Merge pull request #5 from zainasir/setup

fix database connection issuue

.github/workflows/lint-test.yaml

@@ -1,6 +1,6 @@
 name: Lint and Test Charts
 
-on: workflow_dispatch
+on: pull_request
 
 jobs:
   lint-test:

.github/workflows/release.yaml

@@ -1,6 +1,9 @@
 name: Release Charts
 
-on: workflow_dispatch
+on:
+  push:
+    branches:
+      - main
 
 jobs:
   release:

charts/templates/deployment.yaml

@@ -43,8 +43,14 @@ spec:
       {{- end }}
       containers:
         - envFrom:
+            {{- if .Values.configMapRef.enabled }}
             - configMapRef:
-                name: {{ .Values.container.configMapRef }}
+                name: {{ .Values.configMapRef.ref }}
+            {{- end }}
+            {{- if .Values.secretRef.enabled }}
+            - secretRef:
+                name: {{ .Values.secretRef.ref }}
+            {{- end }}
           {{- if .Values.container.env }}
           env:
             {{- toYaml .Values.container.env | nindent 12 }}
@@ -81,7 +87,7 @@ spec:
           terminationMessagePolicy: {{ .Values.terminationMessagePolicy }}
       # run on eks-public-cbioportal node group
       nodeSelector:
-        eks.amazonaws.com/nodegroup: {{ .Values.nodeGroup }}
+        {{ required ".Values.nodeSelector.key is required!" .Values.nodeSelector.key }}: {{ required ".Values.nodeSelector.value is required!" .Values.nodeSelector.value }}
       {{- if .Values.podTolerations }}
       tolerations:
         {{- toYaml .Values.podTolerations | nindent 8 }}

charts/values.yaml

@@ -22,18 +22,15 @@ creationTimestamp: "null"
 generation: 1
 
 # Pod volumes
-podVolumes:
-  - name: cbioportal-frontend-config-volume
-    configMap:
-      name: single-cell-frontend-config
+podVolumes: {}
 
 # Pod Volume Mounts
-podVolumeMounts:
-  - name: cbioportal-frontend-config-volume
-    mountPath: /cbioportal/
+podVolumeMounts: {}
 
 # Node group
-nodeGroup: eks-public-cbioportal
+nodeSelector:
+  key:
+  value:
 
 # Pod strategy
 rollingUpdate:
@@ -43,9 +40,17 @@ rollingUpdate:
 # Pod labels
 podLabels: {}
 
+# Enable/Disable and define configmaps and secrets
+configMapRef:
+  enabled: 0
+  ref: {}
+
+secretRef:
+  enabled: 0
+  ref: {}
+
 # Primary container
 container:
-  configMapRef: cbioportal-public6
   image: cbioportal/cbioportal:6.0.17-web-shenandoah
   cmd: "java"
   env:
@@ -86,18 +91,13 @@ containerPorts:
     protocol: TCP
 
 # Container resources
-containerResources:
-  requests:
-    cpu: 1500m
-    memory: 15Gi
-  limits:
-    memory: 26Gi
+containerResources: {}
 
 # Pod tolerations
 podTolerations:
   - key: "dedicated"
     operator: "Equal"
-    value: "eks-public-cbioportal"
+    value: "cbioportal"
     effect: "NoSchedule"
 
 terminationMessagePath: /dev/termination-log
@@ -116,7 +116,7 @@ terminationGracePeriodSeconds: 30
 status: {}
 
 # Service Name
-serviceName: cbioportal-helm
+serviceName: cbioportal
 
 # Service ports
 servicePorts:
@@ -126,19 +126,12 @@ servicePorts:
 
 # Args for the java command in the container
 containerArgs: [
-  # from https://developers.redhat.com/blog/2017/04/04/openjdk-and-containers/
   "-Xms100m",
   "-Xmx25g",
   "-XX:+UnlockExperimentalVMOptions",
   "-XX:+UseShenandoahGC",
   "-XX:ShenandoahUncommitDelay=1000",
   "-XX:ShenandoahGuaranteedGCInterval=10000",
-  #"-XX:+AlwaysPreTouch",
-  #"-XX:+UseTransparentHugePages",
-  #"-XX:+UseNUMA",
-  #"-XX:+PrintGCDetails",
-  #"-XX:+UseParallelGC",
-  #"-XX:+PrintGCDateStamps",
   #"-XX:ParallelGCThreads=4",
   #"-XX:+UseG1GC",
   #"-XX:+AggressiveHeap",
@@ -159,13 +152,13 @@ containerArgs: [
   "-jar",
   "/cbioportal-webapp/app.jar",
   # enable remote debug
-  "--com.sun.management.jmxremote.rmi.port=8849",
-  "--com.sun.management.jmxremote=false",
-  "--com.sun.management.jmxremote.port=8849",
-  "--com.sun.management.jmxremote.ssl=false",
-  "--com.sun.management.jmxremote.authenticate=false",
-  "--com.sun.management.jmxremote.local.only=false",
-  "--java.rmi.server.hostname=localhost",
+  #"--com.sun.management.jmxremote.rmi.port=8849",
+  #"--com.sun.management.jmxremote=false",
+  #"--com.sun.management.jmxremote.port=8849",
+  #"--com.sun.management.jmxremote.ssl=false",
+  #"--com.sun.management.jmxremote.authenticate=false",
+  #"--com.sun.management.jmxremote.local.only=false",
+  #"--java.rmi.server.hostname=localhost",
   # /enable remote debug
   "--frontend.url=https://frontend.cbioportal.org/",
   "--enable_cross_study_expression=(studies)=>(studies.filter(s=>/pan_can_atlas/.test(s.studyId) === false).length === 0 || studies.filter(s=>/tcga_gdc/.test(s.studyId) === false).length === 0)",
@@ -179,36 +172,36 @@ containerArgs: [
   "--installation_map_url=https://installationmap.netlify.app/",
   "--app.name=public-portal",
   # connecting over dbcp
-  "--dbconnector=dbcp",
+  #"--dbconnector=dbcp",
   # Authentication settings
-  "--authenticate=optional_oauth2",
-  "--authorization=false",
-  "--security.method_authorization_enabled=false",
-  "--always_show_study_group=PUBLIC",
-  "--spring.security.oauth2.client.registration.google.clientId=$(GOOGLE_PLUS_CONSUMER_KEY)",
-  "--spring.security.oauth2.client.registration.google.clientSecret=$(GOOGLE_PLUS_CONSUMER_SECRET)",
-  "--spring.security.oauth2.client.provider.google.user-name-attribute=email",
+  #"--authenticate=optional_oauth2",
+  #"--authorization=false",
+  #"--security.method_authorization_enabled=false",
+  #"--always_show_study_group=PUBLIC",
+  #"--spring.security.oauth2.client.registration.google.clientId=$(GOOGLE_PLUS_CONSUMER_KEY)",
+  #"--spring.security.oauth2.client.registration.google.clientSecret=$(GOOGLE_PLUS_CONSUMER_SECRET)",
+  #"--spring.security.oauth2.client.provider.google.user-name-attribute=email",
   # "--logging.level.org.springframework.security=DEBUG",
-  "--spring.security.oauth2.client.registration.azure.client-id=$(MICROSOFT_LIVE_CONSUMER_KEY)",
-  "--spring.security.oauth2.client.registration.azure.clientSecret=$(MICROSOFT_LIVE_CONSUMER_SECRET)",
-  "--spring.security.oauth2.client.registration.azure.authorization-grant-type=authorization_code",
-  "--spring.security.oauth2.client.registration.azure.redirect-uri={baseUrl}/login/oauth2/code/azure",
-  "--spring.security.oauth2.client.registration.azure.scope=openid,profile,email",
-  "--spring.security.oauth2.client.provider.azure.user-name-attribute=email",
-  "--spring.security.oauth2.client.provider.azure.authorization-uri=https://login.microsoftonline.com/common/oauth2/v2.0/authorize",
-  "--spring.security.oauth2.client.provider.azure.token-uri=https://login.microsoftonline.com/common/oauth2/v2.0/token",
-  "--spring.security.oauth2.client.provider.azure.jwk-set-uri=https://login.microsoftonline.com/common/discovery/v2.0/keys",
+  #"--spring.security.oauth2.client.registration.azure.client-id=$(MICROSOFT_LIVE_CONSUMER_KEY)",
+  #"--spring.security.oauth2.client.registration.azure.clientSecret=$(MICROSOFT_LIVE_CONSUMER_SECRET)",
+  #"--spring.security.oauth2.client.registration.azure.authorization-grant-type=authorization_code",
+  #"--spring.security.oauth2.client.registration.azure.redirect-uri={baseUrl}/login/oauth2/code/azure",
+  #"--spring.security.oauth2.client.registration.azure.scope=openid,profile,email",
+  #"--spring.security.oauth2.client.provider.azure.user-name-attribute=email",
+  #"--spring.security.oauth2.client.provider.azure.authorization-uri=https://login.microsoftonline.com/common/oauth2/v2.0/authorize",
+  #"--spring.security.oauth2.client.provider.azure.token-uri=https://login.microsoftonline.com/common/oauth2/v2.0/token",
+  #"--spring.security.oauth2.client.provider.azure.jwk-set-uri=https://login.microsoftonline.com/common/discovery/v2.0/keys",
   "--security.cors.allowed-origins=*",
   # db settings
   "--db.user=$(DB_USER)",
   "--db.password=$(DB_PASSWORD)",
   "--spring.datasource.driver-class-name=com.mysql.jdbc.Driver",
-  "--spring.jpa.database-platform=org.hibernate.dialect.MySQL5InnoDBDialect",
-  "--spring.datasource.url=jdbc:mysql://publicdb.cbioportal.org:3306/cgds_public_v5?zeroDateTimeBehavior=convertToNull&useSSL=false&allowPublicKeyRetrieval=true",
+  #"--spring.jpa.database-platform=org.hibernate.dialect.MySQL5InnoDBDialect",
+  "--spring.datasource.url=$(DB_CONNECTION_STRING)",
   "--spring.datasource.username=$(DB_USER)",
   "--spring.datasource.password=$(DB_PASSWORD)",
   #            "-Ddb.connection_string=$(DB_CONNECTION_STRING)",
-  "--tomcat.catalina.scope=runtime",
+  #"--tomcat.catalina.scope=runtime",
   "--show.transcript_dropdown=true",
   "--skin.show_tweet_button=$(SKIN_SHOW_TWEET_BUTTON)",
   "[email protected]",
@@ -222,60 +215,60 @@ containerArgs: [
   "--priority_studies=PanCancer Studies#msk_impact_2017,metastatic_solid_tumors_mich_2017,mixed_allen_2018,summit_2018,tmb_mskcc_2018,ntrk_msk_2019,msk_ch_2020,pan_origimed_2020,pancan_pcawg_2020,msk_met_2021;Pediatric Cancer Studies#pptc_2019,all_phase2_target_2018_pub,rt_target_2018_pub,wt_target_2018_pub,aml_target_2018_pub,nbl_target_2018_pub,pediatric_dkfz_2017,mixed_pipseq_2017,all_stjude_2016,all_stjude_2015,es_dfarber_broad_2014,es_iocurie_2014,mbl_pcgp,nbl_msk_2023,pancan_mappyacts_2022;Immunogenomic Studies#gbm_columbia_2019,skcm_dfci_2015,skcm_mskcc_2014,mel_ucla_2016,nsclc_mskcc_2018,nsclc_mskcc_2015,tmb_mskcc_2018,ccrcc_dfci_2019;Cell lines#ccle_broad_2019,cellline_ccle_broad,cellline_nci60;PreCancerous Studies#crc_hta11_htan_2021",
   "--studyview.max_samples_selected=100000",
   "--study_download_url=https://cbioportal-datahub.s3.amazonaws.com/",
-  "--session.service.url=https://session-service.cbioportal.org/api/sessions/public_portal/",
-  "--session.service.origin=*",
-  "--session.service.user=$(SESSION_SERVICE_USER_NAME)",
-  "--session.service.password=$(SESSION_SERVICE_USER_PASSWORD)",
-  "--google_analytics_profile_id=G-5260NDGD6Z",
-  "--bitly.url=$(BITLY_URL)",
-  "--bitly.access.token=$(BITLY_ACCESS_TOKEN)",
-  "--sentry.dsn=$(SENTRY_DSN)",
-  "--sentry.factory=org.cbioportal.logging.SentryClientFactory",
-  "--sentry.traces-sample-rate=1.0",
-  "--sentry.exception-resolver-order=-2147483647",
+  "--session.service.url=https://cbioportal-session-service.herokuapp.com/session_service/api/sessions/heroku_portal/",
+  #"--session.service.origin=*",
+  #"--session.service.user=$(SESSION_SERVICE_USER_NAME)",
+  #"--session.service.password=$(SESSION_SERVICE_USER_PASSWORD)",
+  #"--google_analytics_profile_id=G-5260NDGD6Z",
+  #"--bitly.url=$(BITLY_URL)",
+  #"--bitly.access.token=$(BITLY_ACCESS_TOKEN)",
+  #"--sentry.dsn=$(SENTRY_DSN)",
+  #"--sentry.factory=org.cbioportal.logging.SentryClientFactory",
+  #"--sentry.traces-sample-rate=1.0",
+  #"--sentry.exception-resolver-order=-2147483647",
   #"--sentryjs.frontend_project_endpoint=$(SENTRY_FRONTEND_DSN)",
   "--db.suppress_schema_version_mismatch_errors=true",
   "--sitemaps=true",
-  "--oncokb.public_api.url=https://www.oncokb.org/api/v1",
-  "--oncokb.token=$(ONCOKB_TOKEN)",
-  "--genomenexus.url=https://v1.genomenexus.org",
-  "--show.genomenexus.annotation_sources=mutation_assessor",
-  "--matchminer.url=http://ec2-54-158-52-176.compute-1.amazonaws.com:5555",
-  "--matchminer.token=$(MATCHMINER_TOKEN)",
+  "--oncokb.public_api.url=https://public.api.oncokb.org/api/v1",
+  #"--oncokb.token=$(ONCOKB_TOKEN)",
+  #"--genomenexus.url=https://v1.genomenexus.org",
+  #"--show.genomenexus.annotation_sources=mutation_assessor",
+  #"--matchminer.url=http://ec2-54-158-52-176.compute-1.amazonaws.com:5555",
+  #"--matchminer.token=$(MATCHMINER_TOKEN)",
   # redis session store settings (different from redis persistence cache)
-  "--spring.session.store-type=redis",
+  #"--spring.session.store-type=redis",
   # "--server.servlet.session.timeout=10s", (not sure what this should be)
-  "--spring.data.redis.host=$(REDIS_SESSION_HOST)",
-  "--spring.data.redis.port=$(REDIS_SESSION_PORT)",
-  "--spring.data.redis.password=$(REDIS_SESSION_PASSWORD)",
+  #"--spring.data.redis.host=$(REDIS_SESSION_HOST)",
+  #"--spring.data.redis.port=$(REDIS_SESSION_PORT)",
+  #"--spring.data.redis.password=$(REDIS_SESSION_PASSWORD)",
   # To enable redis session store, we need to set
   # spring.autoconfigure.exclude to a random value to override the
   # property in applications.properties.EXAMPLE
-  "--spring.autoconfigure.exclude=dontexcludeanythingplz",
+  #"--spring.autoconfigure.exclude=dontexcludeanythingplz",
 
   # redis cache settings (currently redis)
   #"--cache.statistics_endpoint_enabled=false",
   # "--logging.level.org.cbioportal.persistence=DEBUG",
   # persistence cache settings (currently redis)
   #"-Dcache.statistics_endpoint_enabled=false",
-  "--persistence.cache_type=redis",
-  "--redis.leader_address=redis://cbioportal-public-persistence-redis-master:6379",
-  "--redis.follower_address=redis://cbioportal-public-persistence-redis-replicas:6379",
-  "--redis.database=8",
-  "--redis.password=$(REDIS_PERSISTENCE_PASSWORD)",
-  "--redis.clear_on_startup=true",
-  "--cache.endpoint.enabled=true",
-  "--cache.endpoint.api-key=1kmfbftTb2iY",
+  #"--persistence.cache_type=redis",
+  #"--redis.leader_address=redis://cbioportal-public-persistence-redis-master:6379",
+  #"--redis.follower_address=redis://cbioportal-public-persistence-redis-replicas:6379",
+  #"--redis.database=8",
+  #"--redis.password=$(REDIS_PERSISTENCE_PASSWORD)",
+  #"--redis.clear_on_startup=true",
+  #"--cache.endpoint.enabled=true",
+  #"--cache.endpoint.api-key=1kmfbftTb2iY",
   # disable ehcache
   #            ??? Are we still using ehcache?
   #            "--ehcache.cache_type=none",
   # misc frontend settings (this is NOT for backend persistence layer caching)
   #"--enable_persistent_cache=true",
   # compress on client side
-  "--enable_request_body_gzip_compression=true",
+  #"--enable_request_body_gzip_compression=true",
   # for single cell plugin
-  "--frontend.config=/cbioportal/frontendConfig.json",
-  "--frontend_authenticate=optional_oauth2",
+  #"--frontend.config=/cbioportal/frontendConfig.json",
+  #"--frontend_authenticate=optional_oauth2",
   # this addresses same issue as
   # https://github.com/cBioPortal/cbioportal/issues/2328 one needs to
   # set this if one doesn't want to forward https -> http -> https