Fix 2210

qiita_db/test/test_util.py

@@ -852,20 +852,21 @@ def test_get_artifacts_information(self):
 
         exp = [
             {'files': ['1_study_1001_closed_reference_otu_table.biom'],
-             'target_subfragment': ['V4'], 'data_type': '18S',
+             'target_subfragment': ['V4'], 'artifact_id': 4,
+             'algorithm': ('Pick closed-reference OTUs, QIIMEv1.9.1 |'
+                           ' barcode_type 8, defaults'),
+             'data_type': '18S', 'prep_samples': 27,
              'parameters': {
                 'reference': 1, 'similarity': 0.97, 'sortmerna_e_value': 1,
                 'sortmerna_max_pos': 10000, 'input_data': 2, 'threads': 1,
-                'sortmerna_coverage': 0.97}, 'name': 'BIOM',
-                'algorithm': ('Pick closed-reference OTUs, QIIMEv1.9.1 '
-                              '| barcode_type 8, defaults'), 'artifact_id': 4},
-            {'files': [], 'target_subfragment': ['V4'], 'data_type': '16S',
-             'parameters': {}, 'name': 'BIOM', 'algorithm': '',
-             'artifact_id': 7},
+                'sortmerna_coverage': 0.97}, 'name': 'BIOM'},
+            {'files': [], 'target_subfragment': ['V4'], 'algorithm': '',
+             'artifact_id': 7, 'data_type': '16S', 'prep_samples': 27,
+             'parameters': {}, 'name': 'BIOM'},
             {'files': ['biom_table.biom'], 'target_subfragment': [],
-             'data_type': '18S', 'parameters': {}, 'name': 'noname',
-             'algorithm': '', 'artifact_id': 8}]
-        self.assertEqual(obs, exp)
+             'algorithm': '', 'artifact_id': 8, 'data_type': '18S',
+             'prep_samples': 0, 'parameters': {}, 'name': 'noname'}]
+        self.assertItemsEqual(obs, exp)
 
 
 if __name__ == '__main__':

qiita_db/util.py

@@ -1382,7 +1382,7 @@ def get_artifacts_information(artifact_ids, only_biom=True):
                         WHERE table_name = 'prep_' || CAST(
                             prep_template_id AS TEXT)
                         AND column_name='target_subfragment')
-                    THEN prep_template_id ELSE NULL END
+                    THEN prep_template_id ELSE NULL END, prep_template_id
                 FROM main_query
                 LEFT JOIN qiita.prep_template pt ON (
                     main_query.root_id = pt.artifact_id)
@@ -1409,10 +1409,13 @@ def get_artifacts_information(artifact_ids, only_biom=True):
                       qdb.sql_connection.TRN.execute_fetchindex()}
 
             # now let's get the actual artifacts
+            ts = {}
+            ps = {}
+            PT = qdb.metadata_template.prep_template.PrepTemplate
             qdb.sql_connection.TRN.add(sql, [tuple(artifact_ids)])
             for row in qdb.sql_connection.TRN.execute_fetchindex():
                 aid, name, cid, gt, aparams, dt, pid, pparams, filepaths, _, \
-                    target = row
+                    target, prep_template_id = row
 
                 # cleaning fields:
                 # - [0] due to the array_agg
@@ -1449,30 +1452,32 @@ def get_artifacts_information(artifact_ids, only_biom=True):
 
                     algorithm = '%s | %s' % (commands[cid], pparams)
 
+                if target is None:
+                    target = []
+                else:
+                    if target not in ts:
+                        qdb.sql_connection.TRN.add(sql_ts, [target])
+                        ts[target] = \
+                            qdb.sql_connection.TRN.execute_fetchflatten()
+                    target = ts[target]
+
+                if prep_template_id is None:
+                    prep_samples = 0
+                else:
+                    if prep_template_id not in ps:
+                        ps[prep_template_id] = len(list(
+                            PT(prep_template_id).keys()))
+                    prep_samples = ps[prep_template_id]
+
                 results.append({
                     'artifact_id': aid,
                     'target_subfragment': target,
+                    'prep_samples': prep_samples,
                     'name': name,
                     'data_type': dt,
                     'timestamp': str(gt),
                     'parameters': aparams,
                     'algorithm': algorithm,
                     'files': filepaths})
 
-            # let's get the values for target_subfragment from the
-            # prep_template, note that we have to do it in a separate sql
-            # doing crosstab is really difficult and in another loop cause we
-            # need to loop over all execute_fetchindex before doing another
-            # query
-            ts = {}
-            for i, r in enumerate(results):
-                pid = r['target_subfragment']
-                if pid is None:
-                    results[i]['target_subfragment'] = []
-                else:
-                    if pid not in ts:
-                        qdb.sql_connection.TRN.add(sql_ts, [pid])
-                        ts[pid] = qdb.sql_connection.TRN.execute_fetchflatten()
-                    results[i]['target_subfragment'] = ts[pid]
-
             return results

qiita_pet/handlers/api_proxy/tests/test_artifact.py

@@ -223,27 +223,34 @@ def test_artifact_get_info(self):
         obs = artifact_get_info('test@foo.bar', [5, 6, 7])
         data = [
             {'files': ['1_study_1001_closed_reference_otu_table_Silva.biom'],
-             'target_subfragment': ['V4'], 'algorithm': (
-                'Pick closed-reference OTUs, QIIMEv1.9.1 | barcode_type 8, '
-                'defaults'), 'artifact_id': 6, 'data_type': '16S',
-             'timestamp': '2012-10-02 17:30:00', 'parameters': {
-                'reference': 2, 'similarity': 0.97, 'sortmerna_e_value': 1,
+             'target_subfragment': ['V4'],
+             'algorithm': ('Pick closed-reference OTUs, QIIMEv1.9.1 | '
+                           'barcode_type 8, defaults'),
+             'artifact_id': 6, 'data_type': '16S',
+             'timestamp': '2012-10-02 17:30:00', 'prep_samples': 27,
+             'parameters': {
+                'reference': 2, 'similarity': 0.97, u'sortmerna_e_value': 1,
                 'sortmerna_max_pos': 10000, 'input_data': 2, 'threads': 1,
                 'sortmerna_coverage': 0.97}, 'name': 'BIOM'},
             {'files': ['1_study_1001_closed_reference_otu_table.biom'],
-             'target_subfragment': ['V4'], 'algorithm': (
-                'Pick closed-reference OTUs, QIIMEv1.9.1 | barcode_type 8, '
-                'defaults'), 'artifact_id': 5, 'data_type': '18S',
-                'timestamp': '2012-10-02 17:30:00', 'parameters': {
-                    'reference': 1, 'similarity': 0.97, 'sortmerna_e_value': 1,
-                    'sortmerna_max_pos': 10000, 'input_data': 2, 'threads': 1,
-                    'sortmerna_coverage': 0.97}, 'name': 'BIOM'},
+             'target_subfragment': ['V4'],
+             'algorithm': ('Pick closed-reference OTUs, QIIMEv1.9.1 | '
+                           'barcode_type 8, defaults'),
+             'artifact_id': 5, 'data_type': '18S',
+             'timestamp': '2012-10-02 17:30:00', 'prep_samples': 27,
+             'parameters': {
+                'reference': 1, 'similarity': 0.97, 'sortmerna_e_value': 1,
+                'sortmerna_max_pos': 10000, 'input_data': 2, 'threads': 1,
+                'sortmerna_coverage': 0.97}, 'name': 'BIOM'},
             {'files': [], 'target_subfragment': ['V4'], 'algorithm': '',
              'artifact_id': 7, 'data_type': '16S',
-             'timestamp': '2012-10-02 17:30:00', 'parameters': {},
-             'name': 'BIOM'}]
+             'timestamp': '2012-10-02 17:30:00', 'prep_samples': 27,
+             'parameters': {}, 'name': 'BIOM'}]
         exp = {'status': 'success', 'msg': '', 'data': data}
-        self.assertEqual(obs, exp)
+        self.assertItemsEqual(obs.keys(), exp.keys())
+        self.assertEqual(obs['status'], exp['status'])
+        self.assertEqual(obs['msg'], exp['msg'])
+        self.assertItemsEqual(obs['data'], exp['data'])
 
     def test_artifact_post_req(self):
         # Create new prep template to attach artifact to

qiita_pet/handlers/study_handlers/tests/test_artifact.py

@@ -164,19 +164,25 @@ def test_get(self):
         self.assertEqual(response.code, 200)
         data = [
             {'files': ['1_study_1001_closed_reference_otu_table_Silva.biom'],
-             'target_subfragment': ['V4'], 'algorithm': (
-                'Pick closed-reference OTUs, QIIMEv1.9.1 | barcode_type 8, '
-                'defaults'), 'artifact_id': 6, 'data_type': '16S',
-             'timestamp': '2012-10-02 17:30:00', 'parameters': {
+             'target_subfragment': ['V4'], 'artifact_id': 6,
+             'data_type': '16S', 'timestamp': '2012-10-02 17:30:00',
+             'prep_samples': 27,
+             'algorithm': 'Pick closed-reference OTUs, QIIMEv1.9.1 | '
+                          'barcode_type 8, defaults',
+             'parameters': {
                 'reference': 2, 'similarity': 0.97, 'sortmerna_e_value': 1,
                 'sortmerna_max_pos': 10000, 'input_data': 2, 'threads': 1,
                 'sortmerna_coverage': 0.97}, 'name': 'BIOM'},
-            {'files': [], 'target_subfragment': ['V4'], 'algorithm': '',
-             'artifact_id': 7, 'data_type': '16S',
-             'timestamp': '2012-10-02 17:30:00', 'parameters': {},
+            {'files': [], 'target_subfragment': ['V4'], 'artifact_id': 7,
+             'data_type': '16S', 'timestamp': '2012-10-02 17:30:00',
+             'prep_samples': 27, 'algorithm': '', 'parameters': {},
              'name': 'BIOM'}]
         exp = {'status': 'success', 'msg': '', 'data': data}
-        self.assertEqual(loads(response.body), exp)
+        obs = loads(response.body)
+        self.assertItemsEqual(obs.keys(), exp.keys())
+        self.assertEqual(obs['status'], exp['status'])
+        self.assertEqual(obs['msg'], exp['msg'])
+        self.assertItemsEqual(obs['data'], exp['data'])
 
 
 class ArtifactAdminAJAXTestsReadOnly(TestHandlerBase):

qiita_pet/templates/analysis_selected.html

@@ -96,7 +96,7 @@ <h2><a href="{% raw qiita_config.portal_dir %}/study/description/{{study.id}}">{
     <h4>Processed Data</h4>
     <table class='table table-striped' id='study{{study.id}}-table'>
     <tr>
-      <th class="col-sm-1">id</th><th class="col-sm-1">Datatype</th><th class="col-sm-2">Processed Date</th><th class="col-sm-2">Algorithm</th><th class="col-sm-2">Parameters</th><th class="col-sm-1">Samples</th><th></th><th></th>
+      <th class="col-sm-1">id</th><th class="col-sm-1">Datatype</th><th class="col-sm-2">Processed Date</th><th class="col-sm-2">Algorithm</th><th class="col-sm-2">Parameters</th><th class="col-sm-1">Samples selected from Prep Info</th><th></th><th></th>
     </tr>
   {% for pid, samples in viewitems(proc_datas) %}
     <tr id="proc{{pid}}">

qiita_pet/templates/list_studies.html

@@ -90,6 +90,7 @@
     proc_data_table += '<th>Data type</th>';
     proc_data_table += '<th>Processing method</th>';
     proc_data_table += '<th>Parameters</th>';
+    proc_data_table += '<th>Samples in Prep Info</th>';
     proc_data_table += '<th>Files</th>';
     proc_data_table += '</tr>';
 
@@ -106,6 +107,7 @@
           params += '<i>' + key + '</i>: ' + info.parameters[key] + '<br/>';
         }
         proc_data_table += '<td><small>' + params + '</small></td>';
+        proc_data_table += '<td>' + info.prep_samples + '</td>';
         proc_data_table += '<td><small>' + info.files.join('<br/>')  + '</small></td>';
 
         proc_data_table += '</tr>';