# Copyright 2022 Observational Health Data Sciences and Informatics
#
# This file is part of ConceptSetDiagnostics
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
#' Given a concept set expression, get the resolved concepts
#'
#' @description
#' Given a concept set expression, get the resolved concepts
#'
#' @template Connection
#'
#' @template ConceptSetExpression
#'
#' @template VocabularyDatabaseSchema
#'
#' @template TempEmulationSchema
#'
#' @return
#' Returns a tibble data frame.
#'
#' @export
getExcludedConceptsInConceptSetExpression <-
function(conceptSetExpression,
connection = NULL,
connectionDetails = NULL,
tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
vocabularyDatabaseSchema = "vocabulary") {
if (is.null(connection)) {
connection <- DatabaseConnector::connect(connectionDetails)
on.exit(DatabaseConnector::disconnect(connection))
}
conceptSetDataFrame <-
convertConceptSetExpressionToDataFrame(conceptSetExpression = conceptSetExpression)
if (!"isExcluded" %in% colnames(conceptSetDataFrame)) {
return(NULL)
}
excludeRows <- conceptSetDataFrame %>%
dplyr::filter(.data$isExcluded == TRUE)
excludeRowsDescendants <- excludeRows %>%
dplyr::filter(.data$includeDescendants == TRUE)
excludeRowsNoDescendants <- excludeRows %>%
dplyr::filter(.data$includeDescendants == FALSE)
excludeConceptIdsWithDescendants <-
getConceptDescendant(
conceptIds = excludeRowsDescendants$conceptId,
connection = connection,
vocabularyDatabaseSchema = vocabularyDatabaseSchema,
tempEmulationSchema = tempEmulationSchema
)
allExcludedConceptIds <-
dplyr::bind_rows(
excludeConceptIdsWithDescendants %>%
dplyr::select(.data$descendantConceptId) %>%
dplyr::rename("conceptId" = .data$descendantConceptId),
excludeRowsNoDescendants %>% dplyr::select(.data$conceptId)
) %>%
dplyr::distinct() %>%
dplyr::arrange(.data$conceptId)
data <-
getConceptIdDetails(
conceptIds = allExcludedConceptIds$conceptId %>% unique(),
connection = connection,
vocabularyDatabaseSchema = vocabularyDatabaseSchema
)
return(data)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.