init public release

2026-09-08 10:59:05 +02:00
commit 9cdf012717
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+MODE= #possible values: none or testserver
+COMPLEX_PATIENTS= #TRUE if only complex patients should be used otherwise FALSE
+COMPLEX_FHIR_SEARCH= #URL for the patient selection on the server, e.g. all gout patients:
+IS_SYNTHEA= #TRUE if synthea data is used otherwise FALSE
+FHIR_SERVER_URL= #URL to the FHIR server, e.g. http://hapi.fhir.org/baseR4; use http://blaze:8080/fhir when COMPOSE_PROFILES includes blaze
+BOLT_ADVERTISED_ADDRESS=localhost:8081 #change in production
+NEO4J_AUTH= # set if the server needs authentification: none otherwise true
+ENABLE_BOLT_TLS= #true to require TLS on the bolt connector (needs real certs in ./neo4j-certs/bolt/, used in production); leave unset/false for local runs
+
+DISABLE_IMPORT= #true if only neo4j should be started and load existing import data, false if the complete pipeline should run
+
+### Settings for deployment - might be adapted depending on the network its deployed in and
+#FHIR_SERVER_USER=
+#FHIR_SERVER_PW=
+#HTTP_PROXY=
+#HTTPS_PROXY=
+#NO_PROXY=
+
+### Settings for how to get the data
+NUMBER_OF_PATIENTS=2 # depends on the goal, very high to get all patients, lower numbers for testing; depends on disk space, plan with 30GB per 60k patients
+BATCH_SIZE=10 # depends on the computational power, plan with 12GB per 250 patients; higher batch sizes improve the needed time to run the pipeline
+
+# MDM
+MDM_MODE= #biocypher or mdm (beta)
+
+#OAUTH2_COOKIE_SECURE=true # or: NEO4J_COOKIE_SECRET= #for local setup
+
+
+#Keycloak settings if a local keycloak instance is used
+#KEYCLOAK_ISSUER_URL=https://---your productive keycloak url---/realms/yourRealm    #if using the setup with a local keycloak use: http://localhost:4040/realms/testPipeline
+#NEO4J_OAUTH_CLIENT_ID=neo4j-client
+#NEO4J_OAUTH_SECRET=secret-from-production-keycloak or secret from local keycloak setup
+
+#NEO4J_PROXY_REDIRECT_URL=https://your-domain.com/oauth2/callback
+
+COMPOSE_PROFILES= #comma-separated: blaze, keycloak, proxy, server - activates parts of docker compose depending on the setup (see README)
+
+#Test vars
+TEST_MODE=FALSE
+TEST_DEPTH=4