more changes for suggestions

Author: squirrelo

qiita_pet/handlers/study_handlers/listing_handlers.py

@@ -52,6 +52,12 @@ def _build_single_study_info(study, info, study_proc, proc_samples):
         The study to build information for
     info : dict
         Information from Study.get_info
+    study_proc : dict of lists
+        Dictionary keyed on study_id that lists all processed data associated
+        with that study.
+    proc_samples : dict of lists
+        Dictionary keyed on proc_data_id that lists all samples associated with
+        that processed data.
 
     Returns
     -------
@@ -76,20 +82,18 @@ def _build_single_study_info(study, info, study_proc, proc_samples):
     del info["principal_investigator_id"]
     del info["email"]
     # Build the proc data info list for the child row in datatable
-    info["proc_data_info"] = _build_single_proc_data_info(
-        study, study_proc, proc_samples)
+    info["proc_data_info"] = [
+        _build_single_proc_data_info(pd_id, proc_samples[pd_id])
+        for pd_id in study_proc[study.id]]
     return info
 
 
-def _build_single_proc_data_info(study, study_proc, proc_samples):
+def _build_single_proc_data_info(proc_data_id, samples):
     """Build the proc data info list for the child row in datatable
 
-
     Parameters
     ----------
-    study : Study object
-        The study to build information for
-    study_proc : dict of lists
+    proc_data_id : int
         The processed data attached to he study, in the form
         {study_id: [proc_data_id, proc_data_id, ...], ...}
     proc_samples : dict of lists
@@ -98,24 +102,20 @@ def _build_single_proc_data_info(study, study_proc, proc_samples):
 
     Returns
     -------
-    dict of dicts
-        The information for the processed data, in the form
-        {proc_data_id: {info: value, ...}, ...}
+    dict
+        The information for the processed data, in the form {info: value, ...}
     """
-    proc_data_info = []
-    for pid in study_proc[study.id]:
-        proc_data = ProcessedData(pid)
-        proc_info = proc_data.processing_info
-        proc_info['pid'] = pid
-        proc_info['data_type'] = proc_data.data_type()
-        proc_info['samples'] = sorted(proc_samples[pid])
-        proc_info['processed_date'] = str(proc_info['processed_date'])
-        proc_data_info.append(proc_info)
-    return proc_data_info
+    proc_data = ProcessedData(proc_data_id)
+    proc_info = proc_data.processing_info
+    proc_info['pid'] = proc_data_id
+    proc_info['data_type'] = proc_data.data_type()
+    proc_info['samples'] = sorted(samples)
+    proc_info['processed_date'] = str(proc_info['processed_date'])
+    return proc_info
 
 
 def _build_study_info(user, study_proc=None, proc_samples=None):
-    """builds list of dicts for studies table, with all html formatted
+    """Builds list of dicts for studies table, with all HTML formatted
 
     Parameters
     ----------
@@ -171,11 +171,11 @@ def _build_study_info(user, study_proc=None, proc_samples=None):
         study = Study(info['study_id'])
         # Build the processed data info for the study if none passed
         if build_samples:
-                proc_data = study.processed_data()
-                proc_samples = {}
-                study_proc = {study.id: proc_data}
-                for pid in proc_data:
-                    proc_samples[pid] = ProcessedData(pid).samples
+            proc_data = study.processed_data()
+            proc_samples = {}
+            study_proc = {study.id: proc_data}
+            for pid in proc_data:
+                proc_samples[pid] = ProcessedData(pid).samples
 
         study_info = _build_single_study_info(study, info, study_proc,
                                               proc_samples)

qiita_pet/templates/list_studies.html

@@ -81,7 +81,7 @@
         });
     // Add event listener for opening and closing details
     $('#studies-table tbody').on('click', 'td.details-control', function () {
-      var table = $('#studies-table').DataTable();
+        var table = $('#studies-table').DataTable();
         var tr = $(this).closest('tr');
         var row = table.row( tr );
 

qiita_pet/test/test_study_handlers.py

@@ -2,6 +2,7 @@
 from json import loads
 
 from qiita_pet.test.tornado_test_base import TestHandlerBase
+from qiita_core.exceptions import IncompetentQiitaDeveloperError
 from qiita_db.study import StudyPerson, Study
 from qiita_db.util import get_count, check_count
 from qiita_db.user import User
@@ -14,7 +15,7 @@ class TestHelpers(TestHandlerBase):
     database = True
 
     def setUp(self):
-        self.proc_data_exp = [{
+        self.proc_data_exp = {
             'pid': 1,
             'processed_date': '2012-10-01 09:30:27',
             'data_type': '18S',
@@ -36,7 +37,7 @@ def setUp(self):
                         '1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
                         '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
                         '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']
-        }]
+        }
         self.single_exp = {
             'study_id': 1,
             'status': 'private',
@@ -64,7 +65,7 @@ def setUp(self):
                     '//www.ncbi.nlm.nih.gov/pubmed/7891011">7891011</a>',
             'pi': '<a target="_blank" href="mailto:PI_dude@foo.bar">'
                   'PIDude</a>',
-            'proc_data_info': self.proc_data_exp
+            'proc_data_info': [self.proc_data_exp]
         }
         self.exp = [self.single_exp]
         super(TestHelpers, self).setUp()
@@ -76,7 +77,7 @@ def test_get_shared_links_for_study(self):
 
     def test_build_single_study_info(self):
         study_proc = {1: [1]}
-        proc_samples = {1: self.proc_data_exp[0]['samples']}
+        proc_samples = {1: self.proc_data_exp['samples']}
         study_info = {
             'study_id': 1,
             'email': 'test@foo.bar',
@@ -104,15 +105,18 @@ def test_build_single_study_info(self):
         self.assertEqual(obs, self.single_exp)
 
     def test_build_single_proc_data_info(self):
-        study_proc = {1: [1]}
-        proc_samples = {1: self.proc_data_exp[0]['samples']}
-        obs = _build_single_proc_data_info(Study(1), study_proc, proc_samples)
+        obs = _build_single_proc_data_info(1, self.proc_data_exp['samples'])
         self.assertEqual(obs, self.proc_data_exp)
 
     def test_build_study_info(self):
         obs = _build_study_info(User('test@foo.bar'))
         self.assertEqual(obs, self.exp)
 
+        with self.assertRaises(IncompetentQiitaDeveloperError):
+            obs = _build_study_info(User('test@foo.bar'), study_proc={})
+        with self.assertRaises(IncompetentQiitaDeveloperError):
+            obs = _build_study_info(User('test@foo.bar'), proc_samples={})
+
     def test_build_study_info_new_study(self):
         info = {
             'timeseries_type_id': 1,