Merge pull request #23 from antgonza/update-qiita_db.artifacts

update qiita_db.artifacts

Author: charles-cowart

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

@@ -77,17 +77,17 @@ jobs:
       - name: Install Qiita plugins
         shell: bash -l {0}
         run: |
-          conda create --quiet --yes -n qp-target-gene python=2.7 pip numpy pigz
+          conda create --override-channels -c defaults --quiet --yes -n qp-target-gene python=2.7
           conda activate qp-target-gene
-          conda install --quiet --yes -c bioconda -c biocore "VSEARCH=2.7.0" MAFFT=7.310 SortMeRNA=2.0 fragment-insertion numpy==1.13.0 cython
+          conda install --yes -c bioconda -c biocore SortMeRNA==2.0 numpy==1.13.1 pigz
 
           export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt
           export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
           pip --quiet install -U pip
           pip --quiet install .
           pip --quiet install coveralls
 
-          configure_qp_target_gene --env-script "source /home/runner/.profile; conda activate qp-target-gene" --server-cert $QIITA_SERVER_CERT
+          configure_target_gene --env-script "source /home/runner/.profile; conda activate qp-target-gene" --server-cert $QIITA_SERVER_CERT
 
           echo "Available Qiita plugins"
           ls ~/.qiita_plugins/
@@ -146,7 +146,7 @@ jobs:
     - name: flake8
       uses: actions/setup-python@v2
       with:
-        python-version: 3.6
+        python-version: 3.9
     - name: install dependencies
       run: python -m pip install --upgrade pip
     - name: Check out repository code

README.rst

@@ -7,5 +7,5 @@ Qiita (canonically pronounced *cheetah*) is an analysis environment for microbio
 
 This package includes the target gene plugin for Qiita. This makes the functionality to analyze target gene data available in the Qiita installation.
 
-.. |Build Status| image:: https://travis-ci.com/qiita-spots/qp-target-gene.svg?branch=master
-   :target: https://travis-ci.com/qiita-spots/qp-target-gene
+.. |Build Status| image:: https://github.com/qiita-spots/qp-target-gene/actions/workflows/qiita-plugin-ci.yml/badge.svg
+   :target: https://github.com/qiita-spots/qp-target-gene/actions/workflows/qiita-plugin-ci.yml

qp_target_gene/pick_otus.py

@@ -154,7 +154,7 @@ def pick_closed_reference_otus(qclient, job_id, parameters, out_dir):
     qclient.update_job_step(job_id, "Step 1 of 4: Collecting information")
     artifact_id = parameters['input_data']
     a_info = qclient.get("/qiita_db/artifacts/%s/" % artifact_id)
-    fps = a_info['files']
+    fps = {k: [vv['filepath'] for vv in v] for k, v in a_info['files'].items()}
 
     qclient.update_job_step(job_id, "Step 2 of 4: Generating command")
     command, pick_out = generate_pick_closed_reference_otus_cmd(

qp_target_gene/split_libraries/tests/test_split_libraries_fastq.py

@@ -352,6 +352,7 @@ def test_split_libraries_fastq(self):
 
         # Create the files that Qiita returns (they don't exist in the test)
         files = self.qclient.get('/qiita_db/artifacts/1/')['files']
+        files = {k: [vv['filepath'] for vv in v] for k, v in files.items()}
         bcds_fp = files['raw_barcodes'][0]
         self._clean_up_files.append(bcds_fp)
         with GzipFile(bcds_fp, mode='w') as fh:

qp_target_gene/split_libraries/util.py

@@ -37,7 +37,8 @@ def get_artifact_information(qclient, artifact_id, out_dir):
     """
     # Get the artifact filepath information
     artifact_info = qclient.get("/qiita_db/artifacts/%s/" % artifact_id)
-    fps = artifact_info['files']
+    fps = {k: [vv['filepath'] for vv in v]
+           for k, v in artifact_info['files'].items()}
     # Get the artifact type
     artifact_type = artifact_info['type']
     # Get the artifact metadata

qp_target_gene/tests/test_pick_otus.py

@@ -109,7 +109,7 @@ def test_pick_closed_reference_otus(self):
 
         # These filepaths do not exist in Qiita - create them
         fps = self.qclient.get('/qiita_db/artifacts/2/')['files']
-        fasta_fp = fps['preprocessed_fasta'][0]
+        fasta_fp = fps['preprocessed_fasta'][0]['filepath']
         self.parameters['reference-seq'] = '/tmp/seq.fna'
         self.parameters['reference-tax'] = '/tmp/tax.txt'
         with open(fasta_fp, 'w') as f:

qp_target_gene/trimming.py

@@ -78,7 +78,7 @@ def trimming(qclient, job_id, parameters, out_dir):
     qclient.update_job_step(job_id, "Step 1 of 3: Collecting information")
     artifact_id = parameters['input_data']
     a_info = qclient.get("/qiita_db/artifacts/%s/" % artifact_id)
-    fps = a_info['files']
+    fps = {k: [vv['filepath'] for vv in v] for k, v in a_info['files'].items()}
     if 'preprocessed_demux' not in fps:
         error_msg = "Artifact doesn't contain a preprocessed demux"
         return False, None, error_msg

setup.py

@@ -43,7 +43,7 @@
       package_data={'qp_target_gene': ['support_files/config_file.cfg']},
       scripts=glob('scripts/*'),
       extras_require={'test': ["nose >= 0.10.1", "pep8"]},
-      install_requires=['click >= 3.3', 'future', 'requests', 'pandas >= 0.15',
+      install_requires=['click >= 3.3', 'future', 'requests', 'pandas==0.20.3',
                         'biom-format <= 2.1.7',
                         'h5py >= 2.3.1', 'qiime >= 1.9.0, < 1.10.0',
                         'qiita-files @ https://github.com/'