mrkcoordload.config.default

#format: sh
#
#  Configuration for mrkcoordload
#
#  This file sets up environment variables that are needed for a Coordinate load
#
###########################################################################

#
#  If the MGICONFIG environment variable does not have a local override,
#  use the default "live" settings.
#
if [ "${MGICONFIG}" = "" ]
then
    MGICONFIG=/usr/local/mgi/live/mgiconfig
    export MGICONFIG
fi

CONFIG_MASTER=${MGICONFIG}/master.config.sh

export CONFIG_MASTER

. ${CONFIG_MASTER}

##########################################################################
#
#  JAVA SETTINGS
#
###########################################################################

JAVARUNTIMEOPTS="-Xms1500m -Xmx1500m"

JAVA_LIB=${MGI_JAVALIB}/core.jar:${MGI_JAVALIB}/dbsmgd.jar:${MGI_JAVALIB}/dbsrdr.jar:${MGI_JAVALIB}/dla.jar

CLASSPATH=.:${JAVA_LIB}:${COMMON_CLASSPATH}

export JAVARUNTIMEOPTS JAVA_LIB CLASSPATH


###########################################################################
#
#  LOAD SPECIFIC SETTINGS
#
###########################################################################

# Full path the the logs, reports, and archive directories 
FILEDIR=${DATALOADSOUTPUT}/mgi/mrkcoordload

# Full path to the input, output, logs, reports and archive directories.
#
INPUTDIR=${FILEDIR}/input
LOGDIR=${FILEDIR}/logs
RPTDIR=${FILEDIR}/reports
OUTPUTDIR=${FILEDIR}/output
ARCHIVEDIR=${FILEDIR}/archive

export INPUTDIR FILEDIR LOGDIR RPTDIR OUTPUTDIR ARCHIVEDIR

# Full path name of the curated marker coordload input file (the 
# file we parse into separate files by collection)
INPUT_FILE_DEFAULT="${INPUTDIR}/mrkcoordload.txt"

# Full path to the "cleaned up" QC-ready input file that is created and used
# by the sanity/QC report script.
#
INPUT_FILE_QC=${OUTPUTDIR}/mrkcoordload_qc.txt

export INPUT_FILE_DEFAULT INPUT_FILE_QC

# Minimum number of lines expected for the input files (for sanity check).
#
FILE_MINIMUM_SIZE=2000

# Full path to the load-ready coordinate file that is
# created by the sanity/QC report script and used as input 
# to the marker coordinate load
#
INPUT_FILE_LOAD=${OUTPUTDIR}/mrkcoordload_load.txt

export INPUT_FILE_LOAD

# Full path to the bcp file for loading the input file into the temp table.
#
INPUT_FILE_BCP=${OUTPUTDIR}/mrkcoordload_temp.bcp

export INPUT_FILE_BCP

# Full path to the  sanity/QC log.
#
MRKCOORDQC_LOGFILE=${LOGDIR}/mrkcoordQC.log

export MRKCOORDQC_LOGFILE

# Temp table that will be loaded from the input files.
#
TEMP_TABLE=mrkcoord_temp

export TEMP_TABLE

# Full path to the sanity/QC reports.
#
SANITY_RPT=${RPTDIR}/sanity.rpt
INVALID_MARKER_RPT=${RPTDIR}/invalid_marker.rpt
SEC_MARKER_RPT=${RPTDIR}/secondary_marker.rpt
INVALID_CHR_RPT=${RPTDIR}/invalid_chr.rpt
CHR_DISCREP_RPT=${RPTDIR}/chr_discrep.rpt
INVALID_COORD_STRAND_RPT=${RPTDIR}/invalid_coord_strand.rpt
NON_MIRNA_MARKER_RPT=${RPTDIR}/non_mirna_marker.rpt
MIRBASE_DELETE_RPT=${RPTDIR}/mirbase_delete.rpt
MIRBASE_DUP_RPT=${RPTDIR}/mirbase_dup.rpt
MIRBASE_OTHER_MKR_RPT=${RPTDIR}/mirbase_other_mkr.rpt
MIRBASE_INVALID_ID_RPT=${RPTDIR}/mirbase_invalid_id.rpt
SOURCE_DISPLAY_RPT=${RPTDIR}/source_display.rpt
BUILD_RPT=${RPTDIR}/build.rpt
RPT_NAMES_RPT=${RPTDIR}/reportsWithDiscrepancies.rpt

export SANITY_RPT INVALID_MARKER_RPT SEC_MARKER_RPT
export INVALID_CHR_RPT CHR_DISCREP_RPT INVALID_COORD_STRAND_RPT
export NON_MIRNA_MARKER_RPT MIRBASE_DELETE_RPT MIRBASE_OTHER_MKR_RPT 
export MIRBASE_DUP_RPT MIRBASE_INVALID_ID_RPT SOURCE_DISPLAY_RPT BUILD_RPT RPT_NAMES_RPT

# Number of columns expected for the input file (for sanity check).
#
MRKCOORD_FILE_COLUMNS=8

export MRKCOORD_FILE_COLUMNS


# Temp table that will be loaded from the input file.
#
MRKCOORD_TEMP_TABLE=MRKCoordLoad

export MRKCOORD_TEMP_TABLE

# Full path to QC/sanity scripts.
#
LOAD_QC=${MRKCOORDLOAD}/bin/mrkcoordQC.py
LOAD_QC_SH=${MRKCOORDLOAD}/bin/mrkcoordQC.sh

export LOAD_QC LOAD_QC_SH

#  Full path name of a coordinate load input file. The
# wrapper script will set suffix for each individual load by collection
# e.g. INFILE_NAME=${INFILE_NAME}.qtl export INFILE_NAME
INFILE_NAME="${INPUTDIR}/mrkcoordload" 

# Full path to the file listing all the coordinate load input files
COORD_FILES="${INPUTDIR}/coordinateFileList.txt"

export INFILE_NAME COORD_FILES

# US 35 - create assocload file for mirbase id/marker associations
# mirbase assocload configuration values
ASSOCLOADER_SH=${ASSOCLOAD}/bin/AssocLoad2.sh
ASSOCLOADCONFIG=${MRKCOORDLOAD}/assocload.config
ASSOCDATADIR=${INPUTDIR}
MIRBASE_ASSOC_FILE="${INPUTDIR}/mirbase_assocload.txt"

export ASSOCLOADER_SH ASSOCLOADCONFIG ASSOCDATADIR MIRBASE_ASSOC_FILE

#
# general settings
#
#  Java applications
DLA_LOADER=org.jax.mgi.shr.dla.loader.coord.CoordLoader
DLA_START=org.jax.mgi.shr.dla.loader.DLAStart
COORD_INTERPRETER=org.jax.mgi.shr.dla.input.mgs.MGSCoordinateFormatInterpreter
COORD_PROCESSOR=org.jax.mgi.dbs.mgd.loads.Coord.ChromosomeCoordMapProcessor

export DLA_LOADER DLA_START COORD_INTERPRETER COORD_PROCESSOR

# SQL STREAM
DLA_LOAD_STREAM=org.jax.mgi.shr.dbutils.dao.BCP_Stream
DLA_RADAR_STREAM=org.jax.mgi.shr.dbutils.dao.BCP_Stream

# prefix of Configuration variable names for the load database
# e.g. prefixes DBSERVER, DBNAME, BCP_PATH, etc
DLA_DB_PREFIX=MGD

export DLA_LOAD_STREAM DLA_RADAR_STREAM DLA_DB_PREFIX

# turn off searches for associated clones in the MSProcessor
MS_OK_TO_SEARCH_ASSOC_CLONES=false

export MS_OK_TO_SEARCH_ASSOC_CLONES

#  Full path name of the log files
LOG_PROC=${LOGDIR}/mrkcoordload.proc.log
LOG_DIAG=${LOGDIR}/mrkcoordload.diag.log
LOG_CUR=${LOGDIR}/mrkcoordload.cur.log
LOG_VAL=${LOGDIR}/mrkcoordload.val.log

export LOG_PROC LOG_DIAG LOG_CUR LOG_VAL

# Send debug messages to the diagnostic log
LOG_DEBUG=false
DBDEBUG=false
CACHE_DEBUG=false

# log factory class so classes can get their own logger
LOG_FACTORY=org.jax.mgi.shr.dla.log.DLALoggerFactory

export LOG_DEBUG DBDEBUG CACHE_DEBUG LOG_FACTORY

# this load's login value for DB table CreatedBy and ModifiedBy
JOBSTREAM=mrk_coordload

export JOBSTREAM

# add or delete_reload or reload_by_object
COORD_LOAD_MODE=delete_reload

export COORD_LOAD_MODE

# logical db name for this data provider
# always MGI for markers
COORD_LOGICALDB=MGI

# MGI type name of the feature, always Marker
COORD_FEATURE_MGITYPE=Marker

# name of organism 
COORD_ORGANISM="mouse, laboratory"

# version of the  assembly the coordinates are based on
# e.g. "NCBI Build 36"
# this will be set by wrapper from input file now
#COORD_VERSION=...

export COORD_LOGICALDB COORD_FEATURE_MGITYPE COORD_ORGANISM 

# coordinate map collection to which this load belongs
# e.g. "MGI QTL"
# this will be set by the wrapper for each collection
# file it invokes
#COORD_COLLECTION_NAME=...

# abbreviation for the coordinate collection
# if no value assigned will be same as COORD_COLLECTION
COORD_COLLECTION_ABBREV=

# coordinate map type
COORD_TYPE=Assembly

# the coordinate map units
COORD_UNITS="base pair"

export COORD_COLLECTION_NAME COORD_COLLECTION_ABBREV COORD_TYPE
export COORD_UNITS 

# full path to coordinate repeat file
COORD_REPEAT_FILE=${OUTPUTDIR}/coordrepeats.out

export COORD_REPEAT_FILE

# okay to load multiple coordinates per object?
COORD_REPEATS_OK=false

export COORD_REPEATS_OK

###########################################################################
#
#  BCP MANAGER SETTINGS BY DATABASE
#
###########################################################################

#  Settings used to create a BCP manager for the MGD database
MGD_BCP_PATH=${OUTPUTDIR}
MGD_BCP_PREVENT_EXECUTE=false
MGD_BCP_TRUNCATE_LOG=true
MGD_BCP_DROP_INDEXES=false
MGD_BCP_RECORD_STAMPING=false
MGD_BCP_AUTO_FLUSH=false
MGD_BCP_OK_TO_OVERWRITE=false

export MGD_BCP_PATH MGD_BCP_PREVENT_EXECUTE MGD_BCP_TRUNCATE_LOG
export MGD_BCP_DROP_INDEXES MGD_BCP_RECORD_STAMPING MGD_BCP_AUTO_FLUSH
export MGD_BCP_OK_TO_OVERWRITE

#  Settings used to create a BCP manager for the MGD database
RADAR_BCP_PATH=${OUTPUTDIR}
RADAR_BCP_PREVENT_EXECUTE=false
RADAR_BCP_TRUNCATE_LOG=true
RADAR_BCP_DROP_INDEXES=false
RADAR_BCP_RECORD_STAMPING=false
RADAR_BCP_AUTO_FLUSH=false
RADAR_BCP_OK_TO_OVERWRITE=false

export RADAR_BCP_PATH RADAR_BCP_PREVENT_EXECUTE RADAR_BCP_TRUNCATE_LOG
export RADAR_BCP_DROP_INDEXES RADAR_BCP_RECORD_STAMPING RADAR_BCP_AUTO_FLUSH
export RADAR_BCP_OK_TO_OVERWRITE

###########################################################################
#
#  MISCELLANEOUS SETTINGS
#
###########################################################################
#  The name of the load for the subject of an email notification
# will be set by wrapper based on collection for each load
MAIL_LOADNAME="Marker Coordinate Load"

export MAIL_LOADNAME

#  INSTALLDIR expected by dlautils/DLAInstall
INSTALLDIR=${MRKCOORDLOAD}

export INSTALLDIR