Merge pull request #34 from OHDSI/develop

Fix guid issue in Concept Set Expression creation, add createConceptDataframe CohortGenerator and CohortDiagnostics, and fix documentation

.gitignore

@@ -1,9 +1,7 @@
 .Rhistory
 .Rproj.user
-inst/doc
 .DS_Store
 errorReportSql.txt
 *.log
-/doc/
 /Meta/
 work/*

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Capr
 Title: Cohort definition Application Programming in R
-Version: 1.0.2
+Version: 1.0.3
 Authors@R: 
     person(given = "Martin",
            family = "Lavallee",

NAMESPACE

@@ -10,6 +10,7 @@ export(createAgeAtEndAttribute)
 export(createAgeAtStartAttribute)
 export(createAgeAttribute)
 export(createCensoringCriteria)
+export(createCohortDataframe)
 export(createCohortDefinition)
 export(createCohortEra)
 export(createConceptAttribute)
@@ -121,6 +122,7 @@ import(methods)
 importFrom(CirceR,buildCohortQuery)
 importFrom(CirceR,cohortExpressionFromJson)
 importFrom(CirceR,cohortPrintFriendly)
+importFrom(CirceR,createGenerateOptions)
 importFrom(RJSONIO,toJSON)
 importFrom(jsonlite,read_json)
 importFrom(magrittr,"%>%")
@@ -130,6 +132,7 @@ importFrom(methods,slot)
 importFrom(purrr,discard)
 importFrom(purrr,map)
 importFrom(purrr,map2)
+importFrom(purrr,map_chr)
 importFrom(purrr,map_int)
 importFrom(rlang,"!!!")
 importFrom(rlang,"!!")

NEWS.md

@@ -1,3 +1,10 @@
+Capr 1.0.3
+==========
+
+1. Fix bug in guid generation...did not create unique guid each time
+2. Add function to create cohort data frame for CohortGenerator and CohortDiagnostics
+3. Fix pdf documentation in readme
+
 Capr 1.0.2
 ==========
 

R/LowLevelClasses.R

@@ -551,10 +551,7 @@ setMethod("show", "ConceptSetItem", function(object) {
 setClass("ConceptSetExpression",
          slots = c(id = "character",
                    Name = "character",
-                   Expression = "list"),
-         prototype = list(id = uuid::UUIDgenerate(),
-                          Name = NA_character_,
-                          Expression = list()))
+                   Expression = "list"))
 
 setValidity("ConceptSetExpression", function(object) {
   # TODO create validation rules for ConceptSetExpression

R/LowLevelUtilityFn.R

@@ -166,7 +166,7 @@ removeDupCSE <- function(cse){
     }#end duplication check
   }#end for loop
   #discard any concept set expressions not needed
-  cse <- purrr::discard(cse,function(x) is(x)[1] != "ConceptSetExpression")
+  cse <- purrr::discard(cse, function(x) is(x)[1] != "ConceptSetExpression")
   return(cse)
 }
 

R/UserCommands.R

@@ -182,4 +182,52 @@ compileCohortDefinition <- function(CohortDefinition, generateOptions = NULL){
 }
 
 
+########------Create Cohort Dataframe for generation------------#################
+
+#' Create a dataframe that can be used by cohort generator to build cohorts into backend table
+#'
+#' This function converts a list of Cohort definitions into a dataframe that can be used by cohort
+#' generator and cohort diagnostics to build and evaluate cohorts. The dataframe returns an atlasId column and
+#' a cohortId column which are equivalent. Further it creates a column for the ohdisql, json, read and name of
+#' cohort.
+#'
+#' @param cohortList a list of cohorts to turn into a dataframe
+#' @param generateStats select true if you want inclusion rule stats or false for no stats
+#' @importFrom CirceR createGenerateOptions
+#' @importFrom purrr map_chr
+#' @return A data frame of cohort definitions containing meta data
+#' @export
+createCohortDataframe <- function(cohortList, generateStats = TRUE) {
+
+  check <- purrr::map_chr(cohortList, ~methods::is(.x))
+
+  if(!all(check == "CohortDefinition")) {
+    stop("all cohorts need to be a Capr CohortDefinition class")
+  }
+
+  # get cohort names
+  cohortName <-purrr::map_chr(cohortList, ~slot(slot(.x, "CohortDetails"), "Name"))
+
+  #set basic genops for CirceR
+  genOp <- CirceR::createGenerateOptions(generateStats = generateStats)
+
+  #get the info from compiler
+  cohortInfo <- purrr::map(cohortList, ~compileCohortDefinition(.x,
+                                                                generateOptions = genOp))
+
+  #get each element from compile
+  cohortSql <- purrr::map_chr(cohortInfo, ~getElement(.x, "ohdiSQL"))
+  cohortJson <- purrr::map_chr(cohortInfo, ~getElement(.x, "circeJson"))
+  cohortRead <- purrr::map_chr(cohortInfo, ~getElement(.x, "cohortRead"))
+
+
+  #create Data frame
+  df <- data.frame('atlasId' = seq_along(cohortList),
+                   'cohortId' = seq_along(cohortList),
+                   'cohortName'= cohortName,
+                   'sql'= cohortSql,
+                   'json' = cohortJson,
+                   'read' = cohortRead)
+  return(df)
+}
 

R/UserCreateFn.R

@@ -181,7 +181,11 @@ createConceptSetExpression <- function(conceptSet, Name, includeDescendants =TRU
                                    isExcluded = isExcluded,
                                    includeMapped = includeMapped)
   #create the a new concept set expression from the concept set, this also sets the guid concept id
-  cse <- new("ConceptSetExpression", Name = Name, Expression = concepts)
+  cse <- new("ConceptSetExpression", Name = Name,
+             Expression = concepts)
+  #create guid for new cse
+  cse@id <- uuid::UUIDgenerate()
+
 
   #attach the concept set expressions to a component class object
   comp <- createComponent(Name = Name,
@@ -306,7 +310,10 @@ createConceptSetExpressionCustom <- function(conceptSet, Name, conceptMapping =
     }
   }
   #create the a new concept set expression from the concept set, this also sets the guid concept id
-  cse <- new("ConceptSetExpression", Name = Name, Expression = concepts)
+  cse <- new("ConceptSetExpression", Name = Name,
+             Expression = concepts)
+  #create guid for new cse
+  cse@id <- uuid::UUIDgenerate()
 
   #attach the concept set expressions to a component class object
   comp <- createComponent(Name = Name,