Merge branch 'master' of git.metabarcoding.org:lecasofts/LECABashLib

README.md

@@ -376,7 +376,6 @@ If the file does not exist it is created
 
 Closes the current logfile and redirect the logging to stderr.
 
-
 ----------------------------------------------------------
 
 
@@ -486,7 +485,6 @@ Closes the current logfile and redirect the logging to stderr.
     setintersec <SETNAME1> <SETNAME2> <DESTINATION>
 ```
 
-
 ----------------------------------------------------------
 
 
@@ -576,7 +574,6 @@ and the return status is set to *1* instead of *0* usually.
     tempdirectory <VARIABLE> [MINSIZE]
 ```
 
-
 ----------------------------------------------------------
 
 
@@ -598,6 +595,26 @@ and the return status is set to *1* instead of *0* usually.
 ```
 
 ----------------------------------------------------------
+## path
+
+### Activating the module
+
+    	> source $LECABASHHOME/utils.sh
+    	> include path
+
+### Functions provided:
+
+#### relative2absolute
+
+        relative2absolute <PATH>
+#### absolute2relative
+
+```bash
+    absolute2relative <PATH> <RELATIVE_TO>
+```
+
+
+----------------------------------------------------------
 
 ## irods
 
@@ -642,7 +659,6 @@ ex:
         fi
 ```
 
-
 ----------------------------------------------------------
 
 

path.sh

+# LECA Bash library
+#
+# The LECA bash library provides a set of function used for helping
+# development of bash script mainly to write job script on the luke
+# cluster
+#
+# The files from the LECA Bash library must be sourced from your main script
+#
+#
+
+include logging
+
+logdebug "Load path package"
+
+relative2absolute(){
+  local thePath
+  if [[ ! "$1" =~ ^/ ]];then
+    thePath="$PWD/$1"
+  else
+    thePath="$1"
+  fi
+  echo "$thePath"|(
+  IFS=/
+  read -a parr
+  declare -a outp
+  for i in "${parr[@]}";do
+    case "$i" in
+    ''|.) continue ;;
+    ..)
+      len=${#outp[@]}
+      if ((len==0));then
+        continue
+      else
+        unset outp[$((len-1))] 
+      fi
+      ;;
+    *)
+      len=${#outp[@]}
+      outp[$len]="$i"
+      ;;
+    esac
+  done
+  echo /"${outp[*]}"
+)
+}
+
+function absolute2relative() {
+	# both $1 and $2 are absolute paths beginning with /
+	# returns relative path to $2/$target from $1/$source
+	source=$1
+	target=$2
+
+	common_part=$source # for now
+	result="" # for now
+
+	while [[ "${target#$common_part}" == "${target}" ]]; do
+		# no match, means that candidate common part is not correct
+		# go up one level (reduce common part)
+		common_part="$(dirname $common_part)"
+		# and record that we went back, with correct / handling
+		if [[ -z $result ]]; then
+			result=".."
+		else
+			result="../$result"
+		fi
+	done
+
+	if [[ $common_part == "/" ]]; then
+		# special case for root (no common path)
+		result="$result/"
+	fi
+
+	# since we now have identified the common part,
+	# compute the non-common part
+	forward_part="${target#$common_part}"
+
+	# and now stick all parts together
+	if [[ -n $result ]] && [[ -n $forward_part ]]; then
+		result="$result$forward_part"
+	elif [[ -n $forward_part ]]; then
+		# extra slash removal
+		result="${forward_part:1}"
+	fi
+
+	echo $result
+}

utils.sh

@@ -13,6 +13,10 @@ if [[ -z "${LECALIB_UTIL_SH}" ]]; then
 	LECALIB_UTIL_SH=1
 	LECABASHLIB_RELOADING=0
 	
+	if [[ -z "$LECABASHLIB_PATH" ]] ; then
+		export LECABASHLIB_PATH=""
+	fi
+
 	THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
 
     source "${THIS_DIR}/utils.sh"
@@ -40,11 +44,36 @@ if [[ -z "${LECALIB_UTIL_SH}" ]]; then
 		local MODULE=$(upper $1)
 		local LOADED_MODULE_VAR="LECALIB_${MODULE}_SH"
 		local LOADED_MODULE=$(indirect $LOADED_MODULE_VAR)
-		if [[ -z "${LOADED_MODULE}" || "$LECABASHLIB_RELOADING" == 1 ]]; then
+		local found=""
+		
+		for path in $(echo $LECABASHLIB_PATH | sed 's/:/ /g') ; do
+			if [[ -z "$found" && \
+			      ( -z "${LOADED_MODULE}" || \
+			       "$LECABASHLIB_RELOADING" == 1 ) && \
+			       -f "${path}/${1}.sh" ]] ; then
+				source "${path}/${1}.sh"
+				eval $LOADED_MODULE_VAR=1
+				found=1
+			fi
+		done
+		if [[ -z "$found" && \
+			      ( -z "${LOADED_MODULE}" || \
+			       "$LECABASHLIB_RELOADING" == 1 ) && \
+			       -f "${LECALIB_DIR}/${1}.sh" ]] ; then
 			source "${LECALIB_DIR}/${1}.sh"
 			eval $LOADED_MODULE_VAR=1
+			found=1
+		fi
+
+		if (( found == 1 )) ; then
 			if (( LECABASHLIB_RELOADING == 1 )) ; then
-				loginfo "Module $1 reloaded..."
+				logdebug "Module $1 reloaded..."
+		    else
+				logdebug "Module $1 loaded..."
+			fi
+	    else
+	    		if [[ -z "${LOADED_MODULE}" ]] ; then
+	    			logerror "Cannot load module $1"
 	    		fi
 		fi
 	}
@@ -72,5 +101,7 @@ if [[ -z "${LECALIB_UTIL_SH}" ]]; then
     	command popd "$@" > /dev/null
 	}
 	
+	include logging
 
 fi
+