download public prep data

Author: antgonza

qiita_pet/handlers/download.py

@@ -571,7 +571,7 @@ def get(self):
             zip_fn = '%s_%s.zip' % (
                 fname, datetime.now().strftime('%m%d%y-%H%M%S'))
             self._set_nginx_headers(zip_fn)
-        else:
+        elif study_id is not None:
             study_id = int(study_id)
             try:
                 study = Study(study_id)
@@ -612,6 +612,53 @@ def get(self):
                             '%m%d%y-%H%M%S'))
 
                     self._set_nginx_headers(zip_fn)
+        else:
+            prep_id = int(prep_id)
+            try:
+                prep = PrepTemplate(prep_id)
+            except QiitaDBUnknownIDError:
+                raise HTTPError(422, reason='Prep does not exist')
+            else:
+                public_raw_download = Study(prep.study_id).public_raw_download
+                if prep.status != 'public':
+                    raise HTTPError(404, reason='Prep is not public. If this '
+                                    'is a mistake contact: %s' %
+                                    qiita_config.help_email)
+                elif data == 'raw' and not public_raw_download:
+                    raise HTTPError(422, reason='No raw data access. If this '
+                                    'is a mistake contact: %s'
+                                    % qiita_config.help_email)
+                else:
+                    # raw data
+                    if data == 'raw':
+                        artifacts = [prep.artifact]
+                    # bioms
+                    elif data == 'biom':
+                        artifacts = [a for a in
+                                     prep.artifact.descendants.nodes()
+                                     if a.artifact_type == 'BIOM' and
+                                     a.visibility == 'public']
+                    else:
+                        raise HTTPError(
+                            422,
+                            reason='You can only download raw/biom from preps')
+                    for a in artifacts:
+                        if a.visibility != 'public' or a.has_human:
+                            continue
+                        to_download.extend(self._list_artifact_files_nginx(a))
+
+                if not to_download:
+                    raise HTTPError(422, reason='Nothing to download. If '
+                                    'this is a mistake contact: %s'
+                                    % qiita_config.help_email)
+                else:
+                    self._write_nginx_file_list(to_download)
+
+                    zip_fn = 'prep_%d_%s_%s.zip' % (
+                        prep_id, data, datetime.now().strftime(
+                            '%m%d%y-%H%M%S'))
+
+                    self._set_nginx_headers(zip_fn)
 
         self.finish()
 

qiita_pet/test/test_download.py

@@ -535,6 +535,26 @@ def test_download(self):
             'mapping_files/5_mapping_file.txt')
         self.assertRegex(response.body.decode('ascii'), exp)
 
+        # Now let's check download prep with no raw data access
+        response = self.get('/public_download/?data=raw&prep_id=1')
+        self.assertTrue(response.reason.startswith('No raw data access.'))
+
+        # Now success
+        Study(1).public_raw_download = True
+        response = self.get('/public_download/?data=raw&prep_id=1')
+        self.assertEqual(response.code, 200)
+        exp = ('- [0-9]* /protected/raw_data/1_s_G1_L001_sequences.fastq.gz '
+               'raw_data/1_s_G1_L001_sequences.fastq.gz\n- [0-9]* /protected'
+               '/raw_data/1_s_G1_L001_sequences_barcodes.fastq.gz raw_data/'
+               '1_s_G1_L001_sequences_barcodes.fastq.gz\n- [0-9]* /protected/'
+               'templates/1_prep_1_qiime_19700101-000000.txt mapping_files/'
+               '1_mapping_file.txt\n')
+        self.assertRegex(response.body.decode('ascii'), exp)
+
+        # for simplicity, let's just check respose.code
+        response = self.get('/public_download/?data=biom&prep_id=1')
+        self.assertEqual(response.code, 200)
+
     def test_download_sample_information(self):
         response = self.get('/public_artifact_download/')
         self.assertEqual(response.code, 422)