external assets for thesis now handled more robustly

we can now find all external.assets file in the entire assets/ tree
also copy operation does not overwrite

chertex.sh

@@ -30,7 +30,12 @@ else
    echo "--- This job did not request LaTeXMK RC file"
 fi
 
-# define some commands
+# define some constants
+path_wd=${PWD}
+dir_wd=$(basename $path_wd)
+path_thesis="/media/bay/taha/chepec/thesis"
+
+# define some file types
 Rfiletype="R"
 TeXfiletype="tex"
 tikzfiles="*.tikz"
@@ -120,30 +125,23 @@ if [ $# -eq 1 ]; then
    fi
 
 	#### Special treatment for thesis
-   if [[ ${PWD} ==  "/media/bay/taha/chepec/thesis" && $jobname == "thesis" ]]; then
+   if [[ $path_wd == "$path_thesis" && $jobname == "$dir_wd" ]]; then
       # Fetch external assets by reading any assets.external files in assets/ tree
       # NOTE: be careful NOT to leave empty lines in your assets.external files
       echo "<thesis> -------------------------------"
       echo "<thesis> Getting external assets"
       echo "<thesis> -------------------------------"
-		# summary of operations in this if-clause:
-      # trawl the assets/ subdirectories looking for a file "external.assets", if found,
-      # read its contents line-by-line (each line is a path) and copy that file at that path to the current assets/ subdir
-      # note that we only look for assets.external inside the subdirectories, and not in assets/ itself
-      assetsubdirectories="$(find /media/bay/taha/chepec/thesis/assets/ -maxdepth 1 -mindepth 1 -type d)"
-      # loop through $assetdirs, and look for the file external.assets in each path
-      for assetdir in $assetsubdirectories; do
-         assetfilename="assets.external"
-         if [ -e ${assetdir}/${assetfilename} ]; then
+      # find all files named "assets.external" in the assets/ tree
+      assetsexternalfiles=$(find "$path_wd/assets/" -type f -name "assets.external")
+      for externalfilepath in $assetsexternalfiles; do
+         # this weird-looking while-loop reads the assets.external file line-by-line and copies each asset into the target path inside the thesis' assets/ tree
          # https://stackoverflow.com/questions/10929453/read-a-file-line-by-line-assigning-the-value-to-a-variable
-            # $assets is the current assets.external file
-            assets="${assetdir}/${assetfilename}"
          while IFS='' read -r asset || [[ -n "$asset" ]]; do
-               echo "$asset"
-               # copy this filepath into the current assets subdirectory
-               cp --preserve=timestamps $asset $assetdir
-            done < "$assets"
-         fi
+            assetpathtarget=$(dirname "$externalfilepath")
+            echo "Copying $asset to $assetpathtarget"
+            # cp but don't overwwrite existing files
+            cp --preserve=timestamps --no-clobber $asset $assetpathtarget
+         done < "$externalfilepath"
       done
 
       # Create low-res photos on-the-fly from existing photos/
@@ -157,15 +155,15 @@ if [ $# -eq 1 ]; then
       # rsync can't do that. We need to use a different tool. See e.g.
       # https://superuser.com/questions/260092/rsync-switch-to-only-compare-timestamps
       # copy only the "large" photos that have file modtimes more recent than the last time this operation was run
-      photoslastrun="/media/bay/taha/chepec/thesis/assets/photos/.lowres/lastrun"
+      photoslastrun="$path_wd/assets/photos/.lowres/lastrun"
       if [ ! -f "$photoslastrun" ]; then
          # if, for some reason, the lastrun file does not exist
          # copy over everything and then create the file
-         rsync -av /media/bay/taha/chepec/thesis/assets/photos/* /media/bay/taha/chepec/thesis/assets/photos/.lowres/ --exclude /media/bay/taha/chepec/thesis/assets/photos/.lowres/
+         rsync -av "$path_wd/assets/photos/*" "$path_wd/assets/photos/.lowres/" --exclude "$path_wd/assets/photos/.lowres/"
          touch "$photoslastrun"
       fi
       # cd and use --parents arg to preserve directory structure in .lowres target
-      cd /media/bay/taha/chepec/thesis/assets/photos
+      cd "$path_wd/assets/photos"
       newphotos="$(find . -type f -cnewer $photoslastrun ! -path './.lowres/*')"
       if [ -n "$newphotos" ]; then
          for newphoto in $newphotos; do
@@ -175,7 +173,7 @@ if [ $# -eq 1 ]; then
       # revert the effects of cd above. Redirect to null suppresses the output.
       cd - >/dev/null
       # in the low-res tree, find any photo larger than specific size (500kB)
-      largephotos="$(find /media/bay/taha/chepec/thesis/assets/photos/.lowres/ -size +500k)"
+      largephotos="$(find $path_wd/assets/photos/.lowres/ -size +500k)"
       for largephotofilename in $largephotos; do
          # for the next statement to work reliably, we should probably convert other formats to JPEG
          # detect file extension, and based on it, convert to jpg using mogrify
@@ -299,8 +297,8 @@ else
 		#		exit 1
 		#	fi
 		#else
-		#   # There is exactly one *.Rnw file is current directory
-		#	# Fetch the jobname from the .Rnw filename by stripping off the file extension
+		## There is exactly one *.Rnw file is current directory
+		## Fetch the jobname from the .Rnw filename by stripping off the file extension
 		#	Rnwfilename=$(ls -1 $Rnwfiles)
 		#	jobname=${Rnwfilename%.*}
 		#fi
@@ -407,9 +405,7 @@ runtime=$(( $endtime - $starttime ))
 # send push message via Gotify CLI
 # if runtime is longer than X minutes (suitable limit perhaps 3 min)
 if (( $runtime > 180 )); then
-   # cwd is the current directory (basename)
-	cwd=$(basename $PWD)
-	gotify push --quiet --title "$cwd" --priority 5 "chertex.sh $@ \nCompleted in $runtime s"
+	gotify push --quiet --title "$dir_wd" --priority 5 "chertex.sh $@ \nCompleted in $runtime s"
 fi
 
 echo "-------------------------------------"