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Feature/fix db ser event #315

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merged 3 commits into from
Feb 3, 2022
Merged

Feature/fix db ser event #315

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f821a07
fix db serialization of entry
stefanspiska Feb 3, 2022
23c0d6b
add conformace_test to sonar
stefanspiska Feb 3, 2022
915ddc4
edit CHANGELOG.md
stefanspiska Feb 3, 2022
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10 changes: 7 additions & 3 deletions CHANGELOG.md
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Expand Up @@ -10,8 +10,12 @@ Note: version releases in the 0.x.y range may introduce breaking changes.
- Upgrade to Archie 1.0.4 ([#292](https://github.com/ehrbase/openEHR_SDK/pull/292))
- cleanup created templates (https://github.com/ehrbase/openEHR_SDK/issues/298)
- WebTemplate based validation (see https://github.com/ehrbase/openEHR_SDK/pull/309)
- flat: created conformance tests (see https://github.com/ehrbase/openEHR_SDK/pull/310; https://github.com/ehrbase/openEHR_SDK/pull/305; https://github.com/ehrbase/openEHR_SDK/pull/304; https://github.com/ehrbase/openEHR_SDK/pull/301)
- db-serialising: created conformance test (see https://github.com/ehrbase/openEHR_SDK/pull/311)
- flat: created conformance tests (see https://github.com/ehrbase/openEHR_SDK/pull/310
; https://github.com/ehrbase/openEHR_SDK/pull/305; https://github.com/ehrbase/openEHR_SDK/pull/304
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Just as small comment:
I did it by mistake here because I use this format in EHRbase but I am now thinking that we should also use the Markdown for link [<#pr_number>](<pr_url>) here. It would be prettier

; https://github.com/ehrbase/openEHR_SDK/pull/301)
- db-serialising: created conformance test (see https://github.com/ehrbase/openEHR_SDK/pull/311)
- db-serialising: fix handing of guideline_id & work_flow_id &
wf_definition (https://github.com/ehrbase/openEHR_SDK/pull/315)

### Fixed

Expand All @@ -20,7 +24,7 @@ Note: version releases in the 0.x.y range may introduce breaking changes.
- Fix issue in AQL regarding LIMIT and OFFSET (https://github.com/ehrbase/openEHR_SDK/pull/296)
- Fix issue while unmarshalling FLAT composition that contains ELEMENT with children DV_CODED_TEXT and DV_TEXT (https://github.com/ehrbase/openEHR_SDK/pull/300)
- Fix missing 'type' attribute in ExternalRef encoding (https://github.com/ehrbase/openEHR_SDK/pull/303)
-
- Fix db-serialising: date-time dv_order attributes (https://github.com/ehrbase/openEHR_SDK/pull/314)
## 1.16.0

### Added
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8 changes: 6 additions & 2 deletions serialisation/src/main/java/org/ehrbase/serialisation/attributes/CareEntryAttributes.java
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Expand Up @@ -20,10 +20,12 @@
import com.nedap.archie.rm.composition.CareEntry;
import org.ehrbase.serialisation.dbencoding.CompositionSerializer;
import org.ehrbase.serialisation.dbencoding.ItemStack;
import org.ehrbase.serialisation.dbencoding.RmObjectEncoding;

import java.util.Map;

import static org.ehrbase.serialisation.dbencoding.CompositionSerializer.TAG_GUIDELINE_ID;

/** populate the attributes for RM CareEntry */
public abstract class CareEntryAttributes extends EntryAttributes {

Expand All @@ -34,8 +36,10 @@ public CareEntryAttributes(

public Map<String, Object> toMap(CareEntry careEntry) {

if (careEntry.getGuidelineId() != null)
map = toMap(TAG_GUIDELINE_ID, careEntry.getGuidelineId(), careEntry.getName());
if (careEntry.getGuidelineId() != null) {

map.put(TAG_GUIDELINE_ID, new RmObjectEncoding(careEntry.getGuidelineId()).toMap());
}

map = super.toMap(careEntry);

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6 changes: 4 additions & 2 deletions serialisation/src/main/java/org/ehrbase/serialisation/attributes/EntryAttributes.java
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Expand Up @@ -51,8 +51,10 @@ protected Map<String, Object> toMap(Entry entry){
map.put(TAG_ENCODING, new RmObjectEncoding(entry.getEncoding()).toMap());
}

if (entry.getWorkflowId() != null)
map = toMap(TAG_WORKFLOW_ID, entry.getWorkflowId(), entry.getName());
if (entry.getWorkflowId() != null) {

map.put(TAG_WORKFLOW_ID, new RmObjectEncoding(entry.getWorkflowId()).toMap());
}

if (entry.getOtherParticipations() != null && !entry.getOtherParticipations().isEmpty()){
map.put(TAG_OTHER_PARTICIPATIONS, new OtherParticipationAttributes(entry.getOtherParticipations(), compositionSerializer).toMap());
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11 changes: 7 additions & 4 deletions serialisation/src/main/java/org/ehrbase/serialisation/attributes/InstructionAttributes.java
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Expand Up @@ -17,15 +17,15 @@

package org.ehrbase.serialisation.attributes;

import static org.ehrbase.serialisation.dbencoding.CompositionSerializer.TAG_EXPIRY_TIME;
import static org.ehrbase.serialisation.dbencoding.CompositionSerializer.TAG_NARRATIVE;

import com.nedap.archie.rm.composition.Instruction;
import java.util.Map;
import org.ehrbase.serialisation.dbencoding.CompositionSerializer;
import org.ehrbase.serialisation.dbencoding.ItemStack;
import org.ehrbase.serialisation.dbencoding.RmObjectEncoding;

import java.util.Map;

import static org.ehrbase.serialisation.dbencoding.CompositionSerializer.*;

/**
* populate the attributes for RM Instruction (narrative)
*/
Expand All @@ -45,6 +45,9 @@ public Map<String, Object> toMap(Instruction instruction) {
if (instruction.getExpiryTime() != null) {
map.put(TAG_EXPIRY_TIME, new RmObjectEncoding(instruction.getExpiryTime()).toMap());
}
if (instruction.getWfDefinition() != null) {
map.put(TAG_WF_DEFINITION, new RmObjectEncoding(instruction.getWfDefinition()).toMap());
}

map = super.toMap(instruction);

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1 change: 1 addition & 0 deletions serialisation/src/main/java/org/ehrbase/serialisation/dbencoding/CompositionSerializer.java
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Expand Up @@ -96,6 +96,7 @@ public enum WalkerOutputMode {
public static final String TAG_ISM_TRANSITION_REASON = "/careflow_step";
public static final String TAG_TRANSITION = "/transition";
public static final String TAG_WORKFLOW_ID = "/workflow_id";
public static final String TAG_WF_DEFINITION = "/wf_definition";
public static final String TAG_GUIDELINE_ID = "/guideline_id";
public static final String TAG_OTHER_PARTICIPATIONS = "/other_participations";
public static final String TAG_PROVIDER = "/provider"; // care entry provider
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5 changes: 4 additions & 1 deletion serialisation_conformance_test/pom.xml
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Expand Up @@ -36,8 +36,8 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.0.0-M5</version>
<configuration combine.self="override">
<argLine>${surefireArgLine}</argLine>
<dependenciesToScan>com.github.better-care:web-template-tests</dependenciesToScan>
<includes combine.self="override">
<include>AnySomeConstrainedTest</include>
Expand Down Expand Up @@ -91,6 +91,9 @@
<include>WebTemplateContentTest.java</include>
<include>WorkflowIdTestOverwrite</include>
<include>XdsBuilderTest</include>
<include>DbConformanceTest</include>
<include>DbConformanceTest</include>
<include>FlatConformanceTest</include>
</includes>
</configuration>
</plugin>
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125 changes: 0 additions & 125 deletions ...ion_conformance_test/src/test/java/org/ehrbase/conformance_test/db/DbConformanceTest.java
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Expand Up @@ -98,131 +98,6 @@ private static List<Arguments> testRoundTripArguments(){
new String[] {}));
break;

case EHRBASE_CONFORMANCE_OBSERVATION:
case EHRBASE_CONFORMANCE_FEEDER_AUDIT_MULTIMEDIA:
arguments.add(
Arguments.of(
test,
new String[] {},
new String[] {
// see https://jira.vitagroup.ag/browse/CDR-219
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_observation/_guideline_id|type, value: GUIDELINE",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_observation/_guideline_id|namespace, value: HOSPITAL-NS",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_observation/_guideline_id|id, value: 3445",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_observation/_guideline_id|id_scheme, value: HOSPITAL-NS",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_observation/_work_flow_id|type, value: WORKFLOW",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_observation/_work_flow_id|namespace, value: HOSPITAL-NS",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_observation/_work_flow_id|id, value: 335645",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_observation/_work_flow_id|id_scheme, value: HOSPITAL-NS"
},
new String[] {
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-OBSERVATION.conformance_observation.v0, 1]/workflow_id/id",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-OBSERVATION.conformance_observation.v0, 1]/workflow_id/type",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-OBSERVATION.conformance_observation.v0, 1]/workflow_id/namespace",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-OBSERVATION.conformance_observation.v0, 1]/guideline_id/namespace",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-OBSERVATION.conformance_observation.v0, 1]/guideline_id/id",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-OBSERVATION.conformance_observation.v0, 1]/guideline_id/type"
}));
break;

case EHRBASE_CONFORMANCE_EVALUATION:
arguments.add(
Arguments.of(
test,
new String[] {},
new String[] {
// see https://jira.vitagroup.ag/browse/CDR-219
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_evaluation/_guideline_id|type, value: GUIDELINE",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_evaluation/_guideline_id|namespace, value: HOSPITAL-NS",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_evaluation/_guideline_id|id, value: 3445",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_evaluation/_guideline_id|id_scheme, value: HOSPITAL-NS",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_evaluation/_work_flow_id|type, value: WORKFLOW",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_evaluation/_work_flow_id|namespace, value: HOSPITAL-NS",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_evaluation/_work_flow_id|id, value: 335645",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_evaluation/_work_flow_id|id_scheme, value: HOSPITAL-NS"
},
new String[] {
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-EVALUATION.conformance_evaluation.v0, 1]/workflow_id/id",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-EVALUATION.conformance_evaluation.v0, 1]/workflow_id/type",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-EVALUATION.conformance_evaluation.v0, 1]/workflow_id/namespace",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-EVALUATION.conformance_evaluation.v0, 1]/guideline_id/namespace",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-EVALUATION.conformance_evaluation.v0, 1]/guideline_id/id",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-EVALUATION.conformance_evaluation.v0, 1]/guideline_id/type"
}));
break;
case EHRBASE_CONFORMANCE_ACTION:
arguments.add(
Arguments.of(
test,
new String[] {},
new String[] {
// see https://jira.vitagroup.ag/browse/CDR-219
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_action/_guideline_id|type, value: GUIDELINE",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_action/_guideline_id|namespace, value: HOSPITAL-NS",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_action/_guideline_id|id, value: 3445",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_action/_guideline_id|id_scheme, value: HOSPITAL-NS",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_action/_work_flow_id|type, value: WORKFLOW",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_action/_work_flow_id|namespace, value: HOSPITAL-NS",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_action/_work_flow_id|id, value: 335645",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_action/_work_flow_id|id_scheme, value: HOSPITAL-NS"
},
new String[] {
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-ACTION.conformance_action_.v0, 1]/workflow_id/id",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-ACTION.conformance_action_.v0, 1]/workflow_id/type",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-ACTION.conformance_action_.v0, 1]/workflow_id/namespace",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-ACTION.conformance_action_.v0, 1]/guideline_id/namespace",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-ACTION.conformance_action_.v0, 1]/guideline_id/id",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-ACTION.conformance_action_.v0, 1]/guideline_id/type"
}));
break;
case EHRBASE_CONFORMANCE_INSTRUCTION:
arguments.add(
Arguments.of(
test,
new String[] {},
new String[] {
// see https://jira.vitagroup.ag/browse/CDR-219
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_instruction/_guideline_id|type, value: GUIDELINE",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_instruction/_guideline_id|namespace, value: HOSPITAL-NS",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_instruction/_guideline_id|id, value: 3445",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_instruction/_guideline_id|id_scheme, value: HOSPITAL-NS",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_instruction/_work_flow_id|type, value: WORKFLOW",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_instruction/_work_flow_id|namespace, value: HOSPITAL-NS",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_instruction/_work_flow_id|id, value: 335645",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_instruction/_work_flow_id|id_scheme, value: HOSPITAL-NS",
// https://jira.vitagroup.ag/browse/CDR-221
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_instruction/_wf_definition|value, value: wf_definition",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_instruction/_wf_definition|formalism, value: formalism"
},
new String[] {
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-INSTRUCTION.conformance_instruction.v0, 1]/workflow_id/id",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-INSTRUCTION.conformance_instruction.v0, 1]/workflow_id/type",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-INSTRUCTION.conformance_instruction.v0, 1]/workflow_id/namespace",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-INSTRUCTION.conformance_instruction.v0, 1]/guideline_id/namespace",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-INSTRUCTION.conformance_instruction.v0, 1]/guideline_id/id",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-INSTRUCTION.conformance_instruction.v0, 1]/guideline_id/type"
}));
break;

case EHRBASE_CONFORMANCE_ADMIN_ENTRY:
arguments.add(
Arguments.of(
test,
new String[] {},
new String[] {
// see https://jira.vitagroup.ag/browse/CDR-219

"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_work_flow_id|type, value: WORKFLOW",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_work_flow_id|namespace, value: HOSPITAL-NS",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_work_flow_id|id, value: 335645",
"Extra path: conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_work_flow_id|id_scheme, value: HOSPITAL-NS"
},
new String[] {
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-ADMIN_ENTRY.conformance_admin_entry.v0, 1]/workflow_id/id",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-ADMIN_ENTRY.conformance_admin_entry.v0, 1]/workflow_id/type",
"/content[openEHR-EHR-SECTION.conformance_section.v0, 1]/items[openEHR-EHR-ADMIN_ENTRY.conformance_admin_entry.v0, 1]/workflow_id/namespace"
}));
break;

case EHRBASE_CONFORMANCE_DATA_TYPES_DV_EHR_URI:
// see https://jira.vitagroup.ag/browse/CDR-214
Expand Down