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entities.py
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entities.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
class BaseEntity:
def __init__(self):
self.entityType = 'BaseEntity'
def __repr__(self):
print('Trying to print entity of type ', self.entityType)
return str(vars(self))
class BaseScript:
def __init__(self, data):
self.scriptType = 'BaseScript'
self.name = data['name']
def __repr__(self):
print('Trying to print script of type ', self.scriptType)
return str(vars(self))
class SimpleRetrievalEntity(BaseEntity):
def __init__(self, group, fhir_resource, code_system, codes, valueset_oid):
super().__init__()
self.entityType = "SimpleRetrievalEntity"
self.group = group
self.fhir_resource = fhir_resource
self.code_system = code_system
self.codes = codes
self.valueset_oid = valueset_oid
class FreeTextEntity(SimpleRetrievalEntity):
def __init__(self, group, fhir_resource, cql_expression):
self.entityType = "FreeTextEntity"
self.group = group
self.fhir_resource = fhir_resource
self.cql_expression = cql_expression
class TemporalFilterEntity(SimpleRetrievalEntity):
def __init__(self, group, fhir_resource, code_system, codes, valueset_oid, where_clause_attribute, where_clause_during_begin, where_clause_during_after):
self.entityType = "TemporalFilterEntity"
self.group = group
self.fhir_resource = fhir_resource
self.code_system = code_system
self.codes = codes
self.valueset_oid = valueset_oid
self.where_clause_attribute = where_clause_attribute
self.where_clause_during_begin = where_clause_during_begin
self.where_clause_during_after = where_clause_during_after
class ValueFilterEntity(SimpleRetrievalEntity):
def __init__(self, group, fhir_resource, where_clause_attribute, where_clause_value):
self.entityType = "ValueFilterEntity"
self.group = group
self.fhir_resource = fhir_resource
self.where_clause_attribute = where_clause_attribute
self.where_clause_value = where_clause_value
class RelatedEntity(SimpleRetrievalEntity):
def __init__(self, group, fhir_resource, code_system, codes, valueset_oid, relationship_fhir_resource_type, relationship_codes, relationship_code_system, relationship_valueset, relationship_where_clause):
self.entityType = "RelatedEntity"
self.group = group
self.fhir_resource = fhir_resource
self.code_system = code_system
self.codes = codes
self.valueset_oid = valueset_oid
self.relationship_fhir_resource_type = relationship_fhir_resource_type
self.relationship_codes = relationship_codes
self.relationship_code_system = relationship_code_system
self.relationship_valueset = relationship_valueset
self.relationship_where_clause = relationship_where_clause
class NonEntity:
def __init__(self, group, fields):
self.entityType = "NonEntity"
self.group = group
self.fields = fields
class IndexEventAndInclusionScript(BaseScript):
def __init__(self, data):
super().__init__(data)
self.scriptType = 'IndexEventAndInclusionScript'
self.concepts = list(map(lambda x: ConceptEntity(x), data['concepts']))
self.indexEvent = IndexEventEntity(data['indexEvent'])
self.inclusions = list(map(lambda x: InclusionEntity(x), data['inclusions']))
try:
self.deriveds = list(map(lambda x: DerivedEntity(x), data['deriveds']))
except KeyError:
pass
self.returnAggregator = AggregateEntity(data['returnAggregator'])
class ConceptEntity(BaseEntity):
def __init__(self, data):
super().__init__()
self.entityType = 'ConceptEntity'
self.name = data['name']
if type(data['codesets']) == str: self.codesets = data['codesets']
else: self.codesets = list(map(lambda x: CodesetEntity(x), data['codesets']))
class CodesetEntity(BaseEntity):
def __init__(self, data):
super().__init__()
self.entityType = 'CodesetEntity'
self.codelist = data['codelist']
self.system = data['system']
class IndexEventEntity(SimpleRetrievalEntity):
def __init__(self, data):
self.entityType = "IndexEventEntity"
self.name = data['name']
self.fhirResource = data['fhirResource']
self.conceptReference = data['conceptReference']
self.returnField = data['returnField']
self.returnType = data['returnType']
class InclusionEntity(BaseEntity):
def __init__(self, data):
super().__init__()
self.entityType = "InclusionEntity"
self.name = data['name']
self.fhirResource = data['fhirResource']
self.conceptReference = data['conceptReference']
self.filterType = data['filterType']
if checkForTimeFrame(data['timeFrameRelativeToIndexEvent']):
self.timeFrame = TimeFrameEntity(data['timeFrameRelativeToIndexEvent'])
else: self.timeFrame = None
class DerivedEntity(BaseEntity):
def __init__(self, data):
super().__init__()
self.name = data['name']
self.baseInclusion = data['baseInclusion']
self.fhirField = data['fhirField']
self.fhirReturnResource = data['fhirReturnResource']
self.questionConcept = data['questionConcept']
self.answerValue = AnswerValueEntity(data['answerValue'])
self.sourceNote = data['sourceNote']
class AnswerValueEntity(BaseEntity):
def __init__(self, data):
super().__init__()
self.valueType = data['valueType']
self.renderAnswerWithCQL = data['renderAnswerWithCQL']
self.value = data['value']
class AggregateEntity(BaseEntity):
def __init__(self, data):
super().__init__()
self.entityType = "AggregateEntity"
self.aggregateType = data['type']
class TimeFrameEntity(BaseEntity):
def __init__(self, data):
super().__init__()
self.entityType = "TimeFrameEntity"
self.start = data['start']
self.end = data['end']
class AtlasConceptSetEntity(BaseEntity):
def __init__(self, data):
super().__init__()
self.entityType = 'AtlasConceptSetEntity'
self.concepts = list(map(lambda x: AtlasConceptEntity(x), data['items']))
class AtlasConceptEntity(BaseEntity):
def __init__(self, data):
super().__init__()
self.entityType = 'AtlasConceptEntity'
self.CONCEPT_ID = data['concept']['CONCEPT_ID']
self.CONCEPT_NAME = data['concept']['CONCEPT_NAME']
self.STANDARD_CONCEPT = data['concept']['STANDARD_CONCEPT']
self.STANDARD_CONCEPT_CAPTION = data['concept']['STANDARD_CONCEPT_CAPTION']
self.INVALID_REASON = data['concept']['INVALID_REASON']
self.INVALID_REASON_CAPTION = data['concept']['INVALID_REASON_CAPTION']
self.CONCEPT_CODE = data['concept']['CONCEPT_CODE']
self.DOMAIN_ID = data['concept']['DOMAIN_ID']
self.VOCABULARY_ID = data['concept']['VOCABULARY_ID']
self.CONCEPT_CLASS_ID = data['concept']['CONCEPT_CLASS_ID']
def checkForTimeFrame(timeFrame):
if (timeFrame != '' and timeFrame != {} and (timeFrame['start'] != '' or timeFrame['end'] != '')):
return True
else:
return False