Uncouple clientpush

.github/workflows/qiita-plugin-ci.yml

@@ -13,7 +13,7 @@ jobs:
     services:
       postgres:
         # Docker Hub image
-        image: postgres:9.5
+        image: postgres:13.4
         env:
           POSTGRES_DB: postgres
           POSTGRES_USER: postgres
@@ -39,7 +39,7 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          python-version: 3.6
+          python-version: 3.9
 
       - name: Basic dependencies install
         env:
@@ -62,7 +62,7 @@ jobs:
 
           # Setting up main qiita conda environment
           conda config --add channels conda-forge
-          conda create -q --yes -n qiita python=3.6 pip==9.0.3 libgfortran numpy nginx cython redis
+          conda create -q --yes -n qiita python=3.9 libgfortran numpy nginx cython redis
           conda activate qiita
           pip install -U pip
           pip install sphinx sphinx-bootstrap-theme nose-timer codecov Click
@@ -111,7 +111,7 @@ jobs:
           unzip -j filtering/bloom-analyses.zip bloom-analyses-master/data/qiime2-artifacts-for-qiita/*.qza -d filtering/
           export QP_QIIME2_FILTER_QZA=${PWD}/filtering/
 
-          configure_diversity_types --env-script "source /home/runner/.profile; conda activate qiime2" --server-cert $QIITA_SERVER_CERT
+          configure_diversity_types --env-script "source /home/runner/.profile; conda activate qiime2" --ca-cert $QIITA_SERVER_CERT
           configure_visualization_types --env-script "source /home/runner/.profile; conda activate qiime2" --server-cert $QIITA_SERVER_CERT
           configure_qiime2 --env-script "source /home/runner/.profile; conda activate qiime2; export QP_QIIME2_DBS=${PWD}/databases; export QP_QIIME2_FILTER_QZA=${PWD}/filtering/" --server-cert $QIITA_SERVER_CERT
 

qp_qiime2/tests/test_qiime2.py

@@ -7,7 +7,7 @@
 # -----------------------------------------------------------------------------
 
 from unittest import main
-from os import remove, stat
+from os import remove, stat, environ
 from shutil import rmtree, copyfile
 from tempfile import mkdtemp
 from json import dumps
@@ -79,7 +79,7 @@ def test_not_analysis_artifact(self):
         self.assertEqual(msg, 'Artifact "5" is not an analysis artifact.')
 
     def test_feature_classifier(self):
-        dbpath = join(self.basedir, '..', '..', 'databases',
+        dbpath = join(environ.get('QP_QIIME2_DBS'),
                       'gg-13-8-99-515-806-nb-classifier.qza')
         original_params = {
             'qp-hide-method': 'classify_sklearn',
@@ -144,6 +144,7 @@ def test_feature_classifier(self):
         biom_fp_new = join(self.basedir, 'support_files', 'deblur.biom')
         copyfile(biom_fp_old, biom_fp_old_bk)
         copyfile(biom_fp_new, biom_fp_old)
+        self.qclient.push_file_to_central(biom_fp_old)
 
         self.data['command'] = dumps(
             ['qiime2', qiime2_version, 'Pre-fitted sklearn-based '
@@ -164,6 +165,7 @@ def test_feature_classifier(self):
 
         # returning original biom
         copyfile(biom_fp_old_bk, biom_fp_old)
+        self.qclient.push_file_to_central(biom_fp_old)
         obs_files = [ai.files for ai in ainfo]
         obs_artifact_types = [ai.artifact_type for ai in ainfo]
         obs_output_names = [ai.output_name for ai in ainfo]
@@ -1307,7 +1309,7 @@ def test_filter_features(self):
         self.assertEqual(ainfo[0].output_name, 'filtered_table')
 
         # Filter using a qza file
-        qza_path = join(self.basedir, '..', '..', 'filtering', 'blooms-90.qza')
+        qza_path = join(environ.get('QP_QIIME2_FILTER_QZA'), 'blooms-90.qza')
         params.update({
             'Feature metadata used with `where` parameter when selecting '
             'features to retain, or with `exclude_ids` when selecting '

scripts/configure_qiime2

@@ -17,12 +17,14 @@ from qp_qiime2 import plugin
 @click.option('--env-script', prompt='Environment script',
               default='source activate qp-qiime2')
 @click.option('--server-cert', prompt='Server certificate', default='None')
-def config(env_script, server_cert):
+@click.argument('plugincoupling', required=False, default='filesystem')
+def config(env_script, server_cert, plugincoupling):
     """Generates the Qiita configuration files"""
     if server_cert == 'None':
         server_cert = None
     plugin.generate_config(env_script, 'start_qiime2',
-                           server_cert=server_cert)
+                           server_cert=server_cert,
+                           plugin_coupling=plugincoupling)
 
 
 if __name__ == '__main__':