Add tests, vignettes and pathway prediction

.github/workflows/build.yml

@@ -0,0 +1,49 @@
+name: build
+on:
+  push:
+    branches:
+    - devel
+jobs:
+  rworkflows:
+    permissions: write-all
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
+          rspm: ~
+        - os: macOS-latest
+          bioc: devel
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: devel
+          r: auto
+          cont: ~
+          rspm: ~
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ false }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ true }}
+        run_pkgdown: ${{ true }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1
+        docker_registry: ghcr.io

.github/workflows/test.yml

@@ -0,0 +1,52 @@
+name: test
+on:
+  pull-request:
+    branches:
+    - devel
+jobs:
+  rworkflows:
+    permissions: write-all
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
+          rspm: ~
+        - os: macOS-latest
+          bioc: devel
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: devel
+          r: auto
+          cont: ~
+          rspm: ~
+    env:
+      EP_USERNAME: ${{ secrets.EP_USERNAME }}
+      EP_PASSWORD: ${{ secrets.EP_PASSWORD }}
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ true }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ false }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ false }}
+        run_pkgdown: ${{ false }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1
+        docker_registry: ghcr.io

.gitignore

@@ -1,2 +1,7 @@
 .Rproj.user
 .Rhistory
+.Renviron
+inst/doc
+vignettes/*.html
+vignettes/*.R
+docs/

DESCRIPTION

@@ -1,21 +1,35 @@
 Package: enviPathR
 Title: R client for enviPath API
-Version: 0.0.0.9000
-Authors@R: 
-    person("Giulio", "Benedetti", , "giulio.benedetti@utu.fi", role = c("aut", "cre"))
+Version: 0.99.0
+Authors@R:
+    c(person(given = "Giulio", family = "Benedetti", role = c("aut", "cre"),
+          email = "giulio.benedetti@utu.fi",
+          comment = c(ORCID = "0000-0002-8732-7692")))
 Description:
     The environmental pathway database (enviPath) is a key resource for the
     functional annotation and pathway prediction of microbial communities,
     providing knowledge on biotransformation pathways along with the chemical
     reactions and produced compounds. This package enables the programmatic
     access to enviPath by porting the database API from R.
+biocViews:
+    Software, DataImport, Cheminformatics, Microbiome, Annotation, Pathways,
+    Visualization, Network, GraphAndNetwork
 Imports:
+    BiocParallel,
     httr2,
-    jsonlite,
     stats,
     stringr,
     tools
 License: Artistic-2.0
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 8.0.0
+Suggests:
+    BiocStyle,
+    httptest2,
+    igraph,
+    knitr,
+    rmarkdown,
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3
+VignetteBuilder: knitr

NAMESPACE

@@ -4,6 +4,7 @@ export(epGet)
 export(epLink)
 export(epList)
 export(epLogin)
+export(epModel)
 importFrom(BiocParallel,bplapply)
 importFrom(BiocParallel,bpmapply)
 importFrom(httr2,req_body_form)

R/constants.R

@@ -28,7 +28,7 @@
     cache <- R_user_dir("enviPathR", "cache")
     if( !dir.exists(cache) ) dir.create(cache)
     # Preserve cookies between requests
-    eP_env$cookies <- tempfile("cookies", tmpdir = cache, fileext = ".txt")
+    eP_env$cookies <- file.path(cache, "cookies.txt")
     # Add links
     eP_env$links <- .make_ep_links()
     return(eP_env)

R/get.R

@@ -17,9 +17,21 @@
 #' A list of objects
 #' 
 #' @examples
+#' \dontshow{
+#'     username <- Sys.getenv("EP_USERNAME")
+#'     password <- Sys.getenv("EP_PASSWORD")
+#'     
+#'     epLogin(username, password)
+#' 
+#'     library(httptest2)
+#'     start_vignette("httptest/get")
+#' }
 #' rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a"
 #' 
 #' epGet("reaction", rxn_id)
+#' \dontshow{
+#'     end_vignette()
+#' }
 NULL
 
 #' @export

R/link.R

@@ -17,9 +17,21 @@
 #' A data frame with links between from and to.
 #' 
 #' @examples
+#' \dontshow{
+#'     username <- Sys.getenv("EP_USERNAME")
+#'     password <- Sys.getenv("EP_PASSWORD")
+#'     
+#'     epLogin(username, password)
+#' 
+#'     library(httptest2)
+#'     start_vignette("httptest/link")
+#' }
 #' rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a"
 #' 
-#' epGet("reaction", rxn_id)
+#' epLink("reaction", "compound", rxn_id)
+#' \dontshow{
+#'     end_vignette()
+#' }
 NULL
 
 #' @export

R/list.R

@@ -13,9 +13,21 @@
 #' A data frame.
 #' 
 #' @examples
+#' \dontshow{
+#'     username <- Sys.getenv("EP_USERNAME")
+#'     password <- Sys.getenv("EP_PASSWORD")
+#'     
+#'     epLogin(username, password)
+#' 
+#'     library(httptest2)
+#'     start_vignette("httptest/list")
+#' }
 #' epList("package")
 #' 
 #' epList("pathway", pkg = "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1")
+#' \dontshow{
+#'     end_vignette()
+#' }
 NULL
 
 #' @export
@@ -45,7 +57,9 @@ epList <- function(type, pkg = NULL){
     # Remove id prefix
     df$id <- str_remove(df$id, ".*/")
 
-    to_keep <- c("name", "id", "reviewStatus")
+    to_keep <- c("name", "id")
+    # Include review status except for type setting
+    if( type != "setting" ) to_keep <- c(to_keep, "reviewStatus")
 
     if( type == "package" ){
 

R/login.R

@@ -14,8 +14,11 @@
 #' A message upon successful login.
 #' 
 #' @examples
-#' # epLogin("FirstLast", "abc123")
-#' #> Welcome to enviPath!
+#' \dontshow{
+#'     username <- Sys.getenv("EP_USERNAME")
+#'     password <- Sys.getenv("EP_PASSWORD")
+#' }
+#' epLogin(username, password)
 NULL
 
 #' @importFrom httr2 request req_method req_body_form req_cookie_preserve req_perform

R/model.R

@@ -0,0 +1,81 @@
+#' Predict biotransformation pathways for compounds
+#' 
+#' @name epModel
+#' 
+#' @description
+#' epGet returns a raw object from enviPath.
+#' 
+#' @param smiles \code{Character vector}.
+#' 
+#' @param setting \code{Character scalar}.
+#' 
+#' @returns
+#' A list with two data frames with information on nodes and edges,
+#' respectively.
+#' 
+#' @examples
+#' \dontshow{
+#'     username <- Sys.getenv("EP_USERNAME")
+#'     password <- Sys.getenv("EP_PASSWORD")
+#'     
+#'     epLogin(username, password)
+#' }
+#' library(igraph)
+#' 
+#' # Define smiles of interest
+#' smiles <- "ClC(Cl)=C(Cl)Cl"
+#' 
+#' # Perform pathway prediction with enviFormer
+#' former_out <- epModel(smiles)
+#' 
+#' # Set id for PEPPER model setting
+#' set_id <- "3cda8e56-f4ff-47a8-b68c-4cfcfc4e8c2a"
+#' 
+#' # Perform pathway prediction with PEPPER
+#' pepper_out <- epModel(smiles, set_id)
+#' 
+#' # Convert model output to igraph object
+#' path_graph <- graph_from_data_frame(
+#'     pepper_out$edges,
+#'     vertices = pepper_out$nodes
+#' )
+#' 
+#' # Visualise predicted pathway
+#' plot(path_graph)
+NULL
+
+#' @export
+#' @rdname epModel
+#' @importFrom httr2 request req_method req_url_path_append req_body_form req_cookie_preserve req_perform resp_body_json
+epModel <- function(smiles, setting = NULL){
+
+    if( smiles == "" ){
+        stop("'smiles' must be a valid SMILES string.", call. = FALSE)
+    }
+
+    if( is.null(setting) ) setting <- "1d915a48-286a-4394-9693-bfaa187326a5"
+
+    setting <- paste0("https://envipath.org/setting/", setting)
+
+    req <- request(eP_env$url) |>
+        req_method("POST") |>
+        req_url_path_append("util") |>
+        req_body_form(smiles = smiles, settingUri = setting) |>
+        req_cookie_preserve(path = eP_env$cookies)
+
+    resp <- req_perform(req)
+
+    out <- resp_body_json(resp, simplifyVector = TRUE)
+
+    if( is.data.frame(out$edges$rule) ){
+        out$edges$ruleId <- out$edges$rule$uuid
+        out$edges$ruleName <- out$edges$rule$name
+        out$edges$rule <- NULL
+    }
+
+    out$nodes$name <- out$nodes$smiles
+    out$nodes$smiles <- NULL
+
+    out$nodes <- out$nodes[c("id", "name", "depth")]
+    return(out)
+}

README.md

@@ -13,13 +13,13 @@ Bioconductor release version:
 if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
 
-BiocManager::install("mia")
+BiocManager::install("enviPathR")
 ```
 
 Beta version:
 
 ```
-remotes::install_github("Minotau-R/ariadne")
+remotes::install_github("Minotau-R/enviPathR")
 ```
 
 ## References