From f1f6bef0eeb8524107c09953345c8c437591b116 Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Thu, 20 Jul 2023 10:50:28 -0400
Subject: [PATCH 01/83] include sonar in Java CI

---
 .github/workflows/java-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/java-ci.yml b/.github/workflows/java-ci.yml
index 96b9df3fab..218296b127 100644
--- a/.github/workflows/java-ci.yml
+++ b/.github/workflows/java-ci.yml
@@ -50,10 +50,10 @@ jobs:
           distribution: 'adopt'
       - name: Validate Gradle wrapper
         uses: gradle/wrapper-validation-action@e6e38bacfdf1a337459f332974bb2327a31aaf4b
-      - name: Build with Gradle
+      - name: Build and SonarQube scan with Gradle
         uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
         with:
-          arguments: build --info # if you need to see test failure full stacktraces, change this to `build --info`
+          arguments: build sonar --info # if you need to see test failure full stacktraces, change this to `build --info`
 
   # Need to uncomment these in follow up PR, The new Trivy and Tag workflows need to exist on the development branch
   # before the following steps will work

From ea4937662e55177fd0e6fb5a79e93d691cf26e9b Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Thu, 20 Jul 2023 11:06:11 -0400
Subject: [PATCH 02/83] sonar in Java CI

---
 .github/workflows/java-ci.yml | 3 +++
 api-admin/build.gradle        | 2 +-
 api-participant/build.gradle  | 2 +-
 buildSrc/build.gradle         | 2 +-
 4 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/java-ci.yml b/.github/workflows/java-ci.yml
index 218296b127..b16bbc0459 100644
--- a/.github/workflows/java-ci.yml
+++ b/.github/workflows/java-ci.yml
@@ -54,6 +54,9 @@ jobs:
         uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
         with:
           arguments: build sonar --info # if you need to see test failure full stacktraces, change this to `build --info`
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
   # Need to uncomment these in follow up PR, The new Trivy and Tag workflows need to exist on the development branch
   # before the following steps will work
diff --git a/api-admin/build.gradle b/api-admin/build.gradle
index 603a871ace..287727da55 100644
--- a/api-admin/build.gradle
+++ b/api-admin/build.gradle
@@ -66,7 +66,7 @@ test {
     useJUnitPlatform ()
 }
 
-sonarqube {
+sonar {
     properties {
         property 'sonar.projectName', 'terra-java-project-template'
         property 'sonar.projectKey', 'terra-java-project-template'
diff --git a/api-participant/build.gradle b/api-participant/build.gradle
index ea56e710c3..ac447b0f31 100644
--- a/api-participant/build.gradle
+++ b/api-participant/build.gradle
@@ -62,7 +62,7 @@ test {
     useJUnitPlatform ()
 }
 
-sonarqube {
+sonar {
     properties {
         property 'sonar.projectName', 'terra-java-project-template'
         property 'sonar.projectKey', 'terra-java-project-template'
diff --git a/buildSrc/build.gradle b/buildSrc/build.gradle
index 4fdbf72dd8..3f872a3763 100644
--- a/buildSrc/build.gradle
+++ b/buildSrc/build.gradle
@@ -18,7 +18,7 @@ dependencies {
     implementation 'com.github.spotbugs.snom:spotbugs-gradle-plugin:5.0.12'
     implementation 'io.spring.dependency-management:io.spring.dependency-management.gradle.plugin:1.0.15.RELEASE'
     implementation 'org.hidetake.swagger.generator:org.hidetake.swagger.generator.gradle.plugin:2.19.2'
-    implementation 'org.sonarqube:org.sonarqube.gradle.plugin:3.4.0.2513'
+    implementation 'org.sonarqube:org.sonarqube.gradle.plugin:4.2.1.3168'
     implementation 'org.springframework.boot:spring-boot-gradle-plugin:2.7.10'
     implementation 'bio.terra:terra-test-runner:0.1.5-SNAPSHOT'
     // This is required due to a dependency conflict between jib and srcclr. Removing it will cause jib to fail.

From d0fbe58b118d0e58de3fb64af742bda0130d63e3 Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 13:43:51 -0400
Subject: [PATCH 03/83] separate project sonar scans

---
 .github/workflows/java-ci.yml     |  2 +-
 .github/workflows/sonar.yaml      | 53 +++++++++++++++++++++++++------
 README.md                         | 29 ++++++++++++-----
 api-admin/build.gradle            |  5 +--
 api-participant/build.gradle      |  5 +--
 populate/build.gradle             | 10 ++++++
 sonar-project.properties          |  8 -----
 ui-admin/sonar-project.properties |  6 ++++
 8 files changed, 87 insertions(+), 31 deletions(-)
 delete mode 100644 sonar-project.properties
 create mode 100644 ui-admin/sonar-project.properties

diff --git a/.github/workflows/java-ci.yml b/.github/workflows/java-ci.yml
index b16bbc0459..ed790610ed 100644
--- a/.github/workflows/java-ci.yml
+++ b/.github/workflows/java-ci.yml
@@ -53,7 +53,7 @@ jobs:
       - name: Build and SonarQube scan with Gradle
         uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
         with:
-          arguments: build sonar --info # if you need to see test failure full stacktraces, change this to `build --info`
+          arguments: build --info # if you need to see test failure full stacktraces, change this to `build --info`
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 09974b0c5e..e5a1031ca7 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -2,23 +2,56 @@ name: Sonar
 on: workflow_dispatch
 
 jobs:
-  sonar:
+  # sonar:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v3
+
+  #     - name: Set up JDK
+  #       uses: actions/setup-java@v3
+  #       with:
+  #         java-version: '17'
+  #         distribution: 'temurin'
+  #         cache: 'gradle'
+
+  #     - name: SonarCloud Scan (Typescript only)
+  #       uses: SonarSource/sonarcloud-github-action@master
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+
+
+  #     - name: SonarCloud Scan (Java only)
+  #       run: ./gradlew --build-cache compileJava sonar
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+
+  sonar-api-admin:
+    name: SonarCloud api-admin
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-
-      - name: Set up JDK
-        uses: actions/setup-java@v3
         with:
-          java-version: '17'
-          distribution: 'temurin'
-          cache: 'gradle'
+          fetch-depth: 0
+      - name: Scan api-admin via gradle
+        run: ./gradlew --build-cache :api-admin:compileJava :api-admin:sonar
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
-      - name: Build all projects without running tests
-        run: ./gradlew --build-cache compileJava
 
-      - name: SonarCloud Scan
+  sonar-ui-admin:
+    name: SonarCloud ui-admin
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Scan ui-admin via sonarcloud-github-action
         uses: SonarSource/sonarcloud-github-action@master
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        with:
+          projectBaseDir: ui-admin/
diff --git a/README.md b/README.md
index 1fe3ddb85d..ad0aa66f0a 100644
--- a/README.md
+++ b/README.md
@@ -29,7 +29,7 @@ DTOs, and populate services.  the PopulateCliApp can be used to populate specifi
    In development, it serves at localhost:8081.  Lives in `api-participant` directory
 ##### Study Manager UI
    Participant UI is a create-react-app SPA.  Lives in `ui-participant` directory.  Serves on localhost:3001 in development
-   
+
 
 
 ## Local development
@@ -47,7 +47,7 @@ run `./local-dev/run_postgres.sh start`
 This will start a postgres container with a schema and user configured
 
 #### IDE Setup
-Open the root folder in IntelliJ.  
+Open the root folder in IntelliJ.
 
 * **server:**
 
@@ -76,15 +76,15 @@ Open the root folder in IntelliJ.
         * set environment variable: `B2C_POLICY_NAME=B2C_1A_ddp_participant_signup_signin_dev`
         * set environment variable: `B2C_CHANGE_PASSWORD_POLICY_NAME=B2C_1A_ddp_participant_change_password_dev`
         * disable launch optimization
-        
-         
+
+
 ### Running the application
 #### Admin tool (study manager, population)
 * API (api-admin module)
 In intelliJ, you can either run ApiAdminApp (from the api-admin module) directly, or execute the "bootRun" gradle task.
 In basic development mode, this will only serve the API, not the frontend assets.
 
-To make the application useful, you will want to populate some users and studies.  After the admin API is running, 
+To make the application useful, you will want to populate some users and studies.  After the admin API is running,
 from the root project directory, run
 ```
 ./scripts/populate_portal.sh ourhealth
@@ -98,7 +98,7 @@ From the command line:
   REACT_APP_B2C_TENANT_NAME=ddpdevb2c REACT_APP_B2C_CLIENT_ID=$(vault read -field value secret/dsp/ddp/b2c/dev/application_id) npm -w ui-admin start
   ```
 (note that you can just run `npm -w ui-admin start` if you don't need to test B2C login functionality)
-Then go to `localhost:3000` 
+Then go to `localhost:3000`
 
 ##### Participant API (api-participant module)
 In intelliJ, you can either run ApiParticipantApp (from the api-participant module) directly, or execute the "bootRun" gradle task.
@@ -118,9 +118,9 @@ Then go to `sandbox.ourhealth.localhost:3001`
 (Notice how you need the environment name and portal name as subdomains)
 
 
-### Feature Development 
+### Feature Development
 
-#### Adding a new model 
+#### Adding a new model
 1. Create the schema, models, and services
    1. Create your POJO model in `core/src/main/java/bio/terra/pearl/core/model`, you will almost certainly want to extend
    `BaseEntity`
@@ -150,3 +150,16 @@ Then go to `sandbox.ourhealth.localhost:3001`
 #### Adding environment variables
   Helm charts:
   https://github.com/broadinstitute/terra-helmfile/tree/master/values/app/d2p/live
+
+
+### SonarCloud code scanning
+
+Because juniper contains TypeScript projects and Java projects, the scans are run independently
+in each project
+
+Typescript UI subprojects (ui-admin, ui-core, and ui-participant) are scanned using the
+SonarCloud GitHub Action. Analysis (SonarCloud
+runs the scan on its own and comments back results to PRs).
+
+Java subprojects (core, client, api-admin, api-participant) are scanned using gradle with the
+sonarqube plugin.
\ No newline at end of file
diff --git a/api-admin/build.gradle b/api-admin/build.gradle
index 287727da55..529b310da6 100644
--- a/api-admin/build.gradle
+++ b/api-admin/build.gradle
@@ -68,8 +68,9 @@ test {
 
 sonar {
     properties {
-        property 'sonar.projectName', 'terra-java-project-template'
-        property 'sonar.projectKey', 'terra-java-project-template'
+        property 'sonar.projectName', 'juniper-api-admin'
+        property 'sonar.projectKey', 'broadinstitute_juniper-api-admin'
+        property 'sonar.projectBaseDir', '.'
         property 'sonar.organization', 'broad-databiosphere'
         property 'sonar.host.url', 'https://sonarcloud.io'
     }
diff --git a/api-participant/build.gradle b/api-participant/build.gradle
index ac447b0f31..25fc808d4e 100644
--- a/api-participant/build.gradle
+++ b/api-participant/build.gradle
@@ -64,8 +64,9 @@ test {
 
 sonar {
     properties {
-        property 'sonar.projectName', 'terra-java-project-template'
-        property 'sonar.projectKey', 'terra-java-project-template'
+        property 'sonar.projectName', 'juniper-api-participant'
+        property 'sonar.projectKey', 'broadinstitute_juniper-api-participant'
+        property 'sonar.projectBaseDir', '.'
         property 'sonar.organization', 'broad-databiosphere'
         property 'sonar.host.url', 'https://sonarcloud.io'
     }
diff --git a/populate/build.gradle b/populate/build.gradle
index 958e9d0192..a1bd2db72f 100644
--- a/populate/build.gradle
+++ b/populate/build.gradle
@@ -1,6 +1,7 @@
 plugins {
     id "io.freefair.lombok" version "5.3.3.3"
     id 'java'
+    id 'org.sonarqube'
 }
 
 group = 'bio.terra.pearl.core'
@@ -36,3 +37,12 @@ test {
     useJUnitPlatform ()
 }
 
+sonar {
+    properties {
+        property 'sonar.projectName', 'juniper-populate'
+        property 'sonar.projectKey', 'broadinstitute_juniper-populate'
+        property 'sonar.projectBaseDir', '.'
+        property 'sonar.organization', 'broad-databiosphere'
+        property 'sonar.host.url', 'https://sonarcloud.io'
+    }
+}
diff --git a/sonar-project.properties b/sonar-project.properties
deleted file mode 100644
index 95c6464f6e..0000000000
--- a/sonar-project.properties
+++ /dev/null
@@ -1,8 +0,0 @@
-sonar.projectKey=broadinstitute_pearl
-sonar.organization=dsp-appsec
-sonar.projectName=pearl
-sonar.sources=api-admin,api-participant,core,populate,ui-admin,ui-participant
-sonar.sourceEncoding=UTF-8
-sonar.java.binaries=api-admin/build/classes,api-participant/build/classes,core/build/classes
-
-# TODO sonar.coverage.jacoco.xmlReportPaths
\ No newline at end of file
diff --git a/ui-admin/sonar-project.properties b/ui-admin/sonar-project.properties
new file mode 100644
index 0000000000..6d4dc573ef
--- /dev/null
+++ b/ui-admin/sonar-project.properties
@@ -0,0 +1,6 @@
+sonar.projectName=juniper-ui-admin
+sonar.projectKey=broadinstitute_juniper-ui-admin
+sonar.organization=dsp-appsec
+sonar.sourceEncoding=UTF-8
+
+# TODO sonar.coverage.jacoco.xmlReportPaths
\ No newline at end of file

From 2781dab8b06801b3ff6ce3da0bb6f257a276936e Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 14:01:35 -0400
Subject: [PATCH 04/83] sonar-project.properties at root

---
 .../sonar-project.properties => sonar-project.properties     | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)
 rename ui-admin/sonar-project.properties => sonar-project.properties (50%)

diff --git a/ui-admin/sonar-project.properties b/sonar-project.properties
similarity index 50%
rename from ui-admin/sonar-project.properties
rename to sonar-project.properties
index 6d4dc573ef..cb8e1d2a1b 100644
--- a/ui-admin/sonar-project.properties
+++ b/sonar-project.properties
@@ -1,6 +1,7 @@
-sonar.projectName=juniper-ui-admin
-sonar.projectKey=broadinstitute_juniper-ui-admin
+sonar.projectName=juniper-ui
+sonar.projectKey=broadinstitute_juniper
 sonar.organization=dsp-appsec
+sonar.sources=ui-admin,ui-core
 sonar.sourceEncoding=UTF-8
 
 # TODO sonar.coverage.jacoco.xmlReportPaths
\ No newline at end of file

From 702302871e60c76529815c92d8463114de36cb28 Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 14:12:27 -0400
Subject: [PATCH 05/83] combine all java and combine all typescript

---
 .github/workflows/java-ci.yml | 14 +++++++-------
 .github/workflows/sonar.yaml  | 16 +++++++---------
 .github/workflows/ui-ci.yml   | 13 +++++++------
 3 files changed, 21 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/java-ci.yml b/.github/workflows/java-ci.yml
index ed790610ed..2244d35040 100644
--- a/.github/workflows/java-ci.yml
+++ b/.github/workflows/java-ci.yml
@@ -12,12 +12,13 @@
 name: Java CI
 
 on:
-  push:
-    branches: [ development ]
-    paths-ignore: [ '*.md']
-  pull_request:
-    branches: [ '**' ]
-  merge_group:
+  # push:
+  #   branches: [ development ]
+  #   paths-ignore: [ '*.md']
+  # pull_request:
+  #   branches: [ '**' ]
+  # merge_group:
+  workflow_dispatch:
 
 jobs:
   build:
@@ -56,7 +57,6 @@ jobs:
           arguments: build --info # if you need to see test failure full stacktraces, change this to `build --info`
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
   # Need to uncomment these in follow up PR, The new Trivy and Tag workflows need to exist on the development branch
   # before the following steps will work
diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index e5a1031ca7..4f7c0ab443 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -27,31 +27,29 @@ jobs:
   #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
   #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
-  sonar-api-admin:
-    name: SonarCloud api-admin
+  sonar-java:
+    name: SonarCloud Java
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Scan api-admin via gradle
-        run: ./gradlew --build-cache :api-admin:compileJava :api-admin:sonar
+      - name: Scan via gradle
+        run: ./gradlew --build-cache compileJava sonar
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
 
-  sonar-ui-admin:
-    name: SonarCloud ui-admin
+  sonar-typescript:
+    name: SonarCloud TypeScript
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Scan ui-admin via sonarcloud-github-action
+      - name: Scan via sonarcloud-github-action
         uses: SonarSource/sonarcloud-github-action@master
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-        with:
-          projectBaseDir: ui-admin/
diff --git a/.github/workflows/ui-ci.yml b/.github/workflows/ui-ci.yml
index 876acbbb55..6c45e49525 100644
--- a/.github/workflows/ui-ci.yml
+++ b/.github/workflows/ui-ci.yml
@@ -1,12 +1,13 @@
 name: UI CI
 
 on:
-  push:
-    branches: [ development ]
-    paths-ignore: [ '*.md']
-  pull_request:
-    branches: [ '**' ]
-  merge_group:
+  # push:
+  #   branches: [ development ]
+  #   paths-ignore: [ '*.md']
+  # pull_request:
+  #   branches: [ '**' ]
+  # merge_group:
+  workflow_dispatch:
 
 jobs:
   build:

From 50add44b8c3e2d0520d495288db35f853e0b82b6 Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 14:17:18 -0400
Subject: [PATCH 06/83] sonar typescript

---
 .github/workflows/sonar.yaml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 4f7c0ab443..3549fb1599 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -40,16 +40,18 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
-
-  sonar-typescript:
-    name: SonarCloud TypeScript
+  sonar-ui-admin:
+    name: SonarCloud ui-admin
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Scan via sonarcloud-github-action
+      - name: Scan ui-admin via sonarcloud-github-action
         uses: SonarSource/sonarcloud-github-action@master
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        with:
+          projectBaseDir: ui-admin/
+

From c6963e425a7ee22f981ffa1c30ffd5eeadeed99b Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 14:46:16 -0400
Subject: [PATCH 07/83] sonar args in workflow

---
 .github/workflows/sonar.yaml | 55 ++++++++++++++++++++----------------
 sonar-project.properties     |  7 -----
 2 files changed, 30 insertions(+), 32 deletions(-)
 delete mode 100644 sonar-project.properties

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 3549fb1599..eba95fb335 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -2,31 +2,6 @@ name: Sonar
 on: workflow_dispatch
 
 jobs:
-  # sonar:
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v3
-
-  #     - name: Set up JDK
-  #       uses: actions/setup-java@v3
-  #       with:
-  #         java-version: '17'
-  #         distribution: 'temurin'
-  #         cache: 'gradle'
-
-  #     - name: SonarCloud Scan (Typescript only)
-  #       uses: SonarSource/sonarcloud-github-action@master
-  #       env:
-  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
-
-  #     - name: SonarCloud Scan (Java only)
-  #       run: ./gradlew --build-cache compileJava sonar
-  #       env:
-  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
   sonar-java:
     name: SonarCloud Java
     runs-on: ubuntu-latest
@@ -54,4 +29,34 @@ jobs:
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
         with:
           projectBaseDir: ui-admin/
+          args: >
+              -Dsonar.projectName=juniper-ui-admin
+              -Dsonar.organization=dsp-appsec
+              -Dsonar.projectKey=broadinstitute_juniper-ui-admin
+              -Dsonar.verbose=true
+
+  # sonar:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v3
+
+  #     - name: Set up JDK
+  #       uses: actions/setup-java@v3
+  #       with:
+  #         java-version: '17'
+  #         distribution: 'temurin'
+  #         cache: 'gradle'
+
+  #     - name: SonarCloud Scan (Typescript only)
+  #       uses: SonarSource/sonarcloud-github-action@master
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+
+
+  #     - name: SonarCloud Scan (Java only)
+  #       run: ./gradlew --build-cache compileJava sonar
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
diff --git a/sonar-project.properties b/sonar-project.properties
deleted file mode 100644
index cb8e1d2a1b..0000000000
--- a/sonar-project.properties
+++ /dev/null
@@ -1,7 +0,0 @@
-sonar.projectName=juniper-ui
-sonar.projectKey=broadinstitute_juniper
-sonar.organization=dsp-appsec
-sonar.sources=ui-admin,ui-core
-sonar.sourceEncoding=UTF-8
-
-# TODO sonar.coverage.jacoco.xmlReportPaths
\ No newline at end of file

From 64d6e2d134cf4868753c8cbd77fa17f610886a15 Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 14:49:14 -0400
Subject: [PATCH 08/83] sonarscanner

---
 .github/workflows/sonar.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index eba95fb335..6dc83c5629 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -30,9 +30,9 @@ jobs:
         with:
           projectBaseDir: ui-admin/
           args: >
-              -Dsonar.projectName=juniper-ui-admin
+              -Dsonar.projectName=juniper
               -Dsonar.organization=dsp-appsec
-              -Dsonar.projectKey=broadinstitute_juniper-ui-admin
+              -Dsonar.projectKey=broadinstitute_juniper
               -Dsonar.verbose=true
 
   # sonar:

From 481092837582c0b171dd8752e668f521f8b2f5a9 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 13:35:39 -0400
Subject: [PATCH 09/83] work in progress

---
 .gitignore                   |  3 +++
 api-admin/build.gradle       | 11 -----------
 api-participant/build.gradle |  1 -
 build.gradle                 | 14 ++++++++++++++
 client/build.gradle          | 11 +++++++++++
 core/build.gradle            | 10 ++++++++++
 integration/build.gradle     | 11 +++++++++++
 settings.gradle              |  2 +-
 8 files changed, 50 insertions(+), 13 deletions(-)

diff --git a/.gitignore b/.gitignore
index 19ae5a13e1..b06543d7b0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -42,3 +42,6 @@ npm-debug.log*
 .scannerwork
 .sonar-token
 tmp/
+
+# direnv
+.envrc
diff --git a/api-admin/build.gradle b/api-admin/build.gradle
index 529b310da6..23349bfb8d 100644
--- a/api-admin/build.gradle
+++ b/api-admin/build.gradle
@@ -3,7 +3,6 @@ plugins {
     id 'de.undercouch.download'
     id 'com.google.cloud.tools.jib'
     id 'com.srcclr.gradle'
-    id 'org.sonarqube'
 
     id 'com.gorylenko.gradle-git-properties' version '2.3.1'
 }
@@ -65,13 +64,3 @@ jibDockerBuild.dependsOn('copyWebApp')
 test {
     useJUnitPlatform ()
 }
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-api-admin'
-        property 'sonar.projectKey', 'broadinstitute_juniper-api-admin'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}
diff --git a/api-participant/build.gradle b/api-participant/build.gradle
index 25fc808d4e..b4f1353c4a 100644
--- a/api-participant/build.gradle
+++ b/api-participant/build.gradle
@@ -3,7 +3,6 @@ plugins {
     id 'de.undercouch.download'
     id 'com.google.cloud.tools.jib'
     id 'com.srcclr.gradle'
-    id 'org.sonarqube'
 
     id 'com.gorylenko.gradle-git-properties' version '2.3.1'
 }
diff --git a/build.gradle b/build.gradle
index cde2107918..f950171b13 100644
--- a/build.gradle
+++ b/build.gradle
@@ -16,3 +16,17 @@ task bundleAdminUI(type: NpmTask, dependsOn: [npmInstall, buildUICore]) {
 task bundleParticipantUI(type: NpmTask, dependsOn: [npmInstall, buildUICore]) {
     args = ['--workspace=ui-participant', 'run', 'build']
 }
+
+subprojects {
+    apply plugin: 'org.sonarqube'
+
+    sonar {
+        properties {
+            property 'sonar.projectName', "${rootProject.name}-${project.name}"
+            property 'sonar.projectKey', "broadinstitute_${rootProject.name}-${project.name}"
+            property 'sonar.projectBaseDir', "${projectDir}"
+            property 'sonar.organization', 'broad-databiosphere'
+            property 'sonar.host.url', 'https://sonarcloud.io'
+        }
+    }
+}
diff --git a/client/build.gradle b/client/build.gradle
index 1ed4a117bd..c474db7905 100644
--- a/client/build.gradle
+++ b/client/build.gradle
@@ -6,6 +6,7 @@ plugins {
     id 'io.spring.dependency-management'
     id 'com.jfrog.artifactory' version '4.18.2'
     id 'org.hidetake.swagger.generator'
+    id 'org.sonarqube'
 }
 
 dependencyManagement {
@@ -16,3 +17,13 @@ dependencyManagement {
 
 apply from: 'artifactory.gradle'
 apply from: 'swagger.gradle'
+
+sonar {
+    properties {
+        property 'sonar.projectName', 'juniper-client'
+        property 'sonar.projectKey', 'broadinstitute_juniper-client'
+        property 'sonar.projectBaseDir', '.'
+        property 'sonar.organization', 'broad-databiosphere'
+        property 'sonar.host.url', 'https://sonarcloud.io'
+    }
+}
diff --git a/core/build.gradle b/core/build.gradle
index ca2ff9dfa0..8f449f8e5c 100644
--- a/core/build.gradle
+++ b/core/build.gradle
@@ -3,6 +3,7 @@ plugins {
     id 'java'
     id 'org.liquibase.gradle' version '2.1.0'
     id "java-test-fixtures"
+    id 'org.sonarqube'
 }
 
 group = 'bio.terra.pearl.core'
@@ -56,3 +57,12 @@ test {
     useJUnitPlatform ()
 }
 
+sonar {
+    properties {
+        property 'sonar.projectName', 'juniper-core'
+        property 'sonar.projectKey', 'broadinstitute_juniper-core'
+        property 'sonar.projectBaseDir', '.'
+        property 'sonar.organization', 'broad-databiosphere'
+        property 'sonar.host.url', 'https://sonarcloud.io'
+    }
+}
diff --git a/integration/build.gradle b/integration/build.gradle
index e658872b51..2c8110abea 100644
--- a/integration/build.gradle
+++ b/integration/build.gradle
@@ -4,6 +4,7 @@ plugins {
     id 'bio.terra.java-application-conventions'
     id 'io.spring.dependency-management'
     id 'bio.terra.test-runner-plugin'
+    id 'org.sonarqube'
 }
 
 dependencyManagement {
@@ -29,3 +30,13 @@ dependencies {
     // Requires client libraries
     implementation project(':client')
 }
+
+sonar {
+    properties {
+        property 'sonar.projectName', 'juniper-integration'
+        property 'sonar.projectKey', 'broadinstitute_juniper-integration'
+        property 'sonar.projectBaseDir', '.'
+        property 'sonar.organization', 'broad-databiosphere'
+        property 'sonar.host.url', 'https://sonarcloud.io'
+    }
+}
diff --git a/settings.gradle b/settings.gradle
index b58c8e742f..679ceb7af6 100644
--- a/settings.gradle
+++ b/settings.gradle
@@ -1,4 +1,4 @@
-rootProject.name = 'pearl'
+rootProject.name = 'juniper'
 include('core', 'populate', 'api-admin', 'api-participant')
 
 gradle.ext.releaseVersion = '0.0.85'

From dec810d3d036db47c80e5a9ad97da2e7de9291ad Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 17:15:00 -0400
Subject: [PATCH 10/83] multiproject sonar

---
 .gitignore                   |  3 +++
 api-participant/build.gradle | 10 ----------
 build.gradle                 |  5 ++---
 client/build.gradle          | 11 -----------
 core/build.gradle            | 11 -----------
 integration/build.gradle     | 11 -----------
 populate/build.gradle        | 11 -----------
 7 files changed, 5 insertions(+), 57 deletions(-)

diff --git a/.gitignore b/.gitignore
index b06543d7b0..af6569d321 100644
--- a/.gitignore
+++ b/.gitignore
@@ -45,3 +45,6 @@ tmp/
 
 # direnv
 .envrc
+
+*.hprof
+
diff --git a/api-participant/build.gradle b/api-participant/build.gradle
index b4f1353c4a..c4cce86100 100644
--- a/api-participant/build.gradle
+++ b/api-participant/build.gradle
@@ -60,13 +60,3 @@ jibDockerBuild.dependsOn('copyWebApp')
 test {
     useJUnitPlatform ()
 }
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-api-participant'
-        property 'sonar.projectKey', 'broadinstitute_juniper-api-participant'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}
diff --git a/build.gradle b/build.gradle
index f950171b13..af5012bec4 100644
--- a/build.gradle
+++ b/build.gradle
@@ -17,15 +17,14 @@ task bundleParticipantUI(type: NpmTask, dependsOn: [npmInstall, buildUICore]) {
     args = ['--workspace=ui-participant', 'run', 'build']
 }
 
+apply plugin: 'org.sonarqube'
 subprojects {
-    apply plugin: 'org.sonarqube'
-
     sonar {
         properties {
             property 'sonar.projectName', "${rootProject.name}-${project.name}"
             property 'sonar.projectKey', "broadinstitute_${rootProject.name}-${project.name}"
             property 'sonar.projectBaseDir', "${projectDir}"
-            property 'sonar.organization', 'broad-databiosphere'
+            property 'sonar.organization', 'dsp-appsec'
             property 'sonar.host.url', 'https://sonarcloud.io'
         }
     }
diff --git a/client/build.gradle b/client/build.gradle
index c474db7905..1ed4a117bd 100644
--- a/client/build.gradle
+++ b/client/build.gradle
@@ -6,7 +6,6 @@ plugins {
     id 'io.spring.dependency-management'
     id 'com.jfrog.artifactory' version '4.18.2'
     id 'org.hidetake.swagger.generator'
-    id 'org.sonarqube'
 }
 
 dependencyManagement {
@@ -17,13 +16,3 @@ dependencyManagement {
 
 apply from: 'artifactory.gradle'
 apply from: 'swagger.gradle'
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-client'
-        property 'sonar.projectKey', 'broadinstitute_juniper-client'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}
diff --git a/core/build.gradle b/core/build.gradle
index 8f449f8e5c..40f7c6a14f 100644
--- a/core/build.gradle
+++ b/core/build.gradle
@@ -3,7 +3,6 @@ plugins {
     id 'java'
     id 'org.liquibase.gradle' version '2.1.0'
     id "java-test-fixtures"
-    id 'org.sonarqube'
 }
 
 group = 'bio.terra.pearl.core'
@@ -56,13 +55,3 @@ dependencies {
 test {
     useJUnitPlatform ()
 }
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-core'
-        property 'sonar.projectKey', 'broadinstitute_juniper-core'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}
diff --git a/integration/build.gradle b/integration/build.gradle
index 2c8110abea..e658872b51 100644
--- a/integration/build.gradle
+++ b/integration/build.gradle
@@ -4,7 +4,6 @@ plugins {
     id 'bio.terra.java-application-conventions'
     id 'io.spring.dependency-management'
     id 'bio.terra.test-runner-plugin'
-    id 'org.sonarqube'
 }
 
 dependencyManagement {
@@ -30,13 +29,3 @@ dependencies {
     // Requires client libraries
     implementation project(':client')
 }
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-integration'
-        property 'sonar.projectKey', 'broadinstitute_juniper-integration'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}
diff --git a/populate/build.gradle b/populate/build.gradle
index a1bd2db72f..fa651fa441 100644
--- a/populate/build.gradle
+++ b/populate/build.gradle
@@ -1,7 +1,6 @@
 plugins {
     id "io.freefair.lombok" version "5.3.3.3"
     id 'java'
-    id 'org.sonarqube'
 }
 
 group = 'bio.terra.pearl.core'
@@ -36,13 +35,3 @@ dependencies {
 test {
     useJUnitPlatform ()
 }
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-populate'
-        property 'sonar.projectKey', 'broadinstitute_juniper-populate'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}

From b6ebf5fb39a60e403cf7a0c842bff7cb1436b949 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 17:43:31 -0400
Subject: [PATCH 11/83] gradle sonar on single bound project

---
 .github/workflows/sonar.yaml | 48 +-----------------------------------
 build.gradle                 | 20 +++++++--------
 2 files changed, 11 insertions(+), 57 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 6dc83c5629..8c025de952 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -10,53 +10,7 @@ jobs:
         with:
           fetch-depth: 0
       - name: Scan via gradle
-        run: ./gradlew --build-cache compileJava sonar
+        run: ./gradlew --build-cache compileJava sonar -info
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
-  sonar-ui-admin:
-    name: SonarCloud ui-admin
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-      - name: Scan ui-admin via sonarcloud-github-action
-        uses: SonarSource/sonarcloud-github-action@master
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-        with:
-          projectBaseDir: ui-admin/
-          args: >
-              -Dsonar.projectName=juniper
-              -Dsonar.organization=dsp-appsec
-              -Dsonar.projectKey=broadinstitute_juniper
-              -Dsonar.verbose=true
-
-  # sonar:
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v3
-
-  #     - name: Set up JDK
-  #       uses: actions/setup-java@v3
-  #       with:
-  #         java-version: '17'
-  #         distribution: 'temurin'
-  #         cache: 'gradle'
-
-  #     - name: SonarCloud Scan (Typescript only)
-  #       uses: SonarSource/sonarcloud-github-action@master
-  #       env:
-  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
-
-  #     - name: SonarCloud Scan (Java only)
-  #       run: ./gradlew --build-cache compileJava sonar
-  #       env:
-  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
diff --git a/build.gradle b/build.gradle
index af5012bec4..a8c29338d9 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,5 +1,6 @@
 plugins {
     id 'com.github.node-gradle.node' version '5.0.0'
+    id 'org.sonarqube'
 }
 
 apply plugin: 'base'
@@ -17,15 +18,14 @@ task bundleParticipantUI(type: NpmTask, dependsOn: [npmInstall, buildUICore]) {
     args = ['--workspace=ui-participant', 'run', 'build']
 }
 
-apply plugin: 'org.sonarqube'
-subprojects {
-    sonar {
-        properties {
-            property 'sonar.projectName', "${rootProject.name}-${project.name}"
-            property 'sonar.projectKey', "broadinstitute_${rootProject.name}-${project.name}"
-            property 'sonar.projectBaseDir', "${projectDir}"
-            property 'sonar.organization', 'dsp-appsec'
-            property 'sonar.host.url', 'https://sonarcloud.io'
-        }
+sonar {
+    properties {
+        property 'sonar.projectName', "${rootProject.name}"
+        property 'sonar.projectKey', "broadinstitute_${rootProject.name}"
+        property 'sonar.organization', 'dsp-appsec'
+        property 'sonar.host.url', 'https://sonarcloud.io'
     }
 }
+subprojects {
+    apply plugin: 'org.sonarqube'
+}

From 1fe02e2a7166929004d577d0665bfedb3f1be2c7 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 19:10:59 -0400
Subject: [PATCH 12/83] exclude spotless

---
 .github/workflows/sonar.yaml | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 8c025de952..bd3e6fe13e 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -10,7 +10,16 @@ jobs:
         with:
           fetch-depth: 0
       - name: Scan via gradle
-        run: ./gradlew --build-cache compileJava sonar -info
+        run: >-
+          ./gradlew 
+          --build-cache 
+          -x test 
+          -x spotlessJava 
+          -x spotlessJavaApply 
+          -x spotlessJavaCheck 
+          -x spotlessCheck 
+          -x spotlessApply 
+          build sonar -info
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

From becb8989e391498eb2ea8fdb481c07b0a60b1596 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 19:37:34 -0400
Subject: [PATCH 13/83] include resources in sonar

---
 build.gradle | 1 +
 1 file changed, 1 insertion(+)

diff --git a/build.gradle b/build.gradle
index a8c29338d9..4fa3c22c7c 100644
--- a/build.gradle
+++ b/build.gradle
@@ -24,6 +24,7 @@ sonar {
         property 'sonar.projectKey', "broadinstitute_${rootProject.name}"
         property 'sonar.organization', 'dsp-appsec'
         property 'sonar.host.url', 'https://sonarcloud.io'
+        property 'sonar.sources', 'src/main/java,src/main/resources'
     }
 }
 subprojects {

From 6cb22dca4f3ec0f3cd7d029d8bc04866f2753dc6 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 19:48:49 -0400
Subject: [PATCH 14/83] include resources in sonar

---
 build.gradle | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 4fa3c22c7c..bdbcfae5b3 100644
--- a/build.gradle
+++ b/build.gradle
@@ -24,9 +24,11 @@ sonar {
         property 'sonar.projectKey', "broadinstitute_${rootProject.name}"
         property 'sonar.organization', 'dsp-appsec'
         property 'sonar.host.url', 'https://sonarcloud.io'
-        property 'sonar.sources', 'src/main/java,src/main/resources'
     }
 }
 subprojects {
     apply plugin: 'org.sonarqube'
+    sonar {
+        property 'sonar.sources', 'src/main/java,src/main/resources'
+    }
 }

From 288039f2f6f9cc6b28ddd4d4de4f93bb8d6323c9 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 20:57:55 -0400
Subject: [PATCH 15/83] resources

---
 build.gradle | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index bdbcfae5b3..34deabf251 100644
--- a/build.gradle
+++ b/build.gradle
@@ -29,6 +29,8 @@ sonar {
 subprojects {
     apply plugin: 'org.sonarqube'
     sonar {
-        property 'sonar.sources', 'src/main/java,src/main/resources'
+        properties {
+            property 'sonar.sources', 'src/main/java,src/main/resources'
+        }
     }
 }

From b558e2c347d1ee424e3d59f1e58f14be9cedf61a Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 21:19:33 -0400
Subject: [PATCH 16/83] gha sonar

---
 .github/workflows/sonar.yaml | 42 ++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index bd3e6fe13e..47b278d506 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -9,6 +9,23 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
+      - name: Set up JDK 17
+        uses: actions/setup-java@v3
+        with:
+          java-version: '17'
+          distribution: 'adopt'
+      - name: Cache SonarCloud packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.sonar/cache
+          key: ${{ runner.os }}-sonar
+          restore-keys: ${{ runner.os }}-sonar
+      - name: Cache Gradle packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.gradle/caches
+          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
+          restore-keys: ${{ runner.os }}-gradle
       - name: Scan via gradle
         run: >-
           ./gradlew 
@@ -23,3 +40,28 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+
+
+  sonar-typescript:
+    name: SonarCloud ui-admin
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        subproject: ['ui-admin', 'ui-participant']
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Scan ${{ matrix.subproject }} via sonarcloud-github-action
+        uses: SonarSource/sonarcloud-github-action@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        with:
+          projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
+          args: >
+              -Dsonar.projectName=juniper-${{ matrix.subproject }}
+              -Dsonar.organization=dsp-appsec
+              -Dsonar.projectKey=broadinstitute_juniper-${{ matrix.subproject }}
+              -Dsonar.verbose=true

From bbdde7129cef75529d0f800770a6c0416a9c456d Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 21:33:57 -0400
Subject: [PATCH 17/83] gha

---
 .github/workflows/sonar.yaml            | 18 +-----------------
 ui-admin/sonar-project.properties       | 13 +++++++++++++
 ui-participant/sonar-project.properties | 13 +++++++++++++
 3 files changed, 27 insertions(+), 17 deletions(-)
 create mode 100644 ui-admin/sonar-project.properties
 create mode 100644 ui-participant/sonar-project.properties

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 47b278d506..09d23b930d 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -14,18 +14,6 @@ jobs:
         with:
           java-version: '17'
           distribution: 'adopt'
-      - name: Cache SonarCloud packages
-        uses: actions/cache@v3
-        with:
-          path: ~/.sonar/cache
-          key: ${{ runner.os }}-sonar
-          restore-keys: ${{ runner.os }}-sonar
-      - name: Cache Gradle packages
-        uses: actions/cache@v3
-        with:
-          path: ~/.gradle/caches
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
-          restore-keys: ${{ runner.os }}-gradle
       - name: Scan via gradle
         run: >-
           ./gradlew 
@@ -43,12 +31,11 @@ jobs:
 
 
   sonar-typescript:
-    name: SonarCloud ui-admin
+    name: SonarCloud TypeScript
     runs-on: ubuntu-latest
     strategy:
       matrix:
         subproject: ['ui-admin', 'ui-participant']
-
     steps:
       - uses: actions/checkout@v3
         with:
@@ -61,7 +48,4 @@ jobs:
         with:
           projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
           args: >
-              -Dsonar.projectName=juniper-${{ matrix.subproject }}
-              -Dsonar.organization=dsp-appsec
-              -Dsonar.projectKey=broadinstitute_juniper-${{ matrix.subproject }}
               -Dsonar.verbose=true
diff --git a/ui-admin/sonar-project.properties b/ui-admin/sonar-project.properties
new file mode 100644
index 0000000000..0ed872c811
--- /dev/null
+++ b/ui-admin/sonar-project.properties
@@ -0,0 +1,13 @@
+sonar.projectKey=broadinstitute_juniper-ui-admin
+sonar.organization=dsp-appsec
+
+# This is the name and version displayed in the SonarCloud UI.
+sonar.projectName=juniper-ui-admin
+#sonar.projectVersion=1.0
+
+
+# Path is relative to the sonar-project.properties file. Replace "\" by "/" on Windows.
+#sonar.sources=.
+
+# Encoding of the source code. Default is default system encoding
+#sonar.sourceEncoding=UTF-8
diff --git a/ui-participant/sonar-project.properties b/ui-participant/sonar-project.properties
new file mode 100644
index 0000000000..d4d36496c4
--- /dev/null
+++ b/ui-participant/sonar-project.properties
@@ -0,0 +1,13 @@
+sonar.projectKey=broadinstitute_juniper-ui-participant
+sonar.organization=dsp-appsec
+
+# This is the name and version displayed in the SonarCloud UI.
+sonar.projectName=juniper-ui-participant
+#sonar.projectVersion=1.0
+
+
+# Path is relative to the sonar-project.properties file. Replace "\" by "/" on Windows.
+#sonar.sources=.
+
+# Encoding of the source code. Default is default system encoding
+#sonar.sourceEncoding=UTF-8

From 150f883d4a3ca295f40a3430fdbed696f6e7ad9c Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 22:10:34 -0400
Subject: [PATCH 18/83] typescript sonar specify branch

---
 .github/workflows/sonar.yaml            |  8 +++++++-
 ui-admin/sonar-project.properties       | 10 ----------
 ui-participant/sonar-project.properties | 10 ----------
 3 files changed, 7 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 09d23b930d..da58be83fc 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -1,5 +1,10 @@
 name: Sonar
 on: workflow_dispatch
+  push:
+    branches:
+      - master
+  pull_request:
+    types: [opened, synchronize, reopened]
 
 jobs:
   sonar-java:
@@ -48,4 +53,5 @@ jobs:
         with:
           projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
           args: >
-              -Dsonar.verbose=true
+              -Dsonar.branch.target=${{ github.event.repository.default_branch }}
+              -Dsonar.branch.name=${{ github.ref_name }}
diff --git a/ui-admin/sonar-project.properties b/ui-admin/sonar-project.properties
index 0ed872c811..2b785ca773 100644
--- a/ui-admin/sonar-project.properties
+++ b/ui-admin/sonar-project.properties
@@ -1,13 +1,3 @@
 sonar.projectKey=broadinstitute_juniper-ui-admin
 sonar.organization=dsp-appsec
-
-# This is the name and version displayed in the SonarCloud UI.
 sonar.projectName=juniper-ui-admin
-#sonar.projectVersion=1.0
-
-
-# Path is relative to the sonar-project.properties file. Replace "\" by "/" on Windows.
-#sonar.sources=.
-
-# Encoding of the source code. Default is default system encoding
-#sonar.sourceEncoding=UTF-8
diff --git a/ui-participant/sonar-project.properties b/ui-participant/sonar-project.properties
index d4d36496c4..1d55561464 100644
--- a/ui-participant/sonar-project.properties
+++ b/ui-participant/sonar-project.properties
@@ -1,13 +1,3 @@
 sonar.projectKey=broadinstitute_juniper-ui-participant
 sonar.organization=dsp-appsec
-
-# This is the name and version displayed in the SonarCloud UI.
 sonar.projectName=juniper-ui-participant
-#sonar.projectVersion=1.0
-
-
-# Path is relative to the sonar-project.properties file. Replace "\" by "/" on Windows.
-#sonar.sources=.
-
-# Encoding of the source code. Default is default system encoding
-#sonar.sourceEncoding=UTF-8

From 5739af6a8786660061f286162cb55ad677c87d5b Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 22:13:58 -0400
Subject: [PATCH 19/83] sonar on push

---
 .github/workflows/sonar.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index da58be83fc..477faa7783 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -1,5 +1,6 @@
 name: Sonar
-on: workflow_dispatch
+on: 
+  workflow_dispatch:
   push:
     branches:
       - master

From 67f6447957d8303aace61eedab68466448614afc Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 22:26:55 -0400
Subject: [PATCH 20/83] sonar on push

---
 .github/workflows/sonar.yaml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 477faa7783..59f182d13b 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -46,6 +46,9 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
+      - name: Get branch name
+        id: branch-name
+        uses: tj-actions/branch-names@v5
       - name: Scan ${{ matrix.subproject }} via sonarcloud-github-action
         uses: SonarSource/sonarcloud-github-action@master
         env:
@@ -55,4 +58,4 @@ jobs:
           projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
           args: >
               -Dsonar.branch.target=${{ github.event.repository.default_branch }}
-              -Dsonar.branch.name=${{ github.ref_name }}
+              -Dsonar.branch.name=${{ steps.branch-name.outputs.current_branch }}

From a1b489d45a991f0bac2f2ccd0e4f1c9a8e88cb0c Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 22:41:49 -0400
Subject: [PATCH 21/83] sonar on push

---
 .github/workflows/sonar.yaml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 59f182d13b..685f66720a 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -59,3 +59,9 @@ jobs:
           args: >
               -Dsonar.branch.target=${{ github.event.repository.default_branch }}
               -Dsonar.branch.name=${{ steps.branch-name.outputs.current_branch }}
+      - name: Announce
+        run: |
+          gh pr comment ${{ github.event.pull_request.number }} \
+            --body "SonarCloud analyzed branch: ${{ steps.branch-name.outputs.current_branch }}/"
+        env:
+          GH_TOKEN: ${{ github.token }}

From a1eee5d6821d200edeab98392909816515deeca3 Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Thu, 20 Jul 2023 11:06:11 -0400
Subject: [PATCH 22/83] sonar in Java CI

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/java-ci.yml | 3 +++
 api-admin/build.gradle        | 2 +-
 api-participant/build.gradle  | 2 +-
 buildSrc/build.gradle         | 2 +-
 4 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/java-ci.yml b/.github/workflows/java-ci.yml
index 218296b127..b16bbc0459 100644
--- a/.github/workflows/java-ci.yml
+++ b/.github/workflows/java-ci.yml
@@ -54,6 +54,9 @@ jobs:
         uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
         with:
           arguments: build sonar --info # if you need to see test failure full stacktraces, change this to `build --info`
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
   # Need to uncomment these in follow up PR, The new Trivy and Tag workflows need to exist on the development branch
   # before the following steps will work
diff --git a/api-admin/build.gradle b/api-admin/build.gradle
index 603a871ace..287727da55 100644
--- a/api-admin/build.gradle
+++ b/api-admin/build.gradle
@@ -66,7 +66,7 @@ test {
     useJUnitPlatform ()
 }
 
-sonarqube {
+sonar {
     properties {
         property 'sonar.projectName', 'terra-java-project-template'
         property 'sonar.projectKey', 'terra-java-project-template'
diff --git a/api-participant/build.gradle b/api-participant/build.gradle
index ea56e710c3..ac447b0f31 100644
--- a/api-participant/build.gradle
+++ b/api-participant/build.gradle
@@ -62,7 +62,7 @@ test {
     useJUnitPlatform ()
 }
 
-sonarqube {
+sonar {
     properties {
         property 'sonar.projectName', 'terra-java-project-template'
         property 'sonar.projectKey', 'terra-java-project-template'
diff --git a/buildSrc/build.gradle b/buildSrc/build.gradle
index 4fdbf72dd8..3f872a3763 100644
--- a/buildSrc/build.gradle
+++ b/buildSrc/build.gradle
@@ -18,7 +18,7 @@ dependencies {
     implementation 'com.github.spotbugs.snom:spotbugs-gradle-plugin:5.0.12'
     implementation 'io.spring.dependency-management:io.spring.dependency-management.gradle.plugin:1.0.15.RELEASE'
     implementation 'org.hidetake.swagger.generator:org.hidetake.swagger.generator.gradle.plugin:2.19.2'
-    implementation 'org.sonarqube:org.sonarqube.gradle.plugin:3.4.0.2513'
+    implementation 'org.sonarqube:org.sonarqube.gradle.plugin:4.2.1.3168'
     implementation 'org.springframework.boot:spring-boot-gradle-plugin:2.7.10'
     implementation 'bio.terra:terra-test-runner:0.1.5-SNAPSHOT'
     // This is required due to a dependency conflict between jib and srcclr. Removing it will cause jib to fail.

From d3313bcdb2cb7178f768202034a2247abf1476a7 Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 13:43:51 -0400
Subject: [PATCH 23/83] separate project sonar scans

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/java-ci.yml     |  2 +-
 .github/workflows/sonar.yaml      | 53 +++++++++++++++++++++++++------
 README.md                         | 29 ++++++++++++-----
 api-admin/build.gradle            |  5 +--
 api-participant/build.gradle      |  5 +--
 populate/build.gradle             | 10 ++++++
 sonar-project.properties          |  8 -----
 ui-admin/sonar-project.properties |  6 ++++
 8 files changed, 87 insertions(+), 31 deletions(-)
 delete mode 100644 sonar-project.properties
 create mode 100644 ui-admin/sonar-project.properties

diff --git a/.github/workflows/java-ci.yml b/.github/workflows/java-ci.yml
index b16bbc0459..ed790610ed 100644
--- a/.github/workflows/java-ci.yml
+++ b/.github/workflows/java-ci.yml
@@ -53,7 +53,7 @@ jobs:
       - name: Build and SonarQube scan with Gradle
         uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
         with:
-          arguments: build sonar --info # if you need to see test failure full stacktraces, change this to `build --info`
+          arguments: build --info # if you need to see test failure full stacktraces, change this to `build --info`
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 09974b0c5e..e5a1031ca7 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -2,23 +2,56 @@ name: Sonar
 on: workflow_dispatch
 
 jobs:
-  sonar:
+  # sonar:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v3
+
+  #     - name: Set up JDK
+  #       uses: actions/setup-java@v3
+  #       with:
+  #         java-version: '17'
+  #         distribution: 'temurin'
+  #         cache: 'gradle'
+
+  #     - name: SonarCloud Scan (Typescript only)
+  #       uses: SonarSource/sonarcloud-github-action@master
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+
+
+  #     - name: SonarCloud Scan (Java only)
+  #       run: ./gradlew --build-cache compileJava sonar
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+
+  sonar-api-admin:
+    name: SonarCloud api-admin
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-
-      - name: Set up JDK
-        uses: actions/setup-java@v3
         with:
-          java-version: '17'
-          distribution: 'temurin'
-          cache: 'gradle'
+          fetch-depth: 0
+      - name: Scan api-admin via gradle
+        run: ./gradlew --build-cache :api-admin:compileJava :api-admin:sonar
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
-      - name: Build all projects without running tests
-        run: ./gradlew --build-cache compileJava
 
-      - name: SonarCloud Scan
+  sonar-ui-admin:
+    name: SonarCloud ui-admin
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Scan ui-admin via sonarcloud-github-action
         uses: SonarSource/sonarcloud-github-action@master
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        with:
+          projectBaseDir: ui-admin/
diff --git a/README.md b/README.md
index 1fe3ddb85d..ad0aa66f0a 100644
--- a/README.md
+++ b/README.md
@@ -29,7 +29,7 @@ DTOs, and populate services.  the PopulateCliApp can be used to populate specifi
    In development, it serves at localhost:8081.  Lives in `api-participant` directory
 ##### Study Manager UI
    Participant UI is a create-react-app SPA.  Lives in `ui-participant` directory.  Serves on localhost:3001 in development
-   
+
 
 
 ## Local development
@@ -47,7 +47,7 @@ run `./local-dev/run_postgres.sh start`
 This will start a postgres container with a schema and user configured
 
 #### IDE Setup
-Open the root folder in IntelliJ.  
+Open the root folder in IntelliJ.
 
 * **server:**
 
@@ -76,15 +76,15 @@ Open the root folder in IntelliJ.
         * set environment variable: `B2C_POLICY_NAME=B2C_1A_ddp_participant_signup_signin_dev`
         * set environment variable: `B2C_CHANGE_PASSWORD_POLICY_NAME=B2C_1A_ddp_participant_change_password_dev`
         * disable launch optimization
-        
-         
+
+
 ### Running the application
 #### Admin tool (study manager, population)
 * API (api-admin module)
 In intelliJ, you can either run ApiAdminApp (from the api-admin module) directly, or execute the "bootRun" gradle task.
 In basic development mode, this will only serve the API, not the frontend assets.
 
-To make the application useful, you will want to populate some users and studies.  After the admin API is running, 
+To make the application useful, you will want to populate some users and studies.  After the admin API is running,
 from the root project directory, run
 ```
 ./scripts/populate_portal.sh ourhealth
@@ -98,7 +98,7 @@ From the command line:
   REACT_APP_B2C_TENANT_NAME=ddpdevb2c REACT_APP_B2C_CLIENT_ID=$(vault read -field value secret/dsp/ddp/b2c/dev/application_id) npm -w ui-admin start
   ```
 (note that you can just run `npm -w ui-admin start` if you don't need to test B2C login functionality)
-Then go to `localhost:3000` 
+Then go to `localhost:3000`
 
 ##### Participant API (api-participant module)
 In intelliJ, you can either run ApiParticipantApp (from the api-participant module) directly, or execute the "bootRun" gradle task.
@@ -118,9 +118,9 @@ Then go to `sandbox.ourhealth.localhost:3001`
 (Notice how you need the environment name and portal name as subdomains)
 
 
-### Feature Development 
+### Feature Development
 
-#### Adding a new model 
+#### Adding a new model
 1. Create the schema, models, and services
    1. Create your POJO model in `core/src/main/java/bio/terra/pearl/core/model`, you will almost certainly want to extend
    `BaseEntity`
@@ -150,3 +150,16 @@ Then go to `sandbox.ourhealth.localhost:3001`
 #### Adding environment variables
   Helm charts:
   https://github.com/broadinstitute/terra-helmfile/tree/master/values/app/d2p/live
+
+
+### SonarCloud code scanning
+
+Because juniper contains TypeScript projects and Java projects, the scans are run independently
+in each project
+
+Typescript UI subprojects (ui-admin, ui-core, and ui-participant) are scanned using the
+SonarCloud GitHub Action. Analysis (SonarCloud
+runs the scan on its own and comments back results to PRs).
+
+Java subprojects (core, client, api-admin, api-participant) are scanned using gradle with the
+sonarqube plugin.
\ No newline at end of file
diff --git a/api-admin/build.gradle b/api-admin/build.gradle
index 287727da55..529b310da6 100644
--- a/api-admin/build.gradle
+++ b/api-admin/build.gradle
@@ -68,8 +68,9 @@ test {
 
 sonar {
     properties {
-        property 'sonar.projectName', 'terra-java-project-template'
-        property 'sonar.projectKey', 'terra-java-project-template'
+        property 'sonar.projectName', 'juniper-api-admin'
+        property 'sonar.projectKey', 'broadinstitute_juniper-api-admin'
+        property 'sonar.projectBaseDir', '.'
         property 'sonar.organization', 'broad-databiosphere'
         property 'sonar.host.url', 'https://sonarcloud.io'
     }
diff --git a/api-participant/build.gradle b/api-participant/build.gradle
index ac447b0f31..25fc808d4e 100644
--- a/api-participant/build.gradle
+++ b/api-participant/build.gradle
@@ -64,8 +64,9 @@ test {
 
 sonar {
     properties {
-        property 'sonar.projectName', 'terra-java-project-template'
-        property 'sonar.projectKey', 'terra-java-project-template'
+        property 'sonar.projectName', 'juniper-api-participant'
+        property 'sonar.projectKey', 'broadinstitute_juniper-api-participant'
+        property 'sonar.projectBaseDir', '.'
         property 'sonar.organization', 'broad-databiosphere'
         property 'sonar.host.url', 'https://sonarcloud.io'
     }
diff --git a/populate/build.gradle b/populate/build.gradle
index 958e9d0192..a1bd2db72f 100644
--- a/populate/build.gradle
+++ b/populate/build.gradle
@@ -1,6 +1,7 @@
 plugins {
     id "io.freefair.lombok" version "5.3.3.3"
     id 'java'
+    id 'org.sonarqube'
 }
 
 group = 'bio.terra.pearl.core'
@@ -36,3 +37,12 @@ test {
     useJUnitPlatform ()
 }
 
+sonar {
+    properties {
+        property 'sonar.projectName', 'juniper-populate'
+        property 'sonar.projectKey', 'broadinstitute_juniper-populate'
+        property 'sonar.projectBaseDir', '.'
+        property 'sonar.organization', 'broad-databiosphere'
+        property 'sonar.host.url', 'https://sonarcloud.io'
+    }
+}
diff --git a/sonar-project.properties b/sonar-project.properties
deleted file mode 100644
index 95c6464f6e..0000000000
--- a/sonar-project.properties
+++ /dev/null
@@ -1,8 +0,0 @@
-sonar.projectKey=broadinstitute_pearl
-sonar.organization=dsp-appsec
-sonar.projectName=pearl
-sonar.sources=api-admin,api-participant,core,populate,ui-admin,ui-participant
-sonar.sourceEncoding=UTF-8
-sonar.java.binaries=api-admin/build/classes,api-participant/build/classes,core/build/classes
-
-# TODO sonar.coverage.jacoco.xmlReportPaths
\ No newline at end of file
diff --git a/ui-admin/sonar-project.properties b/ui-admin/sonar-project.properties
new file mode 100644
index 0000000000..6d4dc573ef
--- /dev/null
+++ b/ui-admin/sonar-project.properties
@@ -0,0 +1,6 @@
+sonar.projectName=juniper-ui-admin
+sonar.projectKey=broadinstitute_juniper-ui-admin
+sonar.organization=dsp-appsec
+sonar.sourceEncoding=UTF-8
+
+# TODO sonar.coverage.jacoco.xmlReportPaths
\ No newline at end of file

From 6019c524728db740899c6ff5b483ff7075eece94 Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 14:01:35 -0400
Subject: [PATCH 24/83] sonar-project.properties at root

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .../sonar-project.properties => sonar-project.properties     | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)
 rename ui-admin/sonar-project.properties => sonar-project.properties (50%)

diff --git a/ui-admin/sonar-project.properties b/sonar-project.properties
similarity index 50%
rename from ui-admin/sonar-project.properties
rename to sonar-project.properties
index 6d4dc573ef..cb8e1d2a1b 100644
--- a/ui-admin/sonar-project.properties
+++ b/sonar-project.properties
@@ -1,6 +1,7 @@
-sonar.projectName=juniper-ui-admin
-sonar.projectKey=broadinstitute_juniper-ui-admin
+sonar.projectName=juniper-ui
+sonar.projectKey=broadinstitute_juniper
 sonar.organization=dsp-appsec
+sonar.sources=ui-admin,ui-core
 sonar.sourceEncoding=UTF-8
 
 # TODO sonar.coverage.jacoco.xmlReportPaths
\ No newline at end of file

From 69126f498c25dd493f0189d57ac823e6103b9e7f Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 14:12:27 -0400
Subject: [PATCH 25/83] combine all java and combine all typescript

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/java-ci.yml | 14 +++++++-------
 .github/workflows/sonar.yaml  | 16 +++++++---------
 .github/workflows/ui-ci.yml   | 13 +++++++------
 3 files changed, 21 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/java-ci.yml b/.github/workflows/java-ci.yml
index ed790610ed..2244d35040 100644
--- a/.github/workflows/java-ci.yml
+++ b/.github/workflows/java-ci.yml
@@ -12,12 +12,13 @@
 name: Java CI
 
 on:
-  push:
-    branches: [ development ]
-    paths-ignore: [ '*.md']
-  pull_request:
-    branches: [ '**' ]
-  merge_group:
+  # push:
+  #   branches: [ development ]
+  #   paths-ignore: [ '*.md']
+  # pull_request:
+  #   branches: [ '**' ]
+  # merge_group:
+  workflow_dispatch:
 
 jobs:
   build:
@@ -56,7 +57,6 @@ jobs:
           arguments: build --info # if you need to see test failure full stacktraces, change this to `build --info`
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
   # Need to uncomment these in follow up PR, The new Trivy and Tag workflows need to exist on the development branch
   # before the following steps will work
diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index e5a1031ca7..4f7c0ab443 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -27,31 +27,29 @@ jobs:
   #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
   #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
-  sonar-api-admin:
-    name: SonarCloud api-admin
+  sonar-java:
+    name: SonarCloud Java
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Scan api-admin via gradle
-        run: ./gradlew --build-cache :api-admin:compileJava :api-admin:sonar
+      - name: Scan via gradle
+        run: ./gradlew --build-cache compileJava sonar
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
 
-  sonar-ui-admin:
-    name: SonarCloud ui-admin
+  sonar-typescript:
+    name: SonarCloud TypeScript
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Scan ui-admin via sonarcloud-github-action
+      - name: Scan via sonarcloud-github-action
         uses: SonarSource/sonarcloud-github-action@master
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-        with:
-          projectBaseDir: ui-admin/
diff --git a/.github/workflows/ui-ci.yml b/.github/workflows/ui-ci.yml
index 876acbbb55..6c45e49525 100644
--- a/.github/workflows/ui-ci.yml
+++ b/.github/workflows/ui-ci.yml
@@ -1,12 +1,13 @@
 name: UI CI
 
 on:
-  push:
-    branches: [ development ]
-    paths-ignore: [ '*.md']
-  pull_request:
-    branches: [ '**' ]
-  merge_group:
+  # push:
+  #   branches: [ development ]
+  #   paths-ignore: [ '*.md']
+  # pull_request:
+  #   branches: [ '**' ]
+  # merge_group:
+  workflow_dispatch:
 
 jobs:
   build:

From 6b6cff1e8dfaf051000dcc277b3f6c1257d30ba9 Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 14:17:18 -0400
Subject: [PATCH 26/83] sonar typescript

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 4f7c0ab443..3549fb1599 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -40,16 +40,18 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
-
-  sonar-typescript:
-    name: SonarCloud TypeScript
+  sonar-ui-admin:
+    name: SonarCloud ui-admin
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Scan via sonarcloud-github-action
+      - name: Scan ui-admin via sonarcloud-github-action
         uses: SonarSource/sonarcloud-github-action@master
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        with:
+          projectBaseDir: ui-admin/
+

From cc8dbba2b7f0355206f6791a94110404ae4ce42f Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 14:46:16 -0400
Subject: [PATCH 27/83] sonar args in workflow

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 55 ++++++++++++++++++++----------------
 sonar-project.properties     |  7 -----
 2 files changed, 30 insertions(+), 32 deletions(-)
 delete mode 100644 sonar-project.properties

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 3549fb1599..eba95fb335 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -2,31 +2,6 @@ name: Sonar
 on: workflow_dispatch
 
 jobs:
-  # sonar:
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v3
-
-  #     - name: Set up JDK
-  #       uses: actions/setup-java@v3
-  #       with:
-  #         java-version: '17'
-  #         distribution: 'temurin'
-  #         cache: 'gradle'
-
-  #     - name: SonarCloud Scan (Typescript only)
-  #       uses: SonarSource/sonarcloud-github-action@master
-  #       env:
-  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
-
-  #     - name: SonarCloud Scan (Java only)
-  #       run: ./gradlew --build-cache compileJava sonar
-  #       env:
-  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
   sonar-java:
     name: SonarCloud Java
     runs-on: ubuntu-latest
@@ -54,4 +29,34 @@ jobs:
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
         with:
           projectBaseDir: ui-admin/
+          args: >
+              -Dsonar.projectName=juniper-ui-admin
+              -Dsonar.organization=dsp-appsec
+              -Dsonar.projectKey=broadinstitute_juniper-ui-admin
+              -Dsonar.verbose=true
+
+  # sonar:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v3
+
+  #     - name: Set up JDK
+  #       uses: actions/setup-java@v3
+  #       with:
+  #         java-version: '17'
+  #         distribution: 'temurin'
+  #         cache: 'gradle'
+
+  #     - name: SonarCloud Scan (Typescript only)
+  #       uses: SonarSource/sonarcloud-github-action@master
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+
+
+  #     - name: SonarCloud Scan (Java only)
+  #       run: ./gradlew --build-cache compileJava sonar
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
diff --git a/sonar-project.properties b/sonar-project.properties
deleted file mode 100644
index cb8e1d2a1b..0000000000
--- a/sonar-project.properties
+++ /dev/null
@@ -1,7 +0,0 @@
-sonar.projectName=juniper-ui
-sonar.projectKey=broadinstitute_juniper
-sonar.organization=dsp-appsec
-sonar.sources=ui-admin,ui-core
-sonar.sourceEncoding=UTF-8
-
-# TODO sonar.coverage.jacoco.xmlReportPaths
\ No newline at end of file

From c0aab52651d61552eca49abfc5bba763d6eefc87 Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 14:49:14 -0400
Subject: [PATCH 28/83] sonarscanner

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index eba95fb335..6dc83c5629 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -30,9 +30,9 @@ jobs:
         with:
           projectBaseDir: ui-admin/
           args: >
-              -Dsonar.projectName=juniper-ui-admin
+              -Dsonar.projectName=juniper
               -Dsonar.organization=dsp-appsec
-              -Dsonar.projectKey=broadinstitute_juniper-ui-admin
+              -Dsonar.projectKey=broadinstitute_juniper
               -Dsonar.verbose=true
 
   # sonar:

From 3fd955923ebe9ccbf104156ab04de265e19ebdd6 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 13:35:39 -0400
Subject: [PATCH 29/83] work in progress

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .gitignore                   |  3 +++
 api-admin/build.gradle       | 11 -----------
 api-participant/build.gradle |  1 -
 build.gradle                 | 14 ++++++++++++++
 client/build.gradle          | 11 +++++++++++
 core/build.gradle            | 10 ++++++++++
 integration/build.gradle     | 11 +++++++++++
 settings.gradle              |  2 +-
 8 files changed, 50 insertions(+), 13 deletions(-)

diff --git a/.gitignore b/.gitignore
index 19ae5a13e1..b06543d7b0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -42,3 +42,6 @@ npm-debug.log*
 .scannerwork
 .sonar-token
 tmp/
+
+# direnv
+.envrc
diff --git a/api-admin/build.gradle b/api-admin/build.gradle
index 529b310da6..23349bfb8d 100644
--- a/api-admin/build.gradle
+++ b/api-admin/build.gradle
@@ -3,7 +3,6 @@ plugins {
     id 'de.undercouch.download'
     id 'com.google.cloud.tools.jib'
     id 'com.srcclr.gradle'
-    id 'org.sonarqube'
 
     id 'com.gorylenko.gradle-git-properties' version '2.3.1'
 }
@@ -65,13 +64,3 @@ jibDockerBuild.dependsOn('copyWebApp')
 test {
     useJUnitPlatform ()
 }
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-api-admin'
-        property 'sonar.projectKey', 'broadinstitute_juniper-api-admin'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}
diff --git a/api-participant/build.gradle b/api-participant/build.gradle
index 25fc808d4e..b4f1353c4a 100644
--- a/api-participant/build.gradle
+++ b/api-participant/build.gradle
@@ -3,7 +3,6 @@ plugins {
     id 'de.undercouch.download'
     id 'com.google.cloud.tools.jib'
     id 'com.srcclr.gradle'
-    id 'org.sonarqube'
 
     id 'com.gorylenko.gradle-git-properties' version '2.3.1'
 }
diff --git a/build.gradle b/build.gradle
index cde2107918..f950171b13 100644
--- a/build.gradle
+++ b/build.gradle
@@ -16,3 +16,17 @@ task bundleAdminUI(type: NpmTask, dependsOn: [npmInstall, buildUICore]) {
 task bundleParticipantUI(type: NpmTask, dependsOn: [npmInstall, buildUICore]) {
     args = ['--workspace=ui-participant', 'run', 'build']
 }
+
+subprojects {
+    apply plugin: 'org.sonarqube'
+
+    sonar {
+        properties {
+            property 'sonar.projectName', "${rootProject.name}-${project.name}"
+            property 'sonar.projectKey', "broadinstitute_${rootProject.name}-${project.name}"
+            property 'sonar.projectBaseDir', "${projectDir}"
+            property 'sonar.organization', 'broad-databiosphere'
+            property 'sonar.host.url', 'https://sonarcloud.io'
+        }
+    }
+}
diff --git a/client/build.gradle b/client/build.gradle
index 1ed4a117bd..c474db7905 100644
--- a/client/build.gradle
+++ b/client/build.gradle
@@ -6,6 +6,7 @@ plugins {
     id 'io.spring.dependency-management'
     id 'com.jfrog.artifactory' version '4.18.2'
     id 'org.hidetake.swagger.generator'
+    id 'org.sonarqube'
 }
 
 dependencyManagement {
@@ -16,3 +17,13 @@ dependencyManagement {
 
 apply from: 'artifactory.gradle'
 apply from: 'swagger.gradle'
+
+sonar {
+    properties {
+        property 'sonar.projectName', 'juniper-client'
+        property 'sonar.projectKey', 'broadinstitute_juniper-client'
+        property 'sonar.projectBaseDir', '.'
+        property 'sonar.organization', 'broad-databiosphere'
+        property 'sonar.host.url', 'https://sonarcloud.io'
+    }
+}
diff --git a/core/build.gradle b/core/build.gradle
index ca2ff9dfa0..8f449f8e5c 100644
--- a/core/build.gradle
+++ b/core/build.gradle
@@ -3,6 +3,7 @@ plugins {
     id 'java'
     id 'org.liquibase.gradle' version '2.1.0'
     id "java-test-fixtures"
+    id 'org.sonarqube'
 }
 
 group = 'bio.terra.pearl.core'
@@ -56,3 +57,12 @@ test {
     useJUnitPlatform ()
 }
 
+sonar {
+    properties {
+        property 'sonar.projectName', 'juniper-core'
+        property 'sonar.projectKey', 'broadinstitute_juniper-core'
+        property 'sonar.projectBaseDir', '.'
+        property 'sonar.organization', 'broad-databiosphere'
+        property 'sonar.host.url', 'https://sonarcloud.io'
+    }
+}
diff --git a/integration/build.gradle b/integration/build.gradle
index e658872b51..2c8110abea 100644
--- a/integration/build.gradle
+++ b/integration/build.gradle
@@ -4,6 +4,7 @@ plugins {
     id 'bio.terra.java-application-conventions'
     id 'io.spring.dependency-management'
     id 'bio.terra.test-runner-plugin'
+    id 'org.sonarqube'
 }
 
 dependencyManagement {
@@ -29,3 +30,13 @@ dependencies {
     // Requires client libraries
     implementation project(':client')
 }
+
+sonar {
+    properties {
+        property 'sonar.projectName', 'juniper-integration'
+        property 'sonar.projectKey', 'broadinstitute_juniper-integration'
+        property 'sonar.projectBaseDir', '.'
+        property 'sonar.organization', 'broad-databiosphere'
+        property 'sonar.host.url', 'https://sonarcloud.io'
+    }
+}
diff --git a/settings.gradle b/settings.gradle
index b58c8e742f..679ceb7af6 100644
--- a/settings.gradle
+++ b/settings.gradle
@@ -1,4 +1,4 @@
-rootProject.name = 'pearl'
+rootProject.name = 'juniper'
 include('core', 'populate', 'api-admin', 'api-participant')
 
 gradle.ext.releaseVersion = '0.0.85'

From 24d44e675e11074697db455a3cfd5e7f3c03d765 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 17:15:00 -0400
Subject: [PATCH 30/83] multiproject sonar

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .gitignore                   |  3 +++
 api-participant/build.gradle | 10 ----------
 build.gradle                 |  5 ++---
 client/build.gradle          | 11 -----------
 core/build.gradle            | 11 -----------
 integration/build.gradle     | 11 -----------
 populate/build.gradle        | 11 -----------
 7 files changed, 5 insertions(+), 57 deletions(-)

diff --git a/.gitignore b/.gitignore
index b06543d7b0..af6569d321 100644
--- a/.gitignore
+++ b/.gitignore
@@ -45,3 +45,6 @@ tmp/
 
 # direnv
 .envrc
+
+*.hprof
+
diff --git a/api-participant/build.gradle b/api-participant/build.gradle
index b4f1353c4a..c4cce86100 100644
--- a/api-participant/build.gradle
+++ b/api-participant/build.gradle
@@ -60,13 +60,3 @@ jibDockerBuild.dependsOn('copyWebApp')
 test {
     useJUnitPlatform ()
 }
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-api-participant'
-        property 'sonar.projectKey', 'broadinstitute_juniper-api-participant'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}
diff --git a/build.gradle b/build.gradle
index f950171b13..af5012bec4 100644
--- a/build.gradle
+++ b/build.gradle
@@ -17,15 +17,14 @@ task bundleParticipantUI(type: NpmTask, dependsOn: [npmInstall, buildUICore]) {
     args = ['--workspace=ui-participant', 'run', 'build']
 }
 
+apply plugin: 'org.sonarqube'
 subprojects {
-    apply plugin: 'org.sonarqube'
-
     sonar {
         properties {
             property 'sonar.projectName', "${rootProject.name}-${project.name}"
             property 'sonar.projectKey', "broadinstitute_${rootProject.name}-${project.name}"
             property 'sonar.projectBaseDir', "${projectDir}"
-            property 'sonar.organization', 'broad-databiosphere'
+            property 'sonar.organization', 'dsp-appsec'
             property 'sonar.host.url', 'https://sonarcloud.io'
         }
     }
diff --git a/client/build.gradle b/client/build.gradle
index c474db7905..1ed4a117bd 100644
--- a/client/build.gradle
+++ b/client/build.gradle
@@ -6,7 +6,6 @@ plugins {
     id 'io.spring.dependency-management'
     id 'com.jfrog.artifactory' version '4.18.2'
     id 'org.hidetake.swagger.generator'
-    id 'org.sonarqube'
 }
 
 dependencyManagement {
@@ -17,13 +16,3 @@ dependencyManagement {
 
 apply from: 'artifactory.gradle'
 apply from: 'swagger.gradle'
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-client'
-        property 'sonar.projectKey', 'broadinstitute_juniper-client'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}
diff --git a/core/build.gradle b/core/build.gradle
index 8f449f8e5c..40f7c6a14f 100644
--- a/core/build.gradle
+++ b/core/build.gradle
@@ -3,7 +3,6 @@ plugins {
     id 'java'
     id 'org.liquibase.gradle' version '2.1.0'
     id "java-test-fixtures"
-    id 'org.sonarqube'
 }
 
 group = 'bio.terra.pearl.core'
@@ -56,13 +55,3 @@ dependencies {
 test {
     useJUnitPlatform ()
 }
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-core'
-        property 'sonar.projectKey', 'broadinstitute_juniper-core'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}
diff --git a/integration/build.gradle b/integration/build.gradle
index 2c8110abea..e658872b51 100644
--- a/integration/build.gradle
+++ b/integration/build.gradle
@@ -4,7 +4,6 @@ plugins {
     id 'bio.terra.java-application-conventions'
     id 'io.spring.dependency-management'
     id 'bio.terra.test-runner-plugin'
-    id 'org.sonarqube'
 }
 
 dependencyManagement {
@@ -30,13 +29,3 @@ dependencies {
     // Requires client libraries
     implementation project(':client')
 }
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-integration'
-        property 'sonar.projectKey', 'broadinstitute_juniper-integration'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}
diff --git a/populate/build.gradle b/populate/build.gradle
index a1bd2db72f..fa651fa441 100644
--- a/populate/build.gradle
+++ b/populate/build.gradle
@@ -1,7 +1,6 @@
 plugins {
     id "io.freefair.lombok" version "5.3.3.3"
     id 'java'
-    id 'org.sonarqube'
 }
 
 group = 'bio.terra.pearl.core'
@@ -36,13 +35,3 @@ dependencies {
 test {
     useJUnitPlatform ()
 }
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-populate'
-        property 'sonar.projectKey', 'broadinstitute_juniper-populate'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}

From f8e4d1f827c6ecf2435a415785074eff6bfe031d Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 17:43:31 -0400
Subject: [PATCH 31/83] gradle sonar on single bound project

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 48 +-----------------------------------
 build.gradle                 | 20 +++++++--------
 2 files changed, 11 insertions(+), 57 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 6dc83c5629..8c025de952 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -10,53 +10,7 @@ jobs:
         with:
           fetch-depth: 0
       - name: Scan via gradle
-        run: ./gradlew --build-cache compileJava sonar
+        run: ./gradlew --build-cache compileJava sonar -info
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
-  sonar-ui-admin:
-    name: SonarCloud ui-admin
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-      - name: Scan ui-admin via sonarcloud-github-action
-        uses: SonarSource/sonarcloud-github-action@master
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-        with:
-          projectBaseDir: ui-admin/
-          args: >
-              -Dsonar.projectName=juniper
-              -Dsonar.organization=dsp-appsec
-              -Dsonar.projectKey=broadinstitute_juniper
-              -Dsonar.verbose=true
-
-  # sonar:
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v3
-
-  #     - name: Set up JDK
-  #       uses: actions/setup-java@v3
-  #       with:
-  #         java-version: '17'
-  #         distribution: 'temurin'
-  #         cache: 'gradle'
-
-  #     - name: SonarCloud Scan (Typescript only)
-  #       uses: SonarSource/sonarcloud-github-action@master
-  #       env:
-  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
-
-  #     - name: SonarCloud Scan (Java only)
-  #       run: ./gradlew --build-cache compileJava sonar
-  #       env:
-  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
diff --git a/build.gradle b/build.gradle
index af5012bec4..a8c29338d9 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,5 +1,6 @@
 plugins {
     id 'com.github.node-gradle.node' version '5.0.0'
+    id 'org.sonarqube'
 }
 
 apply plugin: 'base'
@@ -17,15 +18,14 @@ task bundleParticipantUI(type: NpmTask, dependsOn: [npmInstall, buildUICore]) {
     args = ['--workspace=ui-participant', 'run', 'build']
 }
 
-apply plugin: 'org.sonarqube'
-subprojects {
-    sonar {
-        properties {
-            property 'sonar.projectName', "${rootProject.name}-${project.name}"
-            property 'sonar.projectKey', "broadinstitute_${rootProject.name}-${project.name}"
-            property 'sonar.projectBaseDir', "${projectDir}"
-            property 'sonar.organization', 'dsp-appsec'
-            property 'sonar.host.url', 'https://sonarcloud.io'
-        }
+sonar {
+    properties {
+        property 'sonar.projectName', "${rootProject.name}"
+        property 'sonar.projectKey', "broadinstitute_${rootProject.name}"
+        property 'sonar.organization', 'dsp-appsec'
+        property 'sonar.host.url', 'https://sonarcloud.io'
     }
 }
+subprojects {
+    apply plugin: 'org.sonarqube'
+}

From 25e12fec91f9218aa746eba8c729aaf8e9c61b98 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 19:10:59 -0400
Subject: [PATCH 32/83] exclude spotless

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 8c025de952..bd3e6fe13e 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -10,7 +10,16 @@ jobs:
         with:
           fetch-depth: 0
       - name: Scan via gradle
-        run: ./gradlew --build-cache compileJava sonar -info
+        run: >-
+          ./gradlew 
+          --build-cache 
+          -x test 
+          -x spotlessJava 
+          -x spotlessJavaApply 
+          -x spotlessJavaCheck 
+          -x spotlessCheck 
+          -x spotlessApply 
+          build sonar -info
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

From 14c05f11c904f8aa64fdadced3605b3b867d71d2 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 19:37:34 -0400
Subject: [PATCH 33/83] include resources in sonar

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 build.gradle | 1 +
 1 file changed, 1 insertion(+)

diff --git a/build.gradle b/build.gradle
index a8c29338d9..4fa3c22c7c 100644
--- a/build.gradle
+++ b/build.gradle
@@ -24,6 +24,7 @@ sonar {
         property 'sonar.projectKey', "broadinstitute_${rootProject.name}"
         property 'sonar.organization', 'dsp-appsec'
         property 'sonar.host.url', 'https://sonarcloud.io'
+        property 'sonar.sources', 'src/main/java,src/main/resources'
     }
 }
 subprojects {

From 166fba7a7916abc49e07d39da9021b9e11a21141 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 19:48:49 -0400
Subject: [PATCH 34/83] include resources in sonar

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 build.gradle | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 4fa3c22c7c..bdbcfae5b3 100644
--- a/build.gradle
+++ b/build.gradle
@@ -24,9 +24,11 @@ sonar {
         property 'sonar.projectKey', "broadinstitute_${rootProject.name}"
         property 'sonar.organization', 'dsp-appsec'
         property 'sonar.host.url', 'https://sonarcloud.io'
-        property 'sonar.sources', 'src/main/java,src/main/resources'
     }
 }
 subprojects {
     apply plugin: 'org.sonarqube'
+    sonar {
+        property 'sonar.sources', 'src/main/java,src/main/resources'
+    }
 }

From 11de4de2a8f56b4db2637d151ad9707b0ba49fb7 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 20:57:55 -0400
Subject: [PATCH 35/83] resources

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 build.gradle | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index bdbcfae5b3..34deabf251 100644
--- a/build.gradle
+++ b/build.gradle
@@ -29,6 +29,8 @@ sonar {
 subprojects {
     apply plugin: 'org.sonarqube'
     sonar {
-        property 'sonar.sources', 'src/main/java,src/main/resources'
+        properties {
+            property 'sonar.sources', 'src/main/java,src/main/resources'
+        }
     }
 }

From bf92e878a4d9297a9ec44bf5127cb5fe9cbb431e Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 21:19:33 -0400
Subject: [PATCH 36/83] gha sonar

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 42 ++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index bd3e6fe13e..47b278d506 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -9,6 +9,23 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
+      - name: Set up JDK 17
+        uses: actions/setup-java@v3
+        with:
+          java-version: '17'
+          distribution: 'adopt'
+      - name: Cache SonarCloud packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.sonar/cache
+          key: ${{ runner.os }}-sonar
+          restore-keys: ${{ runner.os }}-sonar
+      - name: Cache Gradle packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.gradle/caches
+          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
+          restore-keys: ${{ runner.os }}-gradle
       - name: Scan via gradle
         run: >-
           ./gradlew 
@@ -23,3 +40,28 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+
+
+  sonar-typescript:
+    name: SonarCloud ui-admin
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        subproject: ['ui-admin', 'ui-participant']
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Scan ${{ matrix.subproject }} via sonarcloud-github-action
+        uses: SonarSource/sonarcloud-github-action@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        with:
+          projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
+          args: >
+              -Dsonar.projectName=juniper-${{ matrix.subproject }}
+              -Dsonar.organization=dsp-appsec
+              -Dsonar.projectKey=broadinstitute_juniper-${{ matrix.subproject }}
+              -Dsonar.verbose=true

From 5389f6c5a51b34c013958d01f6950670606996b7 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 21:33:57 -0400
Subject: [PATCH 37/83] gha

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml            | 18 +-----------------
 ui-admin/sonar-project.properties       | 13 +++++++++++++
 ui-participant/sonar-project.properties | 13 +++++++++++++
 3 files changed, 27 insertions(+), 17 deletions(-)
 create mode 100644 ui-admin/sonar-project.properties
 create mode 100644 ui-participant/sonar-project.properties

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 47b278d506..09d23b930d 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -14,18 +14,6 @@ jobs:
         with:
           java-version: '17'
           distribution: 'adopt'
-      - name: Cache SonarCloud packages
-        uses: actions/cache@v3
-        with:
-          path: ~/.sonar/cache
-          key: ${{ runner.os }}-sonar
-          restore-keys: ${{ runner.os }}-sonar
-      - name: Cache Gradle packages
-        uses: actions/cache@v3
-        with:
-          path: ~/.gradle/caches
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
-          restore-keys: ${{ runner.os }}-gradle
       - name: Scan via gradle
         run: >-
           ./gradlew 
@@ -43,12 +31,11 @@ jobs:
 
 
   sonar-typescript:
-    name: SonarCloud ui-admin
+    name: SonarCloud TypeScript
     runs-on: ubuntu-latest
     strategy:
       matrix:
         subproject: ['ui-admin', 'ui-participant']
-
     steps:
       - uses: actions/checkout@v3
         with:
@@ -61,7 +48,4 @@ jobs:
         with:
           projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
           args: >
-              -Dsonar.projectName=juniper-${{ matrix.subproject }}
-              -Dsonar.organization=dsp-appsec
-              -Dsonar.projectKey=broadinstitute_juniper-${{ matrix.subproject }}
               -Dsonar.verbose=true
diff --git a/ui-admin/sonar-project.properties b/ui-admin/sonar-project.properties
new file mode 100644
index 0000000000..0ed872c811
--- /dev/null
+++ b/ui-admin/sonar-project.properties
@@ -0,0 +1,13 @@
+sonar.projectKey=broadinstitute_juniper-ui-admin
+sonar.organization=dsp-appsec
+
+# This is the name and version displayed in the SonarCloud UI.
+sonar.projectName=juniper-ui-admin
+#sonar.projectVersion=1.0
+
+
+# Path is relative to the sonar-project.properties file. Replace "\" by "/" on Windows.
+#sonar.sources=.
+
+# Encoding of the source code. Default is default system encoding
+#sonar.sourceEncoding=UTF-8
diff --git a/ui-participant/sonar-project.properties b/ui-participant/sonar-project.properties
new file mode 100644
index 0000000000..d4d36496c4
--- /dev/null
+++ b/ui-participant/sonar-project.properties
@@ -0,0 +1,13 @@
+sonar.projectKey=broadinstitute_juniper-ui-participant
+sonar.organization=dsp-appsec
+
+# This is the name and version displayed in the SonarCloud UI.
+sonar.projectName=juniper-ui-participant
+#sonar.projectVersion=1.0
+
+
+# Path is relative to the sonar-project.properties file. Replace "\" by "/" on Windows.
+#sonar.sources=.
+
+# Encoding of the source code. Default is default system encoding
+#sonar.sourceEncoding=UTF-8

From ec0775cc971305a2e26a7c0b7d63c10e67130334 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 22:10:34 -0400
Subject: [PATCH 38/83] typescript sonar specify branch

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml            |  8 +++++++-
 ui-admin/sonar-project.properties       | 10 ----------
 ui-participant/sonar-project.properties | 10 ----------
 3 files changed, 7 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 09d23b930d..da58be83fc 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -1,5 +1,10 @@
 name: Sonar
 on: workflow_dispatch
+  push:
+    branches:
+      - master
+  pull_request:
+    types: [opened, synchronize, reopened]
 
 jobs:
   sonar-java:
@@ -48,4 +53,5 @@ jobs:
         with:
           projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
           args: >
-              -Dsonar.verbose=true
+              -Dsonar.branch.target=${{ github.event.repository.default_branch }}
+              -Dsonar.branch.name=${{ github.ref_name }}
diff --git a/ui-admin/sonar-project.properties b/ui-admin/sonar-project.properties
index 0ed872c811..2b785ca773 100644
--- a/ui-admin/sonar-project.properties
+++ b/ui-admin/sonar-project.properties
@@ -1,13 +1,3 @@
 sonar.projectKey=broadinstitute_juniper-ui-admin
 sonar.organization=dsp-appsec
-
-# This is the name and version displayed in the SonarCloud UI.
 sonar.projectName=juniper-ui-admin
-#sonar.projectVersion=1.0
-
-
-# Path is relative to the sonar-project.properties file. Replace "\" by "/" on Windows.
-#sonar.sources=.
-
-# Encoding of the source code. Default is default system encoding
-#sonar.sourceEncoding=UTF-8
diff --git a/ui-participant/sonar-project.properties b/ui-participant/sonar-project.properties
index d4d36496c4..1d55561464 100644
--- a/ui-participant/sonar-project.properties
+++ b/ui-participant/sonar-project.properties
@@ -1,13 +1,3 @@
 sonar.projectKey=broadinstitute_juniper-ui-participant
 sonar.organization=dsp-appsec
-
-# This is the name and version displayed in the SonarCloud UI.
 sonar.projectName=juniper-ui-participant
-#sonar.projectVersion=1.0
-
-
-# Path is relative to the sonar-project.properties file. Replace "\" by "/" on Windows.
-#sonar.sources=.
-
-# Encoding of the source code. Default is default system encoding
-#sonar.sourceEncoding=UTF-8

From e240fc75f1b7be1d8296b65fac37e01828a3aa58 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 22:13:58 -0400
Subject: [PATCH 39/83] sonar on push

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index da58be83fc..477faa7783 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -1,5 +1,6 @@
 name: Sonar
-on: workflow_dispatch
+on: 
+  workflow_dispatch:
   push:
     branches:
       - master

From 5d8f8b7a2701b51117314f8dfbb495971ec45d4e Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 22:26:55 -0400
Subject: [PATCH 40/83] sonar on push

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 477faa7783..59f182d13b 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -46,6 +46,9 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
+      - name: Get branch name
+        id: branch-name
+        uses: tj-actions/branch-names@v5
       - name: Scan ${{ matrix.subproject }} via sonarcloud-github-action
         uses: SonarSource/sonarcloud-github-action@master
         env:
@@ -55,4 +58,4 @@ jobs:
           projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
           args: >
               -Dsonar.branch.target=${{ github.event.repository.default_branch }}
-              -Dsonar.branch.name=${{ github.ref_name }}
+              -Dsonar.branch.name=${{ steps.branch-name.outputs.current_branch }}

From 63530f504416087f5429aac087daf260de69e616 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 22:41:49 -0400
Subject: [PATCH 41/83] sonar on push

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 59f182d13b..685f66720a 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -59,3 +59,9 @@ jobs:
           args: >
               -Dsonar.branch.target=${{ github.event.repository.default_branch }}
               -Dsonar.branch.name=${{ steps.branch-name.outputs.current_branch }}
+      - name: Announce
+        run: |
+          gh pr comment ${{ github.event.pull_request.number }} \
+            --body "SonarCloud analyzed branch: ${{ steps.branch-name.outputs.current_branch }}/"
+        env:
+          GH_TOKEN: ${{ github.token }}

From 7a92258e561902abc9b175f8b12f2a60958fb9c3 Mon Sep 17 00:00:00 2001
From: Tom Conner <tconner@broadinstitute.org>
Date: Thu, 27 Jul 2023 21:59:41 -0400
Subject: [PATCH 42/83] announce message

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 685f66720a..29fcd8ef2f 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -62,6 +62,6 @@ jobs:
       - name: Announce
         run: |
           gh pr comment ${{ github.event.pull_request.number }} \
-            --body "SonarCloud analyzed branch: ${{ steps.branch-name.outputs.current_branch }}/"
+            --body "SonarCloud analyzed ${{ matrix.subproject }} on ${{ steps.branch-name.outputs.current_branch }}/"
         env:
           GH_TOKEN: ${{ github.token }}

From fe33a0c351fc846265582027bac51308e2af5172 Mon Sep 17 00:00:00 2001
From: Tom Conner <tconner@broadinstitute.org>
Date: Thu, 27 Jul 2023 22:31:08 -0400
Subject: [PATCH 43/83] revert

---
 .github/workflows/java-ci.yml | 17 +++++++----------
 .github/workflows/ui-ci.yml   | 13 ++++++-------
 README.md                     | 29 ++++++++---------------------
 3 files changed, 21 insertions(+), 38 deletions(-)

diff --git a/.github/workflows/java-ci.yml b/.github/workflows/java-ci.yml
index 2244d35040..96b9df3fab 100644
--- a/.github/workflows/java-ci.yml
+++ b/.github/workflows/java-ci.yml
@@ -12,13 +12,12 @@
 name: Java CI
 
 on:
-  # push:
-  #   branches: [ development ]
-  #   paths-ignore: [ '*.md']
-  # pull_request:
-  #   branches: [ '**' ]
-  # merge_group:
-  workflow_dispatch:
+  push:
+    branches: [ development ]
+    paths-ignore: [ '*.md']
+  pull_request:
+    branches: [ '**' ]
+  merge_group:
 
 jobs:
   build:
@@ -51,12 +50,10 @@ jobs:
           distribution: 'adopt'
       - name: Validate Gradle wrapper
         uses: gradle/wrapper-validation-action@e6e38bacfdf1a337459f332974bb2327a31aaf4b
-      - name: Build and SonarQube scan with Gradle
+      - name: Build with Gradle
         uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
         with:
           arguments: build --info # if you need to see test failure full stacktraces, change this to `build --info`
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
 
   # Need to uncomment these in follow up PR, The new Trivy and Tag workflows need to exist on the development branch
   # before the following steps will work
diff --git a/.github/workflows/ui-ci.yml b/.github/workflows/ui-ci.yml
index 6c45e49525..876acbbb55 100644
--- a/.github/workflows/ui-ci.yml
+++ b/.github/workflows/ui-ci.yml
@@ -1,13 +1,12 @@
 name: UI CI
 
 on:
-  # push:
-  #   branches: [ development ]
-  #   paths-ignore: [ '*.md']
-  # pull_request:
-  #   branches: [ '**' ]
-  # merge_group:
-  workflow_dispatch:
+  push:
+    branches: [ development ]
+    paths-ignore: [ '*.md']
+  pull_request:
+    branches: [ '**' ]
+  merge_group:
 
 jobs:
   build:
diff --git a/README.md b/README.md
index ad0aa66f0a..1fe3ddb85d 100644
--- a/README.md
+++ b/README.md
@@ -29,7 +29,7 @@ DTOs, and populate services.  the PopulateCliApp can be used to populate specifi
    In development, it serves at localhost:8081.  Lives in `api-participant` directory
 ##### Study Manager UI
    Participant UI is a create-react-app SPA.  Lives in `ui-participant` directory.  Serves on localhost:3001 in development
-
+   
 
 
 ## Local development
@@ -47,7 +47,7 @@ run `./local-dev/run_postgres.sh start`
 This will start a postgres container with a schema and user configured
 
 #### IDE Setup
-Open the root folder in IntelliJ.
+Open the root folder in IntelliJ.  
 
 * **server:**
 
@@ -76,15 +76,15 @@ Open the root folder in IntelliJ.
         * set environment variable: `B2C_POLICY_NAME=B2C_1A_ddp_participant_signup_signin_dev`
         * set environment variable: `B2C_CHANGE_PASSWORD_POLICY_NAME=B2C_1A_ddp_participant_change_password_dev`
         * disable launch optimization
-
-
+        
+         
 ### Running the application
 #### Admin tool (study manager, population)
 * API (api-admin module)
 In intelliJ, you can either run ApiAdminApp (from the api-admin module) directly, or execute the "bootRun" gradle task.
 In basic development mode, this will only serve the API, not the frontend assets.
 
-To make the application useful, you will want to populate some users and studies.  After the admin API is running,
+To make the application useful, you will want to populate some users and studies.  After the admin API is running, 
 from the root project directory, run
 ```
 ./scripts/populate_portal.sh ourhealth
@@ -98,7 +98,7 @@ From the command line:
   REACT_APP_B2C_TENANT_NAME=ddpdevb2c REACT_APP_B2C_CLIENT_ID=$(vault read -field value secret/dsp/ddp/b2c/dev/application_id) npm -w ui-admin start
   ```
 (note that you can just run `npm -w ui-admin start` if you don't need to test B2C login functionality)
-Then go to `localhost:3000`
+Then go to `localhost:3000` 
 
 ##### Participant API (api-participant module)
 In intelliJ, you can either run ApiParticipantApp (from the api-participant module) directly, or execute the "bootRun" gradle task.
@@ -118,9 +118,9 @@ Then go to `sandbox.ourhealth.localhost:3001`
 (Notice how you need the environment name and portal name as subdomains)
 
 
-### Feature Development
+### Feature Development 
 
-#### Adding a new model
+#### Adding a new model 
 1. Create the schema, models, and services
    1. Create your POJO model in `core/src/main/java/bio/terra/pearl/core/model`, you will almost certainly want to extend
    `BaseEntity`
@@ -150,16 +150,3 @@ Then go to `sandbox.ourhealth.localhost:3001`
 #### Adding environment variables
   Helm charts:
   https://github.com/broadinstitute/terra-helmfile/tree/master/values/app/d2p/live
-
-
-### SonarCloud code scanning
-
-Because juniper contains TypeScript projects and Java projects, the scans are run independently
-in each project
-
-Typescript UI subprojects (ui-admin, ui-core, and ui-participant) are scanned using the
-SonarCloud GitHub Action. Analysis (SonarCloud
-runs the scan on its own and comments back results to PRs).
-
-Java subprojects (core, client, api-admin, api-participant) are scanned using gradle with the
-sonarqube plugin.
\ No newline at end of file

From 7743265e4f88c77f97ff9f6802e58bd14b85502c Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 13:43:51 -0400
Subject: [PATCH 44/83] separate project sonar scans

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml      | 31 -------------------------------
 ui-admin/sonar-project.properties |  6 ++++++
 2 files changed, 6 insertions(+), 31 deletions(-)
 create mode 100644 ui-admin/sonar-project.properties

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 6dc83c5629..b2102f270a 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -29,34 +29,3 @@ jobs:
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
         with:
           projectBaseDir: ui-admin/
-          args: >
-              -Dsonar.projectName=juniper
-              -Dsonar.organization=dsp-appsec
-              -Dsonar.projectKey=broadinstitute_juniper
-              -Dsonar.verbose=true
-
-  # sonar:
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v3
-
-  #     - name: Set up JDK
-  #       uses: actions/setup-java@v3
-  #       with:
-  #         java-version: '17'
-  #         distribution: 'temurin'
-  #         cache: 'gradle'
-
-  #     - name: SonarCloud Scan (Typescript only)
-  #       uses: SonarSource/sonarcloud-github-action@master
-  #       env:
-  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
-
-  #     - name: SonarCloud Scan (Java only)
-  #       run: ./gradlew --build-cache compileJava sonar
-  #       env:
-  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
diff --git a/ui-admin/sonar-project.properties b/ui-admin/sonar-project.properties
new file mode 100644
index 0000000000..6d4dc573ef
--- /dev/null
+++ b/ui-admin/sonar-project.properties
@@ -0,0 +1,6 @@
+sonar.projectName=juniper-ui-admin
+sonar.projectKey=broadinstitute_juniper-ui-admin
+sonar.organization=dsp-appsec
+sonar.sourceEncoding=UTF-8
+
+# TODO sonar.coverage.jacoco.xmlReportPaths
\ No newline at end of file

From 7d57f7d3931348cc397455621e35ad202c93749d Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 14:01:35 -0400
Subject: [PATCH 45/83] sonar-project.properties at root

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .../sonar-project.properties => sonar-project.properties     | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)
 rename ui-admin/sonar-project.properties => sonar-project.properties (50%)

diff --git a/ui-admin/sonar-project.properties b/sonar-project.properties
similarity index 50%
rename from ui-admin/sonar-project.properties
rename to sonar-project.properties
index 6d4dc573ef..cb8e1d2a1b 100644
--- a/ui-admin/sonar-project.properties
+++ b/sonar-project.properties
@@ -1,6 +1,7 @@
-sonar.projectName=juniper-ui-admin
-sonar.projectKey=broadinstitute_juniper-ui-admin
+sonar.projectName=juniper-ui
+sonar.projectKey=broadinstitute_juniper
 sonar.organization=dsp-appsec
+sonar.sources=ui-admin,ui-core
 sonar.sourceEncoding=UTF-8
 
 # TODO sonar.coverage.jacoco.xmlReportPaths
\ No newline at end of file

From 9a051f7341464cbfdf76639c47164452e023be6b Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 14:12:27 -0400
Subject: [PATCH 46/83] combine all java and combine all typescript

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index b2102f270a..6bc9ab529b 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -9,23 +9,24 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
+      - name: Scan via gradle
+        run: ./gradlew --build-cache compileJava sonar
       - name: Scan via gradle
         run: ./gradlew --build-cache compileJava sonar
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
-  sonar-ui-admin:
-    name: SonarCloud ui-admin
+
+  sonar-typescript:
+    name: SonarCloud TypeScript
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Scan ui-admin via sonarcloud-github-action
+      - name: Scan via sonarcloud-github-action
         uses: SonarSource/sonarcloud-github-action@master
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-        with:
-          projectBaseDir: ui-admin/

From 77927be2bed026dc152397c24ef73550daad6baa Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 14:17:18 -0400
Subject: [PATCH 47/83] sonar typescript

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 6bc9ab529b..98e9605599 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -17,16 +17,18 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
-
-  sonar-typescript:
-    name: SonarCloud TypeScript
+  sonar-ui-admin:
+    name: SonarCloud ui-admin
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Scan via sonarcloud-github-action
+      - name: Scan ui-admin via sonarcloud-github-action
         uses: SonarSource/sonarcloud-github-action@master
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        with:
+          projectBaseDir: ui-admin/
+

From 9564e2f76cc078abbedf63f49d319f0c078ef661 Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 14:46:16 -0400
Subject: [PATCH 48/83] sonar args in workflow

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 30 ++++++++++++++++++++++++++++++
 sonar-project.properties     |  7 -------
 2 files changed, 30 insertions(+), 7 deletions(-)
 delete mode 100644 sonar-project.properties

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 98e9605599..b99aa4095f 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -31,4 +31,34 @@ jobs:
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
         with:
           projectBaseDir: ui-admin/
+          args: >
+              -Dsonar.projectName=juniper-ui-admin
+              -Dsonar.organization=dsp-appsec
+              -Dsonar.projectKey=broadinstitute_juniper-ui-admin
+              -Dsonar.verbose=true
+
+  # sonar:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v3
+
+  #     - name: Set up JDK
+  #       uses: actions/setup-java@v3
+  #       with:
+  #         java-version: '17'
+  #         distribution: 'temurin'
+  #         cache: 'gradle'
+
+  #     - name: SonarCloud Scan (Typescript only)
+  #       uses: SonarSource/sonarcloud-github-action@master
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+
+
+  #     - name: SonarCloud Scan (Java only)
+  #       run: ./gradlew --build-cache compileJava sonar
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
diff --git a/sonar-project.properties b/sonar-project.properties
deleted file mode 100644
index cb8e1d2a1b..0000000000
--- a/sonar-project.properties
+++ /dev/null
@@ -1,7 +0,0 @@
-sonar.projectName=juniper-ui
-sonar.projectKey=broadinstitute_juniper
-sonar.organization=dsp-appsec
-sonar.sources=ui-admin,ui-core
-sonar.sourceEncoding=UTF-8
-
-# TODO sonar.coverage.jacoco.xmlReportPaths
\ No newline at end of file

From 6e9ce5ce369c9493e5354445259b53baa03a3a8a Mon Sep 17 00:00:00 2001
From: TomConner <tconner@broadinstitute.org>
Date: Fri, 21 Jul 2023 14:49:14 -0400
Subject: [PATCH 49/83] sonarscanner

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index b99aa4095f..dc5b3123cc 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -32,9 +32,9 @@ jobs:
         with:
           projectBaseDir: ui-admin/
           args: >
-              -Dsonar.projectName=juniper-ui-admin
+              -Dsonar.projectName=juniper
               -Dsonar.organization=dsp-appsec
-              -Dsonar.projectKey=broadinstitute_juniper-ui-admin
+              -Dsonar.projectKey=broadinstitute_juniper
               -Dsonar.verbose=true
 
   # sonar:

From b26bc64baf2e6388051b173352b2306cbb5a0d35 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 17:15:00 -0400
Subject: [PATCH 50/83] multiproject sonar

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .gitignore                   |  3 +++
 api-participant/build.gradle | 10 ----------
 build.gradle                 |  5 ++---
 client/build.gradle          | 11 -----------
 core/build.gradle            | 11 -----------
 integration/build.gradle     | 11 -----------
 populate/build.gradle        | 11 -----------
 7 files changed, 5 insertions(+), 57 deletions(-)

diff --git a/.gitignore b/.gitignore
index b06543d7b0..af6569d321 100644
--- a/.gitignore
+++ b/.gitignore
@@ -45,3 +45,6 @@ tmp/
 
 # direnv
 .envrc
+
+*.hprof
+
diff --git a/api-participant/build.gradle b/api-participant/build.gradle
index b4f1353c4a..c4cce86100 100644
--- a/api-participant/build.gradle
+++ b/api-participant/build.gradle
@@ -60,13 +60,3 @@ jibDockerBuild.dependsOn('copyWebApp')
 test {
     useJUnitPlatform ()
 }
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-api-participant'
-        property 'sonar.projectKey', 'broadinstitute_juniper-api-participant'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}
diff --git a/build.gradle b/build.gradle
index f950171b13..af5012bec4 100644
--- a/build.gradle
+++ b/build.gradle
@@ -17,15 +17,14 @@ task bundleParticipantUI(type: NpmTask, dependsOn: [npmInstall, buildUICore]) {
     args = ['--workspace=ui-participant', 'run', 'build']
 }
 
+apply plugin: 'org.sonarqube'
 subprojects {
-    apply plugin: 'org.sonarqube'
-
     sonar {
         properties {
             property 'sonar.projectName', "${rootProject.name}-${project.name}"
             property 'sonar.projectKey', "broadinstitute_${rootProject.name}-${project.name}"
             property 'sonar.projectBaseDir', "${projectDir}"
-            property 'sonar.organization', 'broad-databiosphere'
+            property 'sonar.organization', 'dsp-appsec'
             property 'sonar.host.url', 'https://sonarcloud.io'
         }
     }
diff --git a/client/build.gradle b/client/build.gradle
index c474db7905..1ed4a117bd 100644
--- a/client/build.gradle
+++ b/client/build.gradle
@@ -6,7 +6,6 @@ plugins {
     id 'io.spring.dependency-management'
     id 'com.jfrog.artifactory' version '4.18.2'
     id 'org.hidetake.swagger.generator'
-    id 'org.sonarqube'
 }
 
 dependencyManagement {
@@ -17,13 +16,3 @@ dependencyManagement {
 
 apply from: 'artifactory.gradle'
 apply from: 'swagger.gradle'
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-client'
-        property 'sonar.projectKey', 'broadinstitute_juniper-client'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}
diff --git a/core/build.gradle b/core/build.gradle
index 8f449f8e5c..40f7c6a14f 100644
--- a/core/build.gradle
+++ b/core/build.gradle
@@ -3,7 +3,6 @@ plugins {
     id 'java'
     id 'org.liquibase.gradle' version '2.1.0'
     id "java-test-fixtures"
-    id 'org.sonarqube'
 }
 
 group = 'bio.terra.pearl.core'
@@ -56,13 +55,3 @@ dependencies {
 test {
     useJUnitPlatform ()
 }
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-core'
-        property 'sonar.projectKey', 'broadinstitute_juniper-core'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}
diff --git a/integration/build.gradle b/integration/build.gradle
index 2c8110abea..e658872b51 100644
--- a/integration/build.gradle
+++ b/integration/build.gradle
@@ -4,7 +4,6 @@ plugins {
     id 'bio.terra.java-application-conventions'
     id 'io.spring.dependency-management'
     id 'bio.terra.test-runner-plugin'
-    id 'org.sonarqube'
 }
 
 dependencyManagement {
@@ -30,13 +29,3 @@ dependencies {
     // Requires client libraries
     implementation project(':client')
 }
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-integration'
-        property 'sonar.projectKey', 'broadinstitute_juniper-integration'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}
diff --git a/populate/build.gradle b/populate/build.gradle
index a1bd2db72f..fa651fa441 100644
--- a/populate/build.gradle
+++ b/populate/build.gradle
@@ -1,7 +1,6 @@
 plugins {
     id "io.freefair.lombok" version "5.3.3.3"
     id 'java'
-    id 'org.sonarqube'
 }
 
 group = 'bio.terra.pearl.core'
@@ -36,13 +35,3 @@ dependencies {
 test {
     useJUnitPlatform ()
 }
-
-sonar {
-    properties {
-        property 'sonar.projectName', 'juniper-populate'
-        property 'sonar.projectKey', 'broadinstitute_juniper-populate'
-        property 'sonar.projectBaseDir', '.'
-        property 'sonar.organization', 'broad-databiosphere'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}

From 8f95872b7441e213c7497c6d76a0e9f295dc1081 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 17:43:31 -0400
Subject: [PATCH 51/83] gradle sonar on single bound project

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 50 +-----------------------------------
 build.gradle                 | 20 +++++++--------
 2 files changed, 11 insertions(+), 59 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index dc5b3123cc..8c025de952 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -10,55 +10,7 @@ jobs:
         with:
           fetch-depth: 0
       - name: Scan via gradle
-        run: ./gradlew --build-cache compileJava sonar
-      - name: Scan via gradle
-        run: ./gradlew --build-cache compileJava sonar
+        run: ./gradlew --build-cache compileJava sonar -info
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
-  sonar-ui-admin:
-    name: SonarCloud ui-admin
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-      - name: Scan ui-admin via sonarcloud-github-action
-        uses: SonarSource/sonarcloud-github-action@master
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-        with:
-          projectBaseDir: ui-admin/
-          args: >
-              -Dsonar.projectName=juniper
-              -Dsonar.organization=dsp-appsec
-              -Dsonar.projectKey=broadinstitute_juniper
-              -Dsonar.verbose=true
-
-  # sonar:
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v3
-
-  #     - name: Set up JDK
-  #       uses: actions/setup-java@v3
-  #       with:
-  #         java-version: '17'
-  #         distribution: 'temurin'
-  #         cache: 'gradle'
-
-  #     - name: SonarCloud Scan (Typescript only)
-  #       uses: SonarSource/sonarcloud-github-action@master
-  #       env:
-  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
-
-  #     - name: SonarCloud Scan (Java only)
-  #       run: ./gradlew --build-cache compileJava sonar
-  #       env:
-  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-  #         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
diff --git a/build.gradle b/build.gradle
index af5012bec4..a8c29338d9 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,5 +1,6 @@
 plugins {
     id 'com.github.node-gradle.node' version '5.0.0'
+    id 'org.sonarqube'
 }
 
 apply plugin: 'base'
@@ -17,15 +18,14 @@ task bundleParticipantUI(type: NpmTask, dependsOn: [npmInstall, buildUICore]) {
     args = ['--workspace=ui-participant', 'run', 'build']
 }
 
-apply plugin: 'org.sonarqube'
-subprojects {
-    sonar {
-        properties {
-            property 'sonar.projectName', "${rootProject.name}-${project.name}"
-            property 'sonar.projectKey', "broadinstitute_${rootProject.name}-${project.name}"
-            property 'sonar.projectBaseDir', "${projectDir}"
-            property 'sonar.organization', 'dsp-appsec'
-            property 'sonar.host.url', 'https://sonarcloud.io'
-        }
+sonar {
+    properties {
+        property 'sonar.projectName', "${rootProject.name}"
+        property 'sonar.projectKey', "broadinstitute_${rootProject.name}"
+        property 'sonar.organization', 'dsp-appsec'
+        property 'sonar.host.url', 'https://sonarcloud.io'
     }
 }
+subprojects {
+    apply plugin: 'org.sonarqube'
+}

From 7139df98d5e1b5b42696552af651ff23d803528b Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 19:10:59 -0400
Subject: [PATCH 52/83] exclude spotless

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 8c025de952..bd3e6fe13e 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -10,7 +10,16 @@ jobs:
         with:
           fetch-depth: 0
       - name: Scan via gradle
-        run: ./gradlew --build-cache compileJava sonar -info
+        run: >-
+          ./gradlew 
+          --build-cache 
+          -x test 
+          -x spotlessJava 
+          -x spotlessJavaApply 
+          -x spotlessJavaCheck 
+          -x spotlessCheck 
+          -x spotlessApply 
+          build sonar -info
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

From 44739e2592f8a1acb7b3e8df197e396e17ab1b25 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 19:37:34 -0400
Subject: [PATCH 53/83] include resources in sonar

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 build.gradle | 1 +
 1 file changed, 1 insertion(+)

diff --git a/build.gradle b/build.gradle
index a8c29338d9..4fa3c22c7c 100644
--- a/build.gradle
+++ b/build.gradle
@@ -24,6 +24,7 @@ sonar {
         property 'sonar.projectKey', "broadinstitute_${rootProject.name}"
         property 'sonar.organization', 'dsp-appsec'
         property 'sonar.host.url', 'https://sonarcloud.io'
+        property 'sonar.sources', 'src/main/java,src/main/resources'
     }
 }
 subprojects {

From 014f93a2b704eb4794f99a9f0481cc8c05cf95db Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 19:48:49 -0400
Subject: [PATCH 54/83] include resources in sonar

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 build.gradle | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 4fa3c22c7c..bdbcfae5b3 100644
--- a/build.gradle
+++ b/build.gradle
@@ -24,9 +24,11 @@ sonar {
         property 'sonar.projectKey', "broadinstitute_${rootProject.name}"
         property 'sonar.organization', 'dsp-appsec'
         property 'sonar.host.url', 'https://sonarcloud.io'
-        property 'sonar.sources', 'src/main/java,src/main/resources'
     }
 }
 subprojects {
     apply plugin: 'org.sonarqube'
+    sonar {
+        property 'sonar.sources', 'src/main/java,src/main/resources'
+    }
 }

From 46043ed458bec0d5091514052c1fd7f69c412449 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 20:57:55 -0400
Subject: [PATCH 55/83] resources

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 build.gradle | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index bdbcfae5b3..34deabf251 100644
--- a/build.gradle
+++ b/build.gradle
@@ -29,6 +29,8 @@ sonar {
 subprojects {
     apply plugin: 'org.sonarqube'
     sonar {
-        property 'sonar.sources', 'src/main/java,src/main/resources'
+        properties {
+            property 'sonar.sources', 'src/main/java,src/main/resources'
+        }
     }
 }

From a573adbb4211ec91113f49f76e74cff3c49f45d0 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 21:19:33 -0400
Subject: [PATCH 56/83] gha sonar

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 42 ++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index bd3e6fe13e..47b278d506 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -9,6 +9,23 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
+      - name: Set up JDK 17
+        uses: actions/setup-java@v3
+        with:
+          java-version: '17'
+          distribution: 'adopt'
+      - name: Cache SonarCloud packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.sonar/cache
+          key: ${{ runner.os }}-sonar
+          restore-keys: ${{ runner.os }}-sonar
+      - name: Cache Gradle packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.gradle/caches
+          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
+          restore-keys: ${{ runner.os }}-gradle
       - name: Scan via gradle
         run: >-
           ./gradlew 
@@ -23,3 +40,28 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+
+
+  sonar-typescript:
+    name: SonarCloud ui-admin
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        subproject: ['ui-admin', 'ui-participant']
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Scan ${{ matrix.subproject }} via sonarcloud-github-action
+        uses: SonarSource/sonarcloud-github-action@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        with:
+          projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
+          args: >
+              -Dsonar.projectName=juniper-${{ matrix.subproject }}
+              -Dsonar.organization=dsp-appsec
+              -Dsonar.projectKey=broadinstitute_juniper-${{ matrix.subproject }}
+              -Dsonar.verbose=true

From cfe6b3724ad7288352d53715f2493ef70e0bae9d Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 21:33:57 -0400
Subject: [PATCH 57/83] gha

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml            | 18 +-----------------
 ui-admin/sonar-project.properties       | 13 +++++++++++++
 ui-participant/sonar-project.properties | 13 +++++++++++++
 3 files changed, 27 insertions(+), 17 deletions(-)
 create mode 100644 ui-admin/sonar-project.properties
 create mode 100644 ui-participant/sonar-project.properties

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 47b278d506..09d23b930d 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -14,18 +14,6 @@ jobs:
         with:
           java-version: '17'
           distribution: 'adopt'
-      - name: Cache SonarCloud packages
-        uses: actions/cache@v3
-        with:
-          path: ~/.sonar/cache
-          key: ${{ runner.os }}-sonar
-          restore-keys: ${{ runner.os }}-sonar
-      - name: Cache Gradle packages
-        uses: actions/cache@v3
-        with:
-          path: ~/.gradle/caches
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
-          restore-keys: ${{ runner.os }}-gradle
       - name: Scan via gradle
         run: >-
           ./gradlew 
@@ -43,12 +31,11 @@ jobs:
 
 
   sonar-typescript:
-    name: SonarCloud ui-admin
+    name: SonarCloud TypeScript
     runs-on: ubuntu-latest
     strategy:
       matrix:
         subproject: ['ui-admin', 'ui-participant']
-
     steps:
       - uses: actions/checkout@v3
         with:
@@ -61,7 +48,4 @@ jobs:
         with:
           projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
           args: >
-              -Dsonar.projectName=juniper-${{ matrix.subproject }}
-              -Dsonar.organization=dsp-appsec
-              -Dsonar.projectKey=broadinstitute_juniper-${{ matrix.subproject }}
               -Dsonar.verbose=true
diff --git a/ui-admin/sonar-project.properties b/ui-admin/sonar-project.properties
new file mode 100644
index 0000000000..0ed872c811
--- /dev/null
+++ b/ui-admin/sonar-project.properties
@@ -0,0 +1,13 @@
+sonar.projectKey=broadinstitute_juniper-ui-admin
+sonar.organization=dsp-appsec
+
+# This is the name and version displayed in the SonarCloud UI.
+sonar.projectName=juniper-ui-admin
+#sonar.projectVersion=1.0
+
+
+# Path is relative to the sonar-project.properties file. Replace "\" by "/" on Windows.
+#sonar.sources=.
+
+# Encoding of the source code. Default is default system encoding
+#sonar.sourceEncoding=UTF-8
diff --git a/ui-participant/sonar-project.properties b/ui-participant/sonar-project.properties
new file mode 100644
index 0000000000..d4d36496c4
--- /dev/null
+++ b/ui-participant/sonar-project.properties
@@ -0,0 +1,13 @@
+sonar.projectKey=broadinstitute_juniper-ui-participant
+sonar.organization=dsp-appsec
+
+# This is the name and version displayed in the SonarCloud UI.
+sonar.projectName=juniper-ui-participant
+#sonar.projectVersion=1.0
+
+
+# Path is relative to the sonar-project.properties file. Replace "\" by "/" on Windows.
+#sonar.sources=.
+
+# Encoding of the source code. Default is default system encoding
+#sonar.sourceEncoding=UTF-8

From 51f0e3fc5cb6029b0647d311e975fa412e0e6f95 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 22:10:34 -0400
Subject: [PATCH 58/83] typescript sonar specify branch

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml            |  8 +++++++-
 ui-admin/sonar-project.properties       | 10 ----------
 ui-participant/sonar-project.properties | 10 ----------
 3 files changed, 7 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 09d23b930d..da58be83fc 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -1,5 +1,10 @@
 name: Sonar
 on: workflow_dispatch
+  push:
+    branches:
+      - master
+  pull_request:
+    types: [opened, synchronize, reopened]
 
 jobs:
   sonar-java:
@@ -48,4 +53,5 @@ jobs:
         with:
           projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
           args: >
-              -Dsonar.verbose=true
+              -Dsonar.branch.target=${{ github.event.repository.default_branch }}
+              -Dsonar.branch.name=${{ github.ref_name }}
diff --git a/ui-admin/sonar-project.properties b/ui-admin/sonar-project.properties
index 0ed872c811..2b785ca773 100644
--- a/ui-admin/sonar-project.properties
+++ b/ui-admin/sonar-project.properties
@@ -1,13 +1,3 @@
 sonar.projectKey=broadinstitute_juniper-ui-admin
 sonar.organization=dsp-appsec
-
-# This is the name and version displayed in the SonarCloud UI.
 sonar.projectName=juniper-ui-admin
-#sonar.projectVersion=1.0
-
-
-# Path is relative to the sonar-project.properties file. Replace "\" by "/" on Windows.
-#sonar.sources=.
-
-# Encoding of the source code. Default is default system encoding
-#sonar.sourceEncoding=UTF-8
diff --git a/ui-participant/sonar-project.properties b/ui-participant/sonar-project.properties
index d4d36496c4..1d55561464 100644
--- a/ui-participant/sonar-project.properties
+++ b/ui-participant/sonar-project.properties
@@ -1,13 +1,3 @@
 sonar.projectKey=broadinstitute_juniper-ui-participant
 sonar.organization=dsp-appsec
-
-# This is the name and version displayed in the SonarCloud UI.
 sonar.projectName=juniper-ui-participant
-#sonar.projectVersion=1.0
-
-
-# Path is relative to the sonar-project.properties file. Replace "\" by "/" on Windows.
-#sonar.sources=.
-
-# Encoding of the source code. Default is default system encoding
-#sonar.sourceEncoding=UTF-8

From c49b6125fbebe24875d7d000e70ef110e3ca3966 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 22:13:58 -0400
Subject: [PATCH 59/83] sonar on push

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index da58be83fc..477faa7783 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -1,5 +1,6 @@
 name: Sonar
-on: workflow_dispatch
+on: 
+  workflow_dispatch:
   push:
     branches:
       - master

From 8d1492a6cb87402b748b51c325f95b2e0e6f5f3e Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 22:26:55 -0400
Subject: [PATCH 60/83] sonar on push

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 477faa7783..59f182d13b 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -46,6 +46,9 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
+      - name: Get branch name
+        id: branch-name
+        uses: tj-actions/branch-names@v5
       - name: Scan ${{ matrix.subproject }} via sonarcloud-github-action
         uses: SonarSource/sonarcloud-github-action@master
         env:
@@ -55,4 +58,4 @@ jobs:
           projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
           args: >
               -Dsonar.branch.target=${{ github.event.repository.default_branch }}
-              -Dsonar.branch.name=${{ github.ref_name }}
+              -Dsonar.branch.name=${{ steps.branch-name.outputs.current_branch }}

From 61b1e54ba483b2882f2fca713a9261faecb76966 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 22:41:49 -0400
Subject: [PATCH 61/83] sonar on push

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 59f182d13b..685f66720a 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -59,3 +59,9 @@ jobs:
           args: >
               -Dsonar.branch.target=${{ github.event.repository.default_branch }}
               -Dsonar.branch.name=${{ steps.branch-name.outputs.current_branch }}
+      - name: Announce
+        run: |
+          gh pr comment ${{ github.event.pull_request.number }} \
+            --body "SonarCloud analyzed branch: ${{ steps.branch-name.outputs.current_branch }}/"
+        env:
+          GH_TOKEN: ${{ github.token }}

From 9d2a5334617e46f076154c9b0c6761192c4fd021 Mon Sep 17 00:00:00 2001
From: Tom Conner <tconner@broadinstitute.org>
Date: Thu, 27 Jul 2023 21:59:41 -0400
Subject: [PATCH 62/83] announce message

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 685f66720a..29fcd8ef2f 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -62,6 +62,6 @@ jobs:
       - name: Announce
         run: |
           gh pr comment ${{ github.event.pull_request.number }} \
-            --body "SonarCloud analyzed branch: ${{ steps.branch-name.outputs.current_branch }}/"
+            --body "SonarCloud analyzed ${{ matrix.subproject }} on ${{ steps.branch-name.outputs.current_branch }}/"
         env:
           GH_TOKEN: ${{ github.token }}

From 9e76718323c80deda9deee219b61a0c183099e46 Mon Sep 17 00:00:00 2001
From: Devon <devonbush@gmail.com>
Date: Thu, 20 Jul 2023 13:36:13 -0400
Subject: [PATCH 63/83] [JN-490] avoiding error on dupe mailing list signup
 (#482)

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .../MailingListContactController.java         |  9 +++-
 .../service/MailingListContactExtService.java |  7 +++-
 .../MailingListContactExtServiceTests.java    | 42 +++++++++++++++++++
 .../dao/portal/MailingListContactDao.java     |  5 +++
 .../portal/MailingListContactService.java     |  4 ++
 5 files changed, 64 insertions(+), 3 deletions(-)
 create mode 100644 api-participant/src/test/java/bio/terra/pearl/api/participant/service/MailingListContactExtServiceTests.java

diff --git a/api-participant/src/main/java/bio/terra/pearl/api/participant/controller/MailingListContactController.java b/api-participant/src/main/java/bio/terra/pearl/api/participant/controller/MailingListContactController.java
index e5529e885b..ec37e72d99 100644
--- a/api-participant/src/main/java/bio/terra/pearl/api/participant/controller/MailingListContactController.java
+++ b/api-participant/src/main/java/bio/terra/pearl/api/participant/controller/MailingListContactController.java
@@ -32,9 +32,14 @@ public ResponseEntity<Object> create(
       String portalShortcode, String environmentName, MailingListContactDto body) {
     Optional<ParticipantUser> participantUserOpt = requestUtilService.getUserFromRequest(request);
     EnvironmentName envName = EnvironmentName.valueOfCaseInsensitive(environmentName);
+    // do a get or create to avoid leaking information about whether the user has already signed up
     MailingListContact contact =
-        mailingListContactExtService.create(
+        mailingListContactExtService.createOrGet(
             body.getEmail(), body.getName(), portalShortcode, envName, participantUserOpt);
-    return ResponseEntity.ok(contact);
+    // convert to a DTO to avoid leaking when the contact was first created
+    var dto = new MailingListContactDto();
+    dto.setEmail(contact.getEmail());
+    dto.setName(contact.getName());
+    return ResponseEntity.ok(dto);
   }
 }
diff --git a/api-participant/src/main/java/bio/terra/pearl/api/participant/service/MailingListContactExtService.java b/api-participant/src/main/java/bio/terra/pearl/api/participant/service/MailingListContactExtService.java
index 0c71253716..17cc656857 100644
--- a/api-participant/src/main/java/bio/terra/pearl/api/participant/service/MailingListContactExtService.java
+++ b/api-participant/src/main/java/bio/terra/pearl/api/participant/service/MailingListContactExtService.java
@@ -25,7 +25,7 @@ public MailingListContactExtService(
     this.mailingListContactService = mailingListContactService;
   }
 
-  public MailingListContact create(
+  public MailingListContact createOrGet(
       String email,
       String name,
       String portalShortcode,
@@ -33,6 +33,11 @@ public MailingListContact create(
       Optional<ParticipantUser> userOpt) {
     // mailing lists are open-access -- no need to auth anything.  The user is optional
     PortalEnvironment portalEnv = portalEnvironmentService.findOne(portalShortcode, envName).get();
+    Optional<MailingListContact> existing =
+        mailingListContactService.findByPortalEnv(portalEnv.getId(), email);
+    if (existing.isPresent()) {
+      return existing.get();
+    }
     MailingListContact contact =
         MailingListContact.builder()
             .name(name)
diff --git a/api-participant/src/test/java/bio/terra/pearl/api/participant/service/MailingListContactExtServiceTests.java b/api-participant/src/test/java/bio/terra/pearl/api/participant/service/MailingListContactExtServiceTests.java
new file mode 100644
index 0000000000..37a1a87af2
--- /dev/null
+++ b/api-participant/src/test/java/bio/terra/pearl/api/participant/service/MailingListContactExtServiceTests.java
@@ -0,0 +1,42 @@
+package bio.terra.pearl.api.participant.service;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.equalTo;
+
+import bio.terra.pearl.api.participant.BaseSpringBootTest;
+import bio.terra.pearl.core.factory.DaoTestUtils;
+import bio.terra.pearl.core.factory.portal.PortalEnvironmentFactory;
+import bio.terra.pearl.core.model.portal.PortalEnvironment;
+import bio.terra.pearl.core.service.portal.PortalService;
+import java.util.Optional;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+public class MailingListContactExtServiceTests extends BaseSpringBootTest {
+  @Autowired MailingListContactExtService mailingListContactExtService;
+  @Autowired PortalEnvironmentFactory portalEnvironmentFactory;
+  @Autowired PortalService portalService;
+
+  @Test
+  @Transactional
+  public void testGetOrCreate() {
+    PortalEnvironment portalEnv = portalEnvironmentFactory.buildPersisted("testMailingListCreate");
+    String shortcode = portalService.find(portalEnv.getPortalId()).get().getShortcode();
+    var contact =
+        mailingListContactExtService.createOrGet(
+            "test1@test.com",
+            "fakename",
+            shortcode,
+            portalEnv.getEnvironmentName(),
+            Optional.empty());
+    DaoTestUtils.assertGeneratedProperties(contact);
+
+    // check you can create again with same info
+    var contact2 =
+        mailingListContactExtService.createOrGet(
+            "test1@test.com", "fakename", shortcode, portalEnv.getEnvironmentName(), null);
+    DaoTestUtils.assertGeneratedProperties(contact2);
+    assertThat(contact.getId(), equalTo(contact2.getId()));
+  }
+}
diff --git a/core/src/main/java/bio/terra/pearl/core/dao/portal/MailingListContactDao.java b/core/src/main/java/bio/terra/pearl/core/dao/portal/MailingListContactDao.java
index ca05f77048..863d0a03c0 100644
--- a/core/src/main/java/bio/terra/pearl/core/dao/portal/MailingListContactDao.java
+++ b/core/src/main/java/bio/terra/pearl/core/dao/portal/MailingListContactDao.java
@@ -3,6 +3,7 @@
 import bio.terra.pearl.core.dao.BaseJdbiDao;
 import bio.terra.pearl.core.model.portal.MailingListContact;
 import java.util.List;
+import java.util.Optional;
 import java.util.UUID;
 import org.jdbi.v3.core.Jdbi;
 import org.springframework.stereotype.Component;
@@ -22,6 +23,10 @@ public List<MailingListContact> findByPortalEnv(UUID portalEnvId) {
         return findAllByProperty("portal_environment_id", portalEnvId);
     }
 
+    public Optional<MailingListContact> findByPortalEnv(UUID portalEnvId, String emailAddress) {
+        return findByTwoProperties("portal_environment_id", portalEnvId, "email", emailAddress);
+    }
+
     public void deleteByPortalEnvId(UUID portalEnvId) {
         deleteByProperty("portal_environment_id", portalEnvId);
     }
diff --git a/core/src/main/java/bio/terra/pearl/core/service/portal/MailingListContactService.java b/core/src/main/java/bio/terra/pearl/core/service/portal/MailingListContactService.java
index 25753f2fb5..6b0a362f28 100644
--- a/core/src/main/java/bio/terra/pearl/core/service/portal/MailingListContactService.java
+++ b/core/src/main/java/bio/terra/pearl/core/service/portal/MailingListContactService.java
@@ -4,6 +4,7 @@
 import bio.terra.pearl.core.model.portal.MailingListContact;
 import bio.terra.pearl.core.service.ImmutableEntityService;
 import java.util.List;
+import java.util.Optional;
 import java.util.UUID;
 import org.springframework.stereotype.Service;
 
@@ -16,6 +17,9 @@ public MailingListContactService(MailingListContactDao dao) {
     public List<MailingListContact> findByPortalEnv(UUID portalEnvId) {
         return dao.findByPortalEnv(portalEnvId);
     }
+    public Optional<MailingListContact> findByPortalEnv(UUID portalEnvId, String emailAddress) {
+        return dao.findByPortalEnv(portalEnvId, emailAddress);
+    }
     public void deleteByPortalEnvId(UUID portalEnvId) {
         dao.deleteByPortalEnvId(portalEnvId);
     }

From e167a3256ccae6924bb4ce16f964eb324279ad64 Mon Sep 17 00:00:00 2001
From: Devon <devonbush@gmail.com>
Date: Thu, 20 Jul 2023 13:51:19 -0400
Subject: [PATCH 64/83] [JN-477] admin help for export (#481)

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 ui-admin/src/App.tsx                          |   5 +-
 ui-admin/src/help/ExportHelp.tsx              | 115 ++++++++++++++++++
 ui-admin/src/help/HelpPage.tsx                |  12 ++
 ui-admin/src/help/HelpRouter.tsx              |  15 +++
 .../export/ExportDataControl.test.tsx         |  12 +-
 .../participants/export/ExportDataControl.tsx |  13 +-
 6 files changed, 166 insertions(+), 6 deletions(-)
 create mode 100644 ui-admin/src/help/ExportHelp.tsx
 create mode 100644 ui-admin/src/help/HelpPage.tsx
 create mode 100644 ui-admin/src/help/HelpRouter.tsx

diff --git a/ui-admin/src/App.tsx b/ui-admin/src/App.tsx
index 095dd9d144..ea319ac693 100644
--- a/ui-admin/src/App.tsx
+++ b/ui-admin/src/App.tsx
@@ -1,4 +1,4 @@
-import React, { useContext } from 'react'
+import React, { lazy, useContext } from 'react'
 import 'react-notifications-component/dist/theme.css'
 import 'styles/notifications.css'
 import 'survey-core/defaultV2.min.css'
@@ -22,6 +22,7 @@ import UserList from './user/UserList'
 import InvestigatorTermsOfUsePage from './terms/InvestigatorTermsOfUsePage'
 import PrivacyPolicyPage from 'terms/PrivacyPolicyPage'
 import { IdleStatusMonitor } from 'login/IdleStatusMonitor'
+const HelpRouter = lazy(() => import('./help/HelpRouter'))
 
 
 /** container for the app including the router  */
@@ -39,11 +40,13 @@ function App() {
                   <BrowserRouter>
                     <Routes>
                       <Route path="/" element={<PageFrame/>}>
+                        <Route path="help/*" element={<HelpRouter />} />
                         <Route element={<ProtectedRoute/>}>
                           <Route path="users" element={<UserList/>}/>
                           <Route path=":portalShortcode/*" element={<PortalProvider><PortalRouter/></PortalProvider>}/>
                           <Route index element={<PortalList/>}/>
                         </Route>
+
                         <Route path="privacy" element={<PrivacyPolicyPage />} />
                         <Route path="terms" element={<InvestigatorTermsOfUsePage />} />
                         <Route path="*" element={<div>Unknown page</div>}/>
diff --git a/ui-admin/src/help/ExportHelp.tsx b/ui-admin/src/help/ExportHelp.tsx
new file mode 100644
index 0000000000..30802f5db8
--- /dev/null
+++ b/ui-admin/src/help/ExportHelp.tsx
@@ -0,0 +1,115 @@
+import React from 'react'
+
+/** guide to using the participant export/download function */
+export default function ExportHelp() {
+  return <div>
+    <h3>Participant List Export Info</h3>
+    <p>Participant export enables download of tabular files (.tsv or .xlsx) containing all participants
+      except those who have withdrawn from the study.
+            One row will be generated per participant.</p>
+
+    <h4>File format</h4>
+    <div className="panel">
+      <ul>
+        <li>
+          <b>.xlsx</b> will create an Excel spreadsheet of the participant data. Empty cells will represent
+                    null values.
+        </li>
+        <li>
+          <b>.tsv</b> (tab-delimited values). Will export a tab-delimited file. This may be useful in
+                    environments where Excel is unavailable, or if the
+                    number of columns to be exported exceeds 16K. In order to have data be compliant, double-quotes will
+                    be replaced by single quotes, and any values including
+                    tabs or line breaks will be surrounded in double-quotes.
+        </li>
+      </ul>
+
+
+    </div>
+
+    <h4>Human readable / Analysis friendly</h4>
+    <ul>
+      <li>
+        <b>Analysis friendly</b> Each picklist answers will be displayed as a stable id, rather than the
+                displayed text. For multiselects, each answer option will appear in a separate column. For example, the
+                question &quot;Which symptoms have you had?&quot;
+                with options &quot;fever&quot;, &quot;nausea&quot;, and &quot;persisent cough&quot;,
+                will be exported into 3 columns.
+        <table className="table table-striped">
+          <thead>
+            <tr>
+              <td>MEDICAL_HISTORY.SYMTPOMS.FEVER</td>
+              <td>MEDICAL_HISTORY.SYMPTOMS.NAUSEA</td>
+              <td>MEDICAL_HISTORY.SYMPTOMS.COUGH</td>
+            </tr>
+            <tr>
+              <td>fever</td>
+              <td>nausea</td>
+              <td>persistent cough</td>
+            </tr>
+          </thead>
+          <tbody>
+            <tr>
+              <td>0</td>
+              <td>1</td>
+              <td>0</td>
+            </tr>
+            <tr>
+              <td>1</td>
+              <td>1</td>
+              <td>0</td>
+            </tr>
+            <tr>
+              <td>0</td>
+              <td>0</td>
+              <td>0</td>
+            </tr>
+          </tbody>
+        </table>
+
+      </li>
+      <li>
+        <b>Human readable</b> will use display text where possible, and will show multi-select questions as a
+                single column, with a comma-delimited string of the answers given. For example, the question &quot;Which
+                symptoms have you had?&quot;
+                with options &quot;fever&quot;, &quot;nausea&quot;, and &quot;persisent cough&quot;,
+                will be exported into 1 column.
+        <table className="table table-striped">
+          <thead>
+            <tr>
+              <td>MEDICAL_HISTORY.SYMTPOMS</td>
+            </tr>
+            <tr>
+              <td>symptoms</td>
+            </tr>
+          </thead>
+          <tbody>
+            <tr>
+              <td>nausea</td>
+            </tr>
+            <tr>
+              <td>fever, nausea</td>
+            </tr>
+            <tr>
+              <td></td>
+            </tr>
+          </tbody>
+        </table>
+      </li>
+    </ul>
+    <h4>Include all completions of an activity</h4>
+        This option controls how the export will behave if a participant has completed an activity multiple times.
+    <ul>
+      <li>
+        <b>Yes</b> A new set of columns will be added to the export for each time the activity was completed.
+                These will be
+                denoted by _2, _3, etc... Columns will appear in order of *recency*. So e.g. MEDICAL_HISTORY.SYMPTOMS
+                represents the
+                most recent completion, while MEDICAL_HISTORY_2.SYMPTOMS represents the next-most recent, and so on.
+      </li>
+      <li>
+        <b>No</b> Only the most recent completion for each activity will be included in the export.
+      </li>
+    </ul>
+  </div>
+}
diff --git a/ui-admin/src/help/HelpPage.tsx b/ui-admin/src/help/HelpPage.tsx
new file mode 100644
index 0000000000..31f39f528b
--- /dev/null
+++ b/ui-admin/src/help/HelpPage.tsx
@@ -0,0 +1,12 @@
+import React from 'react'
+import { Link } from 'react-router-dom'
+
+/** shows the root help page.  No structure yet */
+export default function HelpPage() {
+  return <div>
+    <h1 className="h3 mb-3">Juniper help topics</h1>
+    <div>
+      <Link to="export">Participant export</Link>
+    </div>
+  </div>
+}
diff --git a/ui-admin/src/help/HelpRouter.tsx b/ui-admin/src/help/HelpRouter.tsx
new file mode 100644
index 0000000000..caaaab66ab
--- /dev/null
+++ b/ui-admin/src/help/HelpRouter.tsx
@@ -0,0 +1,15 @@
+import React from 'react'
+import { Route, Routes } from 'react-router-dom'
+import ExportHelp from './ExportHelp'
+import HelpPage from './HelpPage'
+
+/** routes across individual help pages -- catches any unmatched routes to the main index */
+export default function HelpRouter() {
+  return <div className="container p-4">
+    <Routes>
+      <Route path="export" element={<ExportHelp/>}/>
+      <Route index element={<HelpPage/>}/>
+      <Route path="*" element={<HelpPage/>}/>
+    </Routes>
+  </div>
+}
diff --git a/ui-admin/src/study/participants/export/ExportDataControl.test.tsx b/ui-admin/src/study/participants/export/ExportDataControl.test.tsx
index ec245cbe7e..f177289d58 100644
--- a/ui-admin/src/study/participants/export/ExportDataControl.test.tsx
+++ b/ui-admin/src/study/participants/export/ExportDataControl.test.tsx
@@ -2,8 +2,9 @@ import React from 'react'
 
 import { setupRouterTest } from 'test-utils/router-testing-utils'
 import { mockStudyEnvContext } from 'test-utils/mocking-utils'
-import { render, screen } from '@testing-library/react'
+import { render, screen, waitFor } from '@testing-library/react'
 import ExportDataControl from './ExportDataControl'
+import userEvent from '@testing-library/user-event'
 
 test('renders the file types', async () => {
   const { RoutedComponent } = setupRouterTest(
@@ -13,3 +14,12 @@ test('renders the file types', async () => {
   expect(screen.getByText('Tab-delimted (.tsv)')).toBeInTheDocument()
   expect(screen.getByText('Excel (.xlsx)')).toBeInTheDocument()
 })
+
+test('help page loads', async () => {
+  const { RoutedComponent } = setupRouterTest(
+    // eslint-disable-next-line @typescript-eslint/no-empty-function
+    <ExportDataControl studyEnvContext={mockStudyEnvContext()} show={true} setShow={() => {}}/>)
+  render(RoutedComponent)
+  userEvent.click(screen.getByText('help page'))
+  waitFor(() => expect(screen.getByText('Participant List Export Info')).toBeInTheDocument())
+})
diff --git a/ui-admin/src/study/participants/export/ExportDataControl.tsx b/ui-admin/src/study/participants/export/ExportDataControl.tsx
index 23beedc1f8..fabbd25517 100644
--- a/ui-admin/src/study/participants/export/ExportDataControl.tsx
+++ b/ui-admin/src/study/participants/export/ExportDataControl.tsx
@@ -6,6 +6,7 @@ import Api from 'api/api'
 import { currentIsoDate } from 'util/timeUtils'
 import { failureNotification } from 'util/notifications'
 import { Store } from 'react-notifications-component'
+import { Link } from 'react-router-dom'
 
 const FILE_FORMATS = [{
   label: 'Tab-delimted (.tsv)',
@@ -74,10 +75,9 @@ const ExportDataControl = ({ studyEnvContext, show, setShow }: {studyEnvContext:
 
   return <Modal show={show} onHide={() => setShow(false)}>
     <Modal.Header closeButton>
-      <Modal.Title>Download</Modal.Title>
-      <div className="ms-4">
-        {studyEnvContext.study.name}: {studyEnvContext.currentEnv.environmentName}
-      </div>
+      <Modal.Title>
+        Download
+      </Modal.Title>
     </Modal.Header>
     <Modal.Body>
       <form onSubmit={e => e.preventDefault()}>
@@ -114,6 +114,11 @@ const ExportDataControl = ({ studyEnvContext, show, setShow }: {studyEnvContext:
             {format.label}
           </label>)}
         </div>
+        <hr/>
+        <div>
+          For more information about download formats,
+          see the <Link to={'/help/export'} target="_blank">help page</Link>.
+        </div>
       </form>
     </Modal.Body>
     <Modal.Footer>

From 277da84244ca17180ff7d45de755ffda2e2195f6 Mon Sep 17 00:00:00 2001
From: Matt Bemis <MatthewBemis@users.noreply.github.com>
Date: Thu, 27 Jul 2023 15:22:37 -0400
Subject: [PATCH 65/83] [JN-453] Preserve fields when switching question types
 in new question form (#485)

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .../src/forms/designer/NewQuestionForm.tsx    | 48 +++----------
 .../designer/questions/questionTypes.tsx      | 70 ++++++++++++++++++-
 2 files changed, 77 insertions(+), 41 deletions(-)

diff --git a/ui-admin/src/forms/designer/NewQuestionForm.tsx b/ui-admin/src/forms/designer/NewQuestionForm.tsx
index 5140083731..8c657a9e99 100644
--- a/ui-admin/src/forms/designer/NewQuestionForm.tsx
+++ b/ui-admin/src/forms/designer/NewQuestionForm.tsx
@@ -5,6 +5,8 @@ import { Question, QuestionType } from '@juniper/ui-core'
 import { Button } from 'components/forms/Button'
 import { QuestionDesigner } from './QuestionDesigner'
 import { TextInput } from 'components/forms/TextInput'
+import { baseQuestions } from './questions/questionTypes'
+import _ from 'lodash'
 
 type NewQuestionFormProps = {
     onCreate: (newQuestion: Question) => void
@@ -15,45 +17,9 @@ type NewQuestionFormProps = {
 export const NewQuestionForm = (props: NewQuestionFormProps) => {
   const { onCreate, readOnly } = props
   const [selectedQuestionType, setSelectedQuestionType] = useState<QuestionType>('text')
-  const [questionName, setQuestionName] = useState<string>('')
-
-  const baseQuestions: Record<QuestionType, Question> = {
-    checkbox: {
-      type: 'checkbox',
-      name: questionName,
-      title: '',
-      choices: []
-    },
-    dropdown: {
-      type: 'dropdown',
-      name: questionName,
-      title: '',
-      choices: []
-    },
-    medications: {
-      type: 'medications',
-      name: questionName,
-      title: ''
-    },
-    radiogroup: {
-      type: 'radiogroup',
-      name: questionName,
-      title: '',
-      choices: []
-    },
-    signaturepad: {
-      type: 'signaturepad',
-      name: questionName,
-      title: ''
-    },
-    text: {
-      type: 'text',
-      name: questionName,
-      title: ''
-    }
-  }
 
   const [question, setQuestion] = useState<Question>(baseQuestions[selectedQuestionType])
+  const { name: questionName } = question
 
   return (
     <>
@@ -65,7 +31,6 @@ export const NewQuestionForm = (props: NewQuestionFormProps) => {
               label='Question stable ID'
               value={questionName}
               onChange={value => {
-                setQuestionName(value)
                 setQuestion({ ...question, name: value })
               }}
             />
@@ -75,7 +40,7 @@ export const NewQuestionForm = (props: NewQuestionFormProps) => {
             onChange={e => {
               const newQuestionType = e.target.value as QuestionType
               setSelectedQuestionType(newQuestionType)
-              setQuestion(baseQuestions[newQuestionType])
+              setQuestion({ ...baseQuestions[newQuestionType], ...question, type: newQuestionType } as Question)
             }}>
             <option value="text">Text</option>
             <option value="checkbox">Checkbox</option>
@@ -98,7 +63,10 @@ export const NewQuestionForm = (props: NewQuestionFormProps) => {
         <Button
           variant="primary"
           onClick={() => {
-            onCreate(question)
+            //While preserving the state during editing, we may have accumulated some extra fields
+            //that don't exist on the final question type. So we need to remove them before saving.
+            const sanitizedQuestion = _.pick(question, Object.keys(baseQuestions[selectedQuestionType])) as Question
+            onCreate(sanitizedQuestion)
           }}
         >
           Create question
diff --git a/ui-admin/src/forms/designer/questions/questionTypes.tsx b/ui-admin/src/forms/designer/questions/questionTypes.tsx
index 50b44a886c..adf753af15 100644
--- a/ui-admin/src/forms/designer/questions/questionTypes.tsx
+++ b/ui-admin/src/forms/designer/questions/questionTypes.tsx
@@ -1,4 +1,4 @@
-import { QuestionType } from '@juniper/ui-core'
+import { Question, QuestionType } from '@juniper/ui-core'
 
 export const questionTypeLabels: Record<QuestionType, string> = {
   text: 'Text',
@@ -17,3 +17,71 @@ export const questionTypeDescriptions: Record<QuestionType, string> = {
   signaturepad: 'Prompts the participant to sign a form.',
   medications: 'Prompts the participant to choose medications from a list.'
 }
+
+//Returns an object with all possible fields for each question type
+export const baseQuestions: Record<QuestionType, Question> = {
+  checkbox: {
+    type: 'checkbox',
+    name: '',
+    title: '',
+    description: '',
+    isRequired: false,
+    choices: [],
+    showNoneItem: undefined,
+    noneText: undefined,
+    noneValue: undefined,
+    showOtherItem: undefined,
+    otherText: undefined,
+    otherPlaceholder: undefined,
+    otherErrorText: undefined
+  },
+  dropdown: {
+    type: 'dropdown',
+    name: '',
+    title: '',
+    description: '',
+    isRequired: false,
+    choices: [],
+    showOtherItem: undefined,
+    otherText: undefined,
+    otherPlaceholder: undefined,
+    otherErrorText: undefined
+  },
+  medications: {
+    type: 'medications',
+    name: '',
+    title: '',
+    description: '',
+    isRequired: false
+  },
+  radiogroup: {
+    type: 'radiogroup',
+    name: '',
+    title: '',
+    description: '',
+    isRequired: false,
+    choices: [],
+    showOtherItem: undefined,
+    otherText: undefined,
+    otherPlaceholder: undefined,
+    otherErrorText: undefined
+  },
+  signaturepad: {
+    type: 'signaturepad',
+    name: '',
+    title: '',
+    description: '',
+    isRequired: false
+  },
+  text: {
+    type: 'text',
+    name: '',
+    title: '',
+    description: '',
+    isRequired: false,
+    inputType: 'text',
+    min: undefined,
+    max: undefined,
+    size: undefined
+  }
+}

From edf05e84f5f88a830a50c2fcdefa9fa392bbaf48 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 17:15:00 -0400
Subject: [PATCH 66/83] multiproject sonar

---
 build.gradle | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/build.gradle b/build.gradle
index 34deabf251..6d789d58dd 100644
--- a/build.gradle
+++ b/build.gradle
@@ -18,19 +18,15 @@ task bundleParticipantUI(type: NpmTask, dependsOn: [npmInstall, buildUICore]) {
     args = ['--workspace=ui-participant', 'run', 'build']
 }
 
-sonar {
-    properties {
-        property 'sonar.projectName', "${rootProject.name}"
-        property 'sonar.projectKey', "broadinstitute_${rootProject.name}"
-        property 'sonar.organization', 'dsp-appsec'
-        property 'sonar.host.url', 'https://sonarcloud.io'
-    }
-}
+apply plugin: 'org.sonarqube'
 subprojects {
-    apply plugin: 'org.sonarqube'
     sonar {
         properties {
-            property 'sonar.sources', 'src/main/java,src/main/resources'
+            property 'sonar.projectName', "${rootProject.name}-${project.name}"
+            property 'sonar.projectKey', "broadinstitute_${rootProject.name}-${project.name}"
+            property 'sonar.projectBaseDir', "${projectDir}"
+            property 'sonar.organization', 'dsp-appsec'
+            property 'sonar.host.url', 'https://sonarcloud.io'
         }
     }
 }

From ae9c4a57a1e5f2564589ee981993dbdc00fe24dc Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 17:43:31 -0400
Subject: [PATCH 67/83] gradle sonar on single bound project

---
 .github/workflows/sonar.yaml | 24 +++++++++---------------
 build.gradle                 | 19 +++++++++----------
 2 files changed, 18 insertions(+), 25 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 29fcd8ef2f..ffb80bcfdd 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -1,11 +1,5 @@
 name: Sonar
-on: 
-  workflow_dispatch:
-  push:
-    branches:
-      - master
-  pull_request:
-    types: [opened, synchronize, reopened]
+on: workflow_dispatch
 
 jobs:
   sonar-java:
@@ -22,14 +16,14 @@ jobs:
           distribution: 'adopt'
       - name: Scan via gradle
         run: >-
-          ./gradlew 
-          --build-cache 
-          -x test 
-          -x spotlessJava 
-          -x spotlessJavaApply 
-          -x spotlessJavaCheck 
-          -x spotlessCheck 
-          -x spotlessApply 
+          ./gradlew
+          --build-cache
+          -x test
+          -x spotlessJava
+          -x spotlessJavaApply
+          -x spotlessJavaCheck
+          -x spotlessCheck
+          -x spotlessApply
           build sonar -info
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
diff --git a/build.gradle b/build.gradle
index 6d789d58dd..a8c29338d9 100644
--- a/build.gradle
+++ b/build.gradle
@@ -18,15 +18,14 @@ task bundleParticipantUI(type: NpmTask, dependsOn: [npmInstall, buildUICore]) {
     args = ['--workspace=ui-participant', 'run', 'build']
 }
 
-apply plugin: 'org.sonarqube'
-subprojects {
-    sonar {
-        properties {
-            property 'sonar.projectName', "${rootProject.name}-${project.name}"
-            property 'sonar.projectKey', "broadinstitute_${rootProject.name}-${project.name}"
-            property 'sonar.projectBaseDir', "${projectDir}"
-            property 'sonar.organization', 'dsp-appsec'
-            property 'sonar.host.url', 'https://sonarcloud.io'
-        }
+sonar {
+    properties {
+        property 'sonar.projectName', "${rootProject.name}"
+        property 'sonar.projectKey', "broadinstitute_${rootProject.name}"
+        property 'sonar.organization', 'dsp-appsec'
+        property 'sonar.host.url', 'https://sonarcloud.io'
     }
 }
+subprojects {
+    apply plugin: 'org.sonarqube'
+}

From a5b8fe843e01ebc9cadcf80208979929d25fa4fa Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 19:37:34 -0400
Subject: [PATCH 68/83] include resources in sonar

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 build.gradle | 1 +
 1 file changed, 1 insertion(+)

diff --git a/build.gradle b/build.gradle
index a8c29338d9..4fa3c22c7c 100644
--- a/build.gradle
+++ b/build.gradle
@@ -24,6 +24,7 @@ sonar {
         property 'sonar.projectKey', "broadinstitute_${rootProject.name}"
         property 'sonar.organization', 'dsp-appsec'
         property 'sonar.host.url', 'https://sonarcloud.io'
+        property 'sonar.sources', 'src/main/java,src/main/resources'
     }
 }
 subprojects {

From d6cfbc8738ac6d9d682d6dfaf9d317235b29104d Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 19:48:49 -0400
Subject: [PATCH 69/83] include resources in sonar

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 build.gradle | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 4fa3c22c7c..bdbcfae5b3 100644
--- a/build.gradle
+++ b/build.gradle
@@ -24,9 +24,11 @@ sonar {
         property 'sonar.projectKey', "broadinstitute_${rootProject.name}"
         property 'sonar.organization', 'dsp-appsec'
         property 'sonar.host.url', 'https://sonarcloud.io'
-        property 'sonar.sources', 'src/main/java,src/main/resources'
     }
 }
 subprojects {
     apply plugin: 'org.sonarqube'
+    sonar {
+        property 'sonar.sources', 'src/main/java,src/main/resources'
+    }
 }

From ff52e8c4ec20f5d0562c605450a81558d4939e5e Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 20:57:55 -0400
Subject: [PATCH 70/83] resources

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 build.gradle | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index bdbcfae5b3..34deabf251 100644
--- a/build.gradle
+++ b/build.gradle
@@ -29,6 +29,8 @@ sonar {
 subprojects {
     apply plugin: 'org.sonarqube'
     sonar {
-        property 'sonar.sources', 'src/main/java,src/main/resources'
+        properties {
+            property 'sonar.sources', 'src/main/java,src/main/resources'
+        }
     }
 }

From e379527e10c3232c0b5f9b5c50247889d1d164f8 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 21:19:33 -0400
Subject: [PATCH 71/83] gha sonar

---
 .github/workflows/sonar.yaml | 30 ++++++++++++++++++------------
 1 file changed, 18 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index ffb80bcfdd..807cd8179f 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -14,6 +14,18 @@ jobs:
         with:
           java-version: '17'
           distribution: 'adopt'
+      - name: Cache SonarCloud packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.sonar/cache
+          key: ${{ runner.os }}-sonar
+          restore-keys: ${{ runner.os }}-sonar
+      - name: Cache Gradle packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.gradle/caches
+          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
+          restore-keys: ${{ runner.os }}-gradle
       - name: Scan via gradle
         run: >-
           ./gradlew
@@ -31,18 +43,16 @@ jobs:
 
 
   sonar-typescript:
-    name: SonarCloud TypeScript
+    name: SonarCloud ui-admin
     runs-on: ubuntu-latest
     strategy:
       matrix:
         subproject: ['ui-admin', 'ui-participant']
+
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Get branch name
-        id: branch-name
-        uses: tj-actions/branch-names@v5
       - name: Scan ${{ matrix.subproject }} via sonarcloud-github-action
         uses: SonarSource/sonarcloud-github-action@master
         env:
@@ -51,11 +61,7 @@ jobs:
         with:
           projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
           args: >
-              -Dsonar.branch.target=${{ github.event.repository.default_branch }}
-              -Dsonar.branch.name=${{ steps.branch-name.outputs.current_branch }}
-      - name: Announce
-        run: |
-          gh pr comment ${{ github.event.pull_request.number }} \
-            --body "SonarCloud analyzed ${{ matrix.subproject }} on ${{ steps.branch-name.outputs.current_branch }}/"
-        env:
-          GH_TOKEN: ${{ github.token }}
+              -Dsonar.projectName=juniper-${{ matrix.subproject }}
+              -Dsonar.organization=dsp-appsec
+              -Dsonar.projectKey=broadinstitute_juniper-${{ matrix.subproject }}
+              -Dsonar.verbose=true

From d2f7e14cc160e7076ef63e4373e021b1a1139d8b Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 21:33:57 -0400
Subject: [PATCH 72/83] gha

---
 .github/workflows/sonar.yaml | 18 +-----------------
 1 file changed, 1 insertion(+), 17 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 807cd8179f..957a880257 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -14,18 +14,6 @@ jobs:
         with:
           java-version: '17'
           distribution: 'adopt'
-      - name: Cache SonarCloud packages
-        uses: actions/cache@v3
-        with:
-          path: ~/.sonar/cache
-          key: ${{ runner.os }}-sonar
-          restore-keys: ${{ runner.os }}-sonar
-      - name: Cache Gradle packages
-        uses: actions/cache@v3
-        with:
-          path: ~/.gradle/caches
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
-          restore-keys: ${{ runner.os }}-gradle
       - name: Scan via gradle
         run: >-
           ./gradlew
@@ -43,12 +31,11 @@ jobs:
 
 
   sonar-typescript:
-    name: SonarCloud ui-admin
+    name: SonarCloud TypeScript
     runs-on: ubuntu-latest
     strategy:
       matrix:
         subproject: ['ui-admin', 'ui-participant']
-
     steps:
       - uses: actions/checkout@v3
         with:
@@ -61,7 +48,4 @@ jobs:
         with:
           projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
           args: >
-              -Dsonar.projectName=juniper-${{ matrix.subproject }}
-              -Dsonar.organization=dsp-appsec
-              -Dsonar.projectKey=broadinstitute_juniper-${{ matrix.subproject }}
               -Dsonar.verbose=true

From 3041c6bdb8638630c972cd6340dc9df16018deef Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 22:10:34 -0400
Subject: [PATCH 73/83] typescript sonar specify branch

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 957a880257..478cd69244 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -1,5 +1,10 @@
 name: Sonar
 on: workflow_dispatch
+  push:
+    branches:
+      - master
+  pull_request:
+    types: [opened, synchronize, reopened]
 
 jobs:
   sonar-java:
@@ -48,4 +53,5 @@ jobs:
         with:
           projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
           args: >
-              -Dsonar.verbose=true
+              -Dsonar.branch.target=${{ github.event.repository.default_branch }}
+              -Dsonar.branch.name=${{ github.ref_name }}

From 088f9ecf67c41ebd6b26460c84f6be76ea540d81 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 22:13:58 -0400
Subject: [PATCH 74/83] sonar on push

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 478cd69244..f915a4a8e6 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -1,5 +1,6 @@
 name: Sonar
-on: workflow_dispatch
+on: 
+  workflow_dispatch:
   push:
     branches:
       - master

From e038f2818ff51420832050f29ba32a58eb8bfa0e Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 22:26:55 -0400
Subject: [PATCH 75/83] sonar on push

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index f915a4a8e6..027127683b 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -46,6 +46,9 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
+      - name: Get branch name
+        id: branch-name
+        uses: tj-actions/branch-names@v5
       - name: Scan ${{ matrix.subproject }} via sonarcloud-github-action
         uses: SonarSource/sonarcloud-github-action@master
         env:
@@ -55,4 +58,4 @@ jobs:
           projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
           args: >
               -Dsonar.branch.target=${{ github.event.repository.default_branch }}
-              -Dsonar.branch.name=${{ github.ref_name }}
+              -Dsonar.branch.name=${{ steps.branch-name.outputs.current_branch }}

From 1198dc1d5706ae3649145342c3b1bfa680a56046 Mon Sep 17 00:00:00 2001
From: TomConner <tomconner46@gmail.com>
Date: Mon, 24 Jul 2023 22:41:49 -0400
Subject: [PATCH 76/83] sonar on push

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/sonar.yaml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 027127683b..6f0eaf7080 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -59,3 +59,9 @@ jobs:
           args: >
               -Dsonar.branch.target=${{ github.event.repository.default_branch }}
               -Dsonar.branch.name=${{ steps.branch-name.outputs.current_branch }}
+      - name: Announce
+        run: |
+          gh pr comment ${{ github.event.pull_request.number }} \
+            --body "SonarCloud analyzed branch: ${{ steps.branch-name.outputs.current_branch }}/"
+        env:
+          GH_TOKEN: ${{ github.token }}

From 01bec4d35513651dc93596dc8808afe0f60e812f Mon Sep 17 00:00:00 2001
From: Tom Conner <tconner@broadinstitute.org>
Date: Thu, 27 Jul 2023 22:31:08 -0400
Subject: [PATCH 77/83] revert

Signed-off-by: Tom Conner <tconner@broadinstitute.org>
---
 .github/workflows/java-ci.yml | 17 +++++++----------
 .github/workflows/ui-ci.yml   | 13 ++++++-------
 README.md                     | 29 ++++++++---------------------
 3 files changed, 21 insertions(+), 38 deletions(-)

diff --git a/.github/workflows/java-ci.yml b/.github/workflows/java-ci.yml
index 2244d35040..96b9df3fab 100644
--- a/.github/workflows/java-ci.yml
+++ b/.github/workflows/java-ci.yml
@@ -12,13 +12,12 @@
 name: Java CI
 
 on:
-  # push:
-  #   branches: [ development ]
-  #   paths-ignore: [ '*.md']
-  # pull_request:
-  #   branches: [ '**' ]
-  # merge_group:
-  workflow_dispatch:
+  push:
+    branches: [ development ]
+    paths-ignore: [ '*.md']
+  pull_request:
+    branches: [ '**' ]
+  merge_group:
 
 jobs:
   build:
@@ -51,12 +50,10 @@ jobs:
           distribution: 'adopt'
       - name: Validate Gradle wrapper
         uses: gradle/wrapper-validation-action@e6e38bacfdf1a337459f332974bb2327a31aaf4b
-      - name: Build and SonarQube scan with Gradle
+      - name: Build with Gradle
         uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
         with:
           arguments: build --info # if you need to see test failure full stacktraces, change this to `build --info`
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
 
   # Need to uncomment these in follow up PR, The new Trivy and Tag workflows need to exist on the development branch
   # before the following steps will work
diff --git a/.github/workflows/ui-ci.yml b/.github/workflows/ui-ci.yml
index 6c45e49525..876acbbb55 100644
--- a/.github/workflows/ui-ci.yml
+++ b/.github/workflows/ui-ci.yml
@@ -1,13 +1,12 @@
 name: UI CI
 
 on:
-  # push:
-  #   branches: [ development ]
-  #   paths-ignore: [ '*.md']
-  # pull_request:
-  #   branches: [ '**' ]
-  # merge_group:
-  workflow_dispatch:
+  push:
+    branches: [ development ]
+    paths-ignore: [ '*.md']
+  pull_request:
+    branches: [ '**' ]
+  merge_group:
 
 jobs:
   build:
diff --git a/README.md b/README.md
index ad0aa66f0a..1fe3ddb85d 100644
--- a/README.md
+++ b/README.md
@@ -29,7 +29,7 @@ DTOs, and populate services.  the PopulateCliApp can be used to populate specifi
    In development, it serves at localhost:8081.  Lives in `api-participant` directory
 ##### Study Manager UI
    Participant UI is a create-react-app SPA.  Lives in `ui-participant` directory.  Serves on localhost:3001 in development
-
+   
 
 
 ## Local development
@@ -47,7 +47,7 @@ run `./local-dev/run_postgres.sh start`
 This will start a postgres container with a schema and user configured
 
 #### IDE Setup
-Open the root folder in IntelliJ.
+Open the root folder in IntelliJ.  
 
 * **server:**
 
@@ -76,15 +76,15 @@ Open the root folder in IntelliJ.
         * set environment variable: `B2C_POLICY_NAME=B2C_1A_ddp_participant_signup_signin_dev`
         * set environment variable: `B2C_CHANGE_PASSWORD_POLICY_NAME=B2C_1A_ddp_participant_change_password_dev`
         * disable launch optimization
-
-
+        
+         
 ### Running the application
 #### Admin tool (study manager, population)
 * API (api-admin module)
 In intelliJ, you can either run ApiAdminApp (from the api-admin module) directly, or execute the "bootRun" gradle task.
 In basic development mode, this will only serve the API, not the frontend assets.
 
-To make the application useful, you will want to populate some users and studies.  After the admin API is running,
+To make the application useful, you will want to populate some users and studies.  After the admin API is running, 
 from the root project directory, run
 ```
 ./scripts/populate_portal.sh ourhealth
@@ -98,7 +98,7 @@ From the command line:
   REACT_APP_B2C_TENANT_NAME=ddpdevb2c REACT_APP_B2C_CLIENT_ID=$(vault read -field value secret/dsp/ddp/b2c/dev/application_id) npm -w ui-admin start
   ```
 (note that you can just run `npm -w ui-admin start` if you don't need to test B2C login functionality)
-Then go to `localhost:3000`
+Then go to `localhost:3000` 
 
 ##### Participant API (api-participant module)
 In intelliJ, you can either run ApiParticipantApp (from the api-participant module) directly, or execute the "bootRun" gradle task.
@@ -118,9 +118,9 @@ Then go to `sandbox.ourhealth.localhost:3001`
 (Notice how you need the environment name and portal name as subdomains)
 
 
-### Feature Development
+### Feature Development 
 
-#### Adding a new model
+#### Adding a new model 
 1. Create the schema, models, and services
    1. Create your POJO model in `core/src/main/java/bio/terra/pearl/core/model`, you will almost certainly want to extend
    `BaseEntity`
@@ -150,16 +150,3 @@ Then go to `sandbox.ourhealth.localhost:3001`
 #### Adding environment variables
   Helm charts:
   https://github.com/broadinstitute/terra-helmfile/tree/master/values/app/d2p/live
-
-
-### SonarCloud code scanning
-
-Because juniper contains TypeScript projects and Java projects, the scans are run independently
-in each project
-
-Typescript UI subprojects (ui-admin, ui-core, and ui-participant) are scanned using the
-SonarCloud GitHub Action. Analysis (SonarCloud
-runs the scan on its own and comments back results to PRs).
-
-Java subprojects (core, client, api-admin, api-participant) are scanned using gradle with the
-sonarqube plugin.
\ No newline at end of file

From bf7caa9838ca6927993d7f673712124d670e6d9e Mon Sep 17 00:00:00 2001
From: Tom Conner <tconner@broadinstitute.org>
Date: Fri, 28 Jul 2023 00:46:32 -0400
Subject: [PATCH 78/83] restore

---
 .github/workflows/sonar.yaml | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 3e1a2144bb..a2b3750647 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -36,15 +36,9 @@ jobs:
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
 
-  sonar-typescript:
-    name: SonarCloud TypeScript
-
   sonar-typescript:
     name: SonarCloud TypeScript
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        subproject: ['ui-admin', 'ui-participant']
     strategy:
       matrix:
         subproject: ['ui-admin', 'ui-participant']
@@ -52,10 +46,6 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Get branch name
-        id: branch-name
-        uses: tj-actions/branch-names@v5
-      - name: Scan ${{ matrix.subproject }} via sonarcloud-github-action
       - name: Get branch name
         id: branch-name
         uses: tj-actions/branch-names@v5
@@ -65,7 +55,6 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
         with:
-          projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
           projectBaseDir: ${{ github.workspace }}/${{ matrix.subproject }}
           args: >
               -Dsonar.branch.target=${{ github.event.repository.default_branch }}

From 1a4f8f34ffaebb9f6e323681dff9c3de5717614e Mon Sep 17 00:00:00 2001
From: Tom Conner <tconner@broadinstitute.org>
Date: Fri, 28 Jul 2023 01:04:59 -0400
Subject: [PATCH 79/83] link to branch sonar scan

---
 .github/workflows/sonar.yaml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index a2b3750647..9a301463b0 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -60,8 +60,10 @@ jobs:
               -Dsonar.branch.target=${{ github.event.repository.default_branch }}
               -Dsonar.branch.name=${{ steps.branch-name.outputs.current_branch }}
       - name: Announce
-        run: |
-          gh pr comment ${{ github.event.pull_request.number }} \
-            --body "SonarCloud analyzed ${{ matrix.subproject }} on ${{ steps.branch-name.outputs.current_branch }}/"
+        run: >
+          gh pr comment ${{ github.event.pull_request.number }}
+            --body "SonarCloud [analyzed ${{ matrix.subproject }} on
+            ${{ steps.branch-name.outputs.current_branch }}](https://sonarcloud.io/summary/new_code?id=broadinstitute_juniper-${{ matrix.subproject }}&branch=${{ steps.branch-name.outputs.current_branch }})"
+
         env:
           GH_TOKEN: ${{ github.token }}

From 5012efc926ec031e02e944a54f705b7a03293cea Mon Sep 17 00:00:00 2001
From: Tom Conner <tconner@broadinstitute.org>
Date: Fri, 28 Jul 2023 01:14:30 -0400
Subject: [PATCH 80/83] announce branch scan

---
 .github/workflows/sonar.yaml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 9a301463b0..50539261ad 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -62,8 +62,6 @@ jobs:
       - name: Announce
         run: >
           gh pr comment ${{ github.event.pull_request.number }}
-            --body "SonarCloud [analyzed ${{ matrix.subproject }} on
-            ${{ steps.branch-name.outputs.current_branch }}](https://sonarcloud.io/summary/new_code?id=broadinstitute_juniper-${{ matrix.subproject }}&branch=${{ steps.branch-name.outputs.current_branch }})"
-
+            --body "SonarCloud [analyzed ${{ matrix.subproject }} on ${{ steps.branch-name.outputs.current_branch }}](https://sonarcloud.io/summary/new_code?id=broadinstitute_juniper-${{ matrix.subproject }}&branch=${{ steps.branch-name.outputs.current_branch }})"
         env:
           GH_TOKEN: ${{ github.token }}

From 46e4d67ce4fe715038dec7039ee60faac9085853 Mon Sep 17 00:00:00 2001
From: Tom Conner <tconner@broadinstitute.org>
Date: Fri, 28 Jul 2023 01:19:30 -0400
Subject: [PATCH 81/83] announce branch scan

---
 .github/workflows/sonar.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index 50539261ad..a394342492 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -60,8 +60,8 @@ jobs:
               -Dsonar.branch.target=${{ github.event.repository.default_branch }}
               -Dsonar.branch.name=${{ steps.branch-name.outputs.current_branch }}
       - name: Announce
-        run: >
-          gh pr comment ${{ github.event.pull_request.number }}
+        run: |
+          gh pr comment ${{ github.event.pull_request.number }} \
             --body "SonarCloud [analyzed ${{ matrix.subproject }} on ${{ steps.branch-name.outputs.current_branch }}](https://sonarcloud.io/summary/new_code?id=broadinstitute_juniper-${{ matrix.subproject }}&branch=${{ steps.branch-name.outputs.current_branch }})"
         env:
           GH_TOKEN: ${{ github.token }}

From 13051207783ff205afcde845459551ffae28b39f Mon Sep 17 00:00:00 2001
From: Tom Conner <tconner@broadinstitute.org>
Date: Fri, 28 Jul 2023 10:52:08 -0400
Subject: [PATCH 82/83] add ui-core

---
 .github/workflows/sonar.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/sonar.yaml b/.github/workflows/sonar.yaml
index a394342492..7092ed13d4 100644
--- a/.github/workflows/sonar.yaml
+++ b/.github/workflows/sonar.yaml
@@ -41,7 +41,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        subproject: ['ui-admin', 'ui-participant']
+        subproject: ['ui-admin', 'ui-core', 'ui-participant']
     steps:
       - uses: actions/checkout@v3
         with:

From ae4a1c24b5e7ffefc576309dd11d546ed1cda33d Mon Sep 17 00:00:00 2001
From: Tom Conner <tconner@broadinstitute.org>
Date: Fri, 28 Jul 2023 11:35:33 -0400
Subject: [PATCH 83/83] add ui-core

---
 ui-core/sonar-project.properties | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 ui-core/sonar-project.properties

diff --git a/ui-core/sonar-project.properties b/ui-core/sonar-project.properties
new file mode 100644
index 0000000000..5d7498351c
--- /dev/null
+++ b/ui-core/sonar-project.properties
@@ -0,0 +1,3 @@
+sonar.projectKey=broadinstitute_juniper-ui-core
+sonar.organization=dsp-appsec
+sonar.projectName=juniper-ui-core