uodated to v7 and checked

DESCRIPTION

@@ -9,7 +9,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 Language: en
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 URL: https://github.com/javier-gracia-tabuenca-tuni/ROMOPAPI
 BugReports: https://github.com/javier-gracia-tabuenca-tuni/ROMOPAPI/issues
 Imports:
@@ -35,6 +35,8 @@ Imports:
     ResultModelManager,
     yaml,
     stringr
+Remotes:
+    javier-gracia-tabuenca-tuni/DatabaseConnector@bigquery-DBI-2
 Suggests: 
     testthat (>= 3.0.0),
     bigrquery,

Dockerfile

@@ -21,15 +21,15 @@ RUN apt-get update && apt-get install -y openjdk-8-jdk liblzma-dev libbz2-dev li
 && rm -rf /var/lib/apt/lists/*
 
 # Install renv and restore packages
-ARG ROMOPAPI_BRANCH=master
+ARG ROMOPAPI_BRANCH=main
 ARG BUILD_CACHE_BUSTER=1
 
 # Install renv and restore packages
 RUN --mount=type=secret,id=build_github_pat \
     cp /usr/local/lib/R/etc/Renviron /tmp/Renviron \
     && echo "GITHUB_PAT=$(cat /run/secrets/build_github_pat)" >> /usr/local/lib/R/etc/Renviron \
     && Rscript -e 'install.packages("remotes")' \
-    && Rscript -e 'remotes::install_github("FINNGEN/ROMOPAPI@${ROMOPAPI_BRANCH}")' \
+    && Rscript -e 'remotes::install_github("FINNGEN/ROMOPAPI")' \
     && cp /tmp/Renviron /usr/local/lib/R/etc/Renviron;
 
 # Expose the port that the API will run on

NAMESPACE

@@ -25,10 +25,10 @@ export(runApiServer)
 importFrom(DatabaseConnector,connect)
 importFrom(DatabaseConnector,createConnectionDetails)
 importFrom(DatabaseConnector,createDbiConnectionDetails)
-importFrom(DatabaseConnector,dbGetQuery)
 importFrom(DatabaseConnector,disconnect)
 importFrom(DatabaseConnector,executeSql)
 importFrom(DatabaseConnector,insertTable)
+importFrom(DatabaseConnector,renderTranslateQuerySql)
 importFrom(DiagrammeR,mermaid)
 importFrom(Eunomia,extractLoadData)
 importFrom(R6,R6Class)

R/getCDMSource.R

@@ -11,7 +11,7 @@
 #'
 #' @importFrom checkmate assertClass
 #' @importFrom SqlRender render translate
-#' @importFrom DatabaseConnector dbGetQuery
+#' @importFrom DatabaseConnector renderTranslateQuerySql
 #' @importFrom tibble as_tibble
 #'
 #' @export
@@ -33,9 +33,11 @@ getCDMSource <- function(
     #
 
     sql <- "SELECT * FROM @vocabularyDatabaseSchema.cdm_source;"
-    sql <- SqlRender::render(sql, vocabularyDatabaseSchema = vocabularyDatabaseSchema)
-    sql <- SqlRender::translate(sql, targetDialect = connection@dbms)
-    cdm_source <- DatabaseConnector::dbGetQuery(connection, sql) |> tibble::as_tibble()
+    cdm_source <- DatabaseConnector::renderTranslateQuerySql(
+        connection = connection,
+        sql = sql,
+        vocabularyDatabaseSchema = vocabularyDatabaseSchema
+    ) |> tibble::as_tibble()
 
     return(cdm_source)
 }

R/getCodeCounts.R

@@ -18,7 +18,7 @@
 #'
 #' @importFrom checkmate assertClass assertIntegerish
 #' @importFrom SqlRender render translate
-#' @importFrom DatabaseConnector dbGetQuery
+#' @importFrom DatabaseConnector renderTranslateQuerySql
 #' @importFrom tibble as_tibble
 #' @importFrom dplyr pull bind_rows
 #'
@@ -109,18 +109,16 @@ getCodeCounts <- function(
     WHERE parent_concept_id IN (SELECT DISTINCT child_concept_id FROM temp_tree ) OR child_concept_id IN (@conceptId)
     "
 
-    sql <- SqlRender::render(
-        sql,
+    # Gets tree of descendants and the code counts for each descendant
+    familyTree <- DatabaseConnector::renderTranslateQuerySql(
+        connection = connection,
+        sql = sql,
         vocabularyDatabaseSchema = vocabularyDatabaseSchema,
         conceptId = conceptId,
         resultsDatabaseSchema = resultsDatabaseSchema,
         stratifiedCodeCountsTable = stratifiedCodeCountsTable
-    )
-    sql <- SqlRender::translate(sql, targetDialect = connection@dbms)
-
-    # Gets tree of descendants and the code counts for each descendant
-    familyTree <- DatabaseConnector::dbGetQuery(connection, sql) |>
-        tibble::as_tibble()
+    ) |>
+    tibble::as_tibble()
 
     if (nrow(familyTree) == 0) {
         stop("No family tree found for conceptId: ", conceptId)
@@ -157,14 +155,13 @@ getCodeCounts <- function(
 
     # - Get counts and derive 'Maps to' and 'Mapped from' from that
     sql <- "SELECT * FROM @resultsDatabaseSchema.@stratifiedCodeCountsTable WHERE concept_id IN (@conceptIds) OR maps_to_concept_id IN (@conceptIds);"
-    sql <- SqlRender::render(
-        sql,
+    codeCounts <- DatabaseConnector::renderTranslateQuerySql(
+        connection = connection,
+        sql = sql,
         resultsDatabaseSchema = resultsDatabaseSchema,
         conceptIds = paste(conceptIdsToGetCounts, collapse = ","),
         stratifiedCodeCountsTable = stratifiedCodeCountsTable
-    )
-    sql <- SqlRender::translate(sql, targetDialect = connection@dbms)
-    codeCounts <- DatabaseConnector::dbGetQuery(connection, sql) |>
+    ) |>
         tibble::as_tibble()
 
     # - Derive 'Maps to' and 'Mapped from'

R/getConceptsWithCodeCounts.R

@@ -19,7 +19,7 @@
 #'
 #' @importFrom checkmate assertClass
 #' @importFrom SqlRender render translate
-#' @importFrom DatabaseConnector dbGetQuery
+#' @importFrom DatabaseConnector renderTranslateQuerySql
 #' @importFrom tibble as_tibble
 #' @importFrom dplyr mutate if_else
 #'
@@ -49,9 +49,13 @@ getConceptsWithCodeCounts <- function(
        FROM @vocabularyDatabaseSchema.concept c
        INNER JOIN @resultsDatabaseSchema.@codeCountsTable cc
        ON c.concept_id = cc.concept_id;"
-    sql <- SqlRender::render(sql, vocabularyDatabaseSchema = vocabularyDatabaseSchema, resultsDatabaseSchema = resultsDatabaseSchema, codeCountsTable = codeCountsTable)
-    sql <- SqlRender::translate(sql, targetDialect = connection@dbms)
-    concepts <- DatabaseConnector::dbGetQuery(connection, sql) |>
+    concepts <- DatabaseConnector::renderTranslateQuerySql(
+        connection = connection,
+        sql = sql,
+        vocabularyDatabaseSchema = vocabularyDatabaseSchema,
+        resultsDatabaseSchema = resultsDatabaseSchema,
+        codeCountsTable = codeCountsTable
+    ) |>
         tibble::as_tibble() |>
         dplyr::mutate(standard_concept = dplyr::if_else(is.na(standard_concept), FALSE, TRUE)) |> 
         dplyr::mutate(concept_id = as.double(concept_id))

R/helper.R

@@ -118,8 +118,7 @@ helper_FinnGen_getDatabaseFileCounts <- function() {
 #' @return No return value. Creates a new SQLite database file at the specified path.
 #'
 #' @importFrom checkmate assertClass assertString
-#' @importFrom DatabaseConnector createConnectionDetails connect disconnect insertTable dbGetQuery
-#' @importFrom SqlRender render translate
+#' @importFrom DatabaseConnector createConnectionDetails connect disconnect insertTable renderTranslateQuerySql
 #' @importFrom tibble as_tibble
 #'
 #' @export
@@ -162,13 +161,13 @@ helper_createSqliteDatabaseFromDatabase <- function(
   # Get concept table
   sql <- "SELECT DISTINCT c.* FROM @vocabularyDatabaseSchema.concept c
           WHERE c.concept_id IN (@conceptIdsToExtract)"
-  sql <- SqlRender::render(
-    sql,
+
+  concept <- DatabaseConnector::renderTranslateQuerySql(
+    connection = sourceConnection,
+    sql = sql,
     vocabularyDatabaseSchema = sourceVocabularyDatabaseSchema,
     conceptIdsToExtract = paste(conceptIdsToExtract, collapse = ",")
-  )
-  sql <- SqlRender::translate(sql, targetDialect = sourceConnection@dbms)
-  concept <- DatabaseConnector::dbGetQuery(sourceConnection, sql) |>
+  ) |>
     tibble::as_tibble()
 
   targetConnection |> DatabaseConnector::insertTable(
@@ -182,13 +181,12 @@ helper_createSqliteDatabaseFromDatabase <- function(
   # Concept ancestor table
   sql <- "SELECT DISTINCT ca.* FROM @vocabularyDatabaseSchema.concept_ancestor ca
          WHERE ca.descendant_concept_id IN (@conceptIdsToExtract) "
-  sql <- SqlRender::render(
-    sql,
+  conceptAncestor <- DatabaseConnector::renderTranslateQuerySql(
+    connection = sourceConnection,
+    sql = sql,
     vocabularyDatabaseSchema = sourceVocabularyDatabaseSchema,
     conceptIdsToExtract = paste(conceptIdsToExtract, collapse = ",")
-  )
-  sql <- SqlRender::translate(sql, targetDialect = sourceConnection@dbms)
-  conceptAncestor <- DatabaseConnector::dbGetQuery(sourceConnection, sql) |>
+  ) |>
     tibble::as_tibble()
 
   targetConnection |> DatabaseConnector::insertTable(
@@ -202,14 +200,13 @@ helper_createSqliteDatabaseFromDatabase <- function(
   # Code counts table
   sql <- "SELECT DISTINCT cc.* FROM @resultsDatabaseSchema.@codeCountsTable cc
          WHERE cc.concept_id IN (@conceptIdsToExtract)"
-  sql <- SqlRender::render(
-    sql,
+  codeCounts <- DatabaseConnector::renderTranslateQuerySql(
+    connection = sourceConnection,
+    sql = sql,
     resultsDatabaseSchema = sourceResultsDatabaseSchema,
     conceptIdsToExtract = paste(conceptIdsToExtract, collapse = ","),
     codeCountsTable = codeCountsTable
-  )
-  sql <- SqlRender::translate(sql, targetDialect = sourceConnection@dbms)
-  codeCounts <- DatabaseConnector::dbGetQuery(sourceConnection, sql) |>
+  ) |>
     tibble::as_tibble()
 
   targetConnection |> DatabaseConnector::insertTable(
@@ -223,13 +220,13 @@ helper_createSqliteDatabaseFromDatabase <- function(
   # stratified code counts table
   sql <- "SELECT DISTINCT cc.* FROM @resultsDatabaseSchema.@stratifiedCodeCountsTable cc
          WHERE cc.concept_id IN (@conceptIdsToExtract) OR cc.maps_to_concept_id IN (@conceptIdsToExtract)"
-  sql <- SqlRender::render(sql,
+  stratifiedCodeCounts <- DatabaseConnector::renderTranslateQuerySql(
+    connection = sourceConnection,
+    sql = sql,
     resultsDatabaseSchema = sourceResultsDatabaseSchema,
     conceptIdsToExtract = paste(conceptIdsToExtract, collapse = ","),
     stratifiedCodeCountsTable = paste0("stratified_", codeCountsTable)
-  )
-  sql <- SqlRender::translate(sql, targetDialect = sourceConnection@dbms)
-  stratifiedCodeCounts <- DatabaseConnector::dbGetQuery(sourceConnection, sql) |>
+  ) |>
     tibble::as_tibble()
 
   targetConnection |> DatabaseConnector::insertTable(