update to http api 0.4.0

.gitignore

@@ -3,6 +3,7 @@ docs
 inst/doc
 dev
 !dev/Makefile
+!dev/extract_irods_services_yaml.R
 *.irods
 /doc/
 /Meta/

DESCRIPTION

@@ -33,7 +33,8 @@ Imports:
     stats,
     testthat (>= 3.0.0),
     utils,
-    withr
+    withr,
+    yaml
 Suggests: 
     httptest2,
     kableExtra,

R/docker-yaml.R

@@ -0,0 +1,25 @@
+get_docker_compose_path <- function() {
+  system.file("irods_demo/docker-compose.yml", package = "rirods")
+}
+
+get_docker_yaml <- function() {
+  docker_compose_file <- yaml::read_yaml(get_docker_compose_path(), handlers = list(
+    # make sure that sequences of size one are read as list
+    # (defaults to vector of length one)
+    seq = function(x) {
+      x <- as.list(x)
+      x
+    }
+  ))
+}
+
+is_irods_service_in_yaml <- function(services, docker_compose_file) {
+  docker_compose_service_names <- names(docker_compose_file[["services"]])
+  irods_services_pattern <- paste0(services, collapse = "|")
+  grepl(irods_services_pattern, docker_compose_service_names)
+}
+
+extract_irods_services_names <- function(services) {
+  docker_compose_file <- get_docker_yaml()
+  names(docker_compose_file[["services"]])[is_irods_service_in_yaml(services, docker_compose_file)]
+}

R/irods-demo.R

@@ -118,17 +118,15 @@ stop_irods_demo <- function(verbose = TRUE) {
 #' @examples
 #' is_irods_demo_running()
 is_irods_demo_running <- function(...) {
-  # first check if Docker exist
+  # first check if Docker exists
   if (!check_docker(FALSE)) {
     return(FALSE)
   }
-  # then check if images exist
+  # then check if images exists
   if (!check_irods_images()) {
     return(FALSE)
   }
-  # check for client-icommand is not required (only needed for demo itself)
   ref <- irods_containers_ref()
-  ref <- ref[ref != "irods-demo-irods-client-icommands-1"]
   irods_containers_state <-
     vapply(ref, is_irods_demo_running_, integer(1))
 
@@ -163,9 +161,9 @@ remove_docker_images <- function() {
 
 start_irods <- function(verbose, recreate = TRUE) {
   if (isTRUE(recreate)) {
-    cmd <- " ; docker compose up -d --force-recreate nginx-reverse-proxy irods-client-http-api irods-client-icommands"
+    cmd <- " ; docker compose up -d --force-recreate "
   } else {
-    cmd <- " ; docker compose up -d nginx-reverse-proxy irods-client-http-api irods-client-icommands"
+    cmd <- " ; docker compose up -d "
   }
   system(
     paste0("cd ", path_to_demo(), cmd),
@@ -219,6 +217,7 @@ is_http_server_running_correct <- function(user, pass, host, lpath) {
 is_irods_server_running_correct <- function() {
   system2(
     system.file(package = "rirods", "shell_scripts", "dry-run-irods-icommands.sh"),
+    system.file("irods_demo", package = "rirods"),
     stdout = FALSE,
     stderr = FALSE
   ) == 0
@@ -262,12 +261,9 @@ check_docker <- function(verbose = TRUE) {
   !(Sys.which("bash") == "" || Sys.which("docker") == "" || docker_version == "")
 }
 
-irods_containers_ref <- function() {
-  irods_demo_yml <- system.file("irods_demo", "docker-compose.yml", package = "rirods")
-  irods_demo_file <- readLines(irods_demo_yml)
-  irods_images_ref <- grep("^\\s{4}[[:graph:]]*?:$", irods_demo_file)
-  irods_images <- irods_demo_file[irods_images_ref]
-  paste0("irods-demo-", trimws(gsub( ":$", "", irods_images)), "-1")
+irods_containers_ref <- function(services = c("nginx", "http-api", "icommands", "catalog")) {
+  docker_compose_service_names = extract_irods_services_names(services)
+  paste0("irods-demo-", docker_compose_service_names, "-1")
 }
 
 irods_images <- c(

R/zzz.R

@@ -3,5 +3,5 @@
 
 .onLoad <- function(libname, pkgname) {
   ns <- topenv()
-  ns$.irods_host <- "http://localhost:9001/irods-http-api/0.2.0"
+  ns$.irods_host <- "http://localhost:9001/irods-http-api/0.4.0"
 }

README.Rmd

@@ -80,7 +80,7 @@ substitute(create_irods(x), list(x = rirods:::.irods_host))
 ```
 
 ```{r project, eval=is_irods_demo_running(), echo=FALSE}
-eval(substitute(create_irods(x), list(x = rirods:::.irods_host)))
+eval(substitute(create_irods(x), list(x = URLencode(rirods:::.irods_host))))
 ```
 
 ### Authentication

README.md

@@ -35,7 +35,7 @@ Launch a local demonstration iRODS service (including the HTTP API):
     use_irods_demo("alice", "passWORD")
 
 This will result in the demonstration HTTP API running at
-<http://localhost:9001/irods-http-api/0.2.0>.
+<http://localhost:9001/irods-http-api/0.4.0>.
 
 These Docker containers are designed to easily stand up a
 **DEMONSTRATION** of the iRODS server. It is intended for education and
@@ -49,7 +49,7 @@ To connect to the HTTP API endpoint of your choice, load `rirods`,
 connect with `create_irods()`, and authenticate with your iRODS
 credentials:
 
-    create_irods("http://localhost:9001/irods-http-api/0.2.0")
+    create_irods("http://localhost:9001/irods-http-api/0.4.0")
 
 ### Authentication
 
@@ -70,7 +70,6 @@ session to an iRODS collection. For this, use the `isaveRDS()` command:
 
     # check where we are in the iRODS namespace
     ipwd()
-    #> [1] "/tempZone/home/alice"
 
     # store data in iRODS
     isaveRDS(foo, "foo.rds")
@@ -89,12 +88,6 @@ describes the data object “foo”:
 
     # check if file is stored with associated metadata
     ils(metadata = TRUE)
-    #> 
-    #> ==========
-    #> iRODS Zone
-    #> ==========
-    #>                  logical_path attribute value units
-    #>  /tempZone/home/alice/foo.rds       foo   bar   baz
 
 For more on using metadata, check out `vignette("metadata")`.
 
@@ -105,10 +98,6 @@ current R session, she would use `ireadRDS()`:
 
     # retrieve in native R format
     ireadRDS("foo.rds")
-    #>   x y
-    #> 1 1 x
-    #> 2 8 y
-    #> 3 9 z
 
 ### Other file formats
 
@@ -126,34 +115,13 @@ a file type that can be accessed by other programs. For this, use the
 
     # check whether it is stored
     ils()
-    #> 
-    #> ==========
-    #> iRODS Zone
-    #> ==========
-    #>                  logical_path
-    #>  /tempZone/home/alice/foo.csv
-    #>  /tempZone/home/alice/foo.rds
 
 Later on somebody else might want to download this file again and store
 it locally:
 
     # retrieve it again later
     iget("foo.csv", "foo.csv")
     read_csv("foo.csv")
-    #> Rows: 3 Columns: 2
-    #> ── Column specification ────────────────────────────────────────────────────────
-    #> Delimiter: ","
-    #> chr (1): y
-    #> dbl (1): x
-    #> 
-    #> ℹ Use `spec()` to retrieve the full column specification for this data.
-    #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
-    #> # A tibble: 3 × 2
-    #>       x y    
-    #>   <dbl> <chr>
-    #> 1     1 x    
-    #> 2     8 y    
-    #> 3     9 z
 
 ### Query
 
@@ -163,15 +131,9 @@ future projects. Objects can be searched with General Queries and
 
     # look for objects in the home collection with a wildcard `%`
     iquery("SELECT COLL_NAME, DATA_NAME WHERE COLL_NAME LIKE '/tempZone/home/%'")
-    #>              COLL_NAME DATA_NAME
-    #> 1 /tempZone/home/alice   foo.csv
-    #> 2 /tempZone/home/alice   foo.rds
 
     # or for data objects with a name that starts with "foo"
     iquery("SELECT COLL_NAME, DATA_NAME WHERE DATA_NAME LIKE 'foo%'")
-    #>              COLL_NAME DATA_NAME
-    #> 1 /tempZone/home/alice   foo.csv
-    #> 2 /tempZone/home/alice   foo.rds
 
 For more on querying, check out `vignette("metadata")`.
 
@@ -185,7 +147,6 @@ Finally, we can clean up Alice’s home collection:
 
     # check if objects are removed
     ils()
-    #> This collection does not contain any objects or collections.
 
     # close the server
     stop_irods_demo()

dev/Makefile

@@ -1,19 +1,19 @@
 # prepare for CRAN by removing unneeded irods_demo bagage
 .ONESHELL:
 SHELL = /bin/bash
-PATH_MODULES := ../inst/irods_demo
-DOCKER_MODULES := $(addprefix $(PATH_MODULES)/,irods_client_nfsrods irods_client_zone_management_tool metalnx-db metalnx minio-data)
+PATH_MODULES := ../inst/irods_demo/.
+IRODS_MODULES := nginx http icommands catalog
+SPACE = $(eval) $(eval)
+DOCKER_MODULES = $(subst $(SPACE),\|,$(IRODS_MODULES))
+DOCKER_MODULES_REGEX = ".*\($(DOCKER_MODULES)\).*"
 
-all: update remove clean
+.PHONY: update clean
+
+all: update clean
 
-# update modules
 update:
 	git submodule sync --recursive
 	git submodule update --init --force --recursive --remote
-# delete unnecessary docker modules
-remove:
-	rm -rf $(DOCKER_MODULES)
-# remove lines docker-compose
 clean:
-	head -n 65 '$(PATH_MODULES)/docker-compose.yml' > temp.yml
-	mv temp.yml '$(PATH_MODULES)/docker-compose.yml'
+	$(shell find $(PATH_MODULES) -type d ! -regex $(DOCKER_MODULES_REGEX) -exec rm -rf {} +)
+	Rscript extract_irods_services_yaml.R $(DOCKER_MODULES)

dev/extract_irods_services_yaml.R

@@ -0,0 +1,15 @@
+#!/usr/bin/env Rscript --vanilla
+
+args <- commandArgs(trailingOnly = TRUE)
+
+devtools::load_all()
+
+extract_irods_services <- function(services = args[1]) {
+  new_docker_compose_file <- docker_compose_file <- get_docker_yaml()
+  grep_services <- is_irods_service_in_yaml(services, docker_compose_file)
+  new_docker_compose_file[["services"]] <- docker_compose_file[["services"]][grep_services]
+  yaml::write_yaml(new_docker_compose_file,  get_docker_compose_path())
+  invisible(NULL)
+}
+
+extract_irods_services()

inst/shell_scripts/dry-run-irods-icommands.sh

@@ -1,8 +1,7 @@
 #!/bin/sh
 
-DIR="$(dirname "$(realpath "$0")")"
+DIR=$(realpath $1)
 
 cd $DIR
-cd ../irods_demo
 
 docker exec irods-demo-irods-client-icommands-1 ils