Merge pull request #45 from antgonza/update-qiita_db.artifacts

adding support for new /qiita_db/artifacts

Author: charles-cowart

qtp_sequencing/summary.py

@@ -88,11 +88,19 @@ def generate_html_summary(qclient, job_id, parameters, out_dir):
     """
     # Step 1: gather file information from qiita using REST api
     artifact_id = parameters['input_data']
+    # we are going to use the "raw" code for retrieving artifact_info vs. the
+    # qiita_client.artifact_and_preparation_files method because fqtools
+    # returns 0 (vs. failing, which is nice) on an empty file
+    # $ touch x.fastq
+    # $ gzip x.fastq
+    # $ fqtools count x.fastq.gz
+    # 0
     qclient_url = "/qiita_db/artifacts/%s/" % artifact_id
     artifact_info = qclient.get(qclient_url)
 
     # 1a. getting the file paths
-    filepaths = artifact_info['files']
+    filepaths = {k: [vv['filepath'] for vv in v]
+                 for k, v in artifact_info['files'].items()}
     # 1.b get the artifact type_info
     artifact_type = artifact_info['type']
 

qtp_sequencing/tests/test_plugin.py

@@ -54,11 +54,11 @@ def test_plugin_summary(self):
         files = self.qclient.get(
             '/qiita_db/artifacts/%s/' % artifact_id)['files']
 
-        bcds_fp = files['raw_barcodes'][0]
+        bcds_fp = files['raw_barcodes'][0]['filepath']
         self._clean_up_files.append(bcds_fp)
         with GzipFile(bcds_fp, mode='w', mtime=1) as fh:
             fh.write(BARCODES.encode())
-        fwd_fp = files['raw_forward_seqs'][0]
+        fwd_fp = files['raw_forward_seqs'][0]['filepath']
         self._clean_up_files.append(fwd_fp)
         with GzipFile(fwd_fp, mode='w', mtime=1) as fh:
             fh.write(READS.encode())

qtp_sequencing/tests/test_summary.py

@@ -51,11 +51,11 @@ def test_generate_html_summary_no_demux(self):
         files = self.qclient.get(
             '/qiita_db/artifacts/%s/' % artifact_id)['files']
 
-        bcds_fp = files['raw_barcodes'][0]
+        bcds_fp = files['raw_barcodes'][0]['filepath']
         self._clean_up_files.append(bcds_fp)
         with GzipFile(bcds_fp, mode='w', mtime=1) as fh:
             fh.write(BARCODES.encode())
-        fwd_fp = files['raw_forward_seqs'][0]
+        fwd_fp = files['raw_forward_seqs'][0]['filepath']
         self._clean_up_files.append(fwd_fp)
         with GzipFile(fwd_fp, mode='w', mtime=1) as fh:
             fh.write(READS.encode())
@@ -71,7 +71,7 @@ def test_generate_html_summary_no_demux(self):
 
         # asserting content of html
         res = self.qclient.get("/qiita_db/artifacts/%s/" % artifact_id)
-        html_fp = res['files']['html_summary'][0]
+        html_fp = res['files']['html_summary'][0]['filepath']
         self._clean_up_files.append(html_fp)
         with open(html_fp) as html_f:
             html = html_f.read()
@@ -92,7 +92,7 @@ def test_generate_html_summary_demux(self):
         # files fo not exist create them
         files = self.qclient.get(
             '/qiita_db/artifacts/%s/' % artifact_id)['files']
-        demux_fp = files['preprocessed_demux'][0]
+        demux_fp = files['preprocessed_demux'][0]['filepath']
         copyfile(join(dirname(__file__), 'test_data', '101_seqs.demux'),
                  demux_fp)
         self._clean_up_files.append(demux_fp)
@@ -107,7 +107,7 @@ def test_generate_html_summary_demux(self):
 
         # asserting content of html
         res = self.qclient.get("/qiita_db/artifacts/%s/" % artifact_id)
-        html_fp = res['files']['html_summary'][0]
+        html_fp = res['files']['html_summary'][0]['filepath']
         self._clean_up_files.append(html_fp)
 
         with open(html_fp) as html_f: