Use latest modules for test analysisSpecification.json and and add dp…

…lyr to base R library list for module execution
OHDSI · Sep 6, 2023 · 4468a9b · 4468a9b
1 parent 06ca01d
commit 4468a9b
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Showing 3 changed files with 21 additions and 29 deletions.
diff --git a/R/ModuleEnv.R b/R/ModuleEnv.R
@@ -69,27 +69,14 @@ withModuleRenv <- function(code,
 
   # Enforce attachment of Strategus from calling process - note one inside the renv
   if (useLocalStrategusLibrary) {
-    libPath <- file.path(find.package("Strategus"), "../")
-    script <- c(sprintf("library(Strategus, lib.loc = '%s')", libPath),
-                script)
+    script <- c(.getLocalLibraryScipt("Strategus"), script)
     # Adding Strategus dependencies to the script
-    libPath <- file.path(find.package("R6"), "../")
-    script <- c(
-      sprintf("library(R6, lib.loc = '%s')", libPath),
-      script
-    )
-    libPath <- file.path(find.package("CohortGenerator"), "../")
-    script <- c(sprintf("library(CohortGenerator, lib.loc = '%s')", libPath),
-                script)
-    libPath <- file.path(find.package("DatabaseConnector"), "../")
-    script <- c(sprintf("library(DatabaseConnector, lib.loc = '%s')", libPath),
-                script)
-    libPath <- file.path(find.package("keyring"), "../")
-    script <- c(sprintf("library(keyring, lib.loc = '%s')", libPath),
-                script)
-    libPath <- file.path(find.package("openssl"), "../")
-    script <- c(sprintf("library(openssl, lib.loc = '%s')", libPath),
-                script)
+    c(.getLocalLibraryScipt("R6"), script)
+    c(.getLocalLibraryScipt("CohortGenerator"), script)
+    c(.getLocalLibraryScipt("DatabaseConnector"), script)
+    c(.getLocalLibraryScipt("keyring"), script)
+    c(.getLocalLibraryScipt("openssl"), script)
+    c(.getLocalLibraryScipt("dplyr"), script)
   }
 
   # Write file and execute script inside an renv
@@ -104,3 +91,8 @@ withModuleRenv <- function(code,
   )
   return(invisible(NULL))
 }
+
+.getLocalLibraryScipt <- function(x) {
+  libPath <- file.path(find.package(x), "../")
+  sprintf("library(%s, lib.loc = '%s')", x, libPath)
+}
diff --git a/inst/csv/modules.csv b/inst/csv/modules.csv
@@ -1,8 +1,8 @@
 module,version,remote_repo,remote_username,module_type,main_package,main_package_tag
-CharacterizationModule,v0.3.1,github.com,OHDSI,cdm,Characterization,v0.1.1
+CharacterizationModule,v0.3.2,github.com,OHDSI,cdm,Characterization,v0.1.1
 CohortDiagnosticsModule,v0.0.7,github.com,OHDSI,cdm,CohortDiagnostics,v3.1.2
 CohortGeneratorModule,v0.1.0,github.com,OHDSI,cdm,CohortGenerator,v0.8.0
-CohortIncidenceModule,v0.0.6,github.com,OHDSI,cdm,CohortIncidence,v3.1.2
+CohortIncidenceModule,v0.0.9,github.com,OHDSI,cdm,CohortIncidence,v3.1.4
 CohortMethodModule,v0.1.0,github.com,OHDSI,cdm,CohortMethod,74f017107e0cc1b740a2badc82879ab6ad291b23
 PatientLevelPredictionModule,v0.1.0,github.com,OHDSI,cdm,PatientLevelPrediction,v6.3.1
 SelfControlledCaseSeriesModule,v0.1.3,github.com,OHDSI,cdm,SelfControlledCaseSeries,15918616814b88137f82bf2aa9986e1dcdf39e74

diff --git a/inst/testdata/analysisSpecification.json b/inst/testdata/analysisSpecification.json
@@ -223,7 +223,7 @@
   "moduleSpecifications": [
     {
       "module": "CohortGeneratorModule",
-      "version": "0.2.0-2",
+      "version": "0.2.0-6",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": {
@@ -234,7 +234,7 @@
     },
     {
       "module": "CohortDiagnosticsModule",
-      "version": "0.1.0-1",
+      "version": "0.1.0-5",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": {
@@ -292,7 +292,7 @@
     },
     {
       "module": "CohortIncidenceModule",
-      "version": "0.1.0-2",
+      "version": "0.1.0-6",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": {
@@ -365,7 +365,7 @@
     },
     {
       "module": "CharacterizationModule",
-      "version": "0.4.0-1",
+      "version": "0.4.0-5",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": {
@@ -489,7 +489,7 @@
     },
     {
       "module": "CohortMethodModule",
-      "version": "0.2.0-1",
+      "version": "0.2.0-5",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": {
@@ -1341,7 +1341,7 @@
     },
     {
       "module": "SelfControlledCaseSeriesModule",
-      "version": "0.2.0-1",
+      "version": "0.2.0-5",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": {
@@ -2360,7 +2360,7 @@
     },
     {
       "module": "PatientLevelPredictionModule",
-      "version": "0.2.0-1",
+      "version": "0.2.0-5",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": [