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HISTORY
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TAG: mrkcoordload-6-0-25-1
DATE: 02/03/2025
STAFF: lec
CHANGES:
wts2-1600/e4g-115/Marker Coordinate Load changes
loadadmin/prod/dailytasks.csh
{MRKCOORDLOAD}/bin/mrkcoordload.sh
{MRKCOORDLOAD}/bin/mrkcoordDelete.sh
TAG: mrkcoordload-6-0-22-4
DATE: 04/14/2023
STAFF: sc
CHANGES: FL2b PAR FL2-213/WTS2-1080
TAG: mrkcoordload-6-0-22-3
TAG: mrkcoordload-6-0-22-2
TAG: mrkcoordload-6-0-22-1
DATE: 09/26/2022
STAFF: sc
CHANGES: WTS2-988 - mrkcoordload: update load QC checks
1) add check for min rowcount of input file
2) remove allowing empty columns for delete format (bug from the delete/reload update)
TAG: mrkcoordload-6-0-17-1
DATE: 05/11/2021
STAFF: sc
CHANGES: TR13349 Build39
TAG: mrkcoordload-6-0-16-1
DATE: 08/21/2020
STAFF: sc
CHANGES: TR13204/I20 project/python 3.7 upgrade
TAG: mrkcoordload-6-0-7-1
DATE: 01/05/2017
STAFF: lec
CHANGES:
1) TR12069/obsolete db.setAutoTranslate()
TAG: mrkcoordload-6-0-6-1
DATE: 11/08/2016
STAFF: lec
CHANGES:
TR11083/Retire/Archive Nomenclature Table (NOM_Marker)
_Marker_Status_key = 2 changed to _Marker_Status_key != 1
TAG: mrkcoordload-6-0-5-2
DATE: 09/01/2016
STAFF: lec
CHANGES:
TR11083/Retire/Archive Nomenclature Table (NOM_Marker)
_Marker_Status_key not in (1,3) changed to = 2
TAG: mrkcoordload-6-0-5-1
DATE: 08/30/2016
STAFF: lec
CHANGES:
TR11083/Retire/Archive Nomenclature Table (NOM_Marker)
_Marker_Status_key in (1,3) changed to "= 1"
TAG: mrkcoordload-6-0-4-1
DATE: 04/27/2016
STAFF: lec
CHANGES: TR12069/postgres cleanup
1) convert to Git
2) add "db.setAutoTranslate"
TAG: mrkcoordload-6-0-3-2
DATE: 4/5/2016
STAFF: dbm
CHANGES:
1) Install: Remove use of /hobbiton mount
TAG: mrkcoordload-6-0-3-1
DATE: 03/07/2016
STAFF: lec
CHANGES: TR12083/replace "vachar(30)" with "text"
TAG: mrkcoordload-6-0-1-1
DATE: 12/2/2015
STAFF: dbm
CHANGES: TR11904 & TR12199
1) mrkcoordload.config.default: Remove MAIL_LOG_CUR setting
TAG: mrkcoordload-6-0-0-5
DATE: 09/28/2015
STAFF: lec
CHANGES:
1) bin/createInputFiles.py : add db.commit()
TAG: mrkcoordload-6-0-0-4
DATE: 8/19/2015
STAFF: dbm
CHANGES:
1) bin/mrkcoordQC.sh: Use .pgpass file in the user's HOME directory if
TAG: mrkcoordload-6-0-0-1, mrkcoordload-6-0-0-2, mrkcoordload-6-0-0-3
DATE: 07/24/2015
STAFF: lec
CHANGES:
1) TR11750/postgres
TAG: mrkcoordload-tr11750-MP
DATE: 7/1/15
STAFF: pf
CHANGES: merge point tag
TAG: mrkcoordload-5-2-1-2
DATE: 04/14/2015
STAFF: dbm
CHANGES:
1) bin/mrkcoordload.sh: Use "head -n +1" to get the first line in the file.
TAG: mrkcoordload-5-2-1-1
DATE: 04/10/2015
STAFF: lec
CHANGES:
1) bin/mrkcoordload.sh
changed "cat" command to "cut" for all unix servers
TAG: mrkcoordload-tr11750-1
DATE: 04/10/2015
STAFF: lec
CHANGES:
1) bin/mrkcoordload.sh
changed "cat" command to "cut" for all unix servers
TAG: mrkcoordload-5-1-7-1
DATE: 03/16/2014
STAFF: sc
CHANGES:
1) Bug whereby TABs were allowed in the header which specifies version (build)
in the load ready file. QC was stripping, but original was being written
to load ready file
TAG: mrkcoordload-5-1-4-1
DATE: 07/27/2013
STAFF: dbm
CHANGES:
1) mrkcoordload.config.default: Use sym link for each jar file in JAVA_LIB path
TAG: mrkcoordload-5-1-3-1
DATE: 04/16/2013
STAFF: sc
RELEASE: new homologyload used mrkcoordload in error. Retagging early
for the 5.1.3 release to disambiguate
TAG: mrkcoordload-5-1-1-3
DATE: 11/12/2012
STAFF: sc
RELEASE: C4AM/B38
1) mrkcoordQC.sh - change temp table column mirbaseID to text
2) mrkcoordQC.py - change non-mirna report temp table query to
use 'like "%MI%"' instead of 'is not null' as may only use
like for a text field in where clause
TAG: mrkcoordload-5-1-1-2
DATE: 11/09/2012
STAFF: sc
RELEASE: C4AM/B38
CHANGES: removed some debug
TAG: mrkcoordload-5-1-1-1
DATE: 11/07/2012
STAFF: sc
RELEASE: dev C4AM/B38
CHANGES: US 175 - n-m mirbase IDs
1) bin/mrkcoordQC.py - other mkr report, tab-delim and add 'tab-delim' to report header
2) bin/mrkcoordQC.sh - build= must start header line
TAG: mrkcoordload-5-0-0-14
DATE: 10/31/2012
STAFF: sc
RELEASE: dev C4AM/B38
CHANGES: US 175 - n-m mirbase IDs
1) mrkcoordload.sh - rm checkMirbaseIDS function (this functionality moved to
mrkcoordQC.py), added mirbase dup and other mkr reports to RPT_LIST
2) index.html - added
3) mrkcoordload.config.default - added mirbase dup and other mkr reports
4) createInputFiles.py - delete mirbase ID only from marker in input NOT from
all markers in DB. Commented that column 8 may now be multi-valued
5) mrkcoordQC.py - added mirbase dup and other mkr reports, updated the delete report
TAG: mrkcoordload-5-0-0-13
DATE: 10/23/2012
STAFF: sc
RELEASE: dev
CHANGES: createInputFiles.py - update to use INPUT_FILE_LOAD
(from INPUT_FILE_DEFAULT which was being used prior
to the QC scripts creating INPUT_FILE_LOAD)
TAG: mrkcoordload-5-0-0-12
DATE: 10/15/2012
STAFF: sc
RELEASE: dev
CHANGES:
1) Daves changes for US10 mirbase QC
2) Jon changes to publish
2) createInputFiles.py - delete mirbase ID from all markers, not just marker in the input
3) mrkcoordload.sh - uncomment checking for lastrun file
TAG: mrkcoordload-5-0-0-11
TAG: mrkcoordload-5-0-0-10
DATE: 8/22/2012
STAFF: sc
RELEASE: dev
CHANGES: US 35 - add mirbase ids
1) assocload.config - set delete/reload to false because this deletes
all associations for the load user
2) createInputFiles.py - query was selecting mbID instead of mgiID
added explicit setting of user and passwork in python db module
3) assocload.config - use DATALOADSOUTPUT
TAG: mrkcoordload-5-0-0-9
TAG: mrkcoordload-5-0-0-8
DATE: 8/21/2012
STAFF: sc
RELEASE: dev
CHANGES: US 35 - add mirbase ids
1) Install - add assocload directories
2) runMrkCoordQC - fixed usage statement
3) mrkcoordload.sh - updated to run assocload
4) createInputFiles.py - updated to create assocload input
file -- currently contains debug print statements
5) assocload.config - added
6) mrkcoordload.config.default - added assocload settings
TAG: mrkcoordload-5-0-0-7
TAG: mrkcoordload-5-0-0-6
DATE: 8/02/2012
STAFF: sc
RELEASE: dev
CHANGES: US#92/93 Bug fixes
1) Remove \n in sanity report for missing data/column check
2) report on command line when new source/display
TAG: mrkcoordload-5-0-0-5
DATE: 7/s0/2012
STAFF: sc
RELEASE: dev
CHANGES: US#3 dn US#11 - bug fixes from testing
1) mrkcoordload.config.default - Added INVALID_CHR_RPT=${RPTDIR}/invalid_chr.rpt
2) checkColumns.py - don't strip the tokens before checking for numColumns
removed some debug
3) mrkcoordQC.py - Added support for INVALID_CHR_RPT, exclude annot evid
4) mrkcoordQC.sh - Added support for INVALID_CHR_RPT
TAG: mrkcoordload-5-0-0-4
TAG: mrkcoordload-5-0-0-3
DATE: 7/26/2012
STAFF: sc
RELEASE: dev
CHANGES: US#3 dn US#11
1. Added checkColumns.py, mrkcoordQC.py, mrkcoordQC.sh
runMrkCoordQC
Note that mrkcoordQC.py will need to keep track of good
lines (not rejected because of QC errrors) and write out
to a load ready file when we run QC from the load
2. mrkcoordload.sh - Added RUNTYPE=live default, Added commented
out code to support running QC from the load
Added case insensitivity for determining build
Added commented out code to deal with last run file
Changed config value of input file - will need to do again
when we run QC from the load
3. createInputFiles.py - changed config value of input file
4. mrkcoordload.config.default - added config to support QC
5. Install - added permissions code for running QC scripts from
hobbiton and sym link input file creation to hobbiton
from lindon
TAG: mrkcoordload-5-0-0-2
DATE: 6/5/2012
STAFF: sc
RELEASE: dev
CHANGES:
1. createInputFiles.py - added support of naming files with collection
abbreviation
2. mrkcoordload.sh - added setting abbreviation in the environment
TAG: mrkcoordload-5-0-0-1
DATE: 6/5/2012
STAFF: sc
RELEASE: dev
CHANGES: TR7106 initial tag