Merge pull request #416 from OHDSI/develop

Develop

.github/workflows/R_CMD_check_Hades.yaml

@@ -67,8 +67,6 @@ jobs:
           
       - name: Setup conda
         uses: conda-incubator/setup-miniconda@v2
-        with:
-          activate-environment: "r-reticulate"
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

DESCRIPTION

@@ -2,8 +2,8 @@ Package: PatientLevelPrediction
 Type: Package
 Title: Developing patient level prediction using data in the OMOP Common Data
     Model
-Version: 6.3.5
-Date: 2023-08-15
+Version: 6.3.6
+Date: 2023-10-09
 Authors@R: c(
     person("Jenna", "Reps", email = "[email protected]", role = c("aut", "cre")),
     person("Martijn", "Schuemie", role = c("aut")),

NEWS.md

@@ -1,3 +1,7 @@
+PatientLevelPrediction 6.3.6
+======================
+- fix bug with ohdsi shiny modules version check (issue 415)
+
 PatientLevelPrediction 6.3.5
 ======================
 - Fix sklearnToJson to be compatible with scikit-learn>=1.3

R/HelperFunctions.R

@@ -94,9 +94,10 @@ listAppend <- function(a, b){
 #'
 #' @param envname   A string for the name of the virtual environment (default is 'PLP') 
 #' @param envtype   An option for specifying the environment as'conda' or 'python'.  If NULL then the default is 'conda' for windows users and 'python' for non-windows users 
+#' @param condaPythonVersion String, Python version to use when creating a conda environment
 #'
 #' @export
-configurePython <- function(envname='PLP', envtype=NULL){
+configurePython <- function(envname='PLP', envtype=NULL, condaPythonVersion="3.11"){
 
   if(is.null(envtype)){
     if(getOs()=='windows'){
@@ -113,7 +114,7 @@ configurePython <- function(envname='PLP', envtype=NULL){
       warning(paste0('Conda environment ', envname,' exists.  You can use reticulate::conda_remove() to remove if you want to fresh config'))
     } else {
       ParallelLogger::logInfo(paste0('Creating virtual conda environment called ', envname))
-      location <- reticulate::conda_create(envname=envname, packages = "python", conda = "auto")
+      location <- reticulate::conda_create(envname=envname, packages = paste0("python==", condaPythonVersion), conda = "auto")
     }
     packages <- c('numpy','scipy','scikit-learn', 'pandas','pydotplus','joblib')
     ParallelLogger::logInfo(paste0('Adding python dependancies to ', envname))

R/ViewShinyPlp.R

@@ -154,7 +154,7 @@ viewPlps <- function(databaseSettings){
     )
   } else{
     ohdsiModulesVersion <- strsplit(x = as.character(utils::packageVersion('OhdsiShinyModules')), split = '\\.')[[1]]
-    if(ohdsiModulesVersion[1]>=1 & ohdsiModulesVersion[2]>= 2){
+    if(paste0(ohdsiModulesVersion[1], ".", ohdsiModulesVersion[2])>= 1.2){
       config <- ParallelLogger::loadSettingsFromJson(
         fileName = system.file(
           'shinyConfigUpdate.json', 

R/uploadToDatabase.R

@@ -1145,7 +1145,7 @@ addCohort <- function(
                        targetDialect = targetDialect, 
                        tableName = 'cohort_definition',
                        columnNames = c('cohort_name'), 
-                       values = c(paste0("'",cohortDefinition$cohortName,"'")),
+                       values = c(paste0("'",gsub('\'', '', cohortDefinition$cohortName),"'")),
                        tempEmulationSchema = tempEmulationSchema
   )
 
@@ -1157,12 +1157,12 @@ addCohort <- function(
 
   if(addNew){
     cohortDefinitionId <- result$cohortDefinitionId[result$json %in% json]
-    ParallelLogger::logInfo(paste0('Cohort ',cohortDefinition$cohortName,' exists in cohort_definition with cohort id', result$cohortDefinitionId[result$json %in% json]))
+    ParallelLogger::logInfo(paste0('Cohort ',gsub('\'', '', cohortDefinition$cohortName),' exists in cohort_definition with cohort id', result$cohortDefinitionId[result$json %in% json]))
   } else{
-    ParallelLogger::logInfo(paste0('Adding cohort ',cohortDefinition$cohortName))
+    ParallelLogger::logInfo(paste0('Adding cohort ',gsub('\'', '', cohortDefinition$cohortName)))
 
     data <- data.frame(
-      cohortName = cohortDefinition$cohortName, 
+      cohortName = gsub('\'', '', cohortDefinition$cohortName), 
       cohortDefinitionId = cohortDefinition$cohortId,
       json = json
     )
@@ -1187,7 +1187,7 @@ addCohort <- function(
       targetDialect = targetDialect, 
       tableName = 'cohort_definition',
       columnNames = c('cohort_name', 'cohort_definition_id'), 
-      values = c(paste0("'",cohortDefinition$cohortName,"'"), cohortDefinition$cohortId),
+      values = c(paste0("'",gsub('\'', '', cohortDefinition$cohortName),"'"), cohortDefinition$cohortId),
       tempEmulationSchema = tempEmulationSchema
     )
 
@@ -1202,18 +1202,18 @@ addCohort <- function(
                        targetDialect = targetDialect, 
                        tableName = 'cohorts',
                        columnNames = c('cohort_definition_id','cohort_name'), 
-                       values = c(cohortDefinitionId, paste0("'",cohortDefinition$cohortName,"'")),
+                       values = c(cohortDefinitionId, paste0("'",gsub('\'', '', cohortDefinition$cohortName),"'")),
                        tempEmulationSchema = tempEmulationSchema
   )
 
   if(nrow(result)>0){
-    ParallelLogger::logInfo(paste0('Cohort ',cohortDefinition$cohortName,' exists in cohorts with cohort id', result$cohortId))
+    ParallelLogger::logInfo(paste0('Cohort ',gsub('\'', '', cohortDefinition$cohortName),' exists in cohorts with cohort id', result$cohortId))
   } else{
-    ParallelLogger::logInfo(paste0('Adding cohort ',cohortDefinition$cohortName))
+    ParallelLogger::logInfo(paste0('Adding cohort ',gsub('\'', '', cohortDefinition$cohortName)))
 
     data <- data.frame(
       cohortDefinitionId = cohortDefinitionId,
-      cohortName = cohortDefinition$cohortName
+      cohortName = gsub('\'', '', cohortDefinition$cohortName)
     )
     DatabaseConnector::insertTable(
       connection = conn, 
@@ -1235,7 +1235,7 @@ addCohort <- function(
                          targetDialect = targetDialect, 
                          tableName = 'cohorts',
                          columnNames = c('cohort_definition_id','cohort_name'), 
-                         values = c(cohortDefinitionId, paste0("'",cohortDefinition$cohortName,"'")),
+                         values = c(cohortDefinitionId, paste0("'",gsub('\'', '', cohortDefinition$cohortName),"'")),
                          tempEmulationSchema = tempEmulationSchema
     )
   }

_pkgdown.yml

@@ -20,6 +20,8 @@ navbar:
     - reference
     - articles
     - tutorial
+    - benchmarks
+    - predictors
     - bestpractice
     - news
     right: [hades, github]
@@ -39,6 +41,12 @@ navbar:
     bestpractice:
       text: Best Practices
       href: articles/BestPractices.html
+    benchmarks:
+      text: Benchmarks
+      href: articles/BenchmarkTasks.html
+    predictors:
+      text: Predictors
+      href: articles/ConstrainedPredictors.html
     news:
       text: Changelog
       href: news/index.html