Merge 9e818b5 into 082701a

microsetta_private_api/admin/admin_impl.py

@@ -1,3 +1,4 @@
+import flask
 from flask import jsonify
 
 from microsetta_private_api.repo.account_repo import AccountRepo
@@ -17,6 +18,21 @@ def search_barcode(token_info, sample_barcode):
         return jsonify(diag), 200
 
 
+def scan_barcode(token_info, sample_barcode, body):
+    validate_admin_access(token_info)
+
+    with Transaction() as t:
+        admin_repo = AdminRepo(t)
+        admin_repo.scan_barcode(sample_barcode, body)
+        t.commit()
+
+    response = flask.Response()
+    response.status_code = 201
+    response.headers['Location'] = '/api/admin/search/samples/%s' % \
+                                   sample_barcode
+    return response
+
+
 def validate_admin_access(token_info):
     with Transaction() as t:
         account_repo = AccountRepo(t)

microsetta_private_api/admin/tests/test_admin.py

@@ -1,6 +1,6 @@
 from unittest import TestCase
 
-from werkzeug.exceptions import Unauthorized
+from werkzeug.exceptions import Unauthorized, NotFound
 
 from microsetta_private_api.model.account import Account
 from microsetta_private_api.model.address import Address
@@ -121,3 +121,42 @@ def test_search_barcode(self):
             self.assertIsNone(diag['source'])
             self.assertIsNone(diag['sample'])
             self.assertEqual(len(diag['barcode_info']), 0)
+
+    def test_scan_barcode(self):
+        with Transaction() as t:
+            # TODO FIXME HACK:  Need to build mock barcodes rather than using
+            #  these fixed ones
+
+            TEST_BARCODE = '000000001'
+            TEST_STATUS = "sample-has-inconsistencies"
+            TEST_NOTES = "THIS IS A UNIT TEST"
+            admin_repo = AdminRepo(t)
+
+            diag = admin_repo.retrieve_diagnostics_by_barcode(TEST_BARCODE)
+            prestatus = diag['barcode_info'][0]['status']
+
+            admin_repo.scan_barcode(
+                TEST_BARCODE,
+                {
+                    "sample_status": TEST_STATUS,
+                    "technician_notes": TEST_NOTES
+                }
+            )
+
+            diag = admin_repo.retrieve_diagnostics_by_barcode(TEST_BARCODE)
+            self.assertEqual(diag['barcode_info'][0]['technician_notes'],
+                             TEST_NOTES)
+            self.assertEqual(diag['barcode_info'][0]['sample_status'],
+                             TEST_STATUS)
+            self.assertEqual(diag['barcode_info'][0]['status'],
+                             prestatus)
+
+            with self.assertRaises(NotFound):
+                admin_repo.scan_barcode(
+                    "THIZIZNOTAREALBARCODEISWARE",
+                    {
+                        "sample_status": "Abc",
+                        "technician_notes": "123"
+                    }
+                )
+                self.fail("Shouldn't get here")

microsetta_private_api/api/microsetta_private_api.yaml

@@ -815,7 +815,7 @@ paths:
           $ref: '#/components/responses/422UnprocessableEntity'
 
   # START ADMINISTRATOR PATHS
-  '/admin/search/sample/{sample_barcode}':
+  '/admin/search/samples/{sample_barcode}':
     get:
       operationId: microsetta_private_api.admin.admin_impl.search_barcode
       tags:
@@ -835,6 +835,41 @@ paths:
           $ref: '#/components/responses/401Unauthorized'
         '404':
           $ref: '#/components/responses/404NotFound'
+  '/admin/scan/{sample_barcode}':
+    post:
+      # Note: We might want to be able to differentiate system administrator operations
+      # from technician operations in the future by user accounts and the routes they post to
+      operationId: microsetta_private_api.admin.admin_impl.scan_barcode
+      tags:
+        - Admin
+      summary: Set sample processing information for a barcode
+      description: Set sample processing information for a barcode
+      parameters:
+        - $ref: '#/components/parameters/sample_barcode'
+      requestBody:
+        content:
+          application/json:
+            schema:
+              type: object
+              properties:
+                sample_status:
+                  type: string
+                  enum: ["not-received",
+                         "sample-is-valid",
+                         "no-associated-consent",
+                         "no-registered-account",
+                         "sample-has-inconsistencies"]
+                  example: "sample-has-inconsistencies"
+                technician_notes:
+                  type: string
+                  example: "Sample Processing Complete!"
+      responses:
+        '201':
+          description: Successfully registered new user account
+          headers:
+            Location:
+              schema:
+                type: string
 
 
 components:

microsetta_private_api/db/patches/0054.sql

@@ -0,0 +1,6 @@
+-- This script adds two columns to the barcodes.barcode table to enable
+-- adding information when scanned by a technician
+
+ALTER TABLE barcodes.barcode
+ADD COLUMN sample_status VARCHAR(100),
+ADD COLUMN technician_notes VARCHAR;

microsetta_private_api/repo/admin_repo.py

@@ -1,7 +1,11 @@
+from datetime import date
+
+from microsetta_private_api.exceptions import RepoException
 from microsetta_private_api.repo.account_repo import AccountRepo
 from microsetta_private_api.repo.base_repo import BaseRepo
 from microsetta_private_api.repo.sample_repo import SampleRepo
 from microsetta_private_api.repo.source_repo import SourceRepo
+from werkzeug.exceptions import NotFound
 
 
 class AdminRepo(BaseRepo):
@@ -75,3 +79,31 @@ def retrieve_diagnostics_by_barcode(self, sample_barcode):
             }
 
             return diagnostic
+
+    def scan_barcode(self, sample_barcode, scan_info):
+        update_args = (
+            scan_info['sample_status'],
+            scan_info['technician_notes'],
+            date.today(),  # TODO: Do we need date or datetime here?
+            sample_barcode
+        )
+
+        with self._transaction.cursor() as cur:
+            cur.execute(
+                "UPDATE barcodes.barcode "
+                "SET "
+                "sample_status = %s, "
+                "technician_notes = %s, "
+                "scan_date = %s "
+                "WHERE "
+                "barcode = %s",
+                update_args
+            )
+
+            if cur.rowcount == 0:
+                raise NotFound("No such barcode: %s" % sample_barcode)
+
+            if cur.rowcount > 1:
+                # Note: This "can't" happen.
+                raise RepoException("ERROR: Multiple barcode entries would be "
+                                    "updated by scan, failing out")