Rename from orderly to orderly1

.github/workflows/R-CMD-check-mac.yaml

@@ -34,7 +34,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: orderly.server
 Title: Serve Orderly
-Version: 0.3.31
+Version: 0.3.32
 Description: Run orderly reports as a server.
 License: MIT + file LICENSE
 Author: Rich FitzJohn
@@ -13,11 +13,11 @@ Imports:
     ids,
     jsonlite,
     lgr,
-    orderly (>= 1.4.10),
+    orderly1 (>= 1.7.0),
     porcelain (>= 0.1.9),
     processx,
     redux,
-    rrq (>= 0.6.0),
+    rrq (>= 0.7.1),
     utils,
     yaml
 Suggests:
@@ -30,9 +30,10 @@ Suggests:
     testthat,
     withr,
     zip
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 Encoding: UTF-8
 Remotes:
+    mrc-ide/rrq,
     reside-ic/porcelain,
     ropensci/jsonvalidate,
-    vimc/orderly
+    orderly1=vimc/orderly@vimc-7135

R/api.R

@@ -87,7 +87,7 @@ target_git_fetch <- function(runner) {
   path <- runner$root
   res <- git_fetch(path)
   if (length(res$output) > 0L) {
-    orderly::orderly_log("fetch", res$output)
+    orderly1::orderly_log("fetch", res$output)
   }
   res$output
 }
@@ -102,7 +102,7 @@ endpoint_git_fetch <- function(runner) {
 target_git_pull <- function(runner) {
   res <- git_pull(runner$root)
   if (length(res$output) > 0L) {
-    orderly::orderly_log("pull", res$output)
+    orderly1::orderly_log("pull", res$output)
   }
   res$output
 }
@@ -198,8 +198,8 @@ target_bundle_pack <- function(path, name, parameters = NULL,
   if (!is.null(parameters)) {
     parameters <- jsonlite::fromJSON(parameters)
   }
-  res <- orderly::orderly_bundle_pack(tempfile(), name, parameters, root = path,
-                                      instance = instance)
+  res <- orderly1::orderly_bundle_pack(tempfile(), name, parameters,
+                                       root = path, instance = instance)
   on.exit(unlink(res$path))
   bytes <- readBin(res$path, "raw", n = file.size(res$path))
   bytes <- porcelain::porcelain_add_headers(
@@ -221,7 +221,7 @@ target_bundle_import <- function(path, data) {
   data_path <- tempfile(fileext = ".zip")
   on.exit(unlink(data_path))
   writeBin(data, data_path)
-  orderly::orderly_bundle_import(data_path, root = path)
+  orderly1::orderly_bundle_import(data_path, root = path)
   scalar(TRUE)
 }
 
@@ -237,7 +237,7 @@ endpoint_bundle_import <- function(path, data) {
 }
 
 target_report_info <- function(runner, id, name) {
-  info <- orderly::orderly_info(id, name, root = runner$root)
+  info <- orderly1::orderly_info(id, name, root = runner$root)
   info <- recursive_scalar(info)
   ## Rename parameters to params for consistency with rest of API
   info <- append(info, list(params = info$parameters))
@@ -483,7 +483,7 @@ check_timeout <- function(runner, rate_limit = 2 * 60) {
 }
 
 target_report_version_artefact_hashes <- function(path, name, id) {
-  db <- orderly::orderly_db("destination", root = path)
+  db <- orderly1::orderly_db("destination", root = path)
   get_report_version(db, name, id)
   sql <- paste(
     "select",
@@ -512,7 +512,7 @@ target_reports <- function(path, reports = NULL) {
   if (!is.null(reports)) {
     reports <- unlist(strsplit(reports, split = ","))
   }
-  db <- orderly::orderly_db("destination", root = path)
+  db <- orderly1::orderly_db("destination", root = path)
   get_all_reports(db, reports)
 }
 
@@ -526,7 +526,7 @@ endpoint_reports <- function(path) {
 }
 
 target_report_versions <- function(path, name) {
-  db <- orderly::orderly_db("destination", root = path)
+  db <- orderly1::orderly_db("destination", root = path)
   sql <- paste(
     "select report_version.id",
     "from report_version",
@@ -551,7 +551,7 @@ endpoint_report_versions <- function(path) {
 }
 
 target_report_version_details <- function(path, name, id) {
-  db <- orderly::orderly_db("destination", root = path)
+  db <- orderly1::orderly_db("destination", root = path)
   report_version <- get_report_version(db, name, id)
   artefacts <- get_artefacts_for_version(db, id)
   parameters <- get_parameters_for_versions(db, id)
@@ -586,7 +586,7 @@ endpoint_report_version_details <- function(path) {
 }
 
 target_report_versions_custom_fields <- function(path, versions) {
-  db <- orderly::orderly_db("destination", root = path)
+  db <- orderly1::orderly_db("destination", root = path)
   get_custom_fields_for_versions(db, unlist(strsplit(versions, split = ",")))
 }
 
@@ -600,7 +600,7 @@ endpoint_report_versions_custom_fields <- function(path) {
 }
 
 target_custom_fields <- function(path) {
-  db <- orderly::orderly_db("destination", root = path)
+  db <- orderly1::orderly_db("destination", root = path)
 
   sql <- paste(
     "select custom_fields.id",
@@ -619,7 +619,7 @@ endpoint_custom_fields <- function(path) {
 }
 
 target_report_versions_params <- function(path, versions) {
-  db <- orderly::orderly_db("destination", root = path)
+  db <- orderly1::orderly_db("destination", root = path)
   get_parameters_for_versions(db, unlist(strsplit(versions, split = ",")))
 }
 
@@ -633,7 +633,7 @@ endpoint_report_versions_params <- function(path) {
 }
 
 target_report_version_data_hashes <- function(path, name, id) {
-  db <- orderly::orderly_db("destination", root = path)
+  db <- orderly1::orderly_db("destination", root = path)
   get_report_version(db, name, id)
   sql <- paste(
     "select",
@@ -657,7 +657,7 @@ endpoint_report_version_data_hashes <- function(path) {
 }
 
 target_report_version_resource_hashes <- function(path, name, id) {
-  db <- orderly::orderly_db("destination", root = path)
+  db <- orderly1::orderly_db("destination", root = path)
   get_report_version(db, name, id)
   sql <- paste(
     "select",
@@ -685,7 +685,7 @@ target_report_version_changelog <- function(path,
                                             name,
                                             id,
                                             public_only = FALSE) {
-  db <- orderly::orderly_db("destination", root = path)
+  db <- orderly1::orderly_db("destination", root = path)
   version <- get_report_version(db, name, id)
   if (public_only) {
     version_field <- "changelog.report_version_public"
@@ -743,7 +743,7 @@ build_version <- function(v, custom_fields, params) {
 }
 
 target_all_versions <- function(path) {
-  db <- orderly::orderly_db("destination", root = path)
+  db <- orderly1::orderly_db("destination", root = path)
   versions <- get_all_versions(db)
   custom_fields <- get_custom_fields_for_versions(db, versions$id)
   params <- get_parameters_for_versions(db, versions$id)

R/backup.R

@@ -73,7 +73,7 @@ orderly_backup_ <- R6::R6Class(
       }
       now <- Sys.time()
       message(sprintf("%s - Backing up orderly db", now))
-      orderly:::orderly_backup(self$config)
+      orderly1:::orderly_backup(self$config)
       self$last_backup <- now
       invisible(TRUE)
     }

R/dependencies.R

@@ -1,6 +1,6 @@
 get_dependencies <- function(path, name, id,
                              direction, propagate, max_depth, show_all, use) {
-  report_tree <- orderly::orderly_graph(name = name, id = id,
+  report_tree <- orderly1::orderly_graph(name = name, id = id,
                                        root = path, locate = FALSE,
                                        direction = direction,
                                        propagate = propagate,

R/git.R

@@ -62,13 +62,13 @@ git_checkout_branch <- function(name, force = FALSE, root = NULL,
   ##      ^ this does not return anything sensible when we were in
   ##        detached head state; detect HEAD and get the hash perhaps?
   args <- c("checkout", if (create) "-b", name)
-  orderly::orderly_log("git", sprintf("checkout %s; was %s", name, prev))
+  orderly1::orderly_log("git", sprintf("checkout %s; was %s", name, prev))
   git_run(args, root = root, check = TRUE)
   prev
 }
 
 git_clone_local <- function(source, destination = NULL) {
-  orderly::orderly_log("git", "clone")
+  orderly1::orderly_log("git", "clone")
   if (!length(destination)) {
     destination <- tempfile()
     dir_create(destination)
@@ -83,12 +83,12 @@ git_clone_local <- function(source, destination = NULL) {
 }
 
 git_fetch <- function(root = NULL) {
-  orderly::orderly_log("git", "fetch")
+  orderly1::orderly_log("git", "fetch")
   git_run("fetch", root = root, check = TRUE)
 }
 
 git_pull <- function(root = NULL) {
-  orderly::orderly_log("git", "pull")
+  orderly1::orderly_log("git", "pull")
   git_run("pull", root = root, check = TRUE)
 }
 

R/main.R

@@ -49,8 +49,8 @@ main_worker <- function(args = commandArgs(TRUE)) {
   # nocov start
   args <- main_worker_args(args)
   wait_for_go_signal(NULL, args$go_signal)
-  w <- rrq::rrq_worker_from_config(orderly_queue_id(args$queue_id, TRUE),
-                                   timeout = 30)
+  w <- rrq::rrq_worker(orderly_queue_id(args$queue_id, TRUE),
+                       timeout_config = 30)
   w$loop()
   invisible(TRUE)
   # nocov end

R/runner.R

@@ -26,7 +26,7 @@
 ##' @examples
 ##' available <- redux::redis_available()
 ##' if (available) {
-##'   path <- orderly:::prepare_orderly_git_example()
+##'   path <- orderly1:::prepare_orderly_git_example()
 ##'   runner <- orderly.server::orderly_runner(path[["local"]], workers = 0)
 ##' }
 orderly_runner <- function(path, identity = NULL, queue_id = NULL,
@@ -41,7 +41,7 @@ runner_run <- function(key_report_id, key, root, name, parameters, instance,
   dir.create(bin)
   orderly_bin <- write_script(
     bin,
-    readLines(system.file("script", package = "orderly", mustWork = TRUE)),
+    readLines(system.file("script", package = "orderly1", mustWork = TRUE)),
     versioned = TRUE)
   id_file <- path_id_file(root, key)
   if (!is.null(parameters)) {
@@ -161,12 +161,12 @@ orderly_runner_ <- R6::R6Class(
                           workers, cleanup_on_exit = workers > 0,
                           worker_timeout = Inf) {
       if (is.null(identity)) {
-        self$config <- orderly::orderly_config(root)
+        self$config <- orderly1::orderly_config(root)
       } else {
         self$identity <- identity
         self$config <- withr::with_envvar(
           c(ORDERLY_API_SERVER_IDENTITY = identity),
-          orderly::orderly_config(root))
+          orderly1::orderly_config(root))
       }
       self$root <- self$config$root
       if (!runner_has_git(self$root)) {
@@ -182,7 +182,7 @@ orderly_runner_ <- R6::R6Class(
 
       ## This ensures that the index will be present, which will be
       ## useful if something else wants to access the database!
-      DBI::dbDisconnect(orderly::orderly_db("destination", self$config, FALSE))
+      DBI::dbDisconnect(orderly1::orderly_db("destination", self$config, FALSE))
 
       ## Create directories for storing logs and id files
       dir_create(dirname(path_stderr(self$root, "ignore")))
@@ -195,7 +195,8 @@ orderly_runner_ <- R6::R6Class(
       message("Starting queue")
       self$queue_id <- orderly_queue_id(queue_id)
       self$queue <- rrq::rrq_controller$new(self$queue_id, self$con)
-      self$queue$worker_config_save("localhost", heartbeat_period = 10)
+      config <- rrq::rrq_worker_config(heartbeat_period = 10)
+      self$queue$worker_config_save("localhost", config)
       self$start_workers(workers, worker_timeout)
       self$keys <- orderly_key(self$queue$queue_id)
     },
@@ -204,11 +205,11 @@ orderly_runner_ <- R6::R6Class(
     #' Re-read configuration and set options
     reload = function() {
       if (is.null(self$identity)) {
-        self$config <- orderly::orderly_config(self$root)
+        self$config <- orderly1::orderly_config(self$root)
       } else {
         self$config <- withr::with_envvar(
           c(ORDERLY_API_SERVER_IDENTITY = self$identity),
-          orderly::orderly_config(self$root))
+          orderly1::orderly_config(self$root))
       }
 
       opts <- self$config$server_options()

R/temp.R

@@ -4,7 +4,7 @@ orderly_upstream_dependencies <- function(reports, root = NULL, locate = TRUE,
   if (!is.null(ref)) {
     assert_scalar_character(ref)
   }
-  config <- orderly::orderly_config(root, locate)
+  config <- orderly1::orderly_config(root, locate)
   stats::setNames(lapply(reports, report_dependencies, ref, config), reports)
 }
 

README.md

@@ -18,8 +18,8 @@ All the query stuff is already dealt with in [montagu-reporting-api](https://git
 IMAGE=docker.montagu.dide.ic.ac.uk:5000/orderly.server:master
 docker pull $IMAGE
 mkdir orderly
-docker run --rm --entrypoint Rscript -v ${PWD}/orderly:/orderly --user ${UID} $IMAGE -e 'orderly:::prepare_orderly_git_example("/orderly")'
-docker run --rm --entrypoint Rscript -v ${PWD}/orderly:/orderly --user ${UID} $IMAGE -e 'orderly::orderly_rebuild("/orderly")'
+docker run --rm --entrypoint Rscript -v ${PWD}/orderly:/orderly --user ${UID} $IMAGE -e 'orderly1:::prepare_orderly_git_example("/orderly")'
+docker run --rm --entrypoint Rscript -v ${PWD}/orderly:/orderly --user ${UID} $IMAGE -e 'orderly1::orderly_rebuild("/orderly")'
 docker run --rm -p 8321:8321 -v ${PWD}/orderly:/orderly --user ${UID} $IMAGE /orderly
 ```
 

docker/common

@@ -32,7 +32,7 @@ TAG_LATEST="${PACKAGE_ORG}/${PACKAGE_NAME}:latest"
 ## combined tag so that we never replace an existing tagged
 ## image built off master with an image with a different
 ## version of orderly installed
-ORDERLY_VERSION="${ORDERLY_VERSION:-master}"
+ORDERLY_VERSION="${ORDERLY_VERSION:-vimc-7135}"
 if [ "$ORDERLY_VERSION" != "master" ]; then
     TAG_SHA="$TAG_SHA-$ORDERLY_VERSION"
     buildkite-agent meta-data set "orderly-server-sha" $TAG_SHA

inst/schema/spec.md

@@ -406,7 +406,7 @@ As for the `/reports/:name/run/` endpoint, accepts as `POST` body json that will
 
 Also accepts the query parameter `instance` which can be used to change database instance.
 
-Returns binary data, being the created bundle object for use with `orderly::orderly_bundle_run`
+Returns binary data, being the created bundle object for use with `orderly1::orderly_bundle_run`
 
 ## POST /bundle/import