samply
/
bridgehead
mirror of https://github.com/samply/bridgehead.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Some more adjustments for dktk

This commit is contained in:
root 2022-02-09 10:58:32 +01:00
parent 31525571e1
commit 3244c3db29
6 changed files with 65 additions and 129 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

32
dktk/docker-compose.yml
View File

@ -52,11 +52,10 @@ services:
connector:
container_name: bridgehead_dktk_connector
image: "samply/share-client:dktk-7"
image: "samply/share-client:dktk-pr-148"
environment:
STORE_URL: ${STORE_URL}
POSTGRES_HOST: ${CONNECTOR_DB_HOST}
POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}
POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
volumes:
- "connector_logs:/usr/local/tomcat/logs"
depends_on:
@ -66,9 +65,8 @@ services:
- "traefik.enable=true"
- "traefik.http.routers.dktk_connector.rule=PathPrefix(`/dktk-connector`)"
- "traefik.http.services.dktk_connector.loadbalancer.server.port=8080"
env_file:
###TODO: Move into Image
- internal.env
ports:
- 65395:65395
connector_db:
container_name: bridgehead_dktk_connector_db
@ -88,14 +86,14 @@ services:
image: docker.verbis.dkfz.de/pseudonymisierung/magicpl:release-0.2.0
environment:
TOMCAT_REVERSEPROXY_FQDN: ${HOST}/id-manager
MAGICPL_MAINZELLISTE_API_KEY: ${MAGICPL_MAINZELLISTE_API_KEY}
MAGICPL_API_KEY: ${MAGICPL_API_KEY}
MAGICPL_API_KEY_CONNECTOR: ${MAGICPL_API_KEY_CONNECTOR}
MAGICPL_PASSPHRASE: ${MAGICPL_PASSPHRASE}
MAGICPL_MAINZELLISTE_CENTRAL_API_KEY: ${MAGICPL_MAINZELLISTE_CENTRAL_API_KEY}
MAGICPL_CENTRAL_API_KEY: ${MAGICPL_CENTRAL_API_KEY}
MAGICPL_OIDC_CLIENT_ID: ${MAGICPL_OIDC_CLIENT_ID}
MAGICPL_OIDC_CLIENT_SECRET: ${MAGICPL_OIDC_CLIENT_SECRET}
MAGICPL_MAINZELLISTE_API_KEY: "123"
MAGICPL_API_KEY: "123"
MAGICPL_API_KEY_CONNECTOR: "123"
MAGICPL_PASSPHRASE: "123"
MAGICPL_MAINZELLISTE_CENTRAL_API_KEY: "123"
MAGICPL_CENTRAL_API_KEY: "123"
MAGICPL_OIDC_CLIENT_ID: "123"
MAGICPL_OIDC_CLIENT_SECRET: "123"
TZ: Europe/Berlin
volumes:
- "idmanager_logs:/usr/local/tomcat/logs"
@ -143,9 +141,9 @@ services:
container_name: bridgehead_dktk_patientlist_db
image: postgres:13.1-alpine
environment:
POSTGRES_PORT: 5432
POSTGRES_DB: mainzelliste
POSTGRES_USER: mainzelliste
POSTGRES_PASSWORD: ${ML_DB_PASS}
volumes:
- "patientlist_db_data:/var/lib/postgresql/data"
env_file:
###TODO: Move into Image
- internal.env

16
dktk/internal.env
View File

@ -6,12 +6,11 @@ CONNECTOR_ENABLE_METRICS=false
CONNECTOR_MONITOR_INTERVAL=
CONNECTOR_UPDATE_SERVER=
TOMCAT_REVERSEPROXY_FQDN=${HOST}/dktk-connector
DEPLOYMENT_CONTEXT=dktk-connector
POSTGRES_PORT=5432
POSTGRES_DB=samply.connector
POSTGRES_USER=samply.connector
POSTGRES_DB=share_v2
POSTGRES_USER=samplyweb
HTTP_PROXY_HOST=${PROXY_URL}
HTTP_PROXY_USER=
@ -28,9 +27,14 @@ CCP_CENTRALSEARCH_URL=https://centralsearch-test.dktk.dkfz.de/
CCP_DECENTRALSEARCH_URL=https://decentralsearch-test.ccp-it.dktk.dkfz.de/
CCP_MDR_URL=https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr
MDR_URL=https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr
CCP_MONITOR_URL=
MONITOR_OPTOUT=
PATIENTLIST_URL=http://bridgehead_patientlist:8080/Patientlist
PROJECTPSEUDONYMISATION_URL=http://bridgehead_patientlist:8080/Patientlist
## nNGM
#NNGM_URL=http://bridgeheadstore:8080
#NNGM_PROFILE=http://uk-koeln.de/fhir/StructureDefinition/Patient/nNGM/pseudonymisiert
@ -42,9 +46,9 @@ MDR_NAMESPACE=adt,dktk,marker
MDR_VALIDATION=false
ML_DB_HOST=bridgehead_dktk_patientlist_db
ML_DB_NAME=samply.connector
ML_DB_NAME=mainzelliste
ML_DB_PORT=5432
ML_DB_USER=samply.connector
ML_DB_USER=mainzelliste
CENTRAL_CONTROL_NUMBER_GENERATPR_URL=http://e260-serv-03/central/api
GLOBAL_ID=DKTK
@ -52,6 +56,8 @@ MAINZELLISTE_URL=https://patientlist-test.ccpit.dktk.dkfz.de/mainzelliste
ML_DB_DRIVER=org.postgresql.Driver
ML_DB_TYPE=postgresql
MAGICPL_MAINZELLISTE_URL=http://bridgehead_patientlist:8080
ML_LOG_LEVEL=warning
ML_SITE=BRIDGEHEAD_DKTK_TEST
TZ=Europe/Berlin

40
gbn/docker-compose.yml
View File

@ -15,11 +15,6 @@ services:
- --entrypoints.web.address=:80
- --entrypoints.web-secure.address=:443
- --providers.docker=true
environment:
http_proxy: ""
HTTP_PROXY: ""
https_proxy: ""
HTTPS_PROXY: ""
ports:
- 80:80
- 443:443
@ -58,31 +53,44 @@ services:
connector:
container_name: "bridgehead_gbn_connector"
image: "samply/share-client:gbn-7"
environment:
POSTGRES_HOST: "bridgehead_gbn_connector_db"
POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}
POSTGRES_PORT: 5432
STORE_URL: "http://bridgehead_gbn_blaze_store:8080/fhir"
env_file:
###TODO: Move into Image
- internal.env
labels:
- "traefik.enable=true"
- "traefik.http.routers.gbn_connector.rule=PathPrefix(`/gbn-connector`)"
- "traefik.http.services.gbn_connector.loadbalancer.server.port=8080"
depends_on:
- "connector-db"
environment:
POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}
POSTGRES_HOST: "bridgehead_gbn_connector_db"
MDR_URL: "https://mdr.germanbiobanknode.de/v3/api/mdr"
https_proxy: "http://www-int2.inet.dkfz-heidelberg.de:3128"
HTTP_PROXY_HOST: "http://www-int2.inet.dkfz-heidelberg.de:3128"
HTTPS_PROXY_HOST: "http://www-int2.inet.dkfz-heidelberg.de:3128"
HTTPS_PROXY_USER: ""
HTTP_PROXY_USER: ""
HTTPS_PROXY_PASSWORD: ""
HTTP_PROXY_PASSWORD: ""
HTTP_PROXY: "http://www-int2.inet.dkfz-heidelberg.de:3128"
HTTPS_PROXY: "http://www-int2.inet.dkfz-heidelberg.de:3128"
http_proxy: "http://www-int2.inet.dkfz-heidelberg.de:3128"
CATALINA_OPTS: "-agentlib:jdwp=transport=dt_socket,address=65395,server=y,suspend=n"
ports:
- 65395:65395
restart: "always"
env_file:
###TODO: Move into Image
- internal.env
connector-db:
container_name: "bridgehead_gbn_connector_db"
image: "postgres:10.17"
environment:
POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
POSTGRES_USER: "samply"
POSTGRES_DB: "samply.connector"
POSTGRES_PORT: 5432
volumes:
- "connector-db-data:/var/lib/postgresql/data"
ports:
- 5432:5432
restart: "always"
env_file:
###TODO: Move into Image
- internal.env

64
gbn/gbn.env.dev
View File

@ -1,64 +0,0 @@
SITE=
SITEID=
TESTPROD=
project=gbn
### Bridgehead Operator
# users may see this contact data for support purposes
OPERATOR_FIRST_NAME=
OPERATOR_LAST_NAME=
OPERATOR_EMAIL=
OPERATOR_PHONE=
### Proxy configuration
## ex.: http://my-proxy-host:my-proxy-port
HTTP_PROXY_HOST=
HTTP_PROXY_USER=
HTTP_PROXY_PASSWORD=
HTTPS_PROXY_HOST=
HTTPS_PROXY_USER=
HTTPS_PROXY_PASSWORD=
HTTP_PROXY=
HTTPS_PROXY=
http_proxy=
https_proxy=
NO_PROXY=
no_proxy=
### SMTP Server
## ex.: mailhost.intern.klinik.de
# MAIL_HOST=
# MAIL_PORT=25
## ex.: no-reply@bridgehead.intern.klinik.de
# MAIL_FROM_ADDRESS=
# MAIL_FROM_NAME=Bridgehead Searchbroker
## Connector
CONNECTOR_POSTGRES_HOST=
CONNECTOR_POSTGRES_PORT=
CONNECTOR_POSTGRES_DB=
CONNECTOR_POSTGRES_USER=
CONNECTOR_SHARE_URL=
CONNECTOR_ENABLE_METRICS=
CONNECTOR_MONITOR_INTERVAL=
CONNECTOR_UPDATE_SERVER=
CONNECTOR_QUERY_LANGUAGE=
CATALINA_OPTS=
MDR_URL=
CENTRAL_SEARCH=
DECENTRAL_SEARCH=
MONITOR_URL=
MONITOR_OPTOUT=
LOG_LEVEL=
feature_BBMRI_DIRECTORY_SYNC=false
feature_DKTK_CENTRAL_SEARCH=false
feature_NNGM_CTS=false
LDM_URL=
ID_MANAGER_URL=

14
gbn/internal.env
View File

@ -4,8 +4,6 @@ QUERY_LANGUAGE=CQL
CONNECTOR_SHARE_URL="http://${HOST}:8080"
MDR_URL="https://mdr.germanbiobanknode.de/v3/api/mdr"
MONITOR_URL=https://ccpit.dktk.dkfz.de/dktk.monitor/rest/info
no_proxy=bridgehead_gbn_connector,bridgehead_gbn_blaze_store,bridgehead_gbn_connector_db
TOMCAT_REVERSEPROXY_FQDN=${HOST}/gbn-connector
DEPLOYMENT_CONTEXT=gbn-connector
CONNECTOR_MONITOR_INTERVAL=
CONNECTOR_UPDATE_SERVER=
@ -13,16 +11,6 @@ feature_BBMRI_DIRECTORY_SYNC=false
feature_DKTK_CENTRAL_SEARCH=false
feature_NNGM_CTS=false
LOG_LEVEL=info
HTTP_PROXY_HOST=${PROXY_URL}
HTTP_PROXY_USER=
HTTP_PROXY_PASSWORD=
HTTPS_PROXY_HOST=${PROXY_URL}
HTTPS_PROXY_USER=
HTTPS_PROXY_PASSWORD=
HTTP_PROXY=${PROXY_URL}
HTTPS_PROXY=${PROXY_URL}
http_proxy=${PROXY_URL}
https_proxy=${PROXY_URL}
STORE_URL=http://bridgehead_gbn_blaze_store:8080
CONNECTOR_ENABLE_METRICS=false

26
internal-configuration/magicpl.xml
View File

@ -40,7 +40,7 @@
<iosingle ref="ids" name="ids"/>
</output>
<switch>
<evaluator name="de.mainzelliste.paths.evaluator.IsConsentedEvaluator">
<evaluator name="de.pseudonymisierung.magicpl.evaluator.IsConsentedEvaluator">
<parameters>
<parameter name="key">consented</parameter>
</parameters>
@ -79,7 +79,7 @@
<output>
<iosingle ref="tokenId"/>
</output>
<implementation>de.mainzelliste.paths.processor.PathClient</implementation>
<implementation>de.pseudonymisierung.magicpl.processor.PathClient</implementation>
</step>
<step>
<name>getDktkId</name>
@ -95,7 +95,7 @@
<output>
<iosingle ref="ids" name="ids"/>
</output>
<implementation>de.mainzelliste.paths.processor.MainzellisteClient</implementation>
<implementation>de.pseudonymisierung.magicpl.processor.MainzellisteClient</implementation>
</step>
<step>
<name>mapIdStringToExternalId</name>
@ -108,7 +108,7 @@
<output>
<iosingle ref="extIDs" name="extIDs"/>
</output>
<implementation>de.mainzelliste.paths.processor.InputMapperProcessor</implementation>
<implementation>de.pseudonymisierung.magicpl.processor.InputMapperProcessor</implementation>
</step>
<step>
<name>getLocalTKTExternalId</name>
@ -128,7 +128,7 @@
</output>
<!-- TODO: Implementation für Ticket Erzeugung ohne Kontrolnummer -->
<!-- Wird hier eine neue Klasse benötigt oder kann diese hier entsprechend angepasst werden? -->
<implementation>de.mainzelliste.paths.processor.MainzellisteKNTicketClient</implementation>
<implementation>de.pseudonymisierung.magicpl.processor.MainzellisteKNTicketClient</implementation>
</step>
<step>
<name>generateLocalIdExternalId</name>
@ -146,7 +146,7 @@
<output>
<iosingle ref="ids" name="ids"/>
</output>
<implementation>de.mainzelliste.paths.processor.MainzellisteClient</implementation>
<implementation>de.pseudonymisierung.magicpl.processor.MainzellisteClient</implementation>
</step>
</multipath>
</case>
@ -178,7 +178,7 @@
<iosingle ref="tokenId"/>
</output>
<!-- Wird hier eine neue Klasse benötigt oder kann diese hier entsprechend angepasst werden? -->
<implementation>de.mainzelliste.paths.processor.MainzellisteKNTicketClient</implementation>
<implementation>de.pseudonymisierung.magicpl.processor.MainzellisteKNTicketClient</implementation>
</step>
<step>
<name>generateLocalId</name>
@ -195,7 +195,7 @@
<output>
<iosingle ref="ids" name="ids"/>
</output>
<implementation>de.mainzelliste.paths.processor.MainzellisteClient</implementation>
<implementation>de.pseudonymisierung.magicpl.processor.MainzellisteClient</implementation>
</step>
</multipath>
</case>
@ -223,7 +223,7 @@
<iosingle ref="patients" name="patients"/>
</output>
<switch>
<evaluator name="de.mainzelliste.paths.evaluator.RegexEvaluator">
<evaluator name="de.pseudonymisierung.magicpl.evaluator.RegexEvaluator">
<parameters>
<parameter name="regex">MDS_\*_G-ID</parameter>
<parameter name="fieldName">resultIds</parameter>
@ -255,7 +255,7 @@
<output>
<iosingle ref="tokenId"/>
</output>
<implementation>de.mainzelliste.paths.processor.MainzellisteReadTokenClient</implementation>
<implementation>de.pseudonymisierung.magicpl.processor.MainzellisteReadTokenClient</implementation>
</step>
<step>
<name>resolveReadTokenCentral</name>
@ -269,7 +269,7 @@
<output>
<iosingle ref="patients"/>
</output>
<implementation>de.mainzelliste.paths.processor.MainzellisteReadClient</implementation>
<implementation>de.pseudonymisierung.magicpl.processor.MainzellisteReadClient</implementation>
</step>
</multipath>
</case>
@ -299,7 +299,7 @@
<output>
<iosingle ref="tokenId"/>
</output>
<implementation>de.mainzelliste.paths.processor.MainzellisteReadTokenClient</implementation>
<implementation>de.pseudonymisierung.magicpl.processor.MainzellisteReadTokenClient</implementation>
</step>
<step>
<name>resolveReadToken</name>
@ -313,7 +313,7 @@
<output>
<iosingle ref="patients"/>
</output>
<implementation>de.mainzelliste.paths.processor.MainzellisteReadClient</implementation>
<implementation>de.pseudonymisierung.magicpl.processor.MainzellisteReadClient</implementation>
</step>
</multipath>
</case>