Custom Query (87 matches)

The oml2-server-hook.sh script that is attached to the tutorial instructions and installed on emmy9 will only push results to the appropriate account in irods if the slice name and the user's iRODS account username start with gimi[0-9]. It assumes that the zone on the iRODS server is geniRenci.

NAME=${DBFILE:12:6}; FILE=${DBFILE:12}; LENGTH=${#FILE} SLICE=${FILE:0:$LENGTH-4} DATE=date ${IPUT} ${OPTION} ${DBFILE}

if $NAME =~ ^gimi[0-9] ?; then

echo "Entered..."

ichmod -M own $NAME /geniRenci/home/$NAME/$FILE iput -f ${DBFILE} /geniRenci/home/$NAME/$FILE; imeta add -d /geniRenci/home/$NAME/$FILE Date ${DATE} imeta add -d /geniRenci/home/$NAME/$FILE UserName? $NAME imeta add -d /geniRenci/home/$NAME/$FILE SliceName? $SLICE

fi

The hook script is also very specific to the configuration of the OML server in that it assumes the path to the DB file contains 12 characters. It isn't clear in the instructions that the user will need to adjust the hook script if they want to use it on their own OML server.

An initialization script will be run by the experimenter within their own environment to do the following:

• create an experiment ID
• select slice(s) for the experiment
• create an iticket for the experiment
• create and prepopulate an experiment directory in iRODS
• push sliver manifests to iRODS
• push information about the experiment to the Experiment Registry (on the GIMI server).

This task will create the skeleton (first version) of the script and allow the user to specify the experiment name from which an experiment ID will be created. The remaining tasks will be tracked by other tickets.

The experimenter's iRODS context must be established. The irodsEnv file should be created with default iRODS configuration (which can be overridden later) and iinit should be run to set up the password hash file.