A simple CLI script to import a series of format files corresponding to a ticket

format-import

#!/bin/bash

set -e
set -u

FILE=$1
shift;

# Define environement variables
HOST=${HOST:-localhost}
PORT=${PORT:-4064}
ROOT_PASSWORD=${ROOT_PASSWORD:-omero}
GROUP=${GROUP:-formats}
FORMAT=${FORMAT:-ome-tiff}
USER_PASSWORD=${USER_PASSWORD:-ome}
TICKET=${TICKET:-1}

# Create group and user (named after format to import)
bin/omero login -s $HOST -p $PORT -u root -w $ROOT_PASSWORD
bin/omero group add $GROUP --ignore-existing
bin/omero user add $FORMAT $FORMAT $FORMAT $GROUP -P ome --ignore-existing
bin/omero logout

# Login as format user
bin/omero login -s $HOST -p $PORT -u $FORMAT -w $USER_PASSWORD

# Create dataset named after ticket number
dataset=$(bin/omero obj new Dataset name="#$TICKET" description="http://trac.openmicroscopy.org/ome/ticket/$TICKET")

# Import the file into the dataset via in-place import (ln_s)
handle() {
    bin/omero import -d $dataset -u $FORMAT \
       ---file $TICKET.out ---errs $TICKET.err "$1" -- \
       --transfer=ln_s --checksum_algorithm=File-Size-64
}

while read i; do handle "$i"; done < $FILE

# Logout
bin/omero logout