Merge pull request #4 from antgonza/update-qiita_db.artifacts

adding support for new /qiita_db/artifacts

Author: charles-cowart

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

@@ -145,7 +145,7 @@ 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

qtp_job_output_folder/summary.py

@@ -66,12 +66,15 @@ def generate_html_summary(qclient, job_id, parameters, out_dir):
         The error message, if not successful
     """
     # Step 1: gather file information from qiita using REST api
+    # we are going to use the "raw" code for retrieving artifact_info vs. the
+    # qiita_client.artifact_and_preparation_files method because this only
+    # expects a single filepath
     artifact_id = parameters['input_data']
     qclient_url = "/qiita_db/artifacts/%s/" % artifact_id
     artifact_info = qclient.get(qclient_url)
 
     # [0] there is only one directory
-    folder = artifact_info['files']['directory'][0]
+    folder = artifact_info['files']['directory'][0]['filepath']
 
     # 2. Generate summary
     index_fp, viz_fp = _generate_html_summary(job_id, folder, out_dir)

qtp_job_output_folder/tests/test_summary.py

@@ -61,14 +61,15 @@ def test_summary(self):
         # asserting content of html
         res = self.qclient.get("/qiita_db/artifacts/%s/" % aid)
         # cleaning artifact files, to avoid errors
-        [self._clean_up_files.extend(f) for f in res['files'].values()]
-        html_fp = res['files']['html_summary'][0]
-        self._clean_up_files.append(html_fp)
+        [self._clean_up_files.extend([ff['filepath']])
+         for f in res['files'].values() for ff in f]
+        html_fp = res['files']['html_summary'][0]['filepath']
         with open(html_fp) as html_f:
             html = html_f.read()
 
         self.assertCountEqual(
-            html.split('\n'), EXP_HTML.format(aid=aid).split('\n'))
+            sorted(html.replace('<br/>', '').split('\n')),
+            sorted(EXP_HTML.format(aid=aid).replace('<br/>', '').split('\n')))
 
 
 EXP_HTML = (