Importing batch demographic data into OSCAR

Sometimes it is useful to import a batch of demographic data into OSCAR.

This script takes demographic data from a flat text file and imports it - creating new patient demographic entries in OSCAR.

Instructions, as with all my scripts, on how to install and run an OSCAR perl script are included at the start of the script itself.

Passwordless SSH access

The best tutorial for passwordless SSH access to your OSCAR server using an SSH key is here:

http://www.debian-administration.org/articles/152


If you are using a mac, you will need to create the ssh-copy-id script which OS X is missing (Ubuntu has it installed by default):


sudo vi /usr/bin/ssh-copy-id



Then paste the following text:




#!/bin/sh

# Shell script to install your public key on a remote machine
# Takes the remote machine name as an argument.
# Obviously, the remote machine must accept password authentication,
# or one of the other keys in your ssh-agent, for this to work.

ID_FILE="${HOME}/.ssh/id_rsa.pub"

if [ "-i" = "$1" ]; then
  shift
  # check if we have 2 parameters left, if so the first is the new ID file
  if [ -n "$2" ]; then
    if expr "$1" : ".*\.pub" >/dev/null; then
      ID_FILE="$1"
    else
      ID_FILE="$1.pub"
    fi
    shift         # and this should leave $1 as the target name
  fi
else
  if [ x$SSH_AUTH_SOCK != x ] && ssh-add -L >/dev/null 2>&1; then
    GET_ID="$GET_ID ssh-add -L"
  fi
fi

if [ -z "`eval $GET_ID`" ] && [ -r "${ID_FILE}" ] ; then
  GET_ID="cat ${ID_FILE}"
fi

if [ -z "`eval $GET_ID`" ]; then
  echo "$0: ERROR: No identities found" >&2
  exit 1
fi

if [ "$#" -lt 1 ] || [ "$1" = "-h" ] || [ "$1" = "--help" ]; then
  echo "Usage: $0 [-i [identity_file]] [user@]machine" >&2
  exit 1
fi

{ eval "$GET_ID" ; } | ssh $1 "umask 077; test -d .ssh || mkdir .ssh ; cat >> .ssh/authorized_keys" || exit 1

cat <
Now try logging into the machine, with "ssh '$1'", and check in:

  .ssh/authorized_keys

to make sure we haven't added extra keys that you weren't expecting.

EOF