Merge pull request #8 from apriltuesday/EVA-3491

EVA-3491: Add schema for submission tables

.github/workflows/run-tests.yml

@@ -1,8 +1,8 @@
 name: Run tests
 
 on:
-  push:
-    branches: [ master ]
+  pull_request:
+    branches: [ main ]
 
 jobs:
   build:

.gitlab-ci.yml

@@ -0,0 +1,126 @@
+stages:
+  - test
+  - package
+  - deploy
+
+variables:
+  WS_ARTIFACT_PATH: target/eva-submission-ws-$ENVIRONMENT_NAME.war
+  MAVEN_SETTINGS: maven-settings.xml
+  URL_MAVEN_SETTINGS: https://api.github.com/repos/EBIvariation/configuration/contents/eva-maven-settings.xml
+  MEDIA_TYPE: application/vnd.github.raw
+
+test:
+  stage: test
+  image: maven:3.6.1-jdk-8-alpine
+  script:
+    - mvn test
+  environment:
+    name: test-env
+  only:
+      - master
+      - tags
+
+# Not executed, parent job definition for package
+.package:
+  stage: package
+  image: maven:3.6.1-jdk-8-alpine
+  environment:
+    name: $ENVIRONMENT_NAME
+  before_script:
+    - DATETIME=$(date +%Y-%m-%dT%H-%M-%S)
+    - apk add --update curl
+    - curl -u $GITHUB_USER:$GITHUB_TOKEN -H "Accept:$MEDIA_TYPE" $URL_MAVEN_SETTINGS > $MAVEN_SETTINGS
+  script:
+    - mvn package --settings $MAVEN_SETTINGS -P $MAVEN_PROFILE -DskipTests
+    - cp target/eva-submission-ws*.war.original $WS_ARTIFACT_PATH
+  after_script:
+    - rm $MAVEN_SETTINGS
+  artifacts:
+    paths:
+      - $WS_ARTIFACT_PATH
+
+package-internal:
+  extends: .package
+  variables:
+    ENVIRONMENT_NAME: internal
+    MAVEN_PROFILE: internal
+  only:
+    - master
+
+package-development:
+  extends: .package
+  variables:
+    ENVIRONMENT_NAME: development
+    MAVEN_PROFILE: development
+  only:
+    - master
+
+package-production:
+  extends: .package
+  variables:
+    ENVIRONMENT_NAME: production
+    # Use production_processing to use production rather than public database
+    MAVEN_PROFILE: production_processing
+  only:
+    - tags
+
+# Not executed, parent job definition for deployments
+.deploy-tomcat:
+  stage: deploy
+  image: alpine:3.9.5
+  environment:
+    name: $ENVIRONMENT_NAME
+  script:
+    - DATETIME=$(date +%Y-%m-%dT%H-%M-%S)
+    - apk add --update curl
+    - curl -u $TOMCAT_USER:$TOMCAT_PASSWORD -T "$WS_ARTIFACT_PATH" "http://$TOMCAT_HOST/manager/text/deploy?update=true&path=/eva/webservices/submission-ws&version=$DATETIME" | grep "OK - Deployed application"
+
+deploy-tomcat-internal:
+  extends: .deploy-tomcat
+  variables:
+    ENVIRONMENT_NAME: internal
+    TOMCAT_USER: $TOMCAT_INTERNAL_USER
+    TOMCAT_PASSWORD: $TOMCAT_INTERNAL_PASSWORD
+    TOMCAT_HOST: $TOMCAT_INTERNAL_HOST
+  dependencies:
+    - package-internal
+  only:
+    - master
+
+deploy-tomcat-development:
+  extends: .deploy-tomcat
+  variables:
+    ENVIRONMENT_NAME: development
+    TOMCAT_USER: $TOMCAT_DEVELOPMENT_USER
+    TOMCAT_PASSWORD: $TOMCAT_DEVELOPMENT_PASSWORD
+    TOMCAT_HOST: $TOMCAT_DEVELOPMENT_HOST
+  dependencies:
+    - package-development
+  only:
+    - master
+
+deploy-tomcat-production:
+  extends: .deploy-tomcat
+  when: manual
+  variables:
+    ENVIRONMENT_NAME: production
+    TOMCAT_USER: $TOMCAT_PRODUCTION_USER
+    TOMCAT_PASSWORD: $TOMCAT_PRODUCTION_PASSWORD
+    TOMCAT_HOST: $TOMCAT_PRODUCTION_HOST
+  dependencies:
+    - package-production
+  only:
+    - tags
+
+deploy-tomcat-production-fallback:
+  extends: .deploy-tomcat
+  when: manual
+  variables:
+    ENVIRONMENT_NAME: production
+    TOMCAT_USER: $TOMCAT_PRODUCTION_FALLBACK_USER
+    TOMCAT_PASSWORD: $TOMCAT_PRODUCTION_FALLBACK_PASSWORD
+    TOMCAT_HOST: $TOMCAT_PRODUCTION_FALLBACK_HOST
+  dependencies:
+    - package-production
+  only:
+    - tags

src/main/java/uk/ac/ebi/eva/submission/model/Submission.java

@@ -12,7 +12,7 @@
 import java.util.Objects;
 
 @Entity
-@Table(name = "submission")
+@Table(schema = "eva_submissions", name = "submission")
 public class Submission {
 
     public Submission() {

src/main/java/uk/ac/ebi/eva/submission/model/SubmissionAccount.java

@@ -12,8 +12,10 @@
 import java.util.List;
 
 @Entity
-@Table(name = "submission_account", uniqueConstraints = {@UniqueConstraint(columnNames = {"user_id", "login_type"})})
+@Table(schema = "eva_submissions", name = "submission_account", uniqueConstraints = {@UniqueConstraint(columnNames =
+        {"user_id", "login_type"})})
 public class SubmissionAccount {
+
     @Id
     private String id;
 

src/main/java/uk/ac/ebi/eva/submission/model/SubmissionDetails.java

@@ -8,8 +8,9 @@
 import javax.persistence.Table;
 
 @Entity
-@Table(name = "submission_details")
+@Table(schema = "eva_submissions", name = "submission_details")
 public class SubmissionDetails {
+
     @Id
     @Column(name = "submission_id")
     private String submissionId;
@@ -28,7 +29,7 @@ public SubmissionDetails() {
 
     }
 
-    public SubmissionDetails(Submission submission){
+    public SubmissionDetails(Submission submission) {
         this.submission = submission;
     }
 

src/main/resources/application.properties

@@ -3,6 +3,7 @@ spring.datasource.url=|eva.evapro.jdbc.url|
 spring.datasource.username=|eva.evapro.user|
 spring.datasource.password=|eva.evapro.password|
 spring.jpa.hibernate.ddl-auto=update
+spring.jpa.properties.hibernate.default_schema=eva_submissions
 spring.jmx.default-domain=eva.ebi.ac.uk.submission-ws.|timestamp|
 
 globus.clientId=|globus.client-id|

src/test/java/uk/ac/ebi/eva/submission/integration/SubmissionWSIntegrationTest.java

@@ -69,7 +69,8 @@ public class SubmissionWSIntegrationTest {
     private GlobusDirectoryProvisioner globusDirectoryProvisioner;
 
     @Container
-    static PostgreSQLContainer<?> postgreSQLContainer = new PostgreSQLContainer<>("postgres:9.6");
+    static PostgreSQLContainer<?> postgreSQLContainer = new PostgreSQLContainer<>("postgres:9.6")
+            .withInitScript("init.sql");
 
     @DynamicPropertySource
     static void dataSourceProperties(DynamicPropertyRegistry registry) {

src/test/resources/application.properties

@@ -1,3 +1,5 @@
+spring.jpa.properties.hibernate.default_schema=eva_submissions
+
 globus.clientId=
 globus.clientSecret=
 globus.refreshToken=

src/test/resources/init.sql

@@ -0,0 +1 @@
+CREATE SCHEMA IF NOT EXISTS eva_submissions;