fix merge conflict

darwin-eu · Jan 31, 2024 · 8bad2be · 8bad2be
2 parents 2f96e5a + 3a9b2e6
commit 8bad2be
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Showing 16 changed files with 49 additions and 42 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -40,7 +40,7 @@ Imports:
     fs,
     generics,
     tidyr,
-    omopgenerics
+    omopgenerics (>= 0.0.2)
 Suggests: 
     SqlRender,
     rJava,

diff --git a/NAMESPACE b/NAMESPACE
@@ -40,7 +40,6 @@ export(cohortAttrition)
 export(cohortCount)
 export(cohortErafy)
 export(cohortSet)
-export(cohortTable)
 export(cohortUnion)
 export(cohort_attrition)
 export(cohort_count)
@@ -76,6 +75,7 @@ export(intersectCohorts)
 export(intersect_cohorts)
 export(listTables)
 export(list_tables)
+export(newCohortTable)
 export(newGeneratedCohortSet)
 export(new_generated_cohort_set)
 export(readCohortSet)
@@ -116,10 +116,10 @@ importFrom(jsonlite,read_json)
 importFrom(methods,is)
 importFrom(omopgenerics,attrition)
 importFrom(omopgenerics,cohortCount)
-importFrom(omopgenerics,cohortTable)
 importFrom(omopgenerics,dropTable)
 importFrom(omopgenerics,insertFromSource)
 importFrom(omopgenerics,insertTable)
+importFrom(omopgenerics,newCohortTable)
 importFrom(omopgenerics,settings)
 importFrom(purrr,"%||%")
 importFrom(rlang,"!!")

diff --git a/R/cdm.R b/R/cdm.R
@@ -99,7 +99,7 @@ cdm_from_con <- function(con,
     achillesTables <- list()
   }
 
-  cdm <- omopgenerics::cdmReference(
+  cdm <- omopgenerics::newCdmReference(
     tables = c(cdmTables, achillesTables),
     cdmName = cdm_name,
     cdmVersion = cdm_version
@@ -117,16 +117,15 @@ cdm_from_con <- function(con,
         NULL
       }
     })
-    cohort <- x[[1]]
-    if(is.null(cohort)) {
+    cdm[[cohort_table]] <- x[[1]]
+    if(is.null(cdm[[cohort_table]])) {
       rlang::abort(glue::glue("cohort table `{cohort_table}` not found!"))
     }
-
-    cdm[[cohort_table]] <- omopgenerics::cohortTable(
-      table = cohort,
-      cohortSetRef = x[[2]],
-      cohortAttritionRef = x[[3]]
-    )
+    cdm[[cohort_table]] <- cdm[[cohort_table]] |>
+      omopgenerics::newCohortTable(
+        cohortSetRef = x[[2]],
+        cohortAttritionRef = x[[3]]
+      )
   }
 
   if (dbms(con) == "snowflake") {
@@ -168,7 +167,7 @@ tbl.db_cdm <- function(src, schema, name, ...) {
   fullName <- inSchema(schema = schema, table = name, dbms = dbms(con))
   x <- dplyr::tbl(src = con, fullName) |>
     dplyr::rename_all(tolower) |>
-    omopgenerics::cdmTable(src = src, name = tolower(name))
+    omopgenerics::newCdmTable(src = src, name = tolower(name))
   return(x)
 }
 

diff --git a/R/copy_cdm_to.R b/R/copy_cdm_to.R
@@ -39,7 +39,7 @@ copy_cdm_to <- function(con, cdm, schema, overwrite = FALSE) {
   }
 
   # create cdm object
-  newCdm <- omopgenerics::cdmReference(
+  newCdm <- omopgenerics::newCdmReference(
     tables = cdmTables, cdmName = omopgenerics::cdmName(cdm)
   )
 
@@ -70,7 +70,7 @@ copy_cdm_to <- function(con, cdm, schema, overwrite = FALSE) {
       overwrite = overwrite
     )
     if (cohort) {
-      newCdm[[table_name]] <- omopgenerics::cohortTable(
+      newCdm[[table_name]] <- omopgenerics::newCohortTable(
         table = newCdm[[table_name]],
         cohortSetRef = newCdm[[paste0(table_name, "_set")]],
         cohortAttritionRef = newCdm[[paste0(table_name, "_attrition")]]

diff --git a/R/dbSource.R b/R/dbSource.R
@@ -34,7 +34,7 @@ dbSource <- function(con,
     "write_schema" = writeSchema
   )
   class(source) <- "db_cdm"
-  source <- omopgenerics::cdmSource(src = source, sourceType = dbms(con))
+  source <- omopgenerics::newCdmSource(src = source, sourceType = dbms(con))
   return(source)
 }
 
@@ -56,7 +56,7 @@ insertTable.db_cdm <- function(cdm,
   }
   DBI::dbWriteTable(conn = con, name = fullName, value = table)
   x <- dplyr::tbl(src = con, fullName) |>
-    omopgenerics::cdmTable(src = src, name = name)
+    omopgenerics::newCdmTable(src = src, name = name)
   return(x)
 }
 
@@ -167,7 +167,7 @@ insertFromSource.db_cdm <- function(cdm, value) {
       remoteName <- substr(remoteName, nchar(prefix) + 1, nchar(remoteName))
     }
   }
-  value <- omopgenerics::cdmTable(
+  value <- omopgenerics::newCdmTable(
     table = value, src = attr(cdm, "cdm_source"), name = remoteName
   )
   return(value)

diff --git a/R/generateCohortSet.R b/R/generateCohortSet.R
@@ -403,11 +403,11 @@ generateCohortSet <- function(cdm,
   # }
 
   cdm[[name]] <- cohort_ref |>
-    omopgenerics::cdmTable(src = attr(cdm, "cdm_source"), name = name)
+    omopgenerics::newCdmTable(src = attr(cdm, "cdm_source"), name = name)
 
 # browser()
   # Create the object. Let the constructor handle getting the counts.----
-  cdm[[name]] <- omopgenerics::cohortTable(
+  cdm[[name]] <- omopgenerics::newCohortTable(
     table = cdm[[name]],
     cohortSetRef = cohortSet[,c("cohort_definition_id", "cohort_name")],
     cohortAttritionRef = cohort_attrition_ref)
@@ -437,7 +437,7 @@ generate_cohort_set <- function(cdm,
 #'
 #' `r lifecycle::badge("superseded")`
 #'
-#' Please use `omopgenerics::cohortTable()` instead.
+#' Please use `omopgenerics::newCohortTable()` instead.
 #'
 #' This constructor function is to be used by analytic package developers to
 #' create `cohort_table` objects.
@@ -563,7 +563,7 @@ new_generated_cohort_set <- function(cohort_ref,
   if (!missing(overwrite)) {
     cli::cli_warn("overwrite is no longer a required argument for new_generated_cohort_set")
   }
-  omopgenerics::cohortTable(
+  omopgenerics::newCohortTable(
     table = cohort_ref,
     cohortSetRef = cohort_set_ref,
     cohortAttritionRef = cohort_attrition_ref

diff --git a/R/generateConceptCohortSet.R b/R/generateConceptCohortSet.R
@@ -350,7 +350,7 @@ generateConceptCohortSet <- function(cdm,
       excluded_records = 0,
       excluded_subjects = 0)
 
-  cdm[[name]] <- omopgenerics::cohortTable(
+  cdm[[name]] <- omopgenerics::newCohortTable(
     table = cohortRef,
     cohortSetRef = cohortSetRef,
     cohortAttritionRef = cohortAttritionRef

diff --git a/R/reexports-omopgenerics.R b/R/reexports-omopgenerics.R
@@ -10,9 +10,9 @@ omopgenerics::settings
 #' @export
 omopgenerics::attrition
 
-#' @importFrom omopgenerics cohortTable
+#' @importFrom omopgenerics newCohortTable
 #' @export
-omopgenerics::cohortTable
+omopgenerics::newCohortTable
 
 #' @importFrom omopgenerics insertTable
 #' @export

diff --git a/extras/circe-work.R b/extras/circe-work.R
@@ -226,7 +226,7 @@ DBI::dbRemoveTable(con, inSchema(write_schema, "codesets", dbms(con)))
 
   cdm[[name]] <- cohortRef
 
-  cdm[[name]] <- omopgenerics::cohortTable(
+  cdm[[name]] <- omopgenerics::newCohortTable(
     cohortRef = cdm[[name]], cohortSetRef = cohortSetRef, overwrite = overwrite
   )
 

diff --git a/man/new_generated_cohort_set.Rd b/man/new_generated_cohort_set.Rd
diff --git a/man/reexports.Rd b/man/reexports.Rd
diff --git a/tests/testthat/test-db-generateCohortSet.R b/tests/testthat/test-db-generateCohortSet.R
@@ -189,7 +189,7 @@ test_that("newGeneratedCohortSet works with prefix", {
     ) %>%
     compute(name = "cohort", temporary = FALSE, overwrite = TRUE)
 
-  cdm$cohort <- cohortTable(cdm$cohort)
+  cdm$cohort <- newCohortTable(cdm$cohort)
 
   expect_true("cohort" %in% list_tables(con, write_schema))
   expect_true("test_cohort" %in% list_tables(con, "main"))

diff --git a/tests/testthat/test-db-newGeneratedCohortSet.R b/tests/testthat/test-db-newGeneratedCohortSet.R
@@ -59,7 +59,7 @@ test_new_generated_cohort_set <- function(con, cdm_schema, write_schema) {
   cdm$new_cohort <- x %>%
     compute(name = "new_cohort", temporary = FALSE, overwrite = TRUE)
 
-  cdm$new_cohort <- omopgenerics::cohortTable(
+  cdm$new_cohort <- omopgenerics::newCohortTable(
       cdm$new_cohort,
       cohortSetRef = dplyr::tibble(
         cohort_definition_id = 1,
@@ -117,7 +117,7 @@ test_that("error in newGeneratedCohortSet if cohort_ref has not been computed",
                   "cohort_start_date" = "condition_start_date",
                   "cohort_end_date" = "condition_end_date")
 
-  expect_error(omopgenerics::cohortTable(cohort_ref))
+  expect_error(omopgenerics::newCohortTable(cohort_ref))
 
   DBI::dbDisconnect(con, shutdown = TRUE)
 })
@@ -163,7 +163,7 @@ test_that("no error if cohort is empty", {
 
   cdm$cohort_3b <- cdm$cohort_3 %>%
     dplyr::compute(name = "cohort_3b", temporary = FALSE) |>
-    omopgenerics::cohortTable(cohortSetRef = c_Ref)
+    omopgenerics::newCohortTable(cohortSetRef = c_Ref)
 
   expect_true("cohort_table" %in% class(cdm$cohort_3b))
   expect_false(nrow(settings(cdm$cohort_3b)) == 0)
@@ -196,7 +196,7 @@ test_that("newGeneratedCohortSet handles empty cohort tables", {
     cdm$cohort_3 <- cdm$cohorts2 %>%
       dplyr::filter(cohort_start_date > "2099-01-01") %>%
       compute(name = "cohort_3", temporary = FALSE) %>%
-      omopgenerics::cohortTable()
+      omopgenerics::newCohortTable()
   })
 
   expect_equal(nrow(dplyr::collect(cdm$cohort_3)), 0)

diff --git a/tests/testthat/test-validate.R b/tests/testthat/test-validate.R
@@ -41,10 +41,18 @@ test_that("assert_tables works", {
   # add missing column error to collection
   err3 <- checkmate::makeAssertCollection()
   cdm <- cdm_from_con(con, "main", "main")
-  expect_error({
-    cdm$person <- cdm$person %>%
-       dplyr::select(-"person_id")
-  })
+
+  expect_no_error(cdm$person %>%
+                 dplyr::select(-"person_id"))
+  # but we can't assign it to the cdm
+  expect_error(cdm$person <- cdm$person %>%
+    dplyr::select(-"person_id"))
+
+  cdm$person <- cdm$person %>%
+    dplyr::select(-"ethnicity_source_concept_id")
+  expect_error(assertTables(cdm = cdm, tables = c("person"), add = err3), NA)
+  expect_length(err3$getMessages(), 1) # missing column
+  expect_error(assertTables(cdm = cdm, tables = c("person"), add = NULL)) # without error collection
 
   # use in a function (i.e. the typical use case)
   countDrugsByGender <- function(cdm) {

diff --git a/vignettes/a02_cohorts.Rmd b/vignettes/a02_cohorts.Rmd
@@ -310,7 +310,7 @@ cdm$cohort
 To make this a true generated cohort object use the `cohort_table`
 
 ```{r}
-cdm$cohort <- cohortTable(cdm$cohort)
+cdm$cohort <- newCohortTable(cdm$cohort)
 ```
 
 We can see that this cohort is now has the class "cohort_table" as well as the various metadata tables.
@@ -324,12 +324,12 @@ If you would like to override the attribute tables then pass additional datafram
 
 ```{r}
 cdm <- insertTable(cdm = cdm, name = "cohort2", table = cohort, overwrite = TRUE)
-cdm$cohort2 <- cohortTable(cdm$cohort2)
+cdm$cohort2 <- newCohortTable(cdm$cohort2)
 settings(cdm$cohort2)
 
 cohort_set <- data.frame(cohort_definition_id = 1L,
                          cohort_name = "made_up_cohort")
-cdm$cohort2 <- cohortTable(cdm$cohort2, cohortSetRef = cohort_set)
+cdm$cohort2 <- newCohortTable(cdm$cohort2, cohortSetRef = cohort_set)
 
 settings(cdm$cohort2)
 ```

diff --git a/vignettes/a06_using_cdm_attributes.Rmd b/vignettes/a06_using_cdm_attributes.Rmd
@@ -154,7 +154,7 @@ We can add the required attributes using the `newGeneratedCohortSet` function. T
 ```{r}
 GI_bleed_cohort_ref <- tibble(cohort_definition_id = 1, cohort_name = "custom_gi_bleed")
 
-cdm$gi_bleed <- omopgenerics::cohortTable(
+cdm$gi_bleed <- omopgenerics::newCohortTable(
   table = cdm$gi_bleed, cohortSetRef = GI_bleed_cohort_ref
 )
 ```