Release v0.10

.Rbuildignore

@@ -4,3 +4,9 @@
 ^\.Rproj\.user$
 ^\.idea$
 ^\.github$
+_pkgdown\.yml
+compare_versions
+deploy.sh
+docs
+extras
+man-roxygen

.github/workflows/R_CMD_check_Hades.yaml

@@ -20,9 +20,6 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"}
-          - {os: macOS-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"}
-          - {os: ubuntu-20.04, r: '4.2.3', rtools: '42', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: windows-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}
           - {os: macOS-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}
           - {os: ubuntu-20.04, r: 'release', rtools: '', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
@@ -50,9 +47,23 @@ jobs:
       CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
       CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}
       CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }}
+      CDM_SNOWFLAKE_CDM53_SCHEMA: ${{ secrets.CDM_SNOWFLAKE_CDM53_SCHEMA }}
+      CDM_SNOWFLAKE_OHDSI_SCHEMA: ${{ secrets.CDM_SNOWFLAKE_OHDSI_SCHEMA }}
+      CDM_SNOWFLAKE_PASSWORD: ${{ secrets.CDM_SNOWFLAKE_PASSWORD }}
+      CDM_SNOWFLAKE_CONNECTION_STRING: ${{ secrets.CDM_SNOWFLAKE_CONNECTION_STRING }}
+      CDM_SNOWFLAKE_USER: ${{ secrets.CDM_SNOWFLAKE_USER }}      
+      CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
+      CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
+      CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
+      CDM5_SPARK_CDM_SCHEMA: ${{ secrets.CDM5_SPARK_CDM_SCHEMA }}
+      CDM5_SPARK_OHDSI_SCHEMA: ${{ secrets.CDM5_SPARK_OHDSI_SCHEMA }}
+      CDM_BIG_QUERY_CONNECTION_STRING: ${{ secrets.CDM_BIG_QUERY_CONNECTION_STRING }}
+      CDM_BIG_QUERY_KEY_FILE: ${{ secrets.CDM_BIG_QUERY_KEY_FILE }}
+      CDM_BIG_QUERY_CDM_SCHEMA: ${{ secrets.CDM_BIG_QUERY_CDM_SCHEMA }}
+      CDM_BIG_QUERY_OHDSI_SCHEMA: ${{ secrets.CDM_BIG_QUERY_OHDSI_SCHEMA }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -91,17 +102,21 @@ jobs:
             eval sudo $cmd
           done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
           
-      - name: Reconfigure Java
+      - name: Setup Java
         if: runner.os == 'macOS'
-        run: R CMD javareconf
-
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'corretto'
+          java-version: '8'
+
       - name: Install libssh
         if: runner.os == 'Linux'
         run: |    
           sudo apt-get install libssh-dev
 
       - name: Install dependencies
         run: |
+          install.packages("cachem")
           remotes::install_deps(dependencies = TRUE, INSTALL_opts=c("--no-multiarch"))
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}

.github/workflows/R_CMD_check_main_weekly.yaml

@@ -20,30 +20,41 @@ jobs:
       GITHUB_PAT: ${{ secrets.GH_TOKEN }}
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
-      CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }}
+      CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM54_SCHEMA }}
       CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }}
       CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }}
       CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }}
       CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }}
-      CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }}
+      CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM54_SCHEMA }}
       CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }}
       CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }}
       CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }}
       CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }}
-      CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }}
+      CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM54_SCHEMA }}
       CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }}
       CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
       CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
       CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
-      CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }}
+      CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM54_SCHEMA }}
       CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }}
       CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
       CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}
       CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }}
+      CDM_SNOWFLAKE_CDM53_SCHEMA: ${{ secrets.CDM_SNOWFLAKE_CDM53_SCHEMA }}
+      CDM_SNOWFLAKE_OHDSI_SCHEMA: ${{ secrets.CDM_SNOWFLAKE_OHDSI_SCHEMA }}
+      CDM_SNOWFLAKE_PASSWORD: ${{ secrets.CDM_SNOWFLAKE_PASSWORD }}
+      CDM_SNOWFLAKE_CONNECTION_STRING: ${{ secrets.CDM_SNOWFLAKE_CONNECTION_STRING }}
+      CDM_SNOWFLAKE_USER: ${{ secrets.CDM_SNOWFLAKE_USER }}      
       CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
       CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
       CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
-
+      CDM5_SPARK_CDM_SCHEMA: ${{ secrets.CDM5_SPARK_CDM_SCHEMA }}
+      CDM5_SPARK_OHDSI_SCHEMA: ${{ secrets.CDM5_SPARK_OHDSI_SCHEMA }}
+      CDM_BIG_QUERY_CONNECTION_STRING: ${{ secrets.CDM_BIG_QUERY_CONNECTION_STRING }}
+      CDM_BIG_QUERY_KEY_FILE: ${{ secrets.CDM_BIG_QUERY_KEY_FILE }}
+      CDM_BIG_QUERY_CDM_SCHEMA: ${{ secrets.CDM_BIG_QUERY_CDM_SCHEMA }}
+      CDM_BIG_QUERY_OHDSI_SCHEMA: ${{ secrets.CDM_BIG_QUERY_OHDSI_SCHEMA }}
+
     steps:
       - uses: actions/checkout@v2
 

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: CohortGenerator
 Type: Package
 Title: An R Package for Cohort Generation Against the OMOP CDM
-Version: 0.9.0
-Date: 2024-05-28
+Version: 0.10.0
+Date: 2024-07-14
 Authors@R: c(
   person("Anthony", "Sena", email = "[email protected]", role = c("aut", "cre")),
   person("Jamie", "Gilbert", role = c("aut")),
@@ -22,25 +22,28 @@ Imports:
   digest,
   dplyr,
   lubridate,
+  methods,
   ParallelLogger (>= 3.0.0),
   readr (>= 2.1.0),
   rlang,
   RJSONIO,
   jsonlite,
+  ResultModelManager,
   SqlRender (>= 1.11.1),
-  stringi (>= 1.7.6)
+  stringi (>= 1.7.6),
+  tibble
 Suggests:
   CirceR (>= 1.1.1),
   Eunomia,
   knitr,
   rmarkdown,
   ROhdsiWebApi,
   testthat,
-  withr
+  withr,
+  zip
 Remotes:
-  ohdsi/CirceR,
-  ohdsi/Eunomia,
-  ohdsi/ROhdsiWebApi
+  ohdsi/ResultModelManager,
+  ohdsi/ROhdsiWebApi,
 License: Apache License
 VignetteBuilder: knitr
 URL: https://ohdsi.github.io/CohortGenerator/, https://github.com/OHDSI/CohortGenerator

NAMESPACE

@@ -16,34 +16,42 @@ export(createDemographicSubset)
 export(createEmptyCohortDefinitionSet)
 export(createEmptyNegativeControlOutcomeCohortSet)
 export(createLimitSubset)
+export(createResultsDataModel)
 export(createSubsetCohortWindow)
 export(dropCohortStatsTables)
 export(exportCohortStatsTables)
 export(generateCohortSet)
 export(generateNegativeControlOutcomeCohorts)
 export(getCohortCounts)
 export(getCohortDefinitionSet)
+export(getCohortInclusionRules)
 export(getCohortStats)
 export(getCohortTableNames)
+export(getDataMigrator)
 export(getRequiredTasks)
+export(getResultsDataModelSpecifications)
 export(getSubsetDefinitions)
 export(insertInclusionRuleNames)
 export(isCamelCase)
 export(isCohortDefinitionSet)
 export(isFormattedForDatabaseUpload)
 export(isSnakeCase)
 export(isTaskRequired)
+export(migrateDataModel)
 export(readCsv)
 export(recordTasksDone)
+export(runCohortGeneration)
 export(sampleCohortDefinitionSet)
 export(saveCohortDefinitionSet)
 export(saveCohortSubsetDefinition)
 export(saveIncremental)
+export(uploadResults)
 export(writeCsv)
 import(DatabaseConnector)
 import(R6)
-importFrom(dplyr,"%>%")
+import(dplyr)
 importFrom(grDevices,rgb)
+importFrom(methods,is)
 importFrom(rlang,':=')
 importFrom(rlang,.data)
 importFrom(stats,aggregate)

NEWS.md

@@ -1,3 +1,20 @@
+CohortGenerator 0.10.0
+=======================
+New Features
+- Add `runCohortGeneration` function (Issue #165)
+- Adopt ResultModelManager for handling results data models & uploading. Extend results data model to include information on cohort subsets(#154, #162)
+- Remove REMOTES entries for CirceR and Eunomia which are now in CRAN (#145)
+- Unit tests now running on all OHDSI DB Platforms (#151)
+
+Bug Fixes
+- Negation of cohort subset operator must join on `subject_id` AND `start_date` (#167)
+- Allow integer as cohort ID (#146)
+- Use native messaging functions for output vs. ParallelLogger (#97)
+- Prevent upload of inclusion rule information (#78)
+- Expose `colTypes` when working with .csv files (#59)
+- Remove `bit64` from package (mostly) (#152)
+- Updated documentation for cohort subset negate feature (#111)
+
 CohortGenerator 0.9.0
 =======================
 - Random sample functionality (for development only) (Issue #129)

R/CohortConstruction.R

@@ -76,6 +76,7 @@ generateCohortSet <- function(connectionDetails = NULL,
       "sql"
     )
   )
+  assertLargeInteger(cohortDefinitionSet$cohortId)
   # Verify that cohort IDs are not repeated in the cohort definition
   # set before generating
   if (length(unique(cohortDefinitionSet$cohortId)) != length(cohortDefinitionSet$cohortId)) {
@@ -249,7 +250,7 @@ generateCohort <- function(cohortId = NULL,
       connection <- DatabaseConnector::connect(connectionDetails)
       on.exit(DatabaseConnector::disconnect(connection))
     }
-    ParallelLogger::logInfo(i, "/", nrow(cohortDefinitionSet), "- Generating cohort: ", cohortName, " (id = ", cohortId, ")")
+    rlang::inform(paste0(i, "/", nrow(cohortDefinitionSet), "- Generating cohort: ", cohortName, " (id = ", cohortId, ")"))
     sql <- cohortDefinitionSet$sql[i]
 
     if (!isSubset) {

R/CohortCount.R

@@ -67,7 +67,7 @@ getCohortCounts <- function(connectionDetails = NULL,
   if (tolower(cohortTable) %in% tablesInServer) {
     counts <- DatabaseConnector::querySql(connection, sql, snakeCaseToCamelCase = TRUE)
     delta <- Sys.time() - start
-    ParallelLogger::logInfo(paste("Counting cohorts took", signif(delta, 3), attr(delta, "units")))
+    rlang::inform(paste("Counting cohorts took", signif(delta, 3), attr(delta, "units")))
     if (!is.null(cohortDefinitionSet)) {
       # If the user has NOT specified a list of cohortIds
       # to use to filter the cohortDefinitionSet, then
@@ -77,15 +77,17 @@ getCohortCounts <- function(connectionDetails = NULL,
       }
       counts <- merge(
         x = counts,
-        y = cohortDefinitionSet[cohortDefinitionSet$cohortId %in% cohortIds, ],
+        y = cohortDefinitionSet[cohortDefinitionSet$cohortId %in% cohortIds, , drop = FALSE],
         by = "cohortId",
         all.y = TRUE
       )
-      counts <- transform(
-        counts,
-        cohortEntries = ifelse(is.na(cohortEntries), 0L, cohortEntries),
-        cohortSubjects = ifelse(is.na(cohortSubjects), 0L, cohortSubjects)
-      )
+      counts <- with(counts, {
+        transform(
+          counts,
+          cohortEntries = ifelse(is.na(cohortEntries), 0L, cohortEntries),
+          cohortSubjects = ifelse(is.na(cohortSubjects), 0L, cohortSubjects)
+        )
+      })
     }
     if (!is.null(databaseId)) {
       counts$databaseId <- databaseId