Merge pull request #566 from colts661/ywang_sample_summary_project

Fix sample summary project output

Author: cassidysymons

microsetta_private_api/admin/admin_impl.py

@@ -491,6 +491,7 @@ def query_project_barcode_stats(body, token_info, strip_sampleid):
 def query_barcode_stats(body, token_info, strip_sampleid):
     validate_admin_access(token_info)
     if 'sample_barcodes' in body:
+        project_id = None
         barcodes = body["sample_barcodes"]
     elif 'project_id' in body:
         project_id = body["project_id"]
@@ -502,7 +503,7 @@ def query_barcode_stats(body, token_info, strip_sampleid):
         unprocessed_barcodes = barcodes[1000:]
         barcodes = barcodes[0:1000]
 
-    results = {'samples': per_sample(None, barcodes, strip_sampleid)}
+    results = {'samples': per_sample(project_id, barcodes, strip_sampleid)}
 
     if unprocessed_barcodes:
         results['partial_result'] = True

microsetta_private_api/admin/sample_summary.py

@@ -23,13 +23,12 @@ def per_sample(project, barcodes, strip_sampleid):
         template_repo = SurveyTemplateRepo(t)
         vs_repo = VioscreenSessionRepo(t)
 
-        if project is not None:
-            project_barcodes = admin_repo.get_project_barcodes(project)
-        else:
-            project = 'Unspecified'
-
+        # all associated projects returned for each barcode,
+        # so no universal project needed
         if barcodes is None:
-            barcodes = project_barcodes
+            if project is None:
+                return summaries
+            barcodes = admin_repo.get_project_barcodes(project)
 
         for barcode in barcodes:
             diag = admin_repo.retrieve_diagnostics_by_barcode(barcode)
@@ -44,6 +43,11 @@ def per_sample(project, barcodes, strip_sampleid):
             source_type = None if source is None else source.source_type
             vio_id = None
 
+            # find all projects for barcode
+            projects_info = diag['projects_info']
+            all_projects = [proj_obj['project'] for proj_obj in projects_info]
+            barcode_project = '; '.join(sorted(all_projects))
+
             if source is not None and source_type == Source.SOURCE_TYPE_HUMAN:
 
                 vio_id = template_repo.get_vioscreen_id_if_exists(account.id,
@@ -82,7 +86,7 @@ def per_sample(project, barcodes, strip_sampleid):
 
             summary = {
                 "sampleid": None if strip_sampleid else barcode,
-                "project": project,
+                "project": barcode_project,
                 "source-type": source_type,
                 "site-sampled": sample_site,
                 "sample-date": sample_date,

microsetta_private_api/admin/tests/test_admin_api.py

@@ -1252,6 +1252,57 @@ def test_query_barcode_stats_project_barcodes_with_strip(self):
         self.assertEqual([v['sample-status'] for v in response_obj],
                          exp_status)
 
+    def test_query_barcode_stats_multiple_projects(self):
+        barcodes = ['000005059', '000005078', '000005103']
+        input_json = json.dumps({'sample_barcodes': barcodes})
+
+        response = self.client.post(
+            "api/admin/account_barcode_summary?strip_sampleid=False",
+            content_type='application/json',
+            data=input_json,
+            headers=MOCK_HEADERS
+        )
+        # an empty string project should be unknown
+        self.assertEqual(200, response.status_code)
+
+        response_obj = json.loads(response.data)
+        self.assertIn('samples', response_obj)
+        response_obj = response_obj['samples']
+        self.assertEqual(len(response_obj), 3)
+
+        self.assertEqual([v['sampleid'] for v in response_obj], barcodes)
+        response_projects = [v['project'].split('; ') for v in response_obj]
+        self.assertEqual(len(response_projects[0]), 2)
+        self.assertEqual(len(response_projects[1]), 3)
+        self.assertEqual(len(response_projects[2]), 3)
+        self.assertTrue(all(
+            projs[0] == 'American Gut Project' for projs in response_projects
+        ))
+        # content: should have exactly the same projects
+        self.assertEqual(response_projects[1], response_projects[2])
+
+    def test_query_barcode_stats_by_project(self):
+        input_json = json.dumps({'project_id': 19})  # expect 5 barcodes
+        exp_barcodes = [
+            '000035369', '000035370', '000035371',
+            '000035372', '000035373'
+        ]
+
+        response = self.client.post(
+            "api/admin/account_barcode_summary?strip_sampleid=False",
+            content_type='application/json',
+            data=input_json,
+            headers=MOCK_HEADERS
+        )
+        # an empty string project should be unknown
+        self.assertEqual(200, response.status_code)
+
+        response_obj = json.loads(response.data)
+        self.assertIn('samples', response_obj)
+        response_obj = response_obj['samples']
+        self.assertEqual(len(response_obj), 5)
+        self.assertEqual([v['sampleid'] for v in response_obj], exp_barcodes)
+
     def test_send_email(self):
         def mock_func(*args, **kwargs):
             pass