From a1217969068dddfa03d991323cd7c70130a32d64 Mon Sep 17 00:00:00 2001
From: Marcelle <53578688+m-goggins@users.noreply.github.com>
Date: Wed, 16 Oct 2024 11:45:24 -0400
Subject: [PATCH 1/4] move migration 5 to correct location (#26)

---
 .../flyway/sql/V01_05__insert_nbs_hardcoded_values.sql            | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename {containers/tefca-viewer => query-connector}/flyway/sql/V01_05__insert_nbs_hardcoded_values.sql (100%)

diff --git a/containers/tefca-viewer/flyway/sql/V01_05__insert_nbs_hardcoded_values.sql b/query-connector/flyway/sql/V01_05__insert_nbs_hardcoded_values.sql
similarity index 100%
rename from containers/tefca-viewer/flyway/sql/V01_05__insert_nbs_hardcoded_values.sql
rename to query-connector/flyway/sql/V01_05__insert_nbs_hardcoded_values.sql

From dd3e4a28d631832f94446b920120f3af748d2638 Mon Sep 17 00:00:00 2001
From: Daniel Paseltiner <99684231+DanPaseltiner@users.noreply.github.com>
Date: Wed, 16 Oct 2024 12:07:52 -0400
Subject: [PATCH 2/4] First draft of CD workflow (#27)

---
 .github/workflows/cd.yaml | 43 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 .github/workflows/cd.yaml

diff --git a/.github/workflows/cd.yaml b/.github/workflows/cd.yaml
new file mode 100644
index 000000000..57894ef23
--- /dev/null
+++ b/.github/workflows/cd.yaml
@@ -0,0 +1,43 @@
+name: CD
+
+on:
+  merge_group:
+    types:
+      - checks_requested
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: Build Query Connector Image
+    runs-on: ubuntu-latest
+    permissions:
+      contents: "read"
+      id-token: "write"
+      packages: "write"
+    steps:
+      - name: Check Out Changes
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push
+        uses: docker/build-push-action@v3
+        working-directory: ./query-connector
+        with:
+          push: true
+          tags: [main, latest]

From f4801c39bb5cbe54848f4c419a6df6d94ba3f560 Mon Sep 17 00:00:00 2001
From: Daniel Paseltiner <99684231+DanPaseltiner@users.noreply.github.com>
Date: Wed, 16 Oct 2024 12:26:44 -0400
Subject: [PATCH 3/4] Update cd.yaml (#28)

---
 .github/workflows/cd.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cd.yaml b/.github/workflows/cd.yaml
index 57894ef23..830742367 100644
--- a/.github/workflows/cd.yaml
+++ b/.github/workflows/cd.yaml
@@ -37,7 +37,7 @@ jobs:
 
       - name: Build and push
         uses: docker/build-push-action@v3
-        working-directory: ./query-connector
         with:
+          context: ./query-connector
           push: true
-          tags: [main, latest]
+          tags: ghcr.io/${{ github.repository }}/query-connector:main, ghcr.io/${{ github.repository }}/query-connector:latest

From af54b91ce94198cff7c1ae6c380d99e1b149836d Mon Sep 17 00:00:00 2001
From: Daniel Paseltiner <99684231+DanPaseltiner@users.noreply.github.com>
Date: Wed, 16 Oct 2024 12:56:50 -0400
Subject: [PATCH 4/4] Removing old workflows we don't need anymore (#29)

---
 .github/workflows/buildReleaseContainers.yaml |  82 -----
 .github/workflows/createNewRelease.yaml       | 285 ------------------
 .github/workflows/run-container-workflow.yaml |  19 --
 3 files changed, 386 deletions(-)
 delete mode 100644 .github/workflows/buildReleaseContainers.yaml
 delete mode 100644 .github/workflows/createNewRelease.yaml
 delete mode 100644 .github/workflows/run-container-workflow.yaml

diff --git a/.github/workflows/buildReleaseContainers.yaml b/.github/workflows/buildReleaseContainers.yaml
deleted file mode 100644
index c809d5c37..000000000
--- a/.github/workflows/buildReleaseContainers.yaml
+++ /dev/null
@@ -1,82 +0,0 @@
-name: Build Release Specific Containers
-
-on:
-  workflow_call:
-    inputs:
-      container-tag:
-        type: string
-        required: true
-  workflow_dispatch:
-    inputs:
-      container-tag:
-        type: string
-        required: true
-
-jobs:
-  list-containers:
-    uses: ./.github/workflows/listContainers.yaml
-  build:
-    name: Build containers
-    needs: list-containers
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        container-to-build: ${{fromJson(needs.list-containers.outputs.all-containers)}}
-    permissions:
-      contents: "read"
-      id-token: "write"
-      packages: "write"
-    steps:
-      - name: Check Out Changes
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-          ref: ${{ inputs.container-tag }}
-
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-
-      - name: Log in to the Container registry
-        uses: docker/login-action@v2
-        with:
-          registry: ghcr.io
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Extract metadata (tags, labels) for Docker
-        id: meta
-        uses: docker/metadata-action@v4
-        with:
-          ref: ${{ inputs.container-tag }}
-          images: ghcr.io/${{ github.repository }}/${{matrix.container-to-build}}
-          # this sets the version for tags and labels for each of the containers to be
-          # be the same as the version/tag where the code was pulled from
-          tags: |
-            type=semver,pattern={{raw}},value=${{ inputs.container-tag }}
-            type=ref,event=branch
-            type=ref,event=tag,pattern={{raw}},value=${{ inputs.container-tag }}
-          labels: |
-            org.opencontainers.image.version=${{ inputs.container-tag }}
-
-      - name: Build and push
-        uses: docker/build-push-action@v3
-        if: ${{ !contains(fromJSON('["ecr-viewer", "tefca-viewer"]'), matrix.container-to-build) }}
-        with:
-          context: ./containers/${{matrix.container-to-build}}
-          push: true
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
-
-      - name: Build and push with shared-resources
-        uses: docker/build-push-action@v3
-        if: ${{ contains(fromJSON('["ecr-viewer", "tefca-viewer"]'), matrix.container-to-build) }}
-        with:
-          context: .
-          file: ./containers/${{ matrix.container-to-build }}/Dockerfile
-          push: true
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
diff --git a/.github/workflows/createNewRelease.yaml b/.github/workflows/createNewRelease.yaml
deleted file mode 100644
index 8468c7229..000000000
--- a/.github/workflows/createNewRelease.yaml
+++ /dev/null
@@ -1,285 +0,0 @@
-name: Create New Release
-on:
-  workflow_dispatch:
-  push:
-    branches:
-      - main
-
-# Run all tests before making a release
-jobs:
-  # Only make a release if commit contains [RELEASE]
-  check-commit-message:
-    runs-on: ubuntu-latest
-    outputs:
-      contains_release: ${{ steps.commit_check.outputs.contains_release }}
-    steps:
-      - name: Check out code
-        uses: actions/checkout@v4
-      - name: Check commit message for [RELEASE]
-        id: commit_check
-        run: |
-          if [[ "${{ github.event.head_commit.message }}" == *"[RELEASE]"* ]]; then
-            echo "contains_release=true" >> $GITHUB_OUTPUT
-          else
-            echo "contains_release=false" >> $GITHUB_OUTPUT
-          fi
-  list-containers:
-    needs: check-commit-message
-    if: ${{ needs.check-commit-message.outputs.contains_release == 'true' }}
-    uses: ./.github/workflows/listContainers.yaml
-
-  test-for-release:
-    needs:
-      - check-commit-message
-      - list-containers
-    if: ${{ needs.check-commit-message.outputs.contains_release == 'true' }}
-    strategy:
-      matrix:
-        container: ${{fromJson(needs.list-containers.outputs.all-containers)}}
-    uses: ./.github/workflows/run-container-workflow.yaml
-    with:
-      container: ${{ matrix.container }}
-    secrets: inherit
-
-  tag-release:
-    name: Update phdi init version number
-    needs: test-for-release
-    permissions:
-      contents: write
-    outputs:
-      version: ${{ steps.get_version.outputs.version }}
-    runs-on: ubuntu-22.04
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: "0"
-          ref: "main"
-      - name: Install poetry and dependencies
-        run: |
-          pip install poetry
-      # update the version number in the phdi/__init.py__ file
-      - name: Get PHDI Version
-        id: get_version
-        run: |
-          VERSION_WITH_PHDI=$(poetry version)
-          echo "version=${VERSION_WITH_PHDI:5}" >> $GITHUB_OUTPUT
-      # Create new release tag
-      - name: Set up Git user
-        run: |
-          git config --local user.email "action@github.com"
-          git config --local user.name "GitHub Action"
-      - name: Tag Release
-        uses: EndBug/latest-tag@latest
-        with:
-          ref: ${{ steps.get_version.outputs.version }}
-      # Generate release notes
-      - name: Generate release notes
-        id: release_notes
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          latest_release_date=$(gh api "/repos/$GITHUB_REPOSITORY/releases?per_page=1" | jq ".[0].created_at")
-          prs=$(gh pr list --base main --state closed --json title,number,url,closedAt -q ".[] | select(.closedAt > $latest_release_date) | select(.title | contains(\"RELEASE\") | not)")
-
-          echo "# Release Notes" > release-notes.md
-          echo "" >> release-notes.md
-          echo "" >> release-notes.md
-
-          while IFS= read -r pr; do
-              pr_title=$(echo "$pr" | jq -r ".title")
-              pr_number=$(echo "$pr" | jq -r ".number")
-              pr_url=$(echo "$pr" | jq -r ".url")
-              line_text="- $pr_title ([#$pr_number]($pr_url))"
-              echo $line_text >> release-notes.md
-          done < <(printf '%s' "$prs")
-
-      # Create new release based upon the latest created tag
-      - name: Create Release
-        id: create_release
-        uses: actions/create-release@v1.1.4
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          tag_name: ${{ steps.get_version.outputs.version }}
-          release_name: ${{ steps.get_version.outputs.version }}
-          body_path: release-notes.md
-
-  release-to-pypi:
-    name: Build and publish PHDI to PyPI
-    needs: tag-release
-    runs-on: ubuntu-latest
-    permissions:
-      id-token: write
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: "0"
-          ref: ${{ needs.tag-release.outputs.version }}
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.x"
-      - name: Install pypa/build
-        run: >-
-          python -m
-          pip install
-          build
-          --user
-      - name: Build a binary wheel and a source tarball
-        run: >-
-          python -m
-          build
-          --sdist
-          --wheel
-          --outdir dist/
-          .
-      - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
-
-  # Rebuild all containers for the new release
-  build-containers-for-release:
-    needs:
-      - tag-release
-      - release-to-pypi
-    permissions:
-      contents: read
-      packages: write
-      id-token: write
-    uses: ./.github/workflows/buildReleaseContainers.yaml
-    with:
-      container-tag: ${{ needs.tag-release.outputs.version }}
-
-  # Create updated PHDI docs for the latest release
-  generate-and-update-phdi-docs:
-    needs:
-      - tag-release
-      - build-containers-for-release
-    permissions:
-      contents: write
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: "0"
-          ref: ${{ needs.tag-release.outputs.version }}
-
-      - name: Install poetry and dependencies
-        run: |
-          pip install poetry
-          poetry install
-
-      - name: Set environment variable for pdoc
-        run: echo "PDOC_ALLOW_EXEC=1" >> $GITHUB_ENV
-
-      - name: Clear Poetry Cache
-        run: |
-          poetry cache clear pypi --all
-          poetry cache clear virtualenvs --all
-
-      - name: Generate docs and move to docs branch
-        run: |
-          poetry run pdoc ./phdi -o ./docs/${{ needs.tag-release.outputs.version }}/sdk
-
-      - uses: actions/upload-artifact@v3
-        with:
-          name: phdi-docs
-          path: ./docs/${{ needs.tag-release.outputs.version }}/sdk
-
-  # Create updated container docs for the latest release
-  generate-and-update-container-docs:
-    needs:
-      - tag-release
-      - list-containers
-      - generate-and-update-phdi-docs
-    permissions:
-      contents: write
-    runs-on: ubuntu-latest
-    services:
-      test-db:
-        image: postgres:13-alpine3.16
-        env:
-          POSTGRES_PASSWORD: pw
-          POSTGRES_DB: testdb
-          POSTGRES_USER: postgres
-        # Set health checks to wait until postgres has started
-        options: >-
-          --health-cmd pg_isready
-          --health-interval 10s
-          --health-timeout 5s
-          --health-retries 5
-          --name testdb
-        ports:
-          - 5432:5432
-    strategy:
-      matrix:
-        container: ${{fromJson(needs.list-containers.outputs.python-containers)}}
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: "0"
-          ref: ${{ needs.tag-release.outputs.version }}
-
-      - name: Update Container Documentation
-        env:
-          MPI_DBNAME: testdb
-          MPI_PASSWORD: pw
-          MPI_DB_TYPE: postgres
-          MPI_HOST: localhost
-          MPI_USER: postgres
-          MPI_PORT: 5432
-          MPI_PATIENT_TABLE: patient
-          MPI_PERSON_TABLE: person
-        run: |
-          npm i -g redoc-cli
-          CONTAINER=${{ matrix.container }}
-          cd $GITHUB_WORKSPACE/containers/$CONTAINER
-          cp $GITHUB_WORKSPACE/utils/make_openapi_json.py .
-          pip install -r requirements.txt
-          python make_openapi_json.py
-          redoc-cli build -o $GITHUB_WORKSPACE/docs/${{ needs.tag-release.outputs.version }}/containers/$CONTAINER.html openapi.json
-
-      - uses: actions/upload-artifact@v3
-        with:
-          name: container-docs
-          path: ./docs/${{ needs.tag-release.outputs.version }}/containers
-
-  commit-docs:
-    needs:
-      - tag-release
-      - generate-and-update-phdi-docs
-      - generate-and-update-container-docs
-    permissions:
-      contents: write
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          ref: docs
-
-      - name: Download phdi docs from artifacts
-        uses: actions/download-artifact@v4.1.7
-        with:
-          name: phdi-docs
-          path: ./docs/${{ needs.tag-release.outputs.version }}/sdk
-
-      - name: Download container docs from artifacts
-        uses: actions/download-artifact@v4.1.7
-        with:
-          name: container-docs
-          path: ./docs/${{ needs.tag-release.outputs.version }}/containers
-
-      - name: Copy to latest folder
-        run: |
-          rm -rf ./docs/latest
-          mkdir -p ./docs/latest/sdk
-          mkdir -p ./docs/latest/containers
-          cp -r ./docs/${{ needs.tag-release.outputs.version }}/sdk/* ./docs/latest/sdk
-          cp -r ./docs/${{ needs.tag-release.outputs.version }}/containers/* ./docs/latest/containers
-
-      - name: Commit New Documentation
-        uses: EndBug/add-and-commit@v9
-        with:
-          add: docs
-          message: Automated update of docs for ${{ needs.tag-release.outputs.version }} release.
diff --git a/.github/workflows/run-container-workflow.yaml b/.github/workflows/run-container-workflow.yaml
deleted file mode 100644
index fd942e81f..000000000
--- a/.github/workflows/run-container-workflow.yaml
+++ /dev/null
@@ -1,19 +0,0 @@
-name: "Run Container Workflow"
-on:
-  workflow_call:
-    inputs:
-      container:
-        required: true
-        type: string
-jobs:
-  run-container-workflow:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Run specified workflow
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          gh workflow run .github/workflows/container-${{ inputs.container }}.yaml