lshep · Apr 22, 2025 · Jan 3, 2025 · Jan 6, 2025 · Jan 6, 2025 · Jan 6, 2025
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: AnnotationHub
 Type: Package
 Title: Client to access AnnotationHub resources
-Version: 3.17.0
+Version: 3.99.0
 Authors@R: 
     c(person("Bioconductor Package", "Maintainer", email="maintainer@bioconductor.org",
              role="cre"),
@@ -23,9 +23,9 @@ Description: This package provides a client for the Bioconductor
     files retrieved by the user, helping with quick and reproducible
     access.
 License: Artistic-2.0
-Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1)
+Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 2.99.0)
 Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs,
-    AnnotationDbi (>= 1.31.19), S4Vectors, httr, yaml, dplyr
+    AnnotationDbi (>= 1.31.19), S4Vectors, httr2, yaml, dplyr
 Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools,
     rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser,
     RUnit, txdbmaker, MSnbase, mzR, Biostrings, CompoundDb, keras,

diff --git a/NAMESPACE b/NAMESPACE
@@ -13,11 +13,8 @@ importFrom(grDevices, rgb)
 importFrom(utils, packageVersion, read.csv, read.delim, unzip,
     capture.output, read.table, .DollarNames
 )
-importFrom(httr,
-    GET, content, parse_url, progress, write_disk,
-    stop_for_status, status_code, use_proxy, HEAD, headers
-)
 importFrom(yaml, yaml.load)
+import(httr2)
 
 importMethodsFrom(AnnotationDbi, dbconn, dbfile)
 importFrom(AnnotationDbi, dbFileConnect)
@@ -71,8 +68,8 @@ export(
     .Hub, AnnotationHub,
     removeCache,
     getAnnotationHubOption, setAnnotationHubOption,
-    possibleDates, mcols,
-    .httr_proxy, .hub_option_key, .db_close,
+    possibleDates, mcols, .getProxyValue,
+    .hub_option_key, .db_close,
     recordStatus, DispatchClassList, refreshHub
 )
 

diff --git a/NEWS b/NEWS
@@ -1,3 +1,10 @@
+CHANGES IN VERSION 3.99.0
+----------------------
+
+MAJOR UPDATES
+
+    o Update downloading method from httr to httr2
+
 CHANGES IN VERSION 3.13.0
 -------------------------
 

diff --git a/R/AnnotationHub-class.R b/R/AnnotationHub-class.R
@@ -30,9 +30,7 @@ AnnotationHub <-
     }
     if (!is.null(proxy)) {
         message("Assuming valid proxy connection through '",
-                ifelse(is(proxy,"request"),
-                       paste(unlist(proxy), collapse=":"),
-                       proxy),
+                proxy,
                 "'",
                 "\n If you experience connection issues consider ",
                 "using 'localHub=TRUE'")

diff --git a/R/AnnotationHubOption.R b/R/AnnotationHubOption.R
@@ -29,13 +29,11 @@ setAnnotationHubOption <- function(arg, value)
         stopifnot(isSingleInteger(value))
         value
     }, PROXY={
-        if (is.null(value) || inherits(value, "request"))
+        if (is.null(value) || (isSingleString(value)))
             value
-        else if (isSingleString(value)) {
-            .httr_proxy(value)
-        } else {
-            txt <- "'value' must be an httr proxy request (use_proxy()),
-                    character(1), or NULL"
+        else {
+            txt <-
+                "'value' must be an single string value character(1) in embedded format (e.g. http://my_user:my_password@myproxy:8080), or NULL"
             stop(paste(strwrap(txt, exdent=2), collapse="\n"))
         }
     }, LOCAL={
@@ -47,13 +45,14 @@ setAnnotationHubOption <- function(arg, value)
     })
 }
 
-.httr_proxy <- function(value)
-{
-    rm <- parse_url(value)
-    if (is.null(rm$scheme))
-        stop("PROXY 'value' does not include scheme (e.g., 'http://')")
-    rm$url <- paste0(rm$scheme, "://", rm$hostname)
-    if (!is.null(rm$port))
-        rm$port <- as.integer(rm$port)
-    do.call(use_proxy, rm[c("url", "port", "username", "password")])
-}
+## .httr_proxy <- function(value)
+## {
+##     rm <- parse_url(value)
+##     if (is.null(rm$scheme))
+##         stop("PROXY 'value' does not include scheme (e.g., 'http://')")
+##     rm$url <- paste0(rm$scheme, "://", rm$hostname)
+##     if (!is.null(rm$port))
+##         rm$port <- as.integer(rm$port)
+##     do.call(use_proxy, rm[c("url", "port", "username", "password")])
+## }
+
diff --git a/R/Hub-class.R b/R/Hub-class.R
@@ -29,7 +29,7 @@ setClass("Hub",
     # find snapshot date
     if (!localHub){
         tryCatch({
-            db_date <- .restrictDateByVersion(db_path)
+            db_date <- .restrictDateByVersion(db_path, proxy)
         }, error=function(err) {
             stop("failed to connect",
                  "\n  reason: ", conditionMessage(err),
@@ -127,6 +127,7 @@ setReplaceMethod("isLocalHub", "Hub",
     function(x, value)
 {
     stopifnot(value %in% c(TRUE, FALSE))
+    proxy <- .getProxyValue(x)
     # not a no op
     if (isLocalHub(x) != value){
         # switch from FALSE to TRUE
@@ -136,7 +137,7 @@ setReplaceMethod("isLocalHub", "Hub",
         # switch from TRUE to FALSE
         }else{
             db_path <- x@.db_path
-            db_date <- .restrictDateByVersion(db_path)
+            db_date <- .restrictDateByVersion(db_path, proxy)
             db_uid <- .db_uid0(db_path, db_date, value)
             x <- new(as.character(class(x)), cache=hubCache(x), hub=hubUrl(x),
                      date=db_date, .db_path=db_path, .db_uid=db_uid,
@@ -159,9 +160,10 @@ setReplaceMethod("snapshotDate", "Hub",
     }, error=function(err) {
         stop("'value' must be a single date or character string")
     })
+    proxy <- .getProxyValue(x)
 
     ## 'value' must be < BiocManager::version() release date
-    restrict <- .restrictDateByVersion(dbfile(x))
+    restrict <- .restrictDateByVersion(dbfile(x), proxy)
     dates <- .possibleDates(dbfile(x))
     valid_range <- range(dates[as.POSIXlt(dates) <= as.POSIXlt(restrict)])
     if (as.POSIXlt(value) > max(valid_range) ||
@@ -345,7 +347,8 @@ setReplaceMethod("cache", "Hub",
     localHub <- isLocalHub(x)
     db_path <- x@.db_path
     if (!localHub){
-        db_date <- .restrictDateByVersion(db_path)
+        proxy <- .getProxyValue(x)
+        db_date <- .restrictDateByVersion(db_path, proxy)
     } else {
         dates <-.possibleDates(db_path)
         db_date <- dates[length(dates)]
@@ -419,7 +422,8 @@ setMethod("removeResources", "character",
                 localHub <- isLocalHub(hub)
                 db_path <- hub@.db_path
                 if (!localHub){
-                    db_date <- .restrictDateByVersion(db_path)
+                    proxy <- .getProxyValue(x)
+                    db_date <- .restrictDateByVersion(db_path, proxy)
                 } else {
                     dates <-.possibleDates(db_path)
                     db_date <- dates[length(dates)]
@@ -499,7 +503,10 @@ getSize <- function(hub, tbl)
     vapply(urls,
            FUN=function(url){
                tryCatch({
-                   headers(HEAD(url))$`content-length`
+                   response = request(url) %>% req_method("HEAD") %>% req_perform()
+                   ifelse(resp_header_exists(response, "content-length"),
+                          resp_header(response, "content-length"),
+                          NA_character_)
                }, error = function(err){
                    NA_character_
                })

diff --git a/R/Hub-utils.R b/R/Hub-utils.R
@@ -155,12 +155,20 @@ refreshHub <- function(..., hub, cache, proxy,
 ###
 
 ## returns the release date for BiocManager::version()
-.biocVersionDate <- function(biocversion) {
+.biocVersionDate <- function(biocversion, proxy) {
     if (length(biocversion) > 1L)
         stop("length(biocversion) must == 1")
 
-    yaml <- httr::content(GET("https://bioconductor.org/config.yaml"),
-                    encoding="UTF-8", as="text")
+    if ((proxy == "") || is.null(proxy)){
+        proxy <- NULL
+    }
+
+    req <- request("https://bioconductor.org/config.yaml")
+    # Apply the proxy if it's not NULL
+    if (!is.null(proxy)) {
+        req <- req %>% req_proxy(proxy)
+    }
+    yaml <-  req %>% req_perform() %>% resp_body_string(encoding = "UTF-8")
     obj <- yaml.load(yaml)
     release_dates <- obj$release_dates
     version_date <- release_dates[biocversion == names(release_dates)]
@@ -172,9 +180,9 @@ refreshHub <- function(..., hub, cache, proxy,
 }
 
 ## single date closest to the release date for BiocManager::version()
-.restrictDateByVersion <- function(path) {
+.restrictDateByVersion <- function(path, proxy) {
     dates <- as.POSIXlt(.possibleDates(path), format='%Y-%m-%d')
-    restrict <- as.POSIXlt(.biocVersionDate(BiocManager::version()),
+    restrict <- as.POSIXlt(.biocVersionDate(BiocManager::version(), proxy),
                            format='%Y-%m-%d')
     if (length(restrict))  ## release
         as.character(max(dates[dates <= restrict]))
@@ -197,7 +205,8 @@ refreshHub <- function(..., hub, cache, proxy,
 possibleDates <- function(x) {
     path <- dbfile(x)
     dates <- .possibleDates(path)
-    restrict <- .restrictDateByVersion(path)
+    proxy <- .getProxyValue(x)
+    restrict <- .restrictDateByVersion(path, proxy)
     dates[as.POSIXlt(dates) <= as.POSIXlt(restrict)]
 }
 
@@ -412,3 +421,18 @@ convertHub <- function(oldcachepath=NULL, newcachepath=NULL,
 
     hubCache(hub)
 }
+
+.getProxyValue <- function(x){
+
+    proxy <- NULL
+    if(is(x, "AnnotationHub")){
+        proxy <- getAnnotationHubOption("PROXY")
+    }
+    if(is(x, "ExperimentHub")){
+        proxy <- getExperimentHubOption("PROXY")
+    }
+    if(is.null(proxy) && is(x, "Hub")){
+        proxy <- Sys.getenv("HUB_PROXY")
+    }
+    proxy
+}
diff --git a/man/Hub-utils.Rd b/man/Hub-utils.Rd
@@ -82,8 +82,9 @@ getInfoOnIds(hub, 69303)
 "https://annotationhub.bioconductor.org/fetch/69303"
 
 # or in R
-httr::GET("https://annotationhub.bioconductor.org/fetch/69303",
-	  write_disk(<pathToSave/69303>, overwrite=FALSE))
+library(httr2)
+req <- request("https://annotationhub.bioconductor.org/fetch/69303")
+response <- req_perform(req, path=<pathToSave/69303>, ...)
 
 # 3. To add to a hub cache (not recommended)
 hub <- AnnotationHub()

diff --git a/man/getAnnotationHubOption.Rd b/man/getAnnotationHubOption.Rd
@@ -38,19 +38,24 @@ setAnnotationHubOption(arg, value)
       avoid accidental download of a large number of AnnotationHub
       members.}
 
-    \item{\dQuote{PROXY}:}{\code{request} object returned by
-      \code{httr::use_proxy()}. The \code{request} object describes a proxy
+    \item{\dQuote{PROXY}:}{Describes a proxy
       connection allowing Internet access, usually through a restrictive
       firewall. Setting this option sends all AnnotationHub requests through
-      the proxy. Default: NULL.
+      the proxy. Default: NULL. 
 
-      In \code{setAnnotationHubOption("PROXY", value)}, \code{value} can be one of NULL,
-      a \code{request} object returned by \code{httr::use_proxy()}, or a
-      well-formed URL as character(1). The URL can be completely
+      In \code{setAnnotationHubOption("PROXY", value)}, \code{value} can
+      be NULL or a well-formed URL as character(1). The URL can be completely
       specified by \code{http://username:password@proxy.dom.com:8080};
       \code{username:password} and port (e.g. \code{:8080}) are
-      optional.If behind a proxy it will also be useful to set the
-      \code{httr::set_config(proxy)} with the proxy information.}
+      optional.
+
+      Unfortunately unlike the previously used
+      `httr::set_config`, there is no option to globally set the proxy
+      for httr2 requests. To get around this you can also set a system
+      wide environment variable "ANNOTATION_HUB_PROXY" for AnnotationHub
+      proxy or "HUB_PROXY" that will work across all Hub classes
+      (e.g. AnnotationHub and ExperimentHub)    
+    }
 
     \item{\dQuote{LOCAL}:}{logical(1). TRUE/FALSE should the AnnotationHub
       create a hub consisting only of previously downloaded resourcesd.

diff --git a/vignettes/AnnotationHub.Rmd b/vignettes/AnnotationHub.Rmd
@@ -247,18 +247,24 @@ vignette("TroubleshootingTheHubs", package="AnnotationHub")
 
 # Accessing Behind A Proxy
 
-The AnnotationHub uses CRAN package `httr` functions `HEAD` and `GET` for accessing
-web resources. This can be problematic if operating behind a proxy. The easiest
-solution is to set the `httr::set_config` with the proxy information.
+
+The ExperimentHub and AnnotationHub use CRAN package `httr2` functions for accessing and downloading
+web resources. This can be problematic if operating behind a
+proxy. You can pass proxy information for Hubs by setting the options like the following:
 
 ```
-proxy <- httr::use_proxy("http://my_user:my_password@myproxy:8080")
-## or
-proxy <- httr::use_proxy(Sys.getenv('http_proxy'))
-httr::set_config(proxy)
+proxy <- "http://my_user:my_password@myproxy:8080"
 AnnotationHub::setAnnotationHubOption("PROXY", proxy)
+## or 
+ExperimentHub::setExperimentHubOption("PROXY", proxy)
 ```
 
+Unfortunately unlike the previously used `httr::set_config`, there is no
+option to globally set the proxy for httr2 requests. To get around this you can
+also set a system wide environment variable "ANNOTATION_HUB_PROXY" for
+AnnotationHub, "EXPERIMENT_HUB_PROXY" for ExperimentHub, or "HUB_PROXY" that
+will work across all Hub classes (e.g. AnnotationHub and ExperimentHub)}
+
 
 
 # Session info

diff --git a/vignettes/TroubleshootingTheHubs.Rmd b/vignettes/TroubleshootingTheHubs.Rmd
@@ -30,21 +30,23 @@ asked issues. If the question or answer cannot be found here please ask on the
 
 ## Accessing Behind A Proxy
 
-The ExperimentHub and AnnotationHub use CRAN package `httr` functions `HEAD` and
-`GET` for accessing web resources. This can be problematic if operating behind a
-proxy. The easiest solution is to set the `httr::set_config` with the proxy
-information.
+The ExperimentHub and AnnotationHub use CRAN package `httr2` functions for accessing and downloading
+web resources. This can be problematic if operating behind a
+proxy. You can pass proxy information for Hubs by setting the options like the following:
 
 ```
-proxy <- httr::use_proxy("http://my_user:my_password@myproxy:8080")
-## or
-proxy <- httr::use_proxy(Sys.getenv('http_proxy'))
-httr::set_config(proxy)
+proxy <- "http://my_user:my_password@myproxy:8080"
 AnnotationHub::setAnnotationHubOption("PROXY", proxy)
 ## or 
 ExperimentHub::setExperimentHubOption("PROXY", proxy)
 ```
 
+Unfortunately unlike the previously used `httr::set_config`, there is no
+option to globally set the proxy for httr2 requests. To get around this you can
+also set a system wide environment variable "ANNOTATION_HUB_PROXY" for
+AnnotationHub, "EXPERIMENT_HUB_PROXY" for ExperimentHub, or "HUB_PROXY" that
+will work across all Hub classes (e.g. AnnotationHub and ExperimentHub)}
+
 ## Invalid Cache
 
 An invalid cache ERROR results from a missing sqlite or index file in the Hub's