From 19f52bc88a5f0eade06b026c2fe2bb8fc26922ad Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Fri, 23 Aug 2024 15:58:14 +0200 Subject: [PATCH 1/6] Split up parameter types, add min/max/regex I think it's a lot cleaner that for each parameter type you're only seeing the valid fields. --- schema/v19_09/examples/valid1.yml | 11 ++ schema/v19_09/workflow.yml | 187 ++++++++++++++++++++++++++---- 2 files changed, 173 insertions(+), 25 deletions(-) diff --git a/schema/v19_09/examples/valid1.yml b/schema/v19_09/examples/valid1.yml index b850e66..138a46e 100644 --- a/schema/v19_09/examples/valid1.yml +++ b/schema/v19_09/examples/valid1.yml @@ -5,6 +5,17 @@ inputs: the_input: type: File doc: input doc + the_collection: + type: collection + collection_type: list + the_integer: + type: integer + min: 1 + max: 3 + # the_float: + # type: float + # min: 1 + # max: 3 outputs: the_output: outputSource: cat/out_file1 diff --git a/schema/v19_09/workflow.yml b/schema/v19_09/workflow.yml index 93abf9b..f3bdc1a 100644 --- a/schema/v19_09/workflow.yml +++ b/schema/v19_09/workflow.yml @@ -28,20 +28,39 @@ $graph: - name: GalaxyType type: enum - extends: sld:PrimitiveType + extends: + - sld:PrimitiveType + - GalaxyDataType + - GalaxyDataCollectionType + - GalaxyIntegerType symbols: - - integer - text - - File - - data - - collection doc: - "Extends primitive types with the native Galaxy concepts such datasets and collections." - - "integer: an alias for int type - matches syntax used by Galaxy tools" - "text: an alias for string type - matches syntax used by Galaxy tools" - - "File: an alias for data - there are subtle differences between a plain file, the CWL concept of 'File', and the Galaxy concept of a dataset - this may have subtly difference semantics in the future" + +- name: GalaxyIntegerType + type: enum + symbols: + - integer + doc: + - "integer: an alias for int type - matches syntax used by Galaxy tools" + +- name: GalaxyDataType + type: enum + symbols: + - data + - File + doc: - "data: a Galaxy dataset" - - "collection: a Galaxy dataset collection" + - "File: an alias for data - there are subtle differences between a plain file, the CWL concept of 'File', and the Galaxy concept of a dataset - this may have subtly difference semantics in the future" + +- name: GalaxyDataCollectionType + type: enum + symbols: + - collection + doc: + - "collection: a Galaxy dataset collection" - name: WorkflowStepType type: enum @@ -57,28 +76,12 @@ $graph: - "subworkflow: Run a subworkflow." - "pause: Pause computation on this branch of workflow until user allows it to continue." -- name: WorkflowInputParameter +- name: BaseInputParameter type: record extends: - cwl:InputParameter - gxformat2common:HasStepPosition - docParent: "#GalaxyWorkflow" fields: - - name: type - type: - - GalaxyType - - "null" - - type: array - items: - - GalaxyType - default: data - jsonldPredicate: - "_id": "sld:type" - "_type": "@vocab" - refScope: 2 - typeDSL: True - doc: | - Specify valid types of data that may be assigned to this parameter. - name: optional type: - boolean @@ -86,6 +89,11 @@ $graph: default: false doc: | If set to true, `WorkflowInputParameter` is not required to submit the workflow. + +- name: BaseDataParameter + type: record + extends: [BaseInputParameter] + fields: - name: format doc: | Specify datatype extension for valid input datasets. @@ -93,6 +101,36 @@ $graph: - "null" - type: array items: string + +- name: WorkflowDataParameter + type: record + extends: + - BaseDataParameter + docParent: "#GalaxyWorkflow" + fields: + - name: type + type: + - GalaxyDataType + - "null" + jsonldPredicate: + "_id": "sld:type" + "_type": "@vocab" + refScope: 2 + typeDSL: True + +- name: WorkflowCollectionParameter + type: record + docParent: "#GalaxyWorkflow" + extends: + - BaseDataParameter + fields: + - name: type + type: GalaxyDataCollectionType + jsonldPredicate: + "_id": "sld:type" + "_type": "@vocab" + refScope: 2 + typeDSL: True - name: collection_type doc: | Collection type (defaults to `list` if `type` is `collection`). Nested @@ -101,6 +139,105 @@ $graph: - "null" - string +- name: MinMaxInt + type: record + fields: + - name: min + type: + - int + - "null" + - name: max + type: + - int + - "null" + +# - name: MinMaxFloat +# type: record +# fields: +# - name: min +# type: +# - int +# - float +# - "null" +# - name: max +# type: +# - int +# - float +# - "null" + +- name: WorkflowIntegerParameter + type: record + extends: + - BaseInputParameter + - MinMaxInt + docParent: "#GalaxyWorkflow" + fields: + - name: type + type: + - GalaxyIntegerType + - type: array + items: + - WorkflowIntegerParameter + jsonldPredicate: + "_id": "sld:type" + "_type": "@vocab" + refScope: 2 + typeDSL: True + + +- name: WorkflowFloatParameter + type: record + extends: + - BaseInputParameter + # - MinMaxFloat + docParent: "#GalaxyWorkflow" + fields: + - name: type + type: + - "float" + - "null" + - type: array + items: + - WorkflowFloatParameter + jsonldPredicate: + "_id": "sld:type" + "_type": "@vocab" + refScope: 2 + typeDSL: True + +- name: WorkflowTextParameter + type: record + extends: + - BaseInputParameter + docParent: "#GalaxyWorkflow" + fields: + - name: type + type: + - string + - "null" + - type: array + items: + - WorkflowTextParameter + jsonldPredicate: + "_id": "sld:type" + "_type": "@vocab" + refScope: 2 + typeDSL: True + - name: "regex" + type: + - string + - "null" + +- name: WorkflowInputParameter + type: union + names: + - WorkflowTextParameter + - WorkflowFloatParameter + - WorkflowIntegerParameter + - WorkflowDataParameter + - WorkflowCollectionParameter + docParent: "#GalaxyWorkflow" + - name: WorkflowOutputParameter type: record extends: cwl:OutputParameter From 8625c32a1a9a86fed3f791d41aef2c351717c980 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Tue, 27 Aug 2024 12:46:10 +0200 Subject: [PATCH 2/6] Narrow workflow parameter types --- schema/v19_09/workflow.yml | 53 +++++++++++++++++++------------------- 1 file changed, 27 insertions(+), 26 deletions(-) diff --git a/schema/v19_09/workflow.yml b/schema/v19_09/workflow.yml index f3bdc1a..4290022 100644 --- a/schema/v19_09/workflow.yml +++ b/schema/v19_09/workflow.yml @@ -33,19 +33,33 @@ $graph: - GalaxyDataType - GalaxyDataCollectionType - GalaxyIntegerType - symbols: - - text + - GalaxyTextType + symbols: [] doc: - "Extends primitive types with the native Galaxy concepts such datasets and collections." - "text: an alias for string type - matches syntax used by Galaxy tools" +- name: GalaxyTextType + type: enum + symbols: + - text + - xsd:string + doc: + - "text: and alias for string type - matches syntax used by Galaxy tools" + - name: GalaxyIntegerType type: enum symbols: - integer + - xsd:int doc: - "integer: an alias for int type - matches syntax used by Galaxy tools" +- name: GalaxyFloatType + type: enum + symbols: + - xsd:float + - name: GalaxyDataType type: enum symbols: @@ -139,37 +153,25 @@ $graph: - "null" - string -- name: MinMaxInt +- name: MinMax type: record fields: - name: min type: - - int - - "null" + - int + - float + - "null" - name: max type: - - int - - "null" - -# - name: MinMaxFloat -# type: record -# fields: -# - name: min -# type: -# - int -# - float -# - "null" -# - name: max -# type: -# - int -# - float -# - "null" + - int + - float + - "null" - name: WorkflowIntegerParameter type: record extends: - BaseInputParameter - - MinMaxInt + - MinMax docParent: "#GalaxyWorkflow" fields: - name: type @@ -184,17 +186,16 @@ $graph: refScope: 2 typeDSL: True - - name: WorkflowFloatParameter type: record extends: - BaseInputParameter - # - MinMaxFloat + - MinMax docParent: "#GalaxyWorkflow" fields: - name: type type: - - "float" + - GalaxyFloatType - "null" - type: array items: @@ -213,7 +214,7 @@ $graph: fields: - name: type type: - - string + - GalaxyTextType - "null" - type: array items: From 377b4ff37419ba15d1fb7211db4aafc332659b62 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Tue, 27 Aug 2024 15:24:23 +0200 Subject: [PATCH 3/6] Add RegexMatch validator --- schema/v19_09/examples/valid1.yml | 24 +++++++++++++++--------- schema/v19_09/workflow.yml | 29 ++++++++++++++++++++++++++--- 2 files changed, 41 insertions(+), 12 deletions(-) diff --git a/schema/v19_09/examples/valid1.yml b/schema/v19_09/examples/valid1.yml index 138a46e..b023923 100644 --- a/schema/v19_09/examples/valid1.yml +++ b/schema/v19_09/examples/valid1.yml @@ -2,20 +2,26 @@ class: GalaxyWorkflow doc: | Simple workflow that no-op cats a file. inputs: - the_input: + the input: type: File doc: input doc - the_collection: + the collection: type: collection collection_type: list - the_integer: - type: integer + the integer: + type: int min: 1 max: 3 - # the_float: - # type: float - # min: 1 - # max: 3 + the float: + type: float + min: 1.0 + max: 3.0 + the string: + type: text + validators: + - type: regex_match + regex: ^(?!.*\s).+$ + doc: String must not contain whitespace outputs: the_output: outputSource: cat/out_file1 @@ -24,4 +30,4 @@ steps: tool_id: cat1 doc: cat doc in: - input1: the_input \ No newline at end of file + input1: the input \ No newline at end of file diff --git a/schema/v19_09/workflow.yml b/schema/v19_09/workflow.yml index 4290022..eb86a73 100644 --- a/schema/v19_09/workflow.yml +++ b/schema/v19_09/workflow.yml @@ -206,6 +206,30 @@ $graph: refScope: 2 typeDSL: True +- name: ValidatorTypes + type: enum + symbols: + - regex_match + +- name: RegexMatch + type: record + fields: + - name: type + type: + - ValidatorTypes + - "null" + jsonldPredicate: + "_id": "sld:type" + "_type": "@vocab" + refScope: 2 + typeDSL: True + - name: regex + type: [string] + - name: doc + type: + - string + jsonldPredicate: rdfs:comment + - name: WorkflowTextParameter type: record extends: @@ -224,10 +248,9 @@ $graph: "_type": "@vocab" refScope: 2 typeDSL: True - - name: "regex" + - name: "validators" type: - - string - - "null" + - RegexMatch[] - name: WorkflowInputParameter type: union From 9a5313ee4f675ae4cdc352d16931adf9c7e99aab Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Tue, 27 Aug 2024 15:48:23 +0200 Subject: [PATCH 4/6] Add docs --- schema/v19_09/examples/valid1.yml | 6 +++--- schema/v19_09/workflow.yml | 30 ++++++++++++------------------ 2 files changed, 15 insertions(+), 21 deletions(-) diff --git a/schema/v19_09/examples/valid1.yml b/schema/v19_09/examples/valid1.yml index b023923..1998970 100644 --- a/schema/v19_09/examples/valid1.yml +++ b/schema/v19_09/examples/valid1.yml @@ -19,9 +19,9 @@ inputs: the string: type: text validators: - - type: regex_match - regex: ^(?!.*\s).+$ - doc: String must not contain whitespace + - regex_match: + regex: ^(?!.*\s).+$ + doc: String must not contain whitespace outputs: the_output: outputSource: cat/out_file1 diff --git a/schema/v19_09/workflow.yml b/schema/v19_09/workflow.yml index eb86a73..b26a73a 100644 --- a/schema/v19_09/workflow.yml +++ b/schema/v19_09/workflow.yml @@ -45,7 +45,8 @@ $graph: - text - xsd:string doc: - - "text: and alias for string type - matches syntax used by Galaxy tools" + - "text: an alias for string type - matches syntax used by Galaxy tools" + - "string: string type" - name: GalaxyIntegerType type: enum @@ -110,7 +111,7 @@ $graph: fields: - name: format doc: | - Specify datatype extension for valid input datasets. + Specify datatype extensions for valid input datasets. type: - "null" - type: array @@ -196,7 +197,6 @@ $graph: - name: type type: - GalaxyFloatType - - "null" - type: array items: - WorkflowFloatParameter @@ -206,29 +206,23 @@ $graph: refScope: 2 typeDSL: True -- name: ValidatorTypes - type: enum - symbols: - - regex_match +- name: TextValidators + type: record + fields: + regex_match: + type: [RegexMatch] - name: RegexMatch type: record fields: - - name: type - type: - - ValidatorTypes - - "null" - jsonldPredicate: - "_id": "sld:type" - "_type": "@vocab" - refScope: 2 - typeDSL: True - name: regex type: [string] + doc: Check if a regular expression matches the value. A value is only valid if a match is found. - name: doc type: - string jsonldPredicate: rdfs:comment + doc: Message to provide to user if validator did not succeed. - name: WorkflowTextParameter type: record @@ -239,7 +233,6 @@ $graph: - name: type type: - GalaxyTextType - - "null" - type: array items: - WorkflowTextParameter @@ -250,7 +243,8 @@ $graph: typeDSL: True - name: "validators" type: - - RegexMatch[] + - TextValidators[]? + doc: Apply one more validators to the input value. Input is valid if all validators succeed. - name: WorkflowInputParameter type: union From 2696c0cefd0e429404e33845af88d2d6fd9ddabb Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 28 Aug 2024 12:41:26 +0200 Subject: [PATCH 5/6] Fixup schema --- schema/v19_09/workflow.yml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/schema/v19_09/workflow.yml b/schema/v19_09/workflow.yml index b26a73a..1476b5f 100644 --- a/schema/v19_09/workflow.yml +++ b/schema/v19_09/workflow.yml @@ -29,15 +29,13 @@ $graph: - name: GalaxyType type: enum extends: - - sld:PrimitiveType - GalaxyDataType - GalaxyDataCollectionType - - GalaxyIntegerType - GalaxyTextType + - GalaxyIntegerType + - GalaxyFloatType + - GalaxyBooleanType symbols: [] - doc: - - "Extends primitive types with the native Galaxy concepts such datasets and collections." - - "text: an alias for string type - matches syntax used by Galaxy tools" - name: GalaxyTextType type: enum @@ -61,6 +59,11 @@ $graph: symbols: - xsd:float +- name: GalaxyBooleanType + type: enum + symbols: + - xsd:bool + - name: GalaxyDataType type: enum symbols: From c617262b96078b6e2670388e61a014d454c3bf2b Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Tue, 27 Aug 2024 15:48:36 +0200 Subject: [PATCH 6/6] Rebuild client --- gxformat2/schema/v19_09.py | 3978 ++++++++++++++++- .../gxformat2/v19_09/BaseDataParameter.java | 94 + .../v19_09/BaseDataParameterImpl.java | 303 ++ .../gxformat2/v19_09/BaseInputParameter.java | 83 + .../v19_09/BaseInputParameterImpl.java | 270 ++ .../v19_09/GalaxyDataCollectionType.java | 38 + .../gxformat2/v19_09/GalaxyDataType.java | 39 + .../gxformat2/v19_09/GalaxyFloatType.java | 38 + .../gxformat2/v19_09/GalaxyIntegerType.java | 39 + .../gxformat2/v19_09/GalaxyTextType.java | 39 + .../gxformat2/v19_09/MinMax.java | 28 + .../gxformat2/v19_09/MinMaxImpl.java | 114 + .../gxformat2/v19_09/RegexMatch.java | 44 + .../gxformat2/v19_09/RegexMatchImpl.java | 115 + .../gxformat2/v19_09/TextValidators.java | 29 + .../gxformat2/v19_09/TextValidatorsImpl.java | 87 + .../v19_09/WorkflowCollectionParameter.java | 109 + .../WorkflowCollectionParameterImpl.java | 357 ++ .../v19_09/WorkflowDataParameter.java | 96 + .../v19_09/WorkflowDataParameterImpl.java | 327 ++ .../v19_09/WorkflowFloatParameter.java | 89 + .../v19_09/WorkflowFloatParameterImpl.java | 336 ++ .../v19_09/WorkflowIntegerParameter.java | 89 + .../v19_09/WorkflowIntegerParameterImpl.java | 336 ++ .../v19_09/WorkflowTextParameter.java | 96 + .../v19_09/WorkflowTextParameterImpl.java | 321 ++ typescript/docs/assets/main.js | 4 +- typescript/docs/assets/search.js | 2 +- typescript/docs/classes/ArraySchema.html | 6 +- .../docs/classes/BaseDataParameter.html | 31 + .../docs/classes/BaseInputParameter.html | 29 + typescript/docs/classes/EnumSchema.html | 6 +- typescript/docs/classes/GalaxyWorkflow.html | 26 +- typescript/docs/classes/MinMax.html | 16 + typescript/docs/classes/RecordField.html | 8 +- typescript/docs/classes/RecordSchema.html | 6 +- typescript/docs/classes/RegexMatch.html | 20 + typescript/docs/classes/Report.html | 4 +- typescript/docs/classes/StepPosition.html | 6 +- typescript/docs/classes/TextValidators.html | 16 + .../docs/classes/ToolShedRepository.html | 10 +- .../docs/classes/ValidationException.html | 4 +- .../classes/WorkflowCollectionParameter.html | 34 + .../docs/classes/WorkflowDataParameter.html | 31 + .../docs/classes/WorkflowFloatParameter.html | 29 + .../docs/classes/WorkflowInputParameter.html | 36 - 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.../WorkflowIntegerParameterProperties.html | 16 + .../WorkflowOutputParameterProperties.html | 10 +- .../WorkflowStepInputProperties.html | 8 +- .../WorkflowStepOutputProperties.html | 4 +- .../interfaces/WorkflowStepProperties.html | 30 +- .../WorkflowTextParameterProperties.html | 18 + typescript/docs/modules.html | 4 +- typescript/package-lock.json | 2853 ++++++++---- typescript/src/BaseDataParameter.ts | 298 ++ typescript/src/BaseDataParameterProperties.ts | 48 + typescript/src/BaseInputParameter.ts | 270 ++ .../src/BaseInputParameterProperties.ts | 42 + typescript/src/GalaxyBooleanType.ts | 4 + typescript/src/GalaxyDataCollectionType.ts | 4 + typescript/src/GalaxyDataType.ts | 5 + typescript/src/GalaxyFloatType.ts | 4 + typescript/src/GalaxyIntegerType.ts | 5 + typescript/src/GalaxyTextType.ts | 5 + typescript/src/GalaxyType.ts | 17 +- typescript/src/GalaxyWorkflow.ts | 2 +- typescript/src/GalaxyWorkflowProperties.ts | 2 +- typescript/src/MinMax.ts | 138 + typescript/src/MinMaxProperties.ts | 13 + typescript/src/ProcessProperties.ts | 2 +- typescript/src/RegexMatch.ts | 142 + typescript/src/RegexMatchProperties.ts | 21 + typescript/src/TextValidators.ts | 113 + typescript/src/TextValidatorsProperties.ts | 12 + ...eter.ts => WorkflowCollectionParameter.ts} | 71 +- ... WorkflowCollectionParameterProperties.ts} | 13 +- typescript/src/WorkflowDataParameter.ts | 321 ++ .../src/WorkflowDataParameterProperties.ts | 49 + typescript/src/WorkflowFloatParameter.ts | 337 ++ .../src/WorkflowFloatParameterProperties.ts | 45 + typescript/src/WorkflowIntegerParameter.ts | 337 ++ .../src/WorkflowIntegerParameterProperties.ts | 45 + typescript/src/WorkflowTextParameter.ts | 318 ++ .../src/WorkflowTextParameterProperties.ts | 48 + typescript/src/index.ts | 28 +- typescript/src/test/data/examples/valid1.yml | 21 +- typescript/src/util/Internal.ts | 28 +- typescript/src/util/LoaderInstances.ts | 78 +- typescript/src/util/Vocabs.ts | 54 +- 138 files changed, 12768 insertions(+), 1304 deletions(-) create mode 100644 java/src/main/java/org/galaxyproject/gxformat2/v19_09/BaseDataParameter.java create mode 100644 java/src/main/java/org/galaxyproject/gxformat2/v19_09/BaseDataParameterImpl.java create mode 100644 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typescript/docs/classes/WorkflowTextParameter.html create mode 100644 typescript/docs/enums/GalaxyBooleanType.html create mode 100644 typescript/docs/enums/GalaxyDataCollectionType.html create mode 100644 typescript/docs/enums/GalaxyDataType.html create mode 100644 typescript/docs/enums/GalaxyFloatType.html create mode 100644 typescript/docs/enums/GalaxyIntegerType.html create mode 100644 typescript/docs/enums/GalaxyTextType.html create mode 100644 typescript/docs/interfaces/BaseDataParameterProperties.html create mode 100644 typescript/docs/interfaces/BaseInputParameterProperties.html create mode 100644 typescript/docs/interfaces/MinMaxProperties.html create mode 100644 typescript/docs/interfaces/RegexMatchProperties.html create mode 100644 typescript/docs/interfaces/TextValidatorsProperties.html create mode 100644 typescript/docs/interfaces/WorkflowCollectionParameterProperties.html create mode 100644 typescript/docs/interfaces/WorkflowDataParameterProperties.html create mode 100644 typescript/docs/interfaces/WorkflowFloatParameterProperties.html delete mode 100644 typescript/docs/interfaces/WorkflowInputParameterProperties.html create mode 100644 typescript/docs/interfaces/WorkflowIntegerParameterProperties.html create mode 100644 typescript/docs/interfaces/WorkflowTextParameterProperties.html create mode 100644 typescript/src/BaseDataParameter.ts create mode 100644 typescript/src/BaseDataParameterProperties.ts create mode 100644 typescript/src/BaseInputParameter.ts create mode 100644 typescript/src/BaseInputParameterProperties.ts create mode 100644 typescript/src/GalaxyBooleanType.ts create mode 100644 typescript/src/GalaxyDataCollectionType.ts create mode 100644 typescript/src/GalaxyDataType.ts create mode 100644 typescript/src/GalaxyFloatType.ts create mode 100644 typescript/src/GalaxyIntegerType.ts create mode 100644 typescript/src/GalaxyTextType.ts create mode 100644 typescript/src/MinMax.ts create mode 100644 typescript/src/MinMaxProperties.ts create mode 100644 typescript/src/RegexMatch.ts create mode 100644 typescript/src/RegexMatchProperties.ts create mode 100644 typescript/src/TextValidators.ts create mode 100644 typescript/src/TextValidatorsProperties.ts rename typescript/src/{WorkflowInputParameter.ts => WorkflowCollectionParameter.ts} (87%) rename typescript/src/{WorkflowInputParameterProperties.ts => WorkflowCollectionParameterProperties.ts} (77%) create mode 100644 typescript/src/WorkflowDataParameter.ts create mode 100644 typescript/src/WorkflowDataParameterProperties.ts create mode 100644 typescript/src/WorkflowFloatParameter.ts create mode 100644 typescript/src/WorkflowFloatParameterProperties.ts create mode 100644 typescript/src/WorkflowIntegerParameter.ts create mode 100644 typescript/src/WorkflowIntegerParameterProperties.ts create mode 100644 typescript/src/WorkflowTextParameter.ts create mode 100644 typescript/src/WorkflowTextParameterProperties.ts diff --git a/gxformat2/schema/v19_09.py b/gxformat2/schema/v19_09.py index 5d6778e..bd872ed 100644 --- a/gxformat2/schema/v19_09.py +++ b/gxformat2/schema/v19_09.py @@ -2536,18 +2536,3570 @@ def save( attrs = frozenset(["changeset_revision", "name", "owner", "tool_shed"]) -class WorkflowInputParameter(InputParameter, HasStepPosition): +class BaseInputParameter(InputParameter, HasStepPosition): def __init__( self, + optional: Any, + label: Optional[Any] = None, + doc: Optional[Any] = None, + id: Optional[Any] = None, + default: Optional[Any] = None, + position: Optional[Any] = None, + extension_fields: Optional[Dict[str, Any]] = None, + loadingOptions: Optional[LoadingOptions] = None, + ) -> None: + if extension_fields: + self.extension_fields = extension_fields + else: + self.extension_fields = CommentedMap() + if loadingOptions: + self.loadingOptions = loadingOptions + else: + self.loadingOptions = LoadingOptions() + self.label = label + self.doc = doc + self.id = id + self.default = default + self.position = position + self.optional = optional + + def __eq__(self, other: Any) -> bool: + if isinstance(other, BaseInputParameter): + return bool( + self.label == other.label + and self.doc == other.doc + and self.id == other.id + and self.default == other.default + and self.position == other.position + and self.optional == other.optional + ) + return False + + def __hash__(self) -> int: + return hash( + (self.label, self.doc, self.id, self.default, self.position, self.optional) + ) + + @classmethod + def fromDoc( + cls, + doc: Any, + baseuri: str, + loadingOptions: LoadingOptions, + docRoot: Optional[str] = None + ) -> "BaseInputParameter": + _doc = copy.copy(doc) + + if hasattr(doc, "lc"): + _doc.lc.data = doc.lc.data + _doc.lc.filename = doc.lc.filename + _errors__ = [] + id = None + if "id" in _doc: + try: + id = load_field( + _doc.get("id"), + uri_union_of_None_type_or_strtype_True_False_None_None, + baseuri, + loadingOptions, + lc=_doc.get("id") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `id`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("id")))) + _errors__.append( + ValidationException( + "the `id` field is not valid because:", + SourceLine(_doc, "id", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `id` field is not valid because:", + SourceLine(_doc, "id", str), + [e], + ) + ) + + __original_id_is_none = id is None + if id is None: + if docRoot is not None: + id = docRoot + else: + id = "_:" + str(_uuid__.uuid4()) + if not __original_id_is_none: + baseuri = cast(str, id) + label = None + if "label" in _doc: + try: + label = load_field( + _doc.get("label"), + union_of_None_type_or_strtype, + baseuri, + loadingOptions, + lc=_doc.get("label") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `label`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("label")))) + _errors__.append( + ValidationException( + "the `label` field is not valid because:", + SourceLine(_doc, "label", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `label` field is not valid because:", + SourceLine(_doc, "label", str), + [e], + ) + ) + doc = None + if "doc" in _doc: + try: + doc = load_field( + _doc.get("doc"), + union_of_None_type_or_strtype_or_array_of_strtype, + baseuri, + loadingOptions, + lc=_doc.get("doc") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `doc`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("doc")))) + _errors__.append( + ValidationException( + "the `doc` field is not valid because:", + SourceLine(_doc, "doc", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `doc` field is not valid because:", + SourceLine(_doc, "doc", str), + [e], + ) + ) + default = None + if "default" in _doc: + try: + default = load_field( + _doc.get("default"), + union_of_None_type_or_Any_type, + baseuri, + loadingOptions, + lc=_doc.get("default") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `default`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("default")))) + _errors__.append( + ValidationException( + "the `default` field is not valid because:", + SourceLine(_doc, "default", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `default` field is not valid because:", + SourceLine(_doc, "default", str), + [e], + ) + ) + position = None + if "position" in _doc: + try: + position = load_field( + _doc.get("position"), + union_of_None_type_or_StepPositionLoader, + baseuri, + loadingOptions, + lc=_doc.get("position") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `position`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("position")))) + _errors__.append( + ValidationException( + "the `position` field is not valid because:", + SourceLine(_doc, "position", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `position` field is not valid because:", + SourceLine(_doc, "position", str), + [e], + ) + ) + optional = None + if "optional" in _doc: + try: + optional = load_field( + _doc.get("optional"), + union_of_booltype_or_None_type, + baseuri, + loadingOptions, + lc=_doc.get("optional") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `optional`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("optional")))) + _errors__.append( + ValidationException( + "the `optional` field is not valid because:", + SourceLine(_doc, "optional", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `optional` field is not valid because:", + SourceLine(_doc, "optional", str), + [e], + ) + ) + extension_fields: Dict[str, Any] = {} + for k in _doc.keys(): + if k not in cls.attrs: + if not k: + _errors__.append( + ValidationException("mapping with implicit null key") + ) + elif ":" in k: + ex = expand_url( + k, "", loadingOptions, scoped_id=False, vocab_term=False + ) + extension_fields[ex] = _doc[k] + else: + _errors__.append( + ValidationException( + "invalid field `{}`, expected one of: `label`, `doc`, `id`, `default`, `position`, `optional`".format( + k + ), + SourceLine(_doc, k, str), + ) + ) + + if _errors__: + raise ValidationException("", None, _errors__, "*") + _constructed = cls( + label=label, + doc=doc, + id=id, + default=default, + position=position, + optional=optional, + extension_fields=extension_fields, + loadingOptions=loadingOptions, + ) + loadingOptions.idx[cast(str, id)] = (_constructed, loadingOptions) + return _constructed + + def save( + self, top: bool = False, base_url: str = "", relative_uris: bool = True + ) -> Dict[str, Any]: + r: Dict[str, Any] = {} + + if relative_uris: + for ef in self.extension_fields: + r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef] + else: + for ef in self.extension_fields: + r[ef] = self.extension_fields[ef] + if self.id is not None: + u = save_relative_uri(self.id, base_url, True, None, relative_uris) + r["id"] = u + if self.label is not None: + r["label"] = save( + self.label, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.doc is not None: + r["doc"] = save( + self.doc, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.default is not None: + r["default"] = save( + self.default, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.position is not None: + r["position"] = save( + self.position, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.optional is not None: + r["optional"] = save( + self.optional, top=False, base_url=self.id, relative_uris=relative_uris + ) + + # top refers to the directory level + if top: + if self.loadingOptions.namespaces: + r["$namespaces"] = self.loadingOptions.namespaces + if self.loadingOptions.schemas: + r["$schemas"] = self.loadingOptions.schemas + return r + + attrs = frozenset(["label", "doc", "id", "default", "position", "optional"]) + + +class BaseDataParameter(BaseInputParameter): + def __init__( + self, + optional: Any, + label: Optional[Any] = None, + doc: Optional[Any] = None, + id: Optional[Any] = None, + default: Optional[Any] = None, + position: Optional[Any] = None, + format: Optional[Any] = None, + extension_fields: Optional[Dict[str, Any]] = None, + loadingOptions: Optional[LoadingOptions] = None, + ) -> None: + if extension_fields: + self.extension_fields = extension_fields + else: + self.extension_fields = CommentedMap() + if loadingOptions: + self.loadingOptions = loadingOptions + else: + self.loadingOptions = LoadingOptions() + self.label = label + self.doc = doc + self.id = id + self.default = default + self.position = position + self.optional = optional + self.format = format + + def __eq__(self, other: Any) -> bool: + if isinstance(other, BaseDataParameter): + return bool( + self.label == other.label + and self.doc == other.doc + and self.id == other.id + and self.default == other.default + and self.position == other.position + and self.optional == other.optional + and self.format == other.format + ) + return False + + def __hash__(self) -> int: + return hash( + ( + self.label, + self.doc, + self.id, + self.default, + self.position, + self.optional, + self.format, + ) + ) + + @classmethod + def fromDoc( + cls, + doc: Any, + baseuri: str, + loadingOptions: LoadingOptions, + docRoot: Optional[str] = None + ) -> "BaseDataParameter": + _doc = copy.copy(doc) + + if hasattr(doc, "lc"): + _doc.lc.data = doc.lc.data + _doc.lc.filename = doc.lc.filename + _errors__ = [] + id = None + if "id" in _doc: + try: + id = load_field( + _doc.get("id"), + uri_union_of_None_type_or_strtype_True_False_None_None, + baseuri, + loadingOptions, + lc=_doc.get("id") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `id`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("id")))) + _errors__.append( + ValidationException( + "the `id` field is not valid because:", + SourceLine(_doc, "id", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `id` field is not valid because:", + SourceLine(_doc, "id", str), + [e], + ) + ) + + __original_id_is_none = id is None + if id is None: + if docRoot is not None: + id = docRoot + else: + id = "_:" + str(_uuid__.uuid4()) + if not __original_id_is_none: + baseuri = cast(str, id) + label = None + if "label" in _doc: + try: + label = load_field( + _doc.get("label"), + union_of_None_type_or_strtype, + baseuri, + loadingOptions, + lc=_doc.get("label") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `label`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("label")))) + _errors__.append( + ValidationException( + "the `label` field is not valid because:", + SourceLine(_doc, "label", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `label` field is not valid because:", + SourceLine(_doc, "label", str), + [e], + ) + ) + doc = None + if "doc" in _doc: + try: + doc = load_field( + _doc.get("doc"), + union_of_None_type_or_strtype_or_array_of_strtype, + baseuri, + loadingOptions, + lc=_doc.get("doc") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `doc`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("doc")))) + _errors__.append( + ValidationException( + "the `doc` field is not valid because:", + SourceLine(_doc, "doc", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `doc` field is not valid because:", + SourceLine(_doc, "doc", str), + [e], + ) + ) + default = None + if "default" in _doc: + try: + default = load_field( + _doc.get("default"), + union_of_None_type_or_Any_type, + baseuri, + loadingOptions, + lc=_doc.get("default") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `default`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("default")))) + _errors__.append( + ValidationException( + "the `default` field is not valid because:", + SourceLine(_doc, "default", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `default` field is not valid because:", + SourceLine(_doc, "default", str), + [e], + ) + ) + position = None + if "position" in _doc: + try: + position = load_field( + _doc.get("position"), + union_of_None_type_or_StepPositionLoader, + baseuri, + loadingOptions, + lc=_doc.get("position") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `position`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("position")))) + _errors__.append( + ValidationException( + "the `position` field is not valid because:", + SourceLine(_doc, "position", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `position` field is not valid because:", + SourceLine(_doc, "position", str), + [e], + ) + ) + optional = None + if "optional" in _doc: + try: + optional = load_field( + _doc.get("optional"), + union_of_booltype_or_None_type, + baseuri, + loadingOptions, + lc=_doc.get("optional") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `optional`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("optional")))) + _errors__.append( + ValidationException( + "the `optional` field is not valid because:", + SourceLine(_doc, "optional", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `optional` field is not valid because:", + SourceLine(_doc, "optional", str), + [e], + ) + ) + format = None + if "format" in _doc: + try: + format = load_field( + _doc.get("format"), + union_of_None_type_or_array_of_strtype, + baseuri, + loadingOptions, + lc=_doc.get("format") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `format`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("format")))) + _errors__.append( + ValidationException( + "the `format` field is not valid because:", + SourceLine(_doc, "format", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `format` field is not valid because:", + SourceLine(_doc, "format", str), + [e], + ) + ) + extension_fields: Dict[str, Any] = {} + for k in _doc.keys(): + if k not in cls.attrs: + if not k: + _errors__.append( + ValidationException("mapping with implicit null key") + ) + elif ":" in k: + ex = expand_url( + k, "", loadingOptions, scoped_id=False, vocab_term=False + ) + extension_fields[ex] = _doc[k] + else: + _errors__.append( + ValidationException( + "invalid field `{}`, expected one of: `label`, `doc`, `id`, `default`, `position`, `optional`, `format`".format( + k + ), + SourceLine(_doc, k, str), + ) + ) + + if _errors__: + raise ValidationException("", None, _errors__, "*") + _constructed = cls( + label=label, + doc=doc, + id=id, + default=default, + position=position, + optional=optional, + format=format, + extension_fields=extension_fields, + loadingOptions=loadingOptions, + ) + loadingOptions.idx[cast(str, id)] = (_constructed, loadingOptions) + return _constructed + + def save( + self, top: bool = False, base_url: str = "", relative_uris: bool = True + ) -> Dict[str, Any]: + r: Dict[str, Any] = {} + + if relative_uris: + for ef in self.extension_fields: + r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef] + else: + for ef in self.extension_fields: + r[ef] = self.extension_fields[ef] + if self.id is not None: + u = save_relative_uri(self.id, base_url, True, None, relative_uris) + r["id"] = u + if self.label is not None: + r["label"] = save( + self.label, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.doc is not None: + r["doc"] = save( + self.doc, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.default is not None: + r["default"] = save( + self.default, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.position is not None: + r["position"] = save( + self.position, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.optional is not None: + r["optional"] = save( + self.optional, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.format is not None: + r["format"] = save( + self.format, top=False, base_url=self.id, relative_uris=relative_uris + ) + + # top refers to the directory level + if top: + if self.loadingOptions.namespaces: + r["$namespaces"] = self.loadingOptions.namespaces + if self.loadingOptions.schemas: + r["$schemas"] = self.loadingOptions.schemas + return r + + attrs = frozenset( + ["label", "doc", "id", "default", "position", "optional", "format"] + ) + + +class WorkflowDataParameter(BaseDataParameter): + def __init__( + self, + optional: Any, + type_: Any, + label: Optional[Any] = None, + doc: Optional[Any] = None, + id: Optional[Any] = None, + default: Optional[Any] = None, + position: Optional[Any] = None, + format: Optional[Any] = None, + extension_fields: Optional[Dict[str, Any]] = None, + loadingOptions: Optional[LoadingOptions] = None, + ) -> None: + if extension_fields: + self.extension_fields = extension_fields + else: + self.extension_fields = CommentedMap() + if loadingOptions: + self.loadingOptions = loadingOptions + else: + self.loadingOptions = LoadingOptions() + self.label = label + self.doc = doc + self.id = id + self.default = default + self.position = position + self.optional = optional + self.format = format + self.type_ = type_ + + def __eq__(self, other: Any) -> bool: + if isinstance(other, WorkflowDataParameter): + return bool( + self.label == other.label + and self.doc == other.doc + and self.id == other.id + and self.default == other.default + and self.position == other.position + and self.optional == other.optional + and self.format == other.format + and self.type_ == other.type_ + ) + return False + + def __hash__(self) -> int: + return hash( + ( + self.label, + self.doc, + self.id, + self.default, + self.position, + self.optional, + self.format, + self.type_, + ) + ) + + @classmethod + def fromDoc( + cls, + doc: Any, + baseuri: str, + loadingOptions: LoadingOptions, + docRoot: Optional[str] = None + ) -> "WorkflowDataParameter": + _doc = copy.copy(doc) + + if hasattr(doc, "lc"): + _doc.lc.data = doc.lc.data + _doc.lc.filename = doc.lc.filename + _errors__ = [] + id = None + if "id" in _doc: + try: + id = load_field( + _doc.get("id"), + uri_union_of_None_type_or_strtype_True_False_None_None, + baseuri, + loadingOptions, + lc=_doc.get("id") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `id`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("id")))) + _errors__.append( + ValidationException( + "the `id` field is not valid because:", + SourceLine(_doc, "id", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `id` field is not valid because:", + SourceLine(_doc, "id", str), + [e], + ) + ) + + __original_id_is_none = id is None + if id is None: + if docRoot is not None: + id = docRoot + else: + id = "_:" + str(_uuid__.uuid4()) + if not __original_id_is_none: + baseuri = cast(str, id) + label = None + if "label" in _doc: + try: + label = load_field( + _doc.get("label"), + union_of_None_type_or_strtype, + baseuri, + loadingOptions, + lc=_doc.get("label") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `label`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("label")))) + _errors__.append( + ValidationException( + "the `label` field is not valid because:", + SourceLine(_doc, "label", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `label` field is not valid because:", + SourceLine(_doc, "label", str), + [e], + ) + ) + doc = None + if "doc" in _doc: + try: + doc = load_field( + _doc.get("doc"), + union_of_None_type_or_strtype_or_array_of_strtype, + baseuri, + loadingOptions, + lc=_doc.get("doc") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `doc`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("doc")))) + _errors__.append( + ValidationException( + "the `doc` field is not valid because:", + SourceLine(_doc, "doc", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `doc` field is not valid because:", + SourceLine(_doc, "doc", str), + [e], + ) + ) + default = None + if "default" in _doc: + try: + default = load_field( + _doc.get("default"), + union_of_None_type_or_Any_type, + baseuri, + loadingOptions, + lc=_doc.get("default") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `default`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("default")))) + _errors__.append( + ValidationException( + "the `default` field is not valid because:", + SourceLine(_doc, "default", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `default` field is not valid because:", + SourceLine(_doc, "default", str), + [e], + ) + ) + position = None + if "position" in _doc: + try: + position = load_field( + _doc.get("position"), + union_of_None_type_or_StepPositionLoader, + baseuri, + loadingOptions, + lc=_doc.get("position") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `position`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("position")))) + _errors__.append( + ValidationException( + "the `position` field is not valid because:", + SourceLine(_doc, "position", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `position` field is not valid because:", + SourceLine(_doc, "position", str), + [e], + ) + ) + optional = None + if "optional" in _doc: + try: + optional = load_field( + _doc.get("optional"), + union_of_booltype_or_None_type, + baseuri, + loadingOptions, + lc=_doc.get("optional") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `optional`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("optional")))) + _errors__.append( + ValidationException( + "the `optional` field is not valid because:", + SourceLine(_doc, "optional", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `optional` field is not valid because:", + SourceLine(_doc, "optional", str), + [e], + ) + ) + format = None + if "format" in _doc: + try: + format = load_field( + _doc.get("format"), + union_of_None_type_or_array_of_strtype, + baseuri, + loadingOptions, + lc=_doc.get("format") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `format`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("format")))) + _errors__.append( + ValidationException( + "the `format` field is not valid because:", + SourceLine(_doc, "format", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `format` field is not valid because:", + SourceLine(_doc, "format", str), + [e], + ) + ) + type_ = None + if "type" in _doc: + try: + type_ = load_field( + _doc.get("type"), + typedsl_union_of_GalaxyDataTypeLoader_or_None_type_2, + baseuri, + loadingOptions, + lc=_doc.get("type") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `type`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("type")))) + _errors__.append( + ValidationException( + "the `type` field is not valid because:", + SourceLine(_doc, "type", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `type` field is not valid because:", + SourceLine(_doc, "type", str), + [e], + ) + ) + extension_fields: Dict[str, Any] = {} + for k in _doc.keys(): + if k not in cls.attrs: + if not k: + _errors__.append( + ValidationException("mapping with implicit null key") + ) + elif ":" in k: + ex = expand_url( + k, "", loadingOptions, scoped_id=False, vocab_term=False + ) + extension_fields[ex] = _doc[k] + else: + _errors__.append( + ValidationException( + "invalid field `{}`, expected one of: `label`, `doc`, `id`, `default`, `position`, `optional`, `format`, `type`".format( + k + ), + SourceLine(_doc, k, str), + ) + ) + + if _errors__: + raise ValidationException("", None, _errors__, "*") + _constructed = cls( + label=label, + doc=doc, + id=id, + default=default, + position=position, + optional=optional, + format=format, + type_=type_, + extension_fields=extension_fields, + loadingOptions=loadingOptions, + ) + loadingOptions.idx[cast(str, id)] = (_constructed, loadingOptions) + return _constructed + + def save( + self, top: bool = False, base_url: str = "", relative_uris: bool = True + ) -> Dict[str, Any]: + r: Dict[str, Any] = {} + + if relative_uris: + for ef in self.extension_fields: + r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef] + else: + for ef in self.extension_fields: + r[ef] = self.extension_fields[ef] + if self.id is not None: + u = save_relative_uri(self.id, base_url, True, None, relative_uris) + r["id"] = u + if self.label is not None: + r["label"] = save( + self.label, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.doc is not None: + r["doc"] = save( + self.doc, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.default is not None: + r["default"] = save( + self.default, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.position is not None: + r["position"] = save( + self.position, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.optional is not None: + r["optional"] = save( + self.optional, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.format is not None: + r["format"] = save( + self.format, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.type_ is not None: + r["type"] = save( + self.type_, top=False, base_url=self.id, relative_uris=relative_uris + ) + + # top refers to the directory level + if top: + if self.loadingOptions.namespaces: + r["$namespaces"] = self.loadingOptions.namespaces + if self.loadingOptions.schemas: + r["$schemas"] = self.loadingOptions.schemas + return r + + attrs = frozenset( + ["label", "doc", "id", "default", "position", "optional", "format", "type"] + ) + + +class WorkflowCollectionParameter(BaseDataParameter): + def __init__( + self, + optional: Any, + type_: Any, + label: Optional[Any] = None, + doc: Optional[Any] = None, + id: Optional[Any] = None, + default: Optional[Any] = None, + position: Optional[Any] = None, + format: Optional[Any] = None, + collection_type: Optional[Any] = None, + extension_fields: Optional[Dict[str, Any]] = None, + loadingOptions: Optional[LoadingOptions] = None, + ) -> None: + if extension_fields: + self.extension_fields = extension_fields + else: + self.extension_fields = CommentedMap() + if loadingOptions: + self.loadingOptions = loadingOptions + else: + self.loadingOptions = LoadingOptions() + self.label = label + self.doc = doc + self.id = id + self.default = default + self.position = position + self.optional = optional + self.format = format + self.type_ = type_ + self.collection_type = collection_type + + def __eq__(self, other: Any) -> bool: + if isinstance(other, WorkflowCollectionParameter): + return bool( + self.label == other.label + and self.doc == other.doc + and self.id == other.id + and self.default == other.default + and self.position == other.position + and self.optional == other.optional + and self.format == other.format + and self.type_ == other.type_ + and self.collection_type == other.collection_type + ) + return False + + def __hash__(self) -> int: + return hash( + ( + self.label, + self.doc, + self.id, + self.default, + self.position, + self.optional, + self.format, + self.type_, + self.collection_type, + ) + ) + + @classmethod + def fromDoc( + cls, + doc: Any, + baseuri: str, + loadingOptions: LoadingOptions, + docRoot: Optional[str] = None + ) -> "WorkflowCollectionParameter": + _doc = copy.copy(doc) + + if hasattr(doc, "lc"): + _doc.lc.data = doc.lc.data + _doc.lc.filename = doc.lc.filename + _errors__ = [] + id = None + if "id" in _doc: + try: + id = load_field( + _doc.get("id"), + uri_union_of_None_type_or_strtype_True_False_None_None, + baseuri, + loadingOptions, + lc=_doc.get("id") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `id`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("id")))) + _errors__.append( + ValidationException( + "the `id` field is not valid because:", + SourceLine(_doc, "id", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `id` field is not valid because:", + SourceLine(_doc, "id", str), + [e], + ) + ) + + __original_id_is_none = id is None + if id is None: + if docRoot is not None: + id = docRoot + else: + id = "_:" + str(_uuid__.uuid4()) + if not __original_id_is_none: + baseuri = cast(str, id) + label = None + if "label" in _doc: + try: + label = load_field( + _doc.get("label"), + union_of_None_type_or_strtype, + baseuri, + loadingOptions, + lc=_doc.get("label") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `label`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("label")))) + _errors__.append( + ValidationException( + "the `label` field is not valid because:", + SourceLine(_doc, "label", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `label` field is not valid because:", + SourceLine(_doc, "label", str), + [e], + ) + ) + doc = None + if "doc" in _doc: + try: + doc = load_field( + _doc.get("doc"), + union_of_None_type_or_strtype_or_array_of_strtype, + baseuri, + loadingOptions, + lc=_doc.get("doc") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `doc`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("doc")))) + _errors__.append( + ValidationException( + "the `doc` field is not valid because:", + SourceLine(_doc, "doc", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `doc` field is not valid because:", + SourceLine(_doc, "doc", str), + [e], + ) + ) + default = None + if "default" in _doc: + try: + default = load_field( + _doc.get("default"), + union_of_None_type_or_Any_type, + baseuri, + loadingOptions, + lc=_doc.get("default") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `default`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("default")))) + _errors__.append( + ValidationException( + "the `default` field is not valid because:", + SourceLine(_doc, "default", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `default` field is not valid because:", + SourceLine(_doc, "default", str), + [e], + ) + ) + position = None + if "position" in _doc: + try: + position = load_field( + _doc.get("position"), + union_of_None_type_or_StepPositionLoader, + baseuri, + loadingOptions, + lc=_doc.get("position") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `position`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("position")))) + _errors__.append( + ValidationException( + "the `position` field is not valid because:", + SourceLine(_doc, "position", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `position` field is not valid because:", + SourceLine(_doc, "position", str), + [e], + ) + ) + optional = None + if "optional" in _doc: + try: + optional = load_field( + _doc.get("optional"), + union_of_booltype_or_None_type, + baseuri, + loadingOptions, + lc=_doc.get("optional") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `optional`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("optional")))) + _errors__.append( + ValidationException( + "the `optional` field is not valid because:", + SourceLine(_doc, "optional", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `optional` field is not valid because:", + SourceLine(_doc, "optional", str), + [e], + ) + ) + format = None + if "format" in _doc: + try: + format = load_field( + _doc.get("format"), + union_of_None_type_or_array_of_strtype, + baseuri, + loadingOptions, + lc=_doc.get("format") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `format`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("format")))) + _errors__.append( + ValidationException( + "the `format` field is not valid because:", + SourceLine(_doc, "format", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `format` field is not valid because:", + SourceLine(_doc, "format", str), + [e], + ) + ) + try: + if _doc.get("type") is None: + raise ValidationException("missing required field `type`", None, []) + + type_ = load_field( + _doc.get("type"), + typedsl_GalaxyDataCollectionTypeLoader_2, + baseuri, + loadingOptions, + lc=_doc.get("type") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `type`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("type")))) + _errors__.append( + ValidationException( + "the `type` field is not valid because:", + SourceLine(_doc, "type", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `type` field is not valid because:", + SourceLine(_doc, "type", str), + [e], + ) + ) + collection_type = None + if "collection_type" in _doc: + try: + collection_type = load_field( + _doc.get("collection_type"), + union_of_None_type_or_strtype, + baseuri, + loadingOptions, + lc=_doc.get("collection_type") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `collection_type`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("collection_type")))) + _errors__.append( + ValidationException( + "the `collection_type` field is not valid because:", + SourceLine(_doc, "collection_type", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `collection_type` field is not valid because:", + SourceLine(_doc, "collection_type", str), + [e], + ) + ) + extension_fields: Dict[str, Any] = {} + for k in _doc.keys(): + if k not in cls.attrs: + if not k: + _errors__.append( + ValidationException("mapping with implicit null key") + ) + elif ":" in k: + ex = expand_url( + k, "", loadingOptions, scoped_id=False, vocab_term=False + ) + extension_fields[ex] = _doc[k] + else: + _errors__.append( + ValidationException( + "invalid field `{}`, expected one of: `label`, `doc`, `id`, `default`, `position`, `optional`, `format`, `type`, `collection_type`".format( + k + ), + SourceLine(_doc, k, str), + ) + ) + + if _errors__: + raise ValidationException("", None, _errors__, "*") + _constructed = cls( + label=label, + doc=doc, + id=id, + default=default, + position=position, + optional=optional, + format=format, + type_=type_, + collection_type=collection_type, + extension_fields=extension_fields, + loadingOptions=loadingOptions, + ) + loadingOptions.idx[cast(str, id)] = (_constructed, loadingOptions) + return _constructed + + def save( + self, top: bool = False, base_url: str = "", relative_uris: bool = True + ) -> Dict[str, Any]: + r: Dict[str, Any] = {} + + if relative_uris: + for ef in self.extension_fields: + r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef] + else: + for ef in self.extension_fields: + r[ef] = self.extension_fields[ef] + if self.id is not None: + u = save_relative_uri(self.id, base_url, True, None, relative_uris) + r["id"] = u + if self.label is not None: + r["label"] = save( + self.label, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.doc is not None: + r["doc"] = save( + self.doc, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.default is not None: + r["default"] = save( + self.default, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.position is not None: + r["position"] = save( + self.position, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.optional is not None: + r["optional"] = save( + self.optional, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.format is not None: + r["format"] = save( + self.format, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.type_ is not None: + r["type"] = save( + self.type_, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.collection_type is not None: + r["collection_type"] = save( + self.collection_type, + top=False, + base_url=self.id, + relative_uris=relative_uris, + ) + + # top refers to the directory level + if top: + if self.loadingOptions.namespaces: + r["$namespaces"] = self.loadingOptions.namespaces + if self.loadingOptions.schemas: + r["$schemas"] = self.loadingOptions.schemas + return r + + attrs = frozenset( + [ + "label", + "doc", + "id", + "default", + "position", + "optional", + "format", + "type", + "collection_type", + ] + ) + + +class MinMax(Saveable): + def __init__( + self, + min: Any, + max: Any, + extension_fields: Optional[Dict[str, Any]] = None, + loadingOptions: Optional[LoadingOptions] = None, + ) -> None: + if extension_fields: + self.extension_fields = extension_fields + else: + self.extension_fields = CommentedMap() + if loadingOptions: + self.loadingOptions = loadingOptions + else: + self.loadingOptions = LoadingOptions() + self.min = min + self.max = max + + def __eq__(self, other: Any) -> bool: + if isinstance(other, MinMax): + return bool(self.min == other.min and self.max == other.max) + return False + + def __hash__(self) -> int: + return hash((self.min, self.max)) + + @classmethod + def fromDoc( + cls, + doc: Any, + baseuri: str, + loadingOptions: LoadingOptions, + docRoot: Optional[str] = None + ) -> "MinMax": + _doc = copy.copy(doc) + + if hasattr(doc, "lc"): + _doc.lc.data = doc.lc.data + _doc.lc.filename = doc.lc.filename + _errors__ = [] + min = None + if "min" in _doc: + try: + min = load_field( + _doc.get("min"), + union_of_inttype_or_floattype_or_None_type, + baseuri, + loadingOptions, + lc=_doc.get("min") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `min`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("min")))) + _errors__.append( + ValidationException( + "the `min` field is not valid because:", + SourceLine(_doc, "min", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `min` field is not valid because:", + SourceLine(_doc, "min", str), + [e], + ) + ) + max = None + if "max" in _doc: + try: + max = load_field( + _doc.get("max"), + union_of_inttype_or_floattype_or_None_type, + baseuri, + loadingOptions, + lc=_doc.get("max") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `max`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("max")))) + _errors__.append( + ValidationException( + "the `max` field is not valid because:", + SourceLine(_doc, "max", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `max` field is not valid because:", + SourceLine(_doc, "max", str), + [e], + ) + ) + extension_fields: Dict[str, Any] = {} + for k in _doc.keys(): + if k not in cls.attrs: + if not k: + _errors__.append( + ValidationException("mapping with implicit null key") + ) + elif ":" in k: + ex = expand_url( + k, "", loadingOptions, scoped_id=False, vocab_term=False + ) + extension_fields[ex] = _doc[k] + else: + _errors__.append( + ValidationException( + "invalid field `{}`, expected one of: `min`, `max`".format( + k + ), + SourceLine(_doc, k, str), + ) + ) + + if _errors__: + raise ValidationException("", None, _errors__, "*") + _constructed = cls( + min=min, + max=max, + extension_fields=extension_fields, + loadingOptions=loadingOptions, + ) + return _constructed + + def save( + self, top: bool = False, base_url: str = "", relative_uris: bool = True + ) -> Dict[str, Any]: + r: Dict[str, Any] = {} + + if relative_uris: + for ef in self.extension_fields: + r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef] + else: + for ef in self.extension_fields: + r[ef] = self.extension_fields[ef] + if self.min is not None: + r["min"] = save( + self.min, top=False, base_url=base_url, relative_uris=relative_uris + ) + if self.max is not None: + r["max"] = save( + self.max, top=False, base_url=base_url, relative_uris=relative_uris + ) + + # top refers to the directory level + if top: + if self.loadingOptions.namespaces: + r["$namespaces"] = self.loadingOptions.namespaces + if self.loadingOptions.schemas: + r["$schemas"] = self.loadingOptions.schemas + return r + + attrs = frozenset(["min", "max"]) + + +class WorkflowIntegerParameter(BaseInputParameter, MinMax): + def __init__( + self, + optional: Any, + min: Any, + max: Any, + type_: Any, + label: Optional[Any] = None, + doc: Optional[Any] = None, + id: Optional[Any] = None, + default: Optional[Any] = None, + position: Optional[Any] = None, + extension_fields: Optional[Dict[str, Any]] = None, + loadingOptions: Optional[LoadingOptions] = None, + ) -> None: + if extension_fields: + self.extension_fields = extension_fields + else: + self.extension_fields = CommentedMap() + if loadingOptions: + self.loadingOptions = loadingOptions + else: + self.loadingOptions = LoadingOptions() + self.label = label + self.doc = doc + self.id = id + self.default = default + self.position = position + self.optional = optional + self.min = min + self.max = max + self.type_ = type_ + + def __eq__(self, other: Any) -> bool: + if isinstance(other, WorkflowIntegerParameter): + return bool( + self.label == other.label + and self.doc == other.doc + and self.id == other.id + and self.default == other.default + and self.position == other.position + and self.optional == other.optional + and self.min == other.min + and self.max == other.max + and self.type_ == other.type_ + ) + return False + + def __hash__(self) -> int: + return hash( + ( + self.label, + self.doc, + self.id, + self.default, + self.position, + self.optional, + self.min, + self.max, + self.type_, + ) + ) + + @classmethod + def fromDoc( + cls, + doc: Any, + baseuri: str, + loadingOptions: LoadingOptions, + docRoot: Optional[str] = None + ) -> "WorkflowIntegerParameter": + _doc = copy.copy(doc) + + if hasattr(doc, "lc"): + _doc.lc.data = doc.lc.data + _doc.lc.filename = doc.lc.filename + _errors__ = [] + id = None + if "id" in _doc: + try: + id = load_field( + _doc.get("id"), + uri_union_of_None_type_or_strtype_True_False_None_None, + baseuri, + loadingOptions, + lc=_doc.get("id") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `id`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("id")))) + _errors__.append( + ValidationException( + "the `id` field is not valid because:", + SourceLine(_doc, "id", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `id` field is not valid because:", + SourceLine(_doc, "id", str), + [e], + ) + ) + + __original_id_is_none = id is None + if id is None: + if docRoot is not None: + id = docRoot + else: + id = "_:" + str(_uuid__.uuid4()) + if not __original_id_is_none: + baseuri = cast(str, id) + label = None + if "label" in _doc: + try: + label = load_field( + _doc.get("label"), + union_of_None_type_or_strtype, + baseuri, + loadingOptions, + lc=_doc.get("label") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `label`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("label")))) + _errors__.append( + ValidationException( + "the `label` field is not valid because:", + SourceLine(_doc, "label", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `label` field is not valid because:", + SourceLine(_doc, "label", str), + [e], + ) + ) + doc = None + if "doc" in _doc: + try: + doc = load_field( + _doc.get("doc"), + union_of_None_type_or_strtype_or_array_of_strtype, + baseuri, + loadingOptions, + lc=_doc.get("doc") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `doc`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("doc")))) + _errors__.append( + ValidationException( + "the `doc` field is not valid because:", + SourceLine(_doc, "doc", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `doc` field is not valid because:", + SourceLine(_doc, "doc", str), + [e], + ) + ) + default = None + if "default" in _doc: + try: + default = load_field( + _doc.get("default"), + union_of_None_type_or_Any_type, + baseuri, + loadingOptions, + lc=_doc.get("default") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `default`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("default")))) + _errors__.append( + ValidationException( + "the `default` field is not valid because:", + SourceLine(_doc, "default", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `default` field is not valid because:", + SourceLine(_doc, "default", str), + [e], + ) + ) + position = None + if "position" in _doc: + try: + position = load_field( + _doc.get("position"), + union_of_None_type_or_StepPositionLoader, + baseuri, + loadingOptions, + lc=_doc.get("position") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `position`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("position")))) + _errors__.append( + ValidationException( + "the `position` field is not valid because:", + SourceLine(_doc, "position", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `position` field is not valid because:", + SourceLine(_doc, "position", str), + [e], + ) + ) + optional = None + if "optional" in _doc: + try: + optional = load_field( + _doc.get("optional"), + union_of_booltype_or_None_type, + baseuri, + loadingOptions, + lc=_doc.get("optional") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `optional`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("optional")))) + _errors__.append( + ValidationException( + "the `optional` field is not valid because:", + SourceLine(_doc, "optional", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `optional` field is not valid because:", + SourceLine(_doc, "optional", str), + [e], + ) + ) + min = None + if "min" in _doc: + try: + min = load_field( + _doc.get("min"), + union_of_inttype_or_floattype_or_None_type, + baseuri, + loadingOptions, + lc=_doc.get("min") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `min`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("min")))) + _errors__.append( + ValidationException( + "the `min` field is not valid because:", + SourceLine(_doc, "min", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `min` field is not valid because:", + SourceLine(_doc, "min", str), + [e], + ) + ) + max = None + if "max" in _doc: + try: + max = load_field( + _doc.get("max"), + union_of_inttype_or_floattype_or_None_type, + baseuri, + loadingOptions, + lc=_doc.get("max") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `max`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("max")))) + _errors__.append( + ValidationException( + "the `max` field is not valid because:", + SourceLine(_doc, "max", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `max` field is not valid because:", + SourceLine(_doc, "max", str), + [e], + ) + ) + try: + if _doc.get("type") is None: + raise ValidationException("missing required field `type`", None, []) + + type_ = load_field( + _doc.get("type"), + typedsl_union_of_GalaxyIntegerTypeLoader_or_array_of_union_of_WorkflowIntegerParameterLoader_2, + baseuri, + loadingOptions, + lc=_doc.get("type") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `type`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("type")))) + _errors__.append( + ValidationException( + "the `type` field is not valid because:", + SourceLine(_doc, "type", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `type` field is not valid because:", + SourceLine(_doc, "type", str), + [e], + ) + ) + extension_fields: Dict[str, Any] = {} + for k in _doc.keys(): + if k not in cls.attrs: + if not k: + _errors__.append( + ValidationException("mapping with implicit null key") + ) + elif ":" in k: + ex = expand_url( + k, "", loadingOptions, scoped_id=False, vocab_term=False + ) + extension_fields[ex] = _doc[k] + else: + _errors__.append( + ValidationException( + "invalid field `{}`, expected one of: `label`, `doc`, `id`, `default`, `position`, `optional`, `min`, `max`, `type`".format( + k + ), + SourceLine(_doc, k, str), + ) + ) + + if _errors__: + raise ValidationException("", None, _errors__, "*") + _constructed = cls( + label=label, + doc=doc, + id=id, + default=default, + position=position, + optional=optional, + min=min, + max=max, + type_=type_, + extension_fields=extension_fields, + loadingOptions=loadingOptions, + ) + loadingOptions.idx[cast(str, id)] = (_constructed, loadingOptions) + return _constructed + + def save( + self, top: bool = False, base_url: str = "", relative_uris: bool = True + ) -> Dict[str, Any]: + r: Dict[str, Any] = {} + + if relative_uris: + for ef in self.extension_fields: + r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef] + else: + for ef in self.extension_fields: + r[ef] = self.extension_fields[ef] + if self.id is not None: + u = save_relative_uri(self.id, base_url, True, None, relative_uris) + r["id"] = u + if self.label is not None: + r["label"] = save( + self.label, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.doc is not None: + r["doc"] = save( + self.doc, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.default is not None: + r["default"] = save( + self.default, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.position is not None: + r["position"] = save( + self.position, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.optional is not None: + r["optional"] = save( + self.optional, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.min is not None: + r["min"] = save( + self.min, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.max is not None: + r["max"] = save( + self.max, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.type_ is not None: + r["type"] = save( + self.type_, top=False, base_url=self.id, relative_uris=relative_uris + ) + + # top refers to the directory level + if top: + if self.loadingOptions.namespaces: + r["$namespaces"] = self.loadingOptions.namespaces + if self.loadingOptions.schemas: + r["$schemas"] = self.loadingOptions.schemas + return r + + attrs = frozenset( + ["label", "doc", "id", "default", "position", "optional", "min", "max", "type"] + ) + + +class WorkflowFloatParameter(BaseInputParameter, MinMax): + def __init__( + self, + optional: Any, + min: Any, + max: Any, type_: Any, + label: Optional[Any] = None, + doc: Optional[Any] = None, + id: Optional[Any] = None, + default: Optional[Any] = None, + position: Optional[Any] = None, + extension_fields: Optional[Dict[str, Any]] = None, + loadingOptions: Optional[LoadingOptions] = None, + ) -> None: + if extension_fields: + self.extension_fields = extension_fields + else: + self.extension_fields = CommentedMap() + if loadingOptions: + self.loadingOptions = loadingOptions + else: + self.loadingOptions = LoadingOptions() + self.label = label + self.doc = doc + self.id = id + self.default = default + self.position = position + self.optional = optional + self.min = min + self.max = max + self.type_ = type_ + + def __eq__(self, other: Any) -> bool: + if isinstance(other, WorkflowFloatParameter): + return bool( + self.label == other.label + and self.doc == other.doc + and self.id == other.id + and self.default == other.default + and self.position == other.position + and self.optional == other.optional + and self.min == other.min + and self.max == other.max + and self.type_ == other.type_ + ) + return False + + def __hash__(self) -> int: + return hash( + ( + self.label, + self.doc, + self.id, + self.default, + self.position, + self.optional, + self.min, + self.max, + self.type_, + ) + ) + + @classmethod + def fromDoc( + cls, + doc: Any, + baseuri: str, + loadingOptions: LoadingOptions, + docRoot: Optional[str] = None + ) -> "WorkflowFloatParameter": + _doc = copy.copy(doc) + + if hasattr(doc, "lc"): + _doc.lc.data = doc.lc.data + _doc.lc.filename = doc.lc.filename + _errors__ = [] + id = None + if "id" in _doc: + try: + id = load_field( + _doc.get("id"), + uri_union_of_None_type_or_strtype_True_False_None_None, + baseuri, + loadingOptions, + lc=_doc.get("id") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `id`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("id")))) + _errors__.append( + ValidationException( + "the `id` field is not valid because:", + SourceLine(_doc, "id", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `id` field is not valid because:", + SourceLine(_doc, "id", str), + [e], + ) + ) + + __original_id_is_none = id is None + if id is None: + if docRoot is not None: + id = docRoot + else: + id = "_:" + str(_uuid__.uuid4()) + if not __original_id_is_none: + baseuri = cast(str, id) + label = None + if "label" in _doc: + try: + label = load_field( + _doc.get("label"), + union_of_None_type_or_strtype, + baseuri, + loadingOptions, + lc=_doc.get("label") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `label`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("label")))) + _errors__.append( + ValidationException( + "the `label` field is not valid because:", + SourceLine(_doc, "label", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `label` field is not valid because:", + SourceLine(_doc, "label", str), + [e], + ) + ) + doc = None + if "doc" in _doc: + try: + doc = load_field( + _doc.get("doc"), + union_of_None_type_or_strtype_or_array_of_strtype, + baseuri, + loadingOptions, + lc=_doc.get("doc") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `doc`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("doc")))) + _errors__.append( + ValidationException( + "the `doc` field is not valid because:", + SourceLine(_doc, "doc", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `doc` field is not valid because:", + SourceLine(_doc, "doc", str), + [e], + ) + ) + default = None + if "default" in _doc: + try: + default = load_field( + _doc.get("default"), + union_of_None_type_or_Any_type, + baseuri, + loadingOptions, + lc=_doc.get("default") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `default`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("default")))) + _errors__.append( + ValidationException( + "the `default` field is not valid because:", + SourceLine(_doc, "default", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `default` field is not valid because:", + SourceLine(_doc, "default", str), + [e], + ) + ) + position = None + if "position" in _doc: + try: + position = load_field( + _doc.get("position"), + union_of_None_type_or_StepPositionLoader, + baseuri, + loadingOptions, + lc=_doc.get("position") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `position`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("position")))) + _errors__.append( + ValidationException( + "the `position` field is not valid because:", + SourceLine(_doc, "position", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `position` field is not valid because:", + SourceLine(_doc, "position", str), + [e], + ) + ) + optional = None + if "optional" in _doc: + try: + optional = load_field( + _doc.get("optional"), + union_of_booltype_or_None_type, + baseuri, + loadingOptions, + lc=_doc.get("optional") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `optional`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("optional")))) + _errors__.append( + ValidationException( + "the `optional` field is not valid because:", + SourceLine(_doc, "optional", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `optional` field is not valid because:", + SourceLine(_doc, "optional", str), + [e], + ) + ) + min = None + if "min" in _doc: + try: + min = load_field( + _doc.get("min"), + union_of_inttype_or_floattype_or_None_type, + baseuri, + loadingOptions, + lc=_doc.get("min") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `min`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("min")))) + _errors__.append( + ValidationException( + "the `min` field is not valid because:", + SourceLine(_doc, "min", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `min` field is not valid because:", + SourceLine(_doc, "min", str), + [e], + ) + ) + max = None + if "max" in _doc: + try: + max = load_field( + _doc.get("max"), + union_of_inttype_or_floattype_or_None_type, + baseuri, + loadingOptions, + lc=_doc.get("max") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `max`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("max")))) + _errors__.append( + ValidationException( + "the `max` field is not valid because:", + SourceLine(_doc, "max", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `max` field is not valid because:", + SourceLine(_doc, "max", str), + [e], + ) + ) + try: + if _doc.get("type") is None: + raise ValidationException("missing required field `type`", None, []) + + type_ = load_field( + _doc.get("type"), + typedsl_union_of_GalaxyFloatTypeLoader_or_array_of_union_of_WorkflowFloatParameterLoader_2, + baseuri, + loadingOptions, + lc=_doc.get("type") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `type`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("type")))) + _errors__.append( + ValidationException( + "the `type` field is not valid because:", + SourceLine(_doc, "type", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `type` field is not valid because:", + SourceLine(_doc, "type", str), + [e], + ) + ) + extension_fields: Dict[str, Any] = {} + for k in _doc.keys(): + if k not in cls.attrs: + if not k: + _errors__.append( + ValidationException("mapping with implicit null key") + ) + elif ":" in k: + ex = expand_url( + k, "", loadingOptions, scoped_id=False, vocab_term=False + ) + extension_fields[ex] = _doc[k] + else: + _errors__.append( + ValidationException( + "invalid field `{}`, expected one of: `label`, `doc`, `id`, `default`, `position`, `optional`, `min`, `max`, `type`".format( + k + ), + SourceLine(_doc, k, str), + ) + ) + + if _errors__: + raise ValidationException("", None, _errors__, "*") + _constructed = cls( + label=label, + doc=doc, + id=id, + default=default, + position=position, + optional=optional, + min=min, + max=max, + type_=type_, + extension_fields=extension_fields, + loadingOptions=loadingOptions, + ) + loadingOptions.idx[cast(str, id)] = (_constructed, loadingOptions) + return _constructed + + def save( + self, top: bool = False, base_url: str = "", relative_uris: bool = True + ) -> Dict[str, Any]: + r: Dict[str, Any] = {} + + if relative_uris: + for ef in self.extension_fields: + r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef] + else: + for ef in self.extension_fields: + r[ef] = self.extension_fields[ef] + if self.id is not None: + u = save_relative_uri(self.id, base_url, True, None, relative_uris) + r["id"] = u + if self.label is not None: + r["label"] = save( + self.label, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.doc is not None: + r["doc"] = save( + self.doc, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.default is not None: + r["default"] = save( + self.default, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.position is not None: + r["position"] = save( + self.position, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.optional is not None: + r["optional"] = save( + self.optional, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.min is not None: + r["min"] = save( + self.min, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.max is not None: + r["max"] = save( + self.max, top=False, base_url=self.id, relative_uris=relative_uris + ) + if self.type_ is not None: + r["type"] = save( + self.type_, top=False, base_url=self.id, relative_uris=relative_uris + ) + + # top refers to the directory level + if top: + if self.loadingOptions.namespaces: + r["$namespaces"] = self.loadingOptions.namespaces + if self.loadingOptions.schemas: + r["$schemas"] = self.loadingOptions.schemas + return r + + attrs = frozenset( + ["label", "doc", "id", "default", "position", "optional", "min", "max", "type"] + ) + + +class TextValidators(Saveable): + def __init__( + self, + regex_match: Any, + extension_fields: Optional[Dict[str, Any]] = None, + loadingOptions: Optional[LoadingOptions] = None, + ) -> None: + if extension_fields: + self.extension_fields = extension_fields + else: + self.extension_fields = CommentedMap() + if loadingOptions: + self.loadingOptions = loadingOptions + else: + self.loadingOptions = LoadingOptions() + self.regex_match = regex_match + + def __eq__(self, other: Any) -> bool: + if isinstance(other, TextValidators): + return bool(self.regex_match == other.regex_match) + return False + + def __hash__(self) -> int: + return hash((self.regex_match)) + + @classmethod + def fromDoc( + cls, + doc: Any, + baseuri: str, + loadingOptions: LoadingOptions, + docRoot: Optional[str] = None + ) -> "TextValidators": + _doc = copy.copy(doc) + + if hasattr(doc, "lc"): + _doc.lc.data = doc.lc.data + _doc.lc.filename = doc.lc.filename + _errors__ = [] + try: + if _doc.get("regex_match") is None: + raise ValidationException("missing required field `regex_match`", None, []) + + regex_match = load_field( + _doc.get("regex_match"), + union_of_RegexMatchLoader, + baseuri, + loadingOptions, + lc=_doc.get("regex_match") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `regex_match`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("regex_match")))) + _errors__.append( + ValidationException( + "the `regex_match` field is not valid because:", + SourceLine(_doc, "regex_match", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `regex_match` field is not valid because:", + SourceLine(_doc, "regex_match", str), + [e], + ) + ) + extension_fields: Dict[str, Any] = {} + for k in _doc.keys(): + if k not in cls.attrs: + if not k: + _errors__.append( + ValidationException("mapping with implicit null key") + ) + elif ":" in k: + ex = expand_url( + k, "", loadingOptions, scoped_id=False, vocab_term=False + ) + extension_fields[ex] = _doc[k] + else: + _errors__.append( + ValidationException( + "invalid field `{}`, expected one of: `regex_match`".format( + k + ), + SourceLine(_doc, k, str), + ) + ) + + if _errors__: + raise ValidationException("", None, _errors__, "*") + _constructed = cls( + regex_match=regex_match, + extension_fields=extension_fields, + loadingOptions=loadingOptions, + ) + return _constructed + + def save( + self, top: bool = False, base_url: str = "", relative_uris: bool = True + ) -> Dict[str, Any]: + r: Dict[str, Any] = {} + + if relative_uris: + for ef in self.extension_fields: + r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef] + else: + for ef in self.extension_fields: + r[ef] = self.extension_fields[ef] + if self.regex_match is not None: + r["regex_match"] = save( + self.regex_match, + top=False, + base_url=base_url, + relative_uris=relative_uris, + ) + + # top refers to the directory level + if top: + if self.loadingOptions.namespaces: + r["$namespaces"] = self.loadingOptions.namespaces + if self.loadingOptions.schemas: + r["$schemas"] = self.loadingOptions.schemas + return r + + attrs = frozenset(["regex_match"]) + + +class RegexMatch(Saveable): + def __init__( + self, + regex: Any, + doc: Any, + extension_fields: Optional[Dict[str, Any]] = None, + loadingOptions: Optional[LoadingOptions] = None, + ) -> None: + if extension_fields: + self.extension_fields = extension_fields + else: + self.extension_fields = CommentedMap() + if loadingOptions: + self.loadingOptions = loadingOptions + else: + self.loadingOptions = LoadingOptions() + self.regex = regex + self.doc = doc + + def __eq__(self, other: Any) -> bool: + if isinstance(other, RegexMatch): + return bool(self.regex == other.regex and self.doc == other.doc) + return False + + def __hash__(self) -> int: + return hash((self.regex, self.doc)) + + @classmethod + def fromDoc( + cls, + doc: Any, + baseuri: str, + loadingOptions: LoadingOptions, + docRoot: Optional[str] = None + ) -> "RegexMatch": + _doc = copy.copy(doc) + + if hasattr(doc, "lc"): + _doc.lc.data = doc.lc.data + _doc.lc.filename = doc.lc.filename + _errors__ = [] + try: + if _doc.get("regex") is None: + raise ValidationException("missing required field `regex`", None, []) + + regex = load_field( + _doc.get("regex"), + union_of_strtype, + baseuri, + loadingOptions, + lc=_doc.get("regex") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `regex`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("regex")))) + _errors__.append( + ValidationException( + "the `regex` field is not valid because:", + SourceLine(_doc, "regex", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `regex` field is not valid because:", + SourceLine(_doc, "regex", str), + [e], + ) + ) + try: + if _doc.get("doc") is None: + raise ValidationException("missing required field `doc`", None, []) + + doc = load_field( + _doc.get("doc"), + union_of_strtype, + baseuri, + loadingOptions, + lc=_doc.get("doc") + ) + + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `doc`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("doc")))) + _errors__.append( + ValidationException( + "the `doc` field is not valid because:", + SourceLine(_doc, "doc", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], + ) + ) + else: + _errors__.append( + ValidationException( + "the `doc` field is not valid because:", + SourceLine(_doc, "doc", str), + [e], + ) + ) + extension_fields: Dict[str, Any] = {} + for k in _doc.keys(): + if k not in cls.attrs: + if not k: + _errors__.append( + ValidationException("mapping with implicit null key") + ) + elif ":" in k: + ex = expand_url( + k, "", loadingOptions, scoped_id=False, vocab_term=False + ) + extension_fields[ex] = _doc[k] + else: + _errors__.append( + ValidationException( + "invalid field `{}`, expected one of: `regex`, `doc`".format( + k + ), + SourceLine(_doc, k, str), + ) + ) + + if _errors__: + raise ValidationException("", None, _errors__, "*") + _constructed = cls( + regex=regex, + doc=doc, + extension_fields=extension_fields, + loadingOptions=loadingOptions, + ) + return _constructed + + def save( + self, top: bool = False, base_url: str = "", relative_uris: bool = True + ) -> Dict[str, Any]: + r: Dict[str, Any] = {} + + if relative_uris: + for ef in self.extension_fields: + r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef] + else: + for ef in self.extension_fields: + r[ef] = self.extension_fields[ef] + if self.regex is not None: + r["regex"] = save( + self.regex, top=False, base_url=base_url, relative_uris=relative_uris + ) + if self.doc is not None: + r["doc"] = save( + self.doc, top=False, base_url=base_url, relative_uris=relative_uris + ) + + # top refers to the directory level + if top: + if self.loadingOptions.namespaces: + r["$namespaces"] = self.loadingOptions.namespaces + if self.loadingOptions.schemas: + r["$schemas"] = self.loadingOptions.schemas + return r + + attrs = frozenset(["regex", "doc"]) + + +class WorkflowTextParameter(BaseInputParameter): + def __init__( + self, optional: Any, + type_: Any, label: Optional[Any] = None, doc: Optional[Any] = None, id: Optional[Any] = None, default: Optional[Any] = None, position: Optional[Any] = None, - format: Optional[Any] = None, - collection_type: Optional[Any] = None, + validators: Optional[Any] = None, extension_fields: Optional[Dict[str, Any]] = None, loadingOptions: Optional[LoadingOptions] = None, ) -> None: @@ -2564,23 +6116,21 @@ def __init__( self.id = id self.default = default self.position = position - self.type_ = type_ self.optional = optional - self.format = format - self.collection_type = collection_type + self.type_ = type_ + self.validators = validators def __eq__(self, other: Any) -> bool: - if isinstance(other, WorkflowInputParameter): + if isinstance(other, WorkflowTextParameter): return bool( self.label == other.label and self.doc == other.doc and self.id == other.id and self.default == other.default and self.position == other.position - and self.type_ == other.type_ and self.optional == other.optional - and self.format == other.format - and self.collection_type == other.collection_type + and self.type_ == other.type_ + and self.validators == other.validators ) return False @@ -2592,10 +6142,9 @@ def __hash__(self) -> int: self.id, self.default, self.position, - self.type_, self.optional, - self.format, - self.collection_type, + self.type_, + self.validators, ) ) @@ -2606,7 +6155,7 @@ def fromDoc( baseuri: str, loadingOptions: LoadingOptions, docRoot: Optional[str] = None - ) -> "WorkflowInputParameter": + ) -> "WorkflowTextParameter": _doc = copy.copy(doc) if hasattr(doc, "lc"): @@ -2827,47 +6376,6 @@ def fromDoc( [e], ) ) - type_ = None - if "type" in _doc: - try: - type_ = load_field( - _doc.get("type"), - typedsl_union_of_GalaxyTypeLoader_or_None_type_or_array_of_union_of_GalaxyTypeLoader_2, - baseuri, - loadingOptions, - lc=_doc.get("type") - ) - - except ValidationException as e: - error_message, to_print, verb_tensage = parse_errors(str(e)) - - if str(e) == "missing required field `type`": - _errors__.append( - ValidationException( - str(e), - None - ) - ) - else: - if error_message != str(e): - val_type = convert_typing(extract_type(type(_doc.get("type")))) - _errors__.append( - ValidationException( - "the `type` field is not valid because:", - SourceLine(_doc, "type", str), - [ValidationException(f"Value is a {val_type}, " - f"but valid {to_print} for this field " - f"{verb_tensage} {error_message}")], - ) - ) - else: - _errors__.append( - ValidationException( - "the `type` field is not valid because:", - SourceLine(_doc, "type", str), - [e], - ) - ) optional = None if "optional" in _doc: try: @@ -2909,62 +6417,63 @@ def fromDoc( [e], ) ) - format = None - if "format" in _doc: - try: - format = load_field( - _doc.get("format"), - union_of_None_type_or_array_of_strtype, - baseuri, - loadingOptions, - lc=_doc.get("format") - ) + try: + if _doc.get("type") is None: + raise ValidationException("missing required field `type`", None, []) - except ValidationException as e: - error_message, to_print, verb_tensage = parse_errors(str(e)) + type_ = load_field( + _doc.get("type"), + typedsl_union_of_GalaxyTextTypeLoader_or_array_of_union_of_WorkflowTextParameterLoader_2, + baseuri, + loadingOptions, + lc=_doc.get("type") + ) - if str(e) == "missing required field `format`": + except ValidationException as e: + error_message, to_print, verb_tensage = parse_errors(str(e)) + + if str(e) == "missing required field `type`": + _errors__.append( + ValidationException( + str(e), + None + ) + ) + else: + if error_message != str(e): + val_type = convert_typing(extract_type(type(_doc.get("type")))) _errors__.append( ValidationException( - str(e), - None + "the `type` field is not valid because:", + SourceLine(_doc, "type", str), + [ValidationException(f"Value is a {val_type}, " + f"but valid {to_print} for this field " + f"{verb_tensage} {error_message}")], ) ) else: - if error_message != str(e): - val_type = convert_typing(extract_type(type(_doc.get("format")))) - _errors__.append( - ValidationException( - "the `format` field is not valid because:", - SourceLine(_doc, "format", str), - [ValidationException(f"Value is a {val_type}, " - f"but valid {to_print} for this field " - f"{verb_tensage} {error_message}")], - ) - ) - else: - _errors__.append( - ValidationException( - "the `format` field is not valid because:", - SourceLine(_doc, "format", str), - [e], - ) + _errors__.append( + ValidationException( + "the `type` field is not valid because:", + SourceLine(_doc, "type", str), + [e], ) - collection_type = None - if "collection_type" in _doc: + ) + validators = None + if "validators" in _doc: try: - collection_type = load_field( - _doc.get("collection_type"), - union_of_None_type_or_strtype, + validators = load_field( + _doc.get("validators"), + union_of_None_type_or_array_of_TextValidatorsLoader, baseuri, loadingOptions, - lc=_doc.get("collection_type") + lc=_doc.get("validators") ) except ValidationException as e: error_message, to_print, verb_tensage = parse_errors(str(e)) - if str(e) == "missing required field `collection_type`": + if str(e) == "missing required field `validators`": _errors__.append( ValidationException( str(e), @@ -2973,11 +6482,11 @@ def fromDoc( ) else: if error_message != str(e): - val_type = convert_typing(extract_type(type(_doc.get("collection_type")))) + val_type = convert_typing(extract_type(type(_doc.get("validators")))) _errors__.append( ValidationException( - "the `collection_type` field is not valid because:", - SourceLine(_doc, "collection_type", str), + "the `validators` field is not valid because:", + SourceLine(_doc, "validators", str), [ValidationException(f"Value is a {val_type}, " f"but valid {to_print} for this field " f"{verb_tensage} {error_message}")], @@ -2986,8 +6495,8 @@ def fromDoc( else: _errors__.append( ValidationException( - "the `collection_type` field is not valid because:", - SourceLine(_doc, "collection_type", str), + "the `validators` field is not valid because:", + SourceLine(_doc, "validators", str), [e], ) ) @@ -3006,7 +6515,7 @@ def fromDoc( else: _errors__.append( ValidationException( - "invalid field `{}`, expected one of: `label`, `doc`, `id`, `default`, `position`, `type`, `optional`, `format`, `collection_type`".format( + "invalid field `{}`, expected one of: `label`, `doc`, `id`, `default`, `position`, `optional`, `type`, `validators`".format( k ), SourceLine(_doc, k, str), @@ -3021,10 +6530,9 @@ def fromDoc( id=id, default=default, position=position, - type_=type_, optional=optional, - format=format, - collection_type=collection_type, + type_=type_, + validators=validators, extension_fields=extension_fields, loadingOptions=loadingOptions, ) @@ -3061,21 +6569,17 @@ def save( r["position"] = save( self.position, top=False, base_url=self.id, relative_uris=relative_uris ) - if self.type_ is not None: - r["type"] = save( - self.type_, top=False, base_url=self.id, relative_uris=relative_uris - ) if self.optional is not None: r["optional"] = save( self.optional, top=False, base_url=self.id, relative_uris=relative_uris ) - if self.format is not None: - r["format"] = save( - self.format, top=False, base_url=self.id, relative_uris=relative_uris + if self.type_ is not None: + r["type"] = save( + self.type_, top=False, base_url=self.id, relative_uris=relative_uris ) - if self.collection_type is not None: - r["collection_type"] = save( - self.collection_type, + if self.validators is not None: + r["validators"] = save( + self.validators, top=False, base_url=self.id, relative_uris=relative_uris, @@ -3090,17 +6594,7 @@ def save( return r attrs = frozenset( - [ - "label", - "doc", - "id", - "default", - "position", - "type", - "optional", - "format", - "collection_type", - ] + ["label", "doc", "id", "default", "position", "optional", "type", "validators"] ) @@ -6211,9 +9705,17 @@ def save( _vocab = { "Any": "https://w3id.org/cwl/salad#Any", "ArraySchema": "https://w3id.org/cwl/salad#ArraySchema", + "BaseDataParameter": "https://galaxyproject.org/gxformat2/v19_09#BaseDataParameter", + "BaseInputParameter": "https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter", "Documented": "https://w3id.org/cwl/salad#Documented", "EnumSchema": "https://w3id.org/cwl/salad#EnumSchema", - "File": "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/File", + "File": "https://galaxyproject.org/gxformat2/v19_09#GalaxyDataType/File", + "GalaxyBooleanType": "https://galaxyproject.org/gxformat2/v19_09#GalaxyBooleanType", + "GalaxyDataCollectionType": "https://galaxyproject.org/gxformat2/v19_09#GalaxyDataCollectionType", + "GalaxyDataType": "https://galaxyproject.org/gxformat2/v19_09#GalaxyDataType", + "GalaxyFloatType": "https://galaxyproject.org/gxformat2/v19_09#GalaxyFloatType", + "GalaxyIntegerType": "https://galaxyproject.org/gxformat2/v19_09#GalaxyIntegerType", + "GalaxyTextType": "https://galaxyproject.org/gxformat2/v19_09#GalaxyTextType", "GalaxyType": "https://galaxyproject.org/gxformat2/v19_09#GalaxyType", "GalaxyWorkflow": "https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow", "HasStepErrors": "https://galaxyproject.org/gxformat2/gxformat2common#HasStepErrors", @@ -6222,6 +9724,7 @@ def save( "Identified": "https://w3id.org/cwl/cwl#Identified", "InputParameter": "https://w3id.org/cwl/cwl#InputParameter", "Labeled": "https://w3id.org/cwl/cwl#Labeled", + "MinMax": "https://galaxyproject.org/gxformat2/v19_09#MinMax", "OutputParameter": "https://w3id.org/cwl/cwl#OutputParameter", "Parameter": "https://w3id.org/cwl/cwl#Parameter", "PrimitiveType": "https://w3id.org/cwl/salad#PrimitiveType", @@ -6229,40 +9732,56 @@ def save( "RecordField": "https://w3id.org/cwl/salad#RecordField", "RecordSchema": "https://w3id.org/cwl/salad#RecordSchema", "ReferencesTool": "https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool", + "RegexMatch": "https://galaxyproject.org/gxformat2/v19_09#RegexMatch", "Report": "https://galaxyproject.org/gxformat2/v19_09#Report", "Sink": "https://galaxyproject.org/gxformat2/v19_09#Sink", "StepPosition": "https://galaxyproject.org/gxformat2/gxformat2common#StepPosition", + "TextValidators": "https://galaxyproject.org/gxformat2/v19_09#TextValidators", "ToolShedRepository": "https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository", + "WorkflowCollectionParameter": "https://galaxyproject.org/gxformat2/v19_09#WorkflowCollectionParameter", + "WorkflowDataParameter": "https://galaxyproject.org/gxformat2/v19_09#WorkflowDataParameter", + "WorkflowFloatParameter": "https://galaxyproject.org/gxformat2/v19_09#WorkflowFloatParameter", "WorkflowInputParameter": "https://galaxyproject.org/gxformat2/v19_09#WorkflowInputParameter", + "WorkflowIntegerParameter": "https://galaxyproject.org/gxformat2/v19_09#WorkflowIntegerParameter", "WorkflowOutputParameter": "https://galaxyproject.org/gxformat2/v19_09#WorkflowOutputParameter", "WorkflowStep": "https://galaxyproject.org/gxformat2/v19_09#WorkflowStep", "WorkflowStepInput": "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepInput", "WorkflowStepOutput": "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput", "WorkflowStepType": "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType", + "WorkflowTextParameter": "https://galaxyproject.org/gxformat2/v19_09#WorkflowTextParameter", "array": "https://w3id.org/cwl/salad#array", + "bool": "http://www.w3.org/2001/XMLSchema#bool", "boolean": "http://www.w3.org/2001/XMLSchema#boolean", - "collection": "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/collection", - "data": "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/data", + "collection": "https://galaxyproject.org/gxformat2/v19_09#GalaxyDataCollectionType/collection", + "data": "https://galaxyproject.org/gxformat2/v19_09#GalaxyDataType/data", "double": "http://www.w3.org/2001/XMLSchema#double", "enum": "https://w3id.org/cwl/salad#enum", "float": "http://www.w3.org/2001/XMLSchema#float", "int": "http://www.w3.org/2001/XMLSchema#int", - "integer": "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/integer", + "integer": "https://galaxyproject.org/gxformat2/v19_09#GalaxyIntegerType/integer", "long": "http://www.w3.org/2001/XMLSchema#long", "null": "https://w3id.org/cwl/salad#null", "pause": "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/pause", "record": "https://w3id.org/cwl/salad#record", "string": "http://www.w3.org/2001/XMLSchema#string", "subworkflow": "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/subworkflow", - "text": "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/text", + "text": "https://galaxyproject.org/gxformat2/v19_09#GalaxyTextType/text", "tool": "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/tool", } _rvocab = { "https://w3id.org/cwl/salad#Any": "Any", "https://w3id.org/cwl/salad#ArraySchema": "ArraySchema", + "https://galaxyproject.org/gxformat2/v19_09#BaseDataParameter": "BaseDataParameter", + "https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter": "BaseInputParameter", "https://w3id.org/cwl/salad#Documented": "Documented", "https://w3id.org/cwl/salad#EnumSchema": "EnumSchema", - "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/File": "File", + "https://galaxyproject.org/gxformat2/v19_09#GalaxyDataType/File": "File", + "https://galaxyproject.org/gxformat2/v19_09#GalaxyBooleanType": "GalaxyBooleanType", + "https://galaxyproject.org/gxformat2/v19_09#GalaxyDataCollectionType": "GalaxyDataCollectionType", + "https://galaxyproject.org/gxformat2/v19_09#GalaxyDataType": "GalaxyDataType", + "https://galaxyproject.org/gxformat2/v19_09#GalaxyFloatType": "GalaxyFloatType", + "https://galaxyproject.org/gxformat2/v19_09#GalaxyIntegerType": "GalaxyIntegerType", + "https://galaxyproject.org/gxformat2/v19_09#GalaxyTextType": "GalaxyTextType", "https://galaxyproject.org/gxformat2/v19_09#GalaxyType": "GalaxyType", "https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow": "GalaxyWorkflow", "https://galaxyproject.org/gxformat2/gxformat2common#HasStepErrors": "HasStepErrors", @@ -6271,6 +9790,7 @@ def save( "https://w3id.org/cwl/cwl#Identified": "Identified", "https://w3id.org/cwl/cwl#InputParameter": "InputParameter", "https://w3id.org/cwl/cwl#Labeled": "Labeled", + "https://galaxyproject.org/gxformat2/v19_09#MinMax": "MinMax", "https://w3id.org/cwl/cwl#OutputParameter": "OutputParameter", "https://w3id.org/cwl/cwl#Parameter": "Parameter", "https://w3id.org/cwl/salad#PrimitiveType": "PrimitiveType", @@ -6278,32 +9798,40 @@ def save( "https://w3id.org/cwl/salad#RecordField": "RecordField", "https://w3id.org/cwl/salad#RecordSchema": "RecordSchema", "https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool": "ReferencesTool", + "https://galaxyproject.org/gxformat2/v19_09#RegexMatch": "RegexMatch", "https://galaxyproject.org/gxformat2/v19_09#Report": "Report", "https://galaxyproject.org/gxformat2/v19_09#Sink": "Sink", "https://galaxyproject.org/gxformat2/gxformat2common#StepPosition": "StepPosition", + "https://galaxyproject.org/gxformat2/v19_09#TextValidators": "TextValidators", "https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository": "ToolShedRepository", + "https://galaxyproject.org/gxformat2/v19_09#WorkflowCollectionParameter": "WorkflowCollectionParameter", + "https://galaxyproject.org/gxformat2/v19_09#WorkflowDataParameter": "WorkflowDataParameter", + "https://galaxyproject.org/gxformat2/v19_09#WorkflowFloatParameter": "WorkflowFloatParameter", "https://galaxyproject.org/gxformat2/v19_09#WorkflowInputParameter": "WorkflowInputParameter", + "https://galaxyproject.org/gxformat2/v19_09#WorkflowIntegerParameter": "WorkflowIntegerParameter", "https://galaxyproject.org/gxformat2/v19_09#WorkflowOutputParameter": "WorkflowOutputParameter", "https://galaxyproject.org/gxformat2/v19_09#WorkflowStep": "WorkflowStep", "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepInput": "WorkflowStepInput", "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput": "WorkflowStepOutput", "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType": "WorkflowStepType", + "https://galaxyproject.org/gxformat2/v19_09#WorkflowTextParameter": "WorkflowTextParameter", "https://w3id.org/cwl/salad#array": "array", + "http://www.w3.org/2001/XMLSchema#bool": "bool", "http://www.w3.org/2001/XMLSchema#boolean": "boolean", - "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/collection": "collection", - "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/data": "data", + "https://galaxyproject.org/gxformat2/v19_09#GalaxyDataCollectionType/collection": "collection", + "https://galaxyproject.org/gxformat2/v19_09#GalaxyDataType/data": "data", "http://www.w3.org/2001/XMLSchema#double": "double", "https://w3id.org/cwl/salad#enum": "enum", "http://www.w3.org/2001/XMLSchema#float": "float", "http://www.w3.org/2001/XMLSchema#int": "int", - "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/integer": "integer", + "https://galaxyproject.org/gxformat2/v19_09#GalaxyIntegerType/integer": "integer", "http://www.w3.org/2001/XMLSchema#long": "long", "https://w3id.org/cwl/salad#null": "null", "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/pause": "pause", "https://w3id.org/cwl/salad#record": "record", "http://www.w3.org/2001/XMLSchema#string": "string", "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/subworkflow": "subworkflow", - "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/text": "text", + "https://galaxyproject.org/gxformat2/v19_09#GalaxyTextType/text": "text", "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/tool": "tool", } @@ -6350,27 +9878,56 @@ def save( ToolShedRepositoryLoader = _RecordLoader(ToolShedRepository, None, None) GalaxyTypeLoader = _EnumLoader( ( - "null", - "boolean", + "data", + "File", + "collection", + "text", + "string", + "integer", "int", - "long", "float", - "double", + "bool", + ), + "GalaxyType", +) +GalaxyTextTypeLoader = _EnumLoader( + ( + "text", "string", + ), + "GalaxyTextType", +) +""" +text: an alias for string type - matches syntax used by Galaxy tools +string: string type +""" +GalaxyIntegerTypeLoader = _EnumLoader( + ( "integer", - "text", - "File", - "data", - "collection", + "int", ), - "GalaxyType", + "GalaxyIntegerType", ) """ -Extends primitive types with the native Galaxy concepts such datasets and collections. integer: an alias for int type - matches syntax used by Galaxy tools -text: an alias for string type - matches syntax used by Galaxy tools -File: an alias for data - there are subtle differences between a plain file, the CWL concept of 'File', and the Galaxy concept of a dataset - this may have subtly difference semantics in the future +""" +GalaxyFloatTypeLoader = _EnumLoader(("float",), "GalaxyFloatType") +GalaxyBooleanTypeLoader = _EnumLoader(("bool",), "GalaxyBooleanType") +GalaxyDataTypeLoader = _EnumLoader( + ( + "data", + "File", + ), + "GalaxyDataType", +) +""" data: a Galaxy dataset +File: an alias for data - there are subtle differences between a plain file, the CWL concept of 'File', and the Galaxy concept of a dataset - this may have subtly difference semantics in the future +""" +GalaxyDataCollectionTypeLoader = _EnumLoader( + ("collection",), "GalaxyDataCollectionType" +) +""" collection: a Galaxy dataset collection """ WorkflowStepTypeLoader = _EnumLoader( @@ -6389,7 +9946,19 @@ def save( subworkflow: Run a subworkflow. pause: Pause computation on this branch of workflow until user allows it to continue. """ -WorkflowInputParameterLoader = _RecordLoader(WorkflowInputParameter, None, None) +BaseInputParameterLoader = _RecordLoader(BaseInputParameter, None, None) +BaseDataParameterLoader = _RecordLoader(BaseDataParameter, None, None) +WorkflowDataParameterLoader = _RecordLoader(WorkflowDataParameter, None, None) +WorkflowCollectionParameterLoader = _RecordLoader( + WorkflowCollectionParameter, None, None +) +MinMaxLoader = _RecordLoader(MinMax, None, None) +WorkflowIntegerParameterLoader = _RecordLoader(WorkflowIntegerParameter, None, None) +WorkflowFloatParameterLoader = _RecordLoader(WorkflowFloatParameter, None, None) +TextValidatorsLoader = _RecordLoader(TextValidators, None, None) +RegexMatchLoader = _RecordLoader(RegexMatch, None, None) +WorkflowTextParameterLoader = _RecordLoader(WorkflowTextParameter, None, None) +WorkflowInputParameterLoader = _UnionLoader((), "WorkflowInputParameterLoader") WorkflowOutputParameterLoader = _RecordLoader(WorkflowOutputParameter, None, None) WorkflowStepLoader = _RecordLoader(WorkflowStep, None, None) WorkflowStepInputLoader = _RecordLoader(WorkflowStepInput, None, None) @@ -6485,12 +10054,12 @@ def save( Any_type, ) ) -union_of_WorkflowInputParameterLoader = _UnionLoader((WorkflowInputParameterLoader,)) -array_of_union_of_WorkflowInputParameterLoader = _ArrayLoader( - union_of_WorkflowInputParameterLoader +union_of_BaseInputParameterLoader = _UnionLoader((BaseInputParameterLoader,)) +array_of_union_of_BaseInputParameterLoader = _ArrayLoader( + union_of_BaseInputParameterLoader ) -idmap_inputs_array_of_union_of_WorkflowInputParameterLoader = _IdMapLoader( - array_of_union_of_WorkflowInputParameterLoader, "id", "type" +idmap_inputs_array_of_union_of_BaseInputParameterLoader = _IdMapLoader( + array_of_union_of_BaseInputParameterLoader, "id", "type" ) union_of_WorkflowOutputParameterLoader = _UnionLoader((WorkflowOutputParameterLoader,)) array_of_union_of_WorkflowOutputParameterLoader = _ArrayLoader( @@ -6517,32 +10086,97 @@ def save( ToolShedRepositoryLoader, ) ) -union_of_GalaxyTypeLoader = _UnionLoader((GalaxyTypeLoader,)) -array_of_union_of_GalaxyTypeLoader = _ArrayLoader(union_of_GalaxyTypeLoader) -union_of_GalaxyTypeLoader_or_None_type_or_array_of_union_of_GalaxyTypeLoader = ( +union_of_booltype_or_None_type = _UnionLoader( + ( + booltype, + None_type, + ) +) +union_of_None_type_or_array_of_strtype = _UnionLoader( + ( + None_type, + array_of_strtype, + ) +) +union_of_GalaxyDataTypeLoader_or_None_type = _UnionLoader( + ( + GalaxyDataTypeLoader, + None_type, + ) +) +typedsl_union_of_GalaxyDataTypeLoader_or_None_type_2 = _TypeDSLLoader( + union_of_GalaxyDataTypeLoader_or_None_type, 2, "v1.1" +) +typedsl_GalaxyDataCollectionTypeLoader_2 = _TypeDSLLoader( + GalaxyDataCollectionTypeLoader, 2, "v1.1" +) +union_of_inttype_or_floattype_or_None_type = _UnionLoader( + ( + inttype, + floattype, + None_type, + ) +) +union_of_WorkflowIntegerParameterLoader = _UnionLoader( + (WorkflowIntegerParameterLoader,) +) +array_of_union_of_WorkflowIntegerParameterLoader = _ArrayLoader( + union_of_WorkflowIntegerParameterLoader +) +union_of_GalaxyIntegerTypeLoader_or_array_of_union_of_WorkflowIntegerParameterLoader = ( _UnionLoader( ( - GalaxyTypeLoader, - None_type, - array_of_union_of_GalaxyTypeLoader, + GalaxyIntegerTypeLoader, + array_of_union_of_WorkflowIntegerParameterLoader, ) ) ) -typedsl_union_of_GalaxyTypeLoader_or_None_type_or_array_of_union_of_GalaxyTypeLoader_2 = _TypeDSLLoader( - union_of_GalaxyTypeLoader_or_None_type_or_array_of_union_of_GalaxyTypeLoader, +typedsl_union_of_GalaxyIntegerTypeLoader_or_array_of_union_of_WorkflowIntegerParameterLoader_2 = _TypeDSLLoader( + union_of_GalaxyIntegerTypeLoader_or_array_of_union_of_WorkflowIntegerParameterLoader, 2, "v1.1", ) -union_of_booltype_or_None_type = _UnionLoader( - ( - booltype, - None_type, +union_of_WorkflowFloatParameterLoader = _UnionLoader((WorkflowFloatParameterLoader,)) +array_of_union_of_WorkflowFloatParameterLoader = _ArrayLoader( + union_of_WorkflowFloatParameterLoader +) +union_of_GalaxyFloatTypeLoader_or_array_of_union_of_WorkflowFloatParameterLoader = ( + _UnionLoader( + ( + GalaxyFloatTypeLoader, + array_of_union_of_WorkflowFloatParameterLoader, + ) ) ) -union_of_None_type_or_array_of_strtype = _UnionLoader( +typedsl_union_of_GalaxyFloatTypeLoader_or_array_of_union_of_WorkflowFloatParameterLoader_2 = _TypeDSLLoader( + union_of_GalaxyFloatTypeLoader_or_array_of_union_of_WorkflowFloatParameterLoader, + 2, + "v1.1", +) +union_of_RegexMatchLoader = _UnionLoader((RegexMatchLoader,)) +union_of_strtype = _UnionLoader((strtype,)) +union_of_WorkflowTextParameterLoader = _UnionLoader((WorkflowTextParameterLoader,)) +array_of_union_of_WorkflowTextParameterLoader = _ArrayLoader( + union_of_WorkflowTextParameterLoader +) +union_of_GalaxyTextTypeLoader_or_array_of_union_of_WorkflowTextParameterLoader = ( + _UnionLoader( + ( + GalaxyTextTypeLoader, + array_of_union_of_WorkflowTextParameterLoader, + ) + ) +) +typedsl_union_of_GalaxyTextTypeLoader_or_array_of_union_of_WorkflowTextParameterLoader_2 = _TypeDSLLoader( + union_of_GalaxyTextTypeLoader_or_array_of_union_of_WorkflowTextParameterLoader, + 2, + "v1.1", +) +array_of_TextValidatorsLoader = _ArrayLoader(TextValidatorsLoader) +union_of_None_type_or_array_of_TextValidatorsLoader = _UnionLoader( ( None_type, - array_of_strtype, + array_of_TextValidatorsLoader, ) ) union_of_None_type_or_GalaxyTypeLoader = _UnionLoader( @@ -6648,6 +10282,16 @@ def save( ) ) +WorkflowInputParameterLoader.add_loaders( + ( + WorkflowTextParameterLoader, + WorkflowFloatParameterLoader, + WorkflowIntegerParameterLoader, + WorkflowDataParameterLoader, + WorkflowCollectionParameterLoader, + ) +) + def load_document( doc: Any, diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/BaseDataParameter.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/BaseDataParameter.java new file mode 100644 index 0000000..14699e9 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/BaseDataParameter.java @@ -0,0 +1,94 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.Saveable; + +/** + * Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#BaseDataParameter + *
+ * This interface is implemented by {@link BaseDataParameterImpl}
+ */ +public interface BaseDataParameter extends BaseInputParameter, Saveable { + /** + * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * + *
+ * + * The unique identifier for this object. * + * + *
+ */ + java.util.Optional getId(); + /** + * Getter for property https://w3id.org/cwl/cwl#Labeled/label
+ * + *
+ * + * A short, human-readable label of this object. * + * + *
+ */ + java.util.Optional getLabel(); + /** + * Getter for property https://w3id.org/cwl/salad#Documented/doc
+ * + *
+ * + * A documentation string for this object, or an array of strings which should be concatenated. * + * + *
+ */ + Object getDoc(); + /** + * Getter for property https://w3id.org/cwl/salad#default
+ * + *
+ * + * The default value to use for this parameter if the parameter is missing from the input object, + * or if the value of the parameter in the input object is `null`. Default values are applied + * before evaluating expressions (e.g. dependent `valueFrom` fields). * + * + *
+ */ + java.util.Optional getDefault(); + /** + * Getter for property + * https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
+ */ + java.util.Optional getPosition(); + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter/optional
+ * + *
+ * + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. * + * + *
+ */ + java.util.Optional getOptional(); + /** + * Getter for property https://galaxyproject.org/gxformat2/v19_09#BaseDataParameter/format + *
+ * + *
+ * + * Specify datatype extensions for valid input datasets. * + * + *
+ */ + java.util.Optional> getFormat(); +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/BaseDataParameterImpl.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/BaseDataParameterImpl.java new file mode 100644 index 0000000..9dabb1a --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/BaseDataParameterImpl.java @@ -0,0 +1,303 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptions; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder; +import org.galaxyproject.gxformat2.v19_09.utils.SaveableImpl; +import org.galaxyproject.gxformat2.v19_09.utils.ValidationException; + +/** + * Auto-generated class implementation for + * https://galaxyproject.org/gxformat2/v19_09#BaseDataParameter
+ */ +public class BaseDataParameterImpl extends SaveableImpl implements BaseDataParameter { + private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); + private java.util.Map extensionFields_ = new java.util.HashMap(); + + private java.util.Optional id; + + /** + * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * + *
+ * + * The unique identifier for this object. * + * + *
+ */ + public java.util.Optional getId() { + return this.id; + } + + private java.util.Optional label; + + /** + * Getter for property https://w3id.org/cwl/cwl#Labeled/label
+ * + *
+ * + * A short, human-readable label of this object. * + * + *
+ */ + public java.util.Optional getLabel() { + return this.label; + } + + private Object doc; + + /** + * Getter for property https://w3id.org/cwl/salad#Documented/doc
+ * + *
+ * + * A documentation string for this object, or an array of strings which should be concatenated. * + * + *
+ */ + public Object getDoc() { + return this.doc; + } + + private java.util.Optional default_; + + /** + * Getter for property https://w3id.org/cwl/salad#default
+ * + *
+ * + * The default value to use for this parameter if the parameter is missing from the input object, + * or if the value of the parameter in the input object is `null`. Default values are applied + * before evaluating expressions (e.g. dependent `valueFrom` fields). * + * + *
+ */ + public java.util.Optional getDefault() { + return this.default_; + } + + private java.util.Optional position; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
+ */ + public java.util.Optional getPosition() { + return this.position; + } + + private java.util.Optional optional; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter/optional
+ * + *
+ * + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. * + * + *
+ */ + public java.util.Optional getOptional() { + return this.optional; + } + + private java.util.Optional> format; + + /** + * Getter for property https://galaxyproject.org/gxformat2/v19_09#BaseDataParameter/format + *
+ * + *
+ * + * Specify datatype extensions for valid input datasets. * + * + *
+ */ + public java.util.Optional> getFormat() { + return this.format; + } + + /** + * Used by {@link org.galaxyproject.gxformat2.v19_09.utils.RootLoader} to construct instances of + * BaseDataParameterImpl. + * + * @param __doc_ Document fragment to load this record object from (presumably a {@link + * java.util.Map}). + * @param __baseUri_ Base URI to generate child document IDs against. + * @param __loadingOptions Context for loading URIs and populating objects. + * @param __docRoot_ ID at this position in the document (if available) (maybe?) + * @throws ValidationException If the document fragment is not a {@link java.util.Map} or + * validation of fields fails. + */ + public BaseDataParameterImpl( + final Object __doc_, + final String __baseUri_, + LoadingOptions __loadingOptions, + final String __docRoot_) { + super(__doc_, __baseUri_, __loadingOptions, __docRoot_); + // Prefix plumbing variables with '__' to reduce likelihood of collision with + // generated names. + String __baseUri = __baseUri_; + String __docRoot = __docRoot_; + if (!(__doc_ instanceof java.util.Map)) { + throw new ValidationException("BaseDataParameterImpl called on non-map"); + } + final java.util.Map __doc = (java.util.Map) __doc_; + final java.util.List __errors = + new java.util.ArrayList(); + if (__loadingOptions != null) { + this.loadingOptions_ = __loadingOptions; + } + java.util.Optional id; + + if (__doc.containsKey("id")) { + try { + id = + LoaderInstances.uri_optional_StringInstance_True_False_None_None.loadField( + __doc.get("id"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + id = null; // won't be used but prevents compiler from complaining. + final String __message = "the `id` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + id = null; + } + + Boolean __original_is_null = id == null; + if (id == null) { + if (__docRoot != null) { + id = java.util.Optional.of(__docRoot); + } else { + id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); + } + } + if (__original_is_null) { + __baseUri = __baseUri_; + } else { + __baseUri = (String) id.orElse(null); + } + java.util.Optional label; + + if (__doc.containsKey("label")) { + try { + label = + LoaderInstances.optional_StringInstance.loadField( + __doc.get("label"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + label = null; // won't be used but prevents compiler from complaining. + final String __message = "the `label` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + label = null; + } + Object doc; + + if (__doc.containsKey("doc")) { + try { + doc = + LoaderInstances.union_of_NullInstance_or_StringInstance_or_array_of_StringInstance + .loadField(__doc.get("doc"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + doc = null; // won't be used but prevents compiler from complaining. + final String __message = "the `doc` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + doc = null; + } + java.util.Optional default_; + + if (__doc.containsKey("default")) { + try { + default_ = + LoaderInstances.optional_AnyInstance.loadField( + __doc.get("default"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + default_ = null; // won't be used but prevents compiler from complaining. + final String __message = "the `default` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + default_ = null; + } + java.util.Optional position; + + if (__doc.containsKey("position")) { + try { + position = + LoaderInstances.optional_StepPosition.loadField( + __doc.get("position"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + position = null; // won't be used but prevents compiler from complaining. + final String __message = "the `position` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + position = null; + } + java.util.Optional optional; + + if (__doc.containsKey("optional")) { + try { + optional = + LoaderInstances.optional_BooleanInstance.loadField( + __doc.get("optional"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + optional = null; // won't be used but prevents compiler from complaining. + final String __message = "the `optional` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + optional = null; + } + java.util.Optional> format; + + if (__doc.containsKey("format")) { + try { + format = + LoaderInstances.optional_array_of_StringInstance.loadField( + __doc.get("format"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + format = null; // won't be used but prevents compiler from complaining. + final String __message = "the `format` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + format = null; + } + if (!__errors.isEmpty()) { + throw new ValidationException("Trying 'RecordField'", __errors); + } + this.label = (java.util.Optional) label; + this.doc = (Object) doc; + this.id = (java.util.Optional) id; + this.default_ = (java.util.Optional) default_; + this.position = (java.util.Optional) position; + this.optional = (java.util.Optional) optional; + this.format = (java.util.Optional>) format; + } +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/BaseInputParameter.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/BaseInputParameter.java new file mode 100644 index 0000000..c9210f2 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/BaseInputParameter.java @@ -0,0 +1,83 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.Saveable; + +/** + * Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter + *
+ * This interface is implemented by {@link BaseInputParameterImpl}
+ */ +public interface BaseInputParameter extends InputParameter, HasStepPosition, Saveable { + /** + * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * + *
+ * + * The unique identifier for this object. * + * + *
+ */ + java.util.Optional getId(); + /** + * Getter for property https://w3id.org/cwl/cwl#Labeled/label
+ * + *
+ * + * A short, human-readable label of this object. * + * + *
+ */ + java.util.Optional getLabel(); + /** + * Getter for property https://w3id.org/cwl/salad#Documented/doc
+ * + *
+ * + * A documentation string for this object, or an array of strings which should be concatenated. * + * + *
+ */ + Object getDoc(); + /** + * Getter for property https://w3id.org/cwl/salad#default
+ * + *
+ * + * The default value to use for this parameter if the parameter is missing from the input object, + * or if the value of the parameter in the input object is `null`. Default values are applied + * before evaluating expressions (e.g. dependent `valueFrom` fields). * + * + *
+ */ + java.util.Optional getDefault(); + /** + * Getter for property + * https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
+ */ + java.util.Optional getPosition(); + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter/optional
+ * + *
+ * + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. * + * + *
+ */ + java.util.Optional getOptional(); +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/BaseInputParameterImpl.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/BaseInputParameterImpl.java new file mode 100644 index 0000000..f691f51 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/BaseInputParameterImpl.java @@ -0,0 +1,270 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptions; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder; +import org.galaxyproject.gxformat2.v19_09.utils.SaveableImpl; +import org.galaxyproject.gxformat2.v19_09.utils.ValidationException; + +/** + * Auto-generated class implementation for + * https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter
+ */ +public class BaseInputParameterImpl extends SaveableImpl implements BaseInputParameter { + private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); + private java.util.Map extensionFields_ = new java.util.HashMap(); + + private java.util.Optional id; + + /** + * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * + *
+ * + * The unique identifier for this object. * + * + *
+ */ + public java.util.Optional getId() { + return this.id; + } + + private java.util.Optional label; + + /** + * Getter for property https://w3id.org/cwl/cwl#Labeled/label
+ * + *
+ * + * A short, human-readable label of this object. * + * + *
+ */ + public java.util.Optional getLabel() { + return this.label; + } + + private Object doc; + + /** + * Getter for property https://w3id.org/cwl/salad#Documented/doc
+ * + *
+ * + * A documentation string for this object, or an array of strings which should be concatenated. * + * + *
+ */ + public Object getDoc() { + return this.doc; + } + + private java.util.Optional default_; + + /** + * Getter for property https://w3id.org/cwl/salad#default
+ * + *
+ * + * The default value to use for this parameter if the parameter is missing from the input object, + * or if the value of the parameter in the input object is `null`. Default values are applied + * before evaluating expressions (e.g. dependent `valueFrom` fields). * + * + *
+ */ + public java.util.Optional getDefault() { + return this.default_; + } + + private java.util.Optional position; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
+ */ + public java.util.Optional getPosition() { + return this.position; + } + + private java.util.Optional optional; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter/optional
+ * + *
+ * + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. * + * + *
+ */ + public java.util.Optional getOptional() { + return this.optional; + } + + /** + * Used by {@link org.galaxyproject.gxformat2.v19_09.utils.RootLoader} to construct instances of + * BaseInputParameterImpl. + * + * @param __doc_ Document fragment to load this record object from (presumably a {@link + * java.util.Map}). + * @param __baseUri_ Base URI to generate child document IDs against. + * @param __loadingOptions Context for loading URIs and populating objects. + * @param __docRoot_ ID at this position in the document (if available) (maybe?) + * @throws ValidationException If the document fragment is not a {@link java.util.Map} or + * validation of fields fails. + */ + public BaseInputParameterImpl( + final Object __doc_, + final String __baseUri_, + LoadingOptions __loadingOptions, + final String __docRoot_) { + super(__doc_, __baseUri_, __loadingOptions, __docRoot_); + // Prefix plumbing variables with '__' to reduce likelihood of collision with + // generated names. + String __baseUri = __baseUri_; + String __docRoot = __docRoot_; + if (!(__doc_ instanceof java.util.Map)) { + throw new ValidationException("BaseInputParameterImpl called on non-map"); + } + final java.util.Map __doc = (java.util.Map) __doc_; + final java.util.List __errors = + new java.util.ArrayList(); + if (__loadingOptions != null) { + this.loadingOptions_ = __loadingOptions; + } + java.util.Optional id; + + if (__doc.containsKey("id")) { + try { + id = + LoaderInstances.uri_optional_StringInstance_True_False_None_None.loadField( + __doc.get("id"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + id = null; // won't be used but prevents compiler from complaining. + final String __message = "the `id` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + id = null; + } + + Boolean __original_is_null = id == null; + if (id == null) { + if (__docRoot != null) { + id = java.util.Optional.of(__docRoot); + } else { + id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); + } + } + if (__original_is_null) { + __baseUri = __baseUri_; + } else { + __baseUri = (String) id.orElse(null); + } + java.util.Optional label; + + if (__doc.containsKey("label")) { + try { + label = + LoaderInstances.optional_StringInstance.loadField( + __doc.get("label"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + label = null; // won't be used but prevents compiler from complaining. + final String __message = "the `label` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + label = null; + } + Object doc; + + if (__doc.containsKey("doc")) { + try { + doc = + LoaderInstances.union_of_NullInstance_or_StringInstance_or_array_of_StringInstance + .loadField(__doc.get("doc"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + doc = null; // won't be used but prevents compiler from complaining. + final String __message = "the `doc` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + doc = null; + } + java.util.Optional default_; + + if (__doc.containsKey("default")) { + try { + default_ = + LoaderInstances.optional_AnyInstance.loadField( + __doc.get("default"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + default_ = null; // won't be used but prevents compiler from complaining. + final String __message = "the `default` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + default_ = null; + } + java.util.Optional position; + + if (__doc.containsKey("position")) { + try { + position = + LoaderInstances.optional_StepPosition.loadField( + __doc.get("position"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + position = null; // won't be used but prevents compiler from complaining. + final String __message = "the `position` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + position = null; + } + java.util.Optional optional; + + if (__doc.containsKey("optional")) { + try { + optional = + LoaderInstances.optional_BooleanInstance.loadField( + __doc.get("optional"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + optional = null; // won't be used but prevents compiler from complaining. + final String __message = "the `optional` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + optional = null; + } + if (!__errors.isEmpty()) { + throw new ValidationException("Trying 'RecordField'", __errors); + } + this.label = (java.util.Optional) label; + this.doc = (Object) doc; + this.id = (java.util.Optional) id; + this.default_ = (java.util.Optional) default_; + this.position = (java.util.Optional) position; + this.optional = (java.util.Optional) optional; + } +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyDataCollectionType.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyDataCollectionType.java new file mode 100644 index 0000000..7f3cd5e --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyDataCollectionType.java @@ -0,0 +1,38 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.ValidationException; + +public enum GalaxyDataCollectionType { + COLLECTION("collection"); + + private static String[] symbols = new String[] {"collection"}; + private String docVal; + + private GalaxyDataCollectionType(final String docVal) { + this.docVal = docVal; + } + + public static GalaxyDataCollectionType fromDocumentVal(final String docVal) { + for (final GalaxyDataCollectionType val : GalaxyDataCollectionType.values()) { + if (val.docVal.equals(docVal)) { + return val; + } + } + throw new ValidationException( + String.format("Expected one of %s", GalaxyDataCollectionType.symbols, docVal)); + } +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyDataType.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyDataType.java new file mode 100644 index 0000000..c7aa104 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyDataType.java @@ -0,0 +1,39 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.ValidationException; + +public enum GalaxyDataType { + DATA("data"), + FILE("File"); + + private static String[] symbols = new String[] {"data", "File"}; + private String docVal; + + private GalaxyDataType(final String docVal) { + this.docVal = docVal; + } + + public static GalaxyDataType fromDocumentVal(final String docVal) { + for (final GalaxyDataType val : GalaxyDataType.values()) { + if (val.docVal.equals(docVal)) { + return val; + } + } + throw new ValidationException( + String.format("Expected one of %s", GalaxyDataType.symbols, docVal)); + } +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyFloatType.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyFloatType.java new file mode 100644 index 0000000..872ab2b --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyFloatType.java @@ -0,0 +1,38 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.ValidationException; + +public enum GalaxyFloatType { + FLOAT("float"); + + private static String[] symbols = new String[] {"float"}; + private String docVal; + + private GalaxyFloatType(final String docVal) { + this.docVal = docVal; + } + + public static GalaxyFloatType fromDocumentVal(final String docVal) { + for (final GalaxyFloatType val : GalaxyFloatType.values()) { + if (val.docVal.equals(docVal)) { + return val; + } + } + throw new ValidationException( + String.format("Expected one of %s", GalaxyFloatType.symbols, docVal)); + } +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyIntegerType.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyIntegerType.java new file mode 100644 index 0000000..41a3122 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyIntegerType.java @@ -0,0 +1,39 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.ValidationException; + +public enum GalaxyIntegerType { + INTEGER("integer"), + INT("int"); + + private static String[] symbols = new String[] {"integer", "int"}; + private String docVal; + + private GalaxyIntegerType(final String docVal) { + this.docVal = docVal; + } + + public static GalaxyIntegerType fromDocumentVal(final String docVal) { + for (final GalaxyIntegerType val : GalaxyIntegerType.values()) { + if (val.docVal.equals(docVal)) { + return val; + } + } + throw new ValidationException( + String.format("Expected one of %s", GalaxyIntegerType.symbols, docVal)); + } +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyTextType.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyTextType.java new file mode 100644 index 0000000..6883136 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyTextType.java @@ -0,0 +1,39 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.ValidationException; + +public enum GalaxyTextType { + TEXT("text"), + STRING("string"); + + private static String[] symbols = new String[] {"text", "string"}; + private String docVal; + + private GalaxyTextType(final String docVal) { + this.docVal = docVal; + } + + public static GalaxyTextType fromDocumentVal(final String docVal) { + for (final GalaxyTextType val : GalaxyTextType.values()) { + if (val.docVal.equals(docVal)) { + return val; + } + } + throw new ValidationException( + String.format("Expected one of %s", GalaxyTextType.symbols, docVal)); + } +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/MinMax.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/MinMax.java new file mode 100644 index 0000000..71d63da --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/MinMax.java @@ -0,0 +1,28 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.Saveable; + +/** + * Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#MinMax
+ * This interface is implemented by {@link MinMaxImpl}
+ */ +public interface MinMax extends Saveable { + /** Getter for property https://galaxyproject.org/gxformat2/v19_09#MinMax/min
*/ + Object getMin(); + /** Getter for property https://galaxyproject.org/gxformat2/v19_09#MinMax/max
*/ + Object getMax(); +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/MinMaxImpl.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/MinMaxImpl.java new file mode 100644 index 0000000..e3cfc70 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/MinMaxImpl.java @@ -0,0 +1,114 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptions; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder; +import org.galaxyproject.gxformat2.v19_09.utils.SaveableImpl; +import org.galaxyproject.gxformat2.v19_09.utils.ValidationException; + +/** + * Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#MinMax + *
+ */ +public class MinMaxImpl extends SaveableImpl implements MinMax { + private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); + private java.util.Map extensionFields_ = new java.util.HashMap(); + + private Object min; + + /** Getter for property https://galaxyproject.org/gxformat2/v19_09#MinMax/min
*/ + public Object getMin() { + return this.min; + } + + private Object max; + + /** Getter for property https://galaxyproject.org/gxformat2/v19_09#MinMax/max
*/ + public Object getMax() { + return this.max; + } + + /** + * Used by {@link org.galaxyproject.gxformat2.v19_09.utils.RootLoader} to construct instances of + * MinMaxImpl. + * + * @param __doc_ Document fragment to load this record object from (presumably a {@link + * java.util.Map}). + * @param __baseUri_ Base URI to generate child document IDs against. + * @param __loadingOptions Context for loading URIs and populating objects. + * @param __docRoot_ ID at this position in the document (if available) (maybe?) + * @throws ValidationException If the document fragment is not a {@link java.util.Map} or + * validation of fields fails. + */ + public MinMaxImpl( + final Object __doc_, + final String __baseUri_, + LoadingOptions __loadingOptions, + final String __docRoot_) { + super(__doc_, __baseUri_, __loadingOptions, __docRoot_); + // Prefix plumbing variables with '__' to reduce likelihood of collision with + // generated names. + String __baseUri = __baseUri_; + String __docRoot = __docRoot_; + if (!(__doc_ instanceof java.util.Map)) { + throw new ValidationException("MinMaxImpl called on non-map"); + } + final java.util.Map __doc = (java.util.Map) __doc_; + final java.util.List __errors = + new java.util.ArrayList(); + if (__loadingOptions != null) { + this.loadingOptions_ = __loadingOptions; + } + Object min; + + if (__doc.containsKey("min")) { + try { + min = + LoaderInstances.union_of_IntegerInstance_or_DoubleInstance_or_NullInstance.loadField( + __doc.get("min"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + min = null; // won't be used but prevents compiler from complaining. + final String __message = "the `min` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + min = null; + } + Object max; + + if (__doc.containsKey("max")) { + try { + max = + LoaderInstances.union_of_IntegerInstance_or_DoubleInstance_or_NullInstance.loadField( + __doc.get("max"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + max = null; // won't be used but prevents compiler from complaining. + final String __message = "the `max` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + max = null; + } + if (!__errors.isEmpty()) { + throw new ValidationException("Trying 'RecordField'", __errors); + } + this.min = (Object) min; + this.max = (Object) max; + } +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/RegexMatch.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/RegexMatch.java new file mode 100644 index 0000000..8d30be4 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/RegexMatch.java @@ -0,0 +1,44 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.Saveable; + +/** + * Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#RegexMatch
+ * This interface is implemented by {@link RegexMatchImpl}
+ */ +public interface RegexMatch extends Saveable { + /** + * Getter for property https://galaxyproject.org/gxformat2/v19_09#RegexMatch/regex
+ * + *
+ * + * Check if a regular expression matches the value. A value is only valid if a match is found. * + * + *
+ */ + String getRegex(); + /** + * Getter for property https://galaxyproject.org/gxformat2/v19_09#RegexMatch/doc
+ * + *
+ * + * Message to provide to user if validator did not succeed. * + * + *
+ */ + String getDoc(); +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/RegexMatchImpl.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/RegexMatchImpl.java new file mode 100644 index 0000000..a86fe49 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/RegexMatchImpl.java @@ -0,0 +1,115 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptions; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder; +import org.galaxyproject.gxformat2.v19_09.utils.SaveableImpl; +import org.galaxyproject.gxformat2.v19_09.utils.ValidationException; + +/** + * Auto-generated class implementation for + * https://galaxyproject.org/gxformat2/v19_09#RegexMatch
+ */ +public class RegexMatchImpl extends SaveableImpl implements RegexMatch { + private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); + private java.util.Map extensionFields_ = new java.util.HashMap(); + + private String regex; + + /** + * Getter for property https://galaxyproject.org/gxformat2/v19_09#RegexMatch/regex
+ * + *
+ * + * Check if a regular expression matches the value. A value is only valid if a match is found. * + * + *
+ */ + public String getRegex() { + return this.regex; + } + + private String doc; + + /** + * Getter for property https://galaxyproject.org/gxformat2/v19_09#RegexMatch/doc
+ * + *
+ * + * Message to provide to user if validator did not succeed. * + * + *
+ */ + public String getDoc() { + return this.doc; + } + + /** + * Used by {@link org.galaxyproject.gxformat2.v19_09.utils.RootLoader} to construct instances of + * RegexMatchImpl. + * + * @param __doc_ Document fragment to load this record object from (presumably a {@link + * java.util.Map}). + * @param __baseUri_ Base URI to generate child document IDs against. + * @param __loadingOptions Context for loading URIs and populating objects. + * @param __docRoot_ ID at this position in the document (if available) (maybe?) + * @throws ValidationException If the document fragment is not a {@link java.util.Map} or + * validation of fields fails. + */ + public RegexMatchImpl( + final Object __doc_, + final String __baseUri_, + LoadingOptions __loadingOptions, + final String __docRoot_) { + super(__doc_, __baseUri_, __loadingOptions, __docRoot_); + // Prefix plumbing variables with '__' to reduce likelihood of collision with + // generated names. + String __baseUri = __baseUri_; + String __docRoot = __docRoot_; + if (!(__doc_ instanceof java.util.Map)) { + throw new ValidationException("RegexMatchImpl called on non-map"); + } + final java.util.Map __doc = (java.util.Map) __doc_; + final java.util.List __errors = + new java.util.ArrayList(); + if (__loadingOptions != null) { + this.loadingOptions_ = __loadingOptions; + } + String regex; + try { + regex = + LoaderInstances.StringInstance.loadField(__doc.get("regex"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + regex = null; // won't be used but prevents compiler from complaining. + final String __message = "the `regex` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + String doc; + try { + doc = LoaderInstances.StringInstance.loadField(__doc.get("doc"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + doc = null; // won't be used but prevents compiler from complaining. + final String __message = "the `doc` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + if (!__errors.isEmpty()) { + throw new ValidationException("Trying 'RecordField'", __errors); + } + this.regex = (String) regex; + this.doc = (String) doc; + } +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/TextValidators.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/TextValidators.java new file mode 100644 index 0000000..7ec839c --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/TextValidators.java @@ -0,0 +1,29 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.Saveable; + +/** + * Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#TextValidators
+ * This interface is implemented by {@link TextValidatorsImpl}
+ */ +public interface TextValidators extends Saveable { + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#TextValidators/regex_match
+ */ + RegexMatch getRegex_match(); +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/TextValidatorsImpl.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/TextValidatorsImpl.java new file mode 100644 index 0000000..fe6b779 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/TextValidatorsImpl.java @@ -0,0 +1,87 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptions; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder; +import org.galaxyproject.gxformat2.v19_09.utils.SaveableImpl; +import org.galaxyproject.gxformat2.v19_09.utils.ValidationException; + +/** + * Auto-generated class implementation for + * https://galaxyproject.org/gxformat2/v19_09#TextValidators
+ */ +public class TextValidatorsImpl extends SaveableImpl implements TextValidators { + private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); + private java.util.Map extensionFields_ = new java.util.HashMap(); + + private RegexMatch regex_match; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#TextValidators/regex_match
+ */ + public RegexMatch getRegex_match() { + return this.regex_match; + } + + /** + * Used by {@link org.galaxyproject.gxformat2.v19_09.utils.RootLoader} to construct instances of + * TextValidatorsImpl. + * + * @param __doc_ Document fragment to load this record object from (presumably a {@link + * java.util.Map}). + * @param __baseUri_ Base URI to generate child document IDs against. + * @param __loadingOptions Context for loading URIs and populating objects. + * @param __docRoot_ ID at this position in the document (if available) (maybe?) + * @throws ValidationException If the document fragment is not a {@link java.util.Map} or + * validation of fields fails. + */ + public TextValidatorsImpl( + final Object __doc_, + final String __baseUri_, + LoadingOptions __loadingOptions, + final String __docRoot_) { + super(__doc_, __baseUri_, __loadingOptions, __docRoot_); + // Prefix plumbing variables with '__' to reduce likelihood of collision with + // generated names. + String __baseUri = __baseUri_; + String __docRoot = __docRoot_; + if (!(__doc_ instanceof java.util.Map)) { + throw new ValidationException("TextValidatorsImpl called on non-map"); + } + final java.util.Map __doc = (java.util.Map) __doc_; + final java.util.List __errors = + new java.util.ArrayList(); + if (__loadingOptions != null) { + this.loadingOptions_ = __loadingOptions; + } + RegexMatch regex_match; + try { + regex_match = + LoaderInstances.RegexMatch.loadField( + __doc.get("regex_match"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + regex_match = null; // won't be used but prevents compiler from complaining. + final String __message = "the `regex_match` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + if (!__errors.isEmpty()) { + throw new ValidationException("Trying 'RecordField'", __errors); + } + this.regex_match = (RegexMatch) regex_match; + } +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowCollectionParameter.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowCollectionParameter.java new file mode 100644 index 0000000..ebdec01 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowCollectionParameter.java @@ -0,0 +1,109 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.Saveable; + +/** + * Auto-generated interface for + * https://galaxyproject.org/gxformat2/v19_09#WorkflowCollectionParameter
+ * This interface is implemented by {@link WorkflowCollectionParameterImpl}
+ */ +public interface WorkflowCollectionParameter extends BaseDataParameter, Saveable { + /** + * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * + *
+ * + * The unique identifier for this object. * + * + *
+ */ + java.util.Optional getId(); + /** + * Getter for property https://w3id.org/cwl/cwl#Labeled/label
+ * + *
+ * + * A short, human-readable label of this object. * + * + *
+ */ + java.util.Optional getLabel(); + /** + * Getter for property https://w3id.org/cwl/salad#Documented/doc
+ * + *
+ * + * A documentation string for this object, or an array of strings which should be concatenated. * + * + *
+ */ + Object getDoc(); + /** + * Getter for property https://w3id.org/cwl/salad#default
+ * + *
+ * + * The default value to use for this parameter if the parameter is missing from the input object, + * or if the value of the parameter in the input object is `null`. Default values are applied + * before evaluating expressions (e.g. dependent `valueFrom` fields). * + * + *
+ */ + java.util.Optional getDefault(); + /** + * Getter for property + * https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
+ */ + java.util.Optional getPosition(); + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter/optional
+ * + *
+ * + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. * + * + *
+ */ + java.util.Optional getOptional(); + /** + * Getter for property https://galaxyproject.org/gxformat2/v19_09#BaseDataParameter/format + *
+ * + *
+ * + * Specify datatype extensions for valid input datasets. * + * + *
+ */ + java.util.Optional> getFormat(); + /** Getter for property https://w3id.org/cwl/salad#type
*/ + GalaxyDataCollectionType getType(); + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#WorkflowCollectionParameter/collection_type + *
+ * + *
+ * + * Collection type (defaults to `list` if `type` is `collection`). Nested collection types are + * separated with colons, e.g. `list:list:paired`. * + * + *
+ */ + java.util.Optional getCollection_type(); +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowCollectionParameterImpl.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowCollectionParameterImpl.java new file mode 100644 index 0000000..b7b3b8e --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowCollectionParameterImpl.java @@ -0,0 +1,357 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptions; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder; +import org.galaxyproject.gxformat2.v19_09.utils.SaveableImpl; +import org.galaxyproject.gxformat2.v19_09.utils.ValidationException; + +/** + * Auto-generated class implementation for + * https://galaxyproject.org/gxformat2/v19_09#WorkflowCollectionParameter
+ */ +public class WorkflowCollectionParameterImpl extends SaveableImpl + implements WorkflowCollectionParameter { + private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); + private java.util.Map extensionFields_ = new java.util.HashMap(); + + private java.util.Optional id; + + /** + * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * + *
+ * + * The unique identifier for this object. * + * + *
+ */ + public java.util.Optional getId() { + return this.id; + } + + private java.util.Optional label; + + /** + * Getter for property https://w3id.org/cwl/cwl#Labeled/label
+ * + *
+ * + * A short, human-readable label of this object. * + * + *
+ */ + public java.util.Optional getLabel() { + return this.label; + } + + private Object doc; + + /** + * Getter for property https://w3id.org/cwl/salad#Documented/doc
+ * + *
+ * + * A documentation string for this object, or an array of strings which should be concatenated. * + * + *
+ */ + public Object getDoc() { + return this.doc; + } + + private java.util.Optional default_; + + /** + * Getter for property https://w3id.org/cwl/salad#default
+ * + *
+ * + * The default value to use for this parameter if the parameter is missing from the input object, + * or if the value of the parameter in the input object is `null`. Default values are applied + * before evaluating expressions (e.g. dependent `valueFrom` fields). * + * + *
+ */ + public java.util.Optional getDefault() { + return this.default_; + } + + private java.util.Optional position; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
+ */ + public java.util.Optional getPosition() { + return this.position; + } + + private java.util.Optional optional; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter/optional
+ * + *
+ * + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. * + * + *
+ */ + public java.util.Optional getOptional() { + return this.optional; + } + + private java.util.Optional> format; + + /** + * Getter for property https://galaxyproject.org/gxformat2/v19_09#BaseDataParameter/format + *
+ * + *
+ * + * Specify datatype extensions for valid input datasets. * + * + *
+ */ + public java.util.Optional> getFormat() { + return this.format; + } + + private GalaxyDataCollectionType type; + + /** Getter for property https://w3id.org/cwl/salad#type
*/ + public GalaxyDataCollectionType getType() { + return this.type; + } + + private java.util.Optional collection_type; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#WorkflowCollectionParameter/collection_type + *
+ * + *
+ * + * Collection type (defaults to `list` if `type` is `collection`). Nested collection types are + * separated with colons, e.g. `list:list:paired`. * + * + *
+ */ + public java.util.Optional getCollection_type() { + return this.collection_type; + } + + /** + * Used by {@link org.galaxyproject.gxformat2.v19_09.utils.RootLoader} to construct instances of + * WorkflowCollectionParameterImpl. + * + * @param __doc_ Document fragment to load this record object from (presumably a {@link + * java.util.Map}). + * @param __baseUri_ Base URI to generate child document IDs against. + * @param __loadingOptions Context for loading URIs and populating objects. + * @param __docRoot_ ID at this position in the document (if available) (maybe?) + * @throws ValidationException If the document fragment is not a {@link java.util.Map} or + * validation of fields fails. + */ + public WorkflowCollectionParameterImpl( + final Object __doc_, + final String __baseUri_, + LoadingOptions __loadingOptions, + final String __docRoot_) { + super(__doc_, __baseUri_, __loadingOptions, __docRoot_); + // Prefix plumbing variables with '__' to reduce likelihood of collision with + // generated names. + String __baseUri = __baseUri_; + String __docRoot = __docRoot_; + if (!(__doc_ instanceof java.util.Map)) { + throw new ValidationException("WorkflowCollectionParameterImpl called on non-map"); + } + final java.util.Map __doc = (java.util.Map) __doc_; + final java.util.List __errors = + new java.util.ArrayList(); + if (__loadingOptions != null) { + this.loadingOptions_ = __loadingOptions; + } + java.util.Optional id; + + if (__doc.containsKey("id")) { + try { + id = + LoaderInstances.uri_optional_StringInstance_True_False_None_None.loadField( + __doc.get("id"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + id = null; // won't be used but prevents compiler from complaining. + final String __message = "the `id` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + id = null; + } + + Boolean __original_is_null = id == null; + if (id == null) { + if (__docRoot != null) { + id = java.util.Optional.of(__docRoot); + } else { + id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); + } + } + if (__original_is_null) { + __baseUri = __baseUri_; + } else { + __baseUri = (String) id.orElse(null); + } + java.util.Optional label; + + if (__doc.containsKey("label")) { + try { + label = + LoaderInstances.optional_StringInstance.loadField( + __doc.get("label"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + label = null; // won't be used but prevents compiler from complaining. + final String __message = "the `label` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + label = null; + } + Object doc; + + if (__doc.containsKey("doc")) { + try { + doc = + LoaderInstances.union_of_NullInstance_or_StringInstance_or_array_of_StringInstance + .loadField(__doc.get("doc"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + doc = null; // won't be used but prevents compiler from complaining. + final String __message = "the `doc` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + doc = null; + } + java.util.Optional default_; + + if (__doc.containsKey("default")) { + try { + default_ = + LoaderInstances.optional_AnyInstance.loadField( + __doc.get("default"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + default_ = null; // won't be used but prevents compiler from complaining. + final String __message = "the `default` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + default_ = null; + } + java.util.Optional position; + + if (__doc.containsKey("position")) { + try { + position = + LoaderInstances.optional_StepPosition.loadField( + __doc.get("position"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + position = null; // won't be used but prevents compiler from complaining. + final String __message = "the `position` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + position = null; + } + java.util.Optional optional; + + if (__doc.containsKey("optional")) { + try { + optional = + LoaderInstances.optional_BooleanInstance.loadField( + __doc.get("optional"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + optional = null; // won't be used but prevents compiler from complaining. + final String __message = "the `optional` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + optional = null; + } + java.util.Optional> format; + + if (__doc.containsKey("format")) { + try { + format = + LoaderInstances.optional_array_of_StringInstance.loadField( + __doc.get("format"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + format = null; // won't be used but prevents compiler from complaining. + final String __message = "the `format` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + format = null; + } + GalaxyDataCollectionType type; + try { + type = + LoaderInstances.typedsl_GalaxyDataCollectionType_2.loadField( + __doc.get("type"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + type = null; // won't be used but prevents compiler from complaining. + final String __message = "the `type` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + java.util.Optional collection_type; + + if (__doc.containsKey("collection_type")) { + try { + collection_type = + LoaderInstances.optional_StringInstance.loadField( + __doc.get("collection_type"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + collection_type = null; // won't be used but prevents compiler from complaining. + final String __message = "the `collection_type` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + collection_type = null; + } + if (!__errors.isEmpty()) { + throw new ValidationException("Trying 'RecordField'", __errors); + } + this.label = (java.util.Optional) label; + this.doc = (Object) doc; + this.id = (java.util.Optional) id; + this.default_ = (java.util.Optional) default_; + this.position = (java.util.Optional) position; + this.optional = (java.util.Optional) optional; + this.format = (java.util.Optional>) format; + this.type = (GalaxyDataCollectionType) type; + this.collection_type = (java.util.Optional) collection_type; + } +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowDataParameter.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowDataParameter.java new file mode 100644 index 0000000..e9ee3d7 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowDataParameter.java @@ -0,0 +1,96 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.Saveable; + +/** + * Auto-generated interface for + * https://galaxyproject.org/gxformat2/v19_09#WorkflowDataParameter
+ * This interface is implemented by {@link WorkflowDataParameterImpl}
+ */ +public interface WorkflowDataParameter extends BaseDataParameter, Saveable { + /** + * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * + *
+ * + * The unique identifier for this object. * + * + *
+ */ + java.util.Optional getId(); + /** + * Getter for property https://w3id.org/cwl/cwl#Labeled/label
+ * + *
+ * + * A short, human-readable label of this object. * + * + *
+ */ + java.util.Optional getLabel(); + /** + * Getter for property https://w3id.org/cwl/salad#Documented/doc
+ * + *
+ * + * A documentation string for this object, or an array of strings which should be concatenated. * + * + *
+ */ + Object getDoc(); + /** + * Getter for property https://w3id.org/cwl/salad#default
+ * + *
+ * + * The default value to use for this parameter if the parameter is missing from the input object, + * or if the value of the parameter in the input object is `null`. Default values are applied + * before evaluating expressions (e.g. dependent `valueFrom` fields). * + * + *
+ */ + java.util.Optional getDefault(); + /** + * Getter for property + * https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
+ */ + java.util.Optional getPosition(); + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter/optional
+ * + *
+ * + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. * + * + *
+ */ + java.util.Optional getOptional(); + /** + * Getter for property https://galaxyproject.org/gxformat2/v19_09#BaseDataParameter/format + *
+ * + *
+ * + * Specify datatype extensions for valid input datasets. * + * + *
+ */ + java.util.Optional> getFormat(); + /** Getter for property https://w3id.org/cwl/salad#type
*/ + java.util.Optional getType(); +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowDataParameterImpl.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowDataParameterImpl.java new file mode 100644 index 0000000..97c7a2d --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowDataParameterImpl.java @@ -0,0 +1,327 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptions; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder; +import org.galaxyproject.gxformat2.v19_09.utils.SaveableImpl; +import org.galaxyproject.gxformat2.v19_09.utils.ValidationException; + +/** + * Auto-generated class implementation for + * https://galaxyproject.org/gxformat2/v19_09#WorkflowDataParameter
+ */ +public class WorkflowDataParameterImpl extends SaveableImpl implements WorkflowDataParameter { + private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); + private java.util.Map extensionFields_ = new java.util.HashMap(); + + private java.util.Optional id; + + /** + * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * + *
+ * + * The unique identifier for this object. * + * + *
+ */ + public java.util.Optional getId() { + return this.id; + } + + private java.util.Optional label; + + /** + * Getter for property https://w3id.org/cwl/cwl#Labeled/label
+ * + *
+ * + * A short, human-readable label of this object. * + * + *
+ */ + public java.util.Optional getLabel() { + return this.label; + } + + private Object doc; + + /** + * Getter for property https://w3id.org/cwl/salad#Documented/doc
+ * + *
+ * + * A documentation string for this object, or an array of strings which should be concatenated. * + * + *
+ */ + public Object getDoc() { + return this.doc; + } + + private java.util.Optional default_; + + /** + * Getter for property https://w3id.org/cwl/salad#default
+ * + *
+ * + * The default value to use for this parameter if the parameter is missing from the input object, + * or if the value of the parameter in the input object is `null`. Default values are applied + * before evaluating expressions (e.g. dependent `valueFrom` fields). * + * + *
+ */ + public java.util.Optional getDefault() { + return this.default_; + } + + private java.util.Optional position; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
+ */ + public java.util.Optional getPosition() { + return this.position; + } + + private java.util.Optional optional; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter/optional
+ * + *
+ * + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. * + * + *
+ */ + public java.util.Optional getOptional() { + return this.optional; + } + + private java.util.Optional> format; + + /** + * Getter for property https://galaxyproject.org/gxformat2/v19_09#BaseDataParameter/format + *
+ * + *
+ * + * Specify datatype extensions for valid input datasets. * + * + *
+ */ + public java.util.Optional> getFormat() { + return this.format; + } + + private java.util.Optional type; + + /** Getter for property https://w3id.org/cwl/salad#type
*/ + public java.util.Optional getType() { + return this.type; + } + + /** + * Used by {@link org.galaxyproject.gxformat2.v19_09.utils.RootLoader} to construct instances of + * WorkflowDataParameterImpl. + * + * @param __doc_ Document fragment to load this record object from (presumably a {@link + * java.util.Map}). + * @param __baseUri_ Base URI to generate child document IDs against. + * @param __loadingOptions Context for loading URIs and populating objects. + * @param __docRoot_ ID at this position in the document (if available) (maybe?) + * @throws ValidationException If the document fragment is not a {@link java.util.Map} or + * validation of fields fails. + */ + public WorkflowDataParameterImpl( + final Object __doc_, + final String __baseUri_, + LoadingOptions __loadingOptions, + final String __docRoot_) { + super(__doc_, __baseUri_, __loadingOptions, __docRoot_); + // Prefix plumbing variables with '__' to reduce likelihood of collision with + // generated names. + String __baseUri = __baseUri_; + String __docRoot = __docRoot_; + if (!(__doc_ instanceof java.util.Map)) { + throw new ValidationException("WorkflowDataParameterImpl called on non-map"); + } + final java.util.Map __doc = (java.util.Map) __doc_; + final java.util.List __errors = + new java.util.ArrayList(); + if (__loadingOptions != null) { + this.loadingOptions_ = __loadingOptions; + } + java.util.Optional id; + + if (__doc.containsKey("id")) { + try { + id = + LoaderInstances.uri_optional_StringInstance_True_False_None_None.loadField( + __doc.get("id"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + id = null; // won't be used but prevents compiler from complaining. + final String __message = "the `id` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + id = null; + } + + Boolean __original_is_null = id == null; + if (id == null) { + if (__docRoot != null) { + id = java.util.Optional.of(__docRoot); + } else { + id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); + } + } + if (__original_is_null) { + __baseUri = __baseUri_; + } else { + __baseUri = (String) id.orElse(null); + } + java.util.Optional label; + + if (__doc.containsKey("label")) { + try { + label = + LoaderInstances.optional_StringInstance.loadField( + __doc.get("label"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + label = null; // won't be used but prevents compiler from complaining. + final String __message = "the `label` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + label = null; + } + Object doc; + + if (__doc.containsKey("doc")) { + try { + doc = + LoaderInstances.union_of_NullInstance_or_StringInstance_or_array_of_StringInstance + .loadField(__doc.get("doc"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + doc = null; // won't be used but prevents compiler from complaining. + final String __message = "the `doc` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + doc = null; + } + java.util.Optional default_; + + if (__doc.containsKey("default")) { + try { + default_ = + LoaderInstances.optional_AnyInstance.loadField( + __doc.get("default"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + default_ = null; // won't be used but prevents compiler from complaining. + final String __message = "the `default` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + default_ = null; + } + java.util.Optional position; + + if (__doc.containsKey("position")) { + try { + position = + LoaderInstances.optional_StepPosition.loadField( + __doc.get("position"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + position = null; // won't be used but prevents compiler from complaining. + final String __message = "the `position` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + position = null; + } + java.util.Optional optional; + + if (__doc.containsKey("optional")) { + try { + optional = + LoaderInstances.optional_BooleanInstance.loadField( + __doc.get("optional"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + optional = null; // won't be used but prevents compiler from complaining. + final String __message = "the `optional` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + optional = null; + } + java.util.Optional> format; + + if (__doc.containsKey("format")) { + try { + format = + LoaderInstances.optional_array_of_StringInstance.loadField( + __doc.get("format"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + format = null; // won't be used but prevents compiler from complaining. + final String __message = "the `format` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + format = null; + } + java.util.Optional type; + + if (__doc.containsKey("type")) { + try { + type = + LoaderInstances.typedsl_optional_GalaxyDataType_2.loadField( + __doc.get("type"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + type = null; // won't be used but prevents compiler from complaining. + final String __message = "the `type` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + type = null; + } + if (!__errors.isEmpty()) { + throw new ValidationException("Trying 'RecordField'", __errors); + } + this.label = (java.util.Optional) label; + this.doc = (Object) doc; + this.id = (java.util.Optional) id; + this.default_ = (java.util.Optional) default_; + this.position = (java.util.Optional) position; + this.optional = (java.util.Optional) optional; + this.format = (java.util.Optional>) format; + this.type = (java.util.Optional) type; + } +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowFloatParameter.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowFloatParameter.java new file mode 100644 index 0000000..f10be86 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowFloatParameter.java @@ -0,0 +1,89 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.Saveable; + +/** + * Auto-generated interface for + * https://galaxyproject.org/gxformat2/v19_09#WorkflowFloatParameter
+ * This interface is implemented by {@link WorkflowFloatParameterImpl}
+ */ +public interface WorkflowFloatParameter extends BaseInputParameter, MinMax, Saveable { + /** + * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * + *
+ * + * The unique identifier for this object. * + * + *
+ */ + java.util.Optional getId(); + /** + * Getter for property https://w3id.org/cwl/cwl#Labeled/label
+ * + *
+ * + * A short, human-readable label of this object. * + * + *
+ */ + java.util.Optional getLabel(); + /** + * Getter for property https://w3id.org/cwl/salad#Documented/doc
+ * + *
+ * + * A documentation string for this object, or an array of strings which should be concatenated. * + * + *
+ */ + Object getDoc(); + /** + * Getter for property https://w3id.org/cwl/salad#default
+ * + *
+ * + * The default value to use for this parameter if the parameter is missing from the input object, + * or if the value of the parameter in the input object is `null`. Default values are applied + * before evaluating expressions (e.g. dependent `valueFrom` fields). * + * + *
+ */ + java.util.Optional getDefault(); + /** + * Getter for property + * https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
+ */ + java.util.Optional getPosition(); + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter/optional
+ * + *
+ * + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. * + * + *
+ */ + java.util.Optional getOptional(); + /** Getter for property https://galaxyproject.org/gxformat2/v19_09#MinMax/min
*/ + Object getMin(); + /** Getter for property https://galaxyproject.org/gxformat2/v19_09#MinMax/max
*/ + Object getMax(); + /** Getter for property https://w3id.org/cwl/salad#type
*/ + Object getType(); +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowFloatParameterImpl.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowFloatParameterImpl.java new file mode 100644 index 0000000..ce93d8e --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowFloatParameterImpl.java @@ -0,0 +1,336 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptions; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder; +import org.galaxyproject.gxformat2.v19_09.utils.SaveableImpl; +import org.galaxyproject.gxformat2.v19_09.utils.ValidationException; + +/** + * Auto-generated class implementation for + * https://galaxyproject.org/gxformat2/v19_09#WorkflowFloatParameter
+ */ +public class WorkflowFloatParameterImpl extends SaveableImpl implements WorkflowFloatParameter { + private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); + private java.util.Map extensionFields_ = new java.util.HashMap(); + + private java.util.Optional id; + + /** + * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * + *
+ * + * The unique identifier for this object. * + * + *
+ */ + public java.util.Optional getId() { + return this.id; + } + + private java.util.Optional label; + + /** + * Getter for property https://w3id.org/cwl/cwl#Labeled/label
+ * + *
+ * + * A short, human-readable label of this object. * + * + *
+ */ + public java.util.Optional getLabel() { + return this.label; + } + + private Object doc; + + /** + * Getter for property https://w3id.org/cwl/salad#Documented/doc
+ * + *
+ * + * A documentation string for this object, or an array of strings which should be concatenated. * + * + *
+ */ + public Object getDoc() { + return this.doc; + } + + private java.util.Optional default_; + + /** + * Getter for property https://w3id.org/cwl/salad#default
+ * + *
+ * + * The default value to use for this parameter if the parameter is missing from the input object, + * or if the value of the parameter in the input object is `null`. Default values are applied + * before evaluating expressions (e.g. dependent `valueFrom` fields). * + * + *
+ */ + public java.util.Optional getDefault() { + return this.default_; + } + + private java.util.Optional position; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
+ */ + public java.util.Optional getPosition() { + return this.position; + } + + private java.util.Optional optional; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter/optional
+ * + *
+ * + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. * + * + *
+ */ + public java.util.Optional getOptional() { + return this.optional; + } + + private Object min; + + /** Getter for property https://galaxyproject.org/gxformat2/v19_09#MinMax/min
*/ + public Object getMin() { + return this.min; + } + + private Object max; + + /** Getter for property https://galaxyproject.org/gxformat2/v19_09#MinMax/max
*/ + public Object getMax() { + return this.max; + } + + private Object type; + + /** Getter for property https://w3id.org/cwl/salad#type
*/ + public Object getType() { + return this.type; + } + + /** + * Used by {@link org.galaxyproject.gxformat2.v19_09.utils.RootLoader} to construct instances of + * WorkflowFloatParameterImpl. + * + * @param __doc_ Document fragment to load this record object from (presumably a {@link + * java.util.Map}). + * @param __baseUri_ Base URI to generate child document IDs against. + * @param __loadingOptions Context for loading URIs and populating objects. + * @param __docRoot_ ID at this position in the document (if available) (maybe?) + * @throws ValidationException If the document fragment is not a {@link java.util.Map} or + * validation of fields fails. + */ + public WorkflowFloatParameterImpl( + final Object __doc_, + final String __baseUri_, + LoadingOptions __loadingOptions, + final String __docRoot_) { + super(__doc_, __baseUri_, __loadingOptions, __docRoot_); + // Prefix plumbing variables with '__' to reduce likelihood of collision with + // generated names. + String __baseUri = __baseUri_; + String __docRoot = __docRoot_; + if (!(__doc_ instanceof java.util.Map)) { + throw new ValidationException("WorkflowFloatParameterImpl called on non-map"); + } + final java.util.Map __doc = (java.util.Map) __doc_; + final java.util.List __errors = + new java.util.ArrayList(); + if (__loadingOptions != null) { + this.loadingOptions_ = __loadingOptions; + } + java.util.Optional id; + + if (__doc.containsKey("id")) { + try { + id = + LoaderInstances.uri_optional_StringInstance_True_False_None_None.loadField( + __doc.get("id"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + id = null; // won't be used but prevents compiler from complaining. + final String __message = "the `id` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + id = null; + } + + Boolean __original_is_null = id == null; + if (id == null) { + if (__docRoot != null) { + id = java.util.Optional.of(__docRoot); + } else { + id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); + } + } + if (__original_is_null) { + __baseUri = __baseUri_; + } else { + __baseUri = (String) id.orElse(null); + } + java.util.Optional label; + + if (__doc.containsKey("label")) { + try { + label = + LoaderInstances.optional_StringInstance.loadField( + __doc.get("label"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + label = null; // won't be used but prevents compiler from complaining. + final String __message = "the `label` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + label = null; + } + Object doc; + + if (__doc.containsKey("doc")) { + try { + doc = + LoaderInstances.union_of_NullInstance_or_StringInstance_or_array_of_StringInstance + .loadField(__doc.get("doc"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + doc = null; // won't be used but prevents compiler from complaining. + final String __message = "the `doc` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + doc = null; + } + java.util.Optional default_; + + if (__doc.containsKey("default")) { + try { + default_ = + LoaderInstances.optional_AnyInstance.loadField( + __doc.get("default"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + default_ = null; // won't be used but prevents compiler from complaining. + final String __message = "the `default` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + default_ = null; + } + java.util.Optional position; + + if (__doc.containsKey("position")) { + try { + position = + LoaderInstances.optional_StepPosition.loadField( + __doc.get("position"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + position = null; // won't be used but prevents compiler from complaining. + final String __message = "the `position` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + position = null; + } + java.util.Optional optional; + + if (__doc.containsKey("optional")) { + try { + optional = + LoaderInstances.optional_BooleanInstance.loadField( + __doc.get("optional"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + optional = null; // won't be used but prevents compiler from complaining. + final String __message = "the `optional` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + optional = null; + } + Object min; + + if (__doc.containsKey("min")) { + try { + min = + LoaderInstances.union_of_IntegerInstance_or_DoubleInstance_or_NullInstance.loadField( + __doc.get("min"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + min = null; // won't be used but prevents compiler from complaining. + final String __message = "the `min` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + min = null; + } + Object max; + + if (__doc.containsKey("max")) { + try { + max = + LoaderInstances.union_of_IntegerInstance_or_DoubleInstance_or_NullInstance.loadField( + __doc.get("max"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + max = null; // won't be used but prevents compiler from complaining. + final String __message = "the `max` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + max = null; + } + Object type; + try { + type = + LoaderInstances.typedsl_union_of_GalaxyFloatType_or_array_of_WorkflowFloatParameter_2 + .loadField(__doc.get("type"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + type = null; // won't be used but prevents compiler from complaining. + final String __message = "the `type` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + if (!__errors.isEmpty()) { + throw new ValidationException("Trying 'RecordField'", __errors); + } + this.label = (java.util.Optional) label; + this.doc = (Object) doc; + this.id = (java.util.Optional) id; + this.default_ = (java.util.Optional) default_; + this.position = (java.util.Optional) position; + this.optional = (java.util.Optional) optional; + this.min = (Object) min; + this.max = (Object) max; + this.type = (Object) type; + } +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowIntegerParameter.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowIntegerParameter.java new file mode 100644 index 0000000..244f1d1 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowIntegerParameter.java @@ -0,0 +1,89 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.Saveable; + +/** + * Auto-generated interface for + * https://galaxyproject.org/gxformat2/v19_09#WorkflowIntegerParameter
+ * This interface is implemented by {@link WorkflowIntegerParameterImpl}
+ */ +public interface WorkflowIntegerParameter extends BaseInputParameter, MinMax, Saveable { + /** + * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * + *
+ * + * The unique identifier for this object. * + * + *
+ */ + java.util.Optional getId(); + /** + * Getter for property https://w3id.org/cwl/cwl#Labeled/label
+ * + *
+ * + * A short, human-readable label of this object. * + * + *
+ */ + java.util.Optional getLabel(); + /** + * Getter for property https://w3id.org/cwl/salad#Documented/doc
+ * + *
+ * + * A documentation string for this object, or an array of strings which should be concatenated. * + * + *
+ */ + Object getDoc(); + /** + * Getter for property https://w3id.org/cwl/salad#default
+ * + *
+ * + * The default value to use for this parameter if the parameter is missing from the input object, + * or if the value of the parameter in the input object is `null`. Default values are applied + * before evaluating expressions (e.g. dependent `valueFrom` fields). * + * + *
+ */ + java.util.Optional getDefault(); + /** + * Getter for property + * https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
+ */ + java.util.Optional getPosition(); + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter/optional
+ * + *
+ * + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. * + * + *
+ */ + java.util.Optional getOptional(); + /** Getter for property https://galaxyproject.org/gxformat2/v19_09#MinMax/min
*/ + Object getMin(); + /** Getter for property https://galaxyproject.org/gxformat2/v19_09#MinMax/max
*/ + Object getMax(); + /** Getter for property https://w3id.org/cwl/salad#type
*/ + Object getType(); +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowIntegerParameterImpl.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowIntegerParameterImpl.java new file mode 100644 index 0000000..a08a9dc --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowIntegerParameterImpl.java @@ -0,0 +1,336 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptions; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder; +import org.galaxyproject.gxformat2.v19_09.utils.SaveableImpl; +import org.galaxyproject.gxformat2.v19_09.utils.ValidationException; + +/** + * Auto-generated class implementation for + * https://galaxyproject.org/gxformat2/v19_09#WorkflowIntegerParameter
+ */ +public class WorkflowIntegerParameterImpl extends SaveableImpl implements WorkflowIntegerParameter { + private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); + private java.util.Map extensionFields_ = new java.util.HashMap(); + + private java.util.Optional id; + + /** + * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * + *
+ * + * The unique identifier for this object. * + * + *
+ */ + public java.util.Optional getId() { + return this.id; + } + + private java.util.Optional label; + + /** + * Getter for property https://w3id.org/cwl/cwl#Labeled/label
+ * + *
+ * + * A short, human-readable label of this object. * + * + *
+ */ + public java.util.Optional getLabel() { + return this.label; + } + + private Object doc; + + /** + * Getter for property https://w3id.org/cwl/salad#Documented/doc
+ * + *
+ * + * A documentation string for this object, or an array of strings which should be concatenated. * + * + *
+ */ + public Object getDoc() { + return this.doc; + } + + private java.util.Optional default_; + + /** + * Getter for property https://w3id.org/cwl/salad#default
+ * + *
+ * + * The default value to use for this parameter if the parameter is missing from the input object, + * or if the value of the parameter in the input object is `null`. Default values are applied + * before evaluating expressions (e.g. dependent `valueFrom` fields). * + * + *
+ */ + public java.util.Optional getDefault() { + return this.default_; + } + + private java.util.Optional position; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
+ */ + public java.util.Optional getPosition() { + return this.position; + } + + private java.util.Optional optional; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter/optional
+ * + *
+ * + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. * + * + *
+ */ + public java.util.Optional getOptional() { + return this.optional; + } + + private Object min; + + /** Getter for property https://galaxyproject.org/gxformat2/v19_09#MinMax/min
*/ + public Object getMin() { + return this.min; + } + + private Object max; + + /** Getter for property https://galaxyproject.org/gxformat2/v19_09#MinMax/max
*/ + public Object getMax() { + return this.max; + } + + private Object type; + + /** Getter for property https://w3id.org/cwl/salad#type
*/ + public Object getType() { + return this.type; + } + + /** + * Used by {@link org.galaxyproject.gxformat2.v19_09.utils.RootLoader} to construct instances of + * WorkflowIntegerParameterImpl. + * + * @param __doc_ Document fragment to load this record object from (presumably a {@link + * java.util.Map}). + * @param __baseUri_ Base URI to generate child document IDs against. + * @param __loadingOptions Context for loading URIs and populating objects. + * @param __docRoot_ ID at this position in the document (if available) (maybe?) + * @throws ValidationException If the document fragment is not a {@link java.util.Map} or + * validation of fields fails. + */ + public WorkflowIntegerParameterImpl( + final Object __doc_, + final String __baseUri_, + LoadingOptions __loadingOptions, + final String __docRoot_) { + super(__doc_, __baseUri_, __loadingOptions, __docRoot_); + // Prefix plumbing variables with '__' to reduce likelihood of collision with + // generated names. + String __baseUri = __baseUri_; + String __docRoot = __docRoot_; + if (!(__doc_ instanceof java.util.Map)) { + throw new ValidationException("WorkflowIntegerParameterImpl called on non-map"); + } + final java.util.Map __doc = (java.util.Map) __doc_; + final java.util.List __errors = + new java.util.ArrayList(); + if (__loadingOptions != null) { + this.loadingOptions_ = __loadingOptions; + } + java.util.Optional id; + + if (__doc.containsKey("id")) { + try { + id = + LoaderInstances.uri_optional_StringInstance_True_False_None_None.loadField( + __doc.get("id"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + id = null; // won't be used but prevents compiler from complaining. + final String __message = "the `id` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + id = null; + } + + Boolean __original_is_null = id == null; + if (id == null) { + if (__docRoot != null) { + id = java.util.Optional.of(__docRoot); + } else { + id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); + } + } + if (__original_is_null) { + __baseUri = __baseUri_; + } else { + __baseUri = (String) id.orElse(null); + } + java.util.Optional label; + + if (__doc.containsKey("label")) { + try { + label = + LoaderInstances.optional_StringInstance.loadField( + __doc.get("label"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + label = null; // won't be used but prevents compiler from complaining. + final String __message = "the `label` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + label = null; + } + Object doc; + + if (__doc.containsKey("doc")) { + try { + doc = + LoaderInstances.union_of_NullInstance_or_StringInstance_or_array_of_StringInstance + .loadField(__doc.get("doc"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + doc = null; // won't be used but prevents compiler from complaining. + final String __message = "the `doc` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + doc = null; + } + java.util.Optional default_; + + if (__doc.containsKey("default")) { + try { + default_ = + LoaderInstances.optional_AnyInstance.loadField( + __doc.get("default"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + default_ = null; // won't be used but prevents compiler from complaining. + final String __message = "the `default` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + default_ = null; + } + java.util.Optional position; + + if (__doc.containsKey("position")) { + try { + position = + LoaderInstances.optional_StepPosition.loadField( + __doc.get("position"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + position = null; // won't be used but prevents compiler from complaining. + final String __message = "the `position` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + position = null; + } + java.util.Optional optional; + + if (__doc.containsKey("optional")) { + try { + optional = + LoaderInstances.optional_BooleanInstance.loadField( + __doc.get("optional"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + optional = null; // won't be used but prevents compiler from complaining. + final String __message = "the `optional` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + optional = null; + } + Object min; + + if (__doc.containsKey("min")) { + try { + min = + LoaderInstances.union_of_IntegerInstance_or_DoubleInstance_or_NullInstance.loadField( + __doc.get("min"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + min = null; // won't be used but prevents compiler from complaining. + final String __message = "the `min` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + min = null; + } + Object max; + + if (__doc.containsKey("max")) { + try { + max = + LoaderInstances.union_of_IntegerInstance_or_DoubleInstance_or_NullInstance.loadField( + __doc.get("max"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + max = null; // won't be used but prevents compiler from complaining. + final String __message = "the `max` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + max = null; + } + Object type; + try { + type = + LoaderInstances.typedsl_union_of_GalaxyIntegerType_or_array_of_WorkflowIntegerParameter_2 + .loadField(__doc.get("type"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + type = null; // won't be used but prevents compiler from complaining. + final String __message = "the `type` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + if (!__errors.isEmpty()) { + throw new ValidationException("Trying 'RecordField'", __errors); + } + this.label = (java.util.Optional) label; + this.doc = (Object) doc; + this.id = (java.util.Optional) id; + this.default_ = (java.util.Optional) default_; + this.position = (java.util.Optional) position; + this.optional = (java.util.Optional) optional; + this.min = (Object) min; + this.max = (Object) max; + this.type = (Object) type; + } +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowTextParameter.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowTextParameter.java new file mode 100644 index 0000000..3a6222e --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowTextParameter.java @@ -0,0 +1,96 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.Saveable; + +/** + * Auto-generated interface for + * https://galaxyproject.org/gxformat2/v19_09#WorkflowTextParameter
+ * This interface is implemented by {@link WorkflowTextParameterImpl}
+ */ +public interface WorkflowTextParameter extends BaseInputParameter, Saveable { + /** + * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * + *
+ * + * The unique identifier for this object. * + * + *
+ */ + java.util.Optional getId(); + /** + * Getter for property https://w3id.org/cwl/cwl#Labeled/label
+ * + *
+ * + * A short, human-readable label of this object. * + * + *
+ */ + java.util.Optional getLabel(); + /** + * Getter for property https://w3id.org/cwl/salad#Documented/doc
+ * + *
+ * + * A documentation string for this object, or an array of strings which should be concatenated. * + * + *
+ */ + Object getDoc(); + /** + * Getter for property https://w3id.org/cwl/salad#default
+ * + *
+ * + * The default value to use for this parameter if the parameter is missing from the input object, + * or if the value of the parameter in the input object is `null`. Default values are applied + * before evaluating expressions (e.g. dependent `valueFrom` fields). * + * + *
+ */ + java.util.Optional getDefault(); + /** + * Getter for property + * https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
+ */ + java.util.Optional getPosition(); + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter/optional
+ * + *
+ * + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. * + * + *
+ */ + java.util.Optional getOptional(); + /** Getter for property https://w3id.org/cwl/salad#type
*/ + Object getType(); + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#WorkflowTextParameter/validators
+ * + *
+ * + * Apply one more validators to the input value. Input is valid if all validators succeed. * + * + *
+ */ + java.util.Optional> getValidators(); +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowTextParameterImpl.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowTextParameterImpl.java new file mode 100644 index 0000000..0679fc8 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/WorkflowTextParameterImpl.java @@ -0,0 +1,321 @@ +// Copyright Common Workflow Language project contributors +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptions; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder; +import org.galaxyproject.gxformat2.v19_09.utils.SaveableImpl; +import org.galaxyproject.gxformat2.v19_09.utils.ValidationException; + +/** + * Auto-generated class implementation for + * https://galaxyproject.org/gxformat2/v19_09#WorkflowTextParameter
+ */ +public class WorkflowTextParameterImpl extends SaveableImpl implements WorkflowTextParameter { + private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); + private java.util.Map extensionFields_ = new java.util.HashMap(); + + private java.util.Optional id; + + /** + * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * + *
+ * + * The unique identifier for this object. * + * + *
+ */ + public java.util.Optional getId() { + return this.id; + } + + private java.util.Optional label; + + /** + * Getter for property https://w3id.org/cwl/cwl#Labeled/label
+ * + *
+ * + * A short, human-readable label of this object. * + * + *
+ */ + public java.util.Optional getLabel() { + return this.label; + } + + private Object doc; + + /** + * Getter for property https://w3id.org/cwl/salad#Documented/doc
+ * + *
+ * + * A documentation string for this object, or an array of strings which should be concatenated. * + * + *
+ */ + public Object getDoc() { + return this.doc; + } + + private java.util.Optional default_; + + /** + * Getter for property https://w3id.org/cwl/salad#default
+ * + *
+ * + * The default value to use for this parameter if the parameter is missing from the input object, + * or if the value of the parameter in the input object is `null`. Default values are applied + * before evaluating expressions (e.g. dependent `valueFrom` fields). * + * + *
+ */ + public java.util.Optional getDefault() { + return this.default_; + } + + private java.util.Optional position; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
+ */ + public java.util.Optional getPosition() { + return this.position; + } + + private java.util.Optional optional; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter/optional
+ * + *
+ * + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. * + * + *
+ */ + public java.util.Optional getOptional() { + return this.optional; + } + + private Object type; + + /** Getter for property https://w3id.org/cwl/salad#type
*/ + public Object getType() { + return this.type; + } + + private java.util.Optional> validators; + + /** + * Getter for property + * https://galaxyproject.org/gxformat2/v19_09#WorkflowTextParameter/validators
+ * + *
+ * + * Apply one more validators to the input value. Input is valid if all validators succeed. * + * + *
+ */ + public java.util.Optional> getValidators() { + return this.validators; + } + + /** + * Used by {@link org.galaxyproject.gxformat2.v19_09.utils.RootLoader} to construct instances of + * WorkflowTextParameterImpl. + * + * @param __doc_ Document fragment to load this record object from (presumably a {@link + * java.util.Map}). + * @param __baseUri_ Base URI to generate child document IDs against. + * @param __loadingOptions Context for loading URIs and populating objects. + * @param __docRoot_ ID at this position in the document (if available) (maybe?) + * @throws ValidationException If the document fragment is not a {@link java.util.Map} or + * validation of fields fails. + */ + public WorkflowTextParameterImpl( + final Object __doc_, + final String __baseUri_, + LoadingOptions __loadingOptions, + final String __docRoot_) { + super(__doc_, __baseUri_, __loadingOptions, __docRoot_); + // Prefix plumbing variables with '__' to reduce likelihood of collision with + // generated names. + String __baseUri = __baseUri_; + String __docRoot = __docRoot_; + if (!(__doc_ instanceof java.util.Map)) { + throw new ValidationException("WorkflowTextParameterImpl called on non-map"); + } + final java.util.Map __doc = (java.util.Map) __doc_; + final java.util.List __errors = + new java.util.ArrayList(); + if (__loadingOptions != null) { + this.loadingOptions_ = __loadingOptions; + } + java.util.Optional id; + + if (__doc.containsKey("id")) { + try { + id = + LoaderInstances.uri_optional_StringInstance_True_False_None_None.loadField( + __doc.get("id"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + id = null; // won't be used but prevents compiler from complaining. + final String __message = "the `id` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + id = null; + } + + Boolean __original_is_null = id == null; + if (id == null) { + if (__docRoot != null) { + id = java.util.Optional.of(__docRoot); + } else { + id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); + } + } + if (__original_is_null) { + __baseUri = __baseUri_; + } else { + __baseUri = (String) id.orElse(null); + } + java.util.Optional label; + + if (__doc.containsKey("label")) { + try { + label = + LoaderInstances.optional_StringInstance.loadField( + __doc.get("label"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + label = null; // won't be used but prevents compiler from complaining. + final String __message = "the `label` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + label = null; + } + Object doc; + + if (__doc.containsKey("doc")) { + try { + doc = + LoaderInstances.union_of_NullInstance_or_StringInstance_or_array_of_StringInstance + .loadField(__doc.get("doc"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + doc = null; // won't be used but prevents compiler from complaining. + final String __message = "the `doc` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + doc = null; + } + java.util.Optional default_; + + if (__doc.containsKey("default")) { + try { + default_ = + LoaderInstances.optional_AnyInstance.loadField( + __doc.get("default"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + default_ = null; // won't be used but prevents compiler from complaining. + final String __message = "the `default` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + default_ = null; + } + java.util.Optional position; + + if (__doc.containsKey("position")) { + try { + position = + LoaderInstances.optional_StepPosition.loadField( + __doc.get("position"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + position = null; // won't be used but prevents compiler from complaining. + final String __message = "the `position` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + position = null; + } + java.util.Optional optional; + + if (__doc.containsKey("optional")) { + try { + optional = + LoaderInstances.optional_BooleanInstance.loadField( + __doc.get("optional"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + optional = null; // won't be used but prevents compiler from complaining. + final String __message = "the `optional` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + optional = null; + } + Object type; + try { + type = + LoaderInstances.typedsl_union_of_GalaxyTextType_or_array_of_WorkflowTextParameter_2 + .loadField(__doc.get("type"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + type = null; // won't be used but prevents compiler from complaining. + final String __message = "the `type` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + java.util.Optional> validators; + + if (__doc.containsKey("validators")) { + try { + validators = + LoaderInstances.optional_array_of_TextValidators.loadField( + __doc.get("validators"), __baseUri, __loadingOptions); + } catch (ValidationException e) { + validators = null; // won't be used but prevents compiler from complaining. + final String __message = "the `validators` field is not valid because:"; + __errors.add(new ValidationException(__message, e)); + } + + } else { + validators = null; + } + if (!__errors.isEmpty()) { + throw new ValidationException("Trying 'RecordField'", __errors); + } + this.label = (java.util.Optional) label; + this.doc = (Object) doc; + this.id = (java.util.Optional) id; + this.default_ = (java.util.Optional) default_; + this.position = (java.util.Optional) position; + this.optional = (java.util.Optional) optional; + this.type = (Object) type; + this.validators = (java.util.Optional>) validators; + } +} diff --git a/typescript/docs/assets/main.js b/typescript/docs/assets/main.js index b13205a..bd45452 100644 --- a/typescript/docs/assets/main.js +++ b/typescript/docs/assets/main.js @@ -1,5 +1,5 @@ -(()=>{var Ce=Object.create;var ue=Object.defineProperty;var Pe=Object.getOwnPropertyDescriptor;var Oe=Object.getOwnPropertyNames;var Re=Object.getPrototypeOf,_e=Object.prototype.hasOwnProperty;var Me=(t,e)=>()=>(e||t((e={exports:{}}).exports,e),e.exports);var De=(t,e,r,n)=>{if(e&&typeof e=="object"||typeof e=="function")for(let i of Oe(e))!_e.call(t,i)&&i!==r&&ue(t,i,{get:()=>e[i],enumerable:!(n=Pe(e,i))||n.enumerable});return t};var Fe=(t,e,r)=>(r=t!=null?Ce(Re(t)):{},De(e||!t||!t.__esModule?ue(r,"default",{value:t,enumerable:!0}):r,t));var pe=Me((de,fe)=>{(function(){var t=function(e){var r=new t.Builder;return r.pipeline.add(t.trimmer,t.stopWordFilter,t.stemmer),r.searchPipeline.add(t.stemmer),e.call(r,r),r.build()};t.version="2.3.9";t.utils={},t.utils.warn=function(e){return function(r){e.console&&console.warn&&console.warn(r)}}(this),t.utils.asString=function(e){return e==null?"":e.toString()},t.utils.clone=function(e){if(e==null)return e;for(var r=Object.create(null),n=Object.keys(e),i=0;i0){var h=t.utils.clone(r)||{};h.position=[a,l],h.index=s.length,s.push(new t.Token(n.slice(a,o),h))}a=o+1}}return s},t.tokenizer.separator=/[\s\-]+/;t.Pipeline=function(){this._stack=[]},t.Pipeline.registeredFunctions=Object.create(null),t.Pipeline.registerFunction=function(e,r){r in this.registeredFunctions&&t.utils.warn("Overwriting existing registered function: "+r),e.label=r,t.Pipeline.registeredFunctions[e.label]=e},t.Pipeline.warnIfFunctionNotRegistered=function(e){var r=e.label&&e.label in this.registeredFunctions;r||t.utils.warn(`Function is not registered with pipeline. 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rent\":{\"527\":{},\"528\":{},\"529\":{},\"530\":{},\"531\":{},\"532\":{},\"533\":{},\"534\":{},\"535\":{}}}]],\"pipeline\":[]}}"); \ No newline at end of file diff --git a/typescript/docs/classes/ArraySchema.html b/typescript/docs/classes/ArraySchema.html index ff08114..dc0407f 100644 --- a/typescript/docs/classes/ArraySchema.html +++ b/typescript/docs/classes/ArraySchema.html @@ -1,10 +1,10 @@ ArraySchema | org.galaxyproject.gxformat2.v19_09
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  • Public/Protected
  • All
Menu

Class ArraySchema

Auto-generated class implementation for https://w3id.org/cwl/salad#ArraySchema

-

Hierarchy

  • Saveable
    • ArraySchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

items

items: string | ArraySchema | RecordSchema | EnumSchema | (string | ArraySchema | RecordSchema | EnumSchema)[]
+

Hierarchy

  • Saveable
    • ArraySchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

items

items: string | RecordSchema | EnumSchema | ArraySchema | (string | RecordSchema | EnumSchema | ArraySchema)[]

Defines the type of the array elements.

-

loadingOptions

loadingOptions: LoadingOptions

type

type: ARRAY
+

loadingOptions

loadingOptions: LoadingOptions

type

type: ARRAY

Must be array

-

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

Hierarchy

  • Saveable
    • GalaxyWorkflow

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: string

Optional creator

creator?: any
+

Hierarchy

  • Saveable
    • GalaxyWorkflow

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: string

Optional creator

creator?: any

Can be a schema.org Person (https://schema.org/Person) or Organization (https://schema.org/Organization) entity

-

Optional doc

doc?: string | string[]
+

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string

The unique identifier for this object.

-

inputs

inputs: WorkflowInputParameter[]
+

inputs

inputs: any[]

Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is @@ -29,25 +29,25 @@

A note about label field.

assigned a value of null (or the value of default for that parameter, if provided) for the purposes of validation and evaluation of expressions.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

Optional license

license?: string
+

Optional license

license?: string

Must be a valid license listed at https://spdx.org/licenses/

-

loadingOptions

loadingOptions: LoadingOptions

outputs

outputs: WorkflowOutputParameter[]
+

loadingOptions

loadingOptions: LoadingOptions

outputs

outputs: WorkflowOutputParameter[]

Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.

-

Optional release

release?: string
+

Optional release

release?: string

If listed should correspond to the release of the workflow in its source reposiory.

-

Optional report

report?: Report
+

Optional report

report?: Report

Workflow invocation report template.

-

steps

steps: WorkflowStep[]
+

steps

steps: WorkflowStep[]

The individual steps that make up the workflow. Each step is executed when all of its input data links are fulfilled.

-

Optional tags

tags?: string[]
+

Optional tags

tags?: string[]

Tags for the workflow.

-

Optional uuid

uuid?: string
+

Optional uuid

uuid?: string

UUID uniquely representing this element.

-

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

Hierarchy

  • Saveable
    • WorkflowOutputParameter

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

Hierarchy

  • Saveable
    • WorkflowOutputParameter

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string

The unique identifier for this object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

loadingOptions

loadingOptions: LoadingOptions

Optional outputSource

outputSource?: string
+

loadingOptions

loadingOptions: LoadingOptions

Optional outputSource

outputSource?: string

Specifies workflow parameter that supply the value of to the output parameter.

-

Optional type

type?: GalaxyType
+

Optional type

type?: GalaxyType

Specify valid types of data that may be assigned to this parameter.

-

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

  • Used to construct instances of .

    throws

    ValidationException If the document fragment is not a {@link Dictionary} or validation of fields fails.

    diff --git a/typescript/docs/classes/WorkflowStep.html b/typescript/docs/classes/WorkflowStep.html index e100ad4..9f4b5d0 100644 --- a/typescript/docs/classes/WorkflowStep.html +++ b/typescript/docs/classes/WorkflowStep.html @@ -14,53 +14,53 @@

    A note about state and tool_state fields.

    Galaxy but shouldn't be written by humans.

    state can contained a typed map. Repeat values can be represented as YAML arrays. An alternative to representing state this way is defining inputs with default values.

    -

Hierarchy

  • Saveable
    • WorkflowStep

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

Hierarchy

  • Saveable
    • WorkflowStep

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional errors

errors?: string
+

Optional errors

errors?: string

During Galaxy export there may be some problem validating the tool state, tool used, etc.. that will be indicated by this field. The Galaxy user should be warned of these problems before the workflow can be used in Galaxy.

This field should not be used in human written Galaxy workflow files.

A typical problem is the referenced tool is not installed, this can be fixed by installed the tool and re-saving the workflow and then re-exporting it.

-

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string

The unique identifier for this object.

-

Optional in_

in_?: WorkflowStepInput[]
+

Optional in_

in_?: WorkflowStepInput[]

Defines the input parameters of the workflow step. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used build a user interface for constructing the input object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

loadingOptions

loadingOptions: LoadingOptions

Optional out

out?: (string | WorkflowStepOutput)[]
+

loadingOptions

loadingOptions: LoadingOptions

Optional out

out?: (string | WorkflowStepOutput)[]

Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.

This can also be called 'outputs' for legacy reasons - but the resulting workflow document is not a valid instance of this schema.

-

Optional position

position?: StepPosition

Optional run

run?: GalaxyWorkflow
+

Optional position

position?: StepPosition

Optional run

run?: GalaxyWorkflow

Specifies a subworkflow to run.

-

Optional runtime_inputs

runtime_inputs?: string[]

Optional state

state?: any
+

Optional runtime_inputs

runtime_inputs?: string[]

Optional state

state?: any

Structured tool state.

-

Optional tool_id

tool_id?: string
+

Optional tool_id

tool_id?: string

The tool ID used to run this step of the workflow (e.g. 'cat1' or 'toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0').

-

Optional tool_shed_repository

tool_shed_repository?: ToolShedRepository
+

Optional tool_shed_repository

tool_shed_repository?: ToolShedRepository

The Galaxy Tool Shed repository that should be installed in order to use this tool.

-

Optional tool_state

tool_state?: any
+

Optional tool_state

tool_state?: any

Unstructured tool state.

-

Optional tool_version

tool_version?: string
+

Optional tool_version

tool_version?: string

The tool version corresponding used to run this step of the workflow. For tool shed installed tools, the ID generally uniquely specifies a version and this field is optional.

-

Optional type

type?: WorkflowStepType
+

Optional type

type?: WorkflowStepType

Workflow step module's type (defaults to 'tool').

-

Optional uuid

uuid?: string
+

Optional uuid

uuid?: string

UUID uniquely representing this element.

-

Optional when

when?: string
+

Optional when

when?: string

If defined, only run the step when the expression evaluates to true. If false the step is skipped. A skipped step produces a null on each output.

Expression should be an ecma5.1 expression.

-

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

Hierarchy

  • Saveable
    • WorkflowStepOutput

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional add_tags

add_tags?: string[]

Optional change_datatype

change_datatype?: string

Optional delete_intermediate_datasets

delete_intermediate_datasets?: boolean

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hide

hide?: boolean

Optional id

id?: string
+

Hierarchy

  • Saveable
    • WorkflowStepOutput

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional add_tags

add_tags?: string[]

Optional change_datatype

change_datatype?: string

Optional delete_intermediate_datasets

delete_intermediate_datasets?: boolean

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hide

hide?: boolean

Optional id

id?: string

The unique identifier for this object.

-

loadingOptions

loadingOptions: LoadingOptions

Optional remove_tags

remove_tags?: string[]

Optional rename

rename?: string

Optional set_columns

set_columns?: string[]

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

loadingOptions

loadingOptions: LoadingOptions

Optional remove_tags

remove_tags?: string[]

Optional rename

rename?: string

Optional set_columns

set_columns?: string[]

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

Hierarchy

Implemented by

Index

Properties

Properties

Optional class_

class_?: string

Optional creator

creator?: any
+

Hierarchy

Implemented by

Index

Properties

Properties

Optional class_

class_?: string

Optional creator

creator?: any

Can be a schema.org Person (https://schema.org/Person) or Organization (https://schema.org/Organization) entity

-

Optional doc

doc?: string | string[]
+

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string

The unique identifier for this object.

-

inputs

inputs: WorkflowInputParameter[]
+

inputs

inputs: any[]

Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is @@ -29,22 +29,22 @@

A note about label field.

assigned a value of null (or the value of default for that parameter, if provided) for the purposes of validation and evaluation of expressions.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

Optional license

license?: string
+

Optional license

license?: string

Must be a valid license listed at https://spdx.org/licenses/

-

outputs

outputs: WorkflowOutputParameter[]
+

outputs

outputs: WorkflowOutputParameter[]

Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.

-

Optional release

release?: string
+

Optional release

release?: string

If listed should correspond to the release of the workflow in its source reposiory.

-

Optional report

report?: Report
+

Optional report

report?: Report

Workflow invocation report template.

-

steps

steps: WorkflowStep[]
+

steps

steps: WorkflowStep[]

The individual steps that make up the workflow. Each step is executed when all of its input data links are fulfilled.

-

Optional tags

tags?: string[]
+

Optional tags

tags?: string[]

Tags for the workflow.

-

Optional uuid

uuid?: string
+

Optional uuid

uuid?: string

UUID uniquely representing this element.

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

Settings

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Generated using TypeDoc

\ No newline at end of file diff --git a/typescript/docs/interfaces/HasStepErrorsProperties.html b/typescript/docs/interfaces/HasStepErrorsProperties.html index d9318f1..1a178ea 100644 --- a/typescript/docs/interfaces/HasStepErrorsProperties.html +++ b/typescript/docs/interfaces/HasStepErrorsProperties.html @@ -1,6 +1,6 @@ HasStepErrorsProperties | org.galaxyproject.gxformat2.v19_09
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Interface HasStepErrorsProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#HasStepErrors

-

Hierarchy

Index

Properties

Properties

Optional errors

errors?: string
+

Hierarchy

Index

Properties

Properties

Optional errors

errors?: string

During Galaxy export there may be some problem validating the tool state, tool used, etc.. that will be indicated by this field. The Galaxy user should be warned of these problems before the workflow can be used in Galaxy.

diff --git a/typescript/docs/interfaces/HasStepPositionProperties.html b/typescript/docs/interfaces/HasStepPositionProperties.html index 495d6ff..ce64931 100644 --- a/typescript/docs/interfaces/HasStepPositionProperties.html +++ b/typescript/docs/interfaces/HasStepPositionProperties.html @@ -1,3 +1,3 @@ HasStepPositionProperties | org.galaxyproject.gxformat2.v19_09
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Interface HasStepPositionProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition

-

Hierarchy

Index

Properties

Properties

Optional position

position?: StepPosition

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

Settings

Theme

Generated using TypeDoc

\ No newline at end of file +

Hierarchy

Index

Properties

Properties

Optional position

position?: StepPosition

Legend

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  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

Settings

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\ No newline at end of file diff --git a/typescript/docs/interfaces/HasUUIDProperties.html b/typescript/docs/interfaces/HasUUIDProperties.html index 9fc339b..e8dfee2 100644 --- a/typescript/docs/interfaces/HasUUIDProperties.html +++ b/typescript/docs/interfaces/HasUUIDProperties.html @@ -1,5 +1,5 @@ HasUUIDProperties | org.galaxyproject.gxformat2.v19_09
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Interface HasUUIDProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#HasUUID

-

Hierarchy

Index

Properties

Properties

Optional uuid

uuid?: string
+

Hierarchy

Index

Properties

Properties

Optional uuid

uuid?: string

UUID uniquely representing this element.

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

Settings

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\ No newline at end of file diff --git a/typescript/docs/interfaces/IdentifiedProperties.html b/typescript/docs/interfaces/IdentifiedProperties.html index ed6990f..3fb36cb 100644 --- a/typescript/docs/interfaces/IdentifiedProperties.html +++ b/typescript/docs/interfaces/IdentifiedProperties.html @@ -1,5 +1,5 @@ IdentifiedProperties | org.galaxyproject.gxformat2.v19_09
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Interface IdentifiedProperties

Auto-generated interface for https://w3id.org/cwl/cwl#Identified

-

Hierarchy

Index

Properties

Properties

Optional id

id?: string
+

Hierarchy

Index

Properties

Properties

Optional id

id?: string

The unique identifier for this object.

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

Settings

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\ No newline at end of file diff --git a/typescript/docs/interfaces/InputParameterProperties.html b/typescript/docs/interfaces/InputParameterProperties.html index efe72cd..27a77ab 100644 --- a/typescript/docs/interfaces/InputParameterProperties.html +++ b/typescript/docs/interfaces/InputParameterProperties.html @@ -1,14 +1,14 @@ InputParameterProperties | org.galaxyproject.gxformat2.v19_09
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Interface InputParameterProperties

Auto-generated interface for https://w3id.org/cwl/cwl#InputParameter

-

Hierarchy

Index

Properties

Properties

Optional default_

default_?: any
+

Hierarchy

Index

Properties

Properties

Optional default_

default_?: any

The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is null. Default values are applied before evaluating expressions (e.g. dependent valueFrom fields).

-

Optional doc

doc?: string | string[]
+

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional id

id?: string
+

Optional id

id?: string

The unique identifier for this object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

Settings

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Generated using TypeDoc

\ No newline at end of file diff --git a/typescript/docs/interfaces/LabeledProperties.html b/typescript/docs/interfaces/LabeledProperties.html index d4c1cb1..9b1c57d 100644 --- a/typescript/docs/interfaces/LabeledProperties.html +++ b/typescript/docs/interfaces/LabeledProperties.html @@ -1,5 +1,5 @@ LabeledProperties | org.galaxyproject.gxformat2.v19_09
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Interface LabeledProperties

Auto-generated interface for https://w3id.org/cwl/cwl#Labeled

-

Hierarchy

Index

Properties

Properties

Optional label

label?: string
+

Hierarchy

Index

Properties

Properties

Optional label

label?: string

A short, human-readable label of this object.

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

Settings

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Generated using TypeDoc

\ No newline at end of file diff --git a/typescript/docs/interfaces/MinMaxProperties.html b/typescript/docs/interfaces/MinMaxProperties.html new file mode 100644 index 0000000..4b73953 --- /dev/null +++ b/typescript/docs/interfaces/MinMaxProperties.html @@ -0,0 +1,3 @@ +MinMaxProperties | org.galaxyproject.gxformat2.v19_09
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Interface MinMaxProperties

+

Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#MinMax

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional max

max?: number

Optional min

min?: number

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

Settings

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Generated using TypeDoc

\ No newline at end of file diff --git a/typescript/docs/interfaces/OutputParameterProperties.html b/typescript/docs/interfaces/OutputParameterProperties.html index 43c2cb1..7a519d7 100644 --- a/typescript/docs/interfaces/OutputParameterProperties.html +++ b/typescript/docs/interfaces/OutputParameterProperties.html @@ -1,9 +1,9 @@ OutputParameterProperties | org.galaxyproject.gxformat2.v19_09
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Interface OutputParameterProperties

Auto-generated interface for https://w3id.org/cwl/cwl#OutputParameter

-

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional id

id?: string
+

Optional id

id?: string

The unique identifier for this object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

Legend

  • Constructor
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  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

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\ No newline at end of file diff --git a/typescript/docs/interfaces/ParameterProperties.html b/typescript/docs/interfaces/ParameterProperties.html index 0788b40..05afec3 100644 --- a/typescript/docs/interfaces/ParameterProperties.html +++ b/typescript/docs/interfaces/ParameterProperties.html @@ -1,10 +1,10 @@ ParameterProperties | org.galaxyproject.gxformat2.v19_09
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Interface ParameterProperties

Auto-generated interface for https://w3id.org/cwl/cwl#Parameter

Define an input or output parameter to a process.

-

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional id

id?: string
+

Optional id

id?: string

The unique identifier for this object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

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\ No newline at end of file diff --git a/typescript/docs/interfaces/ProcessProperties.html b/typescript/docs/interfaces/ProcessProperties.html index ae2f67b..c4c000c 100644 --- a/typescript/docs/interfaces/ProcessProperties.html +++ b/typescript/docs/interfaces/ProcessProperties.html @@ -3,11 +3,11 @@

The base executable type in CWL is the Process object defined by the document. Note that the Process object is abstract and cannot be directly executed.

-

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional id

id?: string
+

Optional id

id?: string

The unique identifier for this object.

-

inputs

inputs: WorkflowInputParameter[]
+

inputs

inputs: BaseInputParameter[]

Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is @@ -18,9 +18,9 @@ assigned a value of null (or the value of default for that parameter, if provided) for the purposes of validation and evaluation of expressions.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

outputs

outputs: WorkflowOutputParameter[]
+

outputs

outputs: WorkflowOutputParameter[]

Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

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\ No newline at end of file diff --git a/typescript/docs/interfaces/RecordFieldProperties.html b/typescript/docs/interfaces/RecordFieldProperties.html index 24c253f..d4ca7f5 100644 --- a/typescript/docs/interfaces/RecordFieldProperties.html +++ b/typescript/docs/interfaces/RecordFieldProperties.html @@ -1,10 +1,10 @@ RecordFieldProperties | org.galaxyproject.gxformat2.v19_09
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Interface RecordFieldProperties

Auto-generated interface for https://w3id.org/cwl/salad#RecordField

A field of a record.

-

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional extensionFields

extensionFields?: Dictionary<any>

name

name: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

name

name: string

The name of the field

-

type

type: string | ArraySchema | RecordSchema | EnumSchema | (string | ArraySchema | RecordSchema | EnumSchema)[]
+

type

type: string | RecordSchema | EnumSchema | ArraySchema | (string | RecordSchema | EnumSchema | ArraySchema)[]

The field type

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

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Generated using TypeDoc

\ No newline at end of file diff --git a/typescript/docs/interfaces/RecordSchemaProperties.html b/typescript/docs/interfaces/RecordSchemaProperties.html index cc95093..6825b20 100644 --- a/typescript/docs/interfaces/RecordSchemaProperties.html +++ b/typescript/docs/interfaces/RecordSchemaProperties.html @@ -1,7 +1,7 @@ RecordSchemaProperties | org.galaxyproject.gxformat2.v19_09
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Interface RecordSchemaProperties

Auto-generated interface for https://w3id.org/cwl/salad#RecordSchema

-

Hierarchy

  • RecordSchemaProperties

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional fields

fields?: RecordField[]
+

Hierarchy

  • RecordSchemaProperties

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional fields

fields?: RecordField[]

Defines the fields of the record.

-

type

type: RECORD
+

type

type: RECORD

Must be record

Legend

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  • Static method
  • Property
  • Inherited property

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\ No newline at end of file diff --git a/typescript/docs/interfaces/ReferencesToolProperties.html b/typescript/docs/interfaces/ReferencesToolProperties.html index eaa0093..3f4a7ae 100644 --- a/typescript/docs/interfaces/ReferencesToolProperties.html +++ b/typescript/docs/interfaces/ReferencesToolProperties.html @@ -1,10 +1,10 @@ ReferencesToolProperties | org.galaxyproject.gxformat2.v19_09
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Interface ReferencesToolProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool

-

Hierarchy

Index

Properties

Properties

Optional tool_id

tool_id?: string
+

Hierarchy

Index

Properties

Properties

Optional tool_id

tool_id?: string

The tool ID used to run this step of the workflow (e.g. 'cat1' or 'toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0').

-

Optional tool_shed_repository

tool_shed_repository?: ToolShedRepository
+

Optional tool_shed_repository

tool_shed_repository?: ToolShedRepository

The Galaxy Tool Shed repository that should be installed in order to use this tool.

-

Optional tool_version

tool_version?: string
+

Optional tool_version

tool_version?: string

The tool version corresponding used to run this step of the workflow. For tool shed installed tools, the ID generally uniquely specifies a version and this field is optional.

Legend

  • Constructor
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  • Method
  • Static property
  • Static method
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  • Inherited property

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\ No newline at end of file diff --git a/typescript/docs/interfaces/RegexMatchProperties.html b/typescript/docs/interfaces/RegexMatchProperties.html new file mode 100644 index 0000000..efc9ed5 --- /dev/null +++ b/typescript/docs/interfaces/RegexMatchProperties.html @@ -0,0 +1,7 @@ +RegexMatchProperties | org.galaxyproject.gxformat2.v19_09
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Interface RegexMatchProperties

+

Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#RegexMatch

+

Hierarchy

  • RegexMatchProperties

Implemented by

Index

Properties

Properties

doc

doc: string
+

Message to provide to user if validator did not succeed.

+

Optional extensionFields

extensionFields?: Dictionary<any>

regex

regex: string
+

Check if a regular expression matches the value. A value is only valid if a match is found.

+

Legend

  • Constructor
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\ No newline at end of file diff --git a/typescript/docs/interfaces/ReportProperties.html b/typescript/docs/interfaces/ReportProperties.html index 9390301..da0f68f 100644 --- a/typescript/docs/interfaces/ReportProperties.html +++ b/typescript/docs/interfaces/ReportProperties.html @@ -2,6 +2,6 @@

Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#Report

Definition of an invocation report for this workflow. Currently the only field is 'markdown'.

-

Hierarchy

  • ReportProperties

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

markdown

markdown: string
+

Hierarchy

  • ReportProperties

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

markdown

markdown: string

Galaxy flavored Markdown to define an invocation report.

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\ No newline at end of file diff --git a/typescript/docs/interfaces/SinkProperties.html b/typescript/docs/interfaces/SinkProperties.html index e1d091b..f0d9395 100644 --- a/typescript/docs/interfaces/SinkProperties.html +++ b/typescript/docs/interfaces/SinkProperties.html @@ -1,6 +1,6 @@ SinkProperties | org.galaxyproject.gxformat2.v19_09
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Interface SinkProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#Sink

-

Hierarchy

Index

Properties

Properties

Optional source

source?: string | string[]
+

Hierarchy

Index

Properties

Properties

Optional source

source?: string | string[]

Specifies one or more workflow parameters that will provide input to the underlying step parameter.

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\ No newline at end of file diff --git a/typescript/docs/interfaces/StepPositionProperties.html b/typescript/docs/interfaces/StepPositionProperties.html index 7ec7939..c1935f9 100644 --- a/typescript/docs/interfaces/StepPositionProperties.html +++ b/typescript/docs/interfaces/StepPositionProperties.html @@ -1,8 +1,8 @@ StepPositionProperties | org.galaxyproject.gxformat2.v19_09
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Interface StepPositionProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#StepPosition

This field specifies the location of the step's node when rendered in the workflow editor.

-

Hierarchy

  • StepPositionProperties

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

left

left: number
+

Hierarchy

  • StepPositionProperties

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

left

left: number

Relative horizontal position of the step's node when rendered in the workflow editor.

-

top

top: number
+

top

top: number

Relative vertical position of the step's node when rendered in the workflow editor.

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\ No newline at end of file diff --git a/typescript/docs/interfaces/TextValidatorsProperties.html b/typescript/docs/interfaces/TextValidatorsProperties.html new file mode 100644 index 0000000..d06a57f --- /dev/null +++ b/typescript/docs/interfaces/TextValidatorsProperties.html @@ -0,0 +1,3 @@ +TextValidatorsProperties | org.galaxyproject.gxformat2.v19_09
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Interface TextValidatorsProperties

+

Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#TextValidators

+

Hierarchy

  • TextValidatorsProperties

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

regex_match

regex_match: RegexMatch

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\ No newline at end of file diff --git a/typescript/docs/interfaces/ToolShedRepositoryProperties.html b/typescript/docs/interfaces/ToolShedRepositoryProperties.html index 3200632..1d87147 100644 --- a/typescript/docs/interfaces/ToolShedRepositoryProperties.html +++ b/typescript/docs/interfaces/ToolShedRepositoryProperties.html @@ -1,11 +1,11 @@ ToolShedRepositoryProperties | org.galaxyproject.gxformat2.v19_09
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Interface ToolShedRepositoryProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository

-

Hierarchy

  • ToolShedRepositoryProperties

Implemented by

Index

Properties

Properties

changeset_revision

changeset_revision: string
+

Hierarchy

  • ToolShedRepositoryProperties

Implemented by

Index

Properties

Properties

changeset_revision

changeset_revision: string

The revision of the tool shed repository this tool can be found in.

-

Optional extensionFields

extensionFields?: Dictionary<any>

name

name: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

name

name: string

The name of the tool shed repository this tool can be found in.

-

owner

owner: string
+

owner

owner: string

The owner of the tool shed repository this tool can be found in.

-

tool_shed

tool_shed: string
+

tool_shed

tool_shed: string

The URI of the tool shed containing the repository this tool can be found in - typically this should be toolshed.g2.bx.psu.edu.

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\ No newline at end of file diff --git a/typescript/docs/interfaces/WorkflowCollectionParameterProperties.html b/typescript/docs/interfaces/WorkflowCollectionParameterProperties.html new file mode 100644 index 0000000..76685ef --- /dev/null +++ b/typescript/docs/interfaces/WorkflowCollectionParameterProperties.html @@ -0,0 +1,21 @@ +WorkflowCollectionParameterProperties | org.galaxyproject.gxformat2.v19_09
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Interface WorkflowCollectionParameterProperties

+

Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowCollectionParameter

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional collection_type

collection_type?: string
+

Collection type (defaults to list if type is collection). Nested +collection types are separated with colons, e.g. list:list:paired.

+

Optional default_

default_?: any
+

The default value to use for this parameter if the parameter is missing +from the input object, or if the value of the parameter in the input +object is null. Default values are applied before evaluating expressions +(e.g. dependent valueFrom fields).

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string[]
+

Specify datatype extensions for valid input datasets.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional optional

optional?: boolean
+

If set to true, WorkflowInputParameter is not required to submit the workflow.

+

Optional position

position?: StepPosition

type

type: COLLECTION

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\ No newline at end of file diff --git a/typescript/docs/interfaces/WorkflowDataParameterProperties.html b/typescript/docs/interfaces/WorkflowDataParameterProperties.html new file mode 100644 index 0000000..3bac5c2 --- /dev/null +++ b/typescript/docs/interfaces/WorkflowDataParameterProperties.html @@ -0,0 +1,18 @@ +WorkflowDataParameterProperties | org.galaxyproject.gxformat2.v19_09
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Interface WorkflowDataParameterProperties

+

Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowDataParameter

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional default_

default_?: any
+

The default value to use for this parameter if the parameter is missing +from the input object, or if the value of the parameter in the input +object is null. Default values are applied before evaluating expressions +(e.g. dependent valueFrom fields).

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string[]
+

Specify datatype extensions for valid input datasets.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional optional

optional?: boolean
+

If set to true, WorkflowInputParameter is not required to submit the workflow.

+

Optional position

position?: StepPosition

Optional type

type?: GalaxyDataType

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\ No newline at end of file diff --git a/typescript/docs/interfaces/WorkflowFloatParameterProperties.html b/typescript/docs/interfaces/WorkflowFloatParameterProperties.html new file mode 100644 index 0000000..2f391b6 --- /dev/null +++ b/typescript/docs/interfaces/WorkflowFloatParameterProperties.html @@ -0,0 +1,16 @@ +WorkflowFloatParameterProperties | org.galaxyproject.gxformat2.v19_09
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Interface WorkflowFloatParameterProperties

+

Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowFloatParameter

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional default_

default_?: any
+

The default value to use for this parameter if the parameter is missing +from the input object, or if the value of the parameter in the input +object is null. Default values are applied before evaluating expressions +(e.g. dependent valueFrom fields).

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional max

max?: number

Optional min

min?: number

Optional optional

optional?: boolean
+

If set to true, WorkflowInputParameter is not required to submit the workflow.

+

Optional position

position?: StepPosition

type

type: FLOAT | WorkflowFloatParameter[]

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\ No newline at end of file diff --git a/typescript/docs/interfaces/WorkflowInputParameterProperties.html b/typescript/docs/interfaces/WorkflowInputParameterProperties.html deleted file mode 100644 index 95a00e0..0000000 --- a/typescript/docs/interfaces/WorkflowInputParameterProperties.html +++ /dev/null @@ -1,23 +0,0 @@ -WorkflowInputParameterProperties | org.galaxyproject.gxformat2.v19_09
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Interface WorkflowInputParameterProperties

-

Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowInputParameter

-

Hierarchy

Implemented by

Index

Properties

Properties

Optional collection_type

collection_type?: string
-

Collection type (defaults to list if type is collection). Nested -collection types are separated with colons, e.g. list:list:paired.

-

Optional default_

default_?: any
-

The default value to use for this parameter if the parameter is missing -from the input object, or if the value of the parameter in the input -object is null. Default values are applied before evaluating expressions -(e.g. dependent valueFrom fields).

-

Optional doc

doc?: string | string[]
-

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string[]
-

Specify datatype extension for valid input datasets.

-

Optional id

id?: string
-

The unique identifier for this object.

-

Optional label

label?: string
-

A short, human-readable label of this object.

-

Optional optional

optional?: boolean
-

If set to true, WorkflowInputParameter is not required to submit the workflow.

-

Optional position

position?: StepPosition

Optional type

type?: GalaxyType | GalaxyType[]
-

Specify valid types of data that may be assigned to this parameter.

-

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\ No newline at end of file diff --git a/typescript/docs/interfaces/WorkflowIntegerParameterProperties.html b/typescript/docs/interfaces/WorkflowIntegerParameterProperties.html new file mode 100644 index 0000000..5a05bae --- /dev/null +++ b/typescript/docs/interfaces/WorkflowIntegerParameterProperties.html @@ -0,0 +1,16 @@ +WorkflowIntegerParameterProperties | org.galaxyproject.gxformat2.v19_09
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Interface WorkflowIntegerParameterProperties

+

Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowIntegerParameter

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional default_

default_?: any
+

The default value to use for this parameter if the parameter is missing +from the input object, or if the value of the parameter in the input +object is null. Default values are applied before evaluating expressions +(e.g. dependent valueFrom fields).

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional max

max?: number

Optional min

min?: number

Optional optional

optional?: boolean
+

If set to true, WorkflowInputParameter is not required to submit the workflow.

+

Optional position

position?: StepPosition

type

type: GalaxyIntegerType | WorkflowIntegerParameter[]

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\ No newline at end of file diff --git a/typescript/docs/interfaces/WorkflowOutputParameterProperties.html b/typescript/docs/interfaces/WorkflowOutputParameterProperties.html index 117953a..f871bdf 100644 --- a/typescript/docs/interfaces/WorkflowOutputParameterProperties.html +++ b/typescript/docs/interfaces/WorkflowOutputParameterProperties.html @@ -4,15 +4,15 @@ connected to one parameter defined in the workflow that will provide the value of the output parameter. It is legal to connect a WorkflowInputParameter to a WorkflowOutputParameter.

-

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string

The unique identifier for this object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

Optional outputSource

outputSource?: string
+

Optional outputSource

outputSource?: string

Specifies workflow parameter that supply the value of to the output parameter.

-

Optional type

type?: GalaxyType
+

Optional type

type?: GalaxyType

Specify valid types of data that may be assigned to this parameter.

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\ No newline at end of file diff --git a/typescript/docs/interfaces/WorkflowStepInputProperties.html b/typescript/docs/interfaces/WorkflowStepInputProperties.html index d094fa2..723d5e0 100644 --- a/typescript/docs/interfaces/WorkflowStepInputProperties.html +++ b/typescript/docs/interfaces/WorkflowStepInputProperties.html @@ -1,15 +1,15 @@ WorkflowStepInputProperties | org.galaxyproject.gxformat2.v19_09
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Interface WorkflowStepInputProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowStepInput

TODO:

-

Hierarchy

Implemented by

Index

Properties

Properties

Optional default_

default_?: any
+

Hierarchy

Implemented by

Index

Properties

Properties

Optional default_

default_?: any

The default value for this parameter to use if either there is no source field, or the value produced by the source is null. The default must be applied prior to scattering or evaluating valueFrom.

-

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string

The unique identifier for this object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

Optional source

source?: string | string[]
+

Optional source

source?: string | string[]

Specifies one or more workflow parameters that will provide input to the underlying step parameter.

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\ No newline at end of file diff --git a/typescript/docs/interfaces/WorkflowStepOutputProperties.html b/typescript/docs/interfaces/WorkflowStepOutputProperties.html index 5dcdf25..6f473ca 100644 --- a/typescript/docs/interfaces/WorkflowStepOutputProperties.html +++ b/typescript/docs/interfaces/WorkflowStepOutputProperties.html @@ -7,6 +7,6 @@

A unique identifier for this workflow output parameter. This is the identifier to use in the source field of WorkflowStepInput to connect the output value to downstream parameters.

-

Hierarchy

Implemented by

Index

Properties

Properties

Optional add_tags

add_tags?: string[]

Optional change_datatype

change_datatype?: string

Optional delete_intermediate_datasets

delete_intermediate_datasets?: boolean

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hide

hide?: boolean

Optional id

id?: string
+

Hierarchy

Implemented by

Index

Properties

Properties

Optional add_tags

add_tags?: string[]

Optional change_datatype

change_datatype?: string

Optional delete_intermediate_datasets

delete_intermediate_datasets?: boolean

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hide

hide?: boolean

Optional id

id?: string

The unique identifier for this object.

-

Optional remove_tags

remove_tags?: string[]

Optional rename

rename?: string

Optional set_columns

set_columns?: string[]

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\ No newline at end of file +

Optional remove_tags

remove_tags?: string[]

Optional rename

rename?: string

Optional set_columns

set_columns?: string[]

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\ No newline at end of file diff --git a/typescript/docs/interfaces/WorkflowStepProperties.html b/typescript/docs/interfaces/WorkflowStepProperties.html index 0521066..78ca167 100644 --- a/typescript/docs/interfaces/WorkflowStepProperties.html +++ b/typescript/docs/interfaces/WorkflowStepProperties.html @@ -14,48 +14,48 @@

A note about state and tool_state fields.

Galaxy but shouldn't be written by humans.

state can contained a typed map. Repeat values can be represented as YAML arrays. An alternative to representing state this way is defining inputs with default values.

-

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional errors

errors?: string
+

Optional errors

errors?: string

During Galaxy export there may be some problem validating the tool state, tool used, etc.. that will be indicated by this field. The Galaxy user should be warned of these problems before the workflow can be used in Galaxy.

This field should not be used in human written Galaxy workflow files.

A typical problem is the referenced tool is not installed, this can be fixed by installed the tool and re-saving the workflow and then re-exporting it.

-

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string

The unique identifier for this object.

-

Optional in_

in_?: WorkflowStepInput[]
+

Optional in_

in_?: WorkflowStepInput[]

Defines the input parameters of the workflow step. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used build a user interface for constructing the input object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

Optional out

out?: (string | WorkflowStepOutput)[]
+

Optional out

out?: (string | WorkflowStepOutput)[]

Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.

This can also be called 'outputs' for legacy reasons - but the resulting workflow document is not a valid instance of this schema.

-

Optional position

position?: StepPosition

Optional run

run?: GalaxyWorkflow
+

Optional position

position?: StepPosition

Optional run

run?: GalaxyWorkflow

Specifies a subworkflow to run.

-

Optional runtime_inputs

runtime_inputs?: string[]

Optional state

state?: any
+

Optional runtime_inputs

runtime_inputs?: string[]

Optional state

state?: any

Structured tool state.

-

Optional tool_id

tool_id?: string
+

Optional tool_id

tool_id?: string

The tool ID used to run this step of the workflow (e.g. 'cat1' or 'toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0').

-

Optional tool_shed_repository

tool_shed_repository?: ToolShedRepository
+

Optional tool_shed_repository

tool_shed_repository?: ToolShedRepository

The Galaxy Tool Shed repository that should be installed in order to use this tool.

-

Optional tool_state

tool_state?: any
+

Optional tool_state

tool_state?: any

Unstructured tool state.

-

Optional tool_version

tool_version?: string
+

Optional tool_version

tool_version?: string

The tool version corresponding used to run this step of the workflow. For tool shed installed tools, the ID generally uniquely specifies a version and this field is optional.

-

Optional type

type?: WorkflowStepType
+

Optional type

type?: WorkflowStepType

Workflow step module's type (defaults to 'tool').

-

Optional uuid

uuid?: string
+

Optional uuid

uuid?: string

UUID uniquely representing this element.

-

Optional when

when?: string
+

Optional when

when?: string

If defined, only run the step when the expression evaluates to true. If false the step is skipped. A skipped step produces a null on each output.

diff --git a/typescript/docs/interfaces/WorkflowTextParameterProperties.html b/typescript/docs/interfaces/WorkflowTextParameterProperties.html new file mode 100644 index 0000000..8593951 --- /dev/null +++ b/typescript/docs/interfaces/WorkflowTextParameterProperties.html @@ -0,0 +1,18 @@ +WorkflowTextParameterProperties | org.galaxyproject.gxformat2.v19_09
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Interface WorkflowTextParameterProperties

+

Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowTextParameter

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional default_

default_?: any
+

The default value to use for this parameter if the parameter is missing +from the input object, or if the value of the parameter in the input +object is null. Default values are applied before evaluating expressions +(e.g. dependent valueFrom fields).

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional optional

optional?: boolean
+

If set to true, WorkflowInputParameter is not required to submit the workflow.

+

Optional position

position?: StepPosition

type

type: GalaxyTextType | WorkflowTextParameter[]

Optional validators

validators?: TextValidators[]
+

Apply one more validators to the input value. Input is valid if all validators succeed.

+

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\ No newline at end of file diff --git a/typescript/docs/modules.html b/typescript/docs/modules.html index 88d16b3..9ecea4e 100644 --- a/typescript/docs/modules.html +++ b/typescript/docs/modules.html @@ -1,4 +1,4 @@ -org.galaxyproject.gxformat2.v19_09
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Enumerations

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Interfaces

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Functions

loadDocument

loadDocumentByString

shortname

  • shortname(inputId: string): string

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"resolved": "https://registry.npmjs.org/workerpool/-/workerpool-6.2.0.tgz", + "integrity": "sha512-Rsk5qQHJ9eowMH28Jwhe8HEbmdYDX4lwoMWshiCXugjtHqMD9ZbiqSDLxcsfdqsETPzVUtX5s1Z5kStiIM6l4A==", "dev": true }, "wrap-ansi": { "version": "7.0.0", + "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz", + "integrity": "sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q==", "dev": true, "requires": { "ansi-styles": "^4.0.0", @@ -5222,10 +6385,14 @@ }, "wrappy": { "version": "1.0.2", + "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", + "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==", "dev": true }, "write-file-atomic": { "version": "3.0.3", + "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-3.0.3.tgz", + "integrity": "sha512-AvHcyZ5JnSfq3ioSyjrBkH9yW4m7Ayk8/9My/DD9onKeu/94fwrMocemO2QAJFAlnnDN+ZDS+ZjAR5ua1/PV/Q==", "dev": true, "requires": { "imurmurhash": "^0.1.4", @@ -5236,10 +6403,20 @@ }, "y18n": { "version": "5.0.8", + "resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz", + "integrity": "sha512-0pfFzegeDWJHJIAmTLRP2DwHjdF5s7jo9tuztdQxAhINCdvS+3nGINqPd00AphqJR/0LhANUS6/+7SCb98YOfA==", + "dev": true + }, + "yallist": { + "version": "3.1.1", + "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz", + "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==", "dev": true }, "yargs": { "version": "16.2.0", + "resolved": "https://registry.npmjs.org/yargs/-/yargs-16.2.0.tgz", + "integrity": "sha512-D1mvvtDG0L5ft/jGWkLpG1+m0eQxOfaBvTNELraWj22wSVUMWxZUvYgJYcKh6jGGIkJFhH4IZPQhR4TKpc8mBw==", "dev": true, "requires": { "cliui": "^7.0.2", @@ -5253,10 +6430,14 @@ }, "yargs-parser": { "version": "20.2.4", + "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.4.tgz", + "integrity": 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"https://registry.npmjs.org/yn/-/yn-3.1.1.tgz", + "integrity": "sha512-Ux4ygGWsu2c7isFWe8Yu1YluJmqVhxqK2cLXNQA5AcC3QfbGNpM7fu0Y8b/z16pXLnFxZYvWhd3fhBY9DLmC6Q==", "dev": true }, "yocto-queue": { "version": "0.1.0", + "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", + "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==", "dev": true } } diff --git a/typescript/src/BaseDataParameter.ts b/typescript/src/BaseDataParameter.ts new file mode 100644 index 0000000..76cbe6c --- /dev/null +++ b/typescript/src/BaseDataParameter.ts @@ -0,0 +1,298 @@ + +import { + Dictionary, + expandUrl, + loadField, + LoaderInstances, + LoadingOptions, + Saveable, + ValidationException, + prefixUrl, + save, + saveRelativeUri +} from './util/Internal' +import { v4 as uuidv4 } from 'uuid' +import * as Internal from './util/Internal' + + +/** + * Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#BaseDataParameter + */ +export class BaseDataParameter extends Saveable implements Internal.BaseDataParameterProperties { + extensionFields?: Internal.Dictionary + + /** + * The unique identifier for this object. + */ + id?: undefined | string + + /** + * A short, human-readable label of this object. + */ + label?: undefined | string + + /** + * A documentation string for this object, or an array of strings which should be concatenated. + */ + doc?: undefined | string | Array + + /** + * The default value to use for this parameter if the parameter is missing + * from the input object, or if the value of the parameter in the input + * object is `null`. Default values are applied before evaluating expressions + * (e.g. dependent `valueFrom` fields). + * + */ + default_?: undefined | any + position?: undefined | Internal.StepPosition + + /** + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. + * + */ + optional?: boolean | undefined + + /** + * Specify datatype extensions for valid input datasets. + * + */ + format?: undefined | Array + + + constructor ({loadingOptions, extensionFields, id, label, doc, default_, position, optional, format} : {loadingOptions?: LoadingOptions} & Internal.BaseDataParameterProperties) { + super(loadingOptions) + this.extensionFields = extensionFields ?? {} + this.id = id + this.label = label + this.doc = doc + this.default_ = default_ + this.position = position + this.optional = optional + this.format = format + } + + /** + * Used to construct instances of {@link BaseDataParameter }. + * + * @param __doc Document fragment to load this record object from. + * @param baseuri Base URI to generate child document IDs against. + * @param loadingOptions Context for loading URIs and populating objects. + * @param docRoot ID at this position in the document (if available) + * @returns An instance of {@link BaseDataParameter } + * @throws {@link ValidationException} If the document fragment is not a + * {@link Dictionary} or validation of fields fails. + */ + static override async fromDoc (__doc: any, baseuri: string, loadingOptions: LoadingOptions, + docRoot?: string): Promise { + const _doc = Object.assign({}, __doc) + const __errors: ValidationException[] = [] + + let id + if ('id' in _doc) { + try { + id = await loadField(_doc.id, LoaderInstances.uriunionOfundefinedtypeOrstrtypeTrueFalseNoneNone, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `id` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + const originalidIsUndefined = (id === undefined) + if (originalidIsUndefined ) { + if (docRoot != null) { + id = docRoot + } else { + id = "_" + uuidv4() + } + } else { + baseuri = id as string + } + + let label + if ('label' in _doc) { + try { + label = await loadField(_doc.label, LoaderInstances.unionOfundefinedtypeOrstrtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `label` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let doc + if ('doc' in _doc) { + try { + doc = await loadField(_doc.doc, LoaderInstances.unionOfundefinedtypeOrstrtypeOrarrayOfstrtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `doc` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let default_ + if ('default' in _doc) { + try { + default_ = await loadField(_doc.default, LoaderInstances.unionOfundefinedtypeOranyType, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `default` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let position + if ('position' in _doc) { + try { + position = await loadField(_doc.position, LoaderInstances.unionOfundefinedtypeOrStepPositionLoader, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `position` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let optional + if ('optional' in _doc) { + try { + optional = await loadField(_doc.optional, LoaderInstances.unionOfbooltypeOrundefinedtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `optional` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let format + if ('format' in _doc) { + try { + format = await loadField(_doc.format, LoaderInstances.unionOfundefinedtypeOrarrayOfstrtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `format` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + const extensionFields: Dictionary = {} + for (const [key, value] of Object.entries(_doc)) { + if (!BaseDataParameter.attr.has(key)) { + if ((key as string).includes(':')) { + const ex = expandUrl(key, '', loadingOptions, false, false) + extensionFields[ex] = value + } else { + __errors.push( + new ValidationException(`invalid field ${key as string}, \ + expected one of: \`label\`,\`doc\`,\`id\`,\`default\`,\`position\`,\`optional\`,\`format\``) + ) + break + } + } + } + + if (__errors.length > 0) { + throw new ValidationException("Trying 'BaseDataParameter'", __errors) + } + + const schema = new BaseDataParameter({ + extensionFields: extensionFields, + loadingOptions: loadingOptions, + label: label, + doc: doc, + id: id, + default_: default_, + position: position, + optional: optional, + format: format + }) + return schema + } + + save (top: boolean = false, baseUrl: string = '', relativeUris: boolean = true) + : Dictionary { + const r: Dictionary = {} + for (const ef in this.extensionFields) { + r[prefixUrl(ef, this.loadingOptions.vocab)] = this.extensionFields.ef + } + + if (this.id != null) { + const u = saveRelativeUri(this.id, baseUrl, true, + relativeUris, undefined) + if (u != null) { + r.id = u + } + } + + if (this.label != null) { + r.label = save(this.label, false, this.id, relativeUris) + } + + if (this.doc != null) { + r.doc = save(this.doc, false, this.id, relativeUris) + } + + if (this.default_ != null) { + r.default = save(this.default_, false, this.id, relativeUris) + } + + if (this.position != null) { + r.position = save(this.position, false, this.id, relativeUris) + } + + if (this.optional != null) { + r.optional = save(this.optional, false, this.id, relativeUris) + } + + if (this.format != null) { + r.format = save(this.format, false, this.id, relativeUris) + } + + if (top) { + if (this.loadingOptions.namespaces != null) { + r.$namespaces = this.loadingOptions.namespaces + } + if (this.loadingOptions.schemas != null) { + r.$schemas = this.loadingOptions.schemas + } + } + return r + } + + static attr: Set = new Set(['label','doc','id','default','position','optional','format']) +} diff --git a/typescript/src/BaseDataParameterProperties.ts b/typescript/src/BaseDataParameterProperties.ts new file mode 100644 index 0000000..3e633c5 --- /dev/null +++ b/typescript/src/BaseDataParameterProperties.ts @@ -0,0 +1,48 @@ + +import * as Internal from './util/Internal' + + +/** + * Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#BaseDataParameter + */ +export interface BaseDataParameterProperties extends Internal.BaseInputParameterProperties { + + extensionFields?: Internal.Dictionary + + /** + * The unique identifier for this object. + */ + id?: undefined | string + + /** + * A short, human-readable label of this object. + */ + label?: undefined | string + + /** + * A documentation string for this object, or an array of strings which should be concatenated. + */ + doc?: undefined | string | Array + + /** + * The default value to use for this parameter if the parameter is missing + * from the input object, or if the value of the parameter in the input + * object is `null`. Default values are applied before evaluating expressions + * (e.g. dependent `valueFrom` fields). + * + */ + default_?: undefined | any + position?: undefined | Internal.StepPosition + + /** + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. + * + */ + optional?: boolean | undefined + + /** + * Specify datatype extensions for valid input datasets. + * + */ + format?: undefined | Array +} \ No newline at end of file diff --git a/typescript/src/BaseInputParameter.ts b/typescript/src/BaseInputParameter.ts new file mode 100644 index 0000000..736ad25 --- /dev/null +++ b/typescript/src/BaseInputParameter.ts @@ -0,0 +1,270 @@ + +import { + Dictionary, + expandUrl, + loadField, + LoaderInstances, + LoadingOptions, + Saveable, + ValidationException, + prefixUrl, + save, + saveRelativeUri +} from './util/Internal' +import { v4 as uuidv4 } from 'uuid' +import * as Internal from './util/Internal' + + +/** + * Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter + */ +export class BaseInputParameter extends Saveable implements Internal.BaseInputParameterProperties { + extensionFields?: Internal.Dictionary + + /** + * The unique identifier for this object. + */ + id?: undefined | string + + /** + * A short, human-readable label of this object. + */ + label?: undefined | string + + /** + * A documentation string for this object, or an array of strings which should be concatenated. + */ + doc?: undefined | string | Array + + /** + * The default value to use for this parameter if the parameter is missing + * from the input object, or if the value of the parameter in the input + * object is `null`. Default values are applied before evaluating expressions + * (e.g. dependent `valueFrom` fields). + * + */ + default_?: undefined | any + position?: undefined | Internal.StepPosition + + /** + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. + * + */ + optional?: boolean | undefined + + + constructor ({loadingOptions, extensionFields, id, label, doc, default_, position, optional} : {loadingOptions?: LoadingOptions} & Internal.BaseInputParameterProperties) { + super(loadingOptions) + this.extensionFields = extensionFields ?? {} + this.id = id + this.label = label + this.doc = doc + this.default_ = default_ + this.position = position + this.optional = optional + } + + /** + * Used to construct instances of {@link BaseInputParameter }. + * + * @param __doc Document fragment to load this record object from. + * @param baseuri Base URI to generate child document IDs against. + * @param loadingOptions Context for loading URIs and populating objects. + * @param docRoot ID at this position in the document (if available) + * @returns An instance of {@link BaseInputParameter } + * @throws {@link ValidationException} If the document fragment is not a + * {@link Dictionary} or validation of fields fails. + */ + static override async fromDoc (__doc: any, baseuri: string, loadingOptions: LoadingOptions, + docRoot?: string): Promise { + const _doc = Object.assign({}, __doc) + const __errors: ValidationException[] = [] + + let id + if ('id' in _doc) { + try { + id = await loadField(_doc.id, LoaderInstances.uriunionOfundefinedtypeOrstrtypeTrueFalseNoneNone, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `id` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + const originalidIsUndefined = (id === undefined) + if (originalidIsUndefined ) { + if (docRoot != null) { + id = docRoot + } else { + id = "_" + uuidv4() + } + } else { + baseuri = id as string + } + + let label + if ('label' in _doc) { + try { + label = await loadField(_doc.label, LoaderInstances.unionOfundefinedtypeOrstrtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `label` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let doc + if ('doc' in _doc) { + try { + doc = await loadField(_doc.doc, LoaderInstances.unionOfundefinedtypeOrstrtypeOrarrayOfstrtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `doc` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let default_ + if ('default' in _doc) { + try { + default_ = await loadField(_doc.default, LoaderInstances.unionOfundefinedtypeOranyType, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `default` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let position + if ('position' in _doc) { + try { + position = await loadField(_doc.position, LoaderInstances.unionOfundefinedtypeOrStepPositionLoader, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `position` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let optional + if ('optional' in _doc) { + try { + optional = await loadField(_doc.optional, LoaderInstances.unionOfbooltypeOrundefinedtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `optional` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + const extensionFields: Dictionary = {} + for (const [key, value] of Object.entries(_doc)) { + if (!BaseInputParameter.attr.has(key)) { + if ((key as string).includes(':')) { + const ex = expandUrl(key, '', loadingOptions, false, false) + extensionFields[ex] = value + } else { + __errors.push( + new ValidationException(`invalid field ${key as string}, \ + expected one of: \`label\`,\`doc\`,\`id\`,\`default\`,\`position\`,\`optional\``) + ) + break + } + } + } + + if (__errors.length > 0) { + throw new ValidationException("Trying 'BaseInputParameter'", __errors) + } + + const schema = new BaseInputParameter({ + extensionFields: extensionFields, + loadingOptions: loadingOptions, + label: label, + doc: doc, + id: id, + default_: default_, + position: position, + optional: optional + }) + return schema + } + + save (top: boolean = false, baseUrl: string = '', relativeUris: boolean = true) + : Dictionary { + const r: Dictionary = {} + for (const ef in this.extensionFields) { + r[prefixUrl(ef, this.loadingOptions.vocab)] = this.extensionFields.ef + } + + if (this.id != null) { + const u = saveRelativeUri(this.id, baseUrl, true, + relativeUris, undefined) + if (u != null) { + r.id = u + } + } + + if (this.label != null) { + r.label = save(this.label, false, this.id, relativeUris) + } + + if (this.doc != null) { + r.doc = save(this.doc, false, this.id, relativeUris) + } + + if (this.default_ != null) { + r.default = save(this.default_, false, this.id, relativeUris) + } + + if (this.position != null) { + r.position = save(this.position, false, this.id, relativeUris) + } + + if (this.optional != null) { + r.optional = save(this.optional, false, this.id, relativeUris) + } + + if (top) { + if (this.loadingOptions.namespaces != null) { + r.$namespaces = this.loadingOptions.namespaces + } + if (this.loadingOptions.schemas != null) { + r.$schemas = this.loadingOptions.schemas + } + } + return r + } + + static attr: Set = new Set(['label','doc','id','default','position','optional']) +} diff --git a/typescript/src/BaseInputParameterProperties.ts b/typescript/src/BaseInputParameterProperties.ts new file mode 100644 index 0000000..c15285d --- /dev/null +++ b/typescript/src/BaseInputParameterProperties.ts @@ -0,0 +1,42 @@ + +import * as Internal from './util/Internal' + + +/** + * Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter + */ +export interface BaseInputParameterProperties extends Internal.InputParameterProperties, Internal.HasStepPositionProperties { + + extensionFields?: Internal.Dictionary + + /** + * The unique identifier for this object. + */ + id?: undefined | string + + /** + * A short, human-readable label of this object. + */ + label?: undefined | string + + /** + * A documentation string for this object, or an array of strings which should be concatenated. + */ + doc?: undefined | string | Array + + /** + * The default value to use for this parameter if the parameter is missing + * from the input object, or if the value of the parameter in the input + * object is `null`. Default values are applied before evaluating expressions + * (e.g. dependent `valueFrom` fields). + * + */ + default_?: undefined | any + position?: undefined | Internal.StepPosition + + /** + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. + * + */ + optional?: boolean | undefined +} \ No newline at end of file diff --git a/typescript/src/GalaxyBooleanType.ts b/typescript/src/GalaxyBooleanType.ts new file mode 100644 index 0000000..d6258d2 --- /dev/null +++ b/typescript/src/GalaxyBooleanType.ts @@ -0,0 +1,4 @@ + +export enum GalaxyBooleanType { + BOOL='bool', +} diff --git a/typescript/src/GalaxyDataCollectionType.ts b/typescript/src/GalaxyDataCollectionType.ts new file mode 100644 index 0000000..87748d8 --- /dev/null +++ b/typescript/src/GalaxyDataCollectionType.ts @@ -0,0 +1,4 @@ + +export enum GalaxyDataCollectionType { + COLLECTION='collection', +} diff --git a/typescript/src/GalaxyDataType.ts b/typescript/src/GalaxyDataType.ts new file mode 100644 index 0000000..53ca2da --- /dev/null +++ b/typescript/src/GalaxyDataType.ts @@ -0,0 +1,5 @@ + +export enum GalaxyDataType { + DATA='data', + FILE='File', +} diff --git a/typescript/src/GalaxyFloatType.ts b/typescript/src/GalaxyFloatType.ts new file mode 100644 index 0000000..e1fb502 --- /dev/null +++ b/typescript/src/GalaxyFloatType.ts @@ -0,0 +1,4 @@ + +export enum GalaxyFloatType { + FLOAT='float', +} diff --git a/typescript/src/GalaxyIntegerType.ts b/typescript/src/GalaxyIntegerType.ts new file mode 100644 index 0000000..d07fa95 --- /dev/null +++ b/typescript/src/GalaxyIntegerType.ts @@ -0,0 +1,5 @@ + +export enum GalaxyIntegerType { + INTEGER='integer', + INT='int', +} diff --git a/typescript/src/GalaxyTextType.ts b/typescript/src/GalaxyTextType.ts new file mode 100644 index 0000000..54947fc --- /dev/null +++ b/typescript/src/GalaxyTextType.ts @@ -0,0 +1,5 @@ + +export enum GalaxyTextType { + TEXT='text', + STRING='string', +} diff --git a/typescript/src/GalaxyType.ts b/typescript/src/GalaxyType.ts index 231d274..c5d2dad 100644 --- a/typescript/src/GalaxyType.ts +++ b/typescript/src/GalaxyType.ts @@ -1,15 +1,12 @@ export enum GalaxyType { - NULL='null', - BOOLEAN='boolean', - INT='int', - LONG='long', - FLOAT='float', - DOUBLE='double', - STRING='string', - INTEGER='integer', - TEXT='text', - FILE='File', DATA='data', + FILE='File', COLLECTION='collection', + TEXT='text', + STRING='string', + INTEGER='integer', + INT='int', + FLOAT='float', + BOOL='bool', } diff --git a/typescript/src/GalaxyWorkflow.ts b/typescript/src/GalaxyWorkflow.ts index ac67084..ebd26ef 100644 --- a/typescript/src/GalaxyWorkflow.ts +++ b/typescript/src/GalaxyWorkflow.ts @@ -65,7 +65,7 @@ export class GalaxyWorkflow extends Saveable implements Internal.GalaxyWorkflowP * of expressions. * */ - inputs: Array + inputs: Array /** * Defines the parameters representing the output of the process. May be diff --git a/typescript/src/GalaxyWorkflowProperties.ts b/typescript/src/GalaxyWorkflowProperties.ts index 75b4796..daa5277 100644 --- a/typescript/src/GalaxyWorkflowProperties.ts +++ b/typescript/src/GalaxyWorkflowProperties.ts @@ -53,7 +53,7 @@ export interface GalaxyWorkflowProperties extends Internal.ProcessProperties, In * of expressions. * */ - inputs: Array + inputs: Array /** * Defines the parameters representing the output of the process. May be diff --git a/typescript/src/MinMax.ts b/typescript/src/MinMax.ts new file mode 100644 index 0000000..73e52ad --- /dev/null +++ b/typescript/src/MinMax.ts @@ -0,0 +1,138 @@ + +import { + Dictionary, + expandUrl, + loadField, + LoaderInstances, + LoadingOptions, + Saveable, + ValidationException, + prefixUrl, + save, + saveRelativeUri +} from './util/Internal' +import { v4 as uuidv4 } from 'uuid' +import * as Internal from './util/Internal' + + +/** + * Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#MinMax + */ +export class MinMax extends Saveable implements Internal.MinMaxProperties { + extensionFields?: Internal.Dictionary + min?: number | undefined + max?: number | undefined + + + constructor ({loadingOptions, extensionFields, min, max} : {loadingOptions?: LoadingOptions} & Internal.MinMaxProperties) { + super(loadingOptions) + this.extensionFields = extensionFields ?? {} + this.min = min + this.max = max + } + + /** + * Used to construct instances of {@link MinMax }. + * + * @param __doc Document fragment to load this record object from. + * @param baseuri Base URI to generate child document IDs against. + * @param loadingOptions Context for loading URIs and populating objects. + * @param docRoot ID at this position in the document (if available) + * @returns An instance of {@link MinMax } + * @throws {@link ValidationException} If the document fragment is not a + * {@link Dictionary} or validation of fields fails. + */ + static override async fromDoc (__doc: any, baseuri: string, loadingOptions: LoadingOptions, + docRoot?: string): Promise { + const _doc = Object.assign({}, __doc) + const __errors: ValidationException[] = [] + + let min + if ('min' in _doc) { + try { + min = await loadField(_doc.min, LoaderInstances.unionOfinttypeOrfloattypeOrundefinedtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `min` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let max + if ('max' in _doc) { + try { + max = await loadField(_doc.max, LoaderInstances.unionOfinttypeOrfloattypeOrundefinedtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `max` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + const extensionFields: Dictionary = {} + for (const [key, value] of Object.entries(_doc)) { + if (!MinMax.attr.has(key)) { + if ((key as string).includes(':')) { + const ex = expandUrl(key, '', loadingOptions, false, false) + extensionFields[ex] = value + } else { + __errors.push( + new ValidationException(`invalid field ${key as string}, \ + expected one of: \`min\`,\`max\``) + ) + break + } + } + } + + if (__errors.length > 0) { + throw new ValidationException("Trying 'MinMax'", __errors) + } + + const schema = new MinMax({ + extensionFields: extensionFields, + loadingOptions: loadingOptions, + min: min, + max: max + }) + return schema + } + + save (top: boolean = false, baseUrl: string = '', relativeUris: boolean = true) + : Dictionary { + const r: Dictionary = {} + for (const ef in this.extensionFields) { + r[prefixUrl(ef, this.loadingOptions.vocab)] = this.extensionFields.ef + } + + if (this.min != null) { + r.min = save(this.min, false, baseUrl, relativeUris) + } + + if (this.max != null) { + r.max = save(this.max, false, baseUrl, relativeUris) + } + + if (top) { + if (this.loadingOptions.namespaces != null) { + r.$namespaces = this.loadingOptions.namespaces + } + if (this.loadingOptions.schemas != null) { + r.$schemas = this.loadingOptions.schemas + } + } + return r + } + + static attr: Set = new Set(['min','max']) +} diff --git a/typescript/src/MinMaxProperties.ts b/typescript/src/MinMaxProperties.ts new file mode 100644 index 0000000..076bc7b --- /dev/null +++ b/typescript/src/MinMaxProperties.ts @@ -0,0 +1,13 @@ + +import * as Internal from './util/Internal' + + +/** + * Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#MinMax + */ +export interface MinMaxProperties { + + extensionFields?: Internal.Dictionary + min?: number | undefined + max?: number | undefined +} \ No newline at end of file diff --git a/typescript/src/ProcessProperties.ts b/typescript/src/ProcessProperties.ts index 15e0d40..081364c 100644 --- a/typescript/src/ProcessProperties.ts +++ b/typescript/src/ProcessProperties.ts @@ -42,7 +42,7 @@ export interface ProcessProperties extends Internal.IdentifiedProperties, Intern * of expressions. * */ - inputs: Array + inputs: Array /** * Defines the parameters representing the output of the process. May be diff --git a/typescript/src/RegexMatch.ts b/typescript/src/RegexMatch.ts new file mode 100644 index 0000000..b1844b5 --- /dev/null +++ b/typescript/src/RegexMatch.ts @@ -0,0 +1,142 @@ + +import { + Dictionary, + expandUrl, + loadField, + LoaderInstances, + LoadingOptions, + Saveable, + ValidationException, + prefixUrl, + save, + saveRelativeUri +} from './util/Internal' +import { v4 as uuidv4 } from 'uuid' +import * as Internal from './util/Internal' + + +/** + * Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#RegexMatch + */ +export class RegexMatch extends Saveable implements Internal.RegexMatchProperties { + extensionFields?: Internal.Dictionary + + /** + * Check if a regular expression matches the value. A value is only valid if a match is found. + */ + regex: string + + /** + * Message to provide to user if validator did not succeed. + */ + doc: string + + + constructor ({loadingOptions, extensionFields, regex, doc} : {loadingOptions?: LoadingOptions} & Internal.RegexMatchProperties) { + super(loadingOptions) + this.extensionFields = extensionFields ?? {} + this.regex = regex + this.doc = doc + } + + /** + * Used to construct instances of {@link RegexMatch }. + * + * @param __doc Document fragment to load this record object from. + * @param baseuri Base URI to generate child document IDs against. + * @param loadingOptions Context for loading URIs and populating objects. + * @param docRoot ID at this position in the document (if available) + * @returns An instance of {@link RegexMatch } + * @throws {@link ValidationException} If the document fragment is not a + * {@link Dictionary} or validation of fields fails. + */ + static override async fromDoc (__doc: any, baseuri: string, loadingOptions: LoadingOptions, + docRoot?: string): Promise { + const _doc = Object.assign({}, __doc) + const __errors: ValidationException[] = [] + + let regex + try { + regex = await loadField(_doc.regex, LoaderInstances.unionOfstrtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `regex` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + + let doc + try { + doc = await loadField(_doc.doc, LoaderInstances.unionOfstrtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `doc` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + + const extensionFields: Dictionary = {} + for (const [key, value] of Object.entries(_doc)) { + if (!RegexMatch.attr.has(key)) { + if ((key as string).includes(':')) { + const ex = expandUrl(key, '', loadingOptions, false, false) + extensionFields[ex] = value + } else { + __errors.push( + new ValidationException(`invalid field ${key as string}, \ + expected one of: \`regex\`,\`doc\``) + ) + break + } + } + } + + if (__errors.length > 0) { + throw new ValidationException("Trying 'RegexMatch'", __errors) + } + + const schema = new RegexMatch({ + extensionFields: extensionFields, + loadingOptions: loadingOptions, + regex: regex, + doc: doc + }) + return schema + } + + save (top: boolean = false, baseUrl: string = '', relativeUris: boolean = true) + : Dictionary { + const r: Dictionary = {} + for (const ef in this.extensionFields) { + r[prefixUrl(ef, this.loadingOptions.vocab)] = this.extensionFields.ef + } + + if (this.regex != null) { + r.regex = save(this.regex, false, baseUrl, relativeUris) + } + + if (this.doc != null) { + r.doc = save(this.doc, false, baseUrl, relativeUris) + } + + if (top) { + if (this.loadingOptions.namespaces != null) { + r.$namespaces = this.loadingOptions.namespaces + } + if (this.loadingOptions.schemas != null) { + r.$schemas = this.loadingOptions.schemas + } + } + return r + } + + static attr: Set = new Set(['regex','doc']) +} diff --git a/typescript/src/RegexMatchProperties.ts b/typescript/src/RegexMatchProperties.ts new file mode 100644 index 0000000..04db40e --- /dev/null +++ b/typescript/src/RegexMatchProperties.ts @@ -0,0 +1,21 @@ + +import * as Internal from './util/Internal' + + +/** + * Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#RegexMatch + */ +export interface RegexMatchProperties { + + extensionFields?: Internal.Dictionary + + /** + * Check if a regular expression matches the value. A value is only valid if a match is found. + */ + regex: string + + /** + * Message to provide to user if validator did not succeed. + */ + doc: string +} \ No newline at end of file diff --git a/typescript/src/TextValidators.ts b/typescript/src/TextValidators.ts new file mode 100644 index 0000000..07d0619 --- /dev/null +++ b/typescript/src/TextValidators.ts @@ -0,0 +1,113 @@ + +import { + Dictionary, + expandUrl, + loadField, + LoaderInstances, + LoadingOptions, + Saveable, + ValidationException, + prefixUrl, + save, + saveRelativeUri +} from './util/Internal' +import { v4 as uuidv4 } from 'uuid' +import * as Internal from './util/Internal' + + +/** + * Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#TextValidators + */ +export class TextValidators extends Saveable implements Internal.TextValidatorsProperties { + extensionFields?: Internal.Dictionary + regex_match: Internal.RegexMatch + + + constructor ({loadingOptions, extensionFields, regex_match} : {loadingOptions?: LoadingOptions} & Internal.TextValidatorsProperties) { + super(loadingOptions) + this.extensionFields = extensionFields ?? {} + this.regex_match = regex_match + } + + /** + * Used to construct instances of {@link TextValidators }. + * + * @param __doc Document fragment to load this record object from. + * @param baseuri Base URI to generate child document IDs against. + * @param loadingOptions Context for loading URIs and populating objects. + * @param docRoot ID at this position in the document (if available) + * @returns An instance of {@link TextValidators } + * @throws {@link ValidationException} If the document fragment is not a + * {@link Dictionary} or validation of fields fails. + */ + static override async fromDoc (__doc: any, baseuri: string, loadingOptions: LoadingOptions, + docRoot?: string): Promise { + const _doc = Object.assign({}, __doc) + const __errors: ValidationException[] = [] + + let regex_match + try { + regex_match = await loadField(_doc.regex_match, LoaderInstances.unionOfRegexMatchLoader, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `regex_match` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + + const extensionFields: Dictionary = {} + for (const [key, value] of Object.entries(_doc)) { + if (!TextValidators.attr.has(key)) { + if ((key as string).includes(':')) { + const ex = expandUrl(key, '', loadingOptions, false, false) + extensionFields[ex] = value + } else { + __errors.push( + new ValidationException(`invalid field ${key as string}, \ + expected one of: \`regex_match\``) + ) + break + } + } + } + + if (__errors.length > 0) { + throw new ValidationException("Trying 'TextValidators'", __errors) + } + + const schema = new TextValidators({ + extensionFields: extensionFields, + loadingOptions: loadingOptions, + regex_match: regex_match + }) + return schema + } + + save (top: boolean = false, baseUrl: string = '', relativeUris: boolean = true) + : Dictionary { + const r: Dictionary = {} + for (const ef in this.extensionFields) { + r[prefixUrl(ef, this.loadingOptions.vocab)] = this.extensionFields.ef + } + + if (this.regex_match != null) { + r.regex_match = save(this.regex_match, false, baseUrl, relativeUris) + } + + if (top) { + if (this.loadingOptions.namespaces != null) { + r.$namespaces = this.loadingOptions.namespaces + } + if (this.loadingOptions.schemas != null) { + r.$schemas = this.loadingOptions.schemas + } + } + return r + } + + static attr: Set = new Set(['regex_match']) +} diff --git a/typescript/src/TextValidatorsProperties.ts b/typescript/src/TextValidatorsProperties.ts new file mode 100644 index 0000000..3fb4c18 --- /dev/null +++ b/typescript/src/TextValidatorsProperties.ts @@ -0,0 +1,12 @@ + +import * as Internal from './util/Internal' + + +/** + * Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#TextValidators + */ +export interface TextValidatorsProperties { + + extensionFields?: Internal.Dictionary + regex_match: Internal.RegexMatch +} \ No newline at end of file diff --git a/typescript/src/WorkflowInputParameter.ts b/typescript/src/WorkflowCollectionParameter.ts similarity index 87% rename from typescript/src/WorkflowInputParameter.ts rename to typescript/src/WorkflowCollectionParameter.ts index bf15b28..63e0fbe 100644 --- a/typescript/src/WorkflowInputParameter.ts +++ b/typescript/src/WorkflowCollectionParameter.ts @@ -16,9 +16,9 @@ import * as Internal from './util/Internal' /** - * Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#WorkflowInputParameter + * Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#WorkflowCollectionParameter */ -export class WorkflowInputParameter extends Saveable implements Internal.WorkflowInputParameterProperties { +export class WorkflowCollectionParameter extends Saveable implements Internal.WorkflowCollectionParameterProperties { extensionFields?: Internal.Dictionary /** @@ -46,12 +46,6 @@ export class WorkflowInputParameter extends Saveable implements Internal.Workflo default_?: undefined | any position?: undefined | Internal.StepPosition - /** - * Specify valid types of data that may be assigned to this parameter. - * - */ - type?: Internal.GalaxyType | undefined | Array - /** * If set to true, `WorkflowInputParameter` is not required to submit the workflow. * @@ -59,10 +53,11 @@ export class WorkflowInputParameter extends Saveable implements Internal.Workflo optional?: boolean | undefined /** - * Specify datatype extension for valid input datasets. + * Specify datatype extensions for valid input datasets. * */ format?: undefined | Array + type: Internal.GalaxyDataCollectionType /** * Collection type (defaults to `list` if `type` is `collection`). Nested @@ -72,7 +67,7 @@ export class WorkflowInputParameter extends Saveable implements Internal.Workflo collection_type?: undefined | string - constructor ({loadingOptions, extensionFields, id, label, doc, default_, position, type, optional, format, collection_type} : {loadingOptions?: LoadingOptions} & Internal.WorkflowInputParameterProperties) { + constructor ({loadingOptions, extensionFields, id, label, doc, default_, position, optional, format, type, collection_type} : {loadingOptions?: LoadingOptions} & Internal.WorkflowCollectionParameterProperties) { super(loadingOptions) this.extensionFields = extensionFields ?? {} this.id = id @@ -80,20 +75,20 @@ export class WorkflowInputParameter extends Saveable implements Internal.Workflo this.doc = doc this.default_ = default_ this.position = position - this.type = type this.optional = optional this.format = format + this.type = type this.collection_type = collection_type } /** - * Used to construct instances of {@link WorkflowInputParameter }. + * Used to construct instances of {@link WorkflowCollectionParameter }. * * @param __doc Document fragment to load this record object from. * @param baseuri Base URI to generate child document IDs against. * @param loadingOptions Context for loading URIs and populating objects. * @param docRoot ID at this position in the document (if available) - * @returns An instance of {@link WorkflowInputParameter } + * @returns An instance of {@link WorkflowCollectionParameter } * @throws {@link ValidationException} If the document fragment is not a * {@link Dictionary} or validation of fields fails. */ @@ -193,22 +188,6 @@ export class WorkflowInputParameter extends Saveable implements Internal.Workflo } } - let type - if ('type' in _doc) { - try { - type = await loadField(_doc.type, LoaderInstances.typedslunionOfGalaxyTypeLoaderOrundefinedtypeOrarrayOfunionOfGalaxyTypeLoader2, - baseuri, loadingOptions) - } catch (e) { - if (e instanceof ValidationException) { - __errors.push( - new ValidationException('the `type` field is not valid because: ', [e]) - ) - } else { - throw e - } - } - } - let optional if ('optional' in _doc) { try { @@ -241,6 +220,20 @@ export class WorkflowInputParameter extends Saveable implements Internal.Workflo } } + let type + try { + type = await loadField(_doc.type, LoaderInstances.typedslGalaxyDataCollectionTypeLoader2, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `type` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + let collection_type if ('collection_type' in _doc) { try { @@ -259,14 +252,14 @@ export class WorkflowInputParameter extends Saveable implements Internal.Workflo const extensionFields: Dictionary = {} for (const [key, value] of Object.entries(_doc)) { - if (!WorkflowInputParameter.attr.has(key)) { + if (!WorkflowCollectionParameter.attr.has(key)) { if ((key as string).includes(':')) { const ex = expandUrl(key, '', loadingOptions, false, false) extensionFields[ex] = value } else { __errors.push( new ValidationException(`invalid field ${key as string}, \ - expected one of: \`label\`,\`doc\`,\`id\`,\`default\`,\`position\`,\`type\`,\`optional\`,\`format\`,\`collection_type\``) + expected one of: \`label\`,\`doc\`,\`id\`,\`default\`,\`position\`,\`optional\`,\`format\`,\`type\`,\`collection_type\``) ) break } @@ -274,10 +267,10 @@ export class WorkflowInputParameter extends Saveable implements Internal.Workflo } if (__errors.length > 0) { - throw new ValidationException("Trying 'WorkflowInputParameter'", __errors) + throw new ValidationException("Trying 'WorkflowCollectionParameter'", __errors) } - const schema = new WorkflowInputParameter({ + const schema = new WorkflowCollectionParameter({ extensionFields: extensionFields, loadingOptions: loadingOptions, label: label, @@ -285,9 +278,9 @@ export class WorkflowInputParameter extends Saveable implements Internal.Workflo id: id, default_: default_, position: position, - type: type, optional: optional, format: format, + type: type, collection_type: collection_type }) return schema @@ -324,10 +317,6 @@ export class WorkflowInputParameter extends Saveable implements Internal.Workflo r.position = save(this.position, false, this.id, relativeUris) } - if (this.type != null) { - r.type = save(this.type, false, this.id, relativeUris) - } - if (this.optional != null) { r.optional = save(this.optional, false, this.id, relativeUris) } @@ -336,6 +325,10 @@ export class WorkflowInputParameter extends Saveable implements Internal.Workflo r.format = save(this.format, false, this.id, relativeUris) } + if (this.type != null) { + r.type = save(this.type, false, this.id, relativeUris) + } + if (this.collection_type != null) { r.collection_type = save(this.collection_type, false, this.id, relativeUris) } @@ -351,5 +344,5 @@ export class WorkflowInputParameter extends Saveable implements Internal.Workflo return r } - static attr: Set = new Set(['label','doc','id','default','position','type','optional','format','collection_type']) + static attr: Set = new Set(['label','doc','id','default','position','optional','format','type','collection_type']) } diff --git a/typescript/src/WorkflowInputParameterProperties.ts b/typescript/src/WorkflowCollectionParameterProperties.ts similarity index 77% rename from typescript/src/WorkflowInputParameterProperties.ts rename to typescript/src/WorkflowCollectionParameterProperties.ts index 143063f..4a959a5 100644 --- a/typescript/src/WorkflowInputParameterProperties.ts +++ b/typescript/src/WorkflowCollectionParameterProperties.ts @@ -3,9 +3,9 @@ import * as Internal from './util/Internal' /** - * Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowInputParameter + * Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowCollectionParameter */ -export interface WorkflowInputParameterProperties extends Internal.InputParameterProperties, Internal.HasStepPositionProperties { +export interface WorkflowCollectionParameterProperties extends Internal.BaseDataParameterProperties { extensionFields?: Internal.Dictionary @@ -34,12 +34,6 @@ export interface WorkflowInputParameterProperties extends Internal.InputParamete default_?: undefined | any position?: undefined | Internal.StepPosition - /** - * Specify valid types of data that may be assigned to this parameter. - * - */ - type?: Internal.GalaxyType | undefined | Array - /** * If set to true, `WorkflowInputParameter` is not required to submit the workflow. * @@ -47,10 +41,11 @@ export interface WorkflowInputParameterProperties extends Internal.InputParamete optional?: boolean | undefined /** - * Specify datatype extension for valid input datasets. + * Specify datatype extensions for valid input datasets. * */ format?: undefined | Array + type: Internal.GalaxyDataCollectionType /** * Collection type (defaults to `list` if `type` is `collection`). Nested diff --git a/typescript/src/WorkflowDataParameter.ts b/typescript/src/WorkflowDataParameter.ts new file mode 100644 index 0000000..4542665 --- /dev/null +++ b/typescript/src/WorkflowDataParameter.ts @@ -0,0 +1,321 @@ + +import { + Dictionary, + expandUrl, + loadField, + LoaderInstances, + LoadingOptions, + Saveable, + ValidationException, + prefixUrl, + save, + saveRelativeUri +} from './util/Internal' +import { v4 as uuidv4 } from 'uuid' +import * as Internal from './util/Internal' + + +/** + * Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#WorkflowDataParameter + */ +export class WorkflowDataParameter extends Saveable implements Internal.WorkflowDataParameterProperties { + extensionFields?: Internal.Dictionary + + /** + * The unique identifier for this object. + */ + id?: undefined | string + + /** + * A short, human-readable label of this object. + */ + label?: undefined | string + + /** + * A documentation string for this object, or an array of strings which should be concatenated. + */ + doc?: undefined | string | Array + + /** + * The default value to use for this parameter if the parameter is missing + * from the input object, or if the value of the parameter in the input + * object is `null`. Default values are applied before evaluating expressions + * (e.g. dependent `valueFrom` fields). + * + */ + default_?: undefined | any + position?: undefined | Internal.StepPosition + + /** + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. + * + */ + optional?: boolean | undefined + + /** + * Specify datatype extensions for valid input datasets. + * + */ + format?: undefined | Array + type?: Internal.GalaxyDataType | undefined + + + constructor ({loadingOptions, extensionFields, id, label, doc, default_, position, optional, format, type} : {loadingOptions?: LoadingOptions} & Internal.WorkflowDataParameterProperties) { + super(loadingOptions) + this.extensionFields = extensionFields ?? {} + this.id = id + this.label = label + this.doc = doc + this.default_ = default_ + this.position = position + this.optional = optional + this.format = format + this.type = type + } + + /** + * Used to construct instances of {@link WorkflowDataParameter }. + * + * @param __doc Document fragment to load this record object from. + * @param baseuri Base URI to generate child document IDs against. + * @param loadingOptions Context for loading URIs and populating objects. + * @param docRoot ID at this position in the document (if available) + * @returns An instance of {@link WorkflowDataParameter } + * @throws {@link ValidationException} If the document fragment is not a + * {@link Dictionary} or validation of fields fails. + */ + static override async fromDoc (__doc: any, baseuri: string, loadingOptions: LoadingOptions, + docRoot?: string): Promise { + const _doc = Object.assign({}, __doc) + const __errors: ValidationException[] = [] + + let id + if ('id' in _doc) { + try { + id = await loadField(_doc.id, LoaderInstances.uriunionOfundefinedtypeOrstrtypeTrueFalseNoneNone, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `id` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + const originalidIsUndefined = (id === undefined) + if (originalidIsUndefined ) { + if (docRoot != null) { + id = docRoot + } else { + id = "_" + uuidv4() + } + } else { + baseuri = id as string + } + + let label + if ('label' in _doc) { + try { + label = await loadField(_doc.label, LoaderInstances.unionOfundefinedtypeOrstrtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `label` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let doc + if ('doc' in _doc) { + try { + doc = await loadField(_doc.doc, LoaderInstances.unionOfundefinedtypeOrstrtypeOrarrayOfstrtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `doc` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let default_ + if ('default' in _doc) { + try { + default_ = await loadField(_doc.default, LoaderInstances.unionOfundefinedtypeOranyType, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `default` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let position + if ('position' in _doc) { + try { + position = await loadField(_doc.position, LoaderInstances.unionOfundefinedtypeOrStepPositionLoader, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `position` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let optional + if ('optional' in _doc) { + try { + optional = await loadField(_doc.optional, LoaderInstances.unionOfbooltypeOrundefinedtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `optional` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let format + if ('format' in _doc) { + try { + format = await loadField(_doc.format, LoaderInstances.unionOfundefinedtypeOrarrayOfstrtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `format` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let type + if ('type' in _doc) { + try { + type = await loadField(_doc.type, LoaderInstances.typedslunionOfGalaxyDataTypeLoaderOrundefinedtype2, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `type` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + const extensionFields: Dictionary = {} + for (const [key, value] of Object.entries(_doc)) { + if (!WorkflowDataParameter.attr.has(key)) { + if ((key as string).includes(':')) { + const ex = expandUrl(key, '', loadingOptions, false, false) + extensionFields[ex] = value + } else { + __errors.push( + new ValidationException(`invalid field ${key as string}, \ + expected one of: \`label\`,\`doc\`,\`id\`,\`default\`,\`position\`,\`optional\`,\`format\`,\`type\``) + ) + break + } + } + } + + if (__errors.length > 0) { + throw new ValidationException("Trying 'WorkflowDataParameter'", __errors) + } + + const schema = new WorkflowDataParameter({ + extensionFields: extensionFields, + loadingOptions: loadingOptions, + label: label, + doc: doc, + id: id, + default_: default_, + position: position, + optional: optional, + format: format, + type: type + }) + return schema + } + + save (top: boolean = false, baseUrl: string = '', relativeUris: boolean = true) + : Dictionary { + const r: Dictionary = {} + for (const ef in this.extensionFields) { + r[prefixUrl(ef, this.loadingOptions.vocab)] = this.extensionFields.ef + } + + if (this.id != null) { + const u = saveRelativeUri(this.id, baseUrl, true, + relativeUris, undefined) + if (u != null) { + r.id = u + } + } + + if (this.label != null) { + r.label = save(this.label, false, this.id, relativeUris) + } + + if (this.doc != null) { + r.doc = save(this.doc, false, this.id, relativeUris) + } + + if (this.default_ != null) { + r.default = save(this.default_, false, this.id, relativeUris) + } + + if (this.position != null) { + r.position = save(this.position, false, this.id, relativeUris) + } + + if (this.optional != null) { + r.optional = save(this.optional, false, this.id, relativeUris) + } + + if (this.format != null) { + r.format = save(this.format, false, this.id, relativeUris) + } + + if (this.type != null) { + r.type = save(this.type, false, this.id, relativeUris) + } + + if (top) { + if (this.loadingOptions.namespaces != null) { + r.$namespaces = this.loadingOptions.namespaces + } + if (this.loadingOptions.schemas != null) { + r.$schemas = this.loadingOptions.schemas + } + } + return r + } + + static attr: Set = new Set(['label','doc','id','default','position','optional','format','type']) +} diff --git a/typescript/src/WorkflowDataParameterProperties.ts b/typescript/src/WorkflowDataParameterProperties.ts new file mode 100644 index 0000000..9d46fb0 --- /dev/null +++ b/typescript/src/WorkflowDataParameterProperties.ts @@ -0,0 +1,49 @@ + +import * as Internal from './util/Internal' + + +/** + * Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowDataParameter + */ +export interface WorkflowDataParameterProperties extends Internal.BaseDataParameterProperties { + + extensionFields?: Internal.Dictionary + + /** + * The unique identifier for this object. + */ + id?: undefined | string + + /** + * A short, human-readable label of this object. + */ + label?: undefined | string + + /** + * A documentation string for this object, or an array of strings which should be concatenated. + */ + doc?: undefined | string | Array + + /** + * The default value to use for this parameter if the parameter is missing + * from the input object, or if the value of the parameter in the input + * object is `null`. Default values are applied before evaluating expressions + * (e.g. dependent `valueFrom` fields). + * + */ + default_?: undefined | any + position?: undefined | Internal.StepPosition + + /** + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. + * + */ + optional?: boolean | undefined + + /** + * Specify datatype extensions for valid input datasets. + * + */ + format?: undefined | Array + type?: Internal.GalaxyDataType | undefined +} \ No newline at end of file diff --git a/typescript/src/WorkflowFloatParameter.ts b/typescript/src/WorkflowFloatParameter.ts new file mode 100644 index 0000000..10288ae --- /dev/null +++ b/typescript/src/WorkflowFloatParameter.ts @@ -0,0 +1,337 @@ + +import { + Dictionary, + expandUrl, + loadField, + LoaderInstances, + LoadingOptions, + Saveable, + ValidationException, + prefixUrl, + save, + saveRelativeUri +} from './util/Internal' +import { v4 as uuidv4 } from 'uuid' +import * as Internal from './util/Internal' + + +/** + * Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#WorkflowFloatParameter + */ +export class WorkflowFloatParameter extends Saveable implements Internal.WorkflowFloatParameterProperties { + extensionFields?: Internal.Dictionary + + /** + * The unique identifier for this object. + */ + id?: undefined | string + + /** + * A short, human-readable label of this object. + */ + label?: undefined | string + + /** + * A documentation string for this object, or an array of strings which should be concatenated. + */ + doc?: undefined | string | Array + + /** + * The default value to use for this parameter if the parameter is missing + * from the input object, or if the value of the parameter in the input + * object is `null`. Default values are applied before evaluating expressions + * (e.g. dependent `valueFrom` fields). + * + */ + default_?: undefined | any + position?: undefined | Internal.StepPosition + + /** + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. + * + */ + optional?: boolean | undefined + min?: number | undefined + max?: number | undefined + type: Internal.GalaxyFloatType | Array + + + constructor ({loadingOptions, extensionFields, id, label, doc, default_, position, optional, min, max, type} : {loadingOptions?: LoadingOptions} & Internal.WorkflowFloatParameterProperties) { + super(loadingOptions) + this.extensionFields = extensionFields ?? {} + this.id = id + this.label = label + this.doc = doc + this.default_ = default_ + this.position = position + this.optional = optional + this.min = min + this.max = max + this.type = type + } + + /** + * Used to construct instances of {@link WorkflowFloatParameter }. + * + * @param __doc Document fragment to load this record object from. + * @param baseuri Base URI to generate child document IDs against. + * @param loadingOptions Context for loading URIs and populating objects. + * @param docRoot ID at this position in the document (if available) + * @returns An instance of {@link WorkflowFloatParameter } + * @throws {@link ValidationException} If the document fragment is not a + * {@link Dictionary} or validation of fields fails. + */ + static override async fromDoc (__doc: any, baseuri: string, loadingOptions: LoadingOptions, + docRoot?: string): Promise { + const _doc = Object.assign({}, __doc) + const __errors: ValidationException[] = [] + + let id + if ('id' in _doc) { + try { + id = await loadField(_doc.id, LoaderInstances.uriunionOfundefinedtypeOrstrtypeTrueFalseNoneNone, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `id` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + const originalidIsUndefined = (id === undefined) + if (originalidIsUndefined ) { + if (docRoot != null) { + id = docRoot + } else { + id = "_" + uuidv4() + } + } else { + baseuri = id as string + } + + let label + if ('label' in _doc) { + try { + label = await loadField(_doc.label, LoaderInstances.unionOfundefinedtypeOrstrtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `label` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let doc + if ('doc' in _doc) { + try { + doc = await loadField(_doc.doc, LoaderInstances.unionOfundefinedtypeOrstrtypeOrarrayOfstrtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `doc` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let default_ + if ('default' in _doc) { + try { + default_ = await loadField(_doc.default, LoaderInstances.unionOfundefinedtypeOranyType, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `default` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let position + if ('position' in _doc) { + try { + position = await loadField(_doc.position, LoaderInstances.unionOfundefinedtypeOrStepPositionLoader, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `position` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let optional + if ('optional' in _doc) { + try { + optional = await loadField(_doc.optional, LoaderInstances.unionOfbooltypeOrundefinedtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `optional` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let min + if ('min' in _doc) { + try { + min = await loadField(_doc.min, LoaderInstances.unionOfinttypeOrfloattypeOrundefinedtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `min` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let max + if ('max' in _doc) { + try { + max = await loadField(_doc.max, LoaderInstances.unionOfinttypeOrfloattypeOrundefinedtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `max` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let type + try { + type = await loadField(_doc.type, LoaderInstances.typedslunionOfGalaxyFloatTypeLoaderOrarrayOfunionOfWorkflowFloatParameterLoader2, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `type` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + + const extensionFields: Dictionary = {} + for (const [key, value] of Object.entries(_doc)) { + if (!WorkflowFloatParameter.attr.has(key)) { + if ((key as string).includes(':')) { + const ex = expandUrl(key, '', loadingOptions, false, false) + extensionFields[ex] = value + } else { + __errors.push( + new ValidationException(`invalid field ${key as string}, \ + expected one of: \`label\`,\`doc\`,\`id\`,\`default\`,\`position\`,\`optional\`,\`min\`,\`max\`,\`type\``) + ) + break + } + } + } + + if (__errors.length > 0) { + throw new ValidationException("Trying 'WorkflowFloatParameter'", __errors) + } + + const schema = new WorkflowFloatParameter({ + extensionFields: extensionFields, + loadingOptions: loadingOptions, + label: label, + doc: doc, + id: id, + default_: default_, + position: position, + optional: optional, + min: min, + max: max, + type: type + }) + return schema + } + + save (top: boolean = false, baseUrl: string = '', relativeUris: boolean = true) + : Dictionary { + const r: Dictionary = {} + for (const ef in this.extensionFields) { + r[prefixUrl(ef, this.loadingOptions.vocab)] = this.extensionFields.ef + } + + if (this.id != null) { + const u = saveRelativeUri(this.id, baseUrl, true, + relativeUris, undefined) + if (u != null) { + r.id = u + } + } + + if (this.label != null) { + r.label = save(this.label, false, this.id, relativeUris) + } + + if (this.doc != null) { + r.doc = save(this.doc, false, this.id, relativeUris) + } + + if (this.default_ != null) { + r.default = save(this.default_, false, this.id, relativeUris) + } + + if (this.position != null) { + r.position = save(this.position, false, this.id, relativeUris) + } + + if (this.optional != null) { + r.optional = save(this.optional, false, this.id, relativeUris) + } + + if (this.min != null) { + r.min = save(this.min, false, this.id, relativeUris) + } + + if (this.max != null) { + r.max = save(this.max, false, this.id, relativeUris) + } + + if (this.type != null) { + r.type = save(this.type, false, this.id, relativeUris) + } + + if (top) { + if (this.loadingOptions.namespaces != null) { + r.$namespaces = this.loadingOptions.namespaces + } + if (this.loadingOptions.schemas != null) { + r.$schemas = this.loadingOptions.schemas + } + } + return r + } + + static attr: Set = new Set(['label','doc','id','default','position','optional','min','max','type']) +} diff --git a/typescript/src/WorkflowFloatParameterProperties.ts b/typescript/src/WorkflowFloatParameterProperties.ts new file mode 100644 index 0000000..6abc6bc --- /dev/null +++ b/typescript/src/WorkflowFloatParameterProperties.ts @@ -0,0 +1,45 @@ + +import * as Internal from './util/Internal' + + +/** + * Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowFloatParameter + */ +export interface WorkflowFloatParameterProperties extends Internal.BaseInputParameterProperties, Internal.MinMaxProperties { + + extensionFields?: Internal.Dictionary + + /** + * The unique identifier for this object. + */ + id?: undefined | string + + /** + * A short, human-readable label of this object. + */ + label?: undefined | string + + /** + * A documentation string for this object, or an array of strings which should be concatenated. + */ + doc?: undefined | string | Array + + /** + * The default value to use for this parameter if the parameter is missing + * from the input object, or if the value of the parameter in the input + * object is `null`. Default values are applied before evaluating expressions + * (e.g. dependent `valueFrom` fields). + * + */ + default_?: undefined | any + position?: undefined | Internal.StepPosition + + /** + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. + * + */ + optional?: boolean | undefined + min?: number | undefined + max?: number | undefined + type: Internal.GalaxyFloatType | Array +} \ No newline at end of file diff --git a/typescript/src/WorkflowIntegerParameter.ts b/typescript/src/WorkflowIntegerParameter.ts new file mode 100644 index 0000000..8e450c2 --- /dev/null +++ b/typescript/src/WorkflowIntegerParameter.ts @@ -0,0 +1,337 @@ + +import { + Dictionary, + expandUrl, + loadField, + LoaderInstances, + LoadingOptions, + Saveable, + ValidationException, + prefixUrl, + save, + saveRelativeUri +} from './util/Internal' +import { v4 as uuidv4 } from 'uuid' +import * as Internal from './util/Internal' + + +/** + * Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#WorkflowIntegerParameter + */ +export class WorkflowIntegerParameter extends Saveable implements Internal.WorkflowIntegerParameterProperties { + extensionFields?: Internal.Dictionary + + /** + * The unique identifier for this object. + */ + id?: undefined | string + + /** + * A short, human-readable label of this object. + */ + label?: undefined | string + + /** + * A documentation string for this object, or an array of strings which should be concatenated. + */ + doc?: undefined | string | Array + + /** + * The default value to use for this parameter if the parameter is missing + * from the input object, or if the value of the parameter in the input + * object is `null`. Default values are applied before evaluating expressions + * (e.g. dependent `valueFrom` fields). + * + */ + default_?: undefined | any + position?: undefined | Internal.StepPosition + + /** + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. + * + */ + optional?: boolean | undefined + min?: number | undefined + max?: number | undefined + type: Internal.GalaxyIntegerType | Array + + + constructor ({loadingOptions, extensionFields, id, label, doc, default_, position, optional, min, max, type} : {loadingOptions?: LoadingOptions} & Internal.WorkflowIntegerParameterProperties) { + super(loadingOptions) + this.extensionFields = extensionFields ?? {} + this.id = id + this.label = label + this.doc = doc + this.default_ = default_ + this.position = position + this.optional = optional + this.min = min + this.max = max + this.type = type + } + + /** + * Used to construct instances of {@link WorkflowIntegerParameter }. + * + * @param __doc Document fragment to load this record object from. + * @param baseuri Base URI to generate child document IDs against. + * @param loadingOptions Context for loading URIs and populating objects. + * @param docRoot ID at this position in the document (if available) + * @returns An instance of {@link WorkflowIntegerParameter } + * @throws {@link ValidationException} If the document fragment is not a + * {@link Dictionary} or validation of fields fails. + */ + static override async fromDoc (__doc: any, baseuri: string, loadingOptions: LoadingOptions, + docRoot?: string): Promise { + const _doc = Object.assign({}, __doc) + const __errors: ValidationException[] = [] + + let id + if ('id' in _doc) { + try { + id = await loadField(_doc.id, LoaderInstances.uriunionOfundefinedtypeOrstrtypeTrueFalseNoneNone, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `id` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + const originalidIsUndefined = (id === undefined) + if (originalidIsUndefined ) { + if (docRoot != null) { + id = docRoot + } else { + id = "_" + uuidv4() + } + } else { + baseuri = id as string + } + + let label + if ('label' in _doc) { + try { + label = await loadField(_doc.label, LoaderInstances.unionOfundefinedtypeOrstrtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `label` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let doc + if ('doc' in _doc) { + try { + doc = await loadField(_doc.doc, LoaderInstances.unionOfundefinedtypeOrstrtypeOrarrayOfstrtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `doc` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let default_ + if ('default' in _doc) { + try { + default_ = await loadField(_doc.default, LoaderInstances.unionOfundefinedtypeOranyType, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `default` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let position + if ('position' in _doc) { + try { + position = await loadField(_doc.position, LoaderInstances.unionOfundefinedtypeOrStepPositionLoader, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `position` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let optional + if ('optional' in _doc) { + try { + optional = await loadField(_doc.optional, LoaderInstances.unionOfbooltypeOrundefinedtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `optional` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let min + if ('min' in _doc) { + try { + min = await loadField(_doc.min, LoaderInstances.unionOfinttypeOrfloattypeOrundefinedtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `min` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let max + if ('max' in _doc) { + try { + max = await loadField(_doc.max, LoaderInstances.unionOfinttypeOrfloattypeOrundefinedtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `max` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let type + try { + type = await loadField(_doc.type, LoaderInstances.typedslunionOfGalaxyIntegerTypeLoaderOrarrayOfunionOfWorkflowIntegerParameterLoader2, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `type` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + + const extensionFields: Dictionary = {} + for (const [key, value] of Object.entries(_doc)) { + if (!WorkflowIntegerParameter.attr.has(key)) { + if ((key as string).includes(':')) { + const ex = expandUrl(key, '', loadingOptions, false, false) + extensionFields[ex] = value + } else { + __errors.push( + new ValidationException(`invalid field ${key as string}, \ + expected one of: \`label\`,\`doc\`,\`id\`,\`default\`,\`position\`,\`optional\`,\`min\`,\`max\`,\`type\``) + ) + break + } + } + } + + if (__errors.length > 0) { + throw new ValidationException("Trying 'WorkflowIntegerParameter'", __errors) + } + + const schema = new WorkflowIntegerParameter({ + extensionFields: extensionFields, + loadingOptions: loadingOptions, + label: label, + doc: doc, + id: id, + default_: default_, + position: position, + optional: optional, + min: min, + max: max, + type: type + }) + return schema + } + + save (top: boolean = false, baseUrl: string = '', relativeUris: boolean = true) + : Dictionary { + const r: Dictionary = {} + for (const ef in this.extensionFields) { + r[prefixUrl(ef, this.loadingOptions.vocab)] = this.extensionFields.ef + } + + if (this.id != null) { + const u = saveRelativeUri(this.id, baseUrl, true, + relativeUris, undefined) + if (u != null) { + r.id = u + } + } + + if (this.label != null) { + r.label = save(this.label, false, this.id, relativeUris) + } + + if (this.doc != null) { + r.doc = save(this.doc, false, this.id, relativeUris) + } + + if (this.default_ != null) { + r.default = save(this.default_, false, this.id, relativeUris) + } + + if (this.position != null) { + r.position = save(this.position, false, this.id, relativeUris) + } + + if (this.optional != null) { + r.optional = save(this.optional, false, this.id, relativeUris) + } + + if (this.min != null) { + r.min = save(this.min, false, this.id, relativeUris) + } + + if (this.max != null) { + r.max = save(this.max, false, this.id, relativeUris) + } + + if (this.type != null) { + r.type = save(this.type, false, this.id, relativeUris) + } + + if (top) { + if (this.loadingOptions.namespaces != null) { + r.$namespaces = this.loadingOptions.namespaces + } + if (this.loadingOptions.schemas != null) { + r.$schemas = this.loadingOptions.schemas + } + } + return r + } + + static attr: Set = new Set(['label','doc','id','default','position','optional','min','max','type']) +} diff --git a/typescript/src/WorkflowIntegerParameterProperties.ts b/typescript/src/WorkflowIntegerParameterProperties.ts new file mode 100644 index 0000000..b4259c2 --- /dev/null +++ b/typescript/src/WorkflowIntegerParameterProperties.ts @@ -0,0 +1,45 @@ + +import * as Internal from './util/Internal' + + +/** + * Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowIntegerParameter + */ +export interface WorkflowIntegerParameterProperties extends Internal.BaseInputParameterProperties, Internal.MinMaxProperties { + + extensionFields?: Internal.Dictionary + + /** + * The unique identifier for this object. + */ + id?: undefined | string + + /** + * A short, human-readable label of this object. + */ + label?: undefined | string + + /** + * A documentation string for this object, or an array of strings which should be concatenated. + */ + doc?: undefined | string | Array + + /** + * The default value to use for this parameter if the parameter is missing + * from the input object, or if the value of the parameter in the input + * object is `null`. Default values are applied before evaluating expressions + * (e.g. dependent `valueFrom` fields). + * + */ + default_?: undefined | any + position?: undefined | Internal.StepPosition + + /** + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. + * + */ + optional?: boolean | undefined + min?: number | undefined + max?: number | undefined + type: Internal.GalaxyIntegerType | Array +} \ No newline at end of file diff --git a/typescript/src/WorkflowTextParameter.ts b/typescript/src/WorkflowTextParameter.ts new file mode 100644 index 0000000..e895ea2 --- /dev/null +++ b/typescript/src/WorkflowTextParameter.ts @@ -0,0 +1,318 @@ + +import { + Dictionary, + expandUrl, + loadField, + LoaderInstances, + LoadingOptions, + Saveable, + ValidationException, + prefixUrl, + save, + saveRelativeUri +} from './util/Internal' +import { v4 as uuidv4 } from 'uuid' +import * as Internal from './util/Internal' + + +/** + * Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#WorkflowTextParameter + */ +export class WorkflowTextParameter extends Saveable implements Internal.WorkflowTextParameterProperties { + extensionFields?: Internal.Dictionary + + /** + * The unique identifier for this object. + */ + id?: undefined | string + + /** + * A short, human-readable label of this object. + */ + label?: undefined | string + + /** + * A documentation string for this object, or an array of strings which should be concatenated. + */ + doc?: undefined | string | Array + + /** + * The default value to use for this parameter if the parameter is missing + * from the input object, or if the value of the parameter in the input + * object is `null`. Default values are applied before evaluating expressions + * (e.g. dependent `valueFrom` fields). + * + */ + default_?: undefined | any + position?: undefined | Internal.StepPosition + + /** + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. + * + */ + optional?: boolean | undefined + type: Internal.GalaxyTextType | Array + + /** + * Apply one more validators to the input value. Input is valid if all validators succeed. + */ + validators?: undefined | Array + + + constructor ({loadingOptions, extensionFields, id, label, doc, default_, position, optional, type, validators} : {loadingOptions?: LoadingOptions} & Internal.WorkflowTextParameterProperties) { + super(loadingOptions) + this.extensionFields = extensionFields ?? {} + this.id = id + this.label = label + this.doc = doc + this.default_ = default_ + this.position = position + this.optional = optional + this.type = type + this.validators = validators + } + + /** + * Used to construct instances of {@link WorkflowTextParameter }. + * + * @param __doc Document fragment to load this record object from. + * @param baseuri Base URI to generate child document IDs against. + * @param loadingOptions Context for loading URIs and populating objects. + * @param docRoot ID at this position in the document (if available) + * @returns An instance of {@link WorkflowTextParameter } + * @throws {@link ValidationException} If the document fragment is not a + * {@link Dictionary} or validation of fields fails. + */ + static override async fromDoc (__doc: any, baseuri: string, loadingOptions: LoadingOptions, + docRoot?: string): Promise { + const _doc = Object.assign({}, __doc) + const __errors: ValidationException[] = [] + + let id + if ('id' in _doc) { + try { + id = await loadField(_doc.id, LoaderInstances.uriunionOfundefinedtypeOrstrtypeTrueFalseNoneNone, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `id` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + const originalidIsUndefined = (id === undefined) + if (originalidIsUndefined ) { + if (docRoot != null) { + id = docRoot + } else { + id = "_" + uuidv4() + } + } else { + baseuri = id as string + } + + let label + if ('label' in _doc) { + try { + label = await loadField(_doc.label, LoaderInstances.unionOfundefinedtypeOrstrtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `label` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let doc + if ('doc' in _doc) { + try { + doc = await loadField(_doc.doc, LoaderInstances.unionOfundefinedtypeOrstrtypeOrarrayOfstrtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `doc` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let default_ + if ('default' in _doc) { + try { + default_ = await loadField(_doc.default, LoaderInstances.unionOfundefinedtypeOranyType, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `default` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let position + if ('position' in _doc) { + try { + position = await loadField(_doc.position, LoaderInstances.unionOfundefinedtypeOrStepPositionLoader, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `position` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let optional + if ('optional' in _doc) { + try { + optional = await loadField(_doc.optional, LoaderInstances.unionOfbooltypeOrundefinedtype, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `optional` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + let type + try { + type = await loadField(_doc.type, LoaderInstances.typedslunionOfGalaxyTextTypeLoaderOrarrayOfunionOfWorkflowTextParameterLoader2, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `type` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + + let validators + if ('validators' in _doc) { + try { + validators = await loadField(_doc.validators, LoaderInstances.unionOfundefinedtypeOrarrayOfTextValidatorsLoader, + baseuri, loadingOptions) + } catch (e) { + if (e instanceof ValidationException) { + __errors.push( + new ValidationException('the `validators` field is not valid because: ', [e]) + ) + } else { + throw e + } + } + } + + const extensionFields: Dictionary = {} + for (const [key, value] of Object.entries(_doc)) { + if (!WorkflowTextParameter.attr.has(key)) { + if ((key as string).includes(':')) { + const ex = expandUrl(key, '', loadingOptions, false, false) + extensionFields[ex] = value + } else { + __errors.push( + new ValidationException(`invalid field ${key as string}, \ + expected one of: \`label\`,\`doc\`,\`id\`,\`default\`,\`position\`,\`optional\`,\`type\`,\`validators\``) + ) + break + } + } + } + + if (__errors.length > 0) { + throw new ValidationException("Trying 'WorkflowTextParameter'", __errors) + } + + const schema = new WorkflowTextParameter({ + extensionFields: extensionFields, + loadingOptions: loadingOptions, + label: label, + doc: doc, + id: id, + default_: default_, + position: position, + optional: optional, + type: type, + validators: validators + }) + return schema + } + + save (top: boolean = false, baseUrl: string = '', relativeUris: boolean = true) + : Dictionary { + const r: Dictionary = {} + for (const ef in this.extensionFields) { + r[prefixUrl(ef, this.loadingOptions.vocab)] = this.extensionFields.ef + } + + if (this.id != null) { + const u = saveRelativeUri(this.id, baseUrl, true, + relativeUris, undefined) + if (u != null) { + r.id = u + } + } + + if (this.label != null) { + r.label = save(this.label, false, this.id, relativeUris) + } + + if (this.doc != null) { + r.doc = save(this.doc, false, this.id, relativeUris) + } + + if (this.default_ != null) { + r.default = save(this.default_, false, this.id, relativeUris) + } + + if (this.position != null) { + r.position = save(this.position, false, this.id, relativeUris) + } + + if (this.optional != null) { + r.optional = save(this.optional, false, this.id, relativeUris) + } + + if (this.type != null) { + r.type = save(this.type, false, this.id, relativeUris) + } + + if (this.validators != null) { + r.validators = save(this.validators, false, this.id, relativeUris) + } + + if (top) { + if (this.loadingOptions.namespaces != null) { + r.$namespaces = this.loadingOptions.namespaces + } + if (this.loadingOptions.schemas != null) { + r.$schemas = this.loadingOptions.schemas + } + } + return r + } + + static attr: Set = new Set(['label','doc','id','default','position','optional','type','validators']) +} diff --git a/typescript/src/WorkflowTextParameterProperties.ts b/typescript/src/WorkflowTextParameterProperties.ts new file mode 100644 index 0000000..1fb6745 --- /dev/null +++ b/typescript/src/WorkflowTextParameterProperties.ts @@ -0,0 +1,48 @@ + +import * as Internal from './util/Internal' + + +/** + * Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowTextParameter + */ +export interface WorkflowTextParameterProperties extends Internal.BaseInputParameterProperties { + + extensionFields?: Internal.Dictionary + + /** + * The unique identifier for this object. + */ + id?: undefined | string + + /** + * A short, human-readable label of this object. + */ + label?: undefined | string + + /** + * A documentation string for this object, or an array of strings which should be concatenated. + */ + doc?: undefined | string | Array + + /** + * The default value to use for this parameter if the parameter is missing + * from the input object, or if the value of the parameter in the input + * object is `null`. Default values are applied before evaluating expressions + * (e.g. dependent `valueFrom` fields). + * + */ + default_?: undefined | any + position?: undefined | Internal.StepPosition + + /** + * If set to true, `WorkflowInputParameter` is not required to submit the workflow. + * + */ + optional?: boolean | undefined + type: Internal.GalaxyTextType | Array + + /** + * Apply one more validators to the input value. Input is valid if all validators succeed. + */ + validators?: undefined | Array +} \ No newline at end of file diff --git a/typescript/src/index.ts b/typescript/src/index.ts index d18be8d..b50cb56 100644 --- a/typescript/src/index.ts +++ b/typescript/src/index.ts @@ -6,9 +6,19 @@ export { Any, ArraySchema, ArraySchemaProperties, + BaseDataParameter, + BaseDataParameterProperties, + BaseInputParameter, + BaseInputParameterProperties, DocumentedProperties, EnumSchema, EnumSchemaProperties, + GalaxyBooleanType, + GalaxyDataCollectionType, + GalaxyDataType, + GalaxyFloatType, + GalaxyIntegerType, + GalaxyTextType, GalaxyType, GalaxyWorkflow, GalaxyWorkflowProperties, @@ -18,6 +28,8 @@ export { IdentifiedProperties, InputParameterProperties, LabeledProperties, + MinMax, + MinMaxProperties, OutputParameterProperties, ParameterProperties, PrimitiveType, @@ -27,15 +39,25 @@ export { RecordSchema, RecordSchemaProperties, ReferencesToolProperties, + RegexMatch, + RegexMatchProperties, Report, ReportProperties, SinkProperties, StepPosition, StepPositionProperties, + TextValidators, + TextValidatorsProperties, ToolShedRepository, ToolShedRepositoryProperties, - WorkflowInputParameter, - WorkflowInputParameterProperties, + WorkflowCollectionParameter, + WorkflowCollectionParameterProperties, + WorkflowDataParameter, + WorkflowDataParameterProperties, + WorkflowFloatParameter, + WorkflowFloatParameterProperties, + WorkflowIntegerParameter, + WorkflowIntegerParameterProperties, WorkflowOutputParameter, WorkflowOutputParameterProperties, WorkflowStep, @@ -45,6 +67,8 @@ export { WorkflowStepOutputProperties, WorkflowStepProperties, WorkflowStepType, + WorkflowTextParameter, + WorkflowTextParameterProperties, enum_d062602be0b4b8fd33e69e29a841317b6ab665bc, enum_d961d79c225752b9fadb617367615ab176b47d77, enum_d9cba076fca539106791a4f46d198c7fcfbdb779 diff --git a/typescript/src/test/data/examples/valid1.yml b/typescript/src/test/data/examples/valid1.yml index b850e66..1998970 100644 --- a/typescript/src/test/data/examples/valid1.yml +++ b/typescript/src/test/data/examples/valid1.yml @@ -2,9 +2,26 @@ class: GalaxyWorkflow doc: | Simple workflow that no-op cats a file. inputs: - the_input: + the input: type: File doc: input doc + the collection: + type: collection + collection_type: list + the integer: + type: int + min: 1 + max: 3 + the float: + type: float + min: 1.0 + max: 3.0 + the string: + type: text + validators: + - regex_match: + regex: ^(?!.*\s).+$ + doc: String must not contain whitespace outputs: the_output: outputSource: cat/out_file1 @@ -13,4 +30,4 @@ steps: tool_id: cat1 doc: cat doc in: - input1: the_input \ No newline at end of file + input1: the input \ No newline at end of file diff --git a/typescript/src/util/Internal.ts b/typescript/src/util/Internal.ts index 27e966e..15e6124 100644 --- a/typescript/src/util/Internal.ts +++ b/typescript/src/util/Internal.ts @@ -23,9 +23,19 @@ export * from './Vocabs' export * from '../Any' export * from '../ArraySchema' export * from '../ArraySchemaProperties' +export * from '../BaseDataParameter' +export * from '../BaseDataParameterProperties' +export * from '../BaseInputParameter' +export * from '../BaseInputParameterProperties' export * from '../DocumentedProperties' export * from '../EnumSchema' export * from '../EnumSchemaProperties' +export * from '../GalaxyBooleanType' +export * from '../GalaxyDataCollectionType' +export * from '../GalaxyDataType' +export * from '../GalaxyFloatType' +export * from '../GalaxyIntegerType' +export * from '../GalaxyTextType' export * from '../GalaxyType' export * from '../GalaxyWorkflow' export * from '../GalaxyWorkflowProperties' @@ -35,6 +45,8 @@ export * from '../HasUUIDProperties' export * from '../IdentifiedProperties' export * from '../InputParameterProperties' export * from '../LabeledProperties' +export * from '../MinMax' +export * from '../MinMaxProperties' export * from '../OutputParameterProperties' export * from '../ParameterProperties' export * from '../PrimitiveType' @@ -44,15 +56,25 @@ export * from '../RecordFieldProperties' export * from '../RecordSchema' export * from '../RecordSchemaProperties' export * from '../ReferencesToolProperties' +export * from '../RegexMatch' +export * from '../RegexMatchProperties' export * from '../Report' export * from '../ReportProperties' export * from '../SinkProperties' export * from '../StepPosition' export * from '../StepPositionProperties' +export * from '../TextValidators' +export * from '../TextValidatorsProperties' export * from '../ToolShedRepository' export * from '../ToolShedRepositoryProperties' -export * from '../WorkflowInputParameter' -export * from '../WorkflowInputParameterProperties' +export * from '../WorkflowCollectionParameter' +export * from '../WorkflowCollectionParameterProperties' +export * from '../WorkflowDataParameter' +export * from '../WorkflowDataParameterProperties' +export * from '../WorkflowFloatParameter' +export * from '../WorkflowFloatParameterProperties' +export * from '../WorkflowIntegerParameter' +export * from '../WorkflowIntegerParameterProperties' export * from '../WorkflowOutputParameter' export * from '../WorkflowOutputParameterProperties' export * from '../WorkflowStep' @@ -62,6 +84,8 @@ export * from '../WorkflowStepOutput' export * from '../WorkflowStepOutputProperties' export * from '../WorkflowStepProperties' export * from '../WorkflowStepType' +export * from '../WorkflowTextParameter' +export * from '../WorkflowTextParameterProperties' export * from '../enum_d062602be0b4b8fd33e69e29a841317b6ab665bc' export * from '../enum_d961d79c225752b9fadb617367615ab176b47d77' export * from '../enum_d9cba076fca539106791a4f46d198c7fcfbdb779' diff --git a/typescript/src/util/LoaderInstances.ts b/typescript/src/util/LoaderInstances.ts index 413f2b7..595fc3a 100644 --- a/typescript/src/util/LoaderInstances.ts +++ b/typescript/src/util/LoaderInstances.ts @@ -15,9 +15,19 @@ import { Any, ArraySchema, ArraySchemaProperties, + BaseDataParameter, + BaseDataParameterProperties, + BaseInputParameter, + BaseInputParameterProperties, DocumentedProperties, EnumSchema, EnumSchemaProperties, + GalaxyBooleanType, + GalaxyDataCollectionType, + GalaxyDataType, + GalaxyFloatType, + GalaxyIntegerType, + GalaxyTextType, GalaxyType, GalaxyWorkflow, GalaxyWorkflowProperties, @@ -27,6 +37,8 @@ import { IdentifiedProperties, InputParameterProperties, LabeledProperties, + MinMax, + MinMaxProperties, OutputParameterProperties, ParameterProperties, PrimitiveType, @@ -36,15 +48,25 @@ import { RecordSchema, RecordSchemaProperties, ReferencesToolProperties, + RegexMatch, + RegexMatchProperties, Report, ReportProperties, SinkProperties, StepPosition, StepPositionProperties, + TextValidators, + TextValidatorsProperties, ToolShedRepository, ToolShedRepositoryProperties, - WorkflowInputParameter, - WorkflowInputParameterProperties, + WorkflowCollectionParameter, + WorkflowCollectionParameterProperties, + WorkflowDataParameter, + WorkflowDataParameterProperties, + WorkflowFloatParameter, + WorkflowFloatParameterProperties, + WorkflowIntegerParameter, + WorkflowIntegerParameterProperties, WorkflowOutputParameter, WorkflowOutputParameterProperties, WorkflowStep, @@ -54,6 +76,8 @@ import { WorkflowStepOutputProperties, WorkflowStepProperties, WorkflowStepType, + WorkflowTextParameter, + WorkflowTextParameterProperties, enum_d062602be0b4b8fd33e69e29a841317b6ab665bc, enum_d961d79c225752b9fadb617367615ab176b47d77, enum_d9cba076fca539106791a4f46d198c7fcfbdb779 @@ -74,8 +98,24 @@ export const ArraySchemaLoader = new _RecordLoader(ArraySchema.fromDoc, undefine export const StepPositionLoader = new _RecordLoader(StepPosition.fromDoc, undefined, undefined); export const ToolShedRepositoryLoader = new _RecordLoader(ToolShedRepository.fromDoc, undefined, undefined); export const GalaxyTypeLoader = new _EnumLoader((Object.keys(GalaxyType) as Array).map(key => GalaxyType[key])); +export const GalaxyTextTypeLoader = new _EnumLoader((Object.keys(GalaxyTextType) as Array).map(key => GalaxyTextType[key])); +export const GalaxyIntegerTypeLoader = new _EnumLoader((Object.keys(GalaxyIntegerType) as Array).map(key => GalaxyIntegerType[key])); +export const GalaxyFloatTypeLoader = new _EnumLoader((Object.keys(GalaxyFloatType) as Array).map(key => GalaxyFloatType[key])); +export const GalaxyBooleanTypeLoader = new _EnumLoader((Object.keys(GalaxyBooleanType) as Array).map(key => GalaxyBooleanType[key])); +export const GalaxyDataTypeLoader = new _EnumLoader((Object.keys(GalaxyDataType) as Array).map(key => GalaxyDataType[key])); +export const GalaxyDataCollectionTypeLoader = new _EnumLoader((Object.keys(GalaxyDataCollectionType) as Array).map(key => GalaxyDataCollectionType[key])); export const WorkflowStepTypeLoader = new _EnumLoader((Object.keys(WorkflowStepType) as Array).map(key => WorkflowStepType[key])); -export const WorkflowInputParameterLoader = new _RecordLoader(WorkflowInputParameter.fromDoc, undefined, undefined); +export const BaseInputParameterLoader = new _RecordLoader(BaseInputParameter.fromDoc, undefined, undefined); +export const BaseDataParameterLoader = new _RecordLoader(BaseDataParameter.fromDoc, undefined, undefined); +export const WorkflowDataParameterLoader = new _RecordLoader(WorkflowDataParameter.fromDoc, undefined, undefined); +export const WorkflowCollectionParameterLoader = new _RecordLoader(WorkflowCollectionParameter.fromDoc, undefined, undefined); +export const MinMaxLoader = new _RecordLoader(MinMax.fromDoc, undefined, undefined); +export const WorkflowIntegerParameterLoader = new _RecordLoader(WorkflowIntegerParameter.fromDoc, undefined, undefined); +export const WorkflowFloatParameterLoader = new _RecordLoader(WorkflowFloatParameter.fromDoc, undefined, undefined); +export const TextValidatorsLoader = new _RecordLoader(TextValidators.fromDoc, undefined, undefined); +export const RegexMatchLoader = new _RecordLoader(RegexMatch.fromDoc, undefined, undefined); +export const WorkflowTextParameterLoader = new _RecordLoader(WorkflowTextParameter.fromDoc, undefined, undefined); +export const WorkflowInputParameterLoader = new _UnionLoader([]); export const WorkflowOutputParameterLoader = new _RecordLoader(WorkflowOutputParameter.fromDoc, undefined, undefined); export const WorkflowStepLoader = new _RecordLoader(WorkflowStep.fromDoc, undefined, undefined); export const WorkflowStepInputLoader = new _RecordLoader(WorkflowStepInput.fromDoc, undefined, undefined); @@ -103,21 +143,37 @@ export const typedslenum_d062602be0b4b8fd33e69e29a841317b6ab665bcLoader2 = new _ export const unionOfundefinedtypeOrstrtype = new _UnionLoader([undefinedtype, strtype]); export const uriunionOfundefinedtypeOrstrtypeTrueFalseNoneNone = new _URILoader(unionOfundefinedtypeOrstrtype, true, false, undefined, undefined); export const unionOfundefinedtypeOranyType = new _UnionLoader([undefinedtype, anyType]); -export const unionOfWorkflowInputParameterLoader = new _UnionLoader([WorkflowInputParameterLoader]); -export const arrayOfunionOfWorkflowInputParameterLoader = new _ArrayLoader([unionOfWorkflowInputParameterLoader]); -export const idmapinputsarrayOfunionOfWorkflowInputParameterLoader = new _IdMapLoader(arrayOfunionOfWorkflowInputParameterLoader, 'id', 'type'); +export const unionOfBaseInputParameterLoader = new _UnionLoader([BaseInputParameterLoader]); +export const arrayOfunionOfBaseInputParameterLoader = new _ArrayLoader([unionOfBaseInputParameterLoader]); +export const idmapinputsarrayOfunionOfBaseInputParameterLoader = new _IdMapLoader(arrayOfunionOfBaseInputParameterLoader, 'id', 'type'); export const unionOfWorkflowOutputParameterLoader = new _UnionLoader([WorkflowOutputParameterLoader]); export const arrayOfunionOfWorkflowOutputParameterLoader = new _ArrayLoader([unionOfWorkflowOutputParameterLoader]); export const idmapoutputsarrayOfunionOfWorkflowOutputParameterLoader = new _IdMapLoader(arrayOfunionOfWorkflowOutputParameterLoader, 'id', 'type'); export const unionOfundefinedtypeOrStepPositionLoader = new _UnionLoader([undefinedtype, StepPositionLoader]); export const unionOffloattypeOrinttype = new _UnionLoader([floattype, inttype]); export const unionOfundefinedtypeOrToolShedRepositoryLoader = new _UnionLoader([undefinedtype, ToolShedRepositoryLoader]); -export const unionOfGalaxyTypeLoader = new _UnionLoader([GalaxyTypeLoader]); -export const arrayOfunionOfGalaxyTypeLoader = new _ArrayLoader([unionOfGalaxyTypeLoader]); -export const unionOfGalaxyTypeLoaderOrundefinedtypeOrarrayOfunionOfGalaxyTypeLoader = new _UnionLoader([GalaxyTypeLoader, undefinedtype, arrayOfunionOfGalaxyTypeLoader]); -export const typedslunionOfGalaxyTypeLoaderOrundefinedtypeOrarrayOfunionOfGalaxyTypeLoader2 = new _TypeDSLLoader(unionOfGalaxyTypeLoaderOrundefinedtypeOrarrayOfunionOfGalaxyTypeLoader, 2); export const unionOfbooltypeOrundefinedtype = new _UnionLoader([booltype, undefinedtype]); export const unionOfundefinedtypeOrarrayOfstrtype = new _UnionLoader([undefinedtype, arrayOfstrtype]); +export const unionOfGalaxyDataTypeLoaderOrundefinedtype = new _UnionLoader([GalaxyDataTypeLoader, undefinedtype]); +export const typedslunionOfGalaxyDataTypeLoaderOrundefinedtype2 = new _TypeDSLLoader(unionOfGalaxyDataTypeLoaderOrundefinedtype, 2); +export const typedslGalaxyDataCollectionTypeLoader2 = new _TypeDSLLoader(GalaxyDataCollectionTypeLoader, 2); +export const unionOfinttypeOrfloattypeOrundefinedtype = new _UnionLoader([inttype, floattype, undefinedtype]); +export const unionOfWorkflowIntegerParameterLoader = new _UnionLoader([WorkflowIntegerParameterLoader]); +export const arrayOfunionOfWorkflowIntegerParameterLoader = new _ArrayLoader([unionOfWorkflowIntegerParameterLoader]); +export const unionOfGalaxyIntegerTypeLoaderOrarrayOfunionOfWorkflowIntegerParameterLoader = new _UnionLoader([GalaxyIntegerTypeLoader, arrayOfunionOfWorkflowIntegerParameterLoader]); +export const typedslunionOfGalaxyIntegerTypeLoaderOrarrayOfunionOfWorkflowIntegerParameterLoader2 = new _TypeDSLLoader(unionOfGalaxyIntegerTypeLoaderOrarrayOfunionOfWorkflowIntegerParameterLoader, 2); +export const unionOfWorkflowFloatParameterLoader = new _UnionLoader([WorkflowFloatParameterLoader]); +export const arrayOfunionOfWorkflowFloatParameterLoader = new _ArrayLoader([unionOfWorkflowFloatParameterLoader]); +export const unionOfGalaxyFloatTypeLoaderOrarrayOfunionOfWorkflowFloatParameterLoader = new _UnionLoader([GalaxyFloatTypeLoader, arrayOfunionOfWorkflowFloatParameterLoader]); +export const typedslunionOfGalaxyFloatTypeLoaderOrarrayOfunionOfWorkflowFloatParameterLoader2 = new _TypeDSLLoader(unionOfGalaxyFloatTypeLoaderOrarrayOfunionOfWorkflowFloatParameterLoader, 2); +export const unionOfRegexMatchLoader = new _UnionLoader([RegexMatchLoader]); +export const unionOfstrtype = new _UnionLoader([strtype]); +export const unionOfWorkflowTextParameterLoader = new _UnionLoader([WorkflowTextParameterLoader]); +export const arrayOfunionOfWorkflowTextParameterLoader = new _ArrayLoader([unionOfWorkflowTextParameterLoader]); +export const unionOfGalaxyTextTypeLoaderOrarrayOfunionOfWorkflowTextParameterLoader = new _UnionLoader([GalaxyTextTypeLoader, arrayOfunionOfWorkflowTextParameterLoader]); +export const typedslunionOfGalaxyTextTypeLoaderOrarrayOfunionOfWorkflowTextParameterLoader2 = new _TypeDSLLoader(unionOfGalaxyTextTypeLoaderOrarrayOfunionOfWorkflowTextParameterLoader, 2); +export const arrayOfTextValidatorsLoader = new _ArrayLoader([TextValidatorsLoader]); +export const unionOfundefinedtypeOrarrayOfTextValidatorsLoader = new _UnionLoader([undefinedtype, arrayOfTextValidatorsLoader]); export const unionOfundefinedtypeOrGalaxyTypeLoader = new _UnionLoader([undefinedtype, GalaxyTypeLoader]); export const typedslunionOfundefinedtypeOrGalaxyTypeLoader2 = new _TypeDSLLoader(unionOfundefinedtypeOrGalaxyTypeLoader, 2); export const arrayOfWorkflowStepInputLoader = new _ArrayLoader([WorkflowStepInputLoader]); @@ -146,3 +202,5 @@ export const unionOfarrayOfstrtypeOrundefinedtype = new _UnionLoader([arrayOfstr export const unionOfGalaxyWorkflowLoader = new _UnionLoader([GalaxyWorkflowLoader]); export const arrayOfunionOfGalaxyWorkflowLoader = new _ArrayLoader([unionOfGalaxyWorkflowLoader]); export const unionOfGalaxyWorkflowLoaderOrarrayOfunionOfGalaxyWorkflowLoader = new _UnionLoader([GalaxyWorkflowLoader, arrayOfunionOfGalaxyWorkflowLoader]); + +WorkflowInputParameterLoader.addLoaders([WorkflowTextParameterLoader, WorkflowFloatParameterLoader, WorkflowIntegerParameterLoader, WorkflowDataParameterLoader, WorkflowCollectionParameterLoader]); diff --git a/typescript/src/util/Vocabs.ts b/typescript/src/util/Vocabs.ts index aa2f52e..1634ad7 100644 --- a/typescript/src/util/Vocabs.ts +++ b/typescript/src/util/Vocabs.ts @@ -1,9 +1,17 @@ export const VOCAB = { 'Any': 'https://w3id.org/cwl/salad#Any', 'ArraySchema': 'https://w3id.org/cwl/salad#ArraySchema', + 'BaseDataParameter': 'https://galaxyproject.org/gxformat2/v19_09#BaseDataParameter', + 'BaseInputParameter': 'https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter', 'Documented': 'https://w3id.org/cwl/salad#Documented', 'EnumSchema': 'https://w3id.org/cwl/salad#EnumSchema', - 'File': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyType/File', + 'File': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyDataType/File', + 'GalaxyBooleanType': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyBooleanType', + 'GalaxyDataCollectionType': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyDataCollectionType', + 'GalaxyDataType': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyDataType', + 'GalaxyFloatType': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyFloatType', + 'GalaxyIntegerType': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyIntegerType', + 'GalaxyTextType': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyTextType', 'GalaxyType': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyType', 'GalaxyWorkflow': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow', 'HasStepErrors': 'https://galaxyproject.org/gxformat2/gxformat2common#HasStepErrors', @@ -12,6 +20,7 @@ export const VOCAB = { 'Identified': 'https://w3id.org/cwl/cwl#Identified', 'InputParameter': 'https://w3id.org/cwl/cwl#InputParameter', 'Labeled': 'https://w3id.org/cwl/cwl#Labeled', + 'MinMax': 'https://galaxyproject.org/gxformat2/v19_09#MinMax', 'OutputParameter': 'https://w3id.org/cwl/cwl#OutputParameter', 'Parameter': 'https://w3id.org/cwl/cwl#Parameter', 'PrimitiveType': 'https://w3id.org/cwl/salad#PrimitiveType', @@ -19,40 +28,56 @@ export const VOCAB = { 'RecordField': 'https://w3id.org/cwl/salad#RecordField', 'RecordSchema': 'https://w3id.org/cwl/salad#RecordSchema', 'ReferencesTool': 'https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool', + 'RegexMatch': 'https://galaxyproject.org/gxformat2/v19_09#RegexMatch', 'Report': 'https://galaxyproject.org/gxformat2/v19_09#Report', 'Sink': 'https://galaxyproject.org/gxformat2/v19_09#Sink', 'StepPosition': 'https://galaxyproject.org/gxformat2/gxformat2common#StepPosition', + 'TextValidators': 'https://galaxyproject.org/gxformat2/v19_09#TextValidators', 'ToolShedRepository': 'https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository', + 'WorkflowCollectionParameter': 'https://galaxyproject.org/gxformat2/v19_09#WorkflowCollectionParameter', + 'WorkflowDataParameter': 'https://galaxyproject.org/gxformat2/v19_09#WorkflowDataParameter', + 'WorkflowFloatParameter': 'https://galaxyproject.org/gxformat2/v19_09#WorkflowFloatParameter', 'WorkflowInputParameter': 'https://galaxyproject.org/gxformat2/v19_09#WorkflowInputParameter', + 'WorkflowIntegerParameter': 'https://galaxyproject.org/gxformat2/v19_09#WorkflowIntegerParameter', 'WorkflowOutputParameter': 'https://galaxyproject.org/gxformat2/v19_09#WorkflowOutputParameter', 'WorkflowStep': 'https://galaxyproject.org/gxformat2/v19_09#WorkflowStep', 'WorkflowStepInput': 'https://galaxyproject.org/gxformat2/v19_09#WorkflowStepInput', 'WorkflowStepOutput': 'https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput', 'WorkflowStepType': 'https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType', + 'WorkflowTextParameter': 'https://galaxyproject.org/gxformat2/v19_09#WorkflowTextParameter', 'array': 'https://w3id.org/cwl/salad#array', + 'bool': 'http://www.w3.org/2001/XMLSchema#bool', 'boolean': 'http://www.w3.org/2001/XMLSchema#boolean', - 'collection': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyType/collection', - 'data': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyType/data', + 'collection': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyDataCollectionType/collection', + 'data': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyDataType/data', 'double': 'http://www.w3.org/2001/XMLSchema#double', 'enum': 'https://w3id.org/cwl/salad#enum', 'float': 'http://www.w3.org/2001/XMLSchema#float', 'int': 'http://www.w3.org/2001/XMLSchema#int', - 'integer': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyType/integer', + 'integer': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyIntegerType/integer', 'long': 'http://www.w3.org/2001/XMLSchema#long', 'null': 'https://w3id.org/cwl/salad#null', 'pause': 'https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/pause', 'record': 'https://w3id.org/cwl/salad#record', 'string': 'http://www.w3.org/2001/XMLSchema#string', 'subworkflow': 'https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/subworkflow', - 'text': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyType/text', + 'text': 'https://galaxyproject.org/gxformat2/v19_09#GalaxyTextType/text', 'tool': 'https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/tool' } export const RVOCAB = { 'https://w3id.org/cwl/salad#Any': 'Any', 'https://w3id.org/cwl/salad#ArraySchema': 'ArraySchema', + 'https://galaxyproject.org/gxformat2/v19_09#BaseDataParameter': 'BaseDataParameter', + 'https://galaxyproject.org/gxformat2/v19_09#BaseInputParameter': 'BaseInputParameter', 'https://w3id.org/cwl/salad#Documented': 'Documented', 'https://w3id.org/cwl/salad#EnumSchema': 'EnumSchema', - 'https://galaxyproject.org/gxformat2/v19_09#GalaxyType/File': 'File', + 'https://galaxyproject.org/gxformat2/v19_09#GalaxyDataType/File': 'File', + 'https://galaxyproject.org/gxformat2/v19_09#GalaxyBooleanType': 'GalaxyBooleanType', + 'https://galaxyproject.org/gxformat2/v19_09#GalaxyDataCollectionType': 'GalaxyDataCollectionType', + 'https://galaxyproject.org/gxformat2/v19_09#GalaxyDataType': 'GalaxyDataType', + 'https://galaxyproject.org/gxformat2/v19_09#GalaxyFloatType': 'GalaxyFloatType', + 'https://galaxyproject.org/gxformat2/v19_09#GalaxyIntegerType': 'GalaxyIntegerType', + 'https://galaxyproject.org/gxformat2/v19_09#GalaxyTextType': 'GalaxyTextType', 'https://galaxyproject.org/gxformat2/v19_09#GalaxyType': 'GalaxyType', 'https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow': 'GalaxyWorkflow', 'https://galaxyproject.org/gxformat2/gxformat2common#HasStepErrors': 'HasStepErrors', @@ -61,6 +86,7 @@ export const RVOCAB = { 'https://w3id.org/cwl/cwl#Identified': 'Identified', 'https://w3id.org/cwl/cwl#InputParameter': 'InputParameter', 'https://w3id.org/cwl/cwl#Labeled': 'Labeled', + 'https://galaxyproject.org/gxformat2/v19_09#MinMax': 'MinMax', 'https://w3id.org/cwl/cwl#OutputParameter': 'OutputParameter', 'https://w3id.org/cwl/cwl#Parameter': 'Parameter', 'https://w3id.org/cwl/salad#PrimitiveType': 'PrimitiveType', @@ -68,31 +94,39 @@ export const RVOCAB = { 'https://w3id.org/cwl/salad#RecordField': 'RecordField', 'https://w3id.org/cwl/salad#RecordSchema': 'RecordSchema', 'https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool': 'ReferencesTool', + 'https://galaxyproject.org/gxformat2/v19_09#RegexMatch': 'RegexMatch', 'https://galaxyproject.org/gxformat2/v19_09#Report': 'Report', 'https://galaxyproject.org/gxformat2/v19_09#Sink': 'Sink', 'https://galaxyproject.org/gxformat2/gxformat2common#StepPosition': 'StepPosition', + 'https://galaxyproject.org/gxformat2/v19_09#TextValidators': 'TextValidators', 'https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository': 'ToolShedRepository', + 'https://galaxyproject.org/gxformat2/v19_09#WorkflowCollectionParameter': 'WorkflowCollectionParameter', + 'https://galaxyproject.org/gxformat2/v19_09#WorkflowDataParameter': 'WorkflowDataParameter', + 'https://galaxyproject.org/gxformat2/v19_09#WorkflowFloatParameter': 'WorkflowFloatParameter', 'https://galaxyproject.org/gxformat2/v19_09#WorkflowInputParameter': 'WorkflowInputParameter', + 'https://galaxyproject.org/gxformat2/v19_09#WorkflowIntegerParameter': 'WorkflowIntegerParameter', 'https://galaxyproject.org/gxformat2/v19_09#WorkflowOutputParameter': 'WorkflowOutputParameter', 'https://galaxyproject.org/gxformat2/v19_09#WorkflowStep': 'WorkflowStep', 'https://galaxyproject.org/gxformat2/v19_09#WorkflowStepInput': 'WorkflowStepInput', 'https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput': 'WorkflowStepOutput', 'https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType': 'WorkflowStepType', + 'https://galaxyproject.org/gxformat2/v19_09#WorkflowTextParameter': 'WorkflowTextParameter', 'https://w3id.org/cwl/salad#array': 'array', + 'http://www.w3.org/2001/XMLSchema#bool': 'bool', 'http://www.w3.org/2001/XMLSchema#boolean': 'boolean', - 'https://galaxyproject.org/gxformat2/v19_09#GalaxyType/collection': 'collection', - 'https://galaxyproject.org/gxformat2/v19_09#GalaxyType/data': 'data', + 'https://galaxyproject.org/gxformat2/v19_09#GalaxyDataCollectionType/collection': 'collection', + 'https://galaxyproject.org/gxformat2/v19_09#GalaxyDataType/data': 'data', 'http://www.w3.org/2001/XMLSchema#double': 'double', 'https://w3id.org/cwl/salad#enum': 'enum', 'http://www.w3.org/2001/XMLSchema#float': 'float', 'http://www.w3.org/2001/XMLSchema#int': 'int', - 'https://galaxyproject.org/gxformat2/v19_09#GalaxyType/integer': 'integer', + 'https://galaxyproject.org/gxformat2/v19_09#GalaxyIntegerType/integer': 'integer', 'http://www.w3.org/2001/XMLSchema#long': 'long', 'https://w3id.org/cwl/salad#null': 'null', 'https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/pause': 'pause', 'https://w3id.org/cwl/salad#record': 'record', 'http://www.w3.org/2001/XMLSchema#string': 'string', 'https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/subworkflow': 'subworkflow', - 'https://galaxyproject.org/gxformat2/v19_09#GalaxyType/text': 'text', + 'https://galaxyproject.org/gxformat2/v19_09#GalaxyTextType/text': 'text', 'https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/tool': 'tool' }