added a function getConceptIdDetails

#5

.gitignore

@@ -1,3 +1,5 @@
 .Rproj.user
 inst/doc
 .DS_Store
+errorReportSql.txt
+*.log

NAMESPACE

@@ -73,6 +73,7 @@ export(createVisitOccurrence)
 export(createVisitSourceConceptAttribute)
 export(createVisitTypeExcludeAttribute)
 export(createWindow)
+export(getConceptIdDetails)
 export(getConceptSetExpression)
 export(getConceptSetId)
 export(listAttributeOptions)
@@ -86,6 +87,8 @@ export(readInCirce)
 export(saveComponent)
 export(toggleConceptMapping)
 export(writeCaprCall)
+import(DatabaseConnector)
+import(dplyr)
 import(methods)
 importFrom(CirceR,buildCohortQuery)
 importFrom(CirceR,cohortExpressionFromJson)
@@ -107,6 +110,7 @@ importFrom(purrr,map2)
 importFrom(purrr,map_int)
 importFrom(rlang,"!!!")
 importFrom(rlang,"!!")
+importFrom(rlang,.data)
 importFrom(rlang,call2)
 importFrom(rlang,expr)
 importFrom(rlang,sym)

R/userConceptLookupFn.R

@@ -14,7 +14,55 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-#
+
+
+
+#' get concept id details
+#'
+#' For one or more concept id, get concept id details by querying the
+#' OMOP vocabulary in the database.
+#'
+#' @template     Connection
+#' @template     VocabularyDatabaseSchema
+#' @template     OracleTempSchema
+#' @param        conceptIds a vector of concept ids
+#' @return       a tibble data frame object with conceptId, conceptName, standardConcept,
+#'               standardConceptCaption, invalidReason, invalidReasonCaption, conceptCode,
+#'               domainId, vocabularyId, conceptClassId.
+#'
+#' @export
+getConceptIdDetails <- function(conceptIds,
+                                connectionDetails = NULL,
+                                connection = NULL,
+                                vocabularyDatabaseSchema = NULL,
+                                oracleTempSchema = NULL) {
+
+  errorMessage <- checkmate::makeAssertCollection()
+  checkmate::assertVector(conceptIds, add = errorMessage)
+  checkmate::reportAssertions(collection = errorMessage)
+
+  # Set up connection to server ----------------------------------------------------
+  if (is.null(connection)) {
+    if (!is.null(connectionDetails)) {
+      connection <- DatabaseConnector::connect(connectionDetails)
+      on.exit(DatabaseConnector::disconnect(connection))
+    } else {
+      stop("No connection or connectionDetails provided.")
+    }
+  }
+
+  conceptQuery <- "SELECT * FROM @vocabularyDatabaseSchema.concept WHERE concept_id IN (@conceptId);"
+  conceptDetails <- DatabaseConnector::renderTranslateQuerySql(connection = connection,
+                                                               sql = conceptQuery,
+                                                               snakeCaseToCamelCase = TRUE,
+                                                               vocabularyDatabaseSchema = vocabularyDatabaseSchema,
+                                                               oracleTempSchema = oracleTempSchema,
+                                                               conceptId = conceptIds) %>%
+    dplyr::tibble()
+  return(conceptDetails)
+}
+
+
 ##' Lookup Concepts by OMOP Concept Id
 #'
 #' This function looks up concepts using the OMOP concept id. Function requires a dbms connection to use

man-roxygen/Connection.R

@@ -0,0 +1,9 @@
+#' @param connectionDetails   An object of type \code{connectionDetails} as created using the
+#'                            \code{\link[DatabaseConnector]{createConnectionDetails}} function in the
+#'                            DatabaseConnector package. Can be left NULL if \code{connection} is
+#'                            provided.
+#' @param connection          An object of type \code{connection} as created using the
+#'                            \code{\link[DatabaseConnector]{connect}} function in the
+#'                            DatabaseConnector package. Can be left NULL if \code{connectionDetails}
+#'                            is provided, in which case a new connection will be opened at the start
+#'                            of the function, and closed when the function finishes.

man-roxygen/OracleTempSchema.R

@@ -0,0 +1,2 @@
+#' @param oracleTempSchema   Should be used in Oracle to specify a schema where the user has write
+#'                           privileges for storing temporary tables.

man-roxygen/VocabularyDatabaseSchema.R

@@ -0,0 +1,3 @@
+#' @param vocabularyDatabaseSchema   Schema name where your OMOP vocabulary format resides.
+#'                                   Note that for SQL Server, this should include both the database and
+#'                                   schema name, for example 'vocabulary.dbo'.