make local development easier with regards to google credential json

README.md

@@ -52,8 +52,8 @@ To run locally:
 1. Make sure you have the requirements installed from above. We recommend IntelliJ as an IDE.
 2. Clone the repo (if you see broken inputs build the project to get the generated sources)
 3. Run the commands in `scripts/postgres-init.sql` in your local postgres instance. You will need to be authenticated to access Vault.
-4. Run `scripts/write-config.sh`.  Be sure to follow instructions from output, especially setting the GOOGLE_APPLICATION_CREDENTIALS environment variable
-5. Run `./gradlew bootRun` to spin of the server.
+4. Run `scripts/write-config.sh`
+5. Run `./gradlew bootRun` to spin up the server.
 6. Navigate to [http://localhost:8080/#](http://localhost:8080/#)
 
 #### Local development with debugging

scripts/write-config.sh

@@ -179,10 +179,8 @@ function vaultgetdb {
     jq -r '.username' "${datafile}" > "${outputdir}/${fileprefix}-username.txt"
 }
 
+# grab tsps service account json from vault
 vaultget "secret/dsde/firecloud/${fcenv}/tsps/tsps-account.json" "${outputdir}/tsps-sa.json"
-echo "Run
-GOOGLE_APPLICATION_CREDENTIALS='${outputdir}/tsps-sa.json'
-to set the GOOGLE_APPLICATION_CREDENTIALS environment variable"
 
 # We made it to the end, so record the target and avoid redos
 echo "$target" > "${outputdir}/target.txt"

service/build.gradle

@@ -77,10 +77,15 @@ dependencies {
     testImplementation 'org.testcontainers:postgresql:1.17.3'
 
 }
-// set environment variable for google default credentials when running bootRun
+// workaround for local development
+// set GOOGLE_APPLICATION_CREDENTIALS if this file exists - should only exist when
+// write-config.sh is run.
+// GOOGLE_APPLICATION_CREDENTIALS is set for us when running in a deployed environment
 def googleCredentialsFile = "${rootDir}/config/tsps-sa.json"
 bootRun {
-    environment.put("GOOGLE_APPLICATION_CREDENTIALS", "${googleCredentialsFile}")
+    if(project.file(googleCredentialsFile).exists()) {
+        environment.put("GOOGLE_APPLICATION_CREDENTIALS", "${googleCredentialsFile}")
+    }
 }
 
 test {

service/src/main/java/bio/terra/pipelines/service/ImputationService.java

@@ -36,7 +36,7 @@ public List<ListAppResponse> queryForWorkspaceApps() {
       List<ListAppResponse> getAppsResponse =
           leonardoService.getApps(workspaceId, samService.getTspsServiceAccountToken(), false);
 
-      logger.debug(
+      logger.info(
           "GetAppsResponse for workspace id {}: {}",
           imputationConfiguration.workspaceId(),
           getAppsResponse);

service/src/main/resources/application.yml

@@ -12,13 +12,13 @@ env:
     exportEnabled: ${CLOUD_TRACE_ENABLED:false}
     samplingRate: ${SAMPLING_PROBABILITY:0}
   urls:
-    sam: ${SAM_ADDRESS:https://sam.dsde-dev.broadinstitute.org}
-    leonardo: ${LEONARDO_ADDRESS:https://leonardo.dsde-dev.broadinstitute.org}
+    sam: ${SAM_ADDRESS:https://sam.jsoto-fourth-try.bee.envs-terra.bio/}
+    leonardo: ${LEONARDO_ADDRESS:https://leonardo.jsoto-fourth-try.bee.envs-terra.bio/}
   imputation:
     # default workspace id is for this workspace in the dev environment
-    # https://bvdp-saturn-dev.appspot.com/#workspaces/tsps_dev_BP/Imputation_Control_Workspace_test
-    # should be updated when trying to run on a bee.
-    workspaceId: ${IMPUTATION_WORKSPACE_ID:a2e9cfbb-e4f0-4788-8aa1-de23533205fc}
+    # https://bvdp-saturn-dev.appspot.com/#workspaces/tsps_dev_BP/Imputation_Control_Workspace_test.
+    # this should be updated when trying to run on a bee.
+    workspaceId: ${IMPUTATION_WORKSPACE_ID:5046acb0-32a1-437d-9a18-fac6897c8f03}
 
 # Below here is non-deployment-specific