Install

#!/bin/sh
#
# Installation script for the genemodelload product
#
###########################################################################

cd `dirname $0`

COMMON_CONFIG=genemodel_common.config
PROVIDER_CONFIGS="biotypemapping.config genemodel_ensembl.config genemodel_ncbi.config genemodel_ensemblreg.config genemodel_vistareg.config mgireg.gff3.config"

#
#  Function called when the install fails.
#
installFailed ()
{
    echo "Installation Failed: `date`"
    exit 1
}


#
# Make sure all the configuration files exist.
#
for i in ${COMMON_CONFIG} ${PROVIDER_CONFIGS}
do
    if [ ! -r ${i} ]
    then
        echo "Missing configuration file: ${i}"
        installFailed
    fi
done

#
# Source the common configuration file.
#
. ${COMMON_CONFIG}

#
# Check to see if this is a development installation.
#
DEV=""
if [ "${INSTALL_TYPE}" = "dev" ]
then
    DEV="-d"
fi

#
# Run the DLAInstall.
#
${DLAINSTALL} ${DEV}

#
# The DLAInstall script removes all permissions from shell scripts for
# group "other" on non-development servers. The gene model QC report wrapper
# script needs to have permissions restored to allow the curation staff to run it.
#
chmod -f 755 ${GENEMODEL_QC_SH}

#
# Handle installation tasks specific to each provider.
#
for i in ${PROVIDER_CONFIGS}
do
    #
    # Source the provider configuration file.
    #
    . ${i}

    #
    # For any server, if the association file does not exist already, create one that is writable.
    #
    if [ ! -f ${ASSOC_FILE_DEFAULT} ]
    then
	echo "Creating ${ASSOC_FILE_DEFAULT}"
        touch ${ASSOC_FILE_DEFAULT}
        chmod 664 ${ASSOC_FILE_DEFAULT}
        chgrp mgi ${ASSOC_FILE_DEFAULT}
    fi
done

#
# For any server, the these directories are opened up
# to allow the curation staff to publish new association files.
#
# The config files needs to be open to allow curators to edit them for testing.
#
chmod -fR 777 ${INPUTDIR}

#
# The following steps must all be done on the TEST SERVER: 
# opens up all permissions
#
# once the new curator server is ready:
#	a) replace bhmgidevapp01 with the curator server name
#	b) do not need the MGI_LIVE check because it will use "live"
#
if [ `uname -n` = "bhmgidevapp01" -a "${MGI_LIVE}" = "/usr/local/mgi/test" ]
then
	echo "Setting permissions...${DATALOADSOUTPUT}"
	chgrp mgi *config
	chmod -f 666 *config
	chmod -fR 777 ${DATALOADSOUTPUT}/assembly
	chmod -fR 777 ${DATALOADSOUTPUT}/ensembl
	chmod -fR 777 ${DATALOADSOUTPUT}/mgi/genemodelload
	chmod -fR 777 ${DATALOADSOUTPUT}/mgi/vocload/runTimeBiotype
	chmod -fR 777 ${DATALOADSOUTPUT}/mgi/seqcacheload
	chmod -fR 777 ${DATALOADSOUTPUT}/mgi/mrkcacheload
	chmod -fR 777 ${ASSOCLOAD}
	chmod -fR 777 ${ASSEMBLYSEQLOAD}
	chmod -fR 777 ${SEQSEQASSOCLOAD}
	chmod -f 666 ${ASSEMBLYSEQLOAD}/*.config
	chmod -fR 777 ${DATALOADSOUTPUT}/mgi/pgdbutilities/logs
fi

# copy the scripts for curator use into a standard location which exists in
# their path statements

# trim any trailing slash from MGIBIN variable
DEPLOY_PATH=`echo "${MGIBIN}" | sed 's./$..'`

if [ "${DEPLOY_PATH}" = "" ]; then
        echo "Warning: MGIBIN variable missing from mgiconfig; cannot deploy curator files"
        exit 0
fi

if [ ! -d ${DEPLOY_PATH} ]; then
        # failure to deploy is not a fatal error; could happen during
        # development under a home directory
        echo "Warning: ${DEPLOY_PATH} does not exist; curator scripts were not copied."
        exit 0
fi

if [ -d ${DEPLOY_PATH} ]; then
        # copy files, change permissions, and check for errors
        # deployment errors are non-fatal, as they can occur regularly in an
        # SE's development area

        for file in runGeneModelQC publishAssocFile
        do
                cp bin/${file} ${DEPLOY_PATH}
                if [ $? -ne 0 ]; then
                        echo "Warning: Failed to copy ${file} to ${DEPLOY_PATH}"
                fi

                chmod 755 ${DEPLOY_PATH}/${file}
                if [ $? -ne 0 ]; then
                        echo "Warning: Failed to change permissions on ${DEPLOY_PATH}/${file}"
                fi
        done
        echo "Deployed curator files to ${DEPLOY_PATH}"
fi

exit 0