Merge pull request #62 from jlab/preview_merge_uncouple_clientpush

Preview merge uncouple clientpush

Author: sjanssen2

.github/workflows/buildContainer.yaml

@@ -49,9 +49,9 @@ jobs:
         run: |
           VERSION=$(head -n 1 Images/${{ matrix.container }}/${{ matrix.container }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
           echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
-          cp Images/${{ matrix.container }}/start_${{ matrix.container }}.sh Images/test_plugin.sh Images/nginx/nginx_qiita.conf Images/${{ matrix.container }}/requirements.txt .
+          cp Images/start_plugin.sh Images/test_plugin.sh Images/nginx/nginx_qiita.conf Images/${{ matrix.container }}/requirements.txt Images/nginx/start_nginx.sh .
           cp Images/qiita/config_portal.cfg Images/qiita/config_qiita_oidc.cfg Images/qiita/drop_workflows.py Images/qiita/start_plugin.py Images/qiita/start_qiita-initDB.sh Images/qiita/start_qiita.sh .
-          cp Images/plugin_collector/collect_configs.py Images/plugin_collector/fix_test_db.py Images/plugin_collector/stefan_cert.conf Images/plugin_collector/stefan_csr.conf .
+          cp Images/plugin_collector/collect_configs.py Images/plugin_collector/fix_test_db.py Images/plugin_collector/stefan_cert.conf Images/plugin_collector/stefan_csr.conf Images/plugin_collector/start_plugin_collector.sh .
 
       - name: Download certificates from job build_main
         uses: actions/download-artifact@v4
@@ -119,7 +119,7 @@ jobs:
         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 .
+          cp Images/start_plugin.sh Images/test_plugin.sh Images/${{ matrix.plugin }}/requirements.txt Images/trigger.py .
 
       - name: Download certificates from job build_main
         uses: actions/download-artifact@v4
@@ -196,7 +196,7 @@ jobs:
         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 .
+          cp Images/start_plugin.sh Images/test_plugin.sh Images/${{ matrix.multiplugin }}/requirements.txt Images/trigger.py .
 
       - name: Download certificates from job build_main
         uses: actions/download-artifact@v4
@@ -252,12 +252,6 @@ jobs:
         if: success()
         run: |
           docker push ghcr.io/${{ github.repository }}/${{ matrix.multiplugin }}:testcandidate
-        #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:

Images/nginx/nginx.dockerfile

@@ -10,4 +10,4 @@ RUN chmod 777 start_nginx.sh
 
 RUN mkdir -p /var/log/nginx
 
-CMD ["nginx", "/start_nginx.sh"]
+CMD ["/start_nginx.sh"]

Images/nginx/start_nginx.sh

@@ -2,4 +2,19 @@
 mkdir -p /var/run/nginx/ /usr/local/var/tmp/nginx/
 
 nginx -t -c /qiita_configuration/nginx_qiita.conf
-nginx -c /qiita_configuration/nginx_qiita.conf
+
+# proper listening and reacting to SIGTERM
+cleanup() {
+    echo "Received SIGTERM, stopping..."
+    kill "$PY_PID" 2>/dev/null
+    wait "$PY_PID"
+    exit 0
+}
+trap cleanup SIGTERM SIGINT
+
+# start nginx and safe PID in variable
+nginx -c /qiita_configuration/nginx_qiita.conf &
+PY_PID=$!
+
+# wait till nginx process is terminated
+wait "$PY_PID"

Images/qiita/qiita.dockerfile

@@ -98,4 +98,4 @@ RUN conda install hcc::aspera-cli
 # something is wired with permissions of the git repo?!
 RUN git config --global --add safe.directory /qiita
 
-# CMD ["conda", "run", "-n", "qiita"]
+CMD ["/start_qiita.sh"]

Images/qiita/start_qiita.sh

@@ -2,31 +2,26 @@
 
 CONDA_DIR=/opt/conda
 ENV_NAME=qiita
-#PORT=21174
 
-#sleep 300000
-#export QIITA_CONFIG_FP="/qiita/config_qiita_oidc.cfg"
 if [ -n "${MASTER}" ] && [ ! -d /qiita/qiita_db/__pycache__ ]; then
 	source $CONDA_DIR/etc/profile.d/conda.sh; conda activate $CONDA_DIR/envs/$ENV_NAME; cd /qiita; pip install -e . --no-binary redbiom;
 fi
 
-# # We execute qiita-env make every time. We expect that it will fail always but the very first time, as the qiita DB should exist from then on
-# source $CONDA_DIR/etc/profile.d/conda.sh; conda activate $CONDA_DIR/envs/$ENV_NAME; cd /qiita; qiita-env make --no-load-ontologies 2> .env-make.err || true
-# # To avoid confusing the user, STDERR is written into a file and only reported if it does not contain the text that we expect to see if it just reports the existing DB
-# grep 'already present on the system. You can drop it by running' .env-make.err > /dev/null || cat .env-make.err
+# proper listening and reacting to SIGTERM
+cleanup() {
+    echo "Received SIGTERM, stopping..."
+    kill "$PY_PID" 2>/dev/null
+    wait "$PY_PID"
+    exit 0
+}
+trap cleanup SIGTERM SIGINT
 
-# This was commented out bc it stopped working anymore and i was focusing on fixing something else, if you create the database for the first
-# time you will have to pick the appropriate options.
-#if [ "$( export PGPASSWORD='postgres'; psql -h qiita-db -U postgres -XtAc "SELECT 1 FROM postgres WHERE datname='qiita_test'" )" = '1' ]
-#then
-#    qiita pet webserver --no-build-docs start --port 21174 --master
-#else
-#    qiita-env make --no-load-ontologies
-#    qiita pet webserver --no-build-docs start --port 21174 --master
-#fi
-#qiita-env make --no-load-ontologies; true
-#mkdir -p /qiita/plugins
-#sleep 3
-source $CONDA_DIR/etc/profile.d/conda.sh; conda activate $CONDA_DIR/envs/$ENV_NAME; cd /qiita && qiita pet webserver --no-build-docs start --port $PORT $MASTER 2> /logs/qiita_pet$MASTER.log 1>&2
+source $CONDA_DIR/etc/profile.d/conda.sh
+conda activate $CONDA_DIR/envs/$ENV_NAME
+cd /qiita
+# start Qiita and safe PID in variable
+qiita pet webserver --no-build-docs start --port $PORT $MASTER 2> /logs/qiita_pet$MASTER.log 1>&2 &
+PY_PID=$!
 
-tail -f /dev/null
+# wait till Qiita process is terminated
+wait "$PY_PID"

Images/qp-deblur/qp-deblur.dockerfile

@@ -106,13 +106,13 @@ RUN sed -i "s|/opt/conda/envs/deblur/share/fragment-insertion/sepp/.sepp/bundled
 
 # install tornado based trigger layer in base environment
 RUN pip install -U --no-cache-dir tornado pip-system-certs
-COPY trigger_noconda.py /trigger.py
+COPY trigger.py /trigger.py
 # ^^ 848 MB
 
 WORKDIR /
 
-COPY start_qp-deblur.sh .
-RUN chmod 755 start_qp-deblur.sh
+COPY start_plugin.sh .
+RUN chmod 755 start_plugin.sh
 
 RUN mkdir -p /unshared_plugins
 ENV QIITA_PLUGINS_DIR=/unshared_plugins/
@@ -140,5 +140,5 @@ RUN sed -i "s|source /opt/conda/etc/profile.d/conda.sh; conda activate /opt/cond
 # for testing
 COPY test_plugin.sh /test_plugin.sh
 
-CMD ["./start_qp-deblur.sh"]
+CMD ["./start_plugin.sh"]
 # ^^ 848 MB

Images/qp-deblur/start_qp-deblur.sh

@@ -96,8 +96,8 @@ RUN ln -fs /usr/share/zoneinfo/Etc/UTC /etc/localtime \
 
 WORKDIR /
 
-COPY start_qp-qiime2.sh .
-RUN chmod 755 start_qp-qiime2.sh
+COPY start_plugin.sh .
+RUN chmod 755 start_plugin.sh
 
 RUN mkdir -p /unshared_plugins
 ENV QIITA_PLUGINS_DIR=/unshared_plugins/
@@ -118,4 +118,4 @@ RUN /qp-qiime2/scripts/configure_qiime2 --env-script 'true' --server-cert `find
 # for testing
 COPY test_plugin.sh /test_plugin.sh
 
-CMD ["./start_qp-qiime2.sh"]
+CMD ["./start_plugin.sh"]

Images/qp-qiime2/qp-qiime2.dockerfile

@@ -107,14 +107,14 @@ COPY --from=builder /opt/conda/envs/qp-target-gene/lib/libpython2.7.so.1.0 /usr/
 # "install" pigz
 COPY --from=builder /opt/conda/envs/qp-target-gene/bin/pigz /usr/local/bin/
 
-COPY start_qp-target-gene.sh .
-RUN chmod 755 start_qp-target-gene.sh
+COPY start_plugin.sh .
+RUN chmod 755 start_plugin.sh
 
 RUN mkdir -p /unshared_plugins
 ENV QIITA_PLUGINS_DIR=/unshared_plugins/
 
 RUN pip3 install tornado
-COPY trigger_noconda.py /trigger.py
+COPY trigger.py /trigger.py
 
 # copy sortmerna binaries
 COPY --from=builder /sortmerna-2.0/sortmerna /usr/local/bin/sortmerna
@@ -135,4 +135,4 @@ RUN sed -i -E "s/^START_SCRIPT = .+/START_SCRIPT = python \/start_plugin.py qp-t
 # for testing
 COPY test_plugin.sh /test_plugin.sh
 
-CMD ["./start_qp-target-gene.sh"]
+CMD ["./start_plugin.sh"]