Merge pull request #18 from zainasir/fix/env-vars

add database values and fix container args
cBioPortal · Nov 19, 2024 · 6e557bf · 6e557bf
2 parents edaf3fb + a62a4af
commit 6e557bf
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diff --git a/charts/cbioportal/Chart.yaml b/charts/cbioportal/Chart.yaml
@@ -6,7 +6,7 @@ type: application
 # This is the chart version. This version number should be incremented each time you make changes
 # to the chart and its templates, including the app version.
 # Versions are expected to follow Semantic Versioning (https://semver.org/)
-version: 0.1.6
+version: 0.1.7
 
 # This is the version number of the application being deployed. This version number should be
 # incremented each time you make changes to the application. Versions are not expected to

diff --git a/charts/cbioportal/templates/deployment.yaml b/charts/cbioportal/templates/deployment.yaml
@@ -86,7 +86,7 @@ spec:
           terminationMessagePolicy: {{ .Values.terminationMessagePolicy }}
       # run on eks-public-cbioportal node group
       nodeSelector:
-        {{ required ".Values.nodeSelector.label is required!" .Values.nodeSelector.value }}: {{ required ".Values.nodeSelector.value is required!" .Values.nodeSelector.value }}
+        {{ required ".Values.nodeSelector.label is required!" .Values.nodeSelector.label }}: {{ required ".Values.nodeSelector.value is required!" .Values.nodeSelector.value }}
       {{- if .Values.podTolerations }}
       tolerations:
         {{- toYaml .Values.podTolerations | nindent 8 }}

diff --git a/charts/cbioportal/values.yaml b/charts/cbioportal/values.yaml
@@ -48,10 +48,12 @@ container:
   image: cbioportal/cbioportal:6.0.17-web-shenandoah
   cmd: "java"
   env:
-    - name: DD_PROFILING_ENABLED
-      value: "true"
-    - name: DD_LOGS_INJECTION
-      value: "true"
+    - name: DB_USER
+      value: "db-user"
+    - name: DB_PASSWORD
+      value: "db-pwd"
+    - name: DB_CONNECTION_STRING
+      value: "db-connection-url"
 
 # Pod annotations
 podAnnotations:
@@ -89,7 +91,7 @@ containerResources: {}
 
 # Pod tolerations
 podTolerations:
-  - key: "dedicated"
+  - key: "node-group"
     operator: "Equal"
     value: "cbioportal"
     effect: "NoSchedule"
@@ -120,169 +122,17 @@ servicePorts:
 
 # Args for the java command in the container
 containerArgs: [
-  "-Xms100m",
-  "-Xmx25g",
-  "-XX:+UnlockExperimentalVMOptions",
-  "-XX:+UseShenandoahGC",
-  "-XX:ShenandoahUncommitDelay=1000",
-  "-XX:ShenandoahGuaranteedGCInterval=10000",
-  #"-XX:ParallelGCThreads=4",
-  #"-XX:+UseG1GC",
-  #"-XX:+AggressiveHeap",
-  # non aggressive garbage collection
-  #"-XX:MinHeapFreeRatio=20",
-  #"-XX:MaxHeapFreeRatio=40",
-  #"-XX:GCTimeRatio=19",
-  #"-XX:AdaptiveSizePolicyWeight=90",
-  # This issue says to use maxRAMFraction > 1
-  # https://github.com/akka/akka/issues/23499, but haven't found this
-  # to work v well
-  #"-XX:MaxRAMFraction=1",
-  "-XX:+PrintFlagsFinal",
-  "-XshowSettings:vm",
-  # need to set MaxRAM, somehow the MaxRAMFraction is not picked up
-  # from the limits
-  #"-XX:MaxRAM=6500m",
+  "-Xms2g",
+  "-Xmx4g",
   "-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",
-  # /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)",
-  "--default_cross_cancer_study_session_id=5c8a7d55e4b046111fee2296",
-  "--quick_search.enabled=true",
-  "--skin.footer=",
-  "--skin.right_nav.whats_new_blurb=",
-  "--skin.quick_select_buttons=TCGA PanCancer Atlas Studies#*pan_can_atlas*;Curated set of non-redundant studies|228 studies that are manually curated including TCGA and non-TCGA studies with no overlapping samples#acbc_mskcc_2015,acc_tcga_pan_can_atlas_2018,acyc_fmi_2014,acyc_mda_2015,acyc_mskcc_2013,acyc_sanger_2013,all_phase2_target_2018_pub,all_stjude_2016,aml_target_2018_pub,ampca_bcm_2016,angs_project_painter_2018,bfn_duke_nus_2015,blca_bgi,blca_cornell_2016,blca_dfarber_mskcc_2014,blca_mskcc_solit_2012,blca_mskcc_solit_2014,blca_tcga_pan_can_atlas_2018,brca_bccrc,brca_broad,brca_igr_2015,brca_mbcproject_wagle_2017,brca_metabric,brca_sanger,brca_tcga_pan_can_atlas_2018,ccrcc_irc_2014,ccrcc_utokyo_2013,cesc_tcga_pan_can_atlas_2018,chol_jhu_2013,chol_nccs_2013,chol_nus_2012,chol_tcga_pan_can_atlas_2018,cll_iuopa_2015,cllsll_icgc_2011,coadread_dfci_2016,coadread_genentech,coadread_mskcc,coadread_tcga_pan_can_atlas_2018,cscc_dfarber_2015,cscc_hgsc_bcm_2014,ctcl_columbia_2015,desm_broad_2015,dlbc_tcga_pan_can_atlas_2018,dlbcl_dfci_2018,dlbcl_duke_2017,egc_tmucih_2015,es_dfarber_broad_2014,es_iocurie_2014,esca_broad,esca_tcga_pan_can_atlas_2018,escc_icgc,escc_ucla_2014,gbc_shanghai_2014,gbm_tcga_pan_can_atlas_2018,glioma_msk_2018,hcc_inserm_fr_2015,hcc_msk_venturaa_2018,hnsc_broad,hnsc_jhu,hnsc_mdanderson_2013,hnsc_tcga_pan_can_atlas_2018,kich_tcga_pan_can_atlas_2018,kirc_bgi,kirc_tcga_pan_can_atlas_2018,kirp_tcga_pan_can_atlas_2018,laml_tcga_pan_can_atlas_2018,lcll_broad_2013,lgg_tcga_pan_can_atlas_2018,lgg_ucsf_2014,liad_inserm_fr_2014,lihc_amc_prv,lihc_riken,lihc_tcga_pan_can_atlas_2018,luad_broad,luad_tcga_pan_can_atlas_2018,luad_tsp,lusc_tcga_pan_can_atlas_2018,mbl_broad_2012,mbl_pcgp,mbl_sickkids_2016,mcl_idibips_2013,mds_tokyo_2011,mel_tsam_liang_2017,meso_tcga_pan_can_atlas_2018,mixed_allen_2018,mixed_pipseq_2017,mm_broad,mpnst_mskcc,mrt_bcgsc_2016,msk_impact_2017,nbl_amc_2012,nbl_target_2018_pub,nbl_ucologne_2015,nccrcc_genentech_2014,nepc_wcm_2016,nhl_bcgsc_2011,nhl_bcgsc_2013,npc_nusingapore,nsclc_unito_2016,ov_tcga_pan_can_atlas_2018,paac_jhu_2014,paad_qcmg_uq_2016,paad_tcga_pan_can_atlas_2018,paad_utsw_2015,pact_jhu_2011,panet_arcnet_2017,panet_jhu_2011,panet_shanghai_2013,pcnsl_mayo_2015,pcpg_tcga_pan_can_atlas_2018,pediatric_dkfz_2017,plmeso_nyu_2015,prad_broad,prad_eururol_2017,prad_fhcrc,prad_mich,prad_mpcproject_2018,prad_mskcc,prad_mskcc_cheny1_organoids_2014,prad_tcga_pan_can_atlas_2018,rms_nih_2014,rt_target_2018_pub,sarc_mskcc,sarc_tcga_pan_can_atlas_2018,scco_mskcc,sclc_cancercell_gardner_2017,sclc_jhu,sclc_ucologne_2015,skcm_broad,skcm_broad_brafresist_2012,skcm_tcga_pan_can_atlas_2018,skcm_vanderbilt_mskcc_2015,skcm_yale,stad_pfizer_uhongkong,stad_tcga_pan_can_atlas_2018,stad_utokyo,summit_2018,tet_nci_2014,tgct_tcga_pan_can_atlas_2018,thca_tcga_pan_can_atlas_2018,thym_tcga_pan_can_atlas_2018,uccc_nih_2017,ucec_tcga_pan_can_atlas_2018,ucs_jhu_2014,ucs_tcga_pan_can_atlas_2018,um_qimr_2016,urcc_mskcc_2016,utuc_mskcc_2015,uvm_tcga_pan_can_atlas_2018,vsc_cuk_2018,wt_target_2018_pub,acyc_jhu_2016,prostate_dkfz_2018,histiocytosis_cobi_msk_2019,utuc_cornell_baylor_mdacc_2019,prad_su2c_2019,cll_broad_2015,coad_cptac_2019,brca_mskcc_2019,acc_2019,pptc_2019,prad_msk_2019,ccrcc_dfci_2019,mpn_cimr_2013,nsclc_tracerx_2017,mnm_washu_2016,bcc_unige_2016,coad_caseccc_2015,metastatic_solid_tumors_mich_2017,aml_ohsu_2018,ihch_smmu_2014,nsclc_mskcc_2018,skcm_dfci_2015,skcm_mskcc_2014,mel_ucla_2016,utuc_msk_2019,gbm_columbia_2019,stad_oncosg_2018,brca_smc_2018,luad_oncosg_2020,angs_painter_2020,mel_dfci_2019,lung_smc_2016,utuc_igbmc_2021,cscc_ucsf_2021,chol_icgc_2017,hccihch_pku_2019,ihch_ismms_2015,mbl_dkfz_2017,pan_origimed_2020,crc_nigerian_2020,difg_glass_2019,pancan_pcawg_2020,ucec_cptac_2020,paad_cptac_2021,lusc_cptac_2021,luad_cptac_2020,gbm_cptac_2021,brca_cptac_2020,brain_cptac_2020,mpcproject_broad_2021,brca_hta9_htan_2022,lung_nci_2022,mds_iwg_2022,biliary_tract_summit_2022,pog570_bcgsc_2020,hcc_meric_2021,prostate_pcbm_swiss_2019,ucec_ccr_cfdna_msk_2022,ucec_ccr_msk_2022,mixed_selpercatinib_2020,lgsoc_mapk_msk_2022,mng_utoronto_2021,blca_bcan_hcrn_2022,aml_ohsu_2022,coad_silu_2022,stmyec_wcm_2022,bladder_columbia_msk_2018,sarcoma_msk_2022,cll_broad_2022,coadread_cass_2020,prad_msk_mdanderson_2023,crc_hta11_htan_2021,nbl_msk_2023,pancan_mappyacts_2022,hcc_clca_2024,brca_fuscc_2020",
-  "--skin.example_study_queries=tcga pancancer atlas\ntcga -legacy -pancancer\ntcga or icgc\nmsk-impact\n-\"cell line\"\nbreast\nesophageal OR stomach\nprostate msk\nserous",
-  "--skin.patientview.filter_genes_profiled_all_samples=false",
-  "--installation_map_url=https://installationmap.netlify.app/",
-  "--app.name=public-portal",
-  # connecting over 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",
-  # "--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",
-  "--security.cors.allowed-origins=*",
-  # db settings
+  "--authenticate=false",
+  "--session.service.url=http://cbioportal-session:5001/api/sessions/my_portal/",
   "--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.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",
-  "--show.transcript_dropdown=true",
-  "--skin.show_tweet_button=$(SKIN_SHOW_TWEET_BUTTON)",
-  "[email protected]",
-  "--skin.data_sets_footer=Data sets of published studies were curated from literature. Data sets of legacy TCGA studies were downloaded from the <a href=\"http://gdac.broadinstitute.org\">Broad Institute Firehose</a>, last updated 1/28/2016.",
-  "--skin.data_sets_header=The table below lists the number of available samples per cancer study and data type. It also provides links to download the data for each study. For alternative ways of downloading, see the <a href=\"https://docs.cbioportal.org/5.2-datasets/downloads#introduction\">Download Documentation</a>.",
-  "--skin.authorization_message=Welcome to cBioPortal - sign in with your Google or Microsoft account to store your <a href=\"https://www.cbioportal.org/tutorials#virtual-studies\" target=\"_blank\">virtual studies</a> and <a href=\"https://www.cbioportal.org/tutorials#group-comparison\" target=\"_blank\">groups</a>. This will allow you to access your studies and groups from any computer, and cBioPortal will also remember your study view charts preferences for each study (i.e. order of the charts, type of charts and visibility). Login is optional and not required to access any of the other features of cBioPortal.",
-  "--skin.blurb=",
-  "--show.mdacc.heatmap=true",
-  "--skin.documentation.faq=user-guide/faq.md",
-  "--skin.show_r_matlab_tab=false",
-  "--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://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=$(SENTRY_FRONTEND_DSN)",
-  "--db.suppress_schema_version_mismatch_errors=true",
-  "--sitemaps=true",
-  "--oncokb.public_api.url=https://public.api.oncokb.org/api/v1",
-  #"--oncokb.token=$(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=$(MATCHMINER_TOKEN)",
-  # redis session store settings (different from redis persistence cache)
-  #"--spring.session.store-type=redis",
-  # "--server.servlet.session.timeout=10s", (not sure what this should be)
-  #"--spring.data.redis.host=$(REDIS_SESSION_HOST)",
-  #"--spring.data.redis.port=$(REDIS_SESSION_PORT)",
-  #"--spring.data.redis.password=$(REDIS_SESSION_PASSWORD)",
-  # 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",
-
-  # 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",
-  # 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",
-  # for single cell plugin
-  #"--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
-  # when logging in through google auth. Somehow this goes over http
-  # otherwise.
-  #            ??? How can we translate this?
-  #            "--proxy-base-url",
-  #            "https://www.cbioportal.org",
-  #            "--max-threads",
-  #            "0",
-  #            "--session-store",
-  #            "redis",
-  #            "--session-store-operation-timeout",
-  #            "10000",
-  # Fix long URL https://github.com/cBioPortal/cbioportal/issues/5836
-  "--server.compression.enabled=true",
-  "--server.tomcat.connection-timeout=20000",
-  "--server.tomcat.max-http-response-header-size=16384",
-  #            ??? can we still set port
-  #            "--server.tomcat.port=8888",
-  "--server.max-http-request-header-size=16384",
-  "--show.civic=true"
 ]