Containerize gaia-core and gaia-db (https://github.com/OHDSI/GIS/issu…

…es/184)

.github/workflows/build_gaia_core.yml

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+name: gaia-core Docker image build
+
+on:
+  push:
+    branches:
+      - main
+
+env:
+  REGISTRY: ghcr.io
+  ORG: ohdsi
+
+jobs:
+  build-and-push-images:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        include:
+          - dockerfile: ./docker/gaia-core/Dockerfile
+            image: ghcr.io/ohdsi/gaia-core
+            context: .
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout the code
+        uses: actions/checkout@v2
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to a container registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: <SOME ADMIN USER>
+          password: ${{ secrets.GH_TOKEN }}
+
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v3
+        with:
+          images: ${{ matrix.image }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: ${{ matrix.context }}
+          file: ${{ matrix.dockerfile }}
+          push: true
+          tags: |
+            ${{ steps.meta.outputs.tags }}
+          labels: |
+            ${{ steps.meta.outputs.labels }}
+          platforms: |
+            linux/amd64
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+

.github/workflows/build_gaia_db.yml

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+name: gaia-db Docker image build
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - 'docker/gaia-db/**'
+      - 'inst/csv/**'
+      - 'vocabularies/**'
+
+env:
+  REGISTRY: ghcr.io
+  ORG: ohdsi
+
+jobs:
+  build-and-push-images:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        include:
+          - dockerfile: ./docker/gaia-db/Dockerfile
+            image: ghcr.io/ohdsi/gaia-db
+            context: .
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout the code
+        uses: actions/checkout@v2
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to a container registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: <SOME ADMIN USER>
+          password: ${{ secrets.GH_TOKEN }}
+
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v3
+        with:
+          images: ${{ matrix.image }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: ${{ matrix.context }}
+          file: ${{ matrix.dockerfile }}
+          push: true
+          tags: |
+            ${{ steps.meta.outputs.tags }}
+          labels: |
+            ${{ steps.meta.outputs.labels }}
+          platforms: |
+            linux/amd64
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+

docker/gaia-core/Dockerfile

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+FROM ohdsi/broadsea-hades:4.2.1
+LABEL maintainer="Tufts Medical Center <[email protected]>"
+USER root
+
+RUN Rscript -e 'remotes::install_github("OHDSI/GIS")'
+
+#ENTRYPOINT ["/app/entrypoint.sh"]

docker/gaia-db/Dockerfile

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+FROM postgis/postgis:16-3.4-alpine
+
+RUN mkdir /csv
+COPY inst/csv/data_source.csv /csv/data_source.csv
+COPY inst/csv/variable_source.csv /csv/variable_source.csv
+COPY vocabularies/gis_vocabs_vocabulary_stage_v1.csv /csv/gis_vocabulary_fragment.csv
+COPY vocabularies/gis_vocabs_concept_class_stage_v1.csv /csv/gis_concept_class_fragment.csv
+COPY vocabularies/gis_vocabs_domain_stage_v1.csv /csv/gis_domain_fragment.csv
+COPY vocabularies/gis_vocabs_concept_stage_v1.csv /csv/gis_concept_fragment.csv
+COPY vocabularies/gis_vocabs_relationship_stage_v1.csv /csv/gis_relationship_fragment.csv
+COPY vocabularies/gis_vocabs_concept_relationship_stage_v1.csv /csv/gis_concept_relationship_fragment.csv
+COPY docker/gaia-db/init.sql /docker-entrypoint-initdb.d/init.sql

docker/gaia-db/README.md

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+# Dockerized GAIA-DB
+
+You can run this container directly with the following command:
+
+```bash
+sudo docker run --rm --env POSTGRES_PASSWORD=<YOUR PASSWORD> <IMAGE NAME>:latest
+```
+
+The image contains the PostGIS extension, the backbone schema with the catalog tables loaded, and a vocabulary schema
+with