Merge branch 'release/0.14.4'

Author: HenrikBengtsson

Makefile

@@ -1,4 +1,17 @@
-check: shellcheck spelling
+SHELL=bash
+
+check: shellcheck check-cli spelling
+
+assert_bats:
+	command -v "bats"
+	echo "BATS_SUPPORT_HOME=$${BATS_SUPPORT_HOME:?}"
+	echo "BATS_ASSERT_HOME=$${BATS_ASSERT_HOME:?}"
+
+assert_rstudio:
+	command -v "rserver"
+
+check-cli: assert_bats assert_rstudio
+	(cd tests/; PATH="../bin:$${PATH}" bats *.bats)
 
 shellcheck:
 	(cd bin; \

NEWS.md

@@ -1,3 +1,13 @@
+## Version 0.14.4 [2024-01-16]
+
+### Bug Fixes
+
+ * `rsc start` would generate obscure errors such as `ports.sh: line
+   15: [[:` and `port4me.bash: line 275: 3: Bad file descriptor`.
+   This was due to a teeny, but critical bug in **port4me**
+   0.7.0. Fixed by updating to new **port4me** 0.7.1.
+ 
+
 ## Version 0.14.3 [2024-01-15]
 
 ### New Features

README.md

@@ -333,20 +333,20 @@ As before, the RStudio Server is available at
 
 ```sh
 $ cd /path/to/software
-$ curl -L -O https://github.com/UCSF-CBI/rstudio-server-controller/archive/refs/tags/0.14.3.tar.gz
-$ tar xf 0.14.3.tar.gz
-$ PATH=/path/to/softwarerstudio-server-controller-0.14.3/bin:$PATH
+$ curl -L -O https://github.com/UCSF-CBI/rstudio-server-controller/archive/refs/tags/0.14.4.tar.gz
+$ tar xf 0.14.4.tar.gz
+$ PATH=/path/to/softwarerstudio-server-controller-0.14.4/bin:$PATH
 $ export PATH
 $ rsc --version
-0.14.3
+0.14.4
 ```
 
 To verify that the tool can find R and the RStudio Server executables,
 call:
 
 ```sh
 $ rsc --version --full
-rsc: 0.14.3
+rsc: 0.14.4
 RStudio Server: 2023.06.2+561 (Mountain Hydrangea) for Linux [/path/to/rstudio-server/bin/rstudio-server]
 R: 4.3.1 (2023-06-16) -- "Shortstop Beagle" [/path/to/R/bin/R]
 ```

bin/incl/port4me.bash

@@ -38,7 +38,7 @@
 #' Requirements:
 #' * Bash (>= 4)
 #'
-#' Version: 0.7.0
+#' Version: 0.7.1
 #' Copyright: Henrik Bengtsson (2022-2024)
 #' License: MIT
 #' Source code: https://github.com/HenrikBengtsson/port4me
@@ -293,11 +293,11 @@ _p4m_lcg_port() {
         has_subset=true
     fi
 
-    if ${PORT4ME_DEBUG}; then
+    if ${PORT4ME_DEBUG:-false}; then
         {
             echo "(min,max): ($min,$max)"
             echo "subset: [n=${#subset[@]}]"
-        } >&3
+        }
     fi
 
     ## Sample values in [0,m-2] (sic!), but reject until in [min,max],

bin/rsc

@@ -63,7 +63,7 @@
 ###  rsc config --full
 ###  rsc log
 ###
-### Version: 0.14.3
+### Version: 0.14.4
 ### Copyright: Henrik Bengtsson (2022-2024) and Harry Putnam (2022)
 ### License: ISC
 
@@ -298,7 +298,7 @@ function remove_stray_lockfile {
     mdebug "remove_stray_lockfile() ..."
 
     ## Nothing to do?
-    [[ ! -f "${lockfile}" ]] || [[ -n "$(rserver_pid true)" ]] || [[ -n "$(rsession_pid true)" ]] || [[ -n "$(ssh_revtunnel_pid true)" ]] && return 0;
+    [[ ! -f "${lockfile}" ]] || [[ -n "$(rserver_pid true)" ]] || [[ -n "$(rsession_pid true)" ]] || [[ -n "$(ssh_revtunnel_pid true)" ]] && { mdebug "remove_stray_lockfile() ... done"; return 0; }
 
     ## Here we know that there's neither a rserver PID nor a rsession PID
     rm "${lockfile}"
@@ -398,16 +398,25 @@ function make_rserver_conf {
     local workdir
     local datadir
     local port
+
+    mdebug "make_rserver_conf() ..."
+    
     workdir=$(config_dir)
     assert_dir_exists "${workdir}"
     port=${1:?}
+    mdebug " - workdir=${workdir}"
+    mdebug " - port=${port}"
 
     datadir=$(rserver_data_dir)
 
     if [[ "${port}" == "port4me" ]]; then
+        mdebug "port4me() ..."
         port=$(PORT4ME_TOOL=rsc port4me 2>&1)
         relay_condition "${port}"
+        mdebug "port4me() ... done"
     fi
+    
+    mdebug "port=${port}"
     assert_port_free "${port}"
 
     {
@@ -451,6 +460,8 @@ function make_rserver_conf {
         ## The web port for the RStudio Server
         echo "www-port=${port:?}"
     } > "${workdir}/rserver.conf"
+    
+    mdebug "make_rserver_conf() ... done"
 }
 
 
@@ -1536,10 +1547,12 @@ term_colors enable
 
 ## Remove any stray files
 if ! ${force}; then
+    mdebug "Removing stray files ..."
     remove_stray_pid_file rserver
     remove_stray_pid_file rsession
     remove_stray_pid_file rserver_monitor
     remove_stray_lockfile
+    mdebug "Removing stray files ... done"
 fi    
 
 if [[ "${action}" == "config" ]]; then
@@ -1709,11 +1722,14 @@ elif [[ "${action}" == "wait" ]]; then
     rserver_hostname
     rserver_port
 elif [[ "${action}" == "start" ]]; then    
+    mdebug "Assert sufficient software setup ..."
     ## Assert executables are available
     assert_executable R
     assert_r
     assert_executable rserver
     assert_executable rsession
+    mdebug "Assert sufficient software setup ... done"
+    
     if [[ "${port}" != "port4me" ]]; then
         assert_port_free "${port}"
     fi
@@ -1729,11 +1745,13 @@ elif [[ "${action}" == "start" ]]; then
     make_config_dir
     acquire_lock_file
 
+    mdebug "Setup RStudio Server configurations ..."
     make_database_conf
     make_rserver_conf "${port}"
     make_rsession_envs
     make_rsession_sh
     make_rsession_conf
+    mdebug "Setup RStudio Server configurations ... done"
 
     mdebug "PID for rsc (this process): $$"
 

tests/rsc.bats

@@ -0,0 +1,126 @@
+#!/usr/bin/env bats
+
+setup() {
+    load "${BATS_SUPPORT_HOME:?}/load.bash"
+    load "${BATS_ASSERT_HOME:?}/load.bash"
+    
+    path="$(dirname "${BATS_TEST_FILENAME}")"
+
+    ## Test with a fresh user config and data folder
+    _RSC_TEST_DIR_=$(mktemp -d)
+    export _RSC_TEST_DIR_
+    
+    XDG_CONFIG_HOME=${_RSC_TEST_DIR_}
+    export XDG_CONFIG_HOME
+    XDG_DATA_HOME=${_RSC_TEST_DIR_}
+    export XDG_DATA_HOME
+
+    export RSC_AUTH="auth-via-env"
+    export RSC_PASSWORD="random"
+}
+
+teardown() {
+    rm -rf "${_RSC_TEST_DIR_}"
+}
+
+@test "XDG_CONFIG_HOME is a temporary folder" {
+    run echo "${XDG_CONFIG_HOME:-<not set>}"
+    assert_success
+    refute_output --partial "not set"
+    assert_output --partial "$(dirname "$(mktemp -d)")"
+    
+    run echo "${XDG_DATA_HOME:-<not set>}"
+    assert_success
+    refute_output --partial "not set"
+    assert_output --partial "$(dirname "$(mktemp -d)")"
+}
+
+@test "rsc --version works" {
+    run rsc --version
+    assert_success
+    assert_output --regexp "[[:digit:]]+([.][[:digit:]]+)+(|-[[:digit:]]+)"
+}
+
+@test "rsc --version --full works" {
+    run rsc --version --full
+    assert_success
+    assert_output --regexp "rsc: [[:digit:]]+([.][[:digit:]]+)+(|-[[:digit:]]+)"
+    assert_output --regexp "RStudio Server: "
+    assert_output --regexp "R: [[:digit:]]+([.][[:digit:]]+)+(|-[[:digit:]]+)"
+}
+
+@test "rsc --help works" {
+    run rsc --help
+    assert_success
+    assert_output --partial "rsc"
+    assert_output --partial "RStudio Server Controller"
+    assert_output --partial "Usage:"
+    assert_output --partial "Commands:"
+    assert_output --partial "Options:"
+    assert_output --partial "Version:"
+    assert_output --partial "License:"
+}
+
+@test "rsc status works" {
+    run rsc status
+    assert_success
+    assert_output --partial "rserver: "
+    assert_output --partial "rsession: "
+    assert_output --partial "rserver monitor: "
+    assert_output --partial "SSH reverse tunnel (optional): "
+    assert_output --partial "lock file: "
+}
+
+@test "rsc status --full works" {
+    run rsc status --full
+    assert_success
+    assert_output --partial "rserver: "
+    assert_output --partial "rsession: "
+    assert_output --partial "rserver monitor: "
+    assert_output --partial "SSH reverse tunnel (optional): "
+    assert_output --partial "lock file: "
+}
+
+@test "rsc config works" {
+    run rsc config
+    assert_success
+    assert_output --partial "RStudio Server Controller Storage:"
+    assert_output --partial "RStudio User State Storage:"
+    assert_output --partial "XDG_CONFIG_HOME=$(dirname "$(mktemp -d)")"
+    assert_output --partial "XDG_DATA_HOME=$(dirname "$(mktemp -d)")"
+}
+
+@test "rsc config --full works" {
+    run rsc config --full
+    assert_success
+}
+
+@test "rsc log works" {
+    run rsc log
+    assert_success
+}
+
+@test "rsc reset works" {
+    run rsc reset
+    assert_success
+}
+
+@test "rsc reset --force works" {
+    run rsc reset --force
+    assert_success
+}
+
+@test "rsc stop works" {
+    run rsc stop
+    assert_success
+}
+
+@test "rsc start --debug --dryrun works" {
+    run rsc start --debug --dryrun 2>&1
+    assert_failure
+    assert_output --partial "DRYRUN: rserver --config-file="
+    assert_output --partial "DRYRUN: rserver_monitor launched"
+    assert_output --partial "ERROR: It looks like the RStudio Server failed during launch"
+    assert_output --partial "Shutting down RStudio Server ..."
+    assert_output --partial "Shutting down RStudio Server ... done"
+}