Merge pull request #44 from pneerincx/improved_indentationcheck

Improved indentation check.

.gitattributes

@@ -0,0 +1,6 @@
+* text=auto
+
+*.sh        eol=lf
+*.bash      eol=lf
+*.md        eol=lf
+*.cfg       eol=lf

.gitignore

@@ -0,0 +1,5 @@
+*.DS_Store
+*.project
+*.pydevproject
+*.settings
+*.md.html

README.md

@@ -99,3 +99,4 @@ Navigate to jobs folder. The location of the jobs folder will be outputted at th
 ```BASH
 bash submit.sh
 ```
+

check/indentationcheck.sh

@@ -1,19 +1,11 @@
 #!/bin/bash
 
-#
-# Use either WORKSPACE location for Jenkins or
-# resolve path to scripts we need to check
-# when executed manually outside Jenkins.
-#
-if [[ -z "${WORKSPACE:-}" ]]; then
-	MYDIR="$(cd -P "$(dirname "${0}")" && pwd)"
-	WORKSPACE="$(dirname ${MYDIR})"
-fi
+MYDIR="$(cd -P "$(dirname "${0}")" && pwd)"
 
 echo '#####################################################################################'
 echo '  Bash code must be indented with TABs. Checking for lines indented with spaces ... '
 echo '#####################################################################################'
-grep -n '^[[:space:]]* [[:space:]]*' "${WORKSPACE:-../}/protocols/"*.sh
+grep --recursive --line-number --include='*.*sh' --exclude-dir='deprecated' '^[[:space:]]* [[:space:]]*' "${MYDIR}"/../
 grep_exit_status="${?}"
 if [[ "${grep_exit_status}" -eq 0 ]]; then
 	echo '#####################################################################################'

check/shellcheck.sh

@@ -1,18 +1,19 @@
 #!/bin/bash
 
+set -e
+set -u
+set -o pipefail
+
 #
 # Disable some shellcheck warnings:
 #  * SC2004: $/${} is unnecessary on arithmetic variables.
 #            But for consistency we prefer to always use ${} anyway.
 #  * SC2015: Note that A && B || C is not if-then-else. C may run when A is true.
 #            We know and use this construct regularly to create "transactions"
 #            where C is only executed when both A and B have succeeded.
-#  * SC2154: Due to Molgenis Compute string initialization the warning is not valid 
-#
-#  * SC2148: the shebang is declared in the header.ftl not in the protocols
+#  * SC2148: The shebang is declared in the header.ftl and not in the protocols.
 #
-
-export SHELLCHECK_OPTS="-e SC2004 -e SC2015 -e SC2154 -e SC2148"
+export SHELLCHECK_OPTS="-e SC2004 -e SC2015 -e SC2148"
 
 function showHelp() {
 	#
@@ -35,14 +36,15 @@ EOH
 #
 # Parse commandline options
 #
+declare format='gcc'  # default
 while getopts ":hv" opt
 do
 	case "${opt}" in
 		h)
 			showHelp
 			;;
 		v)
-			verbose='1'
+			format='tty'
 			;;
 		\?)
 			printf '%s\n' "FATAL: Invalid option -${OPTARG}. Try $(basename "${0}") -h for help."
@@ -68,42 +70,23 @@ which shellcheck 2>&1 >/dev/null \
 		exit 1
 	}
 
+MYDIR="$(cd -P "$(dirname "${0}")" && pwd)"
 #
-# Run ShellCheck for all Bash scripts in the bin/ subdir.
-#  * Includes sourced files, so the libraries from the lib/ subfolder 
+# Run ShellCheck for all Bash scripts in the protocols/ subdir.
+#  * Includes sourced files, so files in a subfolder 
 #    are checked too as long a they are used in at least one script.
-#  * Select format and output based on whether this script is 
-#    executed by Jenkins or by a regular user.
 #
-if [[ -n "${WORKSPACE:-}" ]]
+if [[ "${CIRCLECI:-}" == true ]]
 then
 	#
 	# Exclude SC2154 (warning for variables that are referenced but not assigned),
 	# because we cannot easily resolve variables sourced from etc/*.cfg config files.
 	#
 	export SHELLCHECK_OPTS="${SHELLCHECK_OPTS} -e SC2154"
 	#
-	# ShellCheck for Jenkins.
-	#
-	shellcheck -a -x -o all -f checkstyle "${WORKSPACE}"/protocols/*.sh | tee checkstyle-result.xml
-	#
-	# Reformat the generated report to add hyperlinks to the ShellCheck issues on the wiki:
-	#	https://github.com/koalaman/shellcheck/wiki/SC${ISSUENUMBER}
-	# explaining what is wrong with the code / style and how to improve it.
-	#
-	perl -pi -e "s|message='([^']+)'\s+source='ShellCheck.(SC[0-9]+)'|message='<a href="https://github.com/koalaman/shellcheck/wiki/\$2">\$2: 
-\$1</a>' source='ShellCheck.\$2'|" checkstyle-result.xml
-else
-	#
-	# ShellCheck for regular user on the commandline.
+	# Exclude SC2312 (warning for masking return values of command in a subshell when using process substitution) temporarily,
+	# because we did not find a reliable fix yet....
 	#
-	MYDIR="$(cd -P "$(dirname "${0}")" && pwd)"
-	if [[ "${verbose:-0}" -eq 1 ]]
-	then
-		cd "${MYDIR}/.."
-		shellcheck -a -x -o all -f tty protocols/*.sh # cannot use the printf construct used below for non-vebose output as it destroys the terminal colors.
-		cd '-' # Goes back to previous directory before we changed to ${MYDIR}.
-	else
-		printf '%s\n' "$(cd "${MYDIR}/.." && shellcheck -a -x -o all -f gcc protocols/*.sh)"
-	fi
+	export SHELLCHECK_OPTS="${SHELLCHECK_OPTS} -e SC2312"
 fi
+shellcheck -a -x -o all -f "${format}" "${MYDIR}"/../protocols/*.sh | sed "s|${MYDIR}/../||g"

checkEnvironment.sh

@@ -1,6 +1,6 @@
 HOST=$1
 
-if [ -f ./environment_checks.txt ]
+if [[ -f ./environment_checks.txt ]]
 then
 	rm ./environment_checks.txt
 fi
@@ -10,29 +10,25 @@ TMPDIR=""
 GROUP=""
 if [ "${HOST}" == "zinc-finger.gcc.rug.nl" ]
 then
-    	ENVIRONMENT_PARAMETERS="zinc-finger"
-        TMPDIR="tmp05"
+	ENVIRONMENT_PARAMETERS="zinc-finger"
+	TMPDIR="tmp05"
 elif [ "${HOST}" == "leucine-zipper.gcc.rug.nl" ]
 then
-    	ENVIRONMENT_PARAMETERS="leucine-zipper"
-        TMPDIR="tmp06"
-elif [ "${HOST}" == "calculon" ]
-then
-    	ENVIRONMENT_PARAMETERS="calculon"
-        TMPDIR="tmp04"
+	ENVIRONMENT_PARAMETERS="leucine-zipper"
+	TMPDIR="tmp06"
 else
-    	echo "unknown host: running is only possible on calculon,zinc-finger or leucine-zipper"
+	echo "Unknown host: running is only possible on zinc-finger or leucine-zipper."
 fi
 
 THISDIR=$(pwd)
 if [[ $THISDIR == *"/groups/umcg-gaf/"* ]]
 then
 	GROUP="umcg-gaf" 
-elif [[ $THISDIR == *"/groups/umcg-gd/"* ]] 
+elif [[ $THISDIR == *"/groups/umcg-gd/"* ]]
 then
 	GROUP="umcg-gd"
 else
-	echo "this is not a known group, please run only in umcg-gd or umcg-gaf group"
+	echo "This is not a known group. Please run only in umcg-gd or umcg-gaf group."
 fi
 
 printf "${ENVIRONMENT_PARAMETERS}\t${TMPDIR}\t${GROUP}" > ./environment_checks.txt

templates/generate_template.sh

@@ -5,7 +5,7 @@ then
 	echo "RNA pipeline loaded, proceeding"
 else
 	echo "No RNA pipeline loaded, exiting"
-        exit 1
+	exit 1
 fi
 
 module list
@@ -58,7 +58,7 @@ workflow="${EBROOTNGS_RNA}/workflow_${pipeline}.csv"
 
 if [ -f .compute.properties ];
 then
-     rm .compute.properties
+	rm .compute.properties
 fi
 
 perl "${EBROOTNGS_RNA}/convertParametersGitToMolgenis.pl" "${EBROOTNGS_RNA}/parameters.${species}.${build}.csv" > \

test/autotest_generate_template.sh

@@ -20,12 +20,12 @@ PIPELINE="hisat" # hisat, lexogen
 
 WORKFLOW=${EBROOTNGS_RNA}/test_workflow_${PIPELINE}.csv
 
-if [ -f .compute.properties ];
+if [[ -f .compute.properties ]]
 then
-     rm .compute.properties
+	rm .compute.properties
 fi
 
-if [ -f ${GAF}/generatedscripts/${PROJECT}/out.csv  ];
+if [[ -f ${GAF}/generatedscripts/${PROJECT}/out.csv ]]
 then
 	rm -rf ${GAF}/generatedscripts/${PROJECT}/out.csv
 fi

test/protocols/Autotest.sh

@@ -29,11 +29,11 @@ done
 
 if [[ -f "${testResults}/output_NGS_RNA/notInVcf1.txt" || -f "${testResults}/output_NGS_RNA/notInVcf2.txt" || -f "${testResults}/output_NGS_RNA/inconsistent.txt" || -f "${testResults}/output_NGS_RNA/"*.fail ]]
 then
-	echo "there are differences between the test and the original output"
-        echo "please fix the bug or update this test"
-        echo "the stats can be found here: ${testResults}/output_NGS_RNA/vcfStats.txt"
-        exit 1
+	echo "There are differences between the test and the original output."
+	echo "Please fix the bug or update this test."
+	echo "The stats can be found here: ${testResults}/output_NGS_RNA/vcfStats.txt"
+	exit 1
 else
-	echo "test succeeded"
+	echo "Test succeeded."
 	head -2 "${testResults}/output_NGS_RNA/vcfStats.txt"
 fi