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SampleLocator

This project was generated with Angular CLI version 9.0.3.

Development server

Run ng serve for a dev server. Navigate to http://localhost:8085/. The app will automatically reload if you change any of the source files.

Build

Run ng build --prod to build the project. The build artifacts will be stored in the dist/ directory. Use the --prod flag for a production build.

Docker

Run docker build . to build a Docker image. It's not necessary to run ng build --prod before, because a build container is used.

Run (Docker)

Docker

docker build -t sample-locator .

docker run 
    --rm 
    --name=sample-locator
    -p 8085:80 
    -e SEARCHBROKER_URL="http://localhost:8080" 
    -e SAMPLELOCATOR_URL="http://localhost:8085" 
    -e NEGOTIATOR_URL="https://negotiator.bbmri-eric.eu" 
    -e TERMINOLOGY_SERVER_URL="https://r4.ontoserver.csiro.au/fhir"
    -e AUTH_HOST="https://login.bbmri-eric.eu" 
    -e AUTH_CLIENT_ID="88ad6e4f-af9b-430a-8884-394e29cd10c1" 
    -e MDR_API_URL="http://mdr.test.germanbiobanknode.de/v3/api/mdr" 
    -e MDR_NAMESPACE="mdr16" 
    -e MDR_LANGUAGE="en" 
    -e MDR_MAPPING="[{\"nameOfEnum\": \"DONOR\",\"urn\": \"urn:mdr16:dataelementgroup:5:1\"},{\"nameOfEnum\": \"SAMPLE\",\"urn\": \"urn:mdr16:dataelementgroup:3:1\"},{\"nameOfEnum\": \"EVENT\", \"urn\": \"urn:mdr16:dataelementgroup:6:1\"}]" 
    -e MDR_FIELD_PROPERTIES="[{\"urn\": \"urn:mdr16:dataelement:29:1\",\"placeholder\": \"\",\"unit\": \"kg\"},{\"urn\": \"urn:mdr16:dataelement:30:1\",\"placeholder\": \"\",\"unit\": \"cm\"},{\"urn\": \"urn:mdr16:dataelement:28:1\",\"placeholder\": \"\",\"unit\": \"years\"},{\"urn\": \"urn:mdr16:dataelement:14:1\",\"placeholder\": \"\",\"unit\": \"years\"},{\"urn\": \"urn:mdr16:dataelement:27:1\",\"placeholder\": \"e.g. C25.1\",\"unit\": \"\", \"valueSetUrl\": \"http://hl7.org/fhir/ValueSet/condition-code\"}]" 
    -e MDR_HIDDEN="[\"urn:mdr16:dataelement:1:1\",\"urn:mdr16:dataelement:25:1\",\"urn:mdr16:dataelement:34:1\",\"urn:mdr16:dataelement:18:1\",\"urn:mdr16:dataelement:11:1\",\"urn:mdr16:dataelement:19:1\",\"urn:mdr16:dataelement:30:1\",\"urn:mdr16:dataelement:4:1\",\"urn:mdr16:dataelement:21:1\",\"urn:mdr16:dataelement:22:1\",\"urn:mdr16:dataelement:24:1\",\"urn:mdr16:dataelement:13:1\"]" 
    -e MOLGENIS_USERNAME="your_molgenis_username" 
    -e MOLGENIS_PASSWORD="your_molgenis_password" 
    sample-locator:latest
Envionment variable Meaning Default
SAMPLELOCATOR_URL URL of the Sample Locator
SEARCHBROKER_URL URL of the Searchbroker API (Backend)
NEGOTIATOR_URL URL of the Negotiator
TERMINOLOGY_SERVER_URL URL of the terminology server
AUTH_HOST URL of the OpenID Connect provider
AUTH_CLIENT_ID Client-ID of the OpenID Connect Provider
MOLGENIS_USERNAME Username of Molgenis
MOLGENIS_PASSWORD Password of Molgenis
MDR_API_URL URL of the MDR
MDR_NAMESPACE Namespace of the MDR
MDR_LANGUAGE Language code for the MDR
MDR_MAPPING MDR entities and their URNs []
MDR_FIELD_PROPERTIES Specification of placeholder and units for fields []
MDR_HIDDEN Fields to be ignored []
FEATURE_STRATIFIER Feature toggle for stratifications false
FEATURE_STRATIFIER_MIN_NO_BIOBANKS Minimal number of connectors which must send stratifications in order to show stratifications 3

License

Copyright 2020 The Samply Development Community

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

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The sample locator is a graphical user interface for searching bio samples.

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