Merge pull request #22 from EBISPOT/develop

Released 0.0.8

Author: ala-ebi

.gitlab-ci.yml

@@ -56,7 +56,7 @@ deploy-ingest-sandbox:
   - echo "Deploy to sandbox server"
   - mkdir -p /root/.kube
   - echo ${SANBOX_KUBECONF} | base64 -d > /root/.kube/config
-  - helm init
+  - helm init --stable-repo-url https://charts.helm.sh/stable
   - helm delete --purge gwas-ingest-service || true
   - helm install --name gwas-ingest-service --set k8Namespace=gwas,image.repository=$INGEST_REGISTRY_IMAGE,image.tag=$CI_COMMIT_SHA,image.env.secretsName=sandbox-secrets,image.env.secretsKey=db-backend ./k8chart/ --wait
   environment:
@@ -71,7 +71,7 @@ deploy-fallback:
   - echo "Deploy to Production fallback server"
   - mkdir -p /root/.kube
   - echo ${PFALLBACK_KUBECONFIG} | base64 -d > /root/.kube/config
-  - helm init
+  - helm init --stable-repo-url https://charts.helm.sh/stable
   - helm delete --purge gwas-ingest-service || true
   - helm install --name gwas-ingest-service --set k8Namespace=gwas,image.env.envName=prod,image.repository=$INGEST_REGISTRY_IMAGE,image.tag=$CI_COMMIT_SHA,image.env.dbUser=gwasdepo,image.env.secretsName=prod-secrets,image.env.secretsKey=db-backend ./k8chart/ --wait
   environment:
@@ -86,7 +86,7 @@ deploy-live:
   - echo "Deploy to Production server"
   - mkdir -p /root/.kube
   - echo ${PLIVE_KUBECONFIG} | base64 -d > /root/.kube/config
-  - helm init
+  - helm init --stable-repo-url https://charts.helm.sh/stable
   - helm delete --purge gwas-ingest-service || true
   - helm install --name gwas-ingest-service --set k8Namespace=gwas,image.env.envName=prod,image.repository=$INGEST_REGISTRY_IMAGE,image.tag=$CI_COMMIT_SHA,image.env.dbUser=gwasdepo,image.env.secretsName=prod-secrets,image.env.secretsKey=db-backend ./k8chart/ --wait
   environment:

.travis.yml

@@ -0,0 +1,15 @@
+language: java
+sudo: false
+jdk:
+- openjdk8
+
+env:
+  global:
+  - JAVA_OPTS="-XX:+TieredCompilation -XX:TieredStopAtLevel=1 -Xmn48M -Xmx512M"
+addons:
+  sonarcloud:
+    organization: "gwas-ebi"
+    #token:
+      #secure: "LBTAViqGyi7anEYYLzuTyTF1L3Xnq7prupvyzW2mIUWJY6uh9Y3s0TItA+8CSUcbeCUf6MGrj8ydNi4PRLr/DpOCTIrt4FMs5mljaBE4BDfJMgts/hSzLSwSLOa2gKdOJg64ZNpeW+am/hH5/Wbuje6cegeNoNq1yRH4SMBLhnu3/JdmzDLc3pLNuhvNjy6/qX2YPyHLoJ9FE0SfkbULsbzHy7+EDLcxPUVby7aemOD0KUYDxw7Ee4jc5mH9HDrm9sqTFHw+4TWNMA5gsZX4NB3keSElMg9giwVTQT3zLG2sFNbhmhoD2rxs7JxTE+yVeg7ahLSW23LP7mkg4jdc4gR4h1VxB6wwxHIsx+1QZP8MSBOcwYPzLQIp3VyGK37sCVDJHGrpQXZG9SHWZfedmqo6EjabZK8lFCGG8fOTIj5A5FiltfaaHvEfgwbMki12zTm8GftodPJNUT336FNvTHOUlG/RNP3exArWpLXXZXw1gynn57tEVdd5qxdxxpc+QztJiKn2dByWehg5NYh7KwkGcQiNAerYYzMDpIjaVKO1hHeCSouuYFXxp++gBPW0z68Eojp7bVORA/I82nZdY6lkEnFFryHo3RTgU8q6ggDI233r10R/Unsl4bySisQ6z1McPZERQMIton1XMqbAkh3Eb337L+GEGzRSlLehNGM="
+script:
+- mvn clean verify sonar:sonar -Dspring.profiles.active=test -Dmaven.test.failure.ignore=true -Dmaven.test.error.ignore=true -Dsonar.login=0566d66d0cfe16cd2cb8ba02db7fcd0b6d1e7ee6

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>uk.ac.ebi.spot.gwasdepo</groupId>
     <artifactId>gwasdepo-ingest-service</artifactId>
-    <version>0.0.7</version>
+    <version>0.0.8</version>
     <packaging>jar</packaging>
 
     <name>GWAS Deposition App Ingest Service</name>
@@ -20,6 +20,7 @@
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <start-class>uk.ac.ebi.spot.gwas.deposition.ingest.Application</start-class>
+        <sonar.organization>gwas-ebi</sonar.organization>
     </properties>
 
     <scm>
@@ -59,14 +60,50 @@
                 <groupId>org.springframework.boot</groupId>
                 <artifactId>spring-boot-maven-plugin</artifactId>
             </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+            </plugin>
+
+            <plugin>
+                <groupId>org.jacoco</groupId>
+                <artifactId>jacoco-maven-plugin</artifactId>
+                <version>0.7.7.201606060606</version>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>prepare-agent</goal>
+                        </goals>
+                    </execution>
+                    <execution>
+                        <id>report</id>
+                        <goals>
+                            <goal>report</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+
+
         </plugins>
+
+        <pluginManagement>
+            <plugins>
+                <plugin>
+                    <groupId>org.sonarsource.scanner.maven</groupId>
+                    <artifactId>sonar-maven-plugin</artifactId>
+                    <version>3.4.0.905</version>
+                </plugin>
+            </plugins>
+        </pluginManagement>
     </build>
 
     <dependencies>
         <dependency>
             <groupId>uk.ac.ebi.spot.gwasdepo</groupId>
             <artifactId>gwasdepo-commons</artifactId>
-            <version>1.0.13</version>
+            <version>1.0.15</version>
         </dependency>
 
         <dependency>

src/main/java/uk/ac/ebi/spot/gwas/deposition/ingest/rest/dto/StudyDtoAssembler.java

@@ -34,7 +34,8 @@ public static StudyDto assemble(Study study) {
                 study.getCohortId(),
                 null,
                 null,
-                null);
+                null,
+                study.isAgreedToCc0());
     }
 
     public static StudyDto assemble(Study study, List<AssociationDto> associationDtos,
@@ -62,7 +63,8 @@ public static StudyDto assemble(Study study, List<AssociationDto> associationDto
                 study.getCohortId(),
                 associationDtos,
                 sampleDtos,
-                noteDtos);
+                noteDtos,
+                study.isAgreedToCc0());
     }
 
     public static Study disassemble(StudyDto studyDto) {

src/main/java/uk/ac/ebi/spot/gwas/deposition/ingest/service/impl/SubmissionAssemblyServiceImpl.java

@@ -173,6 +173,7 @@ public SubmissionDto assemble(Submission submission) {
                         submission.getAssociations().size(),
                         submission.getSamples().size(),
                         submission.getNotes().size()),
-                ProvenanceDtoAssembler.assemble(submission.getCreated(), userOpt.get()));
+                ProvenanceDtoAssembler.assemble(submission.getCreated(), userOpt.get()),
+                submission.isAgreedToCc0());
     }
 }

src/main/java/uk/ac/ebi/spot/gwas/deposition/ingest/service/impl/SubmissionAssemblyServiceImplV2.java

@@ -100,7 +100,8 @@ public SubmissionDto assemble(Submission submission) {
                         submission.getAssociations().size(),
                         submission.getSamples().size(),
                         submission.getNotes().size()),
-                ProvenanceDtoAssembler.assemble(submission.getCreated(), userOpt.get()));
+                ProvenanceDtoAssembler.assemble(submission.getCreated(), userOpt.get()),
+                submission.isAgreedToCc0());
     }
 
     @Override

src/test/java/uk/ac/ebi/spot/gwas/deposition/ingest/rest/SubmissionsControllerTest.java

@@ -271,7 +271,8 @@ public void shouldUpdateSubmissionStatus() throws Exception {
                 actual.getNotes(),
                 actual.getDateSubmitted(),
                 actual.getMetadata(),
-                actual.getCreated());
+                actual.getCreated(),
+                actual.isAgreedToCc0());
 
         response = mockMvc.perform(put(endpoint)
                 .contentType(MediaType.APPLICATION_JSON).content(mapper.writeValueAsString(updated)))