deprecate search_datasets

R/deprecation.R

@@ -90,8 +90,8 @@ get_taxon_datasets <- function(taxon,
                                raw = getOption("gemma.raw",FALSE), 
                                memoised = getOption("gemma.memoised", FALSE),
                                file = getOption("gemma.file",NA_character_),
-                               overwrite = getOption("gemma.overwrite",FALSE)){
-    warning('get_taxon_datasets is deprecated, please use get_datasets instead')
+                               overwrite = getOption("gemma.overwrite",FALSE),...){
+    warning('get_taxon_datasets is deprecated. please use get_datasets instead')
 
     get_datasets(taxa = taxon,
                  offset = offset,
@@ -102,3 +102,76 @@ get_taxon_datasets <- function(taxon,
                  file = file,
                  overwrite = overwrite)
 }
+
+
+#' Retrieve datasets associated to an annotation tags search
+#'
+#' This function is deprecated in favor of \code{\link{get_datasets}}
+#'
+#' @param query The search query. Either plain text ('traumatic'), or an ontology term URI ('http://purl.obolibrary.org/obo/UBERON_0002048'). Datasets that contain the given string in their short
+#' or full name will also be matched. Can be multiple identifiers separated by commas.
+#' @param taxon Can either be Taxon ID, Taxon NCBI ID, or one of its string identifiers: scientific name, common name.
+#' It is recommended to use Taxon ID for efficiency.
+#' Please note, that not all taxa have all the possible identifiers available.
+#' Use the \code{\link{get_taxa_by_ids}} function to retrieve the necessary information. For convenience, below is a list of officially supported taxa:
+#' \tabular{rllr}{
+#' \strong{ID} \tab \strong{Comm.name} \tab \strong{Scient.name}    \tab \strong{NcbiID}\cr
+#' 1            \tab human               \tab Homo sapiens             \tab 9606            \cr
+#' 2            \tab mouse               \tab Mus musculus             \tab 10090           \cr
+#' 3            \tab rat                 \tab Rattus norvegicus        \tab 10116           \cr
+#' 11           \tab yeast               \tab Saccharomyces cerevisiae \tab 4932            \cr
+#' 12           \tab zebrafish           \tab Danio rerio              \tab 7955            \cr
+#' 13           \tab fly                 \tab Drosophila melanogaster  \tab 7227            \cr
+#' 14           \tab worm                \tab Caenorhabditis elegans   \tab 6239
+#' }
+#' @param offset The offset of the first retrieved result.
+#' @param limit Optional, defaults to 20. Limits the result to specified amount
+#' of objects. Has a maximum value of 100. Use together with \code{offset} and
+#' the \code{totalElements} \link[base:attributes]{attribute} in the output to
+#' compile all data if needed.
+#' @param sort Order results by the given property and direction. The '+' sign indicate ascending order whereas the '-' indicate descending.
+#' @param raw \code{TRUE} to receive results as-is from Gemma, or \code{FALSE} to enable
+#' parsing. Raw results usually contain additional fields and flags that are
+#' omitted in the parsed results.
+#' @param memoised Whether or not to save to cache for future calls with the
+#' same inputs and use the result saved in cache if a result is already saved.
+#' Doing \code{options(gemma.memoised = TRUE)} will ensure that the cache is always
+#' used. Use \code{\link{forget_gemma_memoised}} to clear the cache.
+#' @param file The name of a file to save the results to, or \code{NULL} to not write
+#' results to a file. If \code{raw == TRUE}, the output will be a JSON file. Otherwise,
+#' it will be a RDS file.
+#' @param overwrite Whether or not to overwrite if a file exists at the specified
+#' filename.
+#' @param attributes If \code{TRUE} additional information from the call will be added
+#' into the output object's attributes such as offset and available elements.
+#'
+#' @inherit processDatasets return
+#' @export
+#'
+#'
+#' @examples
+#' search_datasets("bipolar", taxon = "human")
+search_datasets <- function(query, taxon = NA_character_, 
+                            offset = 0L, 
+                            limit = 20L,
+                            sort = "+id",
+                            raw = getOption("gemma.raw", FALSE), memoised = getOption(
+                                "gemma.memoised",
+                                FALSE
+                            ),
+                            file = getOption("gemma.file", NA_character_),
+                            overwrite = getOption("gemma.overwrite", FALSE), attributes = getOption(
+                                "gemma.attributes",
+                                TRUE
+                            ),...){
+    warning("search_datasets is deprecated. please use get_datasets instead")
+
+    get_datasets(query = query,
+                 taxa = taxon,
+                 limit = limit,
+                 sort = sort,
+                 offset = offset,
+                 raw = raw,
+                 file = file,
+                 overwrite = overwrite)
+}