update to http api 0.4.0

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

@@ -1,3 +1,4 @@
+
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 # rirods <a href="https://dplyr.tidyverse.org"><img src="man/figures/logo.png" align="right" height="138" /></a>
@@ -15,27 +16,33 @@ The rirods package is an R client for iRODS.
 
 You can install the latest CRAN version of rirods like so:
 
-    install.packages("rirods")
+``` r
+install.packages("rirods")
+```
 
 Or, the development version from GitHub, like so:
 
-    # install.packages("devtools")
-    devtools::install_github("irods/irods_client_library_rirods")
+``` r
+# install.packages("devtools")
+devtools::install_github("irods/irods_client_library_rirods")
+```
 
 ## Prerequisites
 
 This package connects to the iRODS C++ HTTP API -
-<https://github.com/irods/irods_client_http_api>.
+https://github.com/irods/irods_client_http_api.
 
 Launch a local demonstration iRODS service (including the HTTP API):
 
-    # load
-    library(rirods)
-    # setup a mock iRODS server (https://github.com/irods/irods_demo)
-    use_irods_demo("alice", "passWORD")
+``` r
+# load
+library(rirods)
+# setup a mock iRODS server (https://github.com/irods/irods_demo)
+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/0.2.0.
 
 These Docker containers are designed to easily stand up a
 **DEMONSTRATION** of the iRODS server. It is intended for education and
@@ -57,44 +64,50 @@ In this example Alice is a user of iRODS and she can authenticate
 herself with `iauth("alice")`. This prompts a dialog where you can enter
 your password without hardcoding this information in your scripts.
 
-    # login as alice with password "passWORD"
-    iauth("alice") # or iauth("alice", "passWORD")
+``` r
+# login as alice with password "passWORD"
+iauth("alice") # or iauth("alice", "passWORD")
+```
 
 ### Save R objects
 
 Suppose Alice would like to upload an R object from her current R
 session to an iRODS collection. For this, use the `isaveRDS()` command:
 
-    # some data
-    foo <- data.frame(x = c(1, 8, 9), y = c("x", "y", "z"))
+``` r
+# some data
+foo <- data.frame(x = c(1, 8, 9), y = c("x", "y", "z"))
 
-    # check where we are in the iRODS namespace
-    ipwd()
-    #> [1] "/tempZone/home/alice"
+# check where we are in the iRODS namespace
+ipwd()
+#> [1] "/tempZone/home/alice"
 
-    # store data in iRODS
-    isaveRDS(foo, "foo.rds")
+# store data in iRODS
+isaveRDS(foo, "foo.rds")
+```
 
 ### Metadata
 
 To truly appreciate the strength of iRODS, we can add some metadata that
 describes the data object “foo”:
 
-    # add some metadata
-    imeta(
-      "foo.rds", 
-      operations = 
-        data.frame(operation = "add", attribute = "foo", value = "bar", units = "baz")
-    )
-
-    # 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
+``` r
+# add some metadata
+imeta(
+  "foo.rds", 
+  operations = 
+    data.frame(operation = "add", attribute = "foo", value = "bar", units = "baz")
+)
+
+# 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")`.
 
@@ -103,91 +116,105 @@ For more on using metadata, check out `vignette("metadata")`.
 If Alice wanted to copy the foo R object from an iRODS collection to her
 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
+``` r
+# retrieve in native R format
+ireadRDS("foo.rds")
+#>   x y
+#> 1 1 x
+#> 2 8 y
+#> 3 9 z
+```
 
 ### Other file formats
 
 Possibly Alice does not want a native R object to be stored on iRODS but
 a file type that can be accessed by other programs. For this, use the
 `iput()` command:
 
-    library(readr)
+``` r
+library(readr)
 
-    # creates a csv file of foo
-    write_csv(foo, "foo.csv")
+# creates a csv file of foo
+write_csv(foo, "foo.csv")
 
-    # send file
-    iput("foo.csv", "foo.csv")
+# send file
+iput("foo.csv", "foo.csv")
 
-    # check whether it is stored
-    ils()
-    #> 
-    #> ==========
-    #> iRODS Zone
-    #> ==========
-    #>                  logical_path
-    #>  /tempZone/home/alice/foo.csv
-    #>  /tempZone/home/alice/foo.rds
+# 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
+``` r
+# 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
 
 By adding metadata you and others can more easily discover data in
 future projects. Objects can be searched with General Queries and
 `iquery()`:
 
-    # 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
+``` r
+# 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
+```
+
+``` r
+# 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")`.
 
 ### Cleanup
 
 Finally, we can clean up Alice’s home collection:
 
-    # delete object
-    irm("foo.rds", force = TRUE)
-    irm("foo.csv", force = TRUE)
-
-    # check if objects are removed
-    ils()
-    #> This collection does not contain any objects or collections.
-
-    # close the server
-    stop_irods_demo()
-    # optionally remove the Docker images
-    # irods:::remove_docker_images()
+``` r
+# delete object
+irm("foo.rds", force = TRUE)
+irm("foo.csv", force = TRUE)
+
+# check if objects are removed
+ils()
+#> This collection does not contain any objects or collections.
+```
+
+``` r
+# close the server
+stop_irods_demo()
+# optionally remove the Docker images
+# irods:::remove_docker_images()
+```