Merge pull request #475 from overture-stack/rc/2.1.0

Release Candidate 2.1.0

Author: rtisma

Jenkinsfile

@@ -96,5 +96,46 @@ spec:
                 }
             }
         }
+
+        stage('Deploy to Overture QA') {
+            when {
+                  branch "develop"
+            }
+            steps {
+                container('helm') {
+                    withCredentials([file(credentialsId:'4ed1e45c-b552-466b-8f86-729402993e3b', variable: 'KUBECONFIG')]) {
+                        sh 'env'
+                        sh 'helm init --client-only'
+                        sh "helm ls --kubeconfig $KUBECONFIG"
+                        sh "helm repo add overture https://overture-stack.github.io/charts-server/"
+                        sh """
+                            helm upgrade --kubeconfig $KUBECONFIG --install --namespace=overture-qa song-overture-qa \\
+                            overture/song --reuse-values --set-string image.tag=${commit}
+                           """
+                    }
+                }
+            }
+        }
+
+        stage('Deploy to Overture Staging') {
+            when {
+                  branch "master"
+            }
+            steps {
+                container('helm') {
+                    withCredentials([file(credentialsId:'4ed1e45c-b552-466b-8f86-729402993e3b', variable: 'KUBECONFIG')]) {
+                        sh 'env'
+                        sh 'helm init --client-only'
+                        sh "helm ls --kubeconfig $KUBECONFIG"
+                        sh "helm repo add overture https://overture-stack.github.io/charts-server/"
+                        sh """
+                            helm upgrade --kubeconfig $KUBECONFIG --install --namespace=overture-staging song-overture-staging \\
+                            overture/song --reuse-values --set-string image.tag=${version}
+                           """
+                    }
+                }
+            }
+        }
+
     }
-}
+}

Makefile

@@ -15,3 +15,28 @@ login-psql:
 
 format:
 	@mvn fmt:format
+
+build-server:
+	@mvn package -DskipTests -pl song-server -am 
+
+build-core:
+	@mvn package -DskipTests -pl song-core -am 
+	
+build-client:
+	@mvn package -DskipTests -pl song-client -am 
+
+analyze:
+	@mvn dependency:analyze-report
+
+package-client:
+	@mvn package -pl song-client -am 
+
+package-server:
+	@mvn package -pl song-server -am 
+
+
+build-sdk:
+	@mvn package -DskipTests -pl song-java-sdk -am 
+
+clean:
+	@mvn clean

README.md

@@ -1,5 +1,6 @@
 <h1 align="center">Song</h1>
 
+
 <p align="center">Quickly and reliably track genome metadata scattered across multiple Cloud storage systems.</p>
 
 

dev/example/exampleVariantCall.json

@@ -1,7 +1,10 @@
 {
   "study" : "test",
   "analysisId": "TESTANALYSIS",
-  "analysisTypeId" : "variantCall:1",
+  "analysisType" : {
+    "name" : "variantCall",
+    "version" : 1
+  },
   "experiment": {
     "variantCallingTool": "silver bullet",
     "matchedNormalSampleSubmitterId": "sample x24-11a",

docker-compose.yml

@@ -66,12 +66,9 @@ services:
       AUTH_SERVER_URL: http://localhost:8084/check_token/
       AUTH_SERVER_CLIENTID: 3kJhz9pNtC0pFHAxr2SPkUkGjXrkWWqGcnPC0vBP
       AUTH_SERVER_CLIENTSECRET: v9mjRtuEVwpt7cgqnsq6mxtCa5FbUOpKLGh7WX8a1dWbBKfrM3iV3VYMtE60jr3W7GLWtNeYIaJ8EUxPkaInclWVXf64qKdR3IKwyfpDU7JhvWEwIYQYdwV1YAUZjB2e
-      AUTH_SERVER_SCOPE_STUDY_PREFIX: song
-      AUTH_SERVER_SCOPE_STUDY_FIRSTDELIMITER: "."
-      AUTH_SERVER_SCOPE_STUDY_SECONDDELIMITER: "."
-      AUTH_SERVER_SCOPE_STUDY_SUFFIX: WRITE
-      AUTH_SERVER_SCOPE_SYSTEM_PREFIX: song
-      AUTH_SERVER_SCOPE_SYSTEM_SUFFIX: WRITE
+      AUTH_SERVER_SCOPE_STUDY_PREFIX: song.
+      AUTH_SERVER_SCOPE_STUDY_SUFFIX: .WRITE
+      AUTH_SERVER_SCOPE_SYSTEM: song.WRITE
       SCORE_URL: http://localhost:8087
       SCORE_ACCESSTOKEN: ad83ebde-a55c-11e7-abc4-cec278b6b50a
       MANAGEMENT_SERVER_PORT: 8081