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DIG-1325: Don't add required_but_missing fields to failure list #35

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merged 2 commits into from
Oct 19, 2023
Merged

DIG-1325: Don't add required_but_missing fields to failure list #35

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070d438
Don't add required_but_missing fields to failure list
daisieh Oct 10, 2023
766391c
update tests
daisieh Oct 10, 2023
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2 changes: 1 addition & 1 deletion schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -336,7 +336,7 @@ def validate_schema(self, schema_name, map_json):
}
self.statistics["required_but_missing"][schema_name][f]["total"] += 1
if f not in map_json:
self.warn(f"{f} required for {schema_name}")
# self.warn(f"{f} required for {schema_name}")
self.statistics["required_but_missing"][schema_name][f]["missing"] += 1
if case not in self.statistics["cases_missing_data"]:
self.statistics["cases_missing_data"].append(case)
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3 changes: 1 addition & 2 deletions test_data_ingest.py
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Expand Up @@ -101,15 +101,14 @@ def test_donor_2(packets):
def test_validation(packets, schema):
schema.validate_ingest_map({"donors": packets})
print(schema.validation_failures)
assert len(schema.validation_failures) == 9
assert len(schema.validation_failures) == 8
# should be the following 9 failures:
# DONOR_5: cause_of_death required if is_deceased = Yes
# DONOR_5: date_of_death required if is_deceased = Yes
# DONOR_5 > PD_5: clinical_stage_group is required for clinical_tumour_staging_system Revised International staging system (RISS)
# DONOR_5 > PD_5 > SPECIMEN_6: Tumour specimens require a reference_pathology_confirmed_diagnosis
# DONOR_5 > PD_5 > TR_5 > Radiation 1: Only one radiation is allowed per treatment
# DONOR_5 > PD_5 > TR_5 > Radiation 1: reference_radiation_treatment_id required if radiation_boost = Yes
# DONOR_5 > PD_5 > TR_10: response_to_treatment required for treatments
# DONOR_5 > PD_5 > TR_10: treatment type Immunotherapy should have one or more immunotherapies submitted
# DONOR_6 > PD_6 > TR_9 > Surgery 0: submitter_specimen_id SPECIMEN_43 does not correspond to one of the available specimen_ids ['SPECIMEN_3']

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