branch got out of sync with develop

more things

Author: snf2ye

.github/dependabot.yml

@@ -29,7 +29,7 @@ updates:
       - "dependency"
       - "gradle"
     commit-message:
-      prefix: "[DCJ-400-gradle]"
+      prefix: "[DT-400-gradle]"
     ignore:
       # Google API dependencies use a version format that Dependabot wrongly interprets as semver.
       - dependency-name: "com.google.apis:*"

README.md

@@ -29,13 +29,13 @@ See [started guide](docs/jade-getting-started.md) for information on running con
 ### Run TDR locally
 
 To run TDR locally:
-`./scripts/run local`
+`./scripts/run start_local`
 
 To run TDR in docker:
-`./scripts/run docker`
+`./scripts/run start_docker`
 
 To run TDR locally and wait for debugger to attach on port 5005:
-`./scripts/run local --debug-jvm`
+`./scripts/run start_local --debug-jvm`
 
 To have the code hot reload, enable automatic builds in intellij, go to:
 `Preferences -> Build, Execution, Deployment -> Compiler`

scripts/compose.yaml

@@ -25,7 +25,6 @@ services:
     volumes:
       - /tmp/jade-dev-account.pem:/tmp/jade-dev-account.pem
       - /tmp/jade-dev-account.json:/tmp/jade-dev-account.json
-      - /tmp/buffer-client-sa-account.json:/tmp/buffer-client-sa-account.json
 
   database:
     image: postgres:14

scripts/render-configs.sh

@@ -112,15 +112,9 @@ GOOGLE_SA_CERT=/tmp/jade-dev-account.pem
 # By default, RBS will use the tools project. GCP projects will automatically be deleted after 1 day.
 # Other option: dev - this will allow for projects to persist for longer than 1 day
 if [[ "${RBS_ENV}" == "tools" ]]; then
-    BUFFER_CLIENT_SERVICE_ACCOUNT_VAULT_PATH=secret/dsde/terra/kernel/integration/tools/buffer/client-sa
-    BUFFER_CLIENT_SERVICE_ACCOUNT_GSM_PROJECT=broad-dsde-qa
-    BUFFER_CLIENT_GSM_SECRET=buffer-client-sa-b64-integration
     RBS_POOLID=datarepo_v1
     RBS_INSTANCEURL=https://buffer.tools.integ.envs.broadinstitute.org
 elif [[ "${RBS_ENV}" == "dev" ]]; then
-    BUFFER_CLIENT_SERVICE_ACCOUNT_VAULT_PATH=secret/dsde/terra/kernel/dev/dev/buffer/client-sa
-    BUFFER_CLIENT_SERVICE_ACCOUNT_GSM_PROJECT=broad-jade-dev
-    BUFFER_CLIENT_GSM_SECRET=buffer-client-sa-b64
     RBS_POOLID=datarepo_v3
     RBS_INSTANCEURL=https://buffer.dsde-dev.broadinstitute.org
 else
@@ -131,16 +125,6 @@ fi
 echo $RBS_POOLID > "/tmp/rbs-pool-id.txt"
 echo $RBS_INSTANCEURL > "/tmp/rbs-instance-url.txt"
 
-RBS_CLIENTCREDENTIALFILEPATH=/tmp/buffer-client-sa-account.json
-
-if $USE_VAULT; then
-  vault read -field=key "$BUFFER_CLIENT_SERVICE_ACCOUNT_VAULT_PATH" \
-    | base64 -d > "$RBS_CLIENTCREDENTIALFILEPATH"
-else
-  gcloud secrets versions access latest --project $BUFFER_CLIENT_SERVICE_ACCOUNT_GSM_PROJECT --secret $BUFFER_CLIENT_GSM_SECRET \
-    | jq -r '.key' | base64 -d > "$RBS_CLIENTCREDENTIALFILEPATH"
-fi
-
 
 VARIABLE_NAMES=(AZURE_SYNAPSE_WORKSPACENAME AZURE_CREDENTIALS_HOMETENANTID AZURE_CREDENTIALS_APPLICATIONID AZURE_CREDENTIALS_SECRET AZURE_SYNAPSE_SQLADMINUSER AZURE_SYNAPSE_SQLADMINPASSWORD AZURE_SYNAPSE_ENCRYPTIONKEY GOOGLE_APPLICATION_CREDENTIALS GOOGLE_SA_CERT RBS_POOLID RBS_INSTANCEURL)
 

src/main/java/bio/terra/app/configuration/WebConfig.java

@@ -36,6 +36,6 @@ public void configurePathMatch(PathMatchConfigurer configurer) {
   public void addResourceHandlers(ResourceHandlerRegistry registry) {
     registry
         .addResourceHandler("/webjars/swagger-ui-dist/**")
-        .addResourceLocations("classpath:/META-INF/resources/webjars/swagger-ui-dist/4.3.0/");
+        .addResourceLocations("classpath:/META-INF/resources/webjars/swagger-ui-dist/5.18.2/");
   }
 }

src/main/java/bio/terra/common/PdaoLoadStatistics.java

@@ -1,5 +1,6 @@
 package bio.terra.common;
 
+import com.fasterxml.jackson.annotation.JsonProperty;
 import com.google.cloud.bigquery.JobStatistics;
 import java.time.Instant;
 
@@ -9,7 +10,11 @@ public class PdaoLoadStatistics {
   private final Instant startTime;
   private final Instant endTime;
 
-  public PdaoLoadStatistics(long badRecords, long rowCount, Instant startTime, Instant endTime) {
+  public PdaoLoadStatistics(
+      @JsonProperty("badRecords") long badRecords,
+      @JsonProperty("rowCount") long rowCount,
+      @JsonProperty("startTime") Instant startTime,
+      @JsonProperty("endTime") Instant endTime) {
     this.badRecords = badRecords;
     this.rowCount = rowCount;
     this.startTime = startTime;