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oliverbeumkes-nhsoliverbeumkes-nhs
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[PRM-391] Fix python warnings (#705)
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6 files changed

+52
-17
lines changed

6 files changed

+52
-17
lines changed

‎lambdas/requirements/layers/requirements_data_lambda_layer.txt‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
polars==0.20.25
1+
polars==1.31.0

‎lambdas/services/statistical_report_service.py‎

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -22,7 +22,6 @@
2222

2323
logger = LoggingService(__name__)
2424

25-
2625
class StatisticalReportService:
2726
def __init__(self):
2827
self.dynamo_service = DynamoDBService()
@@ -160,7 +159,7 @@ def summarise_application_data(
160159
pl.concat_list("active_user_ids_hashed")
161160
.flatten()
162161
.unique()
163-
.map_elements(lambda col: str(col.sort().to_list()))
162+
.map_elements(lambda col: str(col.sort().to_list()), return_dtype=pl.Utf8)
164163
.alias("unique_active_user_ids_hashed"),
165164
pl.concat_list("active_user_ids_hashed")
166165
.flatten()
@@ -180,7 +179,7 @@ def join_dataframes_by_ods_code(
180179

181180
for other_dataframe in data_to_report[1:]:
182181
joined_dataframe = joined_dataframe.join(
183-
other_dataframe, on="ods_code", how="outer_coalesce"
182+
other_dataframe, on="ods_code", how='full', coalesce=True
184183
)
185184

186185
return joined_dataframe

‎lambdas/tests/unit/helpers/data/test_stitch_trace.py‎

Lines changed: 34 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,34 @@
1+
from typing import List
2+
from lambdas.enums.trace_status import TraceStatus
3+
from lambdas.models.stitch_trace import StitchTrace
4+
from lambdas.tests.unit.conftest import TEST_NHS_NUMBER
5+
6+
7+
def create_test_stitch_trace() -> StitchTrace:
8+
"""Create a test StitchTrace object with optional overrides."""
9+
stitch_trace = StitchTrace(
10+
nhs_number=TEST_NHS_NUMBER,
11+
expire_at=9999999,
12+
job_status=TraceStatus.PENDING
13+
)
14+
return stitch_trace
15+
16+
def get_list_test_stitch_trace() -> List[StitchTrace]:
17+
"""Create a list of test StitchTrace objects."""
18+
return [
19+
StitchTrace(
20+
nhs_number=TEST_NHS_NUMBER,
21+
expire_at=9999999,
22+
job_status=TraceStatus.PENDING
23+
),
24+
StitchTrace(
25+
nhs_number=TEST_NHS_NUMBER,
26+
expire_at=8888888,
27+
job_status=TraceStatus.PENDING
28+
),
29+
StitchTrace(
30+
nhs_number=TEST_NHS_NUMBER,
31+
expire_at=7777777,
32+
job_status=TraceStatus.PENDING
33+
)
34+
]

‎lambdas/tests/unit/services/test_bulk_upload_metadata_preprocessor_service.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -283,7 +283,7 @@ def test_extract_document_number_from_bulk_upload_file_name_with_no_document_num
283283
("Lloyd_George_Record", "_lloyd_george_12342"),
284284
),
285285
(
286-
"]{\lloyd george?record///person_name",
286+
r"]{\lloyd george?record///person_name",
287287
("Lloyd_George_Record", "///person_name"),
288288
),
289289
("_Lloyd_George-Record_person_name", ("Lloyd_George_Record", "_person_name")),
@@ -352,8 +352,8 @@ def test_extract_person_name_from_bulk_upload_file_name_with_no_person_name(
352352
["input", "expected", "expected_exception"],
353353
[
354354
("_-9991211234-12012024", ("9991211234", "-12012024"), None),
355-
("_-9-99/12?11\/234-12012024", ("9991211234", "-12012024"), None),
356-
("_-9-9l9/12?11\/234-12012024", ("9991211234", "-12012024"), None),
355+
(r"_-9-99/12?11\/234-12012024", ("9991211234", "-12012024"), None),
356+
(r"_-9-9l9/12?11\/234-12012024", ("9991211234", "-12012024"), None),
357357
(
358358
"12_12_12_12_12_12_12_2024.csv",
359359
"incorrect NHS number format",

‎lambdas/tests/unit/services/test_document_deletion_service.py‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,7 @@
55
from enums.lambda_error import LambdaError
66
from enums.snomed_codes import SnomedCodes
77
from enums.supported_document_types import SupportedDocumentTypes
8+
from lambdas.tests.unit.helpers.data.test_stitch_trace import get_list_test_stitch_trace
89
from services.document_deletion_service import DocumentDeletionService
910
from tests.unit.conftest import (
1011
MOCK_ARF_TABLE_NAME,
@@ -26,6 +27,7 @@
2627

2728
TEST_DOC_STORE_REFERENCES = create_test_doc_store_refs()
2829
TEST_LG_DOC_STORE_REFERENCES = create_test_lloyd_george_doc_store_refs()
30+
TEST_STITCH_TRACE_REFERENCES = get_list_test_stitch_trace()
2931
TEST_NHS_NUMBER_WITH_NO_RECORD = "1234567890"
3032
TEST_NHS_NUMBER_WITH_ONLY_LG_RECORD = "234567890"
3133

@@ -250,7 +252,7 @@ def test_delete_specific_doc_type_when_no_record_for_given_patient(
250252

251253
def test_delete_documents_references_in_stitch_table(mock_deletion_service):
252254
mock_deletion_service.stitch_service.query_stitch_trace_with_nhs_number.return_value = (
253-
TEST_LG_DOC_STORE_REFERENCES
255+
TEST_STITCH_TRACE_REFERENCES
254256
)
255257

256258
mock_deletion_service.delete_documents_references_in_stitch_table(TEST_NHS_NUMBER)
@@ -264,7 +266,7 @@ def test_delete_documents_references_in_stitch_table(mock_deletion_service):
264266
key_pair={"ID": record.id},
265267
updated_fields={"Deleted": True},
266268
)
267-
for record in TEST_LG_DOC_STORE_REFERENCES
269+
for record in TEST_STITCH_TRACE_REFERENCES
268270
]
269271
mock_deletion_service.document_service.dynamo_service.update_item.assert_has_calls(
270272
expected_calls

‎lambdas/tests/unit/services/test_statistical_report_service.py‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -97,7 +97,7 @@ def test_make_weekly_summary(set_env, mocker):
9797
expected = EXPECTED_WEEKLY_SUMMARY
9898

9999
assert_frame_equal(
100-
actual, expected, check_row_order=False, check_dtype=False, check_exact=False
100+
actual, expected, check_row_order=False, check_dtypes=False, check_exact=False
101101
)
102102

103103

@@ -142,7 +142,7 @@ def test_summarise_record_store_data(mock_service):
142142

143143
expected = EXPECTED_SUMMARY_RECORD_STORE_DATA
144144

145-
assert_frame_equal(actual, expected, check_row_order=False, check_dtype=False)
145+
assert_frame_equal(actual, expected, check_row_order=False, check_dtypes=False)
146146

147147

148148
def test_summarise_record_store_data_larger_mock_data(mock_service):
@@ -163,7 +163,7 @@ def test_summarise_record_store_data_larger_mock_data(mock_service):
163163

164164
actual = mock_service.summarise_record_store_data(mock_record_store_data)
165165

166-
assert_frame_equal(actual, expected, check_row_order=False, check_dtype=False)
166+
assert_frame_equal(actual, expected, check_row_order=False, check_dtypes=False)
167167

168168

169169
def test_summarise_record_store_data_can_handle_empty_input(mock_service):
@@ -181,7 +181,7 @@ def test_summarise_organisation_data(mock_service):
181181

182182
expected = EXPECTED_SUMMARY_ORGANISATION_DATA
183183

184-
assert_frame_equal(actual, expected, check_row_order=False, check_dtype=False)
184+
assert_frame_equal(actual, expected, check_row_order=False, check_dtypes=False)
185185

186186

187187
def test_summarise_organisation_data_larger_mock_data(mock_service):
@@ -260,7 +260,7 @@ def test_summarise_application_data(mock_service):
260260
assert_frame_equal(
261261
actual,
262262
expected,
263-
check_dtype=False,
263+
check_dtypes=False,
264264
check_row_order=False,
265265
check_column_order=False,
266266
)
@@ -298,7 +298,7 @@ def test_summarise_application_data_larger_mock_data(mock_service):
298298
assert_frame_equal(
299299
actual,
300300
expected,
301-
check_dtype=False,
301+
check_dtypes=False,
302302
check_row_order=False,
303303
check_column_order=False,
304304
)
@@ -336,7 +336,7 @@ def test_join_dataframes_by_ods_code(mock_service):
336336
)
337337
actual = mock_service.join_dataframes_by_ods_code([mock_data_1, mock_data_2])
338338

339-
assert_frame_equal(actual, expected, check_dtype=False, check_row_order=False)
339+
assert_frame_equal(actual, expected, check_dtypes=False, check_row_order=False)
340340

341341

342342
def test_join_dataframes_by_ods_code_can_handle_empty_dataframe(mock_service):
@@ -359,7 +359,7 @@ def test_join_dataframes_by_ods_code_can_handle_empty_dataframe(mock_service):
359359
[mock_data_1, mock_data_2, mock_data_3]
360360
)
361361

362-
assert_frame_equal(actual, expected, check_dtype=False, check_row_order=False)
362+
assert_frame_equal(actual, expected, check_dtypes=False, check_row_order=False)
363363

364364

365365
@freeze_time("20240512T07:00:00Z")

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