Merge pull request #102 from stitam/ena

Fix ena_query()

Author: stitam

.github/workflows/test-coverage.yaml

@@ -5,9 +5,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -16,36 +17,47 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v5
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -8,6 +8,8 @@ Version: 0.1
 Date: 2022-01-05
 Author: Tamas Stirling
 Maintainer: Tamas Stirling <stirling.tamas@gmail.com>
+URL: https://github.com/stitam/webseq
+BugReports: https://github.com/stitam/webseq/issues
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true

R/ena_query.R

@@ -11,6 +11,7 @@
 #'\code{"batch"}: one file for each batch, \code{"all"}: one file altogether.
 #'@param gzip logical; Download the result as a gzip file.
 #'@param set logical; ???
+#'@param include_links logical; ???
 #'@param range character; ???
 #'@param complement logical; ???
 #'@param batch_size integer; Number of accessions to query in a single request.
@@ -34,6 +35,7 @@ ena_query <- function(
     destfile_by = "all",
     gzip = FALSE,
     set = FALSE,
+    include_links = FALSE,
     range = NULL,
     complement = FALSE,
     batch_size = 0,
@@ -45,6 +47,7 @@ ena_query <- function(
   stopifnot(length(download) == 1 && is.logical(download))
   stopifnot(length(gzip) == 1 && is.logical(gzip))
   stopifnot(length(set) == 1 && is.logical(set))
+  stopifnot(length(include_links) == 1 && is.logical(include_links))
   #stopifnot(length(range) == 1 && is.character(range))
   stopifnot(length(complement) == 1 && is.logical(complement))
   stopifnot(length(verbose) == 1 && is.logical(verbose))
@@ -77,16 +80,7 @@ ena_query <- function(
     } else {
       destfile <- paste0(x, ".", mode, ifelse(gzip == "true", ".gz", ""))
     }
-    url <- paste0(
-      "https://www.ebi.ac.uk/ena/browser/api/", mode, "?",
-      "accessions=", x,
-      "&expanded=", expanded,
-      "&annotationOnly=", annotation_only,
-      "&download=", download,
-      "&gzip=", gzip,
-      "&set=", set,
-      "&complement=", complement
-    )
+    url <- paste0("https://www.ebi.ac.uk/ena/browser/api/", mode)
     if (download == "true") {
       # TODO: finalise dev code
       # variations based on number of accessions, batch_size, download_by, gzip
@@ -100,7 +94,28 @@ ena_query <- function(
         mode = mode
       )
     } else {
-      res <- try_url("POST", url)
+      headers <- c(Accept = "text/plain", `Content-Type` = "application/json")
+      body <- list(
+        "accessions" = list(x),
+        "expanded" = expanded,
+        "annotationOnly" = annotation_only,
+        "lineLimit" = 0,
+        "download" = download,
+        "gzip" = gzip,
+        "set" = set,
+        "includeLinks" = include_links,
+        "range" = range,
+        "complement" = complement
+      )
+      res <- try(httr::RETRY(
+        "POST",
+        url,
+        httr::user_agent(package_url()),
+        httr::add_headers(.headers = headers),
+        body = body,
+        encode = "json",
+        terminate_on = 404,
+        quiet = TRUE), silent = TRUE)
       seqs <- ena_parse(res, mode = mode)
       return(seqs)
     }

R/utils.R

@@ -1,3 +1,24 @@
+#' Get package URL
+#'
+#' Look up the DESCRIPTION file of the package that called this function and
+#' return the package URL (the first element of the URL field).
+#'
+#' @return Either a URL
+#' @noRd
+package_url <- function() {
+  # Get package name
+  ns <- parent.frame()
+  pkg <- utils::packageName(ns)
+  if (is.null(pkg)) stop("Could not extract package name.")
+  # Extract URL from DESCRIPTION file
+  desc <- utils::packageDescription(pkg)
+  if (!"URL" %in% names(desc)) stop("Could not extract URL, missing field.")
+  urls <- unlist(strsplit(desc[["URL"]], "[[:space:],]+"))
+  urls <- urls[nzchar(urls)]
+  if (length(urls) == 0) stop("Could not extract URL, empty field.")
+  return(urls[1])
+}
+
 #' Retry a function call
 #' 
 #' @param expr expression; Expression to evaluate.