Merge branch 'master' into installations

Author: jhnwllr

DESCRIPTION

@@ -8,7 +8,7 @@ Description: A programmatic interface to the Web Service methods
     retrieving information on data providers, getting species occurrence
     records, getting counts of occurrence records, and using the GBIF
     tile map service to make rasters summarizing huge amounts of data.
-Version: 3.8.2.3
+Version: 3.8.2.4
 License: MIT + file LICENSE
 Authors@R: c(
     person("Scott", "Chamberlain", role = "aut", comment = c("0000-0003-1444-9135")),
@@ -50,7 +50,7 @@ Suggests:
     magick,
     protolite (>= 2.0),
     sf,
-    vcr (>= 1.2.0),
+    vcr (>= 2.0.0),
     knitr,
     rmarkdown,
     bit64

NAMESPACE

@@ -29,6 +29,8 @@ export(GbifQueue)
 export(as.download)
 export(blanktheme)
 export(check_wkt)
+export(collection_export)
+export(collection_search)
 export(count_facet)
 export(dataset)
 export(dataset_comment)
@@ -78,6 +80,8 @@ export(installation_machinetag)
 export(installation_search)
 export(installation_tag)
 export(installations)
+export(institution_export)
+export(institution_search)
 export(lit_count)
 export(lit_export)
 export(lit_search)

R/collection_search.R

@@ -0,0 +1,320 @@
+#' Search GRSciColl collections
+#'
+#' @param query Simple full text search parameter. The value for this parameter 
+#' can be a simple word or a phrase. Wildcards are not supported.
+#' @param name Name of a GrSciColl institution or collection.
+#' @param fuzzyName It searches by name fuzzily so the parameter doesn't have 
+#' to be the exact name.
+#' @param preservationType Preservation type of a GrSciColl collection. Accepts 
+#' multiple values.
+#' @param contentType Content type of a GrSciColl collection. See here for 
+#' accepted values : 
+#' https://techdocs.gbif.org/en/openapi/v1/registry#/Collections/listCollections
+#' @param numberSpecimens Number of specimens. It supports ranges and a `*` can 
+#' be used as a wildcard.
+#' @param accessionStatus Accession status of a GrSciColl collection. Accepted 
+#' values : INSTITUTIONAL, PROJECT
+#' @param personalCollection Flag for personal GRSciColl collections.
+#' @param sourceId sourceId of MasterSourceMetadata.
+#' @param source Source attribute of MasterSourceMetadata. Accepted values : 
+#' DATASET, ORGANIZATION, IH_IRN
+#' @param code Code of a GrSciColl institution or collection.
+#' @param alternativeCode Alternative code of a GrSciColl institution or 
+#' collection.
+#' @param contact Filters collections and institutions whose contacts contain 
+#' the person key specified.
+#' @param institutionKey Keys of institutions to filter by.
+#' @param country Filters by country given as a ISO 639-1 (2 letter) country 
+#' code.
+#' @param city Filters by the city of the address. It searches in both the 
+#' physical and the mailing address.
+#' @param gbifRegion Filters by a gbif region
+#' Available values : AFRICA, ASIA, EUROPE, NORTH_AMERICA, OCEANIA, 
+#' LATIN_AMERICA, ANTARCTICA.
+#' @param machineTagNamespace Filters for entities with a machine tag in the 
+#' specified namespace.
+#' @param machineTagName Filters for entities with a machine tag with the 
+#' specified name (use in combination with the machineTagNamespace parameter).
+#' @param machineTagValue Filters for entities with a machine tag with the 
+#' specified value (use in combination with the machineTagNamespace and 
+#' machineTagName parameters).
+#' @param identifier An identifier of the type given by the identifierType 
+#' parameter, for example a DOI or UUID.
+#' @param identifierType An identifier type for the identifier parameter. 
+#' Available values : URL, LSID, HANDLER, DOI, UUID, FTP, URI, UNKNOWN, 
+#' GBIF_PORTAL, GBIF_NODE, GBIF_PARTICIPANT, GRSCICOLL_ID, GRSCICOLL_URI, 
+#' IH_IRN, ROR, GRID, CITES, SYMBIOTA_UUID, WIKIDATA, NCBI_BIOCOLLECTION, 
+#' ISIL, CLB_DATASET_KEY.
+#' @param active Active status of a GrSciColl institution or collection.
+#' @param displayOnNHCPortal Flag to show this record in the NHC portal.
+#' @param alternativeCode Alternative code of a GrSciColl institution or 
+#' collection.
+#' @param masterSourceType The master source type of a GRSciColl institution. 
+#' or collection. Available values : GRSCICOLL, GBIF_REGISTRY, IH.
+#' @param replacedBy Key of the entity that replaced another entity.
+#' @param sortBy Field to sort the results by. It only supports the fields 
+#' contained in the enum. Available values : NUMBER_SPECIMENS.
+#' @param sortOrder Sort order to use with the sortBy parameter. 
+#' Available values : ASC, DESC.
+#' @param offset Determines the offset for the search results.
+#' @param limit Controls the number of results in the page. Default 20. 
+#' @param format (character) Format of the export. Default is "TSV". 
+#' Only used for [collection_export].
+#' @param curlopts curlopts options passed on to [crul::HttpClient]. 
+#' 
+#' @details Will return GRSciColl collections data. [collection_export] will 
+#' return all of the results in a single `tibble`, while [collection_search] will 
+#' return a sample of results. 
+#' 
+#' @return a `list`
+#' @export
+#'  
+#' @references 
+#' https://scientific-collections.gbif.org/connected-systems#grscicoll-data-coming-from-other-sources  
+#' @examples \dontrun{
+#'   collection_search(query="insect",limit=2)
+#'   collection_search(name="Insects;Entomology", limit=2)
+#'   collection_search(numberSpecimens = "0,100", limit=1)
+#'   collection_search(institutionKey = "6a6ac6c5-1b8a-48db-91a2-f8661274ff80"
+#'   , limit = 1)
+#'   collection_search(query = "insect", country = "US;GB", limit=1)
+#' } 
+collection_search <- function(
+    query = NULL,
+    name = NULL,
+    fuzzyName = NULL,
+    preservationType = NULL,
+    contentType = NULL,
+    numberSpecimens = NULL,
+    accessionStatus = NULL,
+    personalCollection = NULL,
+    sourceId = NULL,
+    source = NULL,
+    code = NULL,
+    alternativeCode = NULL,
+    contact = NULL,
+    institutionKey = NULL,
+    country = NULL,
+    city = NULL,
+    gbifRegion = NULL,
+    machineTagNamespace = NULL,
+    machineTagName = NULL,
+    machineTagValue = NULL,
+    identifier = NULL,
+    identifierType = NULL,
+    active = NULL,
+    displayOnNHCPortal = NULL,
+    masterSourceType = NULL,
+    replacedBy = NULL,
+    sortBy = NULL,
+    sortOrder = NULL,
+    offset = NULL,
+    limit = NULL,
+    format = NULL,
+    curlopts = list(http_version=2)  
+  ) {
+  
+  assert(query,"character")
+  assert(name,"character")
+  assert(fuzzyName,"character")
+  assert(preservationType,"character")
+  assert(contentType, "character")
+  assert(accessionStatus,"character")
+  assert(personalCollection,"logical")
+  assert(source,"character")
+  assert(code,"character")
+  assert(alternativeCode,"character")
+  assert(contact,"character")
+  assert(institutionKey,"character")
+  assert(country,"character")
+  assert(city,"character")
+  assert(gbifRegion,"character")
+  assert(machineTagNamespace,"character")
+  assert(machineTagName,"character")
+  assert(identifierType,"character")
+  assert(active,"logical")
+  assert(displayOnNHCPortal,"logical")
+  assert(alternativeCode,"character")
+  assert(masterSourceType,"character")
+  assert(replacedBy,"character")
+  assert(sortBy,"character")
+  assert(limit,"numeric")
+  assert(offset,"numeric")
+  
+  # check for valid values 
+  if(!is.null(sortBy)) {
+    match.arg(sortBy, c("NUMBER_SPECIMENS"))
+  }
+  if(!is.null(sortOrder)) {
+    match.arg(sortOrder, c("ASC", "DESC"))
+  }
+
+  args <- as.list(
+    rgbif_compact(c(
+      q = query,
+      numberSpecimens = numberSpecimens,
+      accessionStatus = accessionStatus,
+      active = active,
+      displayOnNHCPortal = displayOnNHCPortal,
+      replacedBy = replacedBy,
+      sortBy = sortBy,
+      sortOrder = sortOrder,
+      offset = offset,
+      limit = limit
+    )))
+  
+  args <- rgbif_compact(c(
+      args,
+      convmany(name),
+      convmany(fuzzyName),
+      convmany(preservationType),
+      convmany(contentType),
+      convmany(personalCollection),
+      convmany(sourceId),
+      convmany(source),
+      convmany(code),
+      convmany(alternativeCode),
+      convmany(contact),
+      convmany(institutionKey),
+      convmany(country),
+      convmany(city),
+      convmany(gbifRegion),
+      convmany(machineTagNamespace),
+      convmany(machineTagName),
+      convmany(machineTagValue),
+      convmany(identifier),
+      convmany(identifierType),
+      convmany(masterSourceType)
+    ))
+  
+  url <- paste0(gbif_base(), '/grscicoll/collection')
+  tt <- gbif_GET(url, args, TRUE, curlopts)
+  
+  meta <- tt[c('offset','limit','endOfRecords','count')]
+  data <- tibble::as_tibble(tt$results)
+  
+  list(meta = as.data.frame(meta), data = data)
+}
+
+#' @export
+#' @rdname collection_search
+collection_export <- function(
+    query = NULL,
+    name = NULL,
+    fuzzyName = NULL,
+    preservationType = NULL,
+    contentType = NULL,
+    numberSpecimens = NULL,
+    accessionStatus = NULL,
+    personalCollection = NULL,
+    sourceId = NULL,
+    source = NULL,
+    code = NULL,
+    alternativeCode = NULL,
+    contact = NULL,
+    institutionKey = NULL,
+    country = NULL,
+    city = NULL,
+    gbifRegion = NULL,
+    machineTagNamespace = NULL,
+    machineTagName = NULL,
+    machineTagValue = NULL,
+    identifier = NULL,
+    identifierType = NULL,
+    active = NULL,
+    displayOnNHCPortal = NULL,
+    masterSourceType = NULL,
+    replacedBy = NULL,
+    sortBy = NULL,
+    sortOrder = NULL,
+    offset = NULL,
+    limit = NULL,
+    format = "TSV",
+    curlopts = list()  
+) {
+  
+  # https://api.gbif.org/v1/grscicoll/collection/export?format=TSV&displayOnNHCPortal=true
+  assert(query,"character")
+  assert(name,"character")
+  assert(fuzzyName,"character")
+  assert(preservationType,"character")
+  assert(contentType, "character")
+  assert(accessionStatus,"character")
+  assert(personalCollection,"logical")
+  assert(source,"character")
+  assert(code,"character")
+  assert(alternativeCode,"character")
+  assert(contact,"character")
+  assert(institutionKey,"character")
+  assert(country,"character")
+  assert(city,"character")
+  assert(gbifRegion,"character")
+  assert(machineTagNamespace,"character")
+  assert(machineTagName,"character")
+  assert(identifierType,"character")
+  assert(active,"logical")
+  assert(displayOnNHCPortal,"logical")
+  assert(alternativeCode,"character")
+  assert(masterSourceType,"character")
+  assert(replacedBy,"character")
+  assert(sortBy,"character")
+  assert(limit,"numeric")
+  assert(offset,"numeric")
+  
+  if(format != "TSV") {
+    warning("Only 'TSV' format is supported for collection_export")
+  }
+  if(!is.null(limit) | !is.null(offset)) {
+    warning("Limit and offset are ignored for collection_export. The full export
+            is returned.")
+  }
+    
+  args <- as.list(
+    rgbif_compact(c(
+      q = query,
+      numberSpecimens = numberSpecimens,
+      accessionStatus = accessionStatus,
+      active = active,
+      displayOnNHCPortal = displayOnNHCPortal,
+      replacedBy = replacedBy,
+      sortBy = sortBy,
+      sortOrder = sortOrder,
+      offset = offset,
+      limit = limit,
+      format = format
+    )))
+  
+  args <- rgbif_compact(c(
+    args,
+    convmany(name),
+    convmany(fuzzyName),
+    convmany(preservationType),
+    convmany(contentType),
+    convmany(personalCollection),
+    convmany(sourceId),
+    convmany(source),
+    convmany(code),
+    convmany(alternativeCode),
+    convmany(contact),
+    convmany(institutionKey),
+    convmany(country),
+    convmany(city),
+    convmany(gbifRegion),
+    convmany(machineTagNamespace),
+    convmany(machineTagName),
+    convmany(machineTagValue),
+    convmany(identifier),
+    convmany(identifierType),
+    convmany(masterSourceType)
+  ))
+  
+  url_query <- paste0(names(args),"=",args,collapse="&")
+  url_query <- utils::URLencode(url_query) 
+  url <- paste0(gbif_base(),"/grscicoll/collection/export?",url_query)
+  temp_file <- tempfile()
+  utils::download.file(url,destfile=temp_file,quiet=TRUE)
+  out <- tibble::as_tibble(data.table::fread(temp_file, showProgress=FALSE))
+  colnames(out) <- to_camel(colnames(out))
+  out 
+}
+

R/dataset_search.r

@@ -137,8 +137,7 @@ dataset_search <- function(query = NULL,
                            limit = 100,
                            start = NULL,
                            description = FALSE,
-                           curlopts = list()) {
-  
+                           curlopts = list(http_version=2)) {
   assert(query,"character")
   assert(type,"character")
   assert(subtype,"character")