Issue 22: migrate to httr2

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: drugfindR
 Title: Investigate iLINCS for candidate repurposable drugs
-Version: 0.99.980
+Version: 0.99.986
 Authors@R: c(
     person(given = c("Ali", "Sajid"),
            family = "Imami",
@@ -34,10 +34,9 @@ URL: https://github.com/CogDisResLab/drugfindR
 BugReports: https://github.com/CogDisResLab/drugfindR/issues
 LazyData: false
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 biocViews: FunctionalPrediction, DifferentialExpression, GeneSetEnrichment
 Imports:
-    httr,
     magrittr,
     tibble,
     rlang,
@@ -47,7 +46,9 @@ Imports:
     stringr,
     stats,
     lifecycle,
-    S4Vectors
+    S4Vectors,
+    httr2,
+    curl
 Depends:
     R (>= 4.4.0)
 Suggests:

NAMESPACE

@@ -9,6 +9,7 @@ export(investigateTarget)
 export(prepareSignature)
 import(lifecycle)
 importFrom(S4Vectors,DataFrame)
+importFrom(curl,form_file)
 importFrom(dplyr,across)
 importFrom(dplyr,any_of)
 importFrom(dplyr,arrange)
@@ -22,10 +23,15 @@ importFrom(dplyr,rename)
 importFrom(dplyr,rename_with)
 importFrom(dplyr,select)
 importFrom(dplyr,ungroup)
-importFrom(httr,POST)
-importFrom(httr,content)
-importFrom(httr,status_code)
-importFrom(httr,upload_file)
+importFrom(httr2,req_method)
+importFrom(httr2,req_perform)
+importFrom(httr2,req_url_path_append)
+importFrom(httr2,req_url_query)
+importFrom(httr2,req_user_agent)
+importFrom(httr2,request)
+importFrom(httr2,resp_body_json)
+importFrom(httr2,resp_body_string)
+importFrom(httr2,resp_status)
 importFrom(lifecycle,deprecated)
 importFrom(magrittr,"%>%")
 importFrom(purrr,flatten_dfr)
@@ -35,6 +41,7 @@ importFrom(purrr,map_dfr)
 importFrom(readr,write_tsv)
 importFrom(rlang,.data)
 importFrom(stats,quantile)
+importFrom(stringr,str_glue)
 importFrom(stringr,str_to_lower)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)

R/getConcordants.R

@@ -16,12 +16,13 @@
 #' @export
 #'
 #' @importFrom readr write_tsv
-#' @importFrom httr POST status_code content upload_file
+#' @importFrom httr2 request req_method req_url_query req_user_agent req_url_path_append req_perform resp_status resp_body_json resp_body_string
 #' @importFrom purrr map flatten_dfr
 #' @importFrom dplyr select any_of mutate filter
 #' @importFrom tibble tibble
 #' @importFrom rlang .data
-#' @importFrom magrittr %>%
+#' @importFrom stringr str_glue
+#' @importFrom curl form_file
 #'
 #' @examples
 #' # Get the L1000 signature for LINCSKD_28
@@ -37,7 +38,7 @@ getConcordants <- function(signature, ilincsLibrary = "CP") {
         stop("signature must be a data frame or data frame like object")
     } else {
         signatureFile <- tempfile(pattern = "ilincs_sig", fileext = ".xls")
-        signature %>%
+        signature |>
             readr::write_tsv(signatureFile)
     }
 
@@ -55,31 +56,32 @@ getConcordants <- function(signature, ilincsLibrary = "CP") {
         CP = "LIB_5"
     )
 
-    if (!ilincsLibrary %in% c("OE", "KD", "CP")) {
-        stop("library must be one of 'OE', 'KD' or 'CP'")
-    }
-
-    url <- "http://www.ilincs.org/api/SignatureMeta/uploadAndAnalyze"
-    query <- list(lib = libMap[ilincsLibrary])
-    body <- list(file = httr::upload_file(signatureFile))
+    stopIfInvalidLibraries(ilincsLibrary)
 
-    request <- httr::POST(url, query = query, body = body)
+    request <- httr2::request(.ilincsBaseUrl()) |>
+        httr2::req_url_path_append("SignatureMeta") |>
+        httr2::req_url_path_append("uploadAndAnalyze") |>
+        httr2::req_url_query(lib = libMap[ilincsLibrary]) |>
+        httr2::req_body_multipart(file = curl::form_file(signatureFile)) |>
+        httr2::req_method("POST") |>
+        httr2::req_user_agent(stringr::str_glue("drugfindR/v{packageVersion('drugfindR')}; https://github.com/CogDisResLab/drugfindR")) |>
+        httr2::req_perform()
 
-    if (httr::status_code(request) == 200L) {
-        concordants <- httr::content(request) %>%
-            purrr::map("concordanceTable") %>%
-            purrr::flatten_dfr() %>%
+    if (httr2::resp_status(request) == 200L) {
+        concordants <- httr2::resp_body_json(request) |>
+            purrr::map("concordanceTable") |>
+            purrr::flatten_dfr() |>
             dplyr::select(dplyr::any_of(c(
                 "signatureid", "compound", "treatment",
                 "concentration", "time", "cellline", "similarity", "pValue"
-            ))) %>%
+            ))) |>
             dplyr::mutate(
                 similarity = round(.data[["similarity"]], 8L),
                 pValue = round(.data[["pValue"]], 20L),
                 sig_direction = sigDirection
             )
         return(concordants)
     } else {
-        httr::stop_for_status(request, "get concardant signatures")
+        stop(httr2::resp_status(request), " ", httr2::resp_body_string(request))
     }
 }

R/getSignature.R

@@ -16,9 +16,8 @@
 #' @return a tibble with the L1000 Signature
 #' @export
 #'
-#' @importFrom httr POST content status_code
+#' @importFrom httr2 request req_method req_url_query req_user_agent req_url_path_append req_perform resp_status resp_body_json resp_body_string
 #' @importFrom tibble tibble as_tibble
-#' @importFrom magrittr %>%
 #' @importFrom rlang .data
 #' @importFrom dplyr select
 #' @importFrom purrr map_dfr
@@ -28,32 +27,32 @@
 #' # Get the L1000 signature for LINCSKD_28
 #' kdSignature <- getSignature("LINCSKD_28")
 getSignature <- function(sigId, l1000 = TRUE) {
-    url <- "http://www.ilincs.org/api/ilincsR/downloadSignature"
-
     if (l1000) {
         numGenes <- 978L
     } else {
         numGenes <- Inf
     }
 
-    query <- list(sigID = sigId, noOfTopGenes = numGenes)
+    request <- httr2::request(.ilincsBaseUrl()) |>
+        httr2::req_url_path_append("ilincsR") |>
+        httr2::req_url_path_append("downloadSignature") |>
+        httr2::req_url_query(sigID = sigId, noOfTopGenes = numGenes) |>
+        httr2::req_method("POST") |>
+        httr2::req_user_agent("drugfindR/v0.99.980; https://github.com/CogDisResLab/drugfindR") |>
+        httr2::req_perform()
 
-    request <- httr::POST(url, query = query)
 
-    if (httr::status_code(request) == 200L) {
-        signature <- httr::content(request) %>%
-            purrr::map("signature") %>%
-            purrr::flatten_dfr() %>%
-            dplyr::select(-"PROBE") %>%
+    if (httr2::resp_status(request) == 200L) {
+        signature <- httr2::resp_body_json(request) |>
+            purrr::map("signature") |>
+            purrr::flatten_dfr() |>
+            dplyr::select(-"PROBE") |>
             dplyr::mutate(
                 ID_geneid = as.character(.data[["ID_geneid"]]),
                 Value_LogDiffExp = round(.data[["Value_LogDiffExp"]], 12L),
                 Significance_pvalue = round(.data[["Significance_pvalue"]], 12L)
             )
-        signature %>%
-            S4Vectors::DataFrame() %>%
-            as_tibble()
     } else {
-        stop(httr::status_code(request), " ", httr::content(request))
+        stop(httr2::resp_status(request), " ", httr2::resp_body_string(request))
     }
 }

R/utilities.R

@@ -21,6 +21,14 @@ targetRename <- function(inputNames) {
     }
 }
 
+#' Parameterize the base URL for the iLINCS API
+#'
+#'
+#' @return a fixed string URL
+.ilincsBaseUrl <- function() {
+    "http://www.ilincs.org/api"
+}
+
 #' Check if the library is valid
 #'
 #' @param lib a string of libraries
@@ -69,3 +77,21 @@ loadMetadata <- function(lib) {
         stop("Invalid library")
     }
 }
+
+
+#' Return the internal iLINCS Library ID for a given library
+#'
+#' @param lib A library name. Can be one of "OE", "KD" or "CP"
+#'
+#' @return A string with the associated library ID
+.return_library <- function(lib) {
+    stopIfInvalidLibraries(lib)
+
+    libMap <- c(
+        OE = "LIB_11",
+        KD = "LIB_6",
+        CP = "LIB_5"
+    )
+
+    libMap[lib]
+}

codemeta.json

@@ -7,7 +7,7 @@
   "codeRepository": "https://github.com/CogDisResLab/drugfindR",
   "issueTracker": "https://github.com/CogDisResLab/drugfindR/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "0.99.980",
+  "version": "0.99.986",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -203,18 +203,6 @@
   ],
   "softwareRequirements": {
     "1": {
-      "@type": "SoftwareApplication",
-      "identifier": "httr",
-      "name": "httr",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=httr"
-    },
-    "2": {
       "@type": "SoftwareApplication",
       "identifier": "magrittr",
       "name": "magrittr",
@@ -226,7 +214,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=magrittr"
     },
-    "3": {
+    "2": {
       "@type": "SoftwareApplication",
       "identifier": "tibble",
       "name": "tibble",
@@ -238,7 +226,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=tibble"
     },
-    "4": {
+    "3": {
       "@type": "SoftwareApplication",
       "identifier": "rlang",
       "name": "rlang",
@@ -250,7 +238,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=rlang"
     },
-    "5": {
+    "4": {
       "@type": "SoftwareApplication",
       "identifier": "dplyr",
       "name": "dplyr",
@@ -262,7 +250,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=dplyr"
     },
-    "6": {
+    "5": {
       "@type": "SoftwareApplication",
       "identifier": "purrr",
       "name": "purrr",
@@ -274,7 +262,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=purrr"
     },
-    "7": {
+    "6": {
       "@type": "SoftwareApplication",
       "identifier": "readr",
       "name": "readr",
@@ -286,7 +274,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=readr"
     },
-    "8": {
+    "7": {
       "@type": "SoftwareApplication",
       "identifier": "stringr",
       "name": "stringr",
@@ -298,12 +286,12 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=stringr"
     },
-    "9": {
+    "8": {
       "@type": "SoftwareApplication",
       "identifier": "stats",
       "name": "stats"
     },
-    "10": {
+    "9": {
       "@type": "SoftwareApplication",
       "identifier": "lifecycle",
       "name": "lifecycle",
@@ -315,7 +303,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=lifecycle"
     },
-    "11": {
+    "10": {
       "@type": "SoftwareApplication",
       "identifier": "S4Vectors",
       "name": "S4Vectors",
@@ -327,7 +315,31 @@
       },
       "sameAs": "https://bioconductor.org/packages/release/bioc/html/S4Vectors.html"
     },
+    "11": {
+      "@type": "SoftwareApplication",
+      "identifier": "httr2",
+      "name": "httr2",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=httr2"
+    },
     "12": {
+      "@type": "SoftwareApplication",
+      "identifier": "curl",
+      "name": "curl",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=curl"
+    },
+    "13": {
       "@type": "SoftwareApplication",
       "identifier": "R",
       "name": "R",
@@ -338,7 +350,7 @@
   "applicationCategory": "Genomics",
   "isPartOf": "https://bioconductor.org",
   "keywords": ["LINCS", "iLINCS", "drugrepurposing", "drugdiscovery", "transcriptomics", "geneexpression", "geneknockdown", "geneoverexpression", "chemicalperturbagen", "drugfindR", "r", "ilincs", "bioinformatics", "bioinformatics-pipeline"],
-  "fileSize": "2083.425KB",
+  "fileSize": "2085.479KB",
   "releaseNotes": "https://github.com/CogDisResLab/drugfindR/blob/master/NEWS.md",
   "readme": "https://github.com/CogDisResLab/drugfindR/blob/devel/README.md",
   "contIntegration": ["https://github.com/CogDisResLab/drugfindR/actions/workflows/rworkflows.yml", "https://app.codecov.io/gh/CogDisResLab/drugfindR?branch=devel"],