Shellcheck and shfmt on bash scripts

.pre-commit-config.yaml

@@ -32,3 +32,8 @@ repos:
     rev: 5.11.5
     hooks:
     -   id: isort
+-   repo: https://github.com/pecigonzalo/pre-commit-shfmt
+    rev: v2.2.0
+    hooks:
+    -   id: shell-fmt-go
+        args: [-l, -w, -s, -fn, -sr, -ci, -i=4, -d]

.shellcheckrc

@@ -1 +1,2 @@
-disable=SC1091  # allow sourcing files that can't immediately be found (pcds_conda)
+disable=SC1091
+# allow sourcing files that can't immediately be found (pcds_conda and variable-dependent paths)

LICENSE.md

@@ -1,39 +1,39 @@
-Copyright (c) 2018, The Board of Trustees of the Leland Stanford Junior 
-University, through SLAC National Accelerator Laboratory (subject to receipt 
-of any required approvals from the U.S. Dept. of Energy). All rights reserved. 
-Redistribution and use in source and binary forms, with or without 
+Copyright (c) 2018, The Board of Trustees of the Leland Stanford Junior
+University, through SLAC National Accelerator Laboratory (subject to receipt
+of any required approvals from the U.S. Dept. of Energy). All rights reserved.
+Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
-
-(1) Redistributions of source code must retain the above copyright notice, 
-    this list of conditions and the following disclaimer. 
 
-(2) Redistributions in binary form must reproduce the above copyright notice, 
-    this list of conditions and the following disclaimer in the documentation 
-    and/or other materials provided with the distribution. 
+(1) Redistributions of source code must retain the above copyright notice,
+    this list of conditions and the following disclaimer.
 
-(3) Neither the name of the Leland Stanford Junior University, SLAC National 
-    Accelerator Laboratory, U.S. Dept. of Energy nor the names of its 
-    contributors may be used to endorse or promote products derived from this 
-    software without specific prior written permission. 
+(2) Redistributions in binary form must reproduce the above copyright notice,
+    this list of conditions and the following disclaimer in the documentation
+    and/or other materials provided with the distribution.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER, THE UNITED STATES GOVERNMENT, 
-OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 
-EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT 
-OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING 
-IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY 
+(3) Neither the name of the Leland Stanford Junior University, SLAC National
+    Accelerator Laboratory, U.S. Dept. of Energy nor the names of its
+    contributors may be used to endorse or promote products derived from this
+    software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER, THE UNITED STATES GOVERNMENT,
+OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
 OF SUCH DAMAGE.
 
-You are under no obligation whatsoever to provide any bug fixes, patches, or 
-upgrades to the features, functionality or performance of the source code 
-("Enhancements") to anyone; however, if you choose to make your Enhancements 
-available either publicly, or directly to SLAC National Accelerator Laboratory, 
-without imposing a separate written license agreement for such Enhancements, 
-then you hereby grant the following license: a non-exclusive, royalty-free 
+You are under no obligation whatsoever to provide any bug fixes, patches, or
+upgrades to the features, functionality or performance of the source code
+("Enhancements") to anyone; however, if you choose to make your Enhancements
+available either publicly, or directly to SLAC National Accelerator Laboratory,
+without imposing a separate written license agreement for such Enhancements,
+then you hereby grant the following license: a non-exclusive, royalty-free
 perpetual license to install, use, modify, prepare derivative works, incorporate
-into other computer software, distribute, and sublicense such Enhancements or 
+into other computer software, distribute, and sublicense such Enhancements or
 derivative works thereof, in binary and source code form.

README.md

@@ -76,7 +76,7 @@ usage: archive-status [-h] PV <br/>
 <tr>
     <td>camViewer</td>
     <td>
-usage: /reg/g/pcds/engineering_tools/latest/scripts/camViewer options<br/>
+usage: /cds/group/pcds/engineering_tools/latest/scripts/camViewer options<br/>
     <br/>
     start the viewer for controls cameras<br/>
     <br/>
@@ -99,7 +99,7 @@ usage: /reg/g/pcds/engineering_tools/latest/scripts/camViewer options<br/>
 <tr>
     <td>check_host</td>
     <td>
-Usage:   /reg/g/pcds/engineering_tools/latest/scripts/check_host HOSTNAME<br/>
+Usage:   /cds/group/pcds/engineering_tools/latest/scripts/check_host HOSTNAME<br/>
     <br/>
     Display host info and run some checks.</br>
     </td>
@@ -178,7 +178,7 @@ Checks epicsArch files for mismatches of PVs and aliases, missing files, and unc
         <br/>
         <br/>
 positional arguments:<br/>
-  filepath        Full filepath of the file to check e.g /reg/g/pcds/dist/pds/xpp/misc/epicsArch.txt
+  filepath        Full filepath of the file to check e.g /cds/group/pcds/dist/pds/xpp/misc/epicsArch.txt
         <br/>
         <br/>
 optional arguments:<br/>
@@ -310,7 +310,7 @@ usage: grep_more_ioc [-h] [-d] patt hutch {print,search} <br/>
 <tr>
     <td>grep_pv</td>
     <td>
-     GREP SEARCHES THROUGH ALL IOCs IN /reg/d/iocData/<br/>
+     GREP SEARCHES THROUGH ALL IOCs IN /cds/data/iocData/<br/>
      FOR PVs THAT MATCH GIVEN KEYWORD/HANDLE.<br/>
      Ideally, find_pv should be used as it gives a lot more information (but can be slow sometimes)<br/>
     </td>
@@ -411,7 +411,7 @@ optional arguments:
 &nbsp;                       $EPICS_SITE_TOP/ioc, or /cds/group/pcds/epics/ioc if
 &nbsp;                       the environment variable is not set. With your current
 &nbsp;                       environment variables, this defaults to
-&nbsp;                       /reg/g/pcds/epics/ioc.
+&nbsp;                       /cds/group/pcds/epics/ioc.
 &nbsp; --path-override PATH_OVERRIDE, -p PATH_OVERRIDE
 &nbsp;                       If provided, ignore all normal path-selection rules in
 &nbsp;                       favor of the specific provided path. This will let you
@@ -456,7 +456,7 @@ optional arguments:
 &nbsp;                       $EPICS_SITE_TOP/ioc, or /cds/group/pcds/epics/ioc if
 &nbsp;                       the environment variable is not set. With your current
 &nbsp;                       environment variables, this defaults to
-&nbsp;                       /reg/g/pcds/epics/ioc.
+&nbsp;                       /cds/group/pcds/epics/ioc.
 &nbsp; --path-override PATH_OVERRIDE, -p PATH_OVERRIDE
 &nbsp;                       If provided, ignore all normal path-selection rules in
 &nbsp;                       favor of the specific provided path. This will let you

rc/bashrc

@@ -21,13 +21,13 @@ if [ -f "${HOME}/.pcds_setup.sh" ]; then
     source "${HOME}/.pcds_setup.sh"
 fi
 
-source /reg/g/pcds/setup/pcds_shortcuts.sh
+source /cds/group/pcds/setup/pcds_shortcuts.sh
 
-export PATH=$PATH:/reg/g/pcds/engineering_tools/latest-released/scripts/
+export PATH=$PATH:/cds/group/pcds/engineering_tools/latest-released/scripts/
 
 ########################################
 ### Specific PCDS environment logins ###
 ########################################
-alias epicsenv='. /reg/g/pcds/setup/epicsenv-cur.sh'
-alias ana_env='source /reg/g/psdm/psconda.sh'
-alias plc_env='. /reg/g/pcds/setup/plcenv.sh'
+alias epicsenv='. /cds/group/pcds/setup/epicsenv-cur.sh'
+alias ana_env='source /cds/group/psdm/psconda.sh'
+alias plc_env='. /cds/group/pcds/setup/plcenv.sh'

rc/vimrc

@@ -24,4 +24,3 @@ au FileType python
     \     autoindent
     \     fileformat=unix
     \     encoding=utf-8
-

scripts/BLmotors

@@ -1,4 +1,4 @@
-#!/reg/g/pcds/pyps/conda/py36/envs/pcds-4.1.6/bin/python
+#!/cds/group/pcds/pyps/conda/py36/envs/pcds-4.1.6/bin/python
 
 
 """
@@ -144,7 +144,7 @@ def assign_full_path(ioc_names):
     """
     lists_path = []
     for name in range(len(ioc_names)):
-        lists_path.append('/reg/d/iocData/' + ioc_names[name] +
+        lists_path.append('/cds/data/iocData/' + ioc_names[name] +
                           '/iocInfo/IOC.pvlist')
     return lists_path
 

scripts/ami_offline_psana

@@ -1,57 +1,56 @@
 #! /bin/bash
 usage()
 {
-cat << EOF
+    cat << EOF
 usage: $0 options
 
 We will run ami_offline
 
 OPTIONS:
--e <expnumber> 
+-e <expnumber>
 -R rebinning (binned to 640x640)
 -n no plugins
 EOF
 }
 
 if [[ ($1 == "--help") || ($1 == "-h") ]]; then
-	usage
-	exit 0
+    usage
+    exit 0
 fi
 
 USER=$(whoami)
 ARGSTR='-Z'
 
-while getopts "u:e:ntR" OPTION
-do
+while getopts "u:e:ntR" OPTION; do
     case $OPTION in
-	e)
-	    EXP=$OPTARG
-	    ;;
-	R)
-	    REBIN=1
-	    ;;
-	n)  
-	    NOPLUG=1
-	    ;;
-	?)
-	    usage
-	    exit
-	    ;;
-	esac
+        e)
+            EXP=$OPTARG
+            ;;
+        R)
+            REBIN=1
+            ;;
+        n)
+            NOPLUG=1
+            ;;
+        ?)
+            usage
+            exit
+            ;;
+    esac
 done
 
 if [ -z "$EXP" ]; then
     echo getting the experiment "$EXP"
     HUTCH=$(get_hutch_name)
     if [ "$HUTCH" == 'unknown_hutch' ]; then
-	read -p 'please enter an experiment name: ' EXP
+        read -rp 'please enter an experiment name: ' EXP
     else
-	EXP=$(get_curr_exp)
+        EXP=$(get_curr_exp)
     fi
 fi
 HUTCH=${EXP:0:3}
 
-if [ -z $REBIN ]; then
+if [[ -z $REBIN ]]; then
     ARGSTR=$ARGSTR' -R'
 fi
 
@@ -66,64 +65,64 @@ if [[ $HUTCH == 'cxi' ]]; then
 fi
 
 #get executable
-ami_base_path=$(grep ami_base_path /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CNF" | grep -v '#' | grep -v 'ami_base_path+' | tail -n 1 | awk 'BEGIN { FS = "=" }; { print $2}' | sed s/\'//g)
-ami_path=$ami_base_path$(grep ami_path /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CNF" | grep -v 'ami_path+' | grep -v '#' | awk 'BEGIN { FS = "= " }; { print $2}' | sed s/ami_base_path+//g | sed s/\'//g)
+ami_base_path=$(grep ami_base_path /cds/group/pcds/dist/pds/"$HUTCH"/scripts/"$CNF" | grep -v '#' | grep -v 'ami_base_path+' | tail -n 1 | awk 'BEGIN { FS = "=" }; { print $2}' | sed s/\'//g)
+ami_path=$ami_base_path$(grep ami_path /cds/group/pcds/dist/pds/"$HUTCH"/scripts/"$CNF" | grep -v 'ami_path+' | grep -v '#' | awk 'BEGIN { FS = "= " }; { print $2}' | sed s/ami_base_path+//g | sed s/\'//g)
 
-if [ ! -f  $ami_path/offline_ami ]; then
+if [[ ! -f $ami_path/offline_ami ]]; then
     echo "could not find offline_ami executable in ""$ami_path"
     exit
 fi
 
 #plugin_path & plugin string.
-pp=$(grep plugin_path /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CNF" | grep ami_base | grep -v '#' | awk 'BEGIN { FS = "= " }; { print $2}' | sed s/ami_base_path+//g | sed s/\'//g)
+pp=$(grep plugin_path /cds/group/pcds/dist/pds/"$HUTCH"/scripts/"$CNF" | grep ami_base | grep -v '#' | awk 'BEGIN { FS = "= " }; { print $2}' | sed s/ami_base_path+//g | sed s/\'//g)
 plugin_path=$ami_base_path$pp
 plugin_str=$plugin_path'/libtimetooldbd.so'
 
-if [ -z $NOPLUG ]; then
+if [[ -z $NOPLUG ]]; then
     ARGSTR=$ARGSTR' -L '$plugin_str
 fi
-#ARGSTR=$ARGSTR -X /reg/neh/operator/$HUTCH\opr/experiments
+#ARGSTR=$ARGSTR -X /cds/home/opr/$HUTCH\opr/experiments
 
 #check hostname - different path for recorder node.
 if [ "${HOSTNAME:0:5}" == 'psana' ]; then
-    XTCDIR=/reg/d/psdm/$HUTCH/$EXP/xtc/
+    XTCDIR=/cds/data/psdm/$HUTCH/$EXP/xtc/
     HAVE_RUNS=$(find "$XTCDIR"/*r* | wc -l)
     if [ "$HAVE_RUNS" == 0 ]; then
-	echo 'did not find any xtc files in /reg/d/psdm/'"$HUTCH"'/'"$EXP"', will exit'
-	exit
-    fi 
+        echo 'did not find any xtc files in /cds/data/psdm/'"$HUTCH"'/'"$EXP"', will exit'
+        exit
+    fi
 elif [ "${HOSTNAME:0:3}" == 'drp' ]; then
     XTCDIR=/cds/data/drpsrcf/$HUTCH/$EXP/xtc/
     HAVE_RUNS=$(find "$XTCDIR"/*r* | wc -l)
     if [ "$HAVE_RUNS" == 0 ]; then
-	echo 'did not find any xtc files in /cds/data/drpsrcf/'"$HUTCH"'/'"$EXP"', will exit'
-	exit
-    fi 
-elif  [ "${HOSTNAME:8:3}" == 'rec' ]; then
+        echo 'did not find any xtc files in /cds/data/drpsrcf/'"$HUTCH"'/'"$EXP"', will exit'
+        exit
+    fi
+elif [ "${HOSTNAME:8:3}" == 'rec' ]; then
     XTCDIR=/u2/REC/daq/xtc/
-elif  [ "${HOSTNAME:8:3}" == 'dss' ]; then
+elif [ "${HOSTNAME:8:3}" == 'dss' ]; then
     EXPID=$(get_info --setExp "$EXP" --experimentNumber)
-    XTCDIR=/u2/pcds/pds/"$HUTCH"/e"$EXPID"/  
+    XTCDIR=/u2/pcds/pds/"$HUTCH"/e"$EXPID"/
 else
     echo 'Please ssh to a psana, recorder or dss node to see data'
     exit
 fi
 
 #change to temporary directory where we'll need the favorites file (&maybe
-if [ ! -d /tmp/ami_offline_"$USER" ] ; then
+if [ ! -d /tmp/ami_offline_"$USER" ]; then
     mkdir /tmp/ami_offline_"$USER"
 fi
 
-ln -sf /reg/neh/operator/"$HUTCH"opr/.ami_favorites ~/.
+ln -sf /cds/home/opr/"$HUTCH"opr/.ami_favorites ~/.
 
 #not sure this is necessary either.
-source /reg/g/pcds/setup/pathmunge.sh
-ldpathmunge /reg/g/pcds/dist/pds/"$HUTCH"/ami-current/build/ami/lib/x86_64-linux-opt
+source /cds/group/pcds/setup/pathmunge.sh
+ldpathmunge /cds/group/pcds/dist/pds/"$HUTCH"/ami-current/build/ami/lib/x86_64-linux-opt
 
-LD_LIBRARY_PATH=/reg/g/pcds/dist/pds/"$HUTCH"/current/build/pds/lib/x86_64-linux/:/reg/g/pcds/dist/pds/xpp/current/build/pdsdata/lib/x86_64-linux/:/reg/g/pcds/dist/pds/xpp/current/build/pdsalg/lib/x86_64-linux/:/reg/g/pcds/dist/pds/xpp/current/build/pdsapp/lib/x86_64-linux/:$LD_LIBRARY_PATH
+LD_LIBRARY_PATH=/cds/group/pcds/dist/pds/"$HUTCH"/current/build/pds/lib/x86_64-linux/:/cds/group/pcds/dist/pds/xpp/current/build/pdsdata/lib/x86_64-linux/:/cds/group/pcds/dist/pds/xpp/current/build/pdsalg/lib/x86_64-linux/:/cds/group/pcds/dist/pds/xpp/current/build/pdsapp/lib/x86_64-linux/:$LD_LIBRARY_PATH
 
 #ARGSTR='-p '$XTCDIR $ARGSTR
 echo '----------------------------------------------'
-echo "$ami_path"/offline_ami $ARGSTR -p $XTCDIR 
+echo "$ami_path"/offline_ami "$ARGSTR" -p "$XTCDIR"
 echo '----------------------------------------------'
-$ami_path/offline_ami $ARGSTR -p $XTCDIR 
+"$ami_path"/offline_ami "$ARGSTR" -p "$XTCDIR"

scripts/archive-resume

@@ -1,7 +1,7 @@
 #!/bin/bash
 usage()
 {
-cat << EOF
+    cat << EOF
 usage: $0 <PV>
 
 Resume archiving of a PV in the archiver, e.g. $0 GDET:FEE1:241:ENRC
@@ -12,13 +12,13 @@ if [[ -z $1 ]]; then
     usage
     exit 1
 fi
-    
+
 if [[ ($1 == "--help") || ($1 == "-h") ]]; then
     usage
     exit 0
 fi
 
 result=$(curl -s "http://pscaa01.slac.stanford.edu:17665/mgmt/bpl/resumeArchivingPV?pv=$1")
 echo
-echo $result | cut -d'{' -f2 | cut -d '}' -f1 | tr ',' '\n'
+echo "$result" | cut -d'{' -f2 | cut -d '}' -f1 | tr ',' '\n'
 echo

scripts/archive-status

@@ -1,7 +1,7 @@
 #!/bin/bash
 usage()
 {
-cat << EOF
+    cat << EOF
 usage: $0 <PV>
 
 Check on the status of a PV in the archiver, e.g. $0 GDET:FEE1:241:ENRC
@@ -12,13 +12,13 @@ if [[ -z $1 ]]; then
     usage
     exit 1
 fi
-    
+
 if [[ ($1 == "--help") || ($1 == "-h") ]]; then
     usage
     exit 0
 fi
 
 result=$(curl -s "http://pscaa01.slac.stanford.edu:17665/mgmt/bpl/getPVStatus?pv=$1")
 echo
-echo $result | cut -d'{' -f2 | cut -d'}' -f1 | tr ',' '\n'
+echo "$result" | cut -d'{' -f2 | cut -d'}' -f1 | tr ',' '\n'
 echo