Release v0.0.5

OHDSI · Apr 13, 2023 · 676fde0 · 676fde0
2 parents a12dee1 + a7d4ef8
commit 676fde0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: Strategus
 Type: Package
 Title: Coordinating and Executing Analytics Using HADES Modules
-Version: 0.0.4
-Date: 2023-03-29
+Version: 0.0.5
+Date: 2023-04-13
 Authors@R: c(
 	person("Martijn", "Schuemie", email = "[email protected]", role = c("aut", "cre")),
 	person("Anthony", "Sena", email = "[email protected]", role = c("aut")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+Strategus 0.0.5
+===============
+
+- Required metadata tables check fails with DatabaseConnector < 6.0 (#61)
+- Update module references and add script to run Strategus on Eunomia in `extras/ExecuteStrategusOnEunomia.R` (#66)
+
 Strategus 0.0.4
 ===============
 

diff --git a/R/DatabaseMetaData.R b/R/DatabaseMetaData.R
@@ -42,7 +42,7 @@ createDatabaseMetaData <- function(executionSettings, keyringName = NULL) {
     connection = connection,
     databaseSchema = executionSettings$cdmDatabaseSchema
   )
-
+  cdmTableList <- tolower(cdmTableList)
 
   if (!length(cdmTableList[which(x = cdmTableList %in% requiredTables)]) == length(requiredTables)) {
     missingCdmTables <- requiredTables[!(requiredTables %in% cdmTableList)]

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/CreatingAnalysisSpecification.html b/docs/articles/CreatingAnalysisSpecification.html
diff --git a/docs/articles/CreatingModules.html b/docs/articles/CreatingModules.html
diff --git a/docs/articles/ExecuteStrategus.html b/docs/articles/ExecuteStrategus.html
diff --git a/docs/articles/IntroductionToStrategus.html b/docs/articles/IntroductionToStrategus.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -6,5 +6,5 @@ articles:
   CreatingModules: CreatingModules.html
   ExecuteStrategus: ExecuteStrategus.html
   IntroductionToStrategus: IntroductionToStrategus.html
-last_built: 2023-03-29T18:18Z
+last_built: 2023-04-13T19:10Z
 
diff --git a/docs/pull_request_template.html b/docs/pull_request_template.html
diff --git a/docs/reference/Strategus-package.html b/docs/reference/Strategus-package.html
diff --git a/docs/reference/addModuleSpecifications.html b/docs/reference/addModuleSpecifications.html
diff --git a/docs/reference/addSharedResources.html b/docs/reference/addSharedResources.html
diff --git a/docs/reference/createCdmExecutionSettings.html b/docs/reference/createCdmExecutionSettings.html
diff --git a/docs/reference/createEmptyAnalysisSpecificiations.html b/docs/reference/createEmptyAnalysisSpecificiations.html
diff --git a/docs/reference/createResultsExecutionSettings.html b/docs/reference/createResultsExecutionSettings.html
diff --git a/docs/reference/ensureAllModulesInstantiated.html b/docs/reference/ensureAllModulesInstantiated.html
diff --git a/docs/reference/execute.html b/docs/reference/execute.html
diff --git a/docs/reference/getModuleList.html b/docs/reference/getModuleList.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/retrieveConnectionDetails.html b/docs/reference/retrieveConnectionDetails.html
diff --git a/docs/reference/storeConnectionDetails.html b/docs/reference/storeConnectionDetails.html
diff --git a/docs/reference/unlockKeyring.html b/docs/reference/unlockKeyring.html
diff --git a/extras/ExecuteStrategusOnEunomia.R b/extras/ExecuteStrategusOnEunomia.R
@@ -0,0 +1,58 @@
+#Install packages required for this script ---------
+#install.packages("remotes")
+#install.packages("ParallelLogger")
+#remotes::install_github("OHDSI/Strategus")
+#remotes::install_github("OHDSI/Eunomia")
+#remotes::install_github("OHDSI/CohortGenerator")
+
+#Run the Eunomia study ---------
+# Set the folder & environment variable for module storage
+moduleFolder <- "C:/temp/strategus/modules"
+studyFolder <- "C:/temp/strategus/EunomiaTestStudy"
+Sys.setenv("INSTANTIATED_MODULES_FOLDER" = moduleFolder)
+
+if (!dir.exists(moduleFolder)) {
+  dir.create(moduleFolder, recursive = TRUE)
+}
+if (!dir.exists(studyFolder)) {
+  dir.create(studyFolder, recursive = TRUE)
+}
+
+# Create the execution settings for Eunomia ----------
+connectionDetails <- Eunomia::getEunomiaConnectionDetails(
+  databaseFile = file.path(studyFolder, "cdm.sqlite")
+)
+
+Strategus::storeConnectionDetails(connectionDetails = connectionDetails,
+                                  connectionDetailsReference = "eunomia")
+
+executionSettings <- Strategus::createCdmExecutionSettings(
+  connectionDetailsReference = "eunomia",
+  workDatabaseSchema = "main",
+  cdmDatabaseSchema = "main",
+  cohortTableNames = CohortGenerator::getCohortTableNames(),
+  workFolder = file.path(studyFolder, "work_folder"),
+  resultsFolder = file.path(studyFolder, "results_folder"),
+  minCellCount = 5
+)
+
+ParallelLogger::saveSettingsToJson(
+  object = executionSettings,
+  file.path(studyFolder, "eunomiaExecutionSettings.json")
+)
+
+# Execute the study ---------
+analysisSpecifications <- ParallelLogger::loadSettingsFromJson(
+  fileName = system.file("testdata/analysisSpecification.json",
+                         package = "Strategus")
+)
+
+executionSettings <- ParallelLogger::loadSettingsFromJson(
+  fileName = file.path(studyFolder, "eunomiaExecutionSettings.json")
+)
+
+Strategus::execute(
+  analysisSpecifications = analysisSpecifications,
+  executionSettings = executionSettings,
+  executionScriptFolder = file.path(studyFolder, "script_folder")
+)
diff --git a/extras/PackageMaintenance.R b/extras/PackageMaintenance.R
@@ -31,6 +31,7 @@ devtools::spell_check()
 
 # Update the module version information based on updates found on GitHub
 library(dplyr)
+# httr::set_config(httr::config(ssl_verifypeer = FALSE))
 updateModuleVersionInfo <- function() {
   modules <- CohortGenerator::readCsv(file = "inst/csv/modules.csv")
   modules <- modules %>%

diff --git a/extras/Strategus.pdf b/extras/Strategus.pdf
diff --git a/inst/csv/modules.csv b/inst/csv/modules.csv
@@ -1,9 +1,9 @@
 module,version,remote_repo,remote_username,module_type,main_package,main_package_tag
-CharacterizationModule,v0.3.0,github.com,OHDSI,cdm,Characterization,v0.1.1
+CharacterizationModule,v0.3.1,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
 CohortMethodModule,v0.1.0,github.com,OHDSI,cdm,CohortMethod,74f017107e0cc1b740a2badc82879ab6ad291b23
-PatientLevelPredictionModule,v0.0.8,github.com,OHDSI,cdm,PatientLevelPrediction,v6.3.1
+PatientLevelPredictionModule,v0.1.0,github.com,OHDSI,cdm,PatientLevelPrediction,v6.3.1
 SelfControlledCaseSeriesModule,v0.1.3,github.com,OHDSI,cdm,SelfControlledCaseSeries,15918616814b88137f82bf2aa9986e1dcdf39e74
 EvidenceSynthesisModule,v0.1.3,github.com,OHDSI,results,EvidenceSynthesis,v0.4.0
diff --git a/inst/doc/CreatingAnalysisSpecification.pdf b/inst/doc/CreatingAnalysisSpecification.pdf
diff --git a/inst/doc/CreatingModules.pdf b/inst/doc/CreatingModules.pdf
diff --git a/inst/doc/ExecuteStrategus.pdf b/inst/doc/ExecuteStrategus.pdf
diff --git a/inst/doc/IntroductionToStrategus.pdf b/inst/doc/IntroductionToStrategus.pdf
diff --git a/inst/testdata/analysisSpecification.json b/inst/testdata/analysisSpecification.json
@@ -365,7 +365,7 @@
     },
     {
       "module": "CharacterizationModule",
-      "version": "0.2.3",
+      "version": "0.3.1",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": {
@@ -2360,7 +2360,7 @@
     },
     {
       "module": "PatientLevelPredictionModule",
-      "version": "0.0.7",
+      "version": "0.1.0",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": [

diff --git a/vignettes/CreatingAnalysisSpecification.Rmd b/vignettes/CreatingAnalysisSpecification.Rmd
@@ -184,7 +184,7 @@ The following code creates the `characterizationModuleSpecifications` to perform
 
 
 ```{r eval=FALSE}
-source("https://raw.githubusercontent.com/OHDSI/CharacterizationModule/v0.3.0/SettingsFunctions.R")
+source("https://raw.githubusercontent.com/OHDSI/CharacterizationModule/v0.3.1/SettingsFunctions.R")
 characterizationModuleSpecifications <- createCharacterizationModuleSpecifications(
   targetIds = c(1, 2),
   outcomeIds = 3,
@@ -421,7 +421,7 @@ sccsModuleSpecifications <- creatSelfControlledCaseSeriesModuleSpecifications(
 The following code creates the `plpModuleSpecifications` to perform a self-controlled case series analysis for this study.
 
 ```{r eval=FALSE}
-source("https://raw.githubusercontent.com/OHDSI/PatientLevelPredictionModule/v0.0.8/SettingsFunctions.R")
+source("https://raw.githubusercontent.com/OHDSI/PatientLevelPredictionModule/v0.1.0/SettingsFunctions.R")
 
 makeModelDesignSettings <- function(targetId, outcomeId, popSettings, covarSettings) {
   invisible(PatientLevelPrediction::createModelDesign(