Merge pull request #574 from ayobi/vocab_samples_issues

cassidysymons · web-flow · commit 233e89c1bbd4 · 2024-07-30T10:50:58.000-07:00
vocab for sample issues
diff --git a/microsetta_private_api/admin/admin_impl.py b/microsetta_private_api/admin/admin_impl.py
@@ -153,6 +153,16 @@ def scan_barcode(token_info, sample_barcode, body):
     return response
 
 
+def get_observations(token_info, sample_barcode):
+    validate_admin_access(token_info)
+
+    with Transaction() as t:
+        admin_repo = AdminRepo(t)
+        observations = admin_repo.\
+            retrieve_observations_by_project(sample_barcode)
+    return jsonify(observations), 200
+
+
 def sample_pulldown_single_survey(token_info,
                                   sample_barcode,
                                   survey_template_id):
diff --git a/microsetta_private_api/admin/tests/test_admin_api.py b/microsetta_private_api/admin/tests/test_admin_api.py
@@ -695,7 +695,8 @@ def test_scan_barcode_success(self):
             scan_info = {
                 "sample_barcode": self.TEST_BARCODE,
                 "sample_status": "sample-is-valid",
-                "technician_notes": ""
+                "technician_notes": "",
+                "observations": []
             }
             input_json = json.dumps(scan_info)
 
diff --git a/microsetta_private_api/admin/tests/test_admin_repo.py b/microsetta_private_api/admin/tests/test_admin_repo.py
@@ -5,6 +5,7 @@
 import psycopg2.extras
 from dateutil.relativedelta import relativedelta
 
+from microsetta_private_api.exceptions import RepoException
 import microsetta_private_api.model.project as p
 
 from werkzeug.exceptions import Unauthorized, NotFound
@@ -323,15 +324,19 @@ def make_tz_datetime(y, m, d):
             "barcode": test_barcode,
             "scan_timestamp": make_tz_datetime(2017, 7, 16),
             "sample_status": 'no-registered-account',
-            "technician_notes": "huh?"
+            "technician_notes": "huh?",
+            "observations": [{'observation_id': None, 'observation': None,
+                              'category': None}]
         }
 
         second_scan = {
             "barcode_scan_id": second_scan_id,
             "barcode": test_barcode,
             "scan_timestamp": make_tz_datetime(2020, 12, 4),
             "sample_status": 'sample-is-valid',
-            "technician_notes": None
+            "technician_notes": None,
+            "observations": [{'observation_id': None, 'observation': None,
+                              'category': None}]
         }
         try:
             add_dummy_scan(first_scan)
@@ -347,6 +352,7 @@ def make_tz_datetime(y, m, d):
                 self.assertGreater(len(diag['projects_info']), 0)
                 self.assertEqual(len(diag['scans_info']), 2)
                 # order matters in the returned vals, so test that
+                print(diag['scans_info'][0], first_scan)
                 self.assertEqual(diag['scans_info'][0], first_scan)
                 self.assertEqual(diag['scans_info'][1], second_scan)
                 self.assertEqual(diag['latest_scan'], second_scan)
@@ -776,30 +782,127 @@ def test_scan_barcode_success(self):
             # TODO FIXME HACK:  Need to build mock barcodes rather than using
             #  these fixed ones
 
-            TEST_BARCODE = '000000001'
+            TEST_BARCODE = '000010860'
             TEST_STATUS = "sample-has-inconsistencies"
             TEST_NOTES = "THIS IS A UNIT TEST"
             admin_repo = AdminRepo(t)
+            with t.dict_cursor() as cur:
+                cur.execute("SELECT observation_id "
+                            "FROM "
+                            "barcodes.sample_observation_project_associations "
+                            "WHERE project_id = 1")
+                observation_id = cur.fetchone()
+
+                # check that before doing a scan,
+                # no scans are recorded for this
+                diag = admin_repo.retrieve_diagnostics_by_barcode(TEST_BARCODE)
+                self.assertEqual(len(diag['scans_info']), 0)
+
+                # do a scan
+                admin_repo.scan_barcode(
+                    TEST_BARCODE,
+                    {
+                        "sample_status": TEST_STATUS,
+                        "technician_notes": TEST_NOTES,
+                        "observations": observation_id
+                    }
+                )
+
+                # show that now a scan is recorded for this barcode
+                diag = admin_repo.retrieve_diagnostics_by_barcode(TEST_BARCODE)
+                self.assertEqual(len(diag['scans_info']), 1)
+                first_scan = diag['scans_info'][0]
+                first_observation = first_scan['observations'][0]
+                scan_observation_id = first_observation['observation_id']
+
+                self.assertEqual(first_scan['technician_notes'], TEST_NOTES)
+                self.assertEqual(first_scan['sample_status'], TEST_STATUS)
+                self.assertEqual(scan_observation_id, observation_id[0])
+
+    def test_scan_with_no_observations(self):
+        with Transaction() as t:
+
+            TEST_BARCODE = '000010860'
+            TEST_NOTES = "THIS IS A UNIT TEST"
+            TEST_STATUS = "sample-has-inconsistencies"
+            admin_repo = AdminRepo(t)
 
             # check that before doing a scan, no scans are recorded for this
             diag = admin_repo.retrieve_diagnostics_by_barcode(TEST_BARCODE)
             self.assertEqual(len(diag['scans_info']), 0)
 
-            # do a scan
             admin_repo.scan_barcode(
                 TEST_BARCODE,
                 {
                     "sample_status": TEST_STATUS,
-                    "technician_notes": TEST_NOTES
+                    "technician_notes": TEST_NOTES,
+                    "observations": None
                 }
             )
-
-            # show that now a scan is recorded for this barcode
             diag = admin_repo.retrieve_diagnostics_by_barcode(TEST_BARCODE)
-            self.assertEqual(len(diag['scans_info']), 1)
             first_scan = diag['scans_info'][0]
-            self.assertEqual(first_scan['technician_notes'], TEST_NOTES)
-            self.assertEqual(first_scan['sample_status'], TEST_STATUS)
+            first_observation = first_scan['observations'][0]
+            scan_observation = first_observation['observation']
+            self.assertEqual(scan_observation, None)
+
+    def test_scan_with_multiple_observations(self):
+        with Transaction() as t:
+
+            TEST_BARCODE = '000010860'
+            TEST_NOTES = "THIS IS A UNIT TEST"
+            TEST_STATUS = "sample-has-inconsistencies"
+            admin_repo = AdminRepo(t)
+
+            with t.dict_cursor() as cur:
+                cur.execute("SELECT observation_id "
+                            "FROM "
+                            "barcodes.sample_observation_project_associations "
+                            "WHERE project_id = 1")
+                rows = cur.fetchmany(2)
+                observation_ids = [row['observation_id'] for row in rows]
+
+                # check that before doing a scan,
+                # no scans are recorded for this
+                diag = admin_repo.retrieve_diagnostics_by_barcode(TEST_BARCODE)
+                self.assertEqual(len(diag['scans_info']), 0)
+
+                admin_repo.scan_barcode(
+                    TEST_BARCODE,
+                    {
+                        "sample_status": TEST_STATUS,
+                        "technician_notes": TEST_NOTES,
+                        "observations": observation_ids
+                    }
+                )
+                diag = admin_repo.retrieve_diagnostics_by_barcode(TEST_BARCODE)
+                scans = [scan['observations'] for scan in diag['scans_info']]
+                scans_observation_ids = [obs['observation_id'] for scan in
+                                         scans for obs in scan]
+
+                self.assertEqual(scans_observation_ids, observation_ids)
+
+    def test_scan_with_wrong_observation(self):
+        with Transaction() as t:
+
+            TEST_BARCODE = '000000001'
+            TEST_NOTES = "THIS IS A UNIT TEST"
+            TEST_STATUS = "sample-has-inconsistencies"
+            TEST_OBSERVATIONS = ["ad374d60-466d-4db0-9a91-5e3e8aec7698"]
+            admin_repo = AdminRepo(t)
+
+            # check that before doing a scan, no scans are recorded for this
+            diag = admin_repo.retrieve_diagnostics_by_barcode(TEST_BARCODE)
+            self.assertEqual(len(diag['scans_info']), 0)
+
+            with self.assertRaises(RepoException):
+                admin_repo.scan_barcode(
+                    TEST_BARCODE,
+                    {
+                        "sample_status": TEST_STATUS,
+                        "technician_notes": TEST_NOTES,
+                        "observations": TEST_OBSERVATIONS
+                    }
+                )
 
     def test_scan_barcode_error_nonexistent(self):
         with Transaction() as t:
diff --git a/microsetta_private_api/api/microsetta_private_api.yaml b/microsetta_private_api/api/microsetta_private_api.yaml
@@ -2546,6 +2546,25 @@ paths:
         '401':
           $ref: '#/components/responses/401Unauthorized'
 
+  '/admin/scan/observations/{sample_barcode}':
+    get:
+      operationId: microsetta_private_api.admin.admin_impl.get_observations
+      tags:
+        - Admin
+      parameters:
+        - $ref: '#/components/parameters/sample_barcode'
+      summary: Return a list of observations
+      description: Return a list of observations
+      responses:
+        '200':
+          description: Array of observations
+          content:
+            application/json:
+              schema:
+                type: array
+        '401':
+          $ref: '#/components/responses/401Unauthorized'
+
   '/admin/scan/{sample_barcode}':
     post:
       # Note: We might want to be able to differentiate system administrator operations
@@ -2578,6 +2597,11 @@ paths:
                 technician_notes:
                   type: string
                   example: "Sample Processing Complete!"
+                observations:
+                  type: array
+                  items:
+                    type: string
+                  example: ["Observation 1", "Observation 2"]
       responses:
         '201':
           description: Successfully recorded new barcode scan
diff --git a/microsetta_private_api/api/tests/test_api.py b/microsetta_private_api/api/tests/test_api.py
@@ -2328,7 +2328,8 @@ def test_associate_sample_locked(self):
         any_status = 'sample-has-inconsistencies'
         post_resp = self.client.post('/api/admin/scan/%s' % BARCODE,
                                      json={'sample_status': any_status,
-                                           'technician_notes': "foobar"},
+                                           'technician_notes': "foobar",
+                                           'observations': []},
                                      headers=make_headers(FAKE_TOKEN_ADMIN))
         self.assertEqual(201, post_resp.status_code)
 
@@ -2383,7 +2384,8 @@ def test_edit_sample_locked(self):
         bad_status = 'sample-has-inconsistencies'
         post_resp = self.client.post('/api/admin/scan/%s' % BARCODE,
                                      json={'sample_status': bad_status,
-                                           'technician_notes': "foobar"},
+                                           'technician_notes': "foobar",
+                                           'observations': []},
                                      headers=make_headers(FAKE_TOKEN_ADMIN))
         self.assertEqual(201, post_resp.status_code)
 
@@ -2448,7 +2450,8 @@ def test_edit_sample_locked(self):
         good_status = "sample-is-valid"
         post_resp = self.client.post('/api/admin/scan/%s' % BARCODE,
                                      json={'sample_status': good_status,
-                                           'technician_notes': "foobar"},
+                                           'technician_notes': "foobar",
+                                           'observations': []},
                                      headers=make_headers(FAKE_TOKEN_ADMIN))
         self.assertEqual(201, post_resp.status_code)
 
@@ -2508,7 +2511,8 @@ def test_dissociate_sample_from_source_locked(self):
                               dummy_is_admin=True)
         post_resp = self.client.post('/api/admin/scan/%s' % BARCODE,
                                      json={'sample_status': 'sample-is-valid',
-                                           'technician_notes': "foobar"},
+                                           'technician_notes': "foobar",
+                                           'observations': []},
                                      headers=make_headers(FAKE_TOKEN_ADMIN))
         self.assertEqual(201, post_resp.status_code)
 
@@ -2563,7 +2567,8 @@ def test_update_sample_association_locked(self):
                               dummy_is_admin=True)
         post_resp = self.client.post('/api/admin/scan/%s' % BARCODE,
                                      json={'sample_status': 'sample-is-valid',
-                                           'technician_notes': "foobar"},
+                                           'technician_notes': "foobar",
+                                           'observations': []},
                                      headers=make_headers(FAKE_TOKEN_ADMIN))
         self.assertEqual(201, post_resp.status_code)
 
diff --git a/microsetta_private_api/db/patches/0141.sql b/microsetta_private_api/db/patches/0141.sql
@@ -0,0 +1,57 @@
+-- May 13, 2024
+-- Create table to store observation categories
+CREATE TABLE barcodes.sample_observation_categories (
+    category VARCHAR(255) PRIMARY KEY
+);
+
+-- Insert predefined observation categories
+INSERT INTO barcodes.sample_observation_categories (category)
+VALUES ('Sample'), ('Swab'), ('Tube');
+
+-- Create table to store sample observations
+CREATE TABLE barcodes.sample_observations (
+    observation_id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
+    category VARCHAR(255) NOT NULL,
+    observation VARCHAR(255) NOT NULL,
+    FOREIGN KEY (category) REFERENCES barcodes.sample_observation_categories(category),
+    UNIQUE (category, observation)
+);
+
+-- Create table to store associations between observations and projects
+CREATE TABLE barcodes.sample_observation_project_associations (
+    id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
+    observation_id UUID NOT NULL,
+    project_id INT NOT NULL,
+    FOREIGN KEY (observation_id) REFERENCES barcodes.sample_observations(observation_id),
+    FOREIGN KEY (project_id) REFERENCES barcodes.project(project_id),
+    UNIQUE (observation_id, project_id)
+);
+
+-- Insert predefined observations and associate them with a project
+WITH inserted_observations AS (
+    INSERT INTO barcodes.sample_observations (category, observation)
+    VALUES
+    ('Tube', 'Tube is not intact'),
+    ('Tube', 'Screw cap is loose'),
+    ('Tube', 'Insufficient ethanol'),
+    ('Tube', 'No ethanol'),
+    ('Swab', 'No swab in tube'),
+    ('Swab', 'Multiple swabs in tube'),
+    ('Swab', 'Incorrect swab type'),
+    ('Sample', 'No visible sample'),
+    ('Sample', 'Excess sample on swab')
+    RETURNING observation_id, category, observation
+)
+INSERT INTO barcodes.sample_observation_project_associations (observation_id, project_id)
+SELECT observation_id, 1
+FROM inserted_observations;
+
+-- Create table to store observation ids associated with barcode scans ids
+CREATE TABLE barcodes.sample_barcode_scan_observations (
+    id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
+    barcode_scan_id UUID NOT NULL,
+    observation_id UUID NOT NULL,
+    FOREIGN KEY (barcode_scan_id) REFERENCES barcodes.barcode_scans(barcode_scan_id),
+    FOREIGN KEY (observation_id) REFERENCES barcodes.sample_observations(observation_id),
+    UNIQUE (barcode_scan_id, observation_id)
+);
diff --git a/microsetta_private_api/repo/admin_repo.py b/microsetta_private_api/repo/admin_repo.py

Original file line number	Diff line number	Diff line change
`@@ -695,7 +695,8 @@ def test_scan_barcode_success(self):`
`695`	`695`	`scan_info = {`
`696`	`696`	`"sample_barcode": self.TEST_BARCODE,`
`697`	`697`	`"sample_status": "sample-is-valid",`
`698`		`- "technician_notes": ""`
	`698`	`+ "technician_notes": "",`
	`699`	`+ "observations": []`
`699`	`700`	`}`
`700`	`701`	`input_json = json.dumps(scan_info)`
`701`	`702`