Bugfixes for switching from Jenkins to CircleCI.

README.md

@@ -2,6 +2,7 @@
 
 Automation using Bash scripts and Cron jobs, inorder to automate the concordance check calculations. 
 
+[![CircleCI](https://dl.circleci.com/status-badge/img/gh/molgenis/ConcordanceCheck/tree/master.svg?style=svg)](https://dl.circleci.com/status-badge/redirect/gh/molgenis/ConcordanceCheck/tree/master)
 
 #### Code style
 

check/indentationcheck.sh

@@ -1,9 +1,11 @@
 #!/bin/bash
 
+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:-../}"/{bin,lib}/*.*sh
+grep -n '^[[:space:]]* [[:space:]]*' "${MYDIR}"/../{bin,lib}/*.*sh
 grep_exit_status="${?}"
 if [[ "${grep_exit_status}" -eq 0 ]]; then
 	echo '#####################################################################################'

check/shellcheck.sh

@@ -1,5 +1,9 @@
 #!/bin/bash
 
+set -e
+set -u
+set -o pipefail
+
 #
 # Disable some shellcheck warnings:
 #  * SC2004: $/${} is unnecessary on arithmetic variables.
@@ -31,14 +35,15 @@ EOH
 #
 # Parse commandline options
 #
-while getopts "hv" opt
+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."
@@ -64,41 +69,23 @@ which shellcheck 2>&1 >/dev/null \
 		exit 1
 	}
 
+MYDIR="$(cd -P "$(dirname "${0}")" && pwd)"
 #
 # Run ShellCheck for all Bash scripts in the bin/ subdir.
 #  * Includes sourced files, so the libraries from the lib/ subfolder 
 #    are checked too as long a they are used in at least one script.
-#  * Select format and output based on whether this script is 
-#    executed by Jenkins or by a regular user.
 #
-if [[ -n "${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 "${WORKSPACE}"/bin/*.sh | tee checkstyle-result.xml
-	#
-	# Reformat the generated report to add hyperlinks to the ShellCheck issues on the wiki:
-	#	https://github.com/koalaman/shellcheck/wiki/SC${ISSUENUMBER}
-	# explaining whatis 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 bin/*.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 "${MYDIR}/.." && shellcheck -a -x -o all -f gcc bin/*.sh)"
-	fi
+	export SHELLCHECK_OPTS="${SHELLCHECK_OPTS} -e SC2312"
 fi
+shellcheck -a -x -o all -f "${format}" "${MYDIR}"/../bin/*.sh | sed "s|${MYDIR}/../||g"