Merge branch 'biocore:master' into japan_locale_change

Author: ayobi

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
@@ -835,6 +836,7 @@ def delete_account(account_id, token_info):
         src_repo = SourceRepo(t)
         samp_repo = SampleRepo(t)
         sar_repo = SurveyAnswersRepo(t)
+        interested_users_repo = InterestedUserRepo(t)
 
         acct = acct_repo.get_account(account_id)
         if acct is None:
@@ -872,6 +874,8 @@ def delete_account(account_id, token_info):
 
         acct_repo.scrub(account_id)
 
+        interested_users_repo.scrub(acct.email)
+
         t.commit()
 
     return None, 204
@@ -885,15 +889,16 @@ def ignore_removal_request(account_id, token_info):
         try:
             # remove the user from the queue, noting the admin who allowed it
             # and the time the action was performed.
-            rq_repo.update_queue(account_id, token_info['email'], 'ignored')
+            rq_repo.update_queue(account_id, token_info['email'],
+                                 'ignored', None)
             t.commit()
         except RepoException as e:
             raise e
 
     return None, 204
 
 
-def allow_removal_request(account_id, token_info):
+def allow_removal_request(account_id, token_info, delete_reason):
     validate_admin_access(token_info)
 
     with Transaction() as t:
@@ -902,7 +907,8 @@ def allow_removal_request(account_id, token_info):
         try:
             # remove the user from the queue, noting the admin who allowed it
             # and the time the action was performed.
-            rq_repo.update_queue(account_id, token_info['email'], 'deleted')
+            rq_repo.update_queue(account_id, token_info['email'],
+                                 'deleted', delete_reason)
             t.commit()
         except RepoException as e:
             raise e

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

microsetta_private_api/api/_removal_queue.py

@@ -15,13 +15,13 @@ def check_request_remove_account(account_id, token_info):
         return jsonify(result), 200
 
 
-def request_remove_account(account_id, token_info):
+def request_remove_account(account_id, token_info, user_delete_reason=None):
     # raises 401 if method fails
     _validate_account_access(token_info, account_id)
 
     with Transaction() as t:
         rq_repo = RemovalQueueRepo(t)
-        rq_repo.request_remove_account(account_id)
+        rq_repo.request_remove_account(account_id, user_delete_reason)
         t.commit()
 
     return jsonify(code=200, message="Request Accepted"), 200

microsetta_private_api/api/microsetta_private_api.yaml

@@ -184,6 +184,12 @@ paths:
       description: Request account to be removed
       parameters:
         - $ref: '#/components/parameters/account_id'
+        - name: user_delete_reason
+          in: query
+          description: Reason for account deletion
+          required: false
+          schema:
+            type: string
       responses:
         '200':
           description: Successfully requested for account to be removed
@@ -199,6 +205,12 @@ paths:
         description: Cancel request for account to be removed
         parameters:
           - $ref: '#/components/parameters/account_id'
+          - name: user_delete_reason
+            in: query
+            description: Reason for account deletion
+            required: false
+            schema:
+              type: string
         responses:
           '200':
             description: Successfully canceled request
@@ -2504,6 +2516,11 @@ paths:
         - Admin
       parameters:
         - $ref: '#/components/parameters/account_id'
+        - name: delete_reason
+          in: query
+          required: true
+          schema:
+            type: string
       responses:
         '200':
           description: Updates queue, log before calling delete_account()

microsetta_private_api/api/tests/test_api.py

@@ -1425,6 +1425,7 @@ def test_request_account_removal(self):
         self.assertFalse(json.loads(response.data)['status'])
 
         # submit a request for this account to be removed.
+        delete_reason = "User requested account removal"
         response = self.client.put(
             f'/api/accounts/{dummy_acct_id}/removal_queue',
             headers=self.dummy_auth)
@@ -1440,8 +1441,9 @@ def test_request_account_removal(self):
             headers=self.dummy_auth)
 
         self.assertEqual(200, response.status_code)
-
-        self.assertTrue(json.loads(response.data)['status'])
+        removal_info = json.loads(response.data)
+        self.assertTrue(removal_info['status'])
+        # self.assertEqual(removal_info['delete_reason'], delete_reason)
 
         # try to request a second time. Verify that an error is returned
         # instead.
@@ -1491,7 +1493,8 @@ def test_request_account_removal(self):
                          "Request Accepted")
 
         response = self.client.put(
-            f'/api/admin/account_removal/{dummy_acct_id}',
+            f'/api/admin/account_removal/{dummy_acct_id}'
+            f'?delete_reason={delete_reason}',
             headers=make_headers(FAKE_TOKEN_ADMIN))
 
         self.assertEqual(204, response.status_code)
@@ -1557,7 +1560,8 @@ def test_request_account_removal(self):
         # functionality; it deletes the id from the delete-queue and logs the
         # deletion in a separate 'log' table, before calling account_delete().
         response = self.client.delete(
-            f'/api/admin/account_removal/{dummy_acct_id}',
+            f'/api/admin/account_removal/{dummy_acct_id}'
+            f'?delete_reason={delete_reason}',
             headers=make_headers(FAKE_TOKEN_ADMIN))
 
         # confirm that the operation was a success.

microsetta_private_api/db/patches/0137.sql

@@ -0,0 +1,7 @@
+-- Feb 5, 2024
+-- Add delete_reason to ag.account_removal_log
+ALTER TABLE ag.account_removal_log
+    ADD COLUMN delete_reason VARCHAR;
+
+COMMENT ON COLUMN ag.account_removal_log.delete_reason
+    IS 'Reason the admin gave for deleting the account.';

microsetta_private_api/db/patches/0138.sql

@@ -0,0 +1,7 @@
+-- Feb 12, 2024
+-- Add user_delete_reason to ag.delete_account_queue
+ALTER TABLE ag.delete_account_queue
+    ADD COLUMN user_delete_reason VARCHAR;
+
+COMMENT ON COLUMN ag.delete_account_queue.user_delete_reason
+    IS 'Reason the user gave for deleting the account.';

microsetta_private_api/model/removal_queue_requests.py

@@ -3,7 +3,7 @@
 
 class RemovalQueueRequest(ModelBase):
     def __init__(self, id, account_id, email, first_name, last_name,
-                 requested_on):
+                 requested_on, user_delete_reason):
         self.id = id
         self.account_id = account_id
         self.email = email
@@ -12,6 +12,7 @@ def __init__(self, id, account_id, email, first_name, last_name,
 
         # 2022-07-27 17:15:33.937458-07:00 -> 2022-07-27 17:15:33
         self.requested_on = str(requested_on).split('.')[0]
+        self.user_delete_reason = user_delete_reason
 
     def to_api(self):
         return self.__dict__.copy()

microsetta_private_api/repo/interested_user_repo.py

@@ -66,6 +66,9 @@ def update_interested_user(self, interested_user):
                 "state = %s, "
                 "postal_code = %s, "
                 "country = %s, "
+                "latitude = %s, "
+                "longitude = %s, "
+                "confirm_consent = %s, "
                 "address_checked = %s, "
                 "address_valid = %s, "
                 "residential_address = %s, "
@@ -82,6 +85,9 @@ def update_interested_user(self, interested_user):
                  interested_user.state,
                  interested_user.postal_code,
                  interested_user.country,
+                 interested_user.latitude,
+                 interested_user.longitude,
+                 interested_user.confirm_consent,
                  interested_user.address_checked,
                  interested_user.address_valid,
                  interested_user.residential_address,
@@ -207,3 +213,41 @@ def verify_address(self, interested_user_id):
                         (interested_user_id,)
                     )
                     return False
+
+    def get_interested_user_by_just_email(self, email):
+        with self._transaction.dict_cursor() as cur:
+            cur.execute(
+                "SELECT * FROM campaign.interested_users "
+                "WHERE lower(email) = lower(%s)",
+                (email,)
+            )
+            rs = cur.fetchall()
+            return [__class__._row_to_interested_user(r) for r in rs]
+
+    def scrub(self, interested_user_email):
+        interested_users = self. \
+            get_interested_user_by_just_email(interested_user_email)
+
+        for interested_user in interested_users:
+            interested_user.first_name = "scrubbed"
+            interested_user.last_name = "scrubbed"
+            interested_user.email = "scrubbed"
+            interested_user.phone = "scrubbed"
+            interested_user.address_1 = "scrubbed"
+            interested_user.address_2 = "scrubbed"
+            interested_user.address_3 = "scrubbed"
+            interested_user.city = "scrubbed"
+            interested_user.state = "scrubbed"
+            interested_user.postal_code = "scrubbed"
+            interested_user.country = "scrubbed"
+            interested_user.latitude = None
+            interested_user.longitude = None
+            interested_user.confirm_consent = False
+            interested_user.ip_address = "scrubbed"
+            interested_user.address_checked = False
+            interested_user.address_valid = False
+            interested_user.residential_address = False
+
+            if not self.update_interested_user(interested_user):
+                raise RepoException("Error scrubbing interested user: "
+                                    + interested_user.interested_user_id)