survey association lock change (#570)

* added lock to qiita repo

* changed where to get survey ids

* moved lock sample to func in qiita repo and added test

* changed location of lock

* added dissociate in test

* added comments

* changed test acct

* removed test in qiita in favor of test_associate_sample_and_survey

* added test

* changes per suggestions

* updated test

* additional changes

* added back commit

* towards moving test into one transaction

* remove commit

* added suggestion

* add commit to qitta metadata update

* Update microsetta_private_api/tasks.py

---------

Co-authored-by: Cassidy Symons <[email protected]>

Author: ayobi

microsetta_private_api/repo/qiita_repo.py

@@ -1,10 +1,33 @@
+from microsetta_private_api.repo.admin_repo import AdminRepo
 from microsetta_private_api.repo.base_repo import BaseRepo
 from microsetta_private_api.qiita import qclient
 from microsetta_private_api.repo.metadata_repo import retrieve_metadata
 from microsetta_private_api.repo.metadata_repo._constants import MISSING_VALUE
+from microsetta_private_api.repo.survey_answers_repo import SurveyAnswersRepo
 
 
 class QiitaRepo(BaseRepo):
+    def lock_completed_surveys_to_barcodes(self, barcodes):
+        # lock survey-sample association
+        admin_repo = AdminRepo(self._transaction)
+        sar_repo = SurveyAnswersRepo(self._transaction)
+
+        for sample_barcode in barcodes:
+            ids = admin_repo._get_ids_relevant_to_barcode(sample_barcode)
+
+            if ids is not None:
+                account_id = ids.get('account_id')
+                source_id = ids.get('source_id')
+                sample_id = ids.get('sample_id')
+
+                survey_ids = sar_repo.list_answered_surveys(
+                    account_id, source_id)
+
+                if survey_ids is not None:
+                    for survey_id in survey_ids:
+                        sar_repo.associate_answered_survey_with_sample(
+                            account_id, source_id, sample_id, survey_id)
+
     def push_metadata_to_qiita(self, barcodes=None):
         """Attempt to format and push metadata for the set of barcodes
 
@@ -35,6 +58,7 @@ def push_metadata_to_qiita(self, barcodes=None):
         list
             Any error detail when constructing metadata
         """
+
         if barcodes is None:
             with self._transaction.cursor() as cur:
                 # obtain all barcodes, which are part of the AG table,
@@ -84,6 +108,9 @@ def push_metadata_to_qiita(self, barcodes=None):
         # calls to this function if and as needed.
         to_push = list(barcodes - samples_in_qiita)[:1000]
 
+        # lock survey-sample association
+        self.lock_completed_surveys_to_barcodes(to_push)
+
         # short circuit if we do not have anything to push
         if len(to_push) == 0:
             return 0, []

microsetta_private_api/repo/tests/test_qiita.py

@@ -1,5 +1,6 @@
 from unittest import TestCase, main
 from unittest.mock import patch
+from microsetta_private_api.repo.survey_answers_repo import SurveyAnswersRepo
 from microsetta_private_api.repo.transaction import Transaction
 from microsetta_private_api.repo.qiita_repo import QiitaRepo
 
@@ -69,6 +70,63 @@ def test_push_metadata_to_qiita(self, test_retrieve_metadata,
                                       "associated with any surveys "
                                       "matching this template id")}])
 
+    def test_lock_completed_surveys_to_barcodes(self):
+
+        test_barcode = '000069747'
+        test_barcodes = [test_barcode]
+
+        with Transaction() as t:
+            with t.dict_cursor() as cur:
+                # first, find the ids for the barcode and survey we're using
+                # as they are dynamically generated.
+                cur.execute("select ag_login_id, source_id from "
+                            "ag_login_surveys a join source_barcodes_surveys b"
+                            " on a.survey_id = b.survey_id and b.barcode = "
+                            "'000069747' and survey_template_id = 1")
+                row = cur.fetchone()
+                account_id = row[0]
+                source_id = row[1]
+
+                cur.execute("select ag_kit_barcode_id from ag_kit_barcodes "
+                            "where barcode = '000069747'")
+                row = cur.fetchone()
+
+                cur.execute("SELECT * FROM source_barcodes_surveys "
+                            "WHERE barcode = '000069747'")
+                rows_before = cur.fetchall()
+
+            # submit a survey for the barcode
+            sar = SurveyAnswersRepo(t)
+            survey_10 = {
+                '22': 'Unspecified',
+                '108': 'Unspecified',
+                '109': 'Unspecified',
+                '110': 'Unspecified',
+                '111': 'Unspecified',
+                '112': '1990',
+                '113': 'Unspecified',
+                '115': 'Unspecified',
+                '148': 'Unspecified',
+                '492': 'Unspecified',
+                '493': 'Unspecified',
+                '502': 'Male'
+            }
+            sar.submit_answered_survey(
+                account_id,
+                source_id,
+                'en_US', 10, survey_10)
+
+            # now lock the barcode to the survey that was recently submitted
+            qiita_repo = QiitaRepo(t)
+            qiita_repo.lock_completed_surveys_to_barcodes(test_barcodes)
+
+            with t.dict_cursor() as cur:
+                cur.execute("SELECT * FROM source_barcodes_surveys "
+                            "WHERE barcode = '000069747'")
+                rows_after = cur.fetchall()
+
+        self.assertGreater(len(rows_after), len(rows_before))
+
 
 if __name__ == '__main__':
     main()

microsetta_private_api/tasks.py

@@ -86,3 +86,4 @@ def update_qiita_metadata():
                        {"what": "qiita metadata push errors",
                         "content": json.dumps(error, indent=2)},
                        EN_US)
+        t.commit()