diff --git a/DockerBuild/Dockerfile b/DockerBuild/Dockerfile index e38facf94..88e12f61e 100644 --- a/DockerBuild/Dockerfile +++ b/DockerBuild/Dockerfile @@ -70,4 +70,4 @@ RUN cd /mnt/data/orangeboard/production/RTX/code/autocomplete && sed -i 's/devED RUN update-rc.d RTX_Complete defaults # setup config.domain -RUN su rt && cd /mnt/data/orangeboard/production/RTX/code/ && echo "arax.ci.transltr.io" > config.domain +RUN su rt && cd /mnt/data/orangeboard/production/RTX/code/ && echo "arax.transltr.io" > config.domain diff --git a/DockerBuild/KG2-Dockerfile b/DockerBuild/KG2-Dockerfile index 2e23b4d04..73fa7165f 100644 --- a/DockerBuild/KG2-Dockerfile +++ b/DockerBuild/KG2-Dockerfile @@ -70,5 +70,4 @@ RUN cd /mnt/data/orangeboard/kg2/RTX/code/autocomplete && sed -i 's/devED/kg2/g' RUN update-rc.d RTX_Complete defaults # setup config.domain -RUN su rt && cd /mnt/data/orangeboard/kg2/RTX/code/ && echo "kg2.ci.transltr.io" > config.domain - +RUN su rt && cd /mnt/data/orangeboard/kg2/RTX/code/ && echo "kg2.transltr.io" > config.domain diff --git a/DockerBuild/Merged-Dockerfile b/DockerBuild/Merged-Dockerfile index 02926b6d2..831f53603 100644 --- a/DockerBuild/Merged-Dockerfile +++ b/DockerBuild/Merged-Dockerfile @@ -29,6 +29,7 @@ RUN chmod -R 700 /home/rt/.ssh RUN mkdir -p /mnt/data/orangeboard/production RUN chown -R rt.rt /mnt/data/orangeboard/production RUN su rt && cd /mnt/data/orangeboard/production && git clone https://github.com/RTXteam/RTX.git +RUN su rt && cd /mnt/data/orangeboard/production/RTX && git checkout production RUN chown -R rt.rt /mnt/data/orangeboard/production/RTX # install apache2 and copy config file @@ -73,6 +74,7 @@ RUN su rt && cd /mnt/data/orangeboard/production/RTX/code/ && echo "Github actio RUN mkdir -p /mnt/data/orangeboard/kg2 RUN chown -R rt.rt /mnt/data/orangeboard/kg2 RUN su rt && cd /mnt/data/orangeboard/kg2 && git clone https://github.com/RTXteam/RTX.git +RUN su rt && cd /mnt/data/orangeboard/kg2/RTX && git checkout production RUN chown -R rt.rt /mnt/data/orangeboard/kg2/RTX COPY kg2-config.js /mnt/data/orangeboard/kg2/RTX/code/UI/interactive/config.js diff --git a/code/UI/OpenAPI/python-flask-server/KG2/openapi_server/openapi/openapi.yaml b/code/UI/OpenAPI/python-flask-server/KG2/openapi_server/openapi/openapi.yaml index 1cb0f8472..7adff4bc0 100644 --- a/code/UI/OpenAPI/python-flask-server/KG2/openapi_server/openapi/openapi.yaml +++ b/code/UI/OpenAPI/python-flask-server/KG2/openapi_server/openapi/openapi.yaml @@ -23,6 +23,11 @@ info: x-trapi: version: 1.4.0 asyncquery: false + test_data_location: + default: + url: https://raw.githubusercontent.com/RTXteam/RTX/production/code/ARAX/KnowledgeSources/RTX_KG2c_test_triples.json + development: + url: https://raw.githubusercontent.com/RTXteam/RTX/kg2integration/code/ARAX/KnowledgeSources/RTX_KG2c_test_triples.json operations: - lookup externalDocs: @@ -33,8 +38,20 @@ externalDocs: description: Documentation for the NCATS Biomedical Translator Reasoners web services url: https://github.com/NCATSTranslator/ReasonerAPI servers: -- description: RTX-KG2 TRAPI 1.4 endpoint - development +- description: RTX-KG2 TRAPI 1.4 endpoint - ITRB production + url: https://kg2.transltr.io/api/rtxkg2/v1.4 + x-maturity: production +- description: RTX-KG2 TRAPI 1.4 endpoint - production url: https://arax.ncats.io/api/rtxkg2/v1.4 + x-maturity: production +- description: RTX-KG2 TRAPI 1.4 endpoint - testing + url: https://kg2.test.transltr.io/api/rtxkg2/v1.4 + x-maturity: testing +- description: RTX-KG2 TRAPI 1.4 endpoint - staging + url: https://kg2.ci.transltr.io/api/rtxkg2/v1.4 + x-maturity: staging +- description: RTX-KG2 TRAPI 1.4 endpoint - development + url: https://arax.ncats.io/beta/api/rtxkg2/v1.4 x-maturity: development tags: - description: Retrieve the meta knowledge graph representation of this TRAPI web diff --git a/code/UI/OpenAPI/python-flask-server/openapi_server/openapi/openapi.yaml b/code/UI/OpenAPI/python-flask-server/openapi_server/openapi/openapi.yaml index 1be2737c8..788145b26 100644 --- a/code/UI/OpenAPI/python-flask-server/openapi_server/openapi/openapi.yaml +++ b/code/UI/OpenAPI/python-flask-server/openapi_server/openapi/openapi.yaml @@ -23,6 +23,7 @@ info: x-trapi: version: 1.4.0 asyncquery: true + test_data_location: https://raw.githubusercontent.com/RTXteam/RTX/master/code/ARAX/Documentation/arax_kps.json operations: - lookup - lookup_and_score @@ -53,8 +54,29 @@ externalDocs: description: Documentation for the NCATS Biomedical Translator Reasoners web services url: https://github.com/NCATSTranslator/ReasonerAPI servers: -- description: ARAX TRAPI 1.4 endpoint - development +- description: ARAX TRAPI 1.4 endpoint - production + url: https://arax.transltr.io/api/arax/v1.4 + x-maturity: production +- description: ARAX TRAPI 1.4 endpoint - production url: https://arax.ncats.io/api/arax/v1.4 + x-maturity: production +- description: ARAX TRAPI 1.4 endpoint - testing + url: https://arax.test.transltr.io/api/arax/v1.4 + x-maturity: testing +- description: ARAX TRAPI 1.4 endpoint - staging + url: https://arax.ci.transltr.io/api/arax/v1.4 + x-maturity: staging +- description: ARAX TRAPI 1.4 endpoint - development + url: https://arax.ncats.io/beta/api/arax/v1.4 + x-maturity: development +- description: ARAX TRAPI 1.4 endpoint - development + url: https://arax.ncats.io/test/api/arax/v1.4 + x-maturity: development +- description: ARAX TRAPI 1.4 endpoint - development + url: https://arax.ncats.io/devED/api/arax/v1.4 + x-maturity: development +- description: ARAX TRAPI 1.4 endpoint - development + url: https://arax.ncats.io/devLM/api/arax/v1.4 x-maturity: development tags: - description: Retrieve the meta knowledge graph representation of this TRAPI web diff --git a/deploy/arax/Jenkinsfile b/deploy/arax/Jenkinsfile-prod similarity index 86% rename from deploy/arax/Jenkinsfile rename to deploy/arax/Jenkinsfile-prod index 7333c7f10..0dbd7f3ce 100644 --- a/deploy/arax/Jenkinsfile +++ b/deploy/arax/Jenkinsfile-prod @@ -11,14 +11,11 @@ pipeline { string(name: 'BUILD_VERSION', defaultValue: '', description: 'The build version to deploy (optional)') string(name: 'AWS_REGION', defaultValue: 'us-east-1', description: 'AWS Region to deploy') } - triggers { - pollSCM('H/5 * * * *') - } environment { IMAGE_NAME = "853771734544.dkr.ecr.us-east-1.amazonaws.com/translator-rtx-arax" DOCKER_REPO_NAME = "translator-rtx-arax" - KUBERNETES_BLUE_CLUSTER_NAME = "translator-eks-ci-blue-cluster" - KUBERNETES_GREEN_CLUSTER_NAME = "translator-eks-ci-green-cluster" + KUBERNETES_BLUE_CLUSTER_NAME = "translator-eks-prod-blue-cluster" + KUBERNETES_GREEN_CLUSTER_NAME = "translator-eks-prod-green-cluster" NAMESPACE = "rtx" SECRET_NAME = "sftp-ssh-key" CFGFILE2DL = "team-expander-ops@sftp.transltr.io:/transltr-063208468694-sftp/team-expander/config_secrets.json" @@ -31,7 +28,7 @@ pipeline { steps{ script { BUILD_VERSION_GENERATED = VersionNumber( - versionNumberString: 'v${BUILD_YEAR, XX}.${BUILD_MONTH, XX}${BUILD_DAY, XX}.${BUILDS_TODAY}', + versionNumberString: 'v${BUILD_YEAR, XX}.${BUILD_MONTH, XX}${BUILD_DAY, XX}.${BUILDS_TODAY}-prod', projectStartDate: '1970-01-01', skipFailedBuilds: true) currentBuild.displayName = BUILD_VERSION_GENERATED @@ -49,7 +46,7 @@ pipeline { stage('Build and Push Docker Image') { when { expression { return env.BUILD == 'true' }} environment { - ENV_BUILD_BRANCH= sh (returnStdout: true, script: 'git rev-parse --abbrev-ref HEAD').trim() + ENV_BUILD_BRANCH='production' } steps { script { @@ -63,7 +60,7 @@ pipeline { } stage('Deploy to AWS EKS Blue') { agent { - label 'translator && ci && deploy' + label 'translator && prod && deploy' } steps { cleanWs() @@ -84,10 +81,5 @@ pipeline { } } } - stage('Clean Up') { - steps { - cleanWs() - } - } } -} \ No newline at end of file +} diff --git a/deploy/arax/templates/deployment.yaml b/deploy/arax/templates/deployment.yaml index 4af445bc4..95bbcf60f 100644 --- a/deploy/arax/templates/deployment.yaml +++ b/deploy/arax/templates/deployment.yaml @@ -51,7 +51,7 @@ spec: httpGet: path: / port: http - periodSeconds: 60 + periodSeconds: 60 volumeMounts: - name: {{ include "arax.fullname" . }}-pvc mountPath: /mnt/data/orangeboard/databases/ diff --git a/deploy/arax/values.yaml b/deploy/arax/values.yaml index 8dd8987a3..25982e614 100644 --- a/deploy/arax/values.yaml +++ b/deploy/arax/values.yaml @@ -73,8 +73,8 @@ affinity: resources: requests: - memory: 50Gi - cpu: 10000m + memory: 48Gi + cpu: 8000m limits: memory: 58Gi cpu: 14000m diff --git a/deploy/kg2/Jenkinsfile b/deploy/kg2/Jenkinsfile-prod similarity index 92% rename from deploy/kg2/Jenkinsfile rename to deploy/kg2/Jenkinsfile-prod index 638313722..da94c2883 100644 --- a/deploy/kg2/Jenkinsfile +++ b/deploy/kg2/Jenkinsfile-prod @@ -11,14 +11,11 @@ pipeline { string(name: 'BUILD_VERSION', defaultValue: '', description: 'The build version to deploy (optional)') string(name: 'AWS_REGION', defaultValue: 'us-east-1', description: 'AWS Region to deploy') } - triggers { - pollSCM('H/5 * * * *') - } environment { IMAGE_NAME = "853771734544.dkr.ecr.us-east-1.amazonaws.com/translator-rtx-kg2" DOCKER_REPO_NAME = "translator-rtx-kg2" - KUBERNETES_BLUE_CLUSTER_NAME = "translator-eks-ci-blue-cluster" - KUBERNETES_GREEN_CLUSTER_NAME = "translator-eks-ci-green-cluster" + KUBERNETES_BLUE_CLUSTER_NAME = "translator-eks-prod-blue-cluster" + KUBERNETES_GREEN_CLUSTER_NAME = "translator-eks-prod-green-cluster" NAMESPACE = "rtx" SECRET_NAME = "sftp-ssh-key" CFGFILE2DL = "team-expander-ops@sftp.transltr.io:/transltr-063208468694-sftp/team-expander/config_secrets.json" @@ -31,7 +28,7 @@ pipeline { steps{ script { BUILD_VERSION_GENERATED = VersionNumber( - versionNumberString: 'v${BUILD_YEAR, XX}.${BUILD_MONTH, XX}${BUILD_DAY, XX}.${BUILDS_TODAY}', + versionNumberString: 'v${BUILD_YEAR, XX}.${BUILD_MONTH, XX}${BUILD_DAY, XX}.${BUILDS_TODAY}-prod', projectStartDate: '1970-01-01', skipFailedBuilds: true) currentBuild.displayName = BUILD_VERSION_GENERATED @@ -63,7 +60,7 @@ pipeline { } stage('Deploy to AWS EKS Blue') { agent { - label 'translator && ci && deploy' + label 'translator && prod && deploy' } steps { cleanWs() @@ -90,4 +87,4 @@ pipeline { } } } -} \ No newline at end of file +} diff --git a/deploy/kg2/values.yaml b/deploy/kg2/values.yaml index 53a23797e..1f0961271 100644 --- a/deploy/kg2/values.yaml +++ b/deploy/kg2/values.yaml @@ -45,7 +45,7 @@ ingress: # toleration to node taint such that this deployment can be scheduled on the tainted node while others without the toleration can not tolerations: - key : "rtx" - value : "kg2" + value : "managed-app" operator : "Equal" effect : "NoSchedule" @@ -59,7 +59,7 @@ affinity: - key: application operator: In values: - - kg2 + - managed-app # this ensures only ONE pod will run on each node podAntiAffinity: requiredDuringSchedulingIgnoredDuringExecution: @@ -68,7 +68,7 @@ affinity: - key: app.kubernetes.io/name operator: In values: - - kg2 + - managed-app topologyKey: "kubernetes.io/hostname" storageClassName: @@ -84,4 +84,4 @@ resources: cpu: 13000m limits: memory: 58Gi - cpu: 14000m \ No newline at end of file + cpu: 14000m