jlab · sjanssen2 · Sep 12, 2025 · Sep 12, 2025 · Sep 12, 2025 · Sep 12, 2025
diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
@@ -3,9 +3,12 @@
 name: docker
 
 on:
+  pull_request:
+    branches:
+      - tinqiita
   push:
     branches:
-      - 'restructure_github_actions'
+      - tinqiita
 
 jobs:
   make_certificates:
@@ -170,89 +173,91 @@ jobs:
           file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
           tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
 
-  # build_mulit_plugins:
-  #   needs:
-  #     - build_plugins
-  #   strategy:
-  #     matrix:
-  #       plugin: ["qp-qiime2"]
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - name: Checkout tinqiita repo
-  #       uses: actions/checkout@v4
-
-  #     - name: Set up Docker Buildx
-  #       uses: docker/setup-buildx-action@v3
-
-  #     - name: Read image version from dockerfile
-  #       id: vars
-  #       run: |
-  #         VERSION=$(head -n 1 Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
-  #         echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
-  #         cp Images/${{ matrix.plugin }}/start_${{ matrix.plugin }}.sh Images/test_plugin.sh Images/${{ matrix.plugin }}/requirements.txt Images/trigger_noconda.py Images/trigger.py .
-
-  #     - name: Download certificates from job build_main
-  #       uses: actions/download-artifact@v4
-  #       with:
-  #         name: certificates
-  #         path: ./
-  #     - name: Download fake references
-  #       uses: actions/download-artifact@v4
-  #       with:
-  #         name: fake_references
-  #         path: ./
-
-  #     - name: Log in to GitHub Container Registry
-  #       uses: docker/login-action@v3
-  #       with:
-  #         registry: ghcr.io
-  #         username: ${{ github.actor }}
-  #         password: ${{ secrets.GITHUB_TOKEN }}
-
-  #     - name: Build plugin images
-  #       uses: docker/build-push-action@v6
-  #       with:
-  #         context: .
-  #         load: true
-  #         file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
-  #         tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
-  #         cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
-  #         cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
-
-  #     - name: adapt compose file to select specific plugin
-  #       run: |
-  #         sed -i "s|||" compose_github.yaml
-  #         sed -i "s/MATRIXPLUGIN/${{ matrix.plugin }}/g" compose_github.yaml
-
-  #     - name: Run docker compose
-  #       uses: hoverkraft-tech/compose-action@v2.0.1
-  #       with:
-  #         compose-file: "compose_github.yaml"
-  #         services: |
-  #           nginx
-
-  #     - name: Execute tests in the running services
-  #       run: |
-  #         sleep 5
-  #         docker compose exec ${{ matrix.plugin }} /bin/bash -c "bash /test_plugin.sh"
-
-  #     - name: Push image to ghcr (only if tests passed)
-  #       if: success()
-  #       uses: docker/build-push-action@v6
-  #       with:
-  #         context: .
-  #         push: true
-  #         file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
-  #         tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
+  # the qp-qiime2 plugin cannot be tested in isolation, it also needs qtp-diversity and qtp-visualization to be active in qiita
+  build_mulit_plugins:
+    needs:
+      - build_plugins
+    strategy:
+      matrix:
+        multiplugin: ["qp-qiime2"]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout tinqiita repo
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Read image version from dockerfile
+        id: vars
+        run: |
+          VERSION=$(head -n 1 Images/${{ matrix.multiplugin }}/${{ matrix.multiplugin }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
+          echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
+          cp Images/${{ matrix.multiplugin }}/start_${{ matrix.multiplugin }}.sh Images/test_plugin.sh Images/${{ matrix.multiplugin }}/requirements.txt Images/trigger_noconda.py Images/trigger.py .
+
+      - name: Download certificates from job build_main
+        uses: actions/download-artifact@v4
+        with:
+          name: certificates
+          path: ./
+      - name: Download fake references
+        uses: actions/download-artifact@v4
+        with:
+          name: fake_references
+          path: ./
+
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build plugin images
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          load: true
+          file: Images/${{ matrix.multiplugin }}/${{ matrix.multiplugin }}.dockerfile
+          tags: ghcr.io/${{ github.repository }}/${{ matrix.multiplugin }}:testcandidate
+          cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
+          cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
+
+      - name: adapt compose file to select specific plugin
+        run: |
+          if [[ "${{ matrix.multiplugin }}" == "qp-qiime2" ]]; then sed -i 's|- QIITA_PLUGINS="MATRIXPLUGIN:"|- QIITA_PLUGINS="${{ matrix.multiplugin }}:qtp-diversity:qtp-visualization:"|' compose_github.yaml; sed -i 's|MATRIXPLUGIN:|${{ matrix.multiplugin }}:\n        condition: service_started\n      qtp-diversity:\n        condition: service_started\n      qtp-visualization:|' compose_github.yaml; fi;
+
+      - name: Run docker compose
+        uses: hoverkraft-tech/compose-action@v2.0.1
+        with:
+          compose-file: "compose_github.yaml"
+          services: |
+            nginx
+
+      - name: Execute tests in the running services
+        run: |
+          sleep 5
+          docker compose exec ${{ matrix.multiplugin }} /bin/bash -c "bash /test_plugin.sh"
+
+      - name: Push image to ghcr (only if tests passed)
+        if: success()
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: true
+          file: Images/${{ matrix.multiplugin }}/${{ matrix.multiplugin }}.dockerfile
+          tags: ghcr.io/${{ github.repository }}/${{ matrix.multiplugin }}:testcandidate
 
   publish_images:
     needs:
       - build_plugins
       - build_main
+      - build_mulit_plugins
     strategy:
       matrix:
         image: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder",
-                 "nginx", "qiita", "plugin_collector"]
+                 "nginx", "qiita", "plugin_collector",
+                 "qp-qiime2"]
     runs-on: ubuntu-latest
     steps:
       - name: Checkout tinqiita repo

diff --git a/Images/qp-qiime2/qp-qiime2.dockerfile b/Images/qp-qiime2/qp-qiime2.dockerfile
@@ -28,14 +28,16 @@ RUN wget https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_
 
 # install tornado based trigger layer in base environment
 RUN pip install -U pip
-RUN conda install tornado
+RUN pip install tornado
 COPY trigger.py /trigger.py
 
 # Download qiime2 yaml
 RUN wget --quiet https://data.qiime2.org/distro/core/qiime2-2023.5-py38-linux-conda.yml
 
 # Create conda env
-RUN conda env create --name qiime2 -y --file qiime2-2023.5-py38-linux-conda.yml
+RUN conda env create --name qiime2 -y --file qiime2-2023.5-py38-linux-conda.yml \
+  && conda clean --all -y \
+  && rm -rf /opt/conda/pkgs
 # Make RUN commands use the new environment:
 # append --format docker to the build command, see https://github.com/containers/podman/issues/8477
 SHELL ["conda", "run", "-p", "/opt/conda/envs/qiime2", "/bin/bash", "-c"]
@@ -61,8 +63,9 @@ RUN export QP_QIIME2_DBS=/databases
 
 # configuring the filtering QZAs available for QIIME 2
 RUN mkdir /filtering
-RUN wget -O /filtering/bloom-analyses.zip https://github.com/knightlab-analyses/bloom-analyses/archive/refs/heads/master.zip
-RUN unzip -j /filtering/bloom-analyses.zip bloom-analyses-master/data/qiime2-artifacts-for-qiita/*.qza -d /filtering/
+RUN wget -O /filtering/bloom-analyses.zip https://github.com/knightlab-analyses/bloom-analyses/archive/refs/heads/master.zip \
+  && unzip -j /filtering/bloom-analyses.zip bloom-analyses-master/data/qiime2-artifacts-for-qiita/*.qza -d /filtering/ \
+  && rm -f /filtering/bloom-analyses.zip
 RUN export QP_QIIME2_FILTER_QZA=/filtering/
 
 # TODO: should the plugin get the server configuration?!

diff --git a/Images/qp-qiime2/requirements.txt b/Images/qp-qiime2/requirements.txt
@@ -0,0 +1,9 @@
+tornado
+q2-umap
+q2-greengenes2
+certifi
+pip-system-certs
+
+-e /qiita_client
+-e /qiita-files
+-e /qp-qiime2
diff --git a/Images/test_plugin.sh b/Images/test_plugin.sh
@@ -11,8 +11,10 @@ else
     REQUESTS_CA_BUNDLE="" pip install pytest;
 fi;
 
-# clone plugin repository
-git clone https://github.com/qiita-spots/${PLUGIN}
+if [ "qp-qiime2" != "$PLUGIN" ]; then
+    # clone plugin repository
+    git clone https://github.com/qiita-spots/${PLUGIN}
+fi;
 
 # NOTE: client api reset only works when communicating with Qitta Master,
 # thus, you need to directly address the port of the master container. Don't
@@ -42,4 +44,8 @@ export QIITA_PORT=21174
 export QIITA_ROOTCA_CERT=$SSL_CERT_FILE
 
 # change into plugin source directory and execute actual tests
-cd ${PLUGIN} && pytest
+if [ "qp-qiime2" == "$PLUGIN" ]; then
+    source /opt/conda/etc/profile.d/conda.sh; conda activate /opt/conda/envs/qiime2; cd ${PLUGIN} && pytest;
+else
+    cd ${PLUGIN} && pytest;
+fi;