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Carry trial conditions and primary completion #13

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Merged
zuhdil merged 3 commits into from
May 13, 2026
Merged

Carry trial conditions and primary completion #13

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eec71dd
Carry new_primarycompletiondate through to the silver layer
zuhdil May 12, 2026
9948d5e
Project conditions and primary completion date onto trial fact
zuhdil May 12, 2026
fa492e0
Apply `ruff format` to the new primary-completion-date test fixture
zuhdil May 13, 2026
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2 changes: 1 addition & 1 deletion src/igh_data_transform/transformations/clinical_trials.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,6 @@
"_owningbusinessunit_value",
"new_resultsfirstposted",
"versionnumber",
"new_primarycompletiondate",
"new_primaryoutcomemeasures",
"timezoneruleversionnumber",
"new_secondaryoutcomemeasures",
Expand All @@ -46,6 +45,7 @@
"vin_ctterminatedreason": "ctterminatedreason",
"vin_clinicaltrialid": "clinicaltrialid",
"new_locations": "locations",
"new_primarycompletiondate": "primarycompletiondate",
"_vin_candidate_value": "candidate_value",
"new_firstposted": "firstposted",
"new_outcomemeasure_secondary": "outcomemeasure_secondary",
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2 changes: 2 additions & 0 deletions src/igh_data_transform/transformations/silver_to_gold/config/schema_map.py
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Expand Up @@ -254,6 +254,8 @@
"collaborator": "collaborator",
"funder_type": "fundertype",
"interventions": "interventions",
"conditions": "conditions",
"primary_completion_date_key": "FK:dim_date.full_date|EXTRACT_DATE:primarycompletiondate",
"outcome_measure": "COALESCE(outcomemeasure_primary, outcomemeasure_secondary)",
"sex": "sex",
"study_design": "study_design",
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12 changes: 10 additions & 2 deletions tests/unit/test_clinical_trials.py
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Expand Up @@ -358,7 +358,10 @@ def _make_input_df(self, overrides=None):
"vin_source": ["ClinicalTrials.gov", "WHO ICTRP"],
"new_resultsfirstposted": [None, None],
"versionnumber": [100, 200],
"new_primarycompletiondate": [None, None],
"new_primarycompletiondate": [
"2024-10-28T13:00:00Z",
"2025-12-31T13:00:00Z",
],
"new_primaryoutcomemeasures": [None, None],
"timezoneruleversionnumber": [0.0, None],
"vin_recentupdates": [None, None],
Expand Down Expand Up @@ -442,7 +445,6 @@ def test_drops_metadata_and_aim1_columns(self):
"_owningbusinessunit_value",
"new_resultsfirstposted",
"versionnumber",
"new_primarycompletiondate",
"new_primaryoutcomemeasures",
"timezoneruleversionnumber",
"new_secondaryoutcomemeasures",
Expand All @@ -455,6 +457,12 @@ def test_drops_metadata_and_aim1_columns(self):
for col in dropped:
assert col not in result.columns

def test_renames_primary_completion_date(self):
df = self._make_input_df()
result, _ = transform_clinical_trials(df)
assert "primarycompletiondate" in result.columns
assert "new_primarycompletiondate" not in result.columns

def test_drops_empty_columns_preserving_valid_to(self):
df = self._make_input_df()
result, _ = transform_clinical_trials(df)
Expand Down