Preserve raw calls and upgrade site to bootstrap 5

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: enviPathR
 Title: Client for the 'enviPath' 'RESTful' API
-Version: 1.0.2
+Version: 1.0.3
 Authors@R:
     c(person(given = "Giulio", family = "Benedetti",
           role = c("aut", "cre", "cph"),
@@ -23,7 +23,7 @@ Imports:
     BiocParallel,
     httr2,
     stats,
-    stringr,
+    stringi,
     tools
 Suggests:
     BiocStyle,
@@ -36,8 +36,8 @@ Suggests:
 License: Artistic-2.0
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 8.0.0
-URL: https://envipath.github.io/enviPathR/
+URL: https://github.com/enviPath/enviPathR, https://envipath.github.io/enviPathR
 BugReports: https://github.com/enviPath/enviPathR/issues
 Config/testthat/edition: 3
 VignetteBuilder: knitr
+Config/roxygen2/version: 8.1.1

NAMESPACE

@@ -7,21 +7,28 @@ export(epLogin)
 export(epLogout)
 export(epModel)
 export(epTypes)
-importFrom(BiocParallel,bplapply)
-importFrom(BiocParallel,bpmapply)
-importFrom(BiocParallel,bpparam)
-importFrom(httr2,req_body_form)
-importFrom(httr2,req_cookie_preserve)
-importFrom(httr2,req_error)
-importFrom(httr2,req_method)
-importFrom(httr2,req_perform)
-importFrom(httr2,req_retry)
-importFrom(httr2,req_throttle)
-importFrom(httr2,req_url_path_append)
-importFrom(httr2,request)
-importFrom(httr2,resp_body_json)
+importFrom(BiocParallel,
+  bplapply,
+  bpmapply,
+  bpparam
+)
+importFrom(httr2,
+  req_body_form,
+  req_cookie_preserve,
+  req_error,
+  req_get_body,
+  req_method,
+  req_perform,
+  req_retry,
+  req_throttle,
+  req_url_path_append,
+  request,
+  resp_body_json,
+  resp_url
+)
 importFrom(stats,complete.cases)
-importFrom(stringr,fixed)
-importFrom(stringr,str_remove)
-importFrom(stringr,str_split)
+importFrom(stringi,
+  stri_replace_first_regex,
+  stri_split_fixed
+)
 importFrom(tools,R_user_dir)

NEWS

@@ -1,5 +1,6 @@
 Changes in version 1.0.x
 * Submitted to CRAN
+* Included raw API calls in output metadata
 
 Changes in version 0.99.x
 * Introduced epTypes, epLogin, epLogout, epList, epLink, epGet and epModel

R/get.R

@@ -1,17 +1,17 @@
 #' Get enviPath objects
 #' 
 #' @name epGet
 #' 
 #' @description
 #' epGet returns raw objects from enviPath.
 #' 
 #' @param type \code{Character scalar}. String specifying the object type to be
 #'   fetched.
 #' 
 #' @param init \code{Character vector}. Vector of strings specifying the initial
 #'   values of \code{type} that should be fetched. When null, all objects
 #'   belonging to \code{type} in \code{pkg} are used. (Default: \code{NULL})
 #' 
 #' @param pkg \code{Character scalar}. String specifying the unique identifier
 #'   of the package from which objects should be fetched. When null, EAWAG-BBD
 #'   is used. (Default: \code{NULL})
@@ -30,7 +30,11 @@
 #'   not serial. (Default: \code{5})
 #' 
 #' @returns
-#' A list of objects.
+#' A list of retrieved objects.
+#' 
+#' @details
+#' For transparency, the performed raw API calls can be accessed with
+#' \code{attr(x, "call")}, where \code{x} is the output of \code{epGet}.
 #' 
 #' @examples
 #' \dontshow{
@@ -76,10 +80,15 @@
         SIMPLIFY = FALSE,
         BPPARAM = BPPARAM
     )
+    # Store raw API calls in corresponding attribute
+    attr(out, "call")$url <- vapply(
+        out, attr, character(1L), "call", USE.NAMES = FALSE
+    )
     return(out)
 } 
 
-#' @importFrom httr2 request req_url_path_append req_cookie_preserve req_throttle resp_body_json
+#' @importFrom httr2 request req_url_path_append req_cookie_preserve
+#'   req_throttle resp_url resp_body_json
 .ep_get <- function(init, type, pkg, property, rate){
     # Prepare get request
     req <- request(eP_env$url) |>
@@ -92,5 +101,7 @@
     resp <- .ep_perform(req)
     # Process response
     out <- resp_body_json(resp, simplifyVector = TRUE)
+    # Store raw API call in corresponding attribute
+    attr(out, "call") <- resp_url(resp)
     return(out)
 }

R/link.R

@@ -32,6 +32,10 @@
 #' @returns
 #' A data frame with links between from and to.
 #' 
+#' @details
+#' For transparency, the performed raw API calls can be accessed with
+#' \code{attr(x, "call")}, where \code{x} is the output of \code{epLink}.
+#' 
 #' @examples
 #' \dontshow{
 #'     username <- Sys.getenv("EP_USERNAME")
@@ -54,7 +58,7 @@ NULL
 #' @export
 #' @rdname epLink
 #' @importFrom BiocParallel bplapply bpparam
-#' @importFrom stringr str_remove
+#' @importFrom stringi stri_replace_first_regex
 #' @importFrom stats complete.cases
 epLink <- function(from, to, init = NULL, pkg = NULL, BPPARAM = bpparam(), rate = 5){
     # Check from
@@ -97,6 +101,8 @@ epLink <- function(from, to, init = NULL, pkg = NULL, BPPARAM = bpparam(), rate
         x = rep(init, lengths(out, use.names = FALSE)),
         y = unlist(out, use.names = FALSE)
     )
+    # Store raw API calls in corresponding attribute
+    attr(linkmap, "call")$url <- vapply(out, attr, character(1L), "call")
     # Set linkmap column names
     colnames(linkmap) <- c(from, to)
     # Remove missing values
@@ -108,19 +114,21 @@ epLink <- function(from, to, init = NULL, pkg = NULL, BPPARAM = bpparam(), rate
     }
     # Remove structure identifier for compounds
     if( by == "pathway2compound" ){
-        linkmap[to] <- str_remove(linkmap[[to]], "/structure/.*")
+        linkmap[to] <- linkmap[[to]] |>
+            stri_replace_first_regex("/structure/.*", "")
     }
     if( by == "pathway2reaction" ){
         rxn_df <- epList("reaction", pkg = pkg)
         linkmap[to] <- rxn_df$id[rxn_df$name %in% linkmap[[to]]]
     }
     # Remove id prefix
-    linkmap[to] <- str_remove(linkmap[[to]], ".*/")
+    linkmap[to] <- stri_replace_first_regex(linkmap[[to]], ".*/", "")
     return(linkmap)
 }
 
 
-#' @importFrom httr2 request req_url_path_append req_cookie_preserve req_throttle resp_body_json
+#' @importFrom httr2 request req_url_path_append req_cookie_preserve
+#'   req_throttle resp_url resp_body_json
 .ep_link <- function(init, from, to, pkg, rate){
     # Prepare link request
     req <- request(eP_env$url) |>
@@ -137,6 +145,8 @@ epLink <- function(from, to, init = NULL, pkg = NULL, BPPARAM = bpparam(), rate
         unlist(use.names = FALSE)
     # Simplify list to single object
     if( is.null(out) ) out <- NA
+    # Store raw API call in corresponding attribute
+    attr(out, "call") <- resp_url(resp)
     return(out)
 }
 

R/list.R

@@ -15,6 +15,10 @@
 #' @returns
 #' A data frame with all objects belonging to \code{type} in \code{pkg}.
 #' 
+#' @details
+#' For transparency, the performed raw API call can be accessed with
+#' \code{attr(x, "call")}, where \code{x} is the output of \code{epList}.
+#' 
 #' @examples
 #' \dontshow{
 #'     username <- Sys.getenv("EP_USERNAME")
@@ -53,8 +57,8 @@ NULL
 
 #' @export
 #' @rdname epList
-#' @importFrom httr2 req_url_path_append req_cookie_preserve resp_body_json
-#' @importFrom stringr str_remove
+#' @importFrom httr2 req_url_path_append req_cookie_preserve resp_url resp_body_json
+#' @importFrom stringi stri_replace_first_regex
 epList <- function(type, pkg = NULL){
     # Check type
     .check_type(type)
@@ -64,36 +68,40 @@ epList <- function(type, pkg = NULL){
     if( type == "package" && is_pkg ){
         stop("'pkg' cannot be defined when listing packages.", call. = FALSE)
     }
-
+    # Initialise request and preserve cookies
     req <- request(eP_env$url) |>
         req_cookie_preserve(eP_env$cookies)
-
+    # Append package id to call url
     if( is_pkg ) req <- req_url_path_append(req, "package", pkg)
-        
+    # Append object type to call url
     req <- req_url_path_append(req, type)
-
+    # Perform query
     resp <- .ep_perform(req)
-
+    # Retrieve result from response
     out <- resp_body_json(resp, simplifyVector = TRUE)
     # Extract data.frame
     df <- out[[1L]]
     # Remove id prefix
-    df$id <- str_remove(df$id, ".*/")
-
+    df$id <- stri_replace_first_regex(df$id, ".*/", "")
+    # Select relevant variables to keep
     to_keep <- c("name", "id")
     # Include review status except for type setting
     if( type != "setting" ) to_keep <- c(to_keep, "reviewStatus")
-
+    # Add package-specific stats
     if( type == "package" ){
-
+        # Retrieve object types
         obj.types <- names(df$links[[1L]])
+        # Count objects for each type
         obj.counts <- vapply(obj.types, .extract_obj_counts, numeric(nrow(df)), df)
-
+        # Combine object counts into table
         df <- cbind(df, obj.counts)
+        # Add description and object counts to relevant variables
         to_keep <- c(to_keep, "description", obj.types)
     }
     # Select relevant columns
     df <- df[ , to_keep]
+    # Store raw API call in corresponding attribute
+    attr(df, "call")$url <- resp_url(resp)
     return(df)
 }
 

R/model.R

@@ -17,6 +17,10 @@
 #' A list with two data frames with information on nodes and edges,
 #' respectively.
 #' 
+#' @details
+#' For transparency, the performed raw API call can be accessed with
+#' \code{attr(x, "call")}, where \code{x} is the output of \code{epModel}.
+#' 
 #' @examples
 #' \dontshow{
 #'     username <- Sys.getenv("EP_USERNAME")
@@ -77,7 +81,8 @@ NULL
 
 #' @export
 #' @rdname epModel
-#' @importFrom httr2 request req_method req_url_path_append req_body_form req_cookie_preserve resp_body_json
+#' @importFrom httr2 request req_method req_url_path_append req_body_form
+#'   req_cookie_preserve req_get_body resp_url resp_body_json
 epModel <- function(smiles, setting = NULL){
     # Check smiles
     if( !is.character(smiles) || !nzchar(smiles) ){
@@ -99,6 +104,9 @@ epModel <- function(smiles, setting = NULL){
     resp <- .ep_perform(req)
     # Process response
     out <- resp_body_json(resp, simplifyVector = TRUE)
+    # Store raw API call in corresponding attribute
+    attr(out, "call")$url <- resp_url(resp)
+    attr(out, "call")$body <- req_get_body(req)
     # Process rule variables
     if( is.data.frame(out$edges$rule) ){
         out$edges$ruleId <- out$edges$rule$uuid

R/types.R

@@ -25,12 +25,12 @@ NULL
 
 #' @export
 #' @rdname epTypes
-#' @importFrom stringr str_split fixed
+#' @importFrom stringi stri_split_fixed
 epTypes <- function(){
     # Retrieve links between object types
     links <- eP_env$links |>
         names() |>
-        str_split(fixed("2"), simplify = TRUE) |>
+        stri_split_fixed("2", simplify = TRUE) |>
         as.data.frame()
     # Give names to link columns
     colnames(links) <- c("from", "to")

README.md

@@ -4,8 +4,8 @@
 [![pulls](https://img.shields.io/github/issues-pr/enviPath/enviPathR)](https://github.com/enviPath/enviPathR/pulls)
 [![CRAN status](https://www.r-pkg.org/badges/version/enviPathR)](https://CRAN.R-project.org/package=enviPathR)
 [![R-CMD-check](https://github.com/enviPath/enviPathR/workflows/build/badge.svg)](https://github.com/enviPath/enviPathR/actions)
-[![](https://cranlogs.r-pkg.org/badges/enviPathR)](https://cran.r-project.org/package=enviPathR)
 [![CodeFactor](https://www.codefactor.io/repository/github/enviPath/envipathr/badge)](https://www.codefactor.io/repository/github/enviPath/envipathr)
+[![downloads](https://cranlogs.r-pkg.org/badges/enviPathR)](https://cran.r-project.org/package=enviPathR)
 
 This package provides a client to the enviPath biotransformation database and
 pathway prediction system. It accesses enviPath resources through its [legacy

pkgdown/_pkgdown.yml

@@ -1,4 +1,12 @@
+url: https://envipath.github.io/enviPathR
 destination: docs
+
+template:
+  bootstrap: 5
+  light-switch: true
+  bslib:
+    navbar-bg: "#142D4A"
+
 reference:
 - title: Work with enviPath API
 - contents: