Merge branch 'tinqiita' of github.com:jlab/qiita-keycloak into unify_trigger

Author: sjanssen2

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?!

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;