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Set user agent to "Bioconductor UCSC.utils" when querying UCSC REST API
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@@ -10,11 +10,20 @@ biocViews: Infrastructure, GenomeAssembly, Annotation, GenomeAnnotation, | |
| DataImport | ||
| URL: https://bioconductor.org/packages/UCSC.utils | ||
| BugReports: https://github.com/Bioconductor/UCSC.utils/issues | ||
| Version: 0.99.1 | ||
| Version: 0.99.2 | ||
| License: Artistic-2.0 | ||
| Encoding: UTF-8 | ||
| Authors@R: person("Hervé", "Pagès", role=c("aut", "cre"), | ||
| email="[email protected]") | ||
| Imports: methods, stats, httr, rjson, S4Vectors | ||
| Suggests: DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle | ||
| VignetteBuilder: knitr | ||
| Collate: 00utils.R | ||
| UCSC.api.url.R | ||
| REST_API.R | ||
| list_UCSC_genomes.R | ||
| get_UCSC_chrom_sizes.R | ||
| list_UCSC_tracks.R | ||
| fetch_UCSC_track_data.R | ||
| UCSC_dbselect.R | ||
| zzz.R | ||
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| ### ========================================================================= | ||
| ### Thin R wrappers to UCSC REST API endpoints | ||
| ### ------------------------------------------------------------------------- | ||
| ### | ||
| ### Nothing in this file is exported. | ||
| ### | ||
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| .API_query <- function(endpoint, query=list(), api.url=UCSC.api.url()) | ||
| { | ||
| stopifnot(isSingleString(endpoint), nzchar(endpoint), | ||
| is.list(query), | ||
| isSingleString(api.url), nzchar(api.url)) | ||
| if (length(query) != 0L) | ||
| stopifnot(!is.null(names(query))) | ||
| url <- paste0(api.url, "/", endpoint) | ||
| GET(url, user_agent("Bioconductor UCSC.utils"), query=query) | ||
| } | ||
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| .parse_json <- function(response) | ||
| { | ||
| parsed_json <- fromJSON(content(response, as="text", encoding="UTF-8")) | ||
| ## Sanity checks. | ||
| stopifnot(is.list(parsed_json), !is.null(names(parsed_json))) | ||
| parsed_json | ||
| } | ||
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| ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| ### We only support the following endpoints at the moment: | ||
| ### - /list/ucscGenomes | ||
| ### - /list/chromosomes | ||
| ### - /list/tracks | ||
| ### - /getData/track | ||
| ### See https://genome.ucsc.edu/goldenPath/help/api.html#Endpoint for the | ||
| ### full list of endpoints. | ||
| ### | ||
| ### All the functions below return parsed JSON. | ||
| ### | ||
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| ### Endpoint /list/ucscGenomes | ||
| API_list_genomes <- function(api.url=UCSC.api.url()) | ||
| { | ||
| endpoint <- "list/ucscGenomes" | ||
| response <- .API_query(endpoint, api.url=api.url) | ||
| if (response[["status_code"]] != 200L) | ||
| stop(wmsg("failed to get list of UCSC genomes from ", api.url)) | ||
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| ans <- .parse_json(response)[["ucscGenomes"]] | ||
| ## Sanity check. | ||
| stopifnot(is.list(ans)) | ||
| ans | ||
| } | ||
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| ### Endpoint /list/chromosomes | ||
| API_list_chromosomes <- function(genome, api.url=UCSC.api.url()) | ||
| { | ||
| stopifnot(isSingleString(genome), nzchar(genome)) | ||
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| endpoint <- "list/chromosomes" | ||
| query <- list(genome=genome) | ||
| response <- .API_query(endpoint, query=query, api.url=api.url) | ||
| if (response[["status_code"]] != 200L) | ||
| stop(wmsg(genome, ": unknown UCSC genome ", | ||
| "(or ", api.url, " is down?)")) | ||
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| ans <- .parse_json(response) | ||
| ## Sanity check. | ||
| stopifnot(identical(ans[["genome"]], genome)) | ||
| ans | ||
| } | ||
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| ### Endpoint /list/tracks | ||
| API_list_tracks <- function(genome, api.url=UCSC.api.url()) | ||
| { | ||
| stopifnot(isSingleString(genome), nzchar(genome)) | ||
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| endpoint <- "list/tracks" | ||
| query <- list(genome=genome) | ||
| response <- .API_query(endpoint, query=query, api.url=api.url) | ||
| if (response[["status_code"]] != 200L) | ||
| stop(wmsg(genome, ": unknown UCSC genome ", | ||
| "(or ", api.url, " is down?)")) | ||
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| ans <- .parse_json(response)[[genome]] | ||
| ## Sanity check. | ||
| stopifnot(is.list(ans)) | ||
| ans | ||
| } | ||
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| ### Endpoint /getData/track | ||
| ### Note that the endpoint expects the supplied 'track' argument to be the | ||
| ### name of the track's primary table rather than the track's name. | ||
| ### E.g. "catLiftOffGenesV1" rather than "CAT/Liftoff Genes". | ||
| API_get_track_data <- function(genome, primary_table, api.url=UCSC.api.url()) | ||
| { | ||
| stopifnot(isSingleString(genome), nzchar(genome), | ||
| isSingleString(primary_table), nzchar(primary_table)) | ||
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| endpoint <- "getData/track" | ||
| query <- list(genome=genome, track=primary_table) | ||
| response <- .API_query(endpoint, query=query, api.url=api.url) | ||
| if (response[["status_code"]] != 200L) | ||
| stop(wmsg(genome, "/", primary_table, ": ", | ||
| "unknown UCSC genome/primary_table ", | ||
| "(or ", api.url, " is down?)")) | ||
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| ans <- .parse_json(response) | ||
| ## Sanity checks. | ||
| stopifnot(identical(ans[["genome"]], genome)) | ||
| if (!is.null(ans[["track"]])) | ||
| stopifnot(identical(ans[["track"]], primary_table)) | ||
| ans | ||
| } | ||
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