Merge pull request #1002 from MetadataConsulting/MET-1745_Batches_and…

…_Actions Met 1745 batches and actions
MetadataConsulting · Jul 25, 2017 · f7e9aa4 · f7e9aa4
2 parents eb7803e + 4c2fbc8
commit f7e9aa4
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Showing 74 changed files with 4,468 additions and 1,564 deletions.
diff --git a/...eCorePluginTestApp/grails-app/assets/javascripts/modelcatalogue/core/ui/bs/actions.coffee b/...eCorePluginTestApp/grails-app/assets/javascripts/modelcatalogue/core/ui/bs/actions.coffee
@@ -260,6 +260,25 @@ angular.module('mc.core.ui.bs.actions', ['mc.util.ui.actions']).config (actionsP
       }
   ]
 
+  actionsProvider.registerActionInRole 'delete-suggestions', actionsProvider.ROLE_LIST_ACTION, ['$scope', 'security',
+      'catalogue', 'modelCatalogueApiRoot', 'enhance', 'rest', 'messages', '$state',
+      ($scope, security, catalogue, modelCatalogueApiRoot, enhance, rest, messages, $state)->
+        return undefined unless security.isUserLoggedIn()
+        return undefined unless $scope.list
+        return undefined unless catalogue.isInstanceOf($scope.list.itemType, 'batch')
+        {
+          position: 100
+          label: 'Delete Suggestions'
+          icon: 'fa fa-flash'
+          type: 'primary'
+          action: ->
+            messages.prompt('Delete Merged Batch', "Delete current list of suggestions", {type: 'delete-suggestions'}).then ->
+              $state.go('.', {page: undefined}, {reload: true})
+
+        }
+    ]
+
+
   actionsProvider.registerActionInRole 'refresh-batches', actionsProvider.ROLE_LIST_ACTION, ['$state', '$scope',
     'security', 'catalogue', ($state, $scope, security, catalogue)->
       return undefined unless security.isUserLoggedIn()

diff --git a/...gueCorePluginTestApp/grails-app/assets/javascripts/modelcatalogue/core/ui/bs/index.coffee b/...gueCorePluginTestApp/grails-app/assets/javascripts/modelcatalogue/core/ui/bs/index.coffee
@@ -64,6 +64,7 @@ angular.module('mc.core.ui.bs', [
   'mc.core.ui.bs.modalPromptRelationshipTypeEdit'
   'mc.core.ui.bs.modalPromptDatModelPolicyEdit'
   'mc.core.ui.bs.modalPromptGenerateSuggestions'
+  'mc.core.ui.bs.modalPromptDeleteSuggestions'
   'mc.core.ui.bs.modalPromptDataElementEdit'
   'mc.core.ui.bs.modalAbout'
   'mc.core.ui.bs.saveOrUpdatePublishedElementCtrl'

diff --git a/...p/assets/javascripts/modelcatalogue/core/ui/bs/modals/modalPromptDeleteSuggestions.coffee b/...p/assets/javascripts/modelcatalogue/core/ui/bs/modals/modalPromptDeleteSuggestions.coffee
@@ -0,0 +1,30 @@
+angular.module('mc.core.ui.bs.modalPromptDeleteSuggestions', ['mc.util.messages', 'mc.util.ui.focusMe']).config ['messagesProvider', (messagesProvider)->
+ messagesProvider.setPromptFactory 'delete-suggestions',  [ '$uibModal', ($uibModal) ->
+   (title, body) ->
+      dialog = $uibModal.open {
+        windowClass: 'messages-modal-prompt'
+        template: '''
+         <div class="modal-header">
+            <h4>''' + title + '''</h4>
+        </div>
+        <div class="modal-footer">
+            <button class="btn btn-primary" ng-click="close()">OK</button>
+            <button class="btn btn-warning" ng-click="$dismiss()">Cancel</button>
+        </div>
+        '''
+        resolve:
+          suggestionsNames: ['$http', 'modelCatalogueApiRoot', ($http, modelCatalogueApiRoot) ->
+            $http.get("#{modelCatalogueApiRoot}/dataArchitect/suggestionsNames").then (response) -> response.data
+          ]
+        controller: ['$scope', 'suggestionsNames', '$uibModalInstance', 'rest', 'modelCatalogueApiRoot', 'messages', ($scope, suggestionsNames, $uibModalInstance, rest, modelCatalogueApiRoot, messages) ->
+          $scope.suggestionsNames = suggestionsNames
+          $scope.close = ->
+            rest(method: 'POST', url: "#{modelCatalogueApiRoot}/dataArchitect/deleteSuggestions", params: {suggestion: $scope.suggestion}).then ->
+              messages.success "Deleting are suggestions in the background. Refresh batch list to see the generated results."
+              $uibModalInstance.close()
+        ]
+      }
+
+      dialog.result
+ ]
+]
diff --git a/...assets/javascripts/modelcatalogue/core/ui/bs/modals/modalPromptGenerateSuggestions.coffee b/...assets/javascripts/modelcatalogue/core/ui/bs/modals/modalPromptGenerateSuggestions.coffee
@@ -8,15 +8,41 @@ angular.module('mc.core.ui.bs.modalPromptGenerateSuggestions', ['mc.util.message
             <h4>''' + title + '''</h4>
         </div>
         <div class="modal-body">
+            <form role="form">
+                <div class="form-group">
+                  <label for="data-model-1" class="">Data Model 1</label>
+                  <elements-as-tags elements="dataModels"></elements-as-tags>
+                  <div class="input-group">
+                    <input type="text" class="form-control" id="data-model-1" placeholder="Name" ng-model="dataModel1" catalogue-element-picker="dataModel"  typeahead-on-select="push('dataModels', 'dataModel')">
+                  </div>
+                </div>
+            </form>
+            <form role="form">
+                <div class="form-group">
+                  <label for="data-model-2" class="">Data Model 2</label>
+                  <elements-as-tags elements="dataModels"></elements-as-tags>
+                  <div class="input-group">
+                    <input type="text" class="form-control" id="data-model-2" placeholder="Name" ng-model="dataModel2" catalogue-element-picker="dataModel"  typeahead-on-select="push('dataModels', 'dataModel')">
+                  </div>
+                </div>
+            </form>
             <form role="form">
               <div class="form-group">
                 <label for="elements">''' + body + '''</label>
                 <select class="form-control" ng-options="name for name in suggestionsNames" ng-model="suggestion"/>
               </div>
             </form>
+
+          <form role="form">
+              <div class="form-group">
+                <label for="min-score"> Min Search Score (default is 10) </label>
+                    <input type="number " class="form-control" max="90" id="min-score" placeholder="Min Score: 10" ng-model="minScore" >
+              </div>
+            </form>
+
         </div>
         <div class="modal-footer">
-            <button class="btn btn-primary" ng-click="close()">OK</button>
+            <button class="btn btn-primary" ng-click="close()" ng-disabled="isEmpty(dataModel1)||isEmpty(dataModel2)||isEmpty(suggestion)">OK</button>
             <button class="btn btn-warning" ng-click="$dismiss()">Cancel</button>
         </div>
         '''
@@ -27,9 +53,12 @@ angular.module('mc.core.ui.bs.modalPromptGenerateSuggestions', ['mc.util.message
         controller: ['$scope', 'suggestionsNames', '$uibModalInstance', 'rest', 'modelCatalogueApiRoot', 'messages', ($scope, suggestionsNames, $uibModalInstance, rest, modelCatalogueApiRoot, messages) ->
           $scope.suggestionsNames = suggestionsNames
           $scope.close = ->
-            rest(method: 'POST', url: "#{modelCatalogueApiRoot}/dataArchitect/generateSuggestions", params: {suggestion: $scope.suggestion}).then ->
+            rest(method: 'POST', url: "#{modelCatalogueApiRoot}/dataArchitect/generateSuggestions", params: {suggestion: $scope.suggestion, dataModel1: $scope.dataModel1.id, dataModel2: $scope.dataModel2.id, minScore: $scope.minScore}).then ->
               messages.success "Suggestions are generating in the background. Refresh batch list to see the generated results."
               $uibModalInstance.close()
+          $scope.isEmpty = (object) ->
+            return true if not object
+            angular.equals object, {}
         ]
       }
 

diff --git a/ModelCatalogueCorePluginTestApp/grails-app/conf/BootStrap.groovy b/ModelCatalogueCorePluginTestApp/grails-app/conf/BootStrap.groovy
@@ -55,21 +55,23 @@ class BootStrap {
                 initSecurity(false)
                 setupDevTestStuff()
             }
-//            modelCatalogueSearchService.reindex(true).all { it }.toBlocking().subscribe {
-//                System.out.println "Reindexed"
-//            }
+
         } else {
             initCatalogueService.initDefaultRelationshipTypes()
-            initPoliciesAndTags()
             initSecurity(!System.getenv('MC_BLANK_DEV'))
         }
 
+        modelCatalogueSearchService.reindex(true).all { it }.toBlocking().subscribe {
+            System.out.println "Reindexed"
+        }
+
         initCatalogueService.setupStoredProcedures()
 
         if (Environment.current == Environment.PRODUCTION) {
             userService.inviteAdmins()
         }
 
+
         //register custom json Marshallers
         //ctx.domainModellerService.modelDomains()
         grailsApplication.mainContext.getBean('modelCatalogueCorePluginCustomObjectMarshallers').register()
@@ -90,7 +92,7 @@ class BootStrap {
         reportsRegistry.register {
             creates asset
             title { "Inventory Report Spreadsheet" }
-            defaultName { "${it.name} report as MS Excel Document" }
+            defaultName { "${it.name} report as MS Excel Document Inventory" }
             depth 3
             type DataModel
             when { DataModel dataModel ->
@@ -99,6 +101,18 @@ class BootStrap {
             link controller: 'dataModel', action: 'inventorySpreadsheet', id: true
         }
 
+        reportsRegistry.register {
+            creates asset
+            title { "Grid Report Spreadsheet" }
+            defaultName { "${it.name} report as MS Excel Document Grid" }
+            depth 3
+            type DataModel
+            when { DataModel dataModel ->
+                dataModel.countDeclares() > 0
+            }
+            link controller: 'dataModel', action: 'gridSpreadsheet', id: true
+        }
+
         reportsRegistry.register {
             creates asset
             title { "Inventory Report Document" }
@@ -129,16 +143,6 @@ class BootStrap {
             link controller: 'dataClass', action: 'inventorySpreadsheet', id: true
         }
 
-//  needs more work
-//        reportsRegistry.register {
-//            creates asset
-//            title { "Changelog Document" }
-//            defaultName { "${it.name} changelog as MS Word Document" }
-//            depth 3
-//            includeMetadata true
-//            type DataClass
-//            link controller: 'dataClass', action: 'changelogDoc', id: true
-//        }
 
         reportsRegistry.register {
             creates link
@@ -169,29 +173,6 @@ class BootStrap {
             link controller: 'genomics', action: 'exportAllRareDiseaseReports', id: true
         }
 
-// needs more work
-//        reportsRegistry.register {
-//            creates asset
-//            title { "GEL Changelog (Word Doc)" }
-//            defaultName { "${it.name} changelog as MS Word Document" }
-//            depth 3
-//            includeMetadata true
-//            type DataModel
-//            when { DataModel dataModel ->
-//                dataModel.ext.get(Metadata.HPO_REPORT_AVAILABLE) == 'true'
-//            }
-//            link controller: 'genomics', action: 'exportChangeLogDocument', id: true
-//        }
-
-//        reportsRegistry.register {
-//            creates asset
-//            title { "GEL Data Specification Report (Word Doc)" }
-//            defaultName { "${it.name} report as MS Word Document" }
-//            depth 3
-//            type DataModel
-//            link controller: 'genomics', action: 'exportGelSpecification', id: true
-//        }
-
         reportsRegistry.register {
             creates link
             title { "Rare Diseases Disorder List (CSV)" }
@@ -212,6 +193,10 @@ class BootStrap {
             link controller: 'genomics', action: 'exportRareDiseaseEligibilityDoc', id: true
         }
 
+
+
+
+
         reportsRegistry.register {
             creates link
             title { "Rare Diseases Phenotypes and Clinical Tests Report (Word Doc)" }
@@ -222,6 +207,17 @@ class BootStrap {
             link controller: 'genomics', action: 'exportRareDiseasePhenotypesAndClinicalTestsDoc', id: true
         }
 
+
+        reportsRegistry.register {
+            creates link
+            title { "Rare Diseases Eligibility Phenotypes Split Docs" }
+            type DataModel
+            when { DataModel dataModel ->
+                dataModel.ext.get(Metadata.HPO_REPORT_AVAILABLE) == 'true'
+            }
+            link controller: 'genomics', action: 'exportRareDiseaseSplitDocs', id: true
+        }
+
         reportsRegistry.register {
             creates link
             title { "Rare Diseases HPO And Clinical Tests (JSON)" }
@@ -275,27 +271,17 @@ class BootStrap {
             link controller: 'genomics', action: 'exportRareDiseaseEligibilityCsv', id: true
         }
 
+        reportsRegistry.register {
+            creates link
+            title { "Rare Diseases Static Website" }
+            type DataModel
+            when { DataModel dataModel ->
+                dataModel.ext.get('Rare Disease Report Available') == 'true' || dataModel.ext.get("All Rare Disease Conditions Reports") == 'true' || dataModel.ext.get(Metadata.ALL_RD_REPORTS) == 'true' || dataModel.ext.get(Metadata.HPO_REPORT_AVAILABLE) == 'true'
+            }
+            link controller: 'genomics', action: 'exportRareDiseasesWebsite', id: true
+        }
+
 
-// needs work before we can release
-//        reportsRegistry.register {
-//            creates link
-//            title { "Cancer Types (JSON)" }
-//            type DataModel
-//            when { DataModel dataModel ->
-//                dataModel.ext.get(Metadata.CANCER_TYPES_AVAILABLE) == 'true'
-//            }
-//            link controller: 'genomics', action: 'exportCancerTypesAsJson', id: true
-//        }
-//
-//        reportsRegistry.register {
-//            creates link
-//            title { "Cancer Types (CSV)" }
-//            type DataModel
-//            when { DataModel dataModel ->
-//                dataModel.ext.get(Metadata.CANCER_TYPES_AVAILABLE) == 'true'
-//            }
-//            link controller: 'genomics', action: 'exportCancerTypesAsCsv', id: true
-//        }
 // needs work before we can release
 //        reportsRegistry.register {
 //            creates link
@@ -322,17 +308,43 @@ class BootStrap {
 //            title { "GEL Data Specification Change Log (Excel)" }
 //            type DataModel
 //            link controller: 'genomics', action: 'exportDataSpecChangeLogAsXls', id: true
+//        }
+        //  needs more work
+//        reportsRegistry.register {
+//            creates asset
+//            title { "Changelog Document" }
+//            defaultName { "${it.name} changelog as MS Word Document" }
+//            depth 3
+//            includeMetadata true
+//            type DataClass
+//            link controller: 'dataClass', action: 'changelogDoc', id: true
 //        }
 
-        reportsRegistry.register {
-            creates link
-            title { "Rare Diseases Static Website" }
-            type DataModel
-            when { DataModel dataModel ->
-                dataModel.ext.get('Rare Disease Report Available') == 'true' || dataModel.ext.get("All Rare Disease Conditions Reports") == 'true' || dataModel.ext.get(Metadata.ALL_RD_REPORTS) == 'true' || dataModel.ext.get(Metadata.HPO_REPORT_AVAILABLE) == 'true'
-            }
-            link controller: 'genomics', action: 'exportRareDiseasesWebsite', id: true
-        }
+// needs more work
+//        reportsRegistry.register {
+//            creates asset
+//            title { "GEL Changelog (Word Doc)" }
+//            defaultName { "${it.name} changelog as MS Word Document" }
+//            depth 3
+//            includeMetadata true
+//            type DataModel
+//            when { DataModel dataModel ->
+//                dataModel.ext.get(Metadata.HPO_REPORT_AVAILABLE) == 'true'
+//            }
+//            link controller: 'genomics', action: 'exportChangeLogDocument', id: true
+//        }
+
+//        reportsRegistry.register {
+//            creates asset
+//            title { "GEL Data Specification Report (Word Doc)" }
+//            defaultName { "${it.name} report as MS Word Document" }
+//            depth 3
+//            type DataModel
+//            link controller: 'genomics', action: 'exportGelSpecification', id: true
+//        }
+
+
+
     }
 
     private static void initSecurity(boolean production) {
@@ -395,6 +407,7 @@ class BootStrap {
                 '/login', '/login.*', '/login/*',
                 '/logout', '/logout.*', '/logout/*',
                 '/register/*', '/errors', '/errors/*',
+                '/load',
                 '/index.gsp'
         ]) {
             createRequestmapIfMissing(url, 'permitAll', null)
@@ -428,11 +441,6 @@ class BootStrap {
         createRequestmapIfMissing('/monitoring/**',                         'ROLE_SUPERVISOR')
         createRequestmapIfMissing('/plugins/console-1.5.0/**',              'ROLE_SUPERVISOR')
 
-//        createRequestmapIfMissing('/api/modelCatalogue/core/dataClass/**', 'IS_AUTHENTICATED_ANONYMOUSLY')
-//        createRequestmapIfMissing('/api/modelCatalogue/core/dataElement/**', 'ROLE_METADATA_CURATOR')
-//        createRequestmapIfMissing('/api/modelCatalogue/core/dataType/**', 'ROLE_USER')
-//        createRequestmapIfMissing('/api/modelCatalogue/core/*/**', 'ROLE_METADATA_CURATOR')
-//        createRequestmapIfMissing('/api/modelCatalogue/core/relationshipTypes/**', 'ROLE_ADMIN')
     }
 
     def initPoliciesAndTags() {
@@ -533,14 +541,25 @@ class BootStrap {
                     dataElement(name: 'Test Element 1') {
                         dataType(name: 'Same Name')
                     }
+                    dataElement(name: 'Test Element 2') {
+                        dataType(name: 'Same Name')
+                    }
                 }
 
+            }
+
+            catalogueBuilder.build {
                 dataModel(name: 'Test 2') {
+                    automatic dataType
                     policy 'Unique of Kind'
                     dataElement(name: 'Test Element 2') {
                         dataType(name: 'Same Name')
                     }
                 }
+            }
+
+            catalogueBuilder.build {
+                automatic dataType
                 dataModel(name: 'Test 3') {
                     dataElement(name: "data element with orphaned data type")
                 }

diff --git a/ModelCatalogueCorePluginTestApp/grails-app/conf/BuildConfig.groovy b/ModelCatalogueCorePluginTestApp/grails-app/conf/BuildConfig.groovy
@@ -73,6 +73,8 @@ grails.project.dependency.resolution = {
         compile "org.modelcatalogue:mc-builder-api:$mcToolkitVersion"
         compile "org.modelcatalogue:mc-datatype-validation:$mcToolkitVersion"
 
+        compile 'me.xdrop:fuzzywuzzy:1.1.7'
+
         compile 'com.craigburke.document:word:0.5.0'
 
         compile 'org.jsoup:jsoup:1.8.3'