Added implementation of 'combination cohorts'. #193
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,250 @@ | ||
| # CombinedCohortOp ------------- | ||
| #' @title A Combined cohort operation used to UNION or INTERSECT cohorts. Note: only UNION supported. | ||
| #' @export | ||
| #' @description | ||
| #' Defines a UNION or INTERSECT on a set of cohorts. | ||
| CombinedCohortOp <- R6::R6Class( | ||
| classname = "CombinedCohortOp", | ||
| private = list( | ||
| .targetCohortIds = NULL, | ||
| .opType = "union" | ||
| ), | ||
| active = list( | ||
| #' @field targetCohortIds The list of cohorts to apply in this group. | ||
| targetCohortIds = function(targetCohortIds) { | ||
| if (missing(targetCohortIds)) { | ||
| return(private$.targetCohortIds) | ||
| } | ||
| checkmate::assertList(as.list(targetCohortIds), types="numeric", min.len = 0) | ||
| private$.targetCohortIds <- targetCohortIds | ||
| return(self) | ||
| }, | ||
| #' @field opType The group operation, either 'union' or 'intersect' | ||
| opType = function(opType) { | ||
| if (missing(opType)) { | ||
| return(private$.opType) | ||
| } | ||
| checkmate::assertChoice(opType, c("union")) | ||
| private$.opType <- opType | ||
| return(self) | ||
| } | ||
| ), | ||
| public = list( | ||
| #' @description | ||
| #' creates a new instance, using the provided data param if provided. | ||
| #' @param data the data (as a json string or list) to initialize with | ||
| initialize = function(data = list()) { | ||
| dataList <- .convertJSON(data) | ||
|
|
||
| if ("targetCohortIds" %in% names (dataList)) self$targetCohortIds <- dataList$targetCohortIds | ||
| if ("opType" %in% names (dataList)) self$opType <- dataList$opType | ||
| }, | ||
| #' @description List representation of object | ||
| toList = function() { | ||
| .removeEmpty(list( | ||
| targetCohortIds = .toJsonArray(private$.targetCohortIds), | ||
| opType = jsonlite::unbox(private$.opType) | ||
| )) | ||
| }, | ||
| #' To JSON | ||
| #' @description json serialized representation of object | ||
| toJSON = function() { | ||
| .toJSON(self$toList()) | ||
| }, | ||
|
|
||
| #' Is Equal to | ||
| #' @description Compare CombinedCohortGroup to another | ||
| #' @param other CombinedCohortGroup instance | ||
| isEqualTo = function(other) { | ||
| checkmate::assertR6(other, "CombinedCohortGroup") | ||
| return(other$toJSON() == self$toJSON()) | ||
| }, | ||
| #' getDependentCohortIds | ||
| #' @description Gets the dependent cohortIds from this operation | ||
| getDependentCohortIds = function() { | ||
| if (length(private$.targetCohortIds) == 0) return(c()) | ||
| return(private$.targetCohortIds) | ||
| } | ||
| ) | ||
| ) | ||
|
|
||
| # CombinedCohortDef ------------- | ||
| #' @title A CombinedCohortDef | ||
| #' @export | ||
| #' @description | ||
| #' Defines the ID, name and operation to produce a new cohort. | ||
| CombinedCohortDef <- R6::R6Class( | ||
| classname = "CombinedCohortDef", | ||
| private = list( | ||
| .cohortId = NA, | ||
| .cohortName = NA, | ||
| .expression = NULL | ||
| ), | ||
| active = list( | ||
| #' @field cohortId The list of cohorts to apply in this group. | ||
| cohortId = function(cohortId) { | ||
| if (missing(cohortId)) { | ||
| return(private$.cohortId) | ||
| } | ||
| checkmate::assertInt(cohortId) | ||
| private$.cohortId <- cohortId | ||
| return(self) | ||
| }, | ||
| #' @field cohortName the name given to this outcome definition | ||
| cohortName = function(cohortName) { | ||
| if (missing(cohortName)) { | ||
| private$.cohortName | ||
| } else { | ||
| # check type | ||
| checkmate::assertCharacter(cohortName) | ||
| private$.cohortName <- cohortName | ||
| self | ||
| } | ||
| }, | ||
| #' @field expression The combo operator that is the root of the definition. | ||
| expression = function(expression) { | ||
| if (missing(expression)) { | ||
| return(private$.expression) | ||
| } | ||
| checkmate::assertClass(expression, classes="CombinedCohortOp") | ||
| private$.expression <- expression | ||
| return(self) | ||
| } | ||
| ), | ||
| public = list( | ||
| #' @description | ||
| #' creates a new instance, using the provided data param if provided. | ||
| #' @param data the data (as a json string or list) to initialize with | ||
| initialize = function(data = list()) { | ||
| dataList <- .convertJSON(data) | ||
|
|
||
| if ("cohortId" %in% names (dataList)) self$targetCohortIds <- dataList$cohortId | ||
| if ("cohortName" %in% names (dataList)) self$cohortName <- dataList$cohortName | ||
| if ("expression" %in% names (dataList)) self$expression<- CohortGenerator::CombinedCohortOp$new(dataList$expression) | ||
| }, | ||
| #' @description List representation of object | ||
| toList = function() { | ||
| .removeEmpty(list( | ||
| cohortId = jsonlite::unbox(private$.cohortId), | ||
| cohortName = jsonlite::unbox(private$.cohortName), | ||
| expression = .r6ToListOrNA(private$.expression) | ||
| )) | ||
| }, | ||
| #' To JSON | ||
| #' @description json serialized representation of object | ||
| toJSON = function() { | ||
| .toJSON(self$toList()) | ||
| }, | ||
|
|
||
| #' Is Equal to | ||
| #' @description Compare CombinedCohortDef to another | ||
| #' @param other CombinedCohortDef instance | ||
| isEqualTo = function(other) { | ||
| checkmate::assertR6(other, "CombinedCohortDef") | ||
| return(other$toJSON() == self$toJSON()) | ||
| } | ||
| ) | ||
| ) | ||
|
|
||
| ### Factory Functions | ||
|
|
||
| #' Create CombinedCohortOp instance | ||
| #' @description | ||
| #' A factory function to create CombinedCohortOp | ||
| #' @export | ||
| #' @param targetCohortIds list of target cohort IDs to combine in this operation | ||
| #' @param opType The op type of this cohort combination, can only be 'union' | ||
| createCombinedCohortOp <- function(targetCohortIds, opType) { | ||
|
|
||
| cohortOp <- CombinedCohortOp$new() | ||
| if (!missing(targetCohortIds)) cohortOp$targetCohortIds <- targetCohortIds | ||
| if (!missing(opType)) cohortOp$opType <- opType | ||
|
|
||
| return (cohortOp); | ||
| } | ||
|
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||
| #' Defines a combined cohort using combined cohort operations | ||
| #' @description | ||
| #' Creates an instance of CombinedCohortDef with the provided cohortId, cohortName and the combine operator expression | ||
| #' @export | ||
| #' @param cohortId The output cohort id from applying the combine expression. | ||
| #' @param cohortName The output cohort name | ||
| #' @param expression The combine operator that will yield the final cohort. | ||
| createCombinedCohortDef <- function(cohortId, cohortName, expression) { | ||
|
|
||
| cohortDef <- CombinedCohortDef$new(); | ||
| if (!missing(cohortId)) cohortDef$cohortId <- cohortId; | ||
| if (!missing(cohortName)) cohortDef$cohortName <- cohortName; | ||
| if (!missing(expression)) cohortDef$expression <- expression; | ||
|
|
||
| return (cohortDef); | ||
| } | ||
|
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| #' Add cohort subset definition to a cohort definition set | ||
| #' @description | ||
| #' Given a subset definition and cohort definition set, this function returns a modified cohortDefinitionSet | ||
| #' That contains cohorts that's have parent's contained within the base cohortDefinitionSet | ||
| #' | ||
| #' Also adds the columns subsetParent and isSubset that denote if the cohort is a subset and what the parent definition | ||
| #' is. | ||
| #' @export | ||
| #' @param cohortDefinitionSet data.frame that conforms to CohortDefinitionSet | ||
| #' @param combinedCohortDefiniton CombinedCohortDefinition instance | ||
| #' @param overwriteExisting Overwrite existing subset definition of the same definitionId if present | ||
| addCombinedCohort <- function(cohortDefinitionSet, | ||
| combinedCohortDefiniton, | ||
| overwriteExisting = FALSE) { | ||
| checkmate::assertTRUE(isCohortDefinitionSet(cohortDefinitionSet)) | ||
| checkmate::assertR6(combinedCohortDefiniton, "CombinedCohortDef") | ||
| checkmate::assertTRUE(!is.null(combinedCohortDefiniton$expression)) | ||
|
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| if (!"dependentCohorts" %in% colnames(cohortDefinitionSet)) { | ||
| cohortDefinitionSet$dependentCohorts <- "" | ||
| } | ||
|
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||
| if (!"isCombinedCohort" %in% colnames(cohortDefinitionSet)) { | ||
| cohortDefinitionSet$isCombinedCohort <- FALSE | ||
| } | ||
|
|
||
| dependentCohortIds <- combinedCohortDefiniton$expression$getDependentCohortIds() | ||
| if (length(dependentCohortIds) > 0) { | ||
| checkmate::assertSubset(dependentCohortIds, cohortDefinitionSet$cohortId) | ||
| } | ||
|
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||
| # TODO: going to just fail if the cohortId exists for now, later we can implement overwrite | ||
| if (!overwriteExisting && nrow(cohortDefinitionSet %>% dplyr::filter(.data$cohortId == combinedCohortDefiniton$cohortId)) > 0) { | ||
| stop("The specified cohortId for this combined cohort already exists in the cohort definition set") | ||
| } else { | ||
| # remove this definition from the set | ||
| cohortDefinitionSet <- cohortDefinitionSet %>% filter(cohortId != combinedCohortDefiniton$cohortId) | ||
| } | ||
|
|
||
| defSql <- SqlRender::readSql(system.file("sql", "sql_server", "combinedCohorts", "CombinedCohortDefinition.sql", package = "CohortGenerator")) | ||
|
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||
| queryBuilder <- CombinedCohortQueryBuilder$new() | ||
| combinationQuery <- queryBuilder$buildQuery(combinedCohortDefiniton) | ||
|
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||
| defSql <- SqlRender::render(defSql, | ||
| output_cohort_id = combinedCohortDefiniton$cohortId, | ||
| combined_cohort_query = combinationQuery) | ||
|
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| cohortDefinitionSet <- | ||
| dplyr::bind_rows( | ||
| cohortDefinitionSet, | ||
| data.frame( | ||
| cohortId = combinedCohortDefiniton$cohortId, | ||
| cohortName = combinedCohortDefiniton$cohortName, | ||
| sql = defSql, | ||
| json = as.character(combinedCohortDefiniton$toJSON()), | ||
| isCombinedCohort = TRUE, | ||
| dependentCohorts = paste0(dependentCohortIds, collapse = ",") | ||
| ) | ||
| ) | ||
|
|
||
| attr(cohortDefinitionSet, "hasCombinedCohorts") <- TRUE | ||
|
|
||
| return(cohortDefinitionSet) | ||
| } | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| CombinedCohortQueryBuilder <- R6::R6Class( | ||
| classname = "CombinedCohortQueryBuilder", | ||
| private = list( | ||
| ), | ||
| public = list( | ||
| buildQuery = function(combinedCohortDefiniton) { | ||
| checkmate::assertR6(combinedCohortDefiniton, "CombinedCohortDef") | ||
| sql <- SqlRender::readSql(system.file("sql", "sql_server", "combinedCohorts", "unionCombine.sql", package = "CohortGenerator")) | ||
| sql <- SqlRender::render(sql, | ||
| target_cohort_ids = combinedCohortDefiniton$expression$targetCohortIds, | ||
| warnOnMissingParameters = TRUE | ||
| ) | ||
| return(sql) | ||
| } | ||
| ) | ||
| ) |
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This was moved around to better work with > 2 cohort types. When it was just the two, it was simpler to say 'either or' in this loop, but arranged this way we can apply different styles of generated cohorts to CohortGenerator.