Merge 3.5 changes before release

.github/workflows/achilles.yml

@@ -0,0 +1,27 @@
+name: achilles profile (Linux)
+on: push
+jobs:
+  achilles:
+    strategy:
+      matrix:
+        os: [ubuntu-22.04]
+        httpType: [http]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Setup Docker on macOS
+        if: runner.os == 'macOS'
+        uses: douglascamata/setup-docker-macos-action@v1-alpha
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Create certs folder
+        run: mkdir -p ./certs
+      - name: Write Github PAT secret file
+        run: echo ${{ secrets.GH_TOKEN }} > ./secrets/github_pat
+      - name: Build and run achilles container
+        run: docker compose --env-file .env --profile achilles up -d
+      - name: Use busybox container to grab log file and verify no errors
+        run: |
+         sleep 30
+         CID=$(docker run -d -v cdm-postprocessing-data:/cdm-postprocessing-data busybox true)
+         docker cp $CID:/cdm-postprocessing-data/achilles/data/demo_cdm/log_achilles.txt ./log_achilles.txt
+         if grep -q "ERROR" ./log_achilles.txt;then exit 1;else exit 0;fi

.github/workflows/default.yml

@@ -0,0 +1,54 @@
+name: default profile (Linux)
+on: push
+jobs:
+  default:
+    strategy:
+      matrix:
+        os: [ubuntu-22.04]
+        httpType: [http, https]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Setup Docker on macOS
+        if: runner.os == 'macOS'
+        uses: douglascamata/setup-docker-macos-action@v1-alpha
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Create certs folder
+        run: mkdir -p ./certs
+      - name: Replace HTTP_TYPE if https (Linux)
+        if: matrix.httpType == 'https' && runner.os == 'Linux'
+        run: sed -i 's/HTTP_TYPE=\"http\"/HTTP_TYPE=\"https\"/g' .env
+      - name: Replace HTTP_TYPE if https (Mac)
+        if: matrix.httpType == 'https' && runner.os == 'macOS'
+        run: sed -i '' 's/HTTP_TYPE=\"http\"/HTTP_TYPE=\"https\"/g' .env
+      - name: Create and trust self signed certs
+        if: matrix.httpType == 'https'
+        run: |
+          openssl req -x509 -out ./certs/broadsea.crt -keyout ./certs/broadsea.key \
+            -newkey rsa:2048 -nodes -sha256 \
+            -subj '/CN=127.0.0.1' -extensions EXT -config <( \
+            printf "[dn]\nCN=127.0.0.1\n[req]\ndistinguished_name = dn\n[EXT]\nsubjectAltName=DNS:127.0.0.1\nkeyUsage=digitalSignature\nextendedKeyUsage=serverAuth")
+      - name: Build traefik container
+        run: docker compose --env-file .env up -d
+      - name: Build default profile
+        run: docker compose --env-file .env --profile default up -d
+      - name: Setup postgres client on Linux
+        if: runner.os == 'Linux'
+        run: sudo apt-get install --yes --no-install-recommends postgresql-client
+      - name: Setup postgres client on MacOS
+        if: runner.os == 'macOS'
+        run: brew install libpq
+      - name: Test atlasdb
+        run: PGPASSWORD=$(cat ./secrets/webapi/WEBAPI_DATASOURCE_PASSWORD) psql -h 127.0.0.1 -p 5432 -U postgres -c "select source_name from webapi.source limit 1"
+      - name: Test traefik container
+        run: docker logs traefik
+      - name: Test content container
+        run: curl -s -k --retry 10 --retry-connrefused ${{matrix.httpType}}://127.0.0.1
+      - name: Test HADES
+        run: curl -s -k --retry 10 --retry-connrefused ${{matrix.httpType}}://127.0.0.1/hades/auth-sign-in
+      - name: Test Atlas
+        run: curl -s -k --retry 10 --retry-connrefused ${{matrix.httpType}}://127.0.0.1/atlas/#/home
+      - name: Test WebAPI info endpoint
+        run: |
+          sleep 30
+          curl -s -k --retry 10 --retry-connrefused ${{matrix.httpType}}://127.0.0.1/WebAPI/info

.github/workflows/perseus.yml

@@ -0,0 +1,27 @@
+name: perseus profile (Linux)
+on: push
+jobs:
+  perseus:
+    strategy:
+      matrix:
+        os: [ubuntu-22.04]
+        httpType: [http]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Setup Docker on macOS
+        if: runner.os == 'macOS'
+        uses: douglascamata/setup-docker-macos-action@v1-alpha
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Create certs folder
+        run: mkdir -p ./certs
+      - name: Build traefik container
+        run: docker compose up -d
+      - name: Check traefik container
+        run: docker logs traefik
+      - name: Build perseus profile
+        run: docker compose --profile perseus up -d
+      - name: Test perseus frontend
+        run: |
+          sleep 30
+          curl -s --retry 10 --retry-connrefused http://127.0.0.1/perseus

.github/workflows/solrvocab.yml

@@ -0,0 +1,44 @@
+name: solr-vocab-no-import profile (Linux)
+on: push
+jobs:
+  solrvocab:
+    strategy:
+      matrix:
+        os: [ubuntu-22.04]
+        httpType: [http, https]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Setup Docker on macOS
+        if: runner.os == 'macOS'
+        uses: douglascamata/setup-docker-macos-action@v1-alpha
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Create certs folder
+        run: mkdir -p ./certs
+      - name: Replace HTTP_TYPE if https (Linux)
+        if: matrix.httpType == 'https' && runner.os == 'Linux'
+        run: sed -i 's/HTTP_TYPE=\"http\"/HTTP_TYPE=\"https\"/g' .env
+      - name: Replace HTTP_TYPE if https (Mac)
+        if: matrix.httpType == 'https' && runner.os == 'macOS'
+        run: sed -i '' 's/HTTP_TYPE=\"http\"/HTTP_TYPE=\"https\"/g' .env
+      - name: Create and trust self signed certs
+        if: matrix.httpType == 'https'
+        run: |
+          openssl req -x509 -out ./certs/broadsea.crt -keyout ./certs/broadsea.key \
+            -newkey rsa:2048 -nodes -sha256 \
+            -subj '/CN=127.0.0.1' -extensions EXT -config <( \
+            printf "[dn]\nCN=127.0.0.1\n[req]\ndistinguished_name = dn\n[EXT]\nsubjectAltName=DNS:127.0.0.1\nkeyUsage=digitalSignature\nextendedKeyUsage=serverAuth")
+      - name: Build traefik container
+        run: docker compose --env-file .env up -d
+      - name: Build atlasdb profile
+        run: docker compose --env-file .env --profile atlasdb up -d
+      - name: Build empty SOLR instance
+        run: docker compose --env-file .env --profile solr-vocab-no-import up -d
+      - name: Build webapi profile with SOLR_VOCAB enabled
+        run: SOLR_VOCAB_ENDPOINT=http://broadsea-solr-vocab:8983/solr docker compose --env-file .env --profile webapi-from-image up -d
+      - name: Test WebAPI info endpoint
+        run: |
+          sleep 30
+          curl -s -k --retry 10 --retry-connrefused ${{matrix.httpType}}://127.0.0.1/WebAPI/info
+      - name: Test SOLR endpoint
+        run: curl -s -k --retry 10 --retry-connrefused ${{matrix.httpType}}://127.0.0.1/solr/

.github/workflows/webapi_auth.yml

@@ -0,0 +1,59 @@
+name: WebAPI Authentication (Linux)
+on: push
+jobs:
+  openldap:
+    strategy:
+      matrix:
+        os: [ubuntu-22.04]
+        httpType: [http]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Setup Docker on macOS
+        if: runner.os == 'macOS'
+        uses: douglascamata/setup-docker-macos-action@v1-alpha
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Create certs folder
+        run: mkdir -p ./certs
+      - name: Build traefik container
+        run: docker compose --env-file .env up -d
+      - name: Build atlasdb profile
+        run: docker compose --env-file .env --profile atlasdb up -d
+      - name: Build webapi profile with ldap enabled
+        run: SECURITY_AUTH_LDAP_ENABLED=true docker compose --env-file .env --profile webapi-from-image up -d
+      - name: Test WebAPI info endpoint
+        run: |
+          sleep 30
+          curl -s -k --retry 10 --retry-connrefused ${{matrix.httpType}}://127.0.0.1/WebAPI/info
+      - name: Build OpenLDAP
+        run: docker compose --env-file .env --profile openldap up -d
+      - name: Test openldap auth in WebAPI
+        run: |
+          curl -d "login=user1&password=$(<./secrets/openldap/OPENLDAP_ACCOUNT_PASSWORDS)" -H "Content-Type: application/x-www-form-urlencoded" -X POST ${{matrix.httpType}}://127.0.0.1/WebAPI/user/login/ldap
+  db:
+    strategy:
+      matrix:
+        os: [ubuntu-22.04]
+        httpType: [http]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Setup Docker on macOS
+        if: runner.os == 'macOS'
+        uses: douglascamata/setup-docker-macos-action@v1-alpha
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Create certs folder
+        run: mkdir -p ./certs
+      - name: Build traefik container
+        run: docker compose --env-file .env up -d
+      - name: Build atlasdb profile
+        run: docker compose --env-file .env --profile atlasdb up -d
+      - name: Build webapi profile with ldap enabled
+        run: SECURITY_AUTH_JDBC_ENABLED=true docker compose --env-file .env --profile webapi-from-image up -d
+      - name: Test WebAPI info endpoint
+        run: |
+          sleep 30
+          curl -s -k --retry 10 --retry-connrefused ${{matrix.httpType}}://127.0.0.1/WebAPI/info
+      - name: Test db auth in WebAPI
+        run: |
+          curl -d "login=ohdsi&password=$(<./secrets/webapi/SECURITY_DB_DATASOURCE_PASSWORD)" -H "Content-Type: application/x-www-form-urlencoded" -X POST ${{matrix.httpType}}://127.0.0.1/WebAPI/user/login/db

.gitignore

@@ -1,4 +1,9 @@
 .DS_Store
 omop_vocab/files
 .env_local
-*.jar
+*.lic
+phoebe/concept_recommended.csv
+phoebe/__MACOSX
+atlas/add_cdm
+.Rproj.user
+strategus/