def test_cdm_csv(self):
cdm_data_rows = resources.cdm_csv()
expected_keys = {
'table_name', 'column_name', 'is_nullable', 'data_type',
'description'
}
expected_table_names = {
'person', 'visit_occurrence', 'condition_occurrence',
'procedure_occurrence', 'drug_exposure', 'measurement'
}
actual_table_names = set()
for row in cdm_data_rows:
keys = set(row.keys())
self.assertSetEqual(expected_keys, keys)
actual_table_names.add(row['table_name'])
for expected_table_name in expected_table_names:
self.assertIn(expected_table_name, actual_table_names)
import resources
import os
CDM_TABLES = set([r['table_name'] for r in resources.cdm_csv()])
CDM_FILES = map(lambda t: t + '.csv', CDM_TABLES)
ACHILLES_INDEX_FILES = resources.achilles_index_files()
ALL_ACHILLES_INDEX_FILES = [
name.split(resources.resource_path + os.sep)[1].strip()
for name in ACHILLES_INDEX_FILES
]
DATASOURCES_JSON = os.path.join(resources.achilles_index_path,
'data/datasources.json')
RESULT_CSV = 'result.csv'
ERRORS_CSV = 'errors.csv'
WARNINGS_CSV = 'warnings.csv'
PROCESSED_TXT = 'processed.txt'
LOG_JSON = 'log.json'
ACHILLES_HEEL_REPORT = 'achillesheel'
PERSON_REPORT = 'person'
DATA_DENSITY_REPORT = 'datadensity'
ALL_REPORTS = [ACHILLES_HEEL_REPORT, PERSON_REPORT, DATA_DENSITY_REPORT]
ALL_REPORT_FILES = map(lambda s: s + '.json', ALL_REPORTS)
IGNORE_LIST = [RESULT_CSV, ERRORS_CSV, WARNINGS_CSV, PROCESSED_TXT
] + ALL_ACHILLES_INDEX_FILES
VOCABULARY_TABLES = [
'concept', 'concept_ancestor', 'concept_class', 'concept_relationship',
'concept_synonym', 'domain', 'drug_strength', 'relationship', 'vocabulary'
]
REQUIRED_TABLES = ['person']
REQUIRED_FILES = [table + '.csv' for table in REQUIRED_TABLES]
ACHILLES_EXPORT_PREFIX_STRING = "curation_report/data/"