Merge branch 'master' of https://github.com/cooperrc/computational-me…

…chanics

middleware/invoke

@@ -4,6 +4,39 @@
 # tool
 #
 
+# Copy all files from a source directory to a target directory that matches
+# a specific file type suffix.
+# Arg 1: The file type. e.g. md, csv, npz
+# Arg 2: The source directory path.
+# Arg 3: The target directory path
+copyFileType () {
+fileType=$1
+sourceDir=$2
+targetDir=$3
+
+# Get a list of file from the source directory that has the file type
+# suffix.
+for file in $(find ${sourceDir} -name "*.${fileType}")
+do
+    # Get the copy file name without the source directory path
+    # attached. Preserve the directory path within the source
+    # directory.
+    copyFile=$(echo ${file} | sed "s:^${sourceDir}/::")
+
+    # Get the directory name of the copyFile
+    copyDir=$(dirname $copyFile)
+
+    # If the directory does not exist within the target directory
+    # create the directory path for the copy file.
+    if [ ! -d ${targetDir}/${copyDir} ]; then
+        mkdir -p ${targetDir}/${copyDir}
+    fi
+
+    # Copy the file from the source directory to the target directory.
+    cp ${file} ${targetDir}/${copyFile}
+done
+}
+
 # Get the middleware and tool directories, the tool directory will be used to copy the
 # symlinks to the user directory.
 middlewareDirectory=$(readlink -f $(dirname $0))
@@ -14,20 +47,26 @@ revision=$(basename $(realpath ${toolDirectory}))
 # containing the links will be ${HOME}/COMPMECH
 userDirectory=${HOME}/COMPMECH/${revision}
 
-# If the user directory path does not exist, then create it.
-mkdir -p ${userDirectory}
-
 # If the user directory does not exist then create the user directory.
-if [ -d ${userDirectory} ]; then
-  # Copy and overrid the symlinks in the user directory.
-  cp -sRf ${toolDirectory}/* ${userDirectory}
+if [ ! -d ${userDirectory} ]; then
+  # Create the user directory.
+  mkdir -p ${userDirectory}
+
+  # Copy all files matching .md, .npz, or .csv file types.
+  copyFileType "md" ${toolDirectory} ${userDirectory}
+  copyFileType "npz" ${toolDirectory} ${userDirectory}
+  copyFileType "csv" ${toolDirectory} ${userDirectory}
+
+  # Copy all other file as symlinks, do not override alreadying
+  # exisiting hard copied files.
+  cp -sRf --no-clobber ${toolDirectory}/* ${userDirectory}
 fi
 
 # Invoke the start_jupyter script, look for the Jupyter files in the user
 # directory containing links to the files.
 /usr/bin/invoke_app "$@" -t compmech \
-                  -C "start_jupyter --themes  README.md" \
+                  -C "start_jupyter --themes" \
                       -u anaconda-7 \
                       -w headless \
-          -d $userDirectory \
+          -d "${HOME}" \
                       -r none