Merge pull request #49 from getwilds/dev

rcromwell v3.3.0 Updates

Author: tefirman

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rcromwell
 Title: Convenience Tools for Managing WDL Workflows via Cromwell
-Version: 3.2.5
+Version: 3.3.0
 Authors@R: c(
     person("Amy", "Paguirigan", role = "aut",
            comment = c(ORCID = "0000-0002-6819-9736")),
@@ -12,30 +12,28 @@ URL: https://getwilds.org/rcromwell, https://github.com/getwilds/rcromwell
 BugReports: https://github.com/getwilds/rcromwell/issues
 Description: A repo containing a basic R package for using Cromwell with WDL workflows via R.
 Imports:
-    httr,
     jsonlite,
     dplyr,
     purrr,
     tidyr,
     lubridate,
     rlang,
-    glue
+    glue,
+    curl,
+    httr2
 License: MIT + file LICENSE
-Depends: R (>= 3.6.0)
+Depends: R (>= 4.1.0)
 Roxygen: list(markdown = TRUE, roclets = c("collate", "namespace", "rd",
     "roxyglobals::global_roclet"))
 RoxygenNote: 7.3.2
 Encoding: UTF-8
 Suggests:
-    curl,
     knitr,
     rmarkdown,
     roxyglobals,
     testthat (>= 3.0.0),
-    vcr (>= 0.6.0),
-    webmockr
-Remotes:
-    ropensci/vcr
+    vcr (>= 1.6.0),
+    webmockr (>= 1.0.0)
 Config/testthat/edition: 3
 Config/roxyglobals/filename: globals.R
 Config/roxyglobals/unique: FALSE

NAMESPACE

@@ -19,18 +19,21 @@ export(cromwell_workflow)
 export(cw_url)
 export(workflow_inputs)
 export(workflow_options)
+importFrom(curl,form_file)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,any_of)
 importFrom(dplyr,as_tibble)
 importFrom(dplyr,relocate)
 importFrom(dplyr,tibble)
 importFrom(glue,glue)
-importFrom(httr,GET)
-importFrom(httr,POST)
-importFrom(httr,content)
-importFrom(httr,status_code)
-importFrom(httr,stop_for_status)
-importFrom(httr,upload_file)
+importFrom(httr2,req_body_multipart)
+importFrom(httr2,req_error)
+importFrom(httr2,req_headers)
+importFrom(httr2,req_method)
+importFrom(httr2,req_perform)
+importFrom(httr2,req_url_query)
+importFrom(httr2,request)
+importFrom(httr2,resp_body_json)
 importFrom(jsonlite,fromJSON)
 importFrom(lubridate,now)
 importFrom(lubridate,with_tz)
@@ -43,7 +46,6 @@ importFrom(purrr,map_dfr)
 importFrom(purrr,pluck)
 importFrom(purrr,reduce)
 importFrom(rlang,abort)
-importFrom(rlang,caller_env)
 importFrom(rlang,has_name)
 importFrom(rlang,is_character)
 importFrom(rlang,is_logical)

NEWS.md

@@ -1,3 +1,7 @@
+# rcromwell 3.3.0
+
+* Swapping `httr` for `httr2` and fixing styling (@sckott in [#48](https://github.com/getwilds/rcromwell/pull/48))
+
 # rcromwell 3.2.5
 
 * gains new function `cromwell_labels` that hits the `/labels` route (#43) (#45)

R/cromwellAbort.R

@@ -9,8 +9,10 @@
 cromwell_abort <- function(workflow_id, url = cw_url(), token = NULL) {
   check_url(url)
   crom_mssg("Aborting job in Cromwell")
-  http_post(make_url(url, "api/workflows/v1", workflow_id, "abort"),
+  http_req_post(
+    url = make_url(url, "api/workflows/v1", workflow_id, "abort"),
     token = token
-  ) %>%
+  ) |>
+    http_perform() |>
     dplyr::as_tibble()
 }

R/cromwellBackends.R

@@ -8,7 +8,11 @@
 cromwell_backends <- function(url = cw_url(), token = NULL) {
   check_url(url)
   crom_mssg("Getting backend options from Cromwell")
-  all <- http_get(make_url(url, "api/workflows/v1/backends"), token = token)
+  all <- http_req_get(
+    url = make_url(url, "api/workflows/v1/backends"),
+    token = token
+  ) |>
+    http_perform()
   all$supportedBackends <- unlist(all$supportedBackends)
   return(all)
 }

R/cromwellCache.R

@@ -20,12 +20,12 @@ cromwell_cache <- function(workflow_id, url = cw_url(), token = NULL) {
 }
 
 cromwell_cache_http <- function(workflow_id, url = cw_url(), token = NULL) {
-  http_get(
+  http_req_get(
     url = make_url(url, "api/workflows/v1", workflow_id, "metadata"),
-    query = list(expandSubWorkflows = "false"),
-    as = "parsed",
     token = token
-  )
+  ) |>
+    req_url_query(expandSubWorkflows = "false") |>
+    http_perform()
 }
 
 #' @autoglobal
@@ -50,7 +50,7 @@ cromwell_cache_process <- function(crommetadata, workflow_id) {
           # add the shard Index associated
           b$shardIndex <- shard_data$shardIndex
         } else {
-          b <- dplyr::as_tibble("shardIndex" = shard_data$shardIndex)
+          b <- dplyr::tibble("shardIndex" = shard_data$shardIndex)
         }
         b$shardIndex <- as.character(b$shardIndex)
         b$workflow_id <- workflow_id

R/cromwellCall.R

@@ -27,12 +27,12 @@ cromwell_call <- function(workflow_id, url = cw_url(), token = NULL) {
   check_url(url)
   crom_mssg(glue("Querying for call metadata for workflow id: {workflow_id}"))
   crommetadata <-
-    http_get(
+    http_req_get(
       url = make_url(url, "api/workflows/v1", workflow_id, "metadata"),
-      query = list(expandSubWorkflows = "true"),
-      as = "parsed",
       token = token
-    )
+    ) |>
+    req_url_query(expandSubWorkflows = "true") |>
+    http_perform()
   # if the response is a character vector, then return it and stop
   if (is.character(crommetadata)) stop(crommetadata)
   # if the response is a list, meaning it has some content, continue

R/cromwellFailures.R

@@ -25,12 +25,12 @@ cromwell_failures <- function(workflow_id, url = cw_url(), token = NULL) {
   ))
 
   response <-
-    http_get(
+    http_req_get(
       url = make_url(url, "api/workflows/v1", workflow_id, "metadata"),
-      query = list(includeKey = "failures", includeKey = "jobId"),
-      as = "parsed",
       token = token
-    )
+    ) |>
+    req_url_query(includeKey = "failures", includeKey = "jobId") |>
+    http_perform()
   cromwell_failures_process(response, workflow_id)
 }
 

R/cromwellGlob.R

@@ -30,10 +30,7 @@ cromwell_glob <- function(
   check_url(url)
   crom_mssg(glue("Querying for metadata for workflow id: {workflow_id}"))
   url <- make_url(url, "api/workflows/v1", workflow_id, "metadata")
-  http_get(
-    url = url,
-    query = list(expandSubWorkflows = tolower(expand_sub_workflows)),
-    as = "parsed",
-    token = token
-  )
+  http_req_get(url = url, token = token) |>
+    req_url_query(expandSubWorkflows = tolower(expand_sub_workflows)) |>
+    http_perform()
 }

R/cromwellJobs.R

@@ -34,10 +34,12 @@ cromwell_jobs <- function(days = 1,
   check_url(url)
   crom_mssg(glue("Querying cromwell for jobs in the last {days} days"))
   query <- cromwell_jobs_query(days, workflow_name, workflow_status)
-  jobs_data <- http_get(
-    make_url(url, "api/workflows/v1/query"),
-    query = query, token = token
-  )
+  jobs_data <- http_req_get(
+    url = make_url(url, "api/workflows/v1/query"),
+    token = token
+  ) |>
+    req_url_query(!!!query) |>
+    http_perform()
   cromwell_jobs_process(jobs_data$results)
 }
 

R/cromwellLogs.R

@@ -20,16 +20,16 @@ cromwell_logs <- function(workflow_id, url = cw_url(), token = NULL) {
 }
 
 cromwell_logs_query <- function(workflow_id, url = cw_url(), token = NULL) {
-  http_get(
+  http_req_get(
     url = make_url(
       url,
       "api/workflows/v1",
       workflow_id,
       "logs"
     ),
-    as = "parsed",
     token = token
-  )
+  ) |>
+    http_perform()
 }
 
 cromwell_logs_process <- function(response, workflow_id) {

R/cromwellOutputs.R

@@ -19,17 +19,17 @@ cromwell_outputs <- function(workflow_id, url = cw_url(), token = NULL) {
 }
 
 cromwell_outputs_query <- function(workflow_id, url = cw_url(), token = NULL) {
-  http_get(
+  http_req_get(
     url =
       make_url(
         url,
         "api/workflows/v1",
         workflow_id,
         "outputs"
       ),
-    as = "parsed",
     token = token
-  )
+  ) |>
+    http_perform()
 }
 
 #' @autoglobal

R/cromwellSubmitBatch.R

@@ -43,7 +43,7 @@ cromwell_submit_batch_query <- function(
     )
   }
   body <- list(
-    workflowSource = httr::upload_file(wdl)
+    workflowSource = curl::form_file(wdl)
   )
 
   if (!is.null(params) && !is.null(batch)) {
@@ -78,10 +78,10 @@ cromwell_submit_batch_query <- function(
 }
 
 cromwell_submit_batch_http <- function(body, url, token) {
-  http_post(
+  http_req_post(
     url = make_url(url, "api/workflows/v1"),
-    body = body,
-    encode = "multipart",
     token = token
-  )
+  ) |>
+    req_body_multipart(!!!body) |>
+    http_perform()
 }

R/cromwellTiming.R

@@ -6,19 +6,17 @@
 #' supplied set the url as the env var `CROMWELLURL`
 #' @inheritSection workflow_options Important
 #' @author Amy Paguirigan, Scott Chamberlain
-#' @details Internally this function uses [httr::BROWSE()] which uses
-#' [utils::browseURL()] - if a auth header is required you'll have to
-#' do that manually
+#' @details Internally this function uses [utils::browseURL()] - if an
+#' auth header is required you'll have to do that manually
 #' @return Opens a timing diagram in a browser
 cromwell_timing <- function(workflow_id, url = cw_url()) {
   check_url(url)
   crom_mssg("Getting timing diagram from Cromwell")
-  httr::BROWSE(
-    make_url(
-      url,
-      "api/workflows/v1",
-      workflow_id,
-      "timing"
-    )
+  url <- make_url(
+    url,
+    "api/workflows/v1",
+    workflow_id,
+    "timing"
   )
+  browse(url)
 }

R/cromwellValidate.R

@@ -15,18 +15,18 @@ cromwell_validate <- function(
   check_url(url)
   crom_mssg("Validating a workflow for Cromwell")
 
-  body <- list(workflowSource = httr::upload_file(wdl))
+  body <- list(workflowSource = curl::form_file(wdl))
   if (!is.null(all_inputs)) {
     body <- c(
       body,
-      workflowInputs = list(httr::upload_file(all_inputs))
+      workflowInputs = list(curl::form_file(all_inputs))
     )
   }
 
-  http_post(
+  http_req_post(
     url = make_url(url, "api/womtool/v1/describe"),
-    body = body,
-    encode = "multipart",
     token = token
-  )
+  ) |>
+    req_body_multipart(!!!body) |>
+    http_perform()
 }

R/cromwellVersion.R

@@ -7,5 +7,6 @@
 #' @return (character) the Cromwell version
 cromwell_version <- function(url = cw_url(), token = NULL) {
   check_url(url)
-  http_get(make_url(url, "engine/v1/version"), token = token)
+  http_req_get(url = make_url(url, "engine/v1/version"), token = token) |>
+    http_perform()
 }

R/cromwellWorkflow.R

@@ -27,12 +27,12 @@ cromwell_workflow <- function(workflow_id, url = cw_url(), token = NULL) {
 }
 
 cromwell_workflow_http <- function(workflow_id, url, token) {
-  http_get(
+  http_req_get(
     url = make_url(url, "api/workflows/v1", workflow_id, "metadata"),
-    query = list(expandSubWorkflows = "false", excludeKey = "calls"),
-    as = "parsed",
     token = token
-  )
+  ) |>
+    req_url_query(expandSubWorkflows = "false", excludeKey = "calls") |>
+    http_perform()
 }
 
 cromwell_workflow_process <- function(meta, workflow_id) {