diff --git a/.github/workflows/image_build_push.yaml b/.github/workflows/image_build_push.yaml index 51543f0fe..d5bfea351 100644 --- a/.github/workflows/image_build_push.yaml +++ b/.github/workflows/image_build_push.yaml @@ -1,10 +1,10 @@ -name: Build Python Base Images and Push to Quay and ECR +name: Build Python Base Images on: push jobs: python_3-9: - name: Python 3.9 Build and Push + name: Python 3.9 uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master with: DOCKERFILE_LOCATION: "./Docker/python-nginx/python3.9-buster/Dockerfile" @@ -17,7 +17,7 @@ jobs: QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }} QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }} python_3-10: - name: Python 3.10 Build and Push + name: Python 3.10 uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master with: DOCKERFILE_LOCATION: "./Docker/python-nginx/python3.10-buster/Dockerfile" @@ -30,7 +30,7 @@ jobs: QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }} QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }} awshelper: - name: AwsHelper Build and Push + name: AwsHelper uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master with: DOCKERFILE_LOCATION: "./Docker/awshelper/Dockerfile" diff --git a/.github/workflows/image_build_push_jenkins.yaml b/.github/workflows/image_build_push_jenkins.yaml index 2d85aedf1..094417fe5 100644 --- a/.github/workflows/image_build_push_jenkins.yaml +++ b/.github/workflows/image_build_push_jenkins.yaml @@ -1,13 +1,14 @@ -name: Build Jenkins images and push to Quay +name: Build Jenkins images on: push: paths: + - .github/workflows/image_build_push_jenkins.yaml - Docker/jenkins/** jobs: jenkins: - name: Jenkins Build and Push + name: Jenkins uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master with: DOCKERFILE_LOCATION: "./Docker/jenkins/Jenkins/Dockerfile" @@ -21,7 +22,7 @@ jobs: QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }} QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }} jenkins2: - name: Jenkins2 Build and Push + name: Jenkins2 uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master with: DOCKERFILE_LOCATION: "./Docker/jenkins/Jenkins2/Dockerfile" @@ -35,7 +36,7 @@ jobs: QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }} QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }} jenkins-ci-worker: - name: Jenkins-CI-Worker Build and Push + name: Jenkins-CI-Worker uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master with: DOCKERFILE_LOCATION: "./Docker/jenkins/Jenkins-CI-Worker/Dockerfile" @@ -49,7 +50,7 @@ jobs: QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }} QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }} jenkins-qa-worker: - name: Jenkins-QA-Worker Build and Push + name: Jenkins-QA-Worker uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master with: DOCKERFILE_LOCATION: "./Docker/jenkins/Jenkins-Worker/Dockerfile" diff --git a/.github/workflows/image_build_push_squid.yaml b/.github/workflows/image_build_push_squid.yaml index 2849f0cc5..ce1761d3c 100644 --- a/.github/workflows/image_build_push_squid.yaml +++ b/.github/workflows/image_build_push_squid.yaml @@ -1,13 +1,14 @@ -name: Build Squid images and push to Quay +name: Build Squid images on: push: paths: + - .github/workflows/image_build_push_squid.yaml - Docker/squid/** jobs: squid: - name: Squid Build and Push + name: Squid image uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master with: DOCKERFILE_LOCATION: "./Docker/squid/Dockerfile" diff --git a/.secrets.baseline b/.secrets.baseline index 919833990..0a8fe9cc9 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -3,7 +3,7 @@ "files": "^.secrets.baseline$", "lines": null }, - "generated_at": "2023-09-18T18:49:22Z", + "generated_at": "2023-10-26T21:32:44Z", "plugins_used": [ { "name": "AWSKeyDetector" @@ -79,7 +79,7 @@ "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", "is_secret": false, "is_verified": false, - "line_number": 122, + "line_number": 121, "type": "Secret Keyword" } ], diff --git a/Docker/jenkins/Jenkins-CI-Worker/Dockerfile b/Docker/jenkins/Jenkins-CI-Worker/Dockerfile index 40fd08fa3..f0da68f69 100644 --- a/Docker/jenkins/Jenkins-CI-Worker/Dockerfile +++ b/Docker/jenkins/Jenkins-CI-Worker/Dockerfile @@ -34,11 +34,10 @@ RUN set -xe && apt-get update \ zlib1g-dev \ zsh \ ca-certificates-java \ - openjdk-11-jre-headless \ && ln -s /usr/bin/lua5.3 /usr/local/bin/lua # Use jdk11 -ENV JAVA_HOME="/usr/lib/jvm/java-11-openjdk-amd64" +ENV JAVA_HOME="/opt/java/openjdk" ENV PATH="$JAVA_HOME/bin:$PATH" COPY ./certfix.sh /certfix.sh @@ -75,7 +74,7 @@ RUN sudo install -m 0755 -d /etc/apt/keyrings \ # install nodejs RUN curl -sL https://deb.nodesource.com/setup_14.x | bash - -RUN apt-get update && apt-get install -y nodejs +RUN apt-get update && apt-get install -y nodejs npm # Install postgres 13 client RUN curl -fsSL https://www.postgresql.org/media/keys/ACCC4CF8.asc| gpg --dearmor -o /etc/apt/trusted.gpg.d/postgresql.gpg && \ @@ -98,7 +97,7 @@ RUN sed -i 's/python3/python3.8/' /usr/bin/lsb_release && \ sed -i 's/python3/python3.8/' /usr/bin/add-apt-repository # install aws cli, poetry, pytest, etc. -RUN set -xe && python3.8 -m pip install --upgrade pip && python3.8 -m pip install awscli --upgrade && python3.8 -m pip install pytest --upgrade && python3.8 -m pip install poetry && python3.8 -m pip install PyYAML --upgrade && python3.8 -m pip install lxml --upgrade && python3.8 -m pip install yq --upgrade && python3.8 -m pip install datadog --upgrade +RUN set -xe && python3.8 -m pip install --upgrade pip setuptools && python3.8 -m pip install awscli --upgrade && python3.8 -m pip install pytest --upgrade && python3.8 -m pip install poetry && python3.8 -m pip install PyYAML --upgrade && python3.8 -m pip install lxml --upgrade && python3.8 -m pip install yq --upgrade && python3.8 -m pip install datadog --upgrade # install terraform RUN curl -o /tmp/terraform.zip https://releases.hashicorp.com/terraform/0.11.15/terraform_0.11.15_linux_amd64.zip \ diff --git a/Docker/jenkins/Jenkins-Worker/Dockerfile b/Docker/jenkins/Jenkins-Worker/Dockerfile index c31e54923..c824690de 100644 --- a/Docker/jenkins/Jenkins-Worker/Dockerfile +++ b/Docker/jenkins/Jenkins-Worker/Dockerfile @@ -8,6 +8,7 @@ RUN set -xe && apt-get update && apt-get install -y apt-utils dnsutils build-ess RUN apt-get update \ && apt-get install -y lsb-release \ + git \ apt-transport-https \ r-base \ libffi-dev \ @@ -36,11 +37,6 @@ RUN apt-get update \ # install Ruby. RUN apt-get install -y ruby-full -# install GIT from buster-backports -RUN echo "deb http://deb.debian.org/debian buster-backports main" > /etc/apt/sources.list.d/buster-backports.list \ - && apt-get update \ - && apt-get -t=buster-backports -y install git=1:2.30.* - # # install docker tools: # diff --git a/kube/services/jobs/usersync-job.yaml b/kube/services/jobs/usersync-job.yaml index 8f148a3b0..8a5471a20 100644 --- a/kube/services/jobs/usersync-job.yaml +++ b/kube/services/jobs/usersync-job.yaml @@ -260,7 +260,7 @@ spec: exit 1 fi #----------------- - echo "awshelper downloading ${userYamlS3Path} to /mnt/shared/useryaml"; + echo "awshelper downloading ${userYamlS3Path} to /mnt/shared/user.yaml"; n=0 until [ $n -ge 5 ]; do echo "Download attempt $n" diff --git a/kube/services/ohdsi-webapi/ohdsi-webapi-config.yaml b/kube/services/ohdsi-webapi/ohdsi-webapi-config.yaml index 5cd46edd9..8eb01ec08 100644 --- a/kube/services/ohdsi-webapi/ohdsi-webapi-config.yaml +++ b/kube/services/ohdsi-webapi/ohdsi-webapi-config.yaml @@ -55,6 +55,9 @@ stringData: security_oauth_callback_api: https://atlas.$hostname/WebAPI/user/oauth/callback security_oauth_callback_urlResolver: query + security_ohdsi_custom_authorization_mode: teamproject + security_ohdsi_custom_authorization_url: $ARBORIST_URL/auth/mapping + logging_level_root: info logging_level_org_ohdsi: info logging_level_org_apache_shiro: info diff --git a/kube/services/ohdsi-webapi/ohdsi-webapi-deploy.yaml b/kube/services/ohdsi-webapi/ohdsi-webapi-deploy.yaml index 65d6ed38c..258aa8f87 100644 --- a/kube/services/ohdsi-webapi/ohdsi-webapi-deploy.yaml +++ b/kube/services/ohdsi-webapi/ohdsi-webapi-deploy.yaml @@ -59,6 +59,13 @@ spec: containers: - name: ohdsi-webapi GEN3_OHDSI-WEBAPI_IMAGE|-image: quay.io/cdis/ohdsi-webapi:latest-| + env: + - name: ARBORIST_URL + valueFrom: + configMapKeyRef: + name: manifest-global + key: arborist_url + optional: true livenessProbe: httpGet: path: /WebAPI/info/