Add DatasetLinks to JSON schema (#1404)

* first try * add functional DatasetLinks schema: any str bigger than len 0 --> uri * add tests * fix lint * use propertyNames feature, instead of not feature * migrated eeg_matchingpennies from GitHub to GIN * fix formatting E501 * Update bids-validator/tests/json.spec.js Co-authored-by: Chris Markiewicz <effigies@gmail.com> * Update bids-validator/validators/json/schemas/dataset_description.json * fix tests Co-authored-by: Chris Markiewicz <effigies@gmail.com>
bids-standard · Jan 20, 2022 · 4feb91b · 4feb91b
1 parent 4d780ec
commit 4feb91b
Show file tree

Hide file tree

Showing 3 changed files with 103 additions and 1 deletion.
diff --git a/bids-validator/bids_validator/test_bids_validator.py b/bids-validator/bids_validator/test_bids_validator.py
@@ -14,7 +14,9 @@
 HOME = os.path.expanduser('~')
 
 TEST_DATA_DICT = {
-    'eeg_matchingpennies': 'https://github.com/sappelhoff/eeg_matchingpennies'
+    'eeg_matchingpennies': (
+        'https://gin.g-node.org/sappelhoff/eeg_matchingpennies'
+    ),
     }
 
 EXCLUDE_KEYWORDS = ['git', 'datalad', 'sourcedata', 'bidsignore']

diff --git a/bids-validator/tests/json.spec.js b/bids-validator/tests/json.spec.js
@@ -467,6 +467,93 @@ describe('JSON', function() {
     relativePath: '/dataset_description.json',
   }
 
+  it('dataset_description.json should validate DatasetLinks', function() {
+    var jsonObj = {
+      Name: 'Example Name',
+      BIDSVersion: '1.4.0',
+      DatasetLinks: {
+        mylink: 'https://www.google.com',
+        deriv1: 'derivatives/derivative1',
+        phantoms: 'file:///data/phantoms',
+        ds000001: 'doi:10.18112/openneuro.ds000001.v1.0.0',
+      },
+    }
+    jsonDict[dataset_description_file.relativePath] = jsonObj
+    validate.JSON(dataset_description_file, jsonDict, function(issues) {
+      assert(issues.length === 0)
+    })
+  })
+
+  it('dataset_description.json should raise on bad keys in DatasetLinks', function() {
+    var jsonObj = {
+      Name: 'Example Name',
+      BIDSVersion: '1.4.0',
+      DatasetLinks: {
+        mylink: 'https://www.google.com',
+        '': 'https://www.yahoo.com',
+        'mylink!': ':/path',
+        'my link': ':/another/path',
+      },
+    }
+    jsonDict[dataset_description_file.relativePath] = jsonObj
+    validate.JSON(dataset_description_file, jsonDict, function(issues) {
+      assert(issues.length === 6)
+      assert(
+        issues[0].evidence ==
+          '.DatasetLinks should NOT be shorter than 1 characters',
+      )
+      assert(issues[1].evidence == ".DatasetLinks property name '' is invalid")
+      assert(
+        issues[2].evidence ==
+          '.DatasetLinks should match pattern "^[a-zA-Z0-9]*$"',
+      )
+      assert(
+        issues[3].evidence ==
+          ".DatasetLinks property name 'mylink!' is invalid",
+      )
+      assert(issues[4].evidence == issues[2].evidence)
+      assert(
+        issues[5].evidence ==
+          ".DatasetLinks property name 'my link' is invalid",
+      )
+    })
+  })
+
+  it('dataset_description.json should raise on non-object value in DatasetLinks', function() {
+    var jsonObj = {
+      Name: 'Example Name',
+      BIDSVersion: '1.4.0',
+      DatasetLinks: 'https://www.google.com',
+    }
+    jsonDict[dataset_description_file.relativePath] = jsonObj
+    validate.JSON(dataset_description_file, jsonDict, function(issues) {
+      assert(issues.length === 1)
+      assert(issues[0].evidence == '.DatasetLinks should be object')
+    })
+  })
+
+  it('dataset_description.json should raise on invalid values in DatasetLinks', function() {
+    var jsonObj = {
+      Name: 'Example Name',
+      BIDSVersion: '1.4.0',
+      DatasetLinks: {
+        mylink1: 'https://www.google.com',
+        mylink2: 1,
+        '': 'https://www.yahoo.com',
+      },
+    }
+    jsonDict[dataset_description_file.relativePath] = jsonObj
+    validate.JSON(dataset_description_file, jsonDict, function(issues) {
+      assert(issues.length === 3)
+      assert(
+        issues[0].evidence ==
+          '.DatasetLinks should NOT be shorter than 1 characters',
+      )
+      assert(issues[1].evidence == ".DatasetLinks property name '' is invalid")
+      assert(issues[2].evidence == ".DatasetLinks['mylink2'] should be string")
+    })
+  })
+
   it('dataset_description.json should validate with enum of DatasetType', function() {
     var jsonObj = {
       Name: 'Example Name',

diff --git a/bids-validator/validators/json/schemas/dataset_description.json b/bids-validator/validators/json/schemas/dataset_description.json
@@ -52,6 +52,19 @@
     "DatasetDOI": {
       "type": "string"
     },
+    "DatasetLinks": {
+      "type": "object",
+      "properties": { },
+      "propertyNames": {
+        "type": "string",
+        "minLength": 1,
+        "pattern": "^[a-zA-Z0-9]*$"
+      },
+      "additionalProperties": {
+        "type": "string",
+        "format": "uri-reference"
+      }
+    },
     "GeneratedBy": {
       "type": "array",
       "minItems": 1,