Development

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ROMOPAPI
 Title: ROMOPAPI
-Version: 2.0.0
+Version: 2.1.0
 Authors@R: 
     person("Javier", "Gracia-Tabuenca", , "javier.graciatabuenca@tuni.fi", role = c("aut", "cre"),
            comment = c(ORCID = "YOUR-ORCID-ID"))

Dockerfile

@@ -22,7 +22,7 @@ RUN apt-get update && apt-get install -y openjdk-8-jdk liblzma-dev libbz2-dev li
 
 # Install renv and restore packages
 ARG ROMOPAPI_BRANCH=main
-ARG BUILD_CACHE_BUSTER=1
+ARG BUILD_CACHE_BUSTER=2
 
 # Install renv and restore packages
 RUN --mount=type=secret,id=build_github_pat \

NAMESPACE

@@ -13,7 +13,7 @@ export(createReport)
 export(createStratifiedCodeCountsTable)
 export(create_api)
 export(fct_setUpLogger)
-export(getCDMSource)
+export(getAPIInfo)
 export(getCodeCounts)
 export(getCodeCounts_memoise)
 export(getConceptsWithCodeCounts)

NEWS.md

@@ -1,3 +1,8 @@
+# ROMOPAPI 2.1.0
+- Added getAPIInfo endpoint to API
+- Updated db with large tree
+- Fixed error in getCodeCounts when conceptId was the root of the tree
+
 # ROMOPAPI 2.0.0
 - Updated to use DatabaseConnector v7
 

R/getCDMSource.R → R/getAPIInfo.R

@@ -1,10 +1,9 @@
-
-#' Get the CDM source information
+#' Get the API information
 #'
 #' @description
 #' Retrieves the CDM source information from the vocabulary schema of an OMOP CDM database.
-#' This includes metadata about the database source, version, and other administrative details.
-#'
+#' Retrieves the API information from the vocabulary schema of an OMOP CDM database.
+#' This includes metadata about the API, version, and other administrative details.
 #' @param CDMdbHandler A CDMdbHandler object that contains database connection details
 #'
 #' @return A tibble containing the CDM source information with columns from the cdm_source table
@@ -16,9 +15,9 @@
 #'
 #' @export
 #'
-getCDMSource <- function(
+getAPIInfo <- function(
     CDMdbHandler) {
-    ParallelLogger::logInfo("getCDMSource: Getting CDM source information")
+    ParallelLogger::logInfo("getAPIInfo: Getting API information")
     #
     # VALIDATE
     #
@@ -39,5 +38,12 @@ getCDMSource <- function(
         vocabularyDatabaseSchema = vocabularyDatabaseSchema
     ) |> tibble::as_tibble()
 
-    return(cdm_source)
+    info <- list(
+        cdm_source_name = cdm_source$cdm_source_name,
+        cdm_source_abbreviation = cdm_source$cdm_source_abbreviation,
+        vocabulary_version = cdm_source$vocabulary_version,
+        romop_api_version = as.character(utils::packageVersion("ROMOPAPI"))
+    )
+
+    return(info)
 }

R/getCodeCounts.R

@@ -106,7 +106,9 @@ getCodeCounts <- function(
     )
     -- take only parents who are someones children, or are the parents  of the concept id
     SELECT * FROM temp_tree tt
-    WHERE parent_concept_id IN (SELECT DISTINCT child_concept_id FROM temp_tree ) OR child_concept_id IN (@conceptId)
+    WHERE parent_concept_id IN (SELECT DISTINCT child_concept_id FROM temp_tree ) OR 
+      child_concept_id IN (@conceptId) OR
+      parent_concept_id IN (@conceptId) -- when concept is top in tree
     "
 
     # Gets tree of descendants and the code counts for each descendant
@@ -173,7 +175,9 @@ getCodeCounts <- function(
             dplyr::distinct(concept_id, maps_to_concept_id) |>
             dplyr::rename(maps_to_concept_id = concept_id, concept_id = maps_to_concept_id) |>
             dplyr::mutate(levels = "Maps to")
-    )
+    ) |> 
+    # If concept maps to itself, bcs concept in concept and source concept columns, dont take it
+    dplyr::filter(concept_id != maps_to_concept_id)
 
     familyTreeWithMappings <- dplyr::bind_rows(
         familyTreeWithInfo,
@@ -194,7 +198,9 @@ getCodeCounts <- function(
         codeCounts |> dplyr::select(-maps_to_concept_id) |> 
             dplyr::group_by(concept_id, calendar_year, gender_concept_id, age_decile) |>
             dplyr::summarise(record_counts = sum(record_counts), .groups = "drop")
-    ) 
+    )  |> 
+    # If concept maps to itself, bcs concept in concept and source concept columns, dont take it
+    dplyr::distinct()
 
     familyTreeDescendants <- familyTreeWithMappings |>
         dplyr::filter(!levels %in% c("Mapped from", "Maps to", "-1", "0")) |>

R/helper.R

@@ -237,6 +237,23 @@ helper_createSqliteDatabaseFromDatabase <- function(
     tempTable = FALSE,
   )
 
+  # get CDMsource 
+  sql <- "SELECT DISTINCT c.* FROM @vocabularyDatabaseSchema.cdm_source c"
+  cdmSource <- DatabaseConnector::renderTranslateQuerySql(
+    connection = sourceConnection,
+    sql = sql,
+    vocabularyDatabaseSchema = sourceVocabularyDatabaseSchema
+  ) |>
+    tibble::as_tibble()
+
+  targetConnection |> DatabaseConnector::insertTable(
+    tableName = "cdm_source",
+    data = cdmSource,
+    dropTableIfExists = TRUE,
+    createTable = TRUE,
+    tempTable = FALSE,
+  )
+
   # disconnect
   targetConnection |> DatabaseConnector::disconnect()
   sourceConnection |> DatabaseConnector::disconnect()

inst/plumber/plumber.R

@@ -45,10 +45,10 @@ function(res, conceptId=0L) {
 }
 
 
-#* Get the CDM source information
-#* @get /getCDMSource
+#* Get the API information
+#* @get /getAPIInfo
 function() {
-  getCDMSource(
+  getAPIInfo(
     CDMdbHandler = CDMdbHandler
   )
 }

inst/testdata/data/createTestingData.R

@@ -8,8 +8,8 @@ conceptIds <- c(
     317009, # Snomed: Asthma
     45596282, # ICD10: Asthma
     21601855, # ATC level 4: C10AA (Statins)
-    #2010001615, # test endpoint
-    320136 # Big graph, parent of Asthma snomed concept (Disorders of the respiratory system)
+    320136, # Big graph, parent of Asthma snomed concept (Disorders of the respiratory system)
+    4024567# biger
 )
 
 CDMdbHandler <- HadesExtras_createCDMdbHandlerFromList(test_cohortTableHandlerConfig, loadConnectionChecksLevel = "basicChecks")
@@ -25,7 +25,7 @@ connection  <- DatabaseConnector::connect(DatabaseConnector::createConnectionDet
 
 DatabaseConnector::dbListTables(connection) |> 
     sort() |>
-    expect_equal(c("code_counts", "concept", "concept_ancestor", "stratified_code_counts"))
+    expect_equal(c("cdm_source", "code_counts", "concept", "concept_ancestor", "stratified_code_counts"))
 
 dplyr::tbl(connection, "concept") |>
     dplyr::count() |>
@@ -47,3 +47,8 @@ dplyr::tbl(connection, "stratified_code_counts") |>
     dplyr::pull(n) |>
     expect_gt(0)
 
+dplyr::tbl(connection, "cdm_source") |>
+    dplyr::count() |>
+    dplyr::pull(n) |>
+    expect_gt(0)
+

tests/testmanual/manualtest-timeplotview.R

@@ -17,7 +17,7 @@ conceptId <- 782748
 
 conceptId <- 21602735
 
-conceptId <- 2010001615 # test endpoint
+conceptId <- 2010001618 # test endpoint
 
 
 results <- getCodeCounts(

tests/testthat/test-getAPIInfo.R

@@ -0,0 +1,20 @@
+# create test for getCDMSource
+
+test_that("getAPIInfo works", {
+  # only works in a full CDM databas
+
+  CDMdbHandler <- HadesExtras_createCDMdbHandlerFromList(test_cohortTableHandlerConfig, loadConnectionChecksLevel = "basicChecks")
+  withr::defer({
+    CDMdbHandler <- NULL
+    gc()
+  })
+
+  api_info <- getAPIInfo(CDMdbHandler)
+
+  # Check column names 
+  api_info |> names() |>
+    expect_equal(c("cdm_source_name", "cdm_source_abbreviation", "vocabulary_version", "romop_api_version"))
+   api_info$romop_api_version |>
+    expect_equal(as.character(utils::packageVersion("ROMOPAPI")))
+
+})