Comments (5)
gowthamrao
commented on July 17, 2024
I was able to parse this into JSON as follows
cdJson <- RJSONIO::toJSON(x = list(cd))
cdJSon <- RJSONIO::fromJSON(content = cdJson)[[1]]
cdJSon <- RJSONIO::toJSON(x = cdJSon, pretty = TRUE)
from capr.
gowthamrao
commented on July 17, 2024
The JSON is below - but it cannot be imported into ATLAs
{
"CohortDetails" : {
"Name" : "Testing Cohort",
"Description" : "Description for Testing Cohort",
"Author" : null,
"cdmVersionRange" : ">=5.0.0"
},
"PrimaryCriteria" : {
"MetaData" : {
"ComponentClass" : "PrimaryCriteria",
"Name" : "Concept Set Condition Occurrence",
"Description" : null
},
"CriteriaExpression" : {
"CriteriaList" : [
{
"Domain" : "ConditionOccurrence",
"CodesetId" : "47ada7d4-56e6-4cdc-909a-91694b48eec8",
"Attributes" : [
{
"Name" : "Age",
"Op" : "lt",
"Contents" : {
"Value" : 10,
"Extent" : null
}
}
]
}
],
"ObservationWindow" : {
"PriorDays" : 0,
"PostDays" : 0
}
},
"Limit" : {
"PrimaryCriteriaLimit" : {
"Type" : "All"
}
},
"ConceptSetExpression" : [
{
"id" : "47ada7d4-56e6-4cdc-909a-91694b48eec8",
"Name" : "Diabetes Melltius",
"Expression" : [
{
"Concept" : {
"CONCEPT_ID" : 201820,
"CONCEPT_NAME" : "Diabetes mellitus",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "73211009",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4008576,
"CONCEPT_NAME" : "Diabetes mellitus without complication",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "111552007",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4058243,
"CONCEPT_NAME" : "Diabetes mellitus during pregnancy, childbirth and the puerperium",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "199223000",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 192691,
"CONCEPT_NAME" : "Diabetes mellitus during pregnancy - baby not yet delivered",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "199227004",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4144583,
"CONCEPT_NAME" : "Diabetes mellitus due to cystic fibrosis",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "427089005",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4192852,
"CONCEPT_NAME" : "Diabetes mellitus due to insulin receptor antibodies",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "75682002",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4240589,
"CONCEPT_NAME" : "Diabetes mellitus associated with hormonal etiology",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "59079001",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4136889,
"CONCEPT_NAME" : "Diabetes mellitus induced by non-steroid drugs without complication",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "413183008",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4079850,
"CONCEPT_NAME" : "Diabetes mellitus in neonate small for gestational age",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "276560009",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4.575747e+07,
"CONCEPT_NAME" : "Diabetes mellitus type 2 without retinopathy",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "1481000119100",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4237068,
"CONCEPT_NAME" : "Diabetes mellitus due to structurally abnormal insulin",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "91352004",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4245270,
"CONCEPT_NAME" : "Diabetes mellitus associated with genetic syndrome",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "5969009",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4178452,
"CONCEPT_NAME" : "Diabetes mellitus associated with pancreatic disease",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "51002006",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4129516,
"CONCEPT_NAME" : "Diabetes-deafness syndrome maternally transmitted",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "237619009",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4322638,
"CONCEPT_NAME" : "Diabetes mellitus AND insipidus with optic atrophy AND deafness",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "70694009",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4235410,
"CONCEPT_NAME" : "Diabetes mellitus induced by non-steroid drugs",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "408540003",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4.575708e+07,
"CONCEPT_NAME" : "Diabetes mellitus due to pancreatic injury",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "105401000119101",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4143529,
"CONCEPT_NAME" : "Diabetes mellitus associated with cystic fibrosis",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "426705001",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4.576605e+07,
"CONCEPT_NAME" : "Diabetes mellitus in remission",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "703136005",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4.575767e+07,
"CONCEPT_NAME" : "Diabetes mellitus type 1 without retinopathy",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "31321000119102",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 3.668483e+07,
"CONCEPT_NAME" : "Diabetes mellitus type 2 with periodontal disease",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "368101000119109",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4.253768e+07,
"CONCEPT_NAME" : "Diabetes mellitus caused by chemical",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "737212004",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4.076934e+07,
"CONCEPT_NAME" : "History of Diabetes (regardless of treatment) [PhenX]",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "66678-4",
"DOMAIN_ID" : "Observation",
"VOCABULARY_ID" : "LOINC",
"CONCEPT_CLASS_ID" : "Clinical Observation"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4.353102e+07,
"CONCEPT_NAME" : "Diabetes mellitus, transient neonatal 2",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "609580007",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
},
{
"Concept" : {
"CONCEPT_ID" : 4.479311e+07,
"CONCEPT_NAME" : "Diabetes mellitus with multiple complications",
"STANDARD_CONCEPT" : "S",
"STANDARD_CONCEPT_CAPTION" : "Standard",
"INVALID_REASON" : "V",
"INVALID_REASON_CAPTION" : "Valid",
"CONCEPT_CODE" : "385041000000108",
"DOMAIN_ID" : "Condition",
"VOCABULARY_ID" : "SNOMED",
"CONCEPT_CLASS_ID" : "Clinical Finding"
},
"isExcluded" : false,
"includeDescendants" : true,
"includeMapped" : false
}
]
}
]
},
"AdditionalCriteria" : {
"MetaData" : {
"ComponentClass" : "Empty",
"Name" : null,
"Description" : null
},
"CriteriaExpression" : [],
"Limit" : [],
"ConceptSetExpression" : []
},
"InclusionRules" : {
"MetaData" : {
"ComponentClass" : "InclusionRules",
"Name" : "Inclusion Rules",
"Description" : null
},
"CriteriaExpression" : [],
"Limit" : {
"ExpressionLimit" : {
"Type" : "First"
}
},
"ConceptSetExpression" : []
},
"EndStrategy" : {
"MetaData" : {
"ComponentClass" : "EndStrategy",
"Name" : "End Strategy Date Offset",
"Description" : null
},
"CriteriaExpression" : [
{
"DateField" : "EndDate",
"Offset" : 0
}
],
"Limit" : [],
"ConceptSetExpression" : []
},
"CensoringCriteria" : {
"MetaData" : {
"ComponentClass" : "Empty",
"Name" : null,
"Description" : null
},
"CriteriaExpression" : [],
"Limit" : [],
"ConceptSetExpression" : []
},
"CohortEra" : {
"MetaData" : {
"ComponentClass" : "CohortEra",
"Name" : "Cohort Era Details",
"Description" : null
},
"CriteriaExpression" : {
"CollapseSettings" : {
"CollapseType" : "ERA",
"EraPad" : 1
},
"CensorWindow" : {
"StartDate" : null,
"EndDate" : null
}
},
"Limit" : [],
"ConceptSetExpression" : []
}
}
from capr.
gowthamrao
commented on July 17, 2024
from capr.
mdlavallee92
commented on July 17, 2024
@gowthamrao Sorry for the delayed response. When you create the cohort definition use Capr::createCohortDefinition this generates the R object version of the cohort definition. In order to get into the ATLAS version of the cohort you need to compile it into the Circe structure. In the vignette go to the next chunk you will see commands that compile the R object into a circe json and ohdisql structure. Capr::compileCohortDefinition(cd,genOps). The genOps object in this call is made from CirceR::createGenerateOptions. Let me know if this is still an issue. Code block below:
cd <- Capr::createCohortDefinition( Name = "Testing Cohort", Description = desc, PrimaryCriteria = pc, InclusionRules = irs, EndStrategy = es, CohortEra = cohortEra)
genOp <- CirceR::createGenerateOptions(cohortIdFieldName = "cohort_definition_id", cohortId = 9999, cdmSchema = connectionDetails$schema, targetTable = "cohort", resultSchema = "results", vocabularySchema = connectionDetails$schema, generateStats = F)
#compile the cohort definition to create json and ohdisql
cohortInfo <- compileCohortDefinition(cd, genOp)
#if no errors preview the json and ohdisql
cat(cohortInfo$circeJson)
cat(cohortInfo$cohortRead)
cat(cohortInfo$ohdiSQL)
from capr.
mdlavallee92
commented on July 17, 2024
This issue should be resolved. Also fixed a bug when compiling cohort definitions without additional criteria or inclusion rules. Can reopen if issue persists
from capr.
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