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https://github.com/samply/bridgehead.git
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tm16-medma
171 lines
5.4 KiB
Plaintext
171 lines
5.4 KiB
Plaintext
BROKER_ID=broker.ccp-it.dktk.dkfz.de
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BROKER_URL=https://${BROKER_ID}
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PROXY_ID=${SITE_ID}.${BROKER_ID}
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FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
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FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
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SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
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PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
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BROKER_URL_FOR_PREREQ=$BROKER_URL
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OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
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OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
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OIDC_PSP_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_PSP"
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OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
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OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
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OIDC_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PUBLIC_CLIENT_ID}/"
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OIDC_PRIVATE_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PRIVATE_CLIENT_ID}/"
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OIDC_GROUP_CLAIM="groups"
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for module in $PROJECT/modules/*.sh
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do
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log DEBUG "sourcing $module"
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source $module
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done
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# ========================================
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# OVIS Bridgehead Module Configuration
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# ========================================
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# Copy this file to ccp/vars and customize for your site.
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# This module supports CCP (FHIR-based) or DEMO (bundled data) import modes.
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# ========================================
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# Enable OVIS module
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ENABLE_OVIS=
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# ========================================
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# IMPORT MODE
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# ========================================
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# Set to "ccp" for FHIR-based Clinical Cancer Profile import
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# Set to "demo" for bundled demo data (no external dependencies)
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OVIS_IMPORT_MODE=demo
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# ========================================
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# ROUTING / TRAEFIK
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# ========================================
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# Hostname for OVIS access
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HOST=localhost
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# Traefik middleware for authentication
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OVIS_AUTH_MIDDLEWARE=traefik-forward-auth
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# CORS origin for backend
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OVIS_CORS_ORIGIN=*
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# ========================================
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# CORE RUNTIME
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# ========================================
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APOLLO_PORT=4001
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CREDOS_PORT=4000
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DB=onc_test
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MONGO_VER=latest
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# Frontend login toggle
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PUBLIC_LOGIN_ENABLED=false
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# ========================================
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# CCP IMPORTER / FHIR SOURCE
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# ========================================
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# Only required when OVIS_IMPORT_MODE=ccp
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# FHIR server URL (defaults to Bridgehead CCP Blaze)
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FHIR_SERVER_URL=http://bridgehead-ccp-blaze:8080/fhir
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FHIR_USERNAME=your-fhir-username
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FHIR_PASSWORD=your-fhir-password
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# Optional ICD10 filter for CCP import
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ICD10_FILTER=
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# ========================================
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# PREPROCESSOR ENDPOINT
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# ========================================
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# URL for uploading omock.json to preprocessing service
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# Uses Bridgehead service name (different from main compose default)
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OVIS_PREPROCESSOR_URL=http://ovis-backend-data-preprocessing:9000/omock
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# ========================================
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# FRONTEND RUNTIME
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# ========================================
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# Catalogue upstream URL (uses Bridgehead service name)
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OVIS_CATALOGUE_UPSTREAM_URL=http://ovis-backend-data-preprocessing:9000/catalogue
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# Express auth configuration
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EXPRESS_AUTH_URL=http://express-auth:5000
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EXPRESS_AUTH_USERNAME=your-express-username
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EXPRESS_AUTH_PASSWORD=your-express-password
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# ========================================
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# PROXY CONFIGURATION (Optional)
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# ========================================
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# Use these only if your server must access the internet through a corporate proxy.
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# Leave all three empty when no proxy is required.
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OVIS_HTTP_PROXY=
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OVIS_HTTPS_PROXY=
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OVIS_NO_PROXY=
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# ========================================
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# PREPROCESSOR OVERRIDES (Optional)
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# ========================================
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# These variables customize preprocessing behavior without code changes.
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# See main compose.yaml for detailed documentation of each variable.
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# Global / patient status
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OVIS_PREPROC_DECEASED_KEYWORDS=["verstorben","dead","deceased","not alive","gestorben"]
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# Rezidiv detection
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OVIS_PREPROC_REZIDIV_PREFIXES=["Rezidiv"]
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OVIS_PREPROC_REZIDIV_CANONICAL=Rezidiv
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OVIS_PREPROC_REZIDIV_LYMPH_STATES=["Rezidiv","Neu"]
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# Progress / DFS
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OVIS_PREPROC_PROGRESS_LABELS=["Progression","Divergentes Geschehen","Rezidiv"]
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OVIS_PREPROC_COMPLETE_REMISSION_LABELS=["Vollremission / Tumorfrei (complete remission)"]
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# DFS start conditions
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OVIS_PREPROC_RCLASS_SUCCESS=["R0"]
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OVIS_PREPROC_LOCAL_RSTATE_SUCCESS=["R0"]
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# Metastasis detection
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OVIS_PREPROC_METASTASIS_PREFIXES=["Rezidiv","Neu"]
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OVIS_PREPROC_METASTASIS_SPREAD_VALUES=["Neu","Rezidiv","Tumornachweis"]
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OVIS_PREPROC_METASTASIS_STRAT_SYNCHRON=Synchrone Metastasierung
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OVIS_PREPROC_METASTASIS_STRAT_NONE=keine synchrone Metastasierung
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# Study phases to treat as null
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OVIS_PREPROC_NULL_STUDY_PHASES=["NOPH","KA"]
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# Therapy mappings
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OVIS_PREPROC_PREV_THERAPY_SURGERY=["operation"]
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OVIS_PREPROC_PREV_THERAPY_SYSTEMIC=["systemic"]
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OVIS_PREPROC_PREV_THERAPY_RADIATION=["radiation"]
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# Consultation mappings
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OVIS_PREPROC_PREV_CONSULTATION_NUTRITION=["nutrition"]
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OVIS_PREPROC_PREV_CONSULTATION_SOCIAL=["social"]
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OVIS_PREPROC_PREV_CONSULTATION_PSYCHO=["psycho"]
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OVIS_PREPROC_PREV_CONSULTATION_GENETIC=["genetic"]
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# Tumorboard patterns (regex)
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OVIS_PREPROC_TUMORBOARD_PATTERN_PRAE=prae|prä|pre
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OVIS_PREPROC_TUMORBOARD_PATTERN_POST=post
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OVIS_PREPROC_TUMORBOARD_PATTERN_MTB=mtb
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# ECOG and distress
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OVIS_PREPROC_ECOG_PREFIX=ECOG
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OVIS_PREPROC_DISTRESS_TYPE=distress
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OVIS_PREPROC_DISTRESS_POSITIVE_VALUES=["Positiv"]
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idManagementSetup
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mtbaSetup
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obds2fhirRestSetup
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blazeSecondarySetup
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for module in modules/*.sh
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do
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log DEBUG "sourcing $module"
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source $module
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done
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transfairSetup
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