Release v1.1.0 preparation

OHDSI · Nov 26, 2024 · bda7af6 · bda7af6
1 parent 6db4f46
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Showing 9 changed files with 13 additions and 10 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+Strategus 1.1.0
+===============
+- Inject cohort schema and table into `createCohortBasedCovariateSettings` (#181)
+- Provide hook to optimize cohort SQL construction (#179)
+- Fixes broken links in R6 class documentation (#183)
+
 Strategus 1.0.0
 ===============
 

diff --git a/R/Module-PatientLevelPrediction.R b/R/Module-PatientLevelPrediction.R
@@ -156,10 +156,9 @@ PatientLevelPredictionModule <- R6::R6Class(
     }
   ),
   private = list(
-    .setCovariateSchemaTable = function(
-        modelDesignList,
-        cohortDatabaseSchema,
-        cohortTable) {
+    .setCovariateSchemaTable = function(modelDesignList,
+                                        cohortDatabaseSchema,
+                                        cohortTable) {
       if (inherits(modelDesignList, "modelDesign")) {
         modelDesignList <- list(modelDesignList)
       }

diff --git a/R/StrategusModule.R b/R/StrategusModule.R
@@ -334,8 +334,8 @@ StrategusModule <- R6::R6Class(
     if (inherits(s, "covariateSettings") && "fun" %in% names(attributes(s))) {
       if (attr(s, "fun") == "getDbCohortBasedCovariatesData") {
         # Set the covariateCohortDatabaseSchema & covariateCohortTable values
-        s$covariateCohortDatabaseSchema = executionSettings$workDatabaseSchema
-        s$covariateCohortTable = executionSettings$cohortTableNames$cohortTable
+        s$covariateCohortDatabaseSchema <- executionSettings$workDatabaseSchema
+        s$covariateCohortTable <- executionSettings$cohortTableNames$cohortTable
       }
     }
     return(s)
@@ -379,5 +379,3 @@ StrategusModule <- R6::R6Class(
   # Call the helper function on the input list
   return(replaceHelper(moduleSettings))
 }
-
-
diff --git a/extras/Strategus.pdf b/extras/Strategus.pdf
diff --git a/inst/doc/CreatingAnalysisSpecification.pdf b/inst/doc/CreatingAnalysisSpecification.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/doc/WorkingWithResults.pdf b/inst/doc/WorkingWithResults.pdf
diff --git a/tests/testthat/test-Settings.R b/tests/testthat/test-Settings.R
@@ -453,8 +453,8 @@ test_that("Test internal function for modifying covariate settings", {
 
   testReplacedModuleSettings <- .replaceCovariateSettings(moduleSettings, executionSettings)
   # For visual inspection
-  #ParallelLogger::saveSettingsToJson(moduleSettings, "before_unit_test.json")
-  #ParallelLogger::saveSettingsToJson(testReplacedModuleSettings, "after_unit_test.json")
+  # ParallelLogger::saveSettingsToJson(moduleSettings, "before_unit_test.json")
+  # ParallelLogger::saveSettingsToJson(testReplacedModuleSettings, "after_unit_test.json")
   expect_equal(testReplacedModuleSettings$analysis$something[[1]]$covariateCohortDatabaseSchema, NULL)
   expect_equal(testReplacedModuleSettings$analysis$something[[1]]$covariateCohortTable, NULL)
   expect_equal(testReplacedModuleSettings$analysis$something[[2]]$covariateCohortDatabaseSchema, workDatabaseSchema)