Merge pull request #324 from wasade/persampe-tweaks

Per sample barcode summaries including email support

microsetta_private_api/admin/admin_impl.py

@@ -5,7 +5,6 @@
 
 from microsetta_private_api.config_manager import SERVER_CONFIG
 from microsetta_private_api.model.log_event import LogEvent
-from microsetta_private_api.model.source import Source
 from microsetta_private_api.model.project import Project
 from microsetta_private_api.model.daklapack_order import DaklapackOrder, \
     ORDER_ID_KEY, SUBMITTER_ACCT_KEY
@@ -18,15 +17,15 @@
 from microsetta_private_api.repo.source_repo import SourceRepo
 from microsetta_private_api.repo.transaction import Transaction
 from microsetta_private_api.repo.admin_repo import AdminRepo
-from microsetta_private_api.repo.survey_template_repo import SurveyTemplateRepo
 from microsetta_private_api.repo.metadata_repo import (retrieve_metadata,
                                                        drop_private_columns)
-from microsetta_private_api.repo.vioscreen_repo import VioscreenSessionRepo
-from microsetta_private_api.tasks import send_email as celery_send_email
+from microsetta_private_api.tasks import send_email as celery_send_email,\
+    per_sample_summary as celery_per_sample_summary
 from microsetta_private_api.admin.email_templates import EmailMessage
 from microsetta_private_api.util.redirects import build_login_redirect
 from microsetta_private_api.admin.daklapack_communication import \
     post_daklapack_order, send_daklapack_hold_email
+from microsetta_private_api.admin.sample_summary import per_sample
 from werkzeug.exceptions import Unauthorized
 
 
@@ -397,83 +396,21 @@ def query_email_stats(body, token_info):
     return jsonify(results), 200
 
 
-def query_barcode_stats(body, token_info):
+def query_project_barcode_stats(body, token_info, strip_sampleid):
     validate_admin_access(token_info)
-
-    barcodes = body.get("sample_barcodes")
+    email = body.get("email")
     project = body["project"]
+    celery_per_sample_summary.delay(email, project, strip_sampleid)
+    return None, 200
 
-    summaries = []
-    with Transaction() as t:
-        admin_repo = AdminRepo(t)
-        sample_repo = SampleRepo(t)
-        template_repo = SurveyTemplateRepo(t)
-        vs_repo = VioscreenSessionRepo(t)
 
-        project_barcodes = admin_repo.get_project_barcodes(project)
-
-        if barcodes is None:
-            barcodes = project_barcodes
-        else:
-            barcodes = [b for b in barcodes if b in set(project_barcodes)]
-            not_found = [b for b in barcodes if b not in set(project_barcodes)]
-            if len(not_found) > 0:
-                nf = ", ".join(not_found)
-                message = f"The following barcodes were not found: '[{nf}]'"
-                return jsonify(code=404, message=message), 404
-
-        for barcode in barcodes:
-            diag = admin_repo.retrieve_diagnostics_by_barcode(barcode)
-            sample = diag['sample']
-            account = diag['account']
-            source = diag['source']
-
-            account_email = None if account is None else account.email
-            source_email = None
-            source_type = None if source is None else source.source_type
-            vio_id = None
-
-            if source is not None and source_type is Source.SOURCE_TYPE_HUMAN:
-                source_email = source.email
-
-                vio_id = template_repo.get_vioscreen_id_if_exists(account.id,
-                                                                  source.id,
-                                                                  sample.id)
-
-            sample_status = sample_repo.get_sample_status(
-                sample.barcode,
-                sample._latest_scan_timestamp
-            )
-
-            ffq_complete, ffq_taken, _ = vs_repo.get_ffq_status_by_sample(
-                sample.id
-            )
-
-            summary = {
-                "sampleid": barcode,
-                "project": project,
-                "source-type": source_type,
-                "site-sampled": sample.site,
-                "source-email": source_email,
-                "account-email": account_email,
-                "vioscreen_username": vio_id,
-                "ffq-taken": ffq_taken,
-                "ffq-complete": ffq_complete,
-                "sample-status": sample_status,
-                "sample-received": sample_status is not None
-            }
-
-            for status in ["sample-is-valid",
-                           "no-associated-source",
-                           "no-registered-account",
-                           "no-collection-info",
-                           "sample-has-inconsistencies",
-                           "received-unknown-validity"]:
-                summary[status] = sample_status == status
-
-            summaries.append(summary)
-
-    return jsonify(summaries), 200
+def query_barcode_stats(body, token_info, strip_sampleid):
+    validate_admin_access(token_info)
+    barcodes = body["sample_barcodes"]
+    if len(barcodes) > 1000:
+        return jsonify({"message": "Too manny barcodes requested"}), 400
+    summary = per_sample(None, barcodes, strip_sampleid)
+    return jsonify(summary), 200
 
 
 def create_daklapack_order(body, token_info):

microsetta_private_api/admin/sample_summary.py

@@ -0,0 +1,88 @@
+from microsetta_private_api.model.source import Source
+from microsetta_private_api.repo.sample_repo import SampleRepo
+from microsetta_private_api.repo.transaction import Transaction
+from microsetta_private_api.repo.admin_repo import AdminRepo
+from microsetta_private_api.repo.survey_template_repo import SurveyTemplateRepo
+from microsetta_private_api.repo.vioscreen_repo import VioscreenSessionRepo
+from werkzeug.exceptions import NotFound
+
+
+def per_sample(project, barcodes, strip_sampleid):
+    summaries = []
+    with Transaction() as t:
+        admin_repo = AdminRepo(t)
+        sample_repo = SampleRepo(t)
+        template_repo = SurveyTemplateRepo(t)
+        vs_repo = VioscreenSessionRepo(t)
+
+        if project is not None:
+            project_barcodes = admin_repo.get_project_barcodes(project)
+        else:
+            project = 'Unspecified'
+
+        if barcodes is None:
+            barcodes = project_barcodes
+
+        for barcode in barcodes:
+            diag = admin_repo.retrieve_diagnostics_by_barcode(barcode)
+            if diag is None:
+                raise NotFound(f"Barcode not found: {barcode}")
+
+            sample = diag['sample']
+            account = diag['account']
+            source = diag['source']
+
+            account_email = None if account is None else account.email
+            source_email = None
+            source_type = None if source is None else source.source_type
+            vio_id = None
+
+            if source is not None and source_type == Source.SOURCE_TYPE_HUMAN:
+                source_email = source.source_data.email
+
+                vio_id = template_repo.get_vioscreen_id_if_exists(account.id,
+                                                                  source.id,
+                                                                  sample.id)
+
+            # at least one sample has been observed that "is_microsetta",
+            # described in the barcodes.project_barcode table, but which is
+            # unexpectedly not present in ag.ag_kit_barcodes
+            if sample is None:
+                sample_status = None
+                sample_site = None
+                ffq_complete = None
+                ffq_taken = None
+            else:
+                sample_status = sample_repo.get_sample_status(
+                    sample.barcode,
+                    sample._latest_scan_timestamp
+                )
+                sample_site = sample.site
+                ffq_complete, ffq_taken, _ = vs_repo.get_ffq_status_by_sample(
+                    sample.id
+                )
+
+            summary = {
+                "sampleid": None if strip_sampleid else barcode,
+                "project": project,
+                "source-type": source_type,
+                "site-sampled": sample_site,
+                "source-email": source_email,
+                "account-email": account_email,
+                "vioscreen_username": vio_id,
+                "ffq-taken": ffq_taken,
+                "ffq-complete": ffq_complete,
+                "sample-status": sample_status,
+                "sample-received": sample_status is not None
+            }
+
+            for status in ["sample-is-valid",
+                           "no-associated-source",
+                           "no-registered-account",
+                           "no-collection-info",
+                           "sample-has-inconsistencies",
+                           "received-unknown-validity"]:
+                summary[status] = sample_status == status
+
+            summaries.append(summary)
+    return summaries

microsetta_private_api/admin/tests/test_admin_api.py

@@ -976,54 +976,72 @@ def test_post_daklapack_orders_failure_dak_api(self):
                 mock_email.side_effect = [True]
                 self._test_post_daklapack_orders(order_info, 401)
 
-    def test_query_barcode_stats_no_project_no_barcodes(self):
-        input_json = json.dumps({'project': 0, 'sample_barcodes': None})
+    def test_query_project_barcode_stats_project_without_strip(self):
+        input_json = json.dumps({'project': 7, 'email': 'foobar'})
 
-        response = self.client.post(
-            "api/admin/account_barcode_summary",
-            content_type='application/json',
-            data=input_json,
-            headers=MOCK_HEADERS
-        )
+        with patch("microsetta_private_api.tasks."
+                   "per_sample_summary.delay") as mock_delay:
+            mock_delay.return_value = None
+            response = self.client.post(
+                "api/admin/account_project_barcode_summary?"
+                "strip_sampleid=false",
+                content_type='application/json',
+                data=input_json,
+                headers=MOCK_HEADERS
+            )
 
-        # an empty string project should be unkown
-        self.assertEqual(404, response.status_code)
+        # ...we assume the system is processing to send an email
+        # so nothing specific to verify on the response data
+        self.assertEqual(200, response.status_code)
 
-    def test_query_barcode_stats_project_no_barcodes(self):
-        input_json = json.dumps({'project': 7, 'sample_barcodes': None})
+    def test_query_project_barcode_stats_project_with_strip(self):
+        input_json = json.dumps({'project': 7, 'email': 'foobar'})
+
+        with patch("microsetta_private_api.tasks."
+                   "per_sample_summary.delay") as mock_delay:
+            mock_delay.return_value = None
+            response = self.client.post(
+                "api/admin/account_project_barcode_summary?"
+                "strip_sampleid=True",
+                content_type='application/json',
+                data=input_json,
+                headers=MOCK_HEADERS
+            )
+
+        # ...we assume the system is processing to send an email
+        # so nothing specific to verify on the response data
+        self.assertEqual(200, response.status_code)
+
+    def test_query_barcode_stats_project_barcodes_without_strip(self):
+        barcodes = ['000010307', '000023344', '000036855']
+        input_json = json.dumps({'sample_barcodes': barcodes})
 
         response = self.client.post(
-            "api/admin/account_barcode_summary",
+            "api/admin/account_barcode_summary?strip_sampleid=False",
             content_type='application/json',
             data=input_json,
             headers=MOCK_HEADERS
         )
-
+        # an empty string project should be unkown
         self.assertEqual(200, response.status_code)
 
         response_obj = json.loads(response.data)
+        self.assertEqual(len(response_obj), 3)
 
-        # there are 24 samples with project 7 in the test db
-        self.assertEqual(len(response_obj), 24)
-
-        # ...10 have been received
-        self.assertEqual(sum([v['sample-received']
-                              for v in response_obj]), 10)
-
-        # ...9 are valid
-        self.assertEqual(sum([v['sample-is-valid']
-                              for v in response_obj]), 9)
-
-        # ...1 is missing a source
-        self.assertEqual(sum([v['no-associated-source']
-                              for v in response_obj]), 1)
+        self.assertEqual([v['sampleid'] for v in response_obj],
+                         barcodes)
+        exp_status = [None, 'no-associated-source', 'sample-is-valid']
+        self.assertEqual([v['sample-status'] for v in response_obj],
+                         exp_status)
+        n_src = sum([v['source-email'] is not None for v in response_obj])
+        self.assertEqual(n_src, 1)
 
-    def test_query_barcode_stats_project_barcodes(self):
+    def test_query_barcode_stats_project_barcodes_with_strip(self):
         barcodes = ['000010307', '000023344', '000036855']
-        input_json = json.dumps({'project': 7, 'sample_barcodes': barcodes})
+        input_json = json.dumps({'sample_barcodes': barcodes})
 
         response = self.client.post(
-            "api/admin/account_barcode_summary",
+            "api/admin/account_barcode_summary?strip_sampleid=True",
             content_type='application/json',
             data=input_json,
             headers=MOCK_HEADERS
@@ -1035,7 +1053,9 @@ def test_query_barcode_stats_project_barcodes(self):
         self.assertEqual(len(response_obj), 3)
 
         self.assertEqual([v['sampleid'] for v in response_obj],
-                         barcodes)
+                         [None] * len(barcodes))
         exp_status = [None, 'no-associated-source', 'sample-is-valid']
         self.assertEqual([v['sample-status'] for v in response_obj],
                          exp_status)
+        n_src = sum([v['source-email'] is not None for v in response_obj])
+        self.assertEqual(n_src, 1)

microsetta_private_api/admin/tests/test_admin_repo.py

@@ -300,6 +300,19 @@ def test_retrieve_diagnostics_by_barcode_not_agp(self):
             self.assertGreater(len(diag['scans_info']), 0)
             self.assertGreater(len(diag['projects_info']), 0)
 
+    def test_get_project_name_fail(self):
+        with Transaction() as t:
+            admin_repo = AdminRepo(t)
+
+            with self.assertRaisesRegex(NotFound, "not found"):
+                admin_repo.get_project_name(9999999)
+
+    def test_get_project_name(self):
+        with Transaction() as t:
+            admin_repo = AdminRepo(t)
+            obs = admin_repo.get_project_name(1)
+            self.assertEqual(obs, 'American Gut Project')
+
     def test_get_project_barcodes_fail(self):
         with Transaction() as t:
             admin_repo = AdminRepo(t)