Merge branch 'release/0.13.7'

UCSF-CBI · Oct 4, 2023 · b95a07b · b95a07b
2 parents e4840d8 + 8f84a1d
commit b95a07b
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diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,14 @@
+## Version 0.13.7 [2023-10-04]
+
+### Miscellaneous
+
+ * `rsc start` attempts to infer the login hostname from ``etc/hosts`,
+   if it only finds an IP number at first.
+
+ * `rsc start` now uses [port4me] 0.6.0, which is the most recent
+   version, for identifying a free TCP port.
+
+
 ## Version 0.13.6 [2023-06-22]
 
 ### Miscellaneous

diff --git a/README.md b/README.md
@@ -333,21 +333,21 @@ 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/0.13.6.tar.gz
-$ tar xf 0.13.6.tar.gz
-$ PATH=/path/to/softwarerstudio-server-controller-0.13.6/bin:$PATH
+$ curl -L -O https://github.com/UCSF-CBI/rstudio-server-controller/archive/refs/tags/0.13.7.tar.gz
+$ tar xf 0.13.7.tar.gz
+$ PATH=/path/to/softwarerstudio-server-controller-0.13.7/bin:$PATH
 $ export PATH
 $ rsc --version
-0.13.6
+0.13.7
 ```
 
 To verify that the tool can find R and the RStudio Server executables,
 call:
 
 ```sh
 $ rsc --version --full
-rsc: 0.13.6
-RStudio Server: 2023.03.0+386 (Cherry Blossom) for Linux [/path/to/rstudio-server/bin/rstudio-server]
+rsc: 0.13.7
+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]
 ```
 

diff --git a/bin/incl/port4me.bash b/bin/incl/port4me.bash
@@ -8,9 +8,14 @@
 #'
 #' - PORT4ME_USER   : The name of the current user (default: ${USER})
 #' - PORT4ME_TOOL   : The name of the software tool (optional)
+#' - PORT4ME_PREPEND: Ports to be considered first (optional)
 #' - PORT4ME_INCLUDE: Ports to be considered (default: 1024-65535)
 #' - PORT4ME_EXCLUDE: Ports to be excluded (optional)
-#' - PORT4ME_PREPEND: Ports to be considered first (optional)
+#' - PORT4ME_EXCLUDE_UNSAFE:
+#'                    Ports to be excluded because they are considered
+#'                    unsafe (defaults: {chrome},{firefox})
+#' - PORT4ME_EXCLUDE_UNSAFE_CHROME: Ports blocked by the Chrome browser
+#' - PORT4ME_EXCLUDE_UNSAFE_FIREFOX: Ports blocked by the Firefox browser
 #' - PORT4ME_SKIP   : Number of ports to skip in the set of ports
 #'                    considered after applying prepended, included,
 #'                    and excluded (optional)
@@ -24,15 +29,26 @@
 #' PORT4ME_EXCLUDE=8787 port4me
 #' PORT4ME_PREPEND=4001-4003 port4me
 #' PORT4ME_LIST=5 port4me
-#' PORT4ME_TEST=4321 port4me
+#' PORT4ME_TEST=4321 port4me && echo "free" || echo "taken"
 #'
-#' Version: 0.4.0-9004
-#' Copyright: Henrik Bengtsson (2022)
-#' License: ISC
+#' Version: 0.6.0
+#' Copyright: Henrik Bengtsson (2022-2023)
+#' License: MIT
 #' Source code: https://github.com/HenrikBengtsson/port4me
 declare -i LCG_SEED
 export LCG_SEED
 
+PORT4ME_EXCLUDE_UNSAFE=${PORT4ME_EXCLUDE_UNSAFE:-"{chrome},{firefox}"}
+export PORT4ME_EXCLUDE_UNSAFE
+
+## Source: https://chromium.googlesource.com/chromium/src.git/+/refs/heads/master/net/base/port_util.cc
+## Last updated: 2022-10-24
+PORT4ME_EXCLUDE_UNSAFE_CHROME=${PORT4ME_EXCLUDE_UNSAFE_CHROME:-"1,7,9,11,13,15,17,19,20,21,22,23,25,37,42,43,53,69,77,79,87,95,101,102,103,104,109,110,111,113,115,117,119,123,135,137,139,143,161,179,389,427,465,512,513,514,515,526,530,531,532,540,548,554,556,563,587,601,636,989,990,993,995,1719,1720,1723,2049,3659,4045,5060,5061,6000,6566,6665,6666,6667,6668,6669,6697,10080"}
+
+## Source: https://www-archive.mozilla.org/projects/netlib/portbanning#portlist
+## Last updated: 2022-10-24
+PORT4ME_EXCLUDE_UNSAFE_FIREFOX=${PORT4ME_EXCLUDE_UNSAFE_FIREFOX:-"1,7,9,11,13,15,17,19,20,21,22,23,25,37,42,43,53,77,79,87,95,101,102,103,104,109,110,111,113,115,117,119,123,135,139,143,179,389,465,512,513,514,515,526,530,531,532,540,556,563,587,601,636,993,995,2049,4045,6000"}
+
 _p4m_error() {
     >&2 echo "ERROR: $1"
     exit 1
@@ -45,11 +61,11 @@ _p4m_error() {
 #' openable=$?
 #'
 #' Requirements:
-#' * either 'nc' or 'ss'
+#' * either 'nc', 'netstat', or 'ss'
 PORT4ME_PORT_COMMAND=
 _p4m_can_port_be_opened() {
     local -i port=${1:?}
-    local cmds=(nc ss)
+    local cmds=(nc netstat ss)
     local cmd
 
     (( port < 1 || port > 65535 )) && _p4m_error "Port is out of range [1,65535]: ${port}"
@@ -74,6 +90,10 @@ _p4m_can_port_be_opened() {
         if ss -H -l -n src :"$port" | grep -q -E ":$port\b"; then
             return 1
         fi
+    elif [[ ${PORT4ME_PORT_COMMAND} == "netstat" ]]; then
+        if netstat -n -l -t | grep -q -E "^tcp\b[^:]+:$port\b"; then
+            return 1
+        fi
     fi
 
     ## FIXME: A port can be free, but it might be that the user
@@ -105,17 +125,21 @@ _p4m_string_to_uint() {
     printf "%d" $hash
 }
 
+
 _p4m_parse_ports() {
     local spec=${1:?}
     local specs
     local -a ports
-
-    ## Prune input
+
+    ## Prune and pre-parse input
+    spec=${spec//\{chrome\}/${PORT4ME_EXCLUDE_UNSAFE_CHROME}}
+    spec=${spec//\{firefox\}/${PORT4ME_EXCLUDE_UNSAFE_FIREFOX}}
     spec=${spec//,/ }
     spec=${spec//+( )/ }
     spec=${spec## }
     spec=${spec%% }
     spec=${spec// /$'\n'}
+    spec=$(sort -n -u <<< "${spec}")
 
     ## Split input into lines
     mapfile -t specs <<< "${spec}"
@@ -190,9 +214,23 @@ port4me() {
         return $?
     fi
 
-    mapfile -t exclude < <(_p4m_parse_ports "${PORT4ME_EXCLUDE},${PORT4ME_EXCLUDE_SITE}")
+    mapfile -t exclude < <(_p4m_parse_ports "${PORT4ME_EXCLUDE},${PORT4ME_EXCLUDE_SITE},${PORT4ME_EXCLUDE_UNSAFE}")
     mapfile -t include < <(_p4m_parse_ports "${PORT4ME_INCLUDE},${PORT4ME_INCLUDE_SITE}")
     mapfile -t prepend < <(_p4m_parse_ports "${PORT4ME_PREPEND},${PORT4ME_PREPEND_SITE}")
+    if ${PORT4ME_DEBUG:-false}; then
+        {
+            echo "PORT4ME_EXCLUDE=${PORT4ME_EXCLUDE}"
+            echo "PORT4ME_EXCLUDE_SITE=${PORT4ME_EXCLUDE_SITE}"
+            echo "PORT4ME_EXCLUDE_UNSAFE=${PORT4ME_EXCLUDE_UNSAFE}"
+            echo "PORT4ME_INCLUDE=${PORT4ME_INCLUDE}"
+            echo "PORT4ME_INCLUDE_SITE=${PORT4ME_INCLUDE_SITE}"
+            echo "PORT4ME_PREPEND=${PORT4ME_PREPEND}"
+            echo "PORT4ME_PREPEND_SITE=${PORT4ME_PREPEND_SITE}"
+            echo "Ports to prepend: [n=${#prepend}] ${prepend[*]}"
+            echo "Ports to include: [n=${#include}] ${include[*]}"
+            echo "Ports to exclude: [n=${#exclude}] ${exclude[*]}"
+        } >&2
+    fi
 
     if (( list > 0 )); then
         max_tries=${list}
@@ -205,11 +243,20 @@ port4me() {
     while (( tries < max_tries )); do
         if (( ${#prepend[@]} > 0 )); then
             port=${prepend[0]}
+            ${PORT4ME_DEBUG:-false} && >&2 printf "Port prepended: %d\n" "$port"
             (( port < 1 || port > 65535 )) && _p4m_error "Prepended port out of range [1,65535]: ${port}"
             prepend=("${prepend[@]:1}") ## drop first element
         else
             _p4m_lcg > /dev/null
+
+            ## Skip?
+            if (( LCG_SEED < 1024 || LCG_SEED > 65535 )); then
+              ${PORT4ME_DEBUG:-false} && >&2 printf "Skip to next, because LCG_SEED is out of range: %d\n" "$LCG_SEED"
+              continue
+            fi
+
             port=${LCG_SEED:?}
+            ${PORT4ME_DEBUG:-false} && >&2 printf "Port drawn: %d\n" "$port"
         fi
 
         ## Skip?
@@ -226,10 +273,8 @@ port4me() {
                 ${PORT4ME_DEBUG:-false} && >&2 printf "Port not included: %d\n" "$port"
                 continue
             fi
-        elif (( LCG_SEED < 1024 || LCG_SEED > 65535 )); then
-            continue
         fi
-
+        
         tries=$(( tries + 1 ))
         count=$((count + 1))
 

diff --git a/bin/rsc b/bin/rsc
@@ -63,7 +63,7 @@
 ###  rsc config --full
 ###  rsc log
 ###
-### Version: 0.13.6
+### Version: 0.13.7
 ### Copyright: Henrik Bengtsson (2022-2023) and Harry Putnam (2022)
 ### License: ISC
 
@@ -554,7 +554,14 @@ function find_login_host_via_who {
         ## Extract the hostname
         bfr=$(echo "${bfr}" | sed -E 's/(.*[[:space:]]+[(]|[)][[:space:]]*)//g')
         mdebug "4. ${bfr}"
-    fi        
+        ## If hostname is an IP number, try to identify hostname
+	if grep -q -E "^[[:digit:]]+[.][[:digit:]]+[.][[:digit:]]+[.][[:digit:]]+$" <<< "${bfr}"; then
+	    if [[ -f /etc/hosts ]] && grep -q -E "\b${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
+            mdebug "5. ${bfr}"
+        fi
+    fi
     echo "${bfr}"
 }