scaffold

#!/bin/bash
#
# scaffold sets up the scaffolding for a new subject.
# Example command is:
#
# ./scaffold new_subject
#
# This will create $PROJ_DIR/subjects/new_subject/
#
# If you make a new function in the $PROJ_DIR/prototype/link directory and you want
# that to be available in a participant's directory then run 
# `./scaffold new_subject` and it will copy over to the participant
# directory. Because that file is linked, you can then make edits to either
# trace
#
# This should mean that scaffolding NEVER deletes or overwrites anything and thus can be done whenever
#
# If you want to run this on all participants than use:
# ./scripts/re-scaffold.sh
#
# Copyright (C) 2010 mason simon (mgsimon@princeton.edu)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.


set -e # stop immediately when an error occurs

#source globals.sh
SUBJECTS_DIR=subjects/

# set global variables
TEMPLATE_DIR=prototype
LINK_DIR=$TEMPLATE_DIR/link
COPY_DIR=$TEMPLATE_DIR/copy
SUBJ_ID_PATTERN='<<SUBJECT_ID>>'


# display usage instructions if this script was run improperly
if [ $# -ne 1 ]; then
  echo "
usage: `basename $0` subject_id

sets up the directory structure and default files (scaffolding) for the subject
with given ID, based on the template in $TEMPLATE_DIR.
if scaffold has already been called for that subject, the subject's directory
will be updated with any files and folders added to the template since the
subject was last scaffolded
  "
  exit
fi

# stick parameters into the right variables
subj=$1
subj_dir=$SUBJECTS_DIR/$subj

if [ ! -d "$SUBJECTS_DIR" ]; then
echo "if this is your first time setting up a subject with NeuroPipe,"
echo "read README.txt in the subject's directory (just created)"
fi

mkdir -p $subj_dir

# link in each file in LINK_DIR, making their parent directories as needed. to
# keep things portable, the code makes relative links, which complicates the
# logic. see the notes within this loop for more explanation
for path in $(find $LINK_DIR/*); do
  rel_path=${path##$LINK_DIR/}   # removes $LINK_DIR from front of path
  rel_dir=$(dirname $rel_path)

  if [ -d "$path" ]; then
    mkdir -p $subj_dir/$rel_path
    continue
  fi

  # because we're recursing into LINK_DIR, we have to build up a prefix of
  # ../'s that gets one longer for each directory we dive into. that's what the
  # following hunk of code does
  p=$path
  prefix=''
  while [ "$(dirname $p)" != '.' ]; do
    prefix="$prefix../"
    p=$(dirname $p)
  done
  
  ln -s -f ${prefix}$path $subj_dir/$rel_path
done

# copy in each file in COPY_DIR, making their parent directories as needed, and
# replacing all instances of $SUBJ_ID_PATTERN with the subject's ID
for path in $(find $COPY_DIR/*); do
  rel_path=${path##$COPY_DIR/}
  rel_dir=$(dirname $rel_path)
  mkdir -p $rel_dir

  if [ -d $path ]; then
    mkdir -p $subj_dir/$rel_path
    continue
  fi

  tmp=$(mktemp -t tmp.XXXXXX)
  cat $path | sed "s:$SUBJ_ID_PATTERN:$subj:g" > $tmp;
  if [ -e "$subj_dir/$rel_path" ] && [ -n "$(diff $tmp $subj_dir/$rel_path)" ]; then
    echo "WARNING: $rel_path has been modified. not updating it" > /dev/stderr
    rm -f $tmp
    continue
  fi

  mv $tmp $subj_dir/$rel_path
  chmod 770 $subj_dir/$rel_path #Change the directory permission
done

echo "created subject directory '$subj_dir'"