Merge pull request #283 from sanger/bugfix_string_comparison

Bugfix string comparison

crawler/.release_version

@@ -0,0 +1 @@
+1.8.1

crawler/helpers/general_helpers.py

@@ -297,7 +297,7 @@ def get_dart_well_index(coordinate: Optional[str]) -> Optional[int]:
 
 
 def is_sample_positive(sample):
-    return sample.get(FIELD_RESULT, False) is POSITIVE_RESULT_VALUE
+    return sample.get(FIELD_RESULT, False) == POSITIVE_RESULT_VALUE
 
 
 def is_sample_important_or_positive(sample):

tests/conftest.py

@@ -374,3 +374,19 @@ def blacklist_for_centre(config):
         yield config
     finally:
         config.CENTRES[0]["file_names_to_ignore"] = []
+
+
+def generate_new_object_for_string(original_str):
+    """
+    For checking bug on comparing strings with 'is'
+    (Pdb) sample.get('Result', False) is 'Positive'
+    <stdin>:1: SyntaxWarning: "is" with a literal. Did you mean "=="?
+    False
+    (Pdb) sample2.get('Result', False) is 'Positive'
+    <stdin>:1: SyntaxWarning: "is" with a literal. Did you mean "=="?
+    True
+    """
+    part1 = original_str[0:2]
+    part2 = original_str[2:]
+    new_str = part1 + part2
+    return new_str

tests/db/test_dart.py

@@ -3,13 +3,21 @@
 import pyodbc
 import pytest
 
-from crawler.constants import DART_STATE, DART_STATE_NO_PLATE, DART_STATE_NO_PROP, DART_STATE_PENDING
+from crawler.constants import (
+    DART_STATE,
+    DART_STATE_NO_PLATE,
+    DART_STATE_NO_PROP,
+    DART_STATE_PENDING,
+    FIELD_RESULT,
+    POSITIVE_RESULT_VALUE,
+)
 from crawler.db.dart import (
     add_dart_plate_if_doesnt_exist,
     create_dart_sql_server_conn,
     get_dart_plate_state,
     set_dart_plate_state_pending,
     set_dart_well_properties,
+    add_dart_well_properties_if_positive,
 )
 from crawler.exceptions import DartStateError
 from crawler.sql_queries import (
@@ -19,6 +27,17 @@
     SQL_DART_SET_WELL_PROPERTY,
 )
 
+from tests.conftest import generate_new_object_for_string
+
+
+def test_add_dart_well_properties_if_positive(mlwh_connection):
+    with patch("crawler.db.dart.add_dart_well_properties") as mock_add_dart_well_properties:
+        cursor = mlwh_connection.cursor(dictionary=True)
+        sample = {FIELD_RESULT: generate_new_object_for_string(POSITIVE_RESULT_VALUE)}
+        plate_barcode = "aBarcode"
+        add_dart_well_properties_if_positive(cursor, sample, plate_barcode)
+        mock_add_dart_well_properties.assert_called_with(cursor, sample, plate_barcode)
+
 
 def test_create_dart_sql_server_conn(config):
     with patch("pyodbc.connect") as mock_connect:

tests/test_file_processing.py

@@ -85,6 +85,7 @@
 from crawler.db.mongo import get_mongo_collection
 from crawler.file_processing import ERRORS_DIR, SUCCESSES_DIR, Centre, CentreFile
 from crawler.types import Config, ModifiedRow
+from tests.conftest import generate_new_object_for_string
 
 # ----- tests helpers -----
 
@@ -1571,7 +1572,7 @@ def test_insert_plates_and_wells_from_docs_into_dart_multiple_new_plates(config)
             FIELD_PLATE_BARCODE: "TC-rna-00000029",
             FIELD_COORDINATE: "A01",
             FIELD_LAB_ID: "AP",
-            FIELD_RESULT: POSITIVE_RESULT_VALUE,
+            FIELD_RESULT: generate_new_object_for_string(POSITIVE_RESULT_VALUE),
         },
         {
             "_id": ObjectId("5f562d9931d9959b92544728"),
@@ -1580,7 +1581,7 @@ def test_insert_plates_and_wells_from_docs_into_dart_multiple_new_plates(config)
             FIELD_PLATE_BARCODE: "TC-rna-00000024",
             FIELD_COORDINATE: "B01",
             FIELD_LAB_ID: "AP",
-            FIELD_RESULT: POSITIVE_RESULT_VALUE,
+            FIELD_RESULT: generate_new_object_for_string(POSITIVE_RESULT_VALUE),
         },
         {
             "_id": ObjectId("5f562d9931d9959b92544728"),
@@ -1650,7 +1651,7 @@ def test_insert_plates_and_wells_from_docs_into_dart_single_new_plate_multiple_w
             FIELD_PLATE_BARCODE: plate_barcode,
             FIELD_COORDINATE: "A01",
             FIELD_LAB_ID: "AP",
-            FIELD_RESULT: POSITIVE_RESULT_VALUE,
+            FIELD_RESULT: generate_new_object_for_string(POSITIVE_RESULT_VALUE),
         },
         {
             "_id": ObjectId("5f562d9931d9959b92544728"),
@@ -1659,7 +1660,7 @@ def test_insert_plates_and_wells_from_docs_into_dart_single_new_plate_multiple_w
             FIELD_PLATE_BARCODE: plate_barcode,
             FIELD_COORDINATE: "A02",
             FIELD_LAB_ID: "AP",
-            FIELD_RESULT: POSITIVE_RESULT_VALUE,
+            FIELD_RESULT: generate_new_object_for_string(POSITIVE_RESULT_VALUE),
         },
         {
             "_id": ObjectId("5f562d9931d9959b92544728"),

tests/test_general_helpers.py

@@ -70,6 +70,8 @@
 )
 from crawler.types import SampleDoc
 
+from tests.conftest import generate_new_object_for_string
+
 
 def test_get_config():
     with pytest.raises(ModuleNotFoundError):
@@ -315,9 +317,9 @@ def test_create_source_plate_doc(freezer):
 
 
 def test_is_sample_positive():
-    negative = "negative"
-    assert is_sample_positive({FIELD_RESULT: negative}) is False
+    assert is_sample_positive({FIELD_RESULT: "negative"}) is False
     assert is_sample_positive({FIELD_RESULT: POSITIVE_RESULT_VALUE}) is True
+    assert is_sample_positive({FIELD_RESULT: generate_new_object_for_string(POSITIVE_RESULT_VALUE)}) is True
 
 
 def test_is_sample_important_or_positive():