Merge branch 'release/4.11.0' into main

MauroDataMapper · Nov 3, 2021 · a99c1da · a99c1da
2 parents 18e0a40 + 8dd6299
commit a99c1da
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Showing 275 changed files with 9,275 additions and 1,238 deletions.
diff --git a/Jenkinsfile b/Jenkinsfile
@@ -133,7 +133,7 @@ pipeline {
                     'mdm-plugin-datamodel',
                     'mdm-plugin-email-proxy',
                     'mdm-plugin-federation',
-                    //                    'mdm-plugin-profile',
+                    'mdm-plugin-profile',
                     'mdm-plugin-referencedata',
                     'mdm-plugin-terminology',
                     'mdm-security',
@@ -393,16 +393,16 @@ pipeline {
                 }
             }
         }
-        //        stage('E2E Profile Functional Test') {
-        //            steps {
-        //                sh "./gradlew -Dgradle.test.package=profile :mdm-testing-functional:integrationTest"
-        //            }
-        //            post {
-        //                always {
-        //                    junit allowEmptyResults: true, testResults: 'mdm-testing-functional/build/test-results/profile/*.xml'
-        //                }
-        //            }
-        //        }
+        stage('E2E Profile Functional Test') {
+            steps {
+                sh "./gradlew -Dgradle.test.package=profile :mdm-testing-functional:integrationTest"
+            }
+            post {
+                always {
+                    junit allowEmptyResults: true, testResults: 'mdm-testing-functional/build/test-results/profile/*.xml'
+                }
+            }
+        }
 
         stage('Compile complete Test Report') {
             steps {

diff --git a/gradle.properties b/gradle.properties
@@ -1,5 +1,5 @@
 # Core Info
-version=4.10.0
+version=4.11.0
 group=uk.ac.ox.softeng.maurodatamapper
 # Gradle
 gradleVersion=6.7.1
@@ -23,6 +23,7 @@ hibernateSearchVersion=2.3.0
 luceneVersion=5.5.5
 ## Core
 commonsTextVersion=1.9
+commonsCsvVersion=1.8
 springBootVersion=2.1.17.RELEASE
 jaxbApiVersion=2.3.1
 assetPipelineVersion=3.3.2

diff --git a/mdm-common/dependencies.gradle b/mdm-common/dependencies.gradle
@@ -11,6 +11,7 @@ dependencies {
 
     implementation group: 'org.grails', name: 'grails-core', version: grailsVersion
     implementation group: 'org.grails', name: 'grails-datastore-gorm'
+    implementation group: 'org.grails', name: 'grails-datastore-gorm-hibernate5'
     implementation group: 'org.grails', name: 'grails-plugin-validation'
     implementation "org.grails.plugins:views-json:$grailsViewsVersion"
 

diff --git a/mdm-common/src/main/groovy/uk/ac/ox/softeng/maurodatamapper/path/Path.groovy b/mdm-common/src/main/groovy/uk/ac/ox/softeng/maurodatamapper/path/Path.groovy
@@ -21,6 +21,8 @@ import uk.ac.ox.softeng.maurodatamapper.traits.domain.CreatorAware
 
 import groovy.transform.stc.ClosureParams
 import groovy.transform.stc.SimpleType
+import uk.ac.ox.softeng.maurodatamapper.traits.domain.PathAware
+import uk.ac.ox.softeng.maurodatamapper.util.Utils
 
 /**
  * @since 28/08/2020
@@ -248,4 +250,16 @@ class Path {
     static boolean isValidPath(String possiblePath) {
         from(possiblePath).toString() == possiblePath
     }
+
+    static Path toPathPrefix(CreatorAware domain, String prefix)
+    {
+        List<CreatorAware> objectsInPath  = []
+        objectsInPath.push(domain)
+
+        while (objectsInPath.first().getPathPrefix() != prefix && Utils.parentClassIsAssignableFromChild(PathAware, objectsInPath.first().class)) {
+            objectsInPath.push(objectsInPath.first().getPathParent())
+        }
+
+        Path.from(objectsInPath)
+    }
 }
diff --git a/...rc/main/groovy/uk/ac/ox/softeng/maurodatamapper/search/bridge/OffsetDateTimeBridge.groovy b/...rc/main/groovy/uk/ac/ox/softeng/maurodatamapper/search/bridge/OffsetDateTimeBridge.groovy
@@ -36,7 +36,7 @@ class OffsetDateTimeBridge implements StringBridge {
     @Override
     String objectToString(Object object) {
         if (object instanceof OffsetDateTime) {
-            return ((OffsetDateTime) object).format(dtf)
+            return ((OffsetDateTime) object).toLocalDate().format(dtf)
         }
         logger.error('Bridge set up to convert object of type {} but it is not an OffsetDateTime', object.getClass())
         return null

diff --git a/...vy/uk/ac/ox/softeng/maurodatamapper/search/bridge/spi/OffsetDateTimeBridgeProvider.groovy b/...vy/uk/ac/ox/softeng/maurodatamapper/search/bridge/spi/OffsetDateTimeBridgeProvider.groovy
@@ -0,0 +1,42 @@
+/*
+ * Copyright 2020 University of Oxford and Health and Social Care Information Centre, also known as NHS Digital
+ *
+ * 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.
+ *
+ * SPDX-License-Identifier: Apache-2.0
+ */
+package uk.ac.ox.softeng.maurodatamapper.search.bridge.spi
+
+
+import uk.ac.ox.softeng.maurodatamapper.search.bridge.OffsetDateTimeBridge
+import uk.ac.ox.softeng.maurodatamapper.util.Utils
+
+import org.hibernate.search.bridge.FieldBridge
+import org.hibernate.search.bridge.spi.BridgeProvider
+import org.hibernate.search.bridge.util.impl.String2FieldBridgeAdaptor
+
+import java.time.OffsetDateTime
+
+/**
+ * @since 13/09/2021
+ */
+class OffsetDateTimeBridgeProvider implements BridgeProvider {
+    @Override
+    FieldBridge provideFieldBridge(BridgeProviderContext bridgeProviderContext) {
+        if (
+        bridgeProviderContext.returnType.simpleName == OffsetDateTime.simpleName && Utils.parentClassIsAssignableFromChild(OffsetDateTime, bridgeProviderContext.returnType)) {
+            return new String2FieldBridgeAdaptor(new OffsetDateTimeBridge())
+        }
+        null
+    }
+}
diff --git a/mdm-common/src/main/groovy/uk/ac/ox/softeng/maurodatamapper/security/User.groovy b/mdm-common/src/main/groovy/uk/ac/ox/softeng/maurodatamapper/security/User.groovy
@@ -53,4 +53,8 @@ trait User extends SecurableResource {
     Boolean getReadableByAuthenticatedUsers() {
         false
     }
+
+    String getFullName() {
+        "${firstName} ${lastName}"
+    }
 }
diff --git a/...mmon/src/main/groovy/uk/ac/ox/softeng/maurodatamapper/security/basic/AnonymousUser.groovy b/...mmon/src/main/groovy/uk/ac/ox/softeng/maurodatamapper/security/basic/AnonymousUser.groovy
@@ -0,0 +1,48 @@
+/*
+ * Copyright 2020 University of Oxford and Health and Social Care Information Centre, also known as NHS Digital
+ *
+ * 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.
+ *
+ * SPDX-License-Identifier: Apache-2.0
+ */
+package uk.ac.ox.softeng.maurodatamapper.security.basic
+
+import uk.ac.ox.softeng.maurodatamapper.security.User
+
+/**
+ * @since 21/10/2019
+ */
+@Singleton
+class AnonymousUser implements User {
+
+    public static final String ANONYMOUS_EMAIL_ADDRESS = 'anonymous@maurodatamapper.com'
+
+    String emailAddress = ANONYMOUS_EMAIL_ADDRESS
+    String firstName = 'Anonymous'
+    String lastName = 'User'
+    String tempPassword
+
+    @Override
+    UUID getId() {
+        UUID.randomUUID()
+    }
+
+    UUID ident() {
+        id
+    }
+
+    @Override
+    String getDomainType() {
+        AnonymousUser
+    }
+}
diff --git a/...apper/core/traits/domain/PathAware.groovy → ...datamapper/traits/domain/PathAware.groovy b/...apper/core/traits/domain/PathAware.groovy → ...datamapper/traits/domain/PathAware.groovy
@@ -15,13 +15,12 @@
  *
  * SPDX-License-Identifier: Apache-2.0
  */
-package uk.ac.ox.softeng.maurodatamapper.core.traits.domain
+package uk.ac.ox.softeng.maurodatamapper.traits.domain
 
 import edu.umd.cs.findbugs.annotations.SuppressFBWarnings
 import grails.compiler.GrailsCompileStatic
 import groovy.transform.SelfType
 import org.grails.datastore.gorm.GormEntity
-import org.grails.datastore.mapping.proxy.EntityProxy
 import org.grails.orm.hibernate.proxy.HibernateProxyHandler
 
 /**

diff --git a/...ommon/src/main/resources/META-INF/services/org.hibernate.search.bridge.spi.BridgeProvider b/...ommon/src/main/resources/META-INF/services/org.hibernate.search.bridge.spi.BridgeProvider
@@ -0,0 +1 @@
+uk.ac.ox.softeng.maurodatamapper.search.bridge.spi.OffsetDateTimeBridgeProvider
diff --git a/mdm-core/dependencies.gradle b/mdm-core/dependencies.gradle
@@ -3,6 +3,7 @@ dependencies {
     compile project(':mdm-common')
 
     compile group: 'org.apache.commons', name: 'commons-text', version: commonsTextVersion
+    compile group: 'org.apache.commons', name: 'commons-csv', version: commonsCsvVersion
     compile group: 'org.simplejavamail', name: 'simple-java-mail', version: javaMailVersion
     compile group: 'com.google.guava', name: 'guava', version: guavaVersion
     compile group: 'commons-beanutils', name: 'commons-beanutils', version: commonsBeanutilsVersion

diff --git a/mdm-core/grails-app/conf/db/migration/core/V2_11_0__allow_emails_to_not_have_a_provider.sql b/mdm-core/grails-app/conf/db/migration/core/V2_11_0__allow_emails_to_not_have_a_provider.sql
@@ -0,0 +1,5 @@
+ALTER TABLE core.email
+    ALTER COLUMN email_service_used DROP NOT NULL;
+
+ALTER TABLE core.email
+    ALTER COLUMN date_time_sent DROP NOT NULL;
diff --git a/mdm-core/grails-app/conf/plugin.yml b/mdm-core/grails-app/conf/plugin.yml
@@ -21,13 +21,16 @@ maurodatamapper:
         public: false
     bootstrap:
         authority: true
+    email:
+        from:
+            address: ''
 ---
 simplejavamail:
     smtp:
-        username: username@gmail.com
-        password: password
-        host: smtp.gmail.com
-        port: 587
+        username: ''
+        password: ''
+        host: ''
+        port: ''
     transportstrategy: SMTP_TLS
     javaxmail.debug: false
 ---
@@ -98,10 +101,18 @@ hibernate:
         batch_size: 30
     order_inserts: true
     order_updates: true
-
+grails:
+    plugins:
+        hibernatesearch:
+            rebuildIndexOnStart: true
 environments:
     development:
         grails:
             views:
                 markup:
-                    cacheTemplates: false
+                    cacheTemplates: false
+    production:
+        grails:
+            plugins:
+                hibernatesearch:
+                    rebuildIndexOnStart: false
diff --git a/mdm-core/grails-app/controllers/uk/ac/ox/softeng/maurodatamapper/core/UrlMappings.groovy b/mdm-core/grails-app/controllers/uk/ac/ox/softeng/maurodatamapper/core/UrlMappings.groovy
@@ -43,6 +43,7 @@ class UrlMappings {
                 '/emails'(resources: 'email', includes: INCLUDES_INDEX_ONLY)
 
                 '/properties'(resources: 'apiProperty', excludes: DEFAULT_EXCLUDES)
+                post '/properties/apply'(controller: 'apiProperty', action: 'apply')
 
                 group "/tree/$containerDomainType/$modelDomainType", {
                     get '/documentationSuperseded'(controller: 'treeItem', action: 'documentationSupersededModels') // New URL
@@ -247,6 +248,7 @@ class UrlMappings {
                     get '/'(controller: 'treeItem', action: 'index')
                     get "/${containerId}"(controller: 'treeItem', action: 'show')
                     get "/${catalogueItemDomainType}/$catalogueItemId"(controller: 'treeItem', action: 'show')
+                    get "/${catalogueItemDomainType}/$catalogueItemId/ancestors"(controller: 'treeItem', action: 'ancestors')
                     get "/search/$searchTerm"(controller: 'treeItem', action: 'search')
                 }
                 "/full/$modelDomainType/$modelId"(controller: 'treeItem', action: 'fullModelTree')

diff --git a/...-app/controllers/uk/ac/ox/softeng/maurodatamapper/core/admin/ApiPropertyController.groovy b/...-app/controllers/uk/ac/ox/softeng/maurodatamapper/core/admin/ApiPropertyController.groovy
@@ -17,18 +17,22 @@
  */
 package uk.ac.ox.softeng.maurodatamapper.core.admin
 
+import grails.gorm.transactions.Transactional
 import uk.ac.ox.softeng.maurodatamapper.api.exception.ApiInternalException
 import uk.ac.ox.softeng.maurodatamapper.core.controller.EditLoggingController
 
 import grails.web.servlet.mvc.GrailsParameterMap
 import groovy.util.logging.Slf4j
+import uk.ac.ox.softeng.maurodatamapper.security.User
 
 @Slf4j
 class ApiPropertyController extends EditLoggingController<ApiProperty> {
 
     ApiPropertyService apiPropertyService
 
-    static responseFormats = ['json', 'xml']
+    static responseFormats = ['json', 'xml', 'csv']
+
+    static includesExcludes = ["include": ["key", "value", "publiclyVisible", "category"]]
 
     ApiPropertyController() {
         super(ApiProperty)
@@ -43,6 +47,26 @@ class ApiPropertyController extends EditLoggingController<ApiProperty> {
         respond res, [model: [userSecurityPolicyManager: currentUserSecurityPolicyManager], view: 'index']
     }
 
+    /**
+     * Override so that we can specify includesExcludes when creating the resource
+     * @return
+     */
+    @Transactional
+    @Override
+    def save() {
+        if (handleReadOnly()) return
+
+        def instance = createResource(includesExcludes)
+
+        if (response.isCommitted()) return
+
+        if (!validateResource(instance, 'create')) return
+
+        saveResource instance
+
+        saveResponse instance
+    }
+
     @Override
     protected ApiProperty saveResource(ApiProperty resource) {
         ApiProperty apiProperty = super.saveResource(resource)
@@ -65,4 +89,53 @@ class ApiPropertyController extends EditLoggingController<ApiProperty> {
         currentUserSecurityPolicyManager.isApplicationAdministrator() ? apiPropertyService.list(params) : []
 
     }
+
+    /**
+     * Save a collection of ApiProperty resources and respond with the index listing
+     * @return
+     */
+    @Transactional
+    def apply() {
+        if (handleReadOnly()) return
+
+        Collection instances = createResources()
+
+        instances.each {instance ->
+            saveResource instance
+        }
+
+        // Respond with the index listing
+        index()
+    }
+
+    /**
+     * Create a collection of resources from the request body
+     * @return
+     */
+    protected Collection<ApiProperty> createResources() {
+
+        // First, bind what was exported to an ApiPropertyCollection (which has properties count and items)
+        // There isn't a way here to specify an includesExcludes list
+        ApiPropertyCollection apiPropertyCollection = new ApiPropertyCollection()
+        bindData apiPropertyCollection, getObjectToBind()
+
+        // Second, iterate the items we just created, and use each instance
+        // to create another cleaned instance. This time, we specify includesExcludes.
+        // At the same time, set the createdBy property of the cleaned instance.
+        Collection<ApiProperty> cleanedInstances = []
+        User creator = getCurrentUser()
+        apiPropertyCollection.items.each {instance ->
+            ApiProperty cleanedInstance = new ApiProperty()
+
+            // Copy the included properties to a cleaned instance
+            includesExcludes["include"].each {
+                cleanedInstance[it] = instance[it]
+            }
+
+            cleanedInstance.createdBy = creator.emailAddress
+            cleanedInstances.add(cleanedInstance)
+        }
+
+        cleanedInstances
+    }
 }