Merge 327fa98 into 082701a

microsetta_private_api/admin/admin_impl.py

@@ -17,6 +17,28 @@ def search_barcode(token_info, sample_barcode):
         return jsonify(diag), 200
 
 
+def search_kit_id(token_info, kit_id):
+    validate_admin_access(token_info)
+
+    with Transaction() as t:
+        admin_repo = AdminRepo(t)
+        diag = admin_repo.retrieve_diagnostics_by_kit_id(kit_id)
+        if diag is None:
+            return jsonify(code=404, message="Kit ID not found"), 404
+        return jsonify(diag), 200
+
+
+def search_email(token_info, email):
+    validate_admin_access(token_info)
+
+    with Transaction() as t:
+        admin_repo = AdminRepo(t)
+        diag = admin_repo.retrieve_diagnostics_by_email(email)
+        if diag is None:
+            return jsonify(code=404, message="Email not found"), 404
+        return jsonify(diag), 200
+
+
 def validate_admin_access(token_info):
     with Transaction() as t:
         account_repo = AccountRepo(t)

microsetta_private_api/admin/tests/test_admin.py

@@ -121,3 +121,27 @@ def test_search_barcode(self):
             self.assertIsNone(diag['source'])
             self.assertIsNone(diag['sample'])
             self.assertEqual(len(diag['barcode_info']), 0)
+
+    def test_search_kit_id(self):
+        with Transaction() as t:
+            admin_repo = AdminRepo(t)
+            diag = admin_repo.retrieve_diagnostics_by_kit_id('test')
+            self.assertIsNotNone(diag)
+            self.assertIsNotNone(diag['kit'])
+
+            diag = admin_repo.retrieve_diagnostics_by_kit_id('NotAKitId!!!!')
+            self.assertIsNone(diag)
+
+    def test_search_email(self):
+        with Transaction() as t:
+            admin_repo = AdminRepo(t)
+            diag = admin_repo.retrieve_diagnostics_by_email(
+                'yqrc&3x9_9@h7yx5.com')
+            self.assertIsNotNone(diag)
+            self.assertEqual(len(diag['accounts']), 1)
+
+            diag = admin_repo.retrieve_diagnostics_by_email(
+                '.com'
+            )
+            self.assertIsNotNone(diag)
+            self.assertGreater(len(diag['accounts']), 1)

microsetta_private_api/api/microsetta_private_api.yaml

@@ -835,6 +835,57 @@ paths:
           $ref: '#/components/responses/401Unauthorized'
         '404':
           $ref: '#/components/responses/404NotFound'
+  '/admin/search/kit/{kit_id}':
+    get:
+      operationId: microsetta_private_api.admin.admin_impl.search_kit_id
+      tags:
+        - Admin
+      summary: Retrieve diagnostic information about a kit by kit_id
+      description: Retrieve diagnostic information about a kit by kit_id
+      parameters:
+        - in: path
+          name: kit_id
+          description: User-facing id of kit
+          schema:
+            $ref: '#/components/schemas/kit_name'
+          required: true
+      responses:
+        '200':
+          description: Object containing linked account (if any), source (if any), sample (if any) and information about the barcode
+          content:
+            application/json:
+              schema:
+                type: object
+        '401':
+          $ref: '#/components/responses/401Unauthorized'
+        '404':
+          $ref: '#/components/responses/404NotFound'
+  '/admin/search/account/{email}':
+    get:
+      operationId: microsetta_private_api.admin.admin_impl.search_email
+      tags:
+        - Admin
+      summary: Retrieve diagnostic information about an account by email
+      description: Retrieve diagnostic information about an account by email
+      parameters:
+        - in: path
+          name: email
+          description: user email address
+          schema:
+            type: string
+            example: "test@test.com"
+          required: true
+      responses:
+        '200':
+          description: Object containing accounts with similar emails (if any)
+          content:
+            application/json:
+              schema:
+                type: object
+        '401':
+          $ref: '#/components/responses/401Unauthorized'
+        '404':
+          $ref: '#/components/responses/404NotFound'
 
 
 components:

microsetta_private_api/repo/account_repo.py

@@ -151,3 +151,11 @@ def delete_account_by_email(self, email):
             cur.execute("DELETE FROM account WHERE account.email = %s",
                         (email,))
             return cur.rowcount == 1
+
+    def get_account_ids_by_email(self, email):
+        email = "%"+email+"%"
+        with self._transaction.cursor() as cur:
+            cur.execute("SELECT id FROM account WHERE email LIKE %s "
+                        "ORDER BY email",
+                        (email,))
+            return [x[0] for x in cur.fetchall()]

microsetta_private_api/repo/admin_repo.py

@@ -1,5 +1,6 @@
 from microsetta_private_api.repo.account_repo import AccountRepo
 from microsetta_private_api.repo.base_repo import BaseRepo
+from microsetta_private_api.repo.kit_repo import KitRepo
 from microsetta_private_api.repo.sample_repo import SampleRepo
 from microsetta_private_api.repo.source_repo import SourceRepo
 
@@ -8,13 +9,14 @@ class AdminRepo(BaseRepo):
     def __init__(self, transaction):
         super().__init__(transaction)
 
-    def retrieve_diagnostics_by_barcode(self, sample_barcode):
+    def retrieve_diagnostics_by_barcode(self, sample_barcode, grab_kit=True):
         with self._transaction.dict_cursor() as cur:
             cur.execute(
                 "SELECT "
                 "ag_kit_barcodes.ag_kit_barcode_id as sample_id, "
                 "source.id as source_id, "
-                "account.id as account_id "
+                "account.id as account_id, "
+                "ag_kit_barcodes.ag_kit_id as kit_id "
                 "FROM "
                 "ag.ag_kit_barcodes "
                 "LEFT OUTER JOIN "
@@ -35,14 +37,17 @@ def retrieve_diagnostics_by_barcode(self, sample_barcode):
                 sample_id = None
                 source_id = None
                 account_id = None
+                kit_id = None
             else:
                 sample_id = row["sample_id"]
                 source_id = row["source_id"]
                 account_id = row["account_id"]
+                kit_id = row["kit_id"]
 
             account = None
             source = None
             sample = None
+            kit = None
 
             if sample_id is not None:
                 sample_repo = SampleRepo(self._transaction)
@@ -54,6 +59,10 @@ def retrieve_diagnostics_by_barcode(self, sample_barcode):
                 account = account_repo.get_account(account_id)
                 source = source_repo.get_source(account_id, source_id)
 
+            if kit_id is not None and grab_kit:
+                kit_repo = KitRepo(self._transaction)
+                kit = kit_repo.get_kit_all_samples_by_kit_id(kit_id)
+
             cur.execute("SELECT * from barcodes.barcode "
                         "LEFT OUTER JOIN barcodes.project_barcode "
                         "USING (barcode) "
@@ -74,4 +83,60 @@ def retrieve_diagnostics_by_barcode(self, sample_barcode):
                 "barcode_info": barcode_info
             }
 
+            if grab_kit:
+                diagnostic["kit"] = kit
+
             return diagnostic
+
+    def retrieve_diagnostics_by_kit_id(self, supplied_kit_id):
+        kit_repo = KitRepo(self._transaction)
+        kit = kit_repo.get_kit_all_samples(supplied_kit_id)
+
+        if kit is None:
+            return None
+
+        sample_assoc = []
+        for sample in kit.samples:
+            sample_assoc.append(
+                self.retrieve_diagnostics_by_barcode(sample.barcode,
+                                                     grab_kit=False))
+
+        with self._transaction.dict_cursor() as cur:
+            cur.execute(
+                "SELECT "
+                "ag_login_id as account_id "
+                "FROM "
+                "ag_kit "
+                "WHERE "
+                "supplied_kit_id = %s",
+                (supplied_kit_id,))
+            row = cur.fetchone()
+
+        pre_microsetta_acct = None
+        if row['account_id'] is not None:
+            acct_repo = AccountRepo(self._transaction)
+            # This kit predated the microsetta migration, let's pull in the
+            # account info associated with it
+            pre_microsetta_acct = acct_repo.get_account(row['account_id'])
+
+        diagnostic = {
+            'kit_id': kit.id,
+            'supplied_kit_id': supplied_kit_id,
+            'kit': kit,
+            'pre_microsetta_acct': pre_microsetta_acct,
+            'sample_diagnostic_info': sample_assoc
+        }
+
+        return diagnostic
+
+    def retrieve_diagnostics_by_email(self, email):
+
+        acct_repo = AccountRepo(self._transaction)
+        ids = acct_repo.get_account_ids_by_email(email)
+
+        accts = [acct_repo.get_account(acct_id) for acct_id in ids]
+        diagnostic = {
+            "accounts": accts
+        }
+
+        return diagnostic

microsetta_private_api/repo/kit_repo.py

@@ -7,6 +7,26 @@ class KitRepo(BaseRepo):
     def __init__(self, transaction):
         super().__init__(transaction)
 
+    # Kit ID is the uuid primary key of ag_kit, as opposed to supplied_kit_id,
+    # the more easily typed string we put on pieces of paper inside the kit
+    def get_kit_all_samples_by_kit_id(self, kit_id):
+        sample_repo = SampleRepo(self._transaction)
+        with self._transaction.cursor() as cur:
+            cur.execute("SELECT "
+                        "ag_kit.ag_kit_id, "
+                        "ag_kit_barcodes.ag_kit_barcode_id "
+                        "FROM ag_kit LEFT JOIN ag_kit_barcodes ON "
+                        "ag_kit.ag_kit_id = ag_kit_barcodes.ag_kit_id "
+                        "WHERE "
+                        "ag_kit.ag_kit_id = %s",
+                        (kit_id,))
+            rows = cur.fetchall()
+            if len(rows) == 0:
+                return None
+            else:
+                samples = [sample_repo._get_sample_by_id(r[1]) for r in rows]
+                return Kit(rows[0][0], samples)
+
     def get_kit_all_samples(self, supplied_kit_id):
         sample_repo = SampleRepo(self._transaction)