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sprivitesprivite
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update mappers
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‎phenex/mappers.py

+111-79
Original file line numberDiff line numberDiff line change
@@ -69,12 +69,14 @@ def get_mapped_tables(self, con) -> Dict[str, PhenexTable]:
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# OMOP Column Mappers
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#
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class OMOPPersonTable(PhenexPersonTable):
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NAME_TABLE = 'PERSON'
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JOIN_KEYS = {
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'OMOPConditionOccurenceTable': ['PERSON_ID'],
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'OMOPVisitDetailTable': ['PERSON_ID']
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}
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class OMOPVisitDetailTable(PhenexVisitDetailTable):
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NAME_TABLE = 'VISIT_DETAIL'
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JOIN_KEYS = {
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'OMOPPersonTable': ['PERSON_ID'],
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'OMOPConditionOccurenceTable': ['PERSON_ID', 'VISIT_DETAIL_ID']
@@ -92,89 +94,119 @@ class OMOPConditionOccurenceTable(CodeTable):
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'CODE': "CONDITION_CONCEPT_ID",
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}
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class OMOPDeathTable(PhenexTable):
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NAME_TABLE = 'DEATH'
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JOIN_KEYS = {
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'OMOPPersonTable': ['PERSON_ID']
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}
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KNOWN_FIELDS = [
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'PERSON_ID',
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'DATE_OF_DEATH'
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]
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DEFAULT_MAPPING = {
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'PERSON_ID': "PERSON_ID",
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'DATE_OF_DEATH': "DEATH_DATE"
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}
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class OMOPProcedureOccurrenceTable(CodeTable):
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NAME_TABLE = 'PROCEDURE_OCCURRENCE'
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JOIN_KEYS = {
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'OMOPPersonTable': ['PERSON_ID'],
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'OMOPVisitDetailTable': ['PERSON_ID', 'VISIT_DETAIL_ID']
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}
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DEFAULT_MAPPING = {
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'PERSON_ID': "PERSON_ID",
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'EVENT_DATE': "PROCEDURE_DATE",
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'CODE': "PROCEDURE_CONCEPT_ID",
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}
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class OMOPDrugExposureTable(CodeTable):
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NAME_TABLE = 'DRUG_EXPOSURE'
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JOIN_KEYS = {
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'OMOPPersonTable': ['PERSON_ID'],
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'OMOPVisitDetailTable': ['PERSON_ID', 'VISIT_DETAIL_ID']
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}
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DEFAULT_MAPPING = {
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'PERSON_ID': "PERSON_ID",
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'EVENT_DATE': "DRUG_EXPOSURE_START_DATE",
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'CODE': "DRUG_CONCEPT_ID",
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}
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class OMOPConditionOccurrenceSourceTable(CodeTable):
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NAME_TABLE = 'CONDITION_OCCURRENCE'
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JOIN_KEYS = {
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'OMOPPersonTable': ['PERSON_ID'],
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'OMOPVisitDetailTable': ['PERSON_ID', 'VISIT_DETAIL_ID']
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}
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DEFAULT_MAPPING = {
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'PERSON_ID': "PERSON_ID",
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'EVENT_DATE': "CONDITION_START_DATE",
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'CODE': "CONDITION_SOURCE_VALUE",
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}
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class OMOPProcedureOccurrenceSourceTable(CodeTable):
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NAME_TABLE = 'PROCEDURE_OCCURRENCE'
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JOIN_KEYS = {
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'OMOPPersonTable': ['PERSON_ID'],
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'OMOPVisitDetailTable': ['PERSON_ID', 'VISIT_DETAIL_ID']
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}
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DEFAULT_MAPPING = {
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'PERSON_ID': "PERSON_ID",
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'EVENT_DATE': "PROCEDURE_DATE",
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'CODE': "PROCEDURE_SOURCE_VALUE",
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}
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class OMOPDrugExposureSourceTable(CodeTable):
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NAME_TABLE = 'DRUG_EXPOSURE'
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JOIN_KEYS = {
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'OMOPPersonTable': ['PERSON_ID'],
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'OMOPVisitDetailTable': ['PERSON_ID', 'VISIT_DETAIL_ID']
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}
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DEFAULT_MAPPING = {
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'PERSON_ID': "PERSON_ID",
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'EVENT_DATE': "DRUG_EXPOSURE_START_DATE",
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'CODE': "DRUG_SOURCE_VALUE",
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}
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class OMOPPersonTableSource(PhenexPersonTable):
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NAME_TABLE = 'PERSON'
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JOIN_KEYS = {
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'OMOPConditionOccurenceTable': ['PERSON_ID'],
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'OMOPVisitDetailTable': ['PERSON_ID']
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}
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DEFAULT_MAPPING = {
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'PERSON_ID': "PERSON_ID",
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'DATE_OF_BIRTH': "BIRTH_DATETIME",
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'YEAR_OF_BIRTH': "YEAR_OF_BIRTH",
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'SEX': "GENDER_SOURCE_VALUE",
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'ETHNICITY': "ETHNICITY_SOURCE_VALUE",
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}
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class OMOPObservationPeriodTable(PhenexObservationPeriodTable):
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NAME_TABLE = 'OBSERVATION_PERIOD'
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JOIN_KEYS = {
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'OMOPPersonTable': ['PERSON_ID']
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}
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DEFAULT_MAPPING = {
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'PERSON_ID': "PERSON_ID",
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'OBSERVATION_PERIOD_START_DATE': "OBSERVATION_PERIOD_START_DATE",
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'OBSERVATION_PERIOD_END_DATE': 'OBSERVATION_PERIOD_END_DATE'
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}
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#
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# Domains
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#
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OMOPs = {
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"PERSON": OMOPPersonTable,
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"VISIT": OMOPVisitDetailTable,
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"VISIT_DETAIL": OMOPVisitDetailTable,
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"CONDITION_OCCURRENCE": OMOPConditionOccurenceTable,
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# "DEATH": OMOPDeathTable,
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# "CONDITION_OCCURRENCE": OMOPConditionOccurrence,
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# "PROCEDURE_OCCURRENCE": OMOPProcedureOccurrence,
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# "DRUG_EXPOSURE": OMOPDrugExposure,
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# "PERSON_SOURCE": OMOPPersonTableSource,
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# "CONDITION_OCCURRENCE_SOURCE": OMOPConditionOccurrenceSource,
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# "PROCEDURE_OCCURRENCE_SOURCE": OMOPProcedureOccurrenceSource,
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# "DRUG_EXPOSURE_SOURCE": OMOPDrugExposureSource,
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# "OBSERVATION_PERIOD": OMOPObservationPeriod,
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"DEATH": OMOPDeathTable,
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"PROCEDURE_OCCURRENCE": OMOPProcedureOccurrenceTable,
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"DRUG_EXPOSURE": OMOPDrugExposureTable,
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"CONDITION_OCCURRENCE_SOURCE": OMOPConditionOccurrenceSourceTable,
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"PROCEDURE_OCCURRENCE_SOURCE": OMOPProcedureOccurrenceSourceTable,
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"DRUG_EXPOSURE_SOURCE": OMOPDrugExposureSourceTable,
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"PERSON_SOURCE": OMOPPersonTableSource,
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"OBSERVATION_PERIOD": OMOPObservationPeriodTable,
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}
112-
OMOPDomains = DomainsDictionary(OMOPs)
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#
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# OLD vvvvv
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#
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# OMOPPersonTable = PersonTable(
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# NAME_TABLE="PERSON",
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# PERSON_ID="PERSON_ID",
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# DATE_OF_BIRTH="BIRTH_DATETIME",
121-
# YEAR_OF_BIRTH="YEAR_OF_BIRTH",
122-
# SEX="GENDER_CONCEPT_ID",
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# ETHNICITY="ETHNICITY_CONCEPT_ID",
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# )
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# OMOPDeathTable = PersonTable(
127-
# NAME_TABLE="DEATH", PERSON_ID="PERSON_ID", DATE_OF_DEATH="DEATH_DATE"
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# )
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# OMOPPersonTableSource = PersonTable(
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# NAME_TABLE="PERSON",
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# PERSON_ID="PERSON_ID",
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# DATE_OF_BIRTH="BIRTH_DATETIME",
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# YEAR_OF_BIRTH="YEAR_OF_BIRTH",
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# SEX="GENDER_SOURCE_VALUE",
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# ETHNICITY="ETHNICITY_SOURCE_VALUE",
137-
# )
138-
139-
# OMOPConditionOccurrence = CodeTable(
140-
# NAME_TABLE="CONDITION_OCCURRENCE",
141-
# EVENT_DATE="CONDITION_START_DATE",
142-
# CODE="CONDITION_CONCEPT_ID",
143-
# )
144-
145-
# OMOPConditionOccurrenceSource = CodeTable(
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# NAME_TABLE="CONDITION_OCCURRENCE",
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# EVENT_DATE="CONDITION_START_DATE",
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# CODE="CONDITION_SOURCE_VALUE",
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# )
150-
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# OMOPProcedureOccurrence = CodeTable(
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# NAME_TABLE="PROCEDURE_OCCURRENCE",
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# EVENT_DATE="PROCEDURE_DATE",
154-
# CODE="PROCEDURE_CONCEPT_ID",
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# )
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# OMOPProcedureOccurrenceSource = CodeTable(
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# NAME_TABLE="PROCEDURE_OCCURRENCE",
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# EVENT_DATE="PROCEDURE_DATE",
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# CODE="PROCEDURE_SOURCE_VALUE",
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# )
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# OMOPDrugExposure = CodeTable(
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# NAME_TABLE="DRUG_EXPOSURE",
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# EVENT_DATE="DRUG_EXPOSURE_START_DATE",
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# CODE="DRUG_CONCEPT_ID",
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# )
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# OMOPDrugExposureSource = CodeTable(
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# NAME_TABLE="DRUG_EXPOSURE",
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# EVENT_DATE="DRUG_EXPOSURE_START_DATE",
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# CODE="DRUG_SOURCE_VALUE",
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# )
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# OMOPObservationPeriod = PhenexObservationPeriodTable(
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# NAME_TABLE="OBSERVATION_PERIOD",
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# PERSON_ID="PERSON_ID",
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# OBSERVATION_PERIOD_START_DATE="OBSERVATION_PERIOD_START_DATE",
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# OBSERVATION_PERIOD_END_DATE="OBSERVATION_PERIOD_END_DATE",
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# )
212+
OMOPDomains = DomainsDictionary(OMOPs)

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