Merge branch 'release/0.14.2' into main

Author: HenrikBengtsson

NEWS.md

@@ -1,3 +1,16 @@
+## Version 0.14.2 [2023-10-23]
+
+### Miscellaneous
+
+ * `rsc start`, `rsc stop`, `rsc status`, `rsc reset`, etc. give more
+   informative error messages when the machine where RStudio Server
+   was most recently running on is not longer available.
+ 
+ * `rsc start --force` suggests calling `rsc reset --force` as a last
+   resort if the machine, where RStudio Server was most recently
+   running on, is not longer available.
+ 
+
 ## Version 0.14.1 [2023-10-16]
 
 ### Miscellaneous

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/0.14.1.tar.gz
-$ tar xf 0.14.1.tar.gz
-$ PATH=/path/to/softwarerstudio-server-controller-0.14.1/bin:$PATH
+$ curl -L -O https://github.com/UCSF-CBI/rstudio-server-controller/archive/refs/tags/0.14.2.tar.gz
+$ tar xf 0.14.2.tar.gz
+$ PATH=/path/to/softwarerstudio-server-controller-0.14.2/bin:$PATH
 $ export PATH
 $ rsc --version
-0.14.1
+0.14.2
 ```
 
 To verify that the tool can find R and the RStudio Server executables,
 call:
 
 ```sh
 $ rsc --version --full
-rsc: 0.14.1
+rsc: 0.14.2
 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/conditions.sh

@@ -33,10 +33,10 @@ function error {
     echo -e "${msg}"
 
     if ${TRACEBACK_ON_ERROR}; then
-       echo -e "${gray}Traceback:"
-       for ((ii = 1; ii < "${#BASH_LINENO[@]}"; ii++ )); do
-           printf "%d: %s() on line #%s in %s\\n" "$ii" "${FUNCNAME[$ii]}" "${BASH_LINENO[$((ii-1))]}" "${BASH_SOURCE[$ii]}"
-       done
+        echo -e "${gray}Traceback:"
+        for ((ii = 1; ii < "${#BASH_LINENO[@]}"; ii++ )); do
+            printf "%d: %s() on line #%s in %s\\n" "$ii" "${FUNCNAME[$ii]}" "${BASH_LINENO[$((ii-1))]}" "${BASH_SOURCE[$ii]}"
+        done
     fi
 
     if [[ -n "${ON_ERROR}" ]]; then
@@ -104,7 +104,24 @@ function message {
 
 
 function relay_condition {
-    grep -q -E "^ERROR: " <<< "${1}" && error "${1#ERROR: }"
-    grep -q -E "^WARNING: " <<< "${1}" && warn "${1#WARNING: }"
+    local bfr=${1}
+    mdebug "relay_condition() ..."
+    for cond in "WARNING" "ERROR"; do
+        bfr=$(sed -n "/${cond}:/,\$p" <<< "${1}")
+        if grep -q -E "${cond}: " <<< "${bfr}"; then
+            # traceback=$(sed -n '/Traceback:/,$p' <<< "${bfr}")
+	    
+	    ## Drop traceback
+            bfr=$(sed '/Traceback:/,$d' <<< "${bfr}")
+	    
+	    [[ ${cond} == "WARNING" ]] && warn  "${bfr#WARNING: }"
+	    [[ ${cond} == "ERROR"   ]] && error "${bfr#ERROR: }"
+	fi
+    done
+    mdebug "relay_condition() ... done"
 }
 
+
+function prune_debug {
+    sed '/DEBUG:/,$d' <<< "${1}"
+}

bin/rsc

@@ -63,7 +63,7 @@
 ###  rsc config --full
 ###  rsc log
 ###
-### Version: 0.14.1
+### Version: 0.14.2
 ### Copyright: Henrik Bengtsson (2022-2023) and Harry Putnam (2022)
 ### License: ISC
 
@@ -270,7 +270,9 @@ function acquire_lock_file {
 
     lockfile=${workdir}/pid.lock
     if [[ -f "${lockfile}" ]]; then
-        error "${USER}, another RStudio Server instance of yours is already running on $(rserver_hostname) on this system. Call '${blue}rsc status --full${undo}' for details on how to reconnect. If you want to start a new instance, please terminate the existing one first by calling '${blue}rsc stop${undo}' from that machine."
+	msg="${USER}, another RStudio Server instance of yours is already running on $(rserver_hostname) on this system. Call '${blue}rsc status --full${undo}' for details on how to reconnect. If you want to start a new instance, please terminate the existing one first by calling '${blue}rsc stop${undo}' from that machine."
+	msg="${msg} As a last resort, for instance, if that machine is no longer available or down for maintenance, try ${blue}rsc reset --force${undo}."
+        error "${msg}"
     fi
     echo "${PPID}" > "${lockfile}"
 }
@@ -313,6 +315,8 @@ function remove_stray_pid_file {
     local -i pid
     local rserver_hostname
     local what
+    local res
+    local -i okay
 
     what=${1:?}
 
@@ -360,8 +364,13 @@ function remove_stray_pid_file {
     mdebug " - hostname=$(hostname)"
 
     ## If this process is not running, remove the PID file
-    pid=$(check_pid "${pid}" "${rserver_hostname}")
-    relay_condition "${pid}"
+    warn_if_check_pid_needs_ssh "${rserver_hostname}"
+    res=$(check_pid "${pid}" "${rserver_hostname}" 2>&1)
+    okay=$?
+    mdebug " - checkpid() exit code: ${okay}"
+    relay_condition "${res}"
+    res=$(prune_debug "${res}")
+    pid=${res}
     if [[ -z ${pid} ]]; then
         rm "${pid_file}"
         warn "Detected a stray PID file (${pid_file}). This file was removed, because it referred to a ${what} process (PID ${pid} on ${rserver_hostname}) which is no longer running."
@@ -473,12 +482,22 @@ function parse_revtunnel {
     echo "${port}"
 }
 
+function warn_if_check_pid_needs_ssh {
+    local hostname
+    hostname=${1:-?}
+    if ${ssh} && [[ "${hostname}" != "$(hostname)" ]]; then
+        mwarn "Needs to SSH to ${hostname} to check whether process ${pid} is still alive. If you don't have SSH key authentication set up, you will be asked to enter your account password below."
+    fi
+ }
+
 function check_pid {
     local -i pid
     local hostname
     local pid_exists
     local asterisk
     local timeout
+    local res
+    local -i okay
 
     ## If 'pid' is assigned an empty value, then it becomes pid=0,
     ## because we declared it as an integer above.
@@ -497,9 +516,16 @@ function check_pid {
             [[ -d "/proc/${pid}" ]] && pid_exists=true
         elif ${ssh}; then
             mdebug "- Checking /proc/${pid} on ${hostname} over SSH ($(ssh_timeout)-second timeout)"
-            mwarn "Needs to SSH to ${hostname} to check whether process ${pid} is still alive. If you don't have SSH key authentication set up, you will be asked to enter your account password below."
             #shellcheck disable=SC2029
-            res=$(ssh -o ConnectTimeout="$(ssh_timeout)" "${hostname}" "[[ -d '/proc/${pid}' ]] && echo true || echo false" 2>&1) || error "Failed to check process PID ${pid} on ${hostname} over SSH. Reason was: ${res}"
+            res=$(ssh -o ConnectTimeout="$(ssh_timeout)" "${hostname}" "[[ -d '/proc/${pid}' ]] && echo true || echo false" 2>&1)
+            okay=$?
+            mdebug "- Result: ${res}"
+            mdebug "- Exit code: ${okay}"
+            if [[ ${okay} -ne 0 ]]; then
+                ## Remove empty leading lines
+                res=$(sed -e '/./,$!d' <<< "${res}")
+                error "Failed to check process PID ${pid} on ${hostname} over SSH. Reason was: ${res}"
+            fi
             [[ "${res}" == "true" ]] && pid_exists=true
         else
             mdebug "- Skipping check of /proc/${pid} on ${hostname}, because --no-ssh"
@@ -566,10 +592,10 @@ function find_login_host_via_who {
         bfr=$(echo "${bfr}" | sed -E 's/(.*[[:space:]]+[(]|[)][[:space:]]*)//g')
         mdebug "4. ${bfr}"
         ## If hostname is an IP number, try to identify hostname
-	if grep -q -E "^[[:digit:]]+[.][[:digit:]]+[.][[:digit:]]+[.][[:digit:]]+$" <<< "${bfr}"; then
-	    if [[ -f /etc/hosts ]] && grep -q -E "\b${bfr}\b" /etc/hosts; then
-		bfr=$(grep -E "\b${bfr}\b" /etc/hosts | sed -E "s/\b${bfr}\b//g" | sed -E 's/[[:space:]]+/ /g' | sed -E 's/(^ | $)//g' | cut -d ' ' -f 1)
-	    fi
+        if grep -q -E "^[[:digit:]]+[.][[:digit:]]+[.][[:digit:]]+[.][[:digit:]]+$" <<< "${bfr}"; then
+            if [[ -f /etc/hosts ]] && grep -q -E "\b${bfr}\b" /etc/hosts; then
+                bfr=$(grep -E "\b${bfr}\b" /etc/hosts | sed -E "s/\b${bfr}\b//g" | sed -E 's/[[:space:]]+/ /g' | sed -E 's/(^ | $)//g' | cut -d ' ' -f 1)
+            fi
             mdebug "5. ${bfr}"
         fi
     fi
@@ -608,15 +634,20 @@ function rs_process_status {
     local pid_info
     local pid_stats
     local tmp
+    local res
     pid=${1}
     hostname=${2}
 
     mdebug "rs_process_status(pid=${pid}, hostname=${hostname}):"
-    
+
     ## Check if PID is still active?
     if [[ ${pid} -ne 0 ]]; then
-        pid=$(check_pid "${pid}" "${hostname}")
-        relay_condition "${pid}"
+	warn_if_check_pid_needs_ssh "${hostname}"
+        res=$(check_pid "${pid}" "${rserver_hostname}" 2>&1)
+        okay=$?
+        relay_condition "${res}"
+        res=$(prune_debug "${res}")
+        pid=${res}
     fi
 
 
@@ -1321,17 +1352,17 @@ function display_access_instructions {
             msg="${msg}  <${blue}http://$(ssh_revtunnel_hostname):$(ssh_revtunnel_port)${undo}>\n"
         elif on_local_machine; then
             msg="${msg}  <${blue}http://127.0.0.1:$(rserver_port)${undo}>\n"
-	fi
+        fi
     else
         hostname=$(rserver_hostname)
         port=$(rserver_port)
         if [[ ${localport} == "port" ]]; then
-	    localport=$port
-	fi
+            localport=$port
+        fi
         msg="${msg}  <${blue}http://127.0.0.1:${port}${undo}>\n"
 
-	if [[ -n ${SSH_CLIENT} ]] || [[ -n ${SSH_CONNECTION} ]] || [[ -n ${SSH_TTY} ]]; then
-	msg="${msg}\nImportantly, if you are running from a remote machine without direct access to ${hostname}, you need to set up SSH port forwarding first, which you can do by running:\n\\n  ${blue}ssh -L ${localport}:${hostname}:${port} ${USER}@$(find_login_host)${undo}\n\nin a second terminal from your local computer.\n"
+        if [[ -n ${SSH_CLIENT} ]] || [[ -n ${SSH_CONNECTION} ]] || [[ -n ${SSH_TTY} ]]; then
+            msg="${msg}\nImportantly, if you are running from a remote machine without direct access to ${hostname}, you need to set up SSH port forwarding first, which you can do by running:\n\\n  ${blue}ssh -L ${localport}:${hostname}:${port} ${USER}@$(find_login_host)${undo}\n\nin a second terminal from your local computer.\n"
         fi
     fi