Merge pull request #504 from MetadataRegistry/develop

GEL Release 20150928
MetadataConsulting · Sep 29, 2015 · b2cb223 · b2cb223
2 parents 0676736 + 6873f11
commit b2cb223
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diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,4 @@
-# FormsPlugin
-/ModelCatalogueFormsPlugin
-*.iml
+**.iml
 **/web-app/*
 **/.idea/*
 **/atlassian-ide-plugin.xml
@@ -15,4 +13,6 @@ ModelCatalogueCorePluginTestApp/test/integration/resources/rare_diseases_combine
 out/**/*
 **/target/**/*
 **/target-eclipse/**/*
-**/*.class
+**/*.class
+**/*.gen.fixture.js
+**/build/**/*
diff --git a/.travis.yml b/.travis.yml
@@ -1,10 +1,27 @@
 language: groovy
+cache:
+  directories:
+    - node_modules
+    - ModelCatalogueCorePlugin/target/work/plugins
+    - ModelCatalogueCorePluginTestApp/target/work/plugins
+    - $HOME/.m2
+    - $HOME/.grails/ivy-cache
+    - $HOME/.grails/wrapper
+
+env:
+  - TEST_SUITE=core_unit
+  - TEST_SUITE=core_integration
+  - TEST_SUITE=core_integration_slow
+  - TEST_SUITE=app_integration
+  - TEST_SUITE=app_functional
+  - TEST_SUITE=forms_integration
+  - TEST_SUITE=gel_integration
 jdk:
-- oraclejdk7
+  - oraclejdk7
 before_install:
   - "export DISPLAY=:99.0"
   - "/sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -ac -screen 0 1920x1080x24"
 script:
   - "./run-all-tests.sh"
-#after_script:
-#  - "./update-gh-pages.sh"
+after_script:
+  - "./update-gh-pages.sh"
diff --git a/ModelCatalogueCorePlugin/ModelCatalogueCoreGrailsPlugin.groovy b/ModelCatalogueCorePlugin/ModelCatalogueCoreGrailsPlugin.groovy
@@ -5,9 +5,13 @@ import org.modelcatalogue.core.*
 import org.modelcatalogue.core.reports.ReportsRegistry
 import org.modelcatalogue.core.util.CatalogueElementDynamicHelper
 import org.modelcatalogue.core.util.ListWrapper
-import org.modelcatalogue.core.util.builder.CatalogueBuilder
+import org.modelcatalogue.core.util.builder.DefaultCatalogueBuilder
 import org.modelcatalogue.core.util.marshalling.*
 import org.modelcatalogue.core.util.marshalling.xlsx.XLSXListRenderer
+import org.modelcatalogue.core.audit.AuditJsonMarshallingCustomizer
+import org.modelcatalogue.core.util.js.FrontendConfigurationProviderRegistry
+import org.modelcatalogue.core.util.js.ApiRootFrontendConfigurationProvider
+import org.modelcatalogue.builder.api.ModelCatalogueTypes
 
 class ModelCatalogueCoreGrailsPlugin {
     // the plugin version
@@ -54,10 +58,25 @@ Model catalogue core plugin (metadata registry)
 
 
     def doWithSpring = {
+        ModelCatalogueTypes.CLASSIFICATION.implementation = Classification
+        ModelCatalogueTypes.MODEL.implementation = Model
+        ModelCatalogueTypes.DATA_ELEMENT.implementation = DataElement
+        ModelCatalogueTypes.VALUE_DOMAIN.implementation = ValueDomain
+        ModelCatalogueTypes.DATA_TYPE.implementation = DataType
+        ModelCatalogueTypes.MEASUREMENT_UNIT.implementation = MeasurementUnit
+        ModelCatalogueTypes.ENUMERATED_TYPE.implementation = EnumeratedType
+
+
         mergeConfig(application)
 
         xlsxListRenderer(XLSXListRenderer)
         reportsRegistry(ReportsRegistry)
+        jsonMarshallingCustomizerRegistry(JsonMarshallingCustomizerRegistry)
+        frontendConfigurationProviderRegistry(FrontendConfigurationProviderRegistry)
+
+        apiRootFrontendConfigurationProvider(ApiRootFrontendConfigurationProvider)
+
+        auditJsonMarshallingCustomizer(AuditJsonMarshallingCustomizer)
 
         modelCatalogueCorePluginCustomObjectMarshallers(ModelCatalogueCorePluginCustomObjectMarshallers) {
             marshallers = [
@@ -67,27 +86,29 @@ Model catalogue core plugin (metadata registry)
                     new DataTypeMarshaller(),
                     new ElementsMarshaller(),
                     new EnumeratedTypeMarshaller(),
-                    new MeasurementUnitMarshallers(),
+                    new MeasurementUnitMarshaller(),
                     new ModelMarshaller(),
                     new RelationshipTypeMarshaller(),
                     new RelationshipMarshallers(),
                     new RelationshipsMarshaller(),
                     new ValueDomainMarshaller(),
-                    new MappingMarshallers(),
+                    new MappingMarshaller(),
                     new MappingsMarshaller(),
                     new ListWithTotalAndTypeWrapperMarshaller(),
                     new BatchMarshaller(),
                     new ActionMarshaller(),
                     new CsvTransformationMarshaller(),
-                    new UserMarshaller()
+                    new UserMarshaller(),
+                    new ChangeMarshaller(),
+
             ]
         }
 
         if (Environment.current == Environment.DEVELOPMENT) {
             springConfig.addAlias('modelCatalogueStorageService','localFilesStorageService')
         }
 
-        catalogueBuilder(CatalogueBuilder, ref('classificationService'), ref('elementService')) { bean ->
+        catalogueBuilder(DefaultCatalogueBuilder, ref('classificationService'), ref('elementService')) { bean ->
             bean.scope = 'prototype'
         }
 
@@ -225,18 +246,50 @@ Model catalogue core plugin (metadata registry)
         xlsxListRenderer.registerRowWriter('NHIC') {
             title "Data Elements to Excel"
             append metadata
-            headers "Classification", "Parent Model Unique Code",
-            "Parent Model", "Model Unique Code", "Model",
-            "Data Item Unique Code", "Data Item Name", "Data Item Description",
-            "Measurement Unit","Measurement Unit Symbol", "Data type", "Metadata"
+            headers "Classification",
+                    "Parent Model Unique Code",
+                    "Parent Model",
+                    "Model Unique Code",
+                    "Model",
+                    "Data Item Unique Code",
+                    "Data Item Name",
+                    "Data Item Description",
+                    "Value Domain Classification",
+                    "Value Domain Unique Code",
+                    "Value Domain",
+                    "Measurement Unit",
+                    "Measurement Unit Symbol",
+                    "Data Type Classification",
+                    "Data Type Unique Code",
+                    "Data Type",
+                    "Metadata"
 
             when { ListWrapper container, RenderContext context ->
                 container.itemType && DataElement.isAssignableFrom(container.itemType)
             } then { DataElement element ->
-                [[getClassificationString(element), getParentModel(element)?.modelCatalogueId,
-                  getParentModel(element)?.name, getContainingModel(element)?.modelCatalogueId, getContainingModel(element)?.name,
-                  element.modelCatalogueId, element.name, element.description,
-                  getUnitOfMeasure(element), getUnitOfMeasureSymbol(element) , getDataType(element), "-"]]
+                Model parent = getParentModel(element)
+                Model model = getContainingModel(element)
+                ValueDomain valueDomain = element.valueDomain
+                DataType dataType = valueDomain?.dataType
+                [[
+                         getClassificationString(element),
+                         parent?.modelCatalogueId ?: parent?.getDefaultModelCatalogueId(true),
+                         parent?.name,
+                         model?.modelCatalogueId  ?: model?.getDefaultModelCatalogueId(true),
+                         model?.name,
+                         element.modelCatalogueId ?: element.getDefaultModelCatalogueId(true),
+                         element.name,
+                         element.description,
+                         getClassificationString(valueDomain),
+                         valueDomain?.modelCatalogueId ?: valueDomain?.getDefaultModelCatalogueId(true),
+                         valueDomain?.name,
+                         getUnitOfMeasure(element),
+                         getUnitOfMeasureSymbol(element) ,
+                         getClassificationString(dataType),
+                         dataType?.modelCatalogueId ?: dataType?.getDefaultModelCatalogueId(true),
+                         getDataType(element),
+                         "-"
+                 ]]
             }
         }
 
@@ -263,6 +316,13 @@ Model catalogue core plugin (metadata registry)
             type Classification
             link controller: 'classification', action: 'gereport', id: true
         }
+
+		reportsRegistry.register {
+			creates link
+			title { "GE Inventory Report Docx" }
+			type Classification
+			link controller: 'classificationReports', action: 'gereportDoc', id: true
+		}
 
         reportsRegistry.register {
             creates link
@@ -348,20 +408,18 @@ Model catalogue core plugin (metadata registry)
                 return ''
             }
             if (dataType instanceof EnumeratedType) {
-                return dataType.enumAsString
+                return dataType.enumerations.collect { key, value -> "$key:$value"}.join('\n')
             }
             return dataType.name
         }
         return null
     }
 
     def static getClassificationString(CatalogueElement dataElement) {
-        String classifications = ""
-        dataElement.classifications.eachWithIndex{ def classification, Integer i ->
-            if (classifications != "") classifications += (stringSeparator + classification.name)
-            else classifications = classification.name
+        if (!dataElement?.classifications) {
+            return ""
         }
-        return classifications
+        dataElement.classifications.first().name
     }
 
     def static getValueDomainString(DataType dataType){

diff --git a/ModelCatalogueCorePlugin/fixtures/assets/A_file.groovy b/ModelCatalogueCorePlugin/fixtures/assets/A_file.groovy
@@ -1,6 +1,6 @@
 import org.modelcatalogue.core.Asset
-import org.modelcatalogue.core.ElementStatus
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture{
     A_file(Asset, name:"file", description: "random file", status: ElementStatus.FINALIZED)

diff --git a/ModelCatalogueCorePlugin/fixtures/assets/A_file1.groovy b/ModelCatalogueCorePlugin/fixtures/assets/A_file1.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.Asset
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture{
     A_file1(Asset, name:"file1", description: "some random file 1", status: ElementStatus.FINALIZED)

diff --git a/ModelCatalogueCorePlugin/fixtures/assets/A_file2.groovy b/ModelCatalogueCorePlugin/fixtures/assets/A_file2.groovy
@@ -1,6 +1,6 @@
 import org.modelcatalogue.core.Asset
-import org.modelcatalogue.core.ElementStatus
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture{
     A_file2(Asset, name:"ASSET", description: "some random file 2", status: ElementStatus.FINALIZED)

diff --git a/ModelCatalogueCorePlugin/fixtures/assets/A_file3.groovy b/ModelCatalogueCorePlugin/fixtures/assets/A_file3.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.Asset
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture{
     A_file3(Asset, name:"A_file3", description: "the random name 3", status: ElementStatus.FINALIZED)

diff --git a/ModelCatalogueCorePlugin/fixtures/assets/A_file4.groovy b/ModelCatalogueCorePlugin/fixtures/assets/A_file4.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.Asset
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture{
     A_file4(Asset, name:"A_file4", description: "some random file 4", status: ElementStatus.FINALIZED)

diff --git a/ModelCatalogueCorePlugin/fixtures/assets/A_file5.groovy b/ModelCatalogueCorePlugin/fixtures/assets/A_file5.groovy
@@ -1,6 +1,6 @@
 import org.modelcatalogue.core.Asset
-import org.modelcatalogue.core.ElementStatus
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture{
     A_file5(Asset, name:"A_file5", description: "random file 5", status: ElementStatus.FINALIZED)

diff --git a/ModelCatalogueCorePlugin/fixtures/assets/A_file6.groovy b/ModelCatalogueCorePlugin/fixtures/assets/A_file6.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.Asset
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture{
     A_file6(Asset, name:"A_file6", description: "random file 6", status: ElementStatus.FINALIZED)

diff --git a/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet1.groovy b/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet1.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.Classification
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture {
     CL_dataSet1(Classification, name: "data set 1", status: ElementStatus.FINALIZED,

diff --git a/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet10.groovy b/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet10.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.Classification
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture {
     CL_dataSet10(Classification, name: "data set 10", status: ElementStatus.FINALIZED,

diff --git a/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet11.groovy b/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet11.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.Classification
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture {
     CL_dataSet11(Classification, name: "data set 11", status: ElementStatus.FINALIZED,

diff --git a/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet12.groovy b/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet12.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.Classification
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture {
     CL_dataSet12(Classification, name: "data set 12", status: ElementStatus.FINALIZED,

diff --git a/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet2.groovy b/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet2.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.Classification
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture {
     CL_dataSet2(Classification, name: "data set 2", status: ElementStatus.FINALIZED,

diff --git a/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet3.groovy b/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet3.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.Classification
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture {
     CL_dataSet3(Classification, name: "data set 3", status: ElementStatus.FINALIZED,

diff --git a/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet4.groovy b/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet4.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.Classification
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture {
     CL_dataSet4(Classification, name: "data set 4", status: ElementStatus.FINALIZED,

diff --git a/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet5.groovy b/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet5.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.Classification
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture {
     CL_dataSet5(Classification, name: "data set 5", status: ElementStatus.FINALIZED,

diff --git a/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet6.groovy b/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet6.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.Classification
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture {
     CL_dataSet6(Classification, name: "data set 6", status: ElementStatus.FINALIZED,

diff --git a/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet7.groovy b/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet7.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.Classification
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture {
     CL_dataSet7(Classification, name: "data set 7", status: ElementStatus.FINALIZED,

diff --git a/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet8.groovy b/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet8.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.Classification
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture {
     CL_dataSet8(Classification, name: "data set 8", status: ElementStatus.FINALIZED,

diff --git a/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet9.groovy b/ModelCatalogueCorePlugin/fixtures/classifications/CL_dataSet9.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.Classification
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture {
     CL_dataSet9(Classification, name: "data set 9", status: ElementStatus.FINALIZED,

diff --git a/ModelCatalogueCorePlugin/fixtures/dataElements/DE_author.groovy b/ModelCatalogueCorePlugin/fixtures/dataElements/DE_author.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.DataElement
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture{
     DE_author(DataElement, name:"DE_author", description: "the DE_author of the book", status: ElementStatus.FINALIZED)

diff --git a/ModelCatalogueCorePlugin/fixtures/dataElements/DE_author1.groovy b/ModelCatalogueCorePlugin/fixtures/dataElements/DE_author1.groovy
@@ -1,6 +1,6 @@
 import org.modelcatalogue.core.DataElement
-import org.modelcatalogue.core.ElementStatus
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture{
     DE_author1(DataElement, name:"DE_author1", description: "the DE_author of the book", status: ElementStatus.FINALIZED)

diff --git a/ModelCatalogueCorePlugin/fixtures/dataElements/DE_author2.groovy b/ModelCatalogueCorePlugin/fixtures/dataElements/DE_author2.groovy
@@ -1,5 +1,5 @@
 import org.modelcatalogue.core.DataElement
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture{
     DE_author2(DataElement, name:"AUTHOR", description: "the DE_author of the book", status: ElementStatus.FINALIZED)

diff --git a/ModelCatalogueCorePlugin/fixtures/dataElements/DE_author3.groovy b/ModelCatalogueCorePlugin/fixtures/dataElements/DE_author3.groovy
@@ -1,6 +1,5 @@
 import org.modelcatalogue.core.DataElement
-import org.modelcatalogue.core.ElementStatus
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture{
     DE_author3(DataElement, name:"auth", description: "the DE_author of the book", status: ElementStatus.FINALIZED)

diff --git a/ModelCatalogueCorePlugin/fixtures/dataElements/DE_author4.groovy b/ModelCatalogueCorePlugin/fixtures/dataElements/DE_author4.groovy
@@ -1,6 +1,6 @@
 import org.modelcatalogue.core.DataElement
-import org.modelcatalogue.core.ElementStatus
-import org.modelcatalogue.core.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
+import org.modelcatalogue.core.api.ElementStatus
 
 fixture{
     DE_author4(DataElement, name:"auth4", description: "the DE_author of the book", status: ElementStatus.FINALIZED)