diff --git a/docker-compose.yaml b/docker-compose.yaml index 2fee04b..98e3d36 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -10,4 +10,5 @@ services: volumes: - /var/run/docker.sock:/var/run/docker.sock:ro - ./pipeline.yaml:/data/pipeline.yaml - - ./log:/log \ No newline at end of file + - ./log:/log + - ./pipeline.env:/data/.env diff --git a/pipeline.yaml b/pipeline.yaml index cd17044..eafdbf9 100644 --- a/pipeline.yaml +++ b/pipeline.yaml @@ -6,7 +6,21 @@ CovidGraphPipeline: dependencies: - CREATE_FULL_TEXT_INDEXES - name: BIOBASE - image_repo: covidgraph/data_biobase + info_link: https://git.connect.dzd-ev.de/dzdconnectpipeline/dataloading_biobase + desc: Load different bio science repos into neo4j + image_repo: registry-gl.connect.dzd-ev.de:443/dzdconnectpipeline/dataloading_biobase + tag: prod + env_vars: + RUN_MODE: NotTest + - name: ONTOLOGIES + info_link: https://git.connect.dzd-ev.de/dzdconnectpipeline/dataloading_ontologies + desc: Load biomedical ontologies and mappings from biomedical entities to ontologies. + image_repo: registry-gl.connect.dzd-ev.de:443/dzdconnectpipeline/dataloading_ontologies + tag: prod + env_vars: + OBO_ONTOLOGIES: go,doid,mp,pato,hp + dependencies: + - BIOBASE - name: LENS_PATENT_DATA image_repo: covidgraph/data-lens-org-covid19-patents - name: CORD19 @@ -35,9 +49,9 @@ CovidGraphPipeline: image_repo: covidgraph/data-biobert dependencies: - CORD19 - #- name: MASYMOS - # image_repo: covidgraph/data_masymos - # env_vars: - # SOURCE: ${MASYMOS_SOURCE_FILE} - # dependencies: - # - CORD19 + - name: MASYMOS + image_repo: covidgraph/data_masymos + env_vars: + SOURCE: ${MASYMOS_SOURCE_FILE} + dependencies: + - CORD19