Uncouple plugins

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

@@ -90,7 +90,7 @@ jobs:
           sed -i "s/f'Entered BaseQiitaPlugin._register_command({command.name})'/'Entered BaseQiitaPlugin._register_command(%s)' % command.name/"  $CONDA_PREFIX/lib/python3.5/site-packages/qiita_client/plugin.py
           pip --quiet install coveralls
 
-          configure_deblur --env-script "source /home/runner/.profile; conda activate deblur" --server-cert $QIITA_ROOTCA_CERT
+          configure_deblur --env-script "source /home/runner/.profile; conda activate deblur" --server-cert $QIITA_ROOTCA_CERT filesystem
 
           echo "Available Qiita plugins"
           ls ~/.qiita_plugins/
@@ -113,6 +113,7 @@ jobs:
           export NGINX_FILE=`pwd`/qiita-dev/qiita_pet/nginx_example.conf
           export NGINX_FILE_NEW=`pwd`/qiita-dev/qiita_pet/nginx_example_local.conf
           sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" ${NGINX_FILE} > ${NGINX_FILE_NEW}
+          sed -i "s#/Users/username/qiita#${PWD}/qiita-dev#g" ${NGINX_FILE_NEW}
           nginx -c ${NGINX_FILE_NEW}
 
           echo "3. Setting up qiita"

qp_deblur/deblur.py

@@ -428,7 +428,8 @@ def deblur(qclient, job_id, parameters, out_dir):
     # Getting preparation information
     prep_info = qclient.get(
         '/qiita_db/prep_template/%s/' % artifact_info['prep_information'][0])
-    df = pd.read_csv(prep_info['prep-file'], sep='\t')
+    df = pd.read_csv(
+        qclient.fetch_file_from_central(prep_info['prep-file']), sep='\t')
     if prep_info['data_type'] not in {'16S', '18S', 'ITS'}:
         error_msg = ('deblur was developed only for amplicon sequencing data')
         return False, None, error_msg
@@ -456,8 +457,9 @@ def deblur(qclient, job_id, parameters, out_dir):
         # using the same number of parallel jobs as defined by the command
         n_jobs = int(parameters['Jobs to start'])
         # [0] cause there should be only 1 file
-        to_per_sample_files(fps['preprocessed_demux'][0],
-                            out_dir=split_out_dir, n_jobs=n_jobs)
+        to_per_sample_files(
+            qclient.fetch_file_from_central(fps['preprocessed_demux'][0]),
+            out_dir=split_out_dir, n_jobs=n_jobs)
 
         qclient.update_job_step(job_id, "Step 2 of 4: Generating per sample "
                                 "from demux (2/2)")
@@ -467,8 +469,10 @@ def deblur(qclient, job_id, parameters, out_dir):
     else:
         qclient.update_job_step(job_id, "Step 2 of 4: Generating deblur "
                                 "command")
-        cmd = generate_deblur_workflow_commands(fps['preprocessed_fastq'],
-                                                out_dir, parameters)
+        cmd = generate_deblur_workflow_commands(
+            list(map(qclient.fetch_file_from_central,
+                     fps['preprocessed_fastq'])),
+            out_dir, parameters)
 
     # Step 3 execute deblur
     qclient.update_job_step(job_id, "Step 3 of 4: Executing deblur job")
@@ -582,14 +586,23 @@ def deblur(qclient, job_id, parameters, out_dir):
     else:
         new_placements = None
 
-    ainfo = [ArtifactInfo('deblur final table', 'BIOM',
-                          [(final_biom, 'biom'),
-                           (final_seqs, 'preprocessed_fasta')])]
+    ainfo = [
+        ArtifactInfo(
+            'deblur final table', 'BIOM',
+            [(qclient.push_file_to_central(final_biom),
+              'biom'),
+             (qclient.push_file_to_central(final_seqs),
+              'preprocessed_fasta')])]
     if fp_phylogeny is not None:
-        ainfo.append(ArtifactInfo('deblur reference hit table', 'BIOM',
-                     [(final_biom_hit, 'biom'),
-                      (final_seqs_hit, 'preprocessed_fasta'),
-                      (fp_phylogeny, 'plain_text')], new_placements))
+        ainfo.append(
+            ArtifactInfo(
+                'deblur reference hit table', 'BIOM',
+                [(qclient.push_file_to_central(final_biom_hit),
+                  'biom'),
+                 (qclient.push_file_to_central(final_seqs_hit),
+                  'preprocessed_fasta'),
+                 (qclient.push_file_to_central(fp_phylogeny),
+                  'plain_text')], new_placements))
 
     return True, ainfo, ""
 

qp_deblur/tests/test_archive.py

@@ -8,14 +8,14 @@
 
 import json
 from unittest import main
-from os import close, remove
+from os import close, remove, environ
 from shutil import copyfile, rmtree
 from tempfile import mkstemp, mkdtemp
 from json import dumps
 from os.path import exists, isdir
 
 from qiita_client.testing import PluginTestCase
-
+from qiita_client.plugin import BaseQiitaPlugin
 
 from qp_deblur import plugin
 from qp_deblur.deblur import deblur
@@ -65,6 +65,11 @@ def setUp(self):
              'CCAGCTGTGAAATCCCCGGGCTCAACCTGGGAATTG')
         ]
 
+        # as we access functions directly, plugin configuration is not parsed,
+        # thus resort to environment variable here
+        self.qclient._plugincoupling = environ.get(
+            'QIITA_PLUGINCOUPLING', BaseQiitaPlugin._DEFAULT_PLUGIN_COUPLINGS)
+
     def tearDown(self):
         for fp in self._clean_up_files:
             if exists(fp):

qp_deblur/tests/test_deblur.py

@@ -7,14 +7,14 @@
 # -----------------------------------------------------------------------------
 
 from unittest import main
-from os import close, remove, chmod
+from os import close, remove, chmod, environ
 from shutil import copyfile, rmtree
 from tempfile import mkstemp, mkdtemp
 from json import dumps, load
 from os.path import exists, isdir, join
-from os import environ
 
 from qiita_client.testing import PluginTestCase
+from qiita_client.plugin import BaseQiitaPlugin
 
 from qp_deblur import plugin
 from qp_deblur.deblur import (
@@ -57,6 +57,11 @@ def setUp(self):
         # saving current value of PATH
         self.oldpath = environ['PATH']
 
+        # as we access functions directly, plugin configuration is not parsed,
+        # thus resort to environment variable here
+        self.qclient._plugincoupling = environ.get(
+            'QIITA_PLUGINCOUPLING', BaseQiitaPlugin._DEFAULT_PLUGIN_COUPLINGS)
+
     def tearDown(self):
         # restore eventually changed PATH env var
         environ['PATH'] = self.oldpath

scripts/configure_deblur

@@ -17,12 +17,14 @@ from qp_deblur import plugin
 @click.option('--env-script', prompt='Environment script',
               default='source activate qp-deblur')
 @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_deblur',
-                           server_cert=server_cert)
+                           server_cert=server_cert,
+                           plugin_coupling=plugincoupling)
 
 if __name__ == '__main__':
     config()