Refine the manuals' "Corresponding API Resources" section for consist…

…ency and syntax
moosa-r · Mar 29, 2024 · bb8f4d3 · bb8f4d3
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diff --git a/R/jaspar.R b/R/jaspar.R
@@ -12,7 +12,7 @@
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#'  "GET "https://jaspar.elixir.no/api/v1/collections/"
+#'  "GET https://jaspar.elixir.no/api/v1/collections/"
 #'
 #' @return A data frame with collections' names and URLs.
 #'
@@ -109,7 +109,7 @@ rba_jaspar_collections <- function(release = 2024,
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#'  "GET "https://jaspar.elixir.no/api/v1/collections/{collection}/"
+#'  "GET https://jaspar.elixir.no/api/v1/collections/\{collection\}/"
 #'
 #' @return A list that contains a data frame with information of matrix
 #'   profiles available in the collection.
@@ -262,7 +262,7 @@ rba_jaspar_collections_matrices <- function(collection,
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#'  "GET "https://jaspar.elixir.no/api/v1/api/v1/matrix/"
+#'  "GET https://jaspar.elixir.no/api/v1/api/v1/matrix/"
 #'
 #' @return A list that contains a data frame of matrix profiles' information.
 #'
@@ -429,7 +429,7 @@ rba_jaspar_matrix_search <- function(term = NULL,
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#'  "GET "https://jaspar.elixir.no/api/v1/matrix/{base_id}/versions/"
+#'  "GET https://jaspar.elixir.no/api/v1/matrix/\{base_id\}/versions/"
 #'
 #' @return A data frame of matrix profiles' versions information.
 #'
@@ -520,7 +520,7 @@ rba_jaspar_matrix_versions <- function(base_id,
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#'  "GET "https://jaspar.elixir.no/api/v1/matrix/{matrix_id}/"
+#'  "GET https://jaspar.elixir.no/api/v1/matrix/\{matrix_id\}/"
 #'
 #' @return A list that contains the PFM along with its details and
 #'   annotations. If file_format was supplied, an un-parsed character string
@@ -638,8 +638,8 @@ rba_jaspar_matrix <- function(matrix_id,
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#' "GET "https://jaspar.elixir.no/api/v1/releases/"
-#'  "GET "https://jaspar.elixir.no/api/v1/releases/{release_number}/"
+#'  "GET https://jaspar.elixir.no/api/v1/releases/"
+#'  \cr "GET https://jaspar.elixir.no/api/v1/releases/\{release_number\}/"
 #'
 #' @return A list that contains all JASPAR database releases' information or
 #'   details of a particular release.
@@ -731,7 +731,7 @@ rba_jaspar_releases  <- function(release_number = NULL,
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#'  "GET "https://jaspar.elixir.no/api/v1/sites/{matrix_id}/"
+#'  "GET https://jaspar.elixir.no/api/v1/sites/\{matrix_id\}/"
 #'
 #' @return A list that contains a data frame with binding sites information.
 #'
@@ -809,7 +809,7 @@ rba_jaspar_sites <- function(matrix_id,
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#'  "GET "https://jaspar.elixir.no/api/v1/species/"
+#'  "GET https://jaspar.elixir.no/api/v1/species/"
 #'
 #' @return A data frame with information of available species.
 #'
@@ -918,7 +918,7 @@ rba_jaspar_species <- function(release = 2024,
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#'  "GET "https://jaspar.elixir.no/api/v1/species/{tax_id}/"
+#'  "GET https://jaspar.elixir.no/api/v1/species/\{tax_id\}/"
 #'
 #' @return A list that contains a data frame with information of matrix
 #'   profiles available for the species.
@@ -1026,7 +1026,7 @@ rba_jaspar_species_matrices <- function(tax_id,
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#'  "GET "https://jaspar.elixir.no/api/v1/taxon/"
+#'  "GET https://jaspar.elixir.no/api/v1/taxon/"
 #'
 #' @return A data frame with information of available species.
 #'
@@ -1122,7 +1122,7 @@ rba_jaspar_taxons <- function(release = 2024,
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#'  "GET "https://jaspar.elixir.no/api/v1/taxon/{tax_group}/"
+#'  "GET https://jaspar.elixir.no/api/v1/taxon/\{tax_group\}/"
 #'
 #' @return A list that contains a data frame with information of matrix
 #'   profiles available for the taxonomic group.
@@ -1261,7 +1261,7 @@ rba_jaspar_taxons_matrices <- function(tax_group,
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#'  "GET "https://jaspar.elixir.no/api/v1/api/v1/tffm/"
+#'  "GET https://jaspar.elixir.no/api/v1/api/v1/tffm/"
 #'
 #' @return A list that contains a data frame with information of query hits'
 #'   TFFMs.
@@ -1376,7 +1376,7 @@ rba_jaspar_tffm_search <- function(term = NULL,
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#'  "GET "https://jaspar.elixir.no/api/v1/fttm/{tffm_id}/"
+#'  "GET https://jaspar.elixir.no/api/v1/fttm/\{tffm_id\}/"
 #'
 #' @return A list that contains the TFFM's information and annotations.
 #'

diff --git a/R/mieaa.R b/R/mieaa.R
@@ -87,7 +87,7 @@
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#'  "GET  "https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/enrichment_categories/{species}/{mirna_type}/"
+#'  "GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/enrichment_categories/\{species\}/\{mirna_type\}/"
 #'
 #' @return a named character vector with the supported categories for
 #'   your supplied input combination.
@@ -442,7 +442,7 @@ rba_mieaa_convert_type <- function(mirna,
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#'  "POST https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/enrichment_analysis/{species}/{type}/{test}/"
+#'  "POST https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/enrichment_analysis/\{species\}/\{type\}/\{test\}/"
 #'
 #' @return A list that contains your submitted job's ID and a URL to
 #'   manually check for your job status.
@@ -605,7 +605,7 @@ rba_mieaa_enrich_submit <- function(test_set,
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#'  "GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/job_status/{job_id}"
+#'  "GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/job_status/\{job_id\}"
 #'
 #' @return A list containing the status value for a analysis that corresponds
 #'   to your supplied job-id.
@@ -679,7 +679,7 @@ rba_mieaa_enrich_status <- function(job_id, ...) {
 #'   arguments manual for more information on available options.
 #'
 #' @section Corresponding API Resources:
-#'  "GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/results/{job_id}"
+#'  "GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/results/\{job_id\}"
 #'
 #' @return A data frame with your enrichment analysis results.
 #'

diff --git a/R/reactome_analysis.R b/R/reactome_analysis.R
@@ -379,8 +379,8 @@ rba_reactome_analysis <- function(input,
 #'   in other formats.
 #'
 #' @section Corresponding API Resources:
-#'  "GET https://reactome.org/AnalysisService/report/{token}/{species}/
-#'  {filename}.pdf"
+#'  "GET https://reactome.org/AnalysisService/report/\{token\}/\{species\}/
+#'  \{filename\}.pdf"
 #'
 #' @param token A token associated to your previous Reactome analysis.
 #' @param species Numeric or Character: NCBI Taxonomy identifier (Human Taxonomy
@@ -547,14 +547,14 @@ rba_reactome_analysis_pdf <- function(token,
 #'   in PDF format.
 #'
 #' @section Corresponding API Resources:
-#' GET https://reactome.org/AnalysisService/download/{token}/entities/
-#' found/{resource}/{filename}.csv"
-#' GET https://reactome.org/AnalysisService//download/{token}/entities/
-#' notfound/{filename}.csv"
-#' GET https://reactome.org/AnalysisService/download/{token}/pathways/
-#' {resource}/{filename}.csv"
-#' GET https://reactome.org/AnalysisService/download/{token}/result.json"
-#' GET https://reactome.org/AnalysisService/download/{token}/result.json.gz"
+#' GET https://reactome.org/AnalysisService/download/\{token\}/entities/
+#' found/\{resource\}/\{filename\}.csv"
+#' \cr GET https://reactome.org/AnalysisService/download/\{token\}/entities/
+#' notfound/\{filename\}.csv"
+#' \cr GET https://reactome.org/AnalysisService/download/\{token\}/pathways/
+#' \{resource\}/\{filename\}.csv"
+#' \cr GET https://reactome.org/AnalysisService/download/\{token\}/result.json"
+#' \cr GET https://reactome.org/AnalysisService/download/\{token\}/result.json.gz"
 #'
 #' @param token A token associated to your previous Reactome analysis.
 #' @param request What to download? Should be one of:\itemize{
@@ -938,7 +938,7 @@ rba_reactome_analysis_mapping <- function(input,
 #'   Reactome Computationally Inferred Events} for more information.
 #'
 #' @section Corresponding API Resources:
-#'  "GET https://reactome.org/AnalysisService/species/homoSapiens/{species}"
+#'  "GET https://reactome.org/AnalysisService/species/homoSapiens/\{species\}"
 #'
 #' @param species_dbid Numeric: Reactome DbId (e.g  Mus musculus is 48892) of
 #'   the species you want to compare with Homo sapiens. See
@@ -1093,7 +1093,7 @@ rba_reactome_analysis_species <- function(species_dbid,
 #'   reactome (using \code{\link{rba_reactome_analysis_import}}) to generate
 #'   a new token.
 #' @section Corresponding API Resources:
-#'  "GET https://reactome.org/AnalysisService/token/{token}"
+#'  "GET https://reactome.org/AnalysisService/token/\{token\}"
 #'
 #' @param token A token associated to your previous Reactome analysis.
 #' @param species Numeric or Character: NCBI Taxonomy identifier (Human