HISTORY

# important info:
# grep ??? access.log.?
# find GET
# cd /data/reports/reports_db/output
# foreach i (*.rpt)
#       ls -l $i
#       grep $i /logs/www/newGondor/access.log.2023.12.11 | grep GET
# bhmgiapp01:/logs/www/newGondor => nslookup 10.3.0.185
# 185.0.3.10.in-addr.arpa name = bhsqldb06wp.jax.org.
# 
# mgimarkerfeed
# It is used in the MGI staging feed, which is triggered every day when JaxStrain ETL is run.
# Scott Rizzo <Scott.Rizzo@jax.org>
#
# these reports are no longer being created, but ouput files still exist.
# so, do NOT remove these files
# bhmgiapp01:/data/reports/reports_db/output
# MGI_GTdbGSS_info.rpt
# MGI_GTDNA.rpt
# MGI_GTGUP.rpt
# MGI_GTRNA.rpt
#

TAG: reports_db-6-0-27-4
DATE: 03/10/2026
STAFF: pf
wts2-1391/HP-MP Lexical Matches report
        new:   weekly/MGI_HpMpLexical.py

TAG: reports_db-6-0-27-3
DATE: 01/28/2026
STAFF: lec
wts2-1793/sprt-204/add genotype IDs to reports with genotypes
        modified:   index.shtml
        modified:   weekly/MGI_GenePheno.py
        modified:   weekly/MGI_PhenoGenoMP.py

TAG: reports_db-6-0-27-2
DATE: 01/22/2026
STAFF: jer
wts2-1792/sprt-202/Report that lists all MP terms associated with an allele
        added:   ALL_Phenotype.py
	updated: index.shtml

TAG: reports_db-6-0-27-1
DATE: 01/21/2026
STAFF: lec
wts2-1790/sprt-201/genotypes missing from MGI_Geno_DiseaseDO.rpt public report 
        modified:   MGI_GenePheno.py

TAG: reports_db-6-0-26-6
DATE: 12/16/2025
STAFF: lec
wts2-1778/sprt-161/Remove Obsolete Public, QC Reports
        deleted:    daily/MGI_Cov_Allele.py
        deleted:    daily/MGI_Cov_Human_Gene.py
        deleted:    daily/MGI_Cov_Mouse_Gene.py
        deleted:    daily/MGI_Cov_Strain.py

TAG: reports_db-6-0-26-5
DATE: 12/12/2025
STAFF: lec
wts2-1771/sprt-153/MGI GPI missing GCRPs as cross reference 
        modified:   GO_gpi.py

TAG: reports_db-6-0-26-4
DATE: 12/02/2025
STAFF: lec
wts2-1764/sprt-143/Update to MGI GPI File
remove all lines that begin with the following identifiers in the first column of the MGI GPI file:
EMBL:
RefSeq:
ENSEMBL:
        modified:   GO_gpi.py

TAG: reports_db-6-0-26-3
DATE: 10/21/2025
STAFF: lec
wts2-1710/sprt-100/NCBI reported having difficullty downloading the MGI logo icon from our Linkout file
	modified:   Configuration.default
        modified:   ncbilinkout/nucleotide_linkout.py
        modified:   ncbilinkout/protein_linkout.py
        modified:   ncbilinkout/pubmed_linkout.py
remove:
<!ENTITY icon https://www.informatics.jax.org/mgihome/homepages/images/MGILinkout.jpg>
<IconUrl>&icon;</IconUrl>

TAG: reports_db-6-0-26-2
TAG: reports_db-6-0-26-1
DATE: 09/17/2025
STAFF: lec
wts2-1725/sprt-59/inconsistencies between MGI GPI and GOA_mouse GPI
        modified:   daily/GO_gpi.py

TAG: reports_db-6-0-25-8
DATE: 06/10/2025
STAFF: lec
wts2-1677/e4g-282/NCBI Linkout Reports - update URLs
        modified:   Configuration.default
        modified:   ncbilinkout/copy_rpt.csh
        modified:   ncbilinkout/ncbilinkout.csh
        modified:   ncbilinkout/providerinfo.xml

TAG: reports_db-6-0-25-7
DATE: 06/02/2025
STAFF: lec
wts2-1669/e4g-264/Python 3.12

TAG: reports_db-6-0-25-6
DATE: 05/15/2025
STAFF: lec
        deleted:    weekly/MGI_MarkerNames.py
Matt Hibbs (Matt.Hibbs@jax.org)
Al Simons (Al.Simons@jax.org)

TAG: reports_db-6-0-25-5
TAG: reports_db-6-0-25-4
TAG: reports_db-6-0-25-3
DATE: 04/28/2025
STAFF: lec
wts2-562/e4g-207/mapping RNA central ids to MGI genes (TR13445)

TAG: reports_db-6-0-25-2
DATE: 03/18/2025
STAFF: lec
wts2-1625/e4g-188/MGI GPI file update/column 8  only

TAG: reports_db-6-0-25-1
DATE: 01/16/2025
STAFF: lec
wts2-1607/e4g-121/Public Reports/NCBI Link Out issue
#	modified:   ncbilinkout/copy_rpt.csh

mirror_wget/bhmgiimsr01.jax.org.imsr_allStrains -> bhmgiimsr02lp.jax.org issue
TAG: reports_db-6-0-24-15
DATE: 11/19/2024
STAFF: lec
mirror_wget/bhmgiimsr01.jax.org.imsr_allStrains -> bhmgiimsr02lp.jax.org issue
#       modified:   Configuration.default

TAG: reports_db-6-0-24-14
DATE: 11/06/2024
STAFF: lec
wts2-1577/e4g-65/Update descriptions for MGI_PhenoGenoMP.rpt

TAG: reports_db-6-0-24-13
TAG: reports_db-6-0-24-12
TAG: reports_db-6-0-24-11
TAG: reports_db-6-0-24-10
TAG: reports_db-6-0-24-9
TAG: reports_db-6-0-24-8
TAG: reports_db-6-0-24-7
TAG: reports_db-6-0-24-6
DATE: 10/04/2024, 10/21/2024, 10/28/2024
STAFF: lec
wts2-495/e4g2/e4g-19/Public Report(s) of Comprehensive GXD RNA-Seq Data
        new file:   gxdrnaseq/GXD_RnaSeq.py
        new file:   run_gxdrnaseq.csh
        modified:   Configuration.default
        modified:   Install

TAG: reports_db-6-0-24-5
DATE: 08/16/2024
STAFF: lec
fl2-948/Create a public report for MGI stat: mouse protein-coding genes with 1-to-1 homology to human
        new file:   weekly/HOM_ProteinCoding.py

TAG: reports_db-6-0-24-4
TAG: reports_db-6-0-24-3
TAG: reports_db-6-0-24-2
TAG: reports_db-6-0-24-1
DATE: 07/18/2024
STAFF: lec
fl2-898/Trouble getting the MRK_Lists to load
        modified:   run_weekly.csh

TAG: reports_db-6-0-23-6
DATE: 06/28/2024
STAFF: lec
wts2-1508/fl2-910/User requested change to MRK_List1.rpt

TAG: reports_db-6-0-23-5
DATE: 06/25/2024
STAFF: lec
wts2-1506/fl2-908/Error in MRK_ENSEMBL.rpt

TAG: reports_db-6-0-23-4
DATE: 06/25/2024
STAFF: lec
wts2-1403/index.shtml

TAG: reports_db-6-0-23-3
DATE: 06/06/2024
STAFF: lec
wts2-1489/fl2-895/archive ma2ncit.obo

TAG: reports_db-6-0-23-2
DATE: 04/05/2024
STAFF: lec
wts2-1455/fl2-815/report BIB_PubMed needs to be re-added
#       added:    weekly/BIB_PubMed.py
#       used by Cc: Murphy, Terence (NIH/NLM/NCBI) [E] <murphyte@ncbi.nlm.nih.gov>
#

TAG: reports_db-6-0-23-1
DATE: 03/29/2024
STAFF: lec
#       deleted:    weekly/BIB_PubMed.py ; no longer used per Stephen Grubb
#       deleted:    weekly/MGI_GTdbGSS_info.py
#       deleted:    weekly/MGI_GTDNA.py
#       deleted:    weekly/MGI_GTGUP.py
#       deleted:    weekly/MGI_GTRNA.py
#       deleted:    weekly/GO_terms.py
#
#       MGI_GT* reports are *not* removed from FTP site
#       deleted:    daily/GO_gene_association.py
#               mgi.gpad
#               gene_association_nonoctua.mgi
#               gene_association_nonoctua_pro.mgi
#               mgi_nonoctua.gpad
#               gene_association.mgi → qcreports_db/mgd/GO_MGIGAF.py
#            

TAG: reports_db-6-0-22-8
DATE: 11/04/2023
STAFF: lec
wts2-1314/fl2-617/Add new file to MP files on FTP site
index.shtml
Configuration.default: setenv MPFILES "MPheno_OBO.ontology mp.owl mp.json mp-international.owl"

TAG: reports_db-6-0-22-7
DATE: 10/24/2023
STAFF: sc
https://mgi-jira.atlassian.net/browse/FL2-564
New report: weekly/TAL_MRK_Nomen_Change.py

TAG: reports_db-6-0-22-6
DATE: 06/15/2023
STAFF: sc
wts2-414 - along with this ticket we discovered some production bugs in the HOM reports and in the
   index file for the HOM reports that were fixed in this tag

TAG: reports_db-6-0-22-5
TAG: reports_db-6-0-22-4
DATE: 05/12/2023, 05/15/2023
STAFF: lec
wts2-1095/fl2-149/Mouse models of human disease report (1)
wts2-1120/fl2-204/Mouse models of human disease report (2)
weekly/MGI_HumanMouseOneToOne.py

TAG: reports_db-6-0-22-3
TAG: reports_db-6-0-22-2
DATE: 03/24/2023
STAFF: lec
wts2-1137/fl2-247/GOA load scripts update to include GO annotations to 'polymorphic pseudogene'
#       modified:   daily/GO_gene_association.py
#       modified:   daily/GO_gpi.py

TAG: reports_db-6-0-22-1
DATE: 02/21/2023
STAFF: lec
wts2-854/fl2-24/Alterations for generating the MGI GPI file.
GO_gpi.py

TAG: reports_db-6-0-21-2
DATE: 07/19/2022
STAFF: lec
wts2-920/Changes to MGI GAF (GO annotations) for consistency of types with those reported in mgi.gpi file
GO_gene_association.py/use SO terms for col 12

TAG: reports_db-6-0-21-1
DATE: 07/18/2022
STAFF: lec
wts2-704/Problem with MGI's latest Europe PMC external links upload
ncbilinkout/pubmed_linkout.py

TAG: reports_db-6-0-20-3
DATE: 06/15/2022
STAFF: sc
added MGIreg.gff3 to index.shtml - apparently this change
    dif not get into 6-0-20-1

TAG: reports_db-6-0-20-2
DATE: 06/14/2022
STAFF: lec
wts2-884/Include more granular Sequence Ontology terms for object types in mgi.gpi

TAG: reports_db-6-0-20-1
DATE: 06/06/2022
STAFF: sc
added MGIreg.gff3 to index.shtml

TAG: reports_db-6-0-19-2
TAG: reports_db-6-0-19-1
DATE: 05/20/2022
STAFF: lec
wts2-857/The Rat iso load for GO is adding go_qualifiers during consumption
GO_gene_association.py

TAG: reports_db-6-0-18-5
TAG: reports_db-6-0-18-4
TAG: reports_db-6-0-18-3
TAG: reports_db-6-0-18-2
DATE: 03/23/2022, 03/30/2022, 04/06/2022
STAFF: lec
wts2-703/tr13272/GO-Noctua
GO_gene_association.py
#       deleted:    weekly/GO_gene_association_nonmouse.py
#       rpt_release.csh/remove copy GO_gene_association_nonmouse
#       run_daily.csh/add mgi_nonoctua.gpad       
#       run_daily.csh/add gene_association_nonoctua.mgi

TAG: reports_db-6-0-18-1
DATE: 02/21/2022
STAFF: lec
wts2-767/mgi_notechunk/mgi_note merge
per YAKS, removing obsolete view/report
#       deleted:    ondemand/MAP_Mapping.py
#       deleted:    ondemand/MGI_CloneSet.py
#       deleted:    ondemand_reports.csh

TAG: reports_db-6-0-17-11
TAG: reports_db-6-0-17-10
DATE: 10/19/2021
STAFF: lec
wts2-710/REVERSE/Allow GO annotations to pseudogenes in the public GPAD and GAF files

TAG: reports_db-6-0-17-9
DATE: 10/04/2021
STAFF: lec
wts2-710/Allow GO annotations to pseudogenes in the public GPAD and GAF files

TAG: reports_db-6-0-17-8
DATE: 08/31/2021
STAFF: sc
CHANGES: WTS2-678  Parse Alliance data files by column header, not by position
Alliance clustered and direct preprocessor updates

TAG: reports_db-6-0-17-7
DATE: 08/17/2021
STAFF: sc
MGI_Cov_Human_Gene.py - YAKS-193, update for input file format change

TAG: reports_db-6-0-17-6
DATE: 06/10/2021
STAFF: sc       
remove extraneous '>' from index page

TAG: reports_db-6-0-17-5
DATE: 06/10/2021
STAFF: lec
wts2-641/Allow additional go_property (is_active_in) to be valid in Noctua load and reexamine how we define duplicate annotations
GO_gene_association.py

TAG: reports_db-6-0-17-4
TAG: reports_db-6-0-17-3
DATE: 06/09/2021
STAFF: sc
merge tr13349 branch to master - was not done prior to release
Merge output my notes with dates for master and branch:
Updating 0851bca..f38d587
Fast-forward
 HISTORY                                            | 10 +++-  OK
 daily/GO_gpi.py                                    | 20 +++++--  master: 4/7 branch: 4/8
 daily/MGI_Cov_Human_Gene.py                        |  6 +--  master: 5/6 branch: 5/11
 index.shtml                                        | 24 ++++----- OK
 runone_postgres_report.csh                         | 63 ----------------------  OK - deleted see b elow
 ...HGNC_homologene.py => HGNC_AllianceHomology.py} | 41 ++++----------  OK
 weekly/HMD_HumanPhenotype.py                       | 53 ++----------------  master:10/30/20 branch: 3/4
 weekly/HOM_AllOrganism.py                          | 44 ++++++++-------  master: 4/2/20 branch: 4/19
 weekly/HOM_MouseHumanSequence.py                   | 35 ++++++------  master: 4/2/20 branch: 4/19
 weekly/MGI_DO.py                                   | 27 ++--------  master: 4/2/20 branch: 3/4
 weekly/MGI_MarkerNames.py                          |  8 ++-  master: 4/2/20 branch: 2/22
 weekly/MGI_iphone_app.py                           | 17 +++---  master: 4/2/20 branch: 2/22
 12 files changed, 116 insertions(+), 232 deletions(-)
 delete mode 100755 runone_postgres_report.csh OK
 rename weekly/{HGNC_homologene.py => HGNC_AllianceHomology.py} (87%) OK
 mode change 100755 => 100644 weekly/MGI_iphone_app.py

TAG: reports_db-6-0-17-2
DATE: 06/07/2021
STAFF: sc
index.shtml - update to GRCm39

DATE: 05/11/2021
STAFF: 
TAG: reports_db-6-0-17-1
DATE: 05/11/2021
STAFF: lec
TR13349/Genome Build 39

TAG: reports_db-6-0-16-22
DATE: 05/06/2021
STAFF: lec
CHANGES:
wts2-605/COV reports showing only headers
reports must run as daily reports so they use the production database : bib_workflow_tag must not be empty

TAG: reports_db-6-0-16-21
DATE: 04/27/2021
STAFF: lec
CHANGES:
wts2-606/Human gene COV report has mouse genes
Configuration.default
setenv ALLIANCE_HUMAN_FILE_GZ  "/data/downloads/fms.alliancegenome.org/download/DISEASE-ALLIANCE_HUMAN.tsv.gz"
setenv ALLIANCE_HUMAN_FILE     "/data/downloads/fms.alliancegenome.org/download/DISEASE-ALLIANCE_HUMAN.tsv"

TAG: reports_db-6-0-16-20
DATE: 04/26/2021
STAFF: lec
CHANGES:
wts2-603/Remove private alleles and strains from the reports for the Coronavirus tables
weekly/MGI_Cov_Allele.py
weekly/MGI_Cov_Strain.py

TAG: reports_db-6-0-16-19
DATE: 04/15/2021
STAFF: lec
CHANGES:
WTS586/Incorrect Evidence Code in MGI GPAD files (TR13494)
daily/GO_gene_association.py

TAG: reports_db-6-0-16-18
DATE: 04/07/2021
STAFF: lec
CHANGES:
TR13491/Add Sanity Check for Withdrawn Markers to MGI/GPI
daily/GO_GPI.py

TAG: reports_db-6-0-16-17
DATE: 04/06/2021
STAFF: sc
CHANGES: Configuration change to static url for input file
TR13459/Coronavirus Reports for Jax Web Resources
MGI_Cov_Human_Gene.py

TAG: reports_db-6-0-16-16
DATE: 04/05/2021
STAFF: lec
CHANGES: 
TR13487/Fix header on non-mouse annotation file

TAG: reports_db-6-0-16-15
DATE: 03/11/2021
STAFF: lec
CHANGES: 
TR13459/Coronavirus Reports for Jax Web Resources
MGI_Cov_Human_Gene.py

TAG: reports_db-6-0-16-14
DATE: 03/02/2021
STAFF: lec
CHANGES: 
TR13272/GO meeting/CalTech/tasks to-do
GO_gene_association.py

TAG: reports_db-6-0-16-13
TAG: reports_db-6-0-16-12
TAG: reports_db-6-0-16-11
TAG: reports_db-6-0-16-10
TAG: reports_db-6-0-16-9
TAG: reports_db-6-0-16-8
TAG: reports_db-6-0-16-7
TAG: reports_db-6-0-16-6
DATE: 02/19/2021
STAFF: lec, sc
CHANGES:
1) update to use Alliance Homology
 # HGNC_homologene.py
 # HOM_AllOrganism.py
 # HOM_MouseHumanSequence.py
 # MGI_DO.py
 # MGI_MarkerNames.py
 # MGI_iphone_app.py
 # MGD_HumandPhenotype.py

TR13459/Coronavirus Reports for Jax Web Resources
GAF 2.2
MGI_Cov_Human_Gene.py
MGI_Cov_Mouse_Gene.py
MGI_Cov_Allele.py
MGI_Cov_Strain.py

TR13272/GO meeting/CalTech/tasks to-do
GO_gene_association.py
GO_gpi.py
GO_gene_association_nonmouse.py

TAG: reports_db-6-0-16-5
DATE: 10/30/2020
STAFF: sc
CHANGES: HMD_HumanPhenotype.py
TR13418 - Missing fields in HMD_HumanPhenotyp.rpt

TAG: reports_db-6-0-16-4
DATE: 09/08/2020
STAFF: dbm
CHANGES: MGI_EntrezGene.py - fixed syntax error

TAG: reports_db-6-0-16-3
TAG: reports_db-6-0-16-2
DATE: 08/25/2020
STAFF: lec
TR13272/GPAD 2.0

TAG: reports_db-6-0-16-1
DATE: 08/21/2020
STAFF: lec
TR13204/Infrastructure Release

TAG: reports_db-6-0-15-10
DATE: 08/19/2020
STAFF: lec
TR13359/Europe's PMC link service error

TAG: reports_db-6-0-15-9
TAG: reports_db-6-0-15-8
DATE: 07/31/2020
STAFF: drs
TR13342 - added a link to the Alliance downloads page

TAG: reports_db-6-0-15-7
TAG: reports_db-6-0-15-6
DATE: 07/07/2020
STAFF: sc
TR13082 - added missing configuration for E PMC

TAG: reports_db-6-0-15-6
DATE: 07/06/2020
STAFF: sc
TR13082  bug fix - PMC configuration missing

TAG: reports_db-6-0-15-5
TAG: reports_db-6-0-15-4
DATE: 03/13/2020
STAFF: lec 
TR13270/GO meeting/add orcid/daily/GO_gene_association.py
backout change : TR13270/GO meeting/add orcid/daily/GO_gene_association.py

TAG: reports_db-6-0-15-3
TAG: reports_db-6-0-15-2
TAG: reports_db-6-0-15-1
DATE: 03/03/2020
STAFF: sc
TR13229, 
1) update Configuration.default MPFILES add mp.json
2) index.shtml - update pheno #1 description and add link
    to mp.json

TAG: reports_db-6-0-14-5
DATE: 10/02/2019
STAFF: sc
TR13082 - change description for pmc_providerinfo.xml (note:NCBI/PubMed does 
    not use the description field.)

TAG: reports_db-6-0-14-4
DATE: 09/25/2019
STAFF: sc
TR13082 - provide NCBI linkout files to E PMC, includes
  adding PMC providerinfo.xml

TAG: reports_db-6-0-14-3
DATE: 08/22/2019
STAFF: lec 
TR13155/daily/GO_gene_association.py/fix doGPADFinish()

TAG: reports_db-6-0-14-2
DATE: 07/16/2019
STAFF: lec 
doGPADFinish/try/except added

TAG: reports_db-6-0-14-1
DATE: 04/03/2019
STAFF: lec 
TR12963/teleuse-to-mgd_java_api

TAG: reports_db-6-0-13-7
DATE: 03/28/2019
STAFF: lec
CHANGES: TR13037/HMD_HumanPhenotype.py/use rollup rules for MP

TAG: reports_db-6-0-13-6
DATE: 03/25/2019
STAFF: sc
CHANGES: TR13040 - index.shtml - fix link to gff3 file, remove link to spec.

TAG: reports_db-6-0-13-5
DATE: 03/05/2019
STAFF: lec
CHANGES: TR13049/GO_gene_association.py/use same assignedBy logic for both GAF and GPAD

TAG: reports_db-6-0-13-4
DATE: 01/22/2019
STAFF: lec
CHANGES: TR13010/GO_gene_association.py/addGPADReportRow/add special processing if inferredFrom=InterPro

TAG: reports_db-6-0-13-3
TAG: reports_db-6-0-13-2
DATE: 10/19/2018
STAFF: sc
CHANGES: TR12115 IMPC Crispr allele load
1) new report: weekly/ALL_IMPC_EM.py

TAG: reports_db-6-0-13-1
DATE: 09/04/2018
STAFF: lec  
CHANGES: TR12734/GenFevah/Mouse Genome Project

TAG: reports_db-6-0-12-15
DATE: 08/29/2018
STAFF: lec
CHANGES: TR12943
Add weekly/MP_EMAPA.py

TAG: reports_db-6-0-12-14
DATE: 08/10/2018
STAFF: sc
CHANGES: TR12909
Add marker name field to MGI_PhenotypicAllele.rpt

TAG: reports_db-6-0-12-13
DATE: 08/09/2018
STAFF: dbm
CHANGES: set file permissions in the Install script

TAG: reports_db-6-0-12-12
DATE: 08/08/2018
STAFF: sc
CHANGES: bug fix MGI_GenePheno.py, If no MP ID, missing TAB. Extra tab after markers

TAG: reports_db-6-0-12-11
DATE: 08/07/2018
STAFF: lec
CHANGES: TR12910/daily/GO_gene_association.py
change order of qualfier (col 3)

TAG: reports_db-6-0-12-10
DATE: 05/16/2018
STAFF: sc
CHANGES: TR12898 - dupes in seq_marker_cache. These are GT seqeunce tags
    that should not be associated with a marker so we set the preferred
    accid bit to 0, exclude these from MGI_GTRNA.rpt

TAG: reports_db-6-0-12-9
DATE: 05/16/2018
STAFF: lec  
CHANGES: TR12868/noctua cleanup
#       modified:   daily/GO_gene_association.py

TAG: reports_db-6-0-12-8
DATE: 05/15/2018
STAFF: sc
CHANGES: TR12811
Add reference column to pub Pheno report
    14.Genotypes with Sex-specific Phenotypes

TAG: reports_db-6-0-12-7
DATE: 05/11/2018
STAFF: lec
CHANGES: TR12834/GO/Noctua
GO_gene_association.py

TAG: reports_db-6-0-12-6
DATE: 05/10/2018
STAFF: sc
CHANGES:
backed out these changes: TR12867/weekly/MP_EMAPA.py
report and index entry is in TR directory

TAG: reports_db-6-0-12-5
TAG: reports_db-6-0-12-4
DATE: 05/09/2018
STAFF: sc
CHANGES:
TR12867/weekly/MP_EMAPA.py

TAG: reports_db-6-0-12-3
DATE: 04/06/2018
STAFF: lec
CHANGES:
TR12834/daily/GO_gene_association.py

TAG: reports_db-6-0-12-2
TAG: reports_db-6-0-12-1
DATE: 03/07/2018, 03/23/2018
STAFF: lec
CHANGES:
TR12662/GMC/removing obsolete note/sequenceNum
weekly/MGI_iphone_app.py
weekly/VOC_MammalianPhenotype.py
weekly/MGI_Recombinase_Full.py
mgimarkerfeed/mgiMarkerFeed.py

TAG: reports_db-6-0-11-7
DATE: 03/06/2018
STAFF: dbm
CHANGES: TR12805
1) weekly/ES_CellLine.py: Added strain MGI ID

TAG: reports_db-6-0-11-6
DATE: 02/28/2018
STAFF: lec
CHANGES: TR12785//GO_gene_association.py/skip if DAG = 0 (obsolete)

TAG: reports_db-6-0-11-5
DATE: 02/21/2018
STAFF: lec
CHANGES: TR12768//GO_gene_association.py/
GAF/col 15, GPAD/col 10 : UniProt, MGI

TAG: reports_db-6-0-11-4
TAG: reports_db-6-0-11-3
DATE: 11/01/2017
STAFF: sc
CHANGES: TR12566 new phenotypes report with sex-specificity

TAG: reports_db-6-0-11-2
DATE: 10/31/2017
STAFF: lec 
CHANGES: 
TR12664/daily/GO_gene_associations.py/noctua-model-id

TAG: reports_db-6-0-11-1
DATE: 10/04/2017
STAFF: lec
CHANGES: 
TR12250/Lit Triage
1) mgimarkerfeed/new reference type

TAG: reports_db-6-0-10-8
DATE: 07/18/2017
STAFF: dbm
CHANGES: 
1) rpt_release_wrapper.csh: removed
2) ncbilinkout/copy_rpt_wrapper.csh; removed

TAG: reports_db-6-0-10-7
DATE: 07/06/2017
STAFF: lec
CHANGES: 
TR12615/exclude obsolete MP terms HMD_HumanPhenotype.py
TR12593/exclude obsolete MP terms MGI_PhenotypicAllele.py

TAG: reports_db-6-0-10-3
DATE: 06/14/2017
STAFF: sc
CHANGES: index.shtml - add HGNC Association? column header to HMD_HumanPhenotype.rpt

TAG: reports_db-6-0-10-6
DATE: 06/13/2017
STAFF: sc
CHANGES: TR12613 - MGI_GenePheno.rpt - add missing TAB btwn 3rd and 4th column.

TAG: reports_db-6-0-10-5
DATE: 06/13/2017
STAFF: sc
CHANGES: index.shtml addede HGNC Assoc? column header for HMD_HumanPhenotype.rpt

TAG: reports_db-6-0-10-4
TAG: reports_db-6-0-10-3
DATE: 06/05/2017
STAFF: lec 
weekly/MGI_DO.py
remove complicated sorting/replace with simple sorting

TAG: reports_db-6-0-10-2
TAG: reports_db-6-0-10-1
DATE: 04/27/2017, 05/08/2017
STAFF: lec 
TR12540/DO (Disease Ontology)
weekly/MGI_DO.py
weekly/MGI_GenePheno.py
weekly/MGI_iphone_app.py
mgimarkerfeed_reports.py
obsolete: weekly/MGI_GeneOMIM.py
HOM* : OMIM ids are for human genes, no change

TAG: reports_db-6-0-8-4
DATE: 03/09/2017
STAFF: lec
CHANGES:
mgimarkerfeed/exclude "reserved" symbols

TAG: reports_db-6-0-8-3
DATE: 3/3/2017
STAFF: dbm
CHANGES:
1) weekly/MGI_IMSRKomp.py: restored the python invocation on line 1 that
                           somehow got lost

TAG: reports_db-6-0-8-2
DATE: 2/23/2017
STAFF: dbm
CHANGES:
1) run_daily.csh: Copy zipped and unzipped files to ftp directory and make
                  sure the pairs of files have the same timestamp. The mgi.gpi
                  report is needed for the GO_GOI_verify QC report, so it can
                  not be removed from the public report output directory.

TAG: reports_db-6-0-8-1
DATE: 11/02/2016, 02/14/2017
STAFF: lec
CHANGES:
TR12427/Disase Ontology (DO)
TR12502/GO_gene_association.py/synonyms pipe needed
mgimarkerfeed/mgiMarkerFeed.py
MGI_GeneOMIM.py : generates both OMIM & DO file
MGI_GenePhenoDO.py/MGI_Geno_DiseaseDO
MGI_GenePhenoDO.py/MGI_Geno_NotDiseaseDO
mgi_DO.py
obsolete : db.setAutoTranslate

TAG: reports_db-6-0-7-3
DATE: 02/08/2017
STAFF: lec
CHANGES:
1) TR12502/GO_gene_association.py/synonym needs pipe

TAG: reports_db-6-0-7-2
DATE: 1/4/2017
STAFF: dbm
CHANGES:
1) Configuration.default: changed IMSR_STRAINS_CSV to use bhmgiimsr01

TAG: reports_db-6-0-7-1
DATE: 12/20/2016
STAFF: dbm
CHANGES: TR12485
1) run_daily.csh: Remove non-zipped files after creating zipped versions

TAG: reports_db-6-0-6-9
DATE: 11/15/2016
STAFF: sc
CHANGES: TR12404
1) modified HMD_HumanPhenotype.py

TAG: reports_db-6-0-6-8
DATE: 10/31/2016
STAFF: lec
CHANGES:
TR12434/Change NCBI LinkOut PubMed XML
#       modified:   Configuration.default
#       modified:   ncbilinkout/nucleotide_linkout.py
#       modified:   ncbilinkout/protein_linkout.py
#       modified:   ncbilinkout/pubmed_linkout.py

TAG: reports_db-6-0-6-7
DATE: ?
STAFF: petefrost
CHANGES:
??

TAG: reports_db-6-0-6-6
DATE: 10/10/2016
STAFF: lec
CHANGES:
GO_gene_association.py

TAG: reports_db-6-0-6-5
DATE: 10/06/2016
STAFF: lec
CHANGES:
Install/synmlink/index.shtml

TAG: reports_db-6-0-6-4
DATE: 10/03/2016
STAFF: lec
CHANGES:
mgimarkerfeed/mgimarkerfeed_reports.csh/copy gzip file to FTPREPORTDIR

TAG: reports_db-6-0-6-3
DATE: 09/19/2016
STAFF: dbm
CHANGES: Split the report copying process because the NCBI linkout reports
         need to be copied from bhmgidb03lp (where ftp is installed) and all
         other reports need to be copied from bhmgiapp01 where sym links to
         files under /data/loads exist
1) public_rpt_release.csh: Remove
2) rpt_release.csh: New
3) rpt_release_wrapper.csh: New
4) copy_rpt_2ncbi.csh: Remove
5) copy_rpt.csh: New
6) copy_rpt_wrapper.csh: New

TAG: reports_db-6-0-6-2
TAG: reports_db-6-0-6-1
DATE: 09/08/2016
STAFF: lec
CHANGES:
TR12349/gone-dor & more
TR12345/GPAD/GPI
1) daily/GO_gene_association
2) daily/GO_gpi.py
_Marker_Status_key in (1,3) changed to = 1
 ncbilinkout/nucleotide_linkout.py
 weekly/GO_gp2protein.py
 weekly/HGNC_homologene.py
 weekly/MGI_EntrezGene.py
 weekly/MGI_GTGUP.py
 weekly/MGI_Gene_Model_Coord.py
 weekly/MGI_MarkerNames.py
 weekly/MGI_OMIM.py
 weekly/MGI_iphone_app.py
 weekly/MRK_GeneTrap.py
 weekly/MRK_List.py
 weekly/MRK_Reference.py
 weekly/MRK_Sequence.py
 weekly/MRK_SwissProt_Sequence.py 
3) added to index.shtml TR12339 - new report weekly/MGI_Nonstandard_Strain.py
4) Install : changes for ftp url
5) includes : new for ftp url
6) mgiMarkerfeed/mgiMarkerFeed.py

TAG: reports_db-6-0-5-7
DATE: 08/25/2016
STAFF: kstone
CHANGES: changed ftp url

TAG: reports_db-6-0-5-2
DATE: 08/10/2016
STAFF: lnh
CHANGES: TR12401
1) Removed weekly/MGI_AllGenes.py

TAG: reports_db-6-0-5-1
DATE: 08/02/2016
STAFF: lec
CHANGES: TR12383/TR 11968 HGNC report
1) fixed index.htmml.default

TAG: reports_db-6-0-4-17
DATE: 08/2/2016
STAFF: lnh
CHANGES: TR12383 and TR12401
    Restored missing report weekly/MGI_AllGenes.py from cvs archived tag reports_db-5-2-1-14

TAG: reports_db-6-0-4-16
DATE: 07/15/2016
STAFF: sc
CHANGES: TR12339 - new report weekly/MGI_Nonstandard_Strain.py

TAG: reports_db-6-0-4-15
TAG: reports_db-6-0-4-14
DATE: 07/14/2016
STAFF: lnh
CHANGES: TR12036
1) ncbilinkout/ncbilinkout.csh: Removed code section that copies reports to NCBI host
2) ncbilinkout/copy_rpt_2ncbi.csh:Added new script to copy reports to NCBI host
3) public_rpt_release.csh: Added a call to copy the linkout reports to NCBI FTP site.

TAG: reports_db-6-0-4-13
DATE: 07/14/2016
STAFF: lnh
CHANGES:
1) weekly/MGI_PhenotypicAllele.py : TR12373 - Remove section of the code 
   that filtered out gene association display for Transgenes.

TAG: reports_db-6-0-4-12
DATE: 07/14/2016
STAFF: lec
CHANGES:
1) Configuration.default:setenv GOAMGI

TAG: reports_db-tr12349
TAG: reports_db-tr12349-BP
DATE: 07/07/2016
STAFF: lec
CHANGES:
1) branch point tag for TR12349/gone-dor & more

TAG: reports_db-6-0-4-11
DATE: 07/05/2016
STAFF: dbm
CHANGES:
1) ncbilinkout/nucleotide_linkout.py: removed reference to rsID dictionary

TAG: reports_db-6-0-4-10
DATE: 06/23/2016
STAFF: lec
CHANGES:
TR12361
1) ndex.html.default: accidentally removed 'NAME="strains"' instead of 'NAME="nomenclature"'

TAG: reports_db-6-0-4-9
TAG: reports_db-6-0-4-8
TAG: reports_db-6-0-4-7
TAG: reports_db-6-0-4-6
DATE: 06/21/2016
STAFF: lec
CHANGES:
TR12345/GO/GPAD file
1) generateGPAD.csh: obsolete
2) daily/GO_eco_association.py : obsolete

TAG: reports_db-6-0-4-5
DATE: 05/26/2016
STAFF: lec
CHANGES:
1) index.html : remove Nomenclature
the python report was obsoleted in 2015 but
the report was never removed from the index.html page

TAG: reports_db-6-0-4-4
TAG: reports_db-6-0-4-3
TAG: reports_db-6-0-4-2
DATE: 05/25/2016, 05/26/2016
STAFF: lnh, lec
CHANGES:
1) weekly/MGI_EntrezGene.py: Added array key exists check to mgiID array after
   this report failed on production this week due to array key error

TAG: reports_db-6-0-4-1
DATE: 05/04/2016
STAFF: lec
CHANGES:
1) TR12223/gxd anatomy II - merged to trunk

TAG: reports_db-6-0-3-3
DATE: 04/25/2016
STAFF: lec
CHANGES: 
1) TR12027/mgimarkerfeed/mgi_relationship

TAG: reports_db-6-0-3-2
DATE: 04/13/2016
STAFF: dbm
CHANGES: 
1) weekly/MGI_IMSRKomp.py: Chnaged path to kompCounts.txt file

TAG: reports_db-6-0-3-1
DATE: 04/06/2016
STAFF: kstone
CHANGES: 
1) Removed MGI_Mutations.py

TAG: reports_db-6-0-2-5
DATE: 03/01/2016
STAFF: dbm
CHANGES:
1) ncbilinkout/ncbilinkout.csh: Remove usage of "_PUB" db settings
2) ondemand_reports.csh: Remove usage of "_PUB" db settings
3) runone_postgres_report.csh: Remove usage of "_PUB" db settings
4) run_weekly.csh: Remove usage of "_PUB" db settings

TAG: reports_db-tr12223-1
DATE: 02/24/2016, 05/04/2016
STAFF: lec
CHANGES:
1) branch point tag for TR12223/gxd anatomy II

TAG: reports_db-?
DATE: 02/24/2016
STAFF: lec
CHANGES:
1) weekly/ALL_OMIM.py : obsolete
2) weekly/MGI_Recombinase_Full.py

TAG: reports_db-tr12223-BP
DATE: 02/24/2016
STAFF: lec
CHANGES:
1) branch point tag for TR12223/gxd anatomy II

TAG: reports_db-6-0-2-4
DATE: 01/25/2016
STAFF: lec
CHANGES:
1) weekly/ALL_OMIM.py

TAG: reports_db-6-0-2-3
DATE: 12/21/2015
STAFF: lec
CHANGES: TR 12122
1) daily/GO_gene_association.py/"!gaf-version: 2.1"

TAG: reports_db-6-0-2-2
DATE: 12/09/2015
STAFF: sc
CHANGES: TR 11968 HGNC report
1) MGI_Gene.py - removed and replaces with HGNC_homologene.rpt
   The report was updated to report the union of HGNC and Homologene

TAG: reports_db-6-0-2-1
DATE: 12/02/2015
STAFF: lec
1) TR12070/daily/GO_gene_association.py

TAG: reports_db-6-0-0-10
DATE: 10/01/2015
STAFF: lec
CHANGES:
1) TR12151/ncbilinkout/providerinfo.xml

TAG: reports_db-6-0-0-9
DATE: 09/16/2015
STAFF: sc
CHANGES: TR11957 
1) remove constraint of requiring Marker assoc to both genbank and refseq 
	sequences to be included in this report
2) add feature type to column 21

TAG: reports_db-tr12070-1
DATE: 12/02/2015
STAFF: lec
1) TR12070/daily/GO_gene_association.py

TAG: reports_db-tr12070-BP
DATE: 09/09/2015
STAFF: kstone
1) branch point tag for TR12070

TAG: reports_db-6-0-0-8
DATE: 09/02/2015
STAFF: lec
CHANGES:
1) weekly/ALL_CellLine_GeneTrap.py

TAG: reports_db-6-0-0-7
DATE: 08/25/2015
STAFF: lec
CHANGES:
1) TR112083/10592/authors/title

TAG: reports_db-6-0-0-6
DATE: 08/19/2015
STAFF: lec
CHANGES:
1) TR12012/daily/GO_gene_association.py

TAG: reports_db-6-0-0-5
TAG: reports_db-6-0-0-4
DATE: 08/13/2015
STAFF: lec
CHANGES:
1) per judy : inparanoid directory/file is obsolete

TAG: reports_db-6-0-0-3
DATE: 08/11/2015
STAFF: lec
CHANGES:
1) mgimarkerfeed/change date format

TAG: reports_db-6-0-0-2
TAG: reports_db-6-0-0-1
DATE: 07/24/2015
STAFF: lec
CHANGES:
1) TR11750/postgres

TAG: reports_db-5-2-2-6
DATE: 06/24/2015
STAFF: lnh
CHANGES:
1) generateGPAD.csh: Added a new script to run gaf_fprocessor.gaf2gpad to convert GAF files to GPAD/GPI
2) run_daily.csh: Removed call to gaf_fprocessor.gaf2gpad 

TAG: reports_db-5-2-2-5
DATE: 06/23/2015
STAFF: lnh
CHANGES:
1) run_daily.csh: Added call to gaf_fprocessor.gaf2gpad to convert GAF files to GPAD/GPI

TAG: reports_db-5-2-2-4
DATE: 06/17/2015
STAFF: dbm
CHANGES:
1) daily/GO_eco_association.py: invoke /usr/local/bin/python so it doesn't
                                fail on Linux

TAG: reports_db-5-2-2-3
DATE: 06/03/2015
STAFF: sc
CHANGES: TR12025
1) weekly/MGI_Gene.rpt - added feature type

TAG: reports_db-5-2-2-2
DATE: 06/03/2015
STAFF: lnh
CHANGES:
 daily/GO_eco_association.py: Fixed missing argument in re.findall() call

TAG: reports_db-5-2-2-1
DATE: 06/02/2015
STAFF: lnh
CHANGES:
 daily/GO_eco_association.py: Code cleanup:parsing Eco code from evidence notes using re.findall()
 
TAG: reports_db-5-2-1-27
DATE: 05/19/2015
STAFF: sc
CHANGE:
protein_linkout.py changed:
<Rule>id=&lo.pacc;</Rule>
to:
<Rule>&lo.pacc;</Rule>

TAG: reports_db-5-2-1-26
TAG: reports_db-5-2-1-25
DATE: 05/15/2015
STAFF: lec
CHANGE:
TR12020/obsolete: allele_marker, allele_markerstatus, allele_markerqualifier
confirmed with Carolyn Blake

TAG: reports_db-5-2-1-24
TAG: reports_db-5-2-1-23
TAG: reports_db-5-2-1-22
DATE: 05/13/2015
STAFF: lec
CHANGE:
TR11652/convert to MRK_Cluster
weekly/MGI_MarkerNames.py
obsolete
weekly/MRK_NomenUpdates.py
runone_sybase_report.csh

TAG: reports_db-5-2-1-21
DATE: 05/11/2015
STAFF: lec
CHANGE:
1) TR12020
weekly/ALL_CellLine_GeneTrap.py
weekly/MGI_CvDC.py
weekly/MGI_iphone_app.py
weekly/MRK_GeneTrap.py
weekly/MGI_Gene.py

TAG: reports_db-5-2-1-20
DATE: 05/11/2015
STAFF: sc
CHANGE:
1) TR11968 new report: weekly/MGI_Gene.py

TAG: reports_db-5-2-1-19
TAG: reports_db-5-2-1-18
DATE: 04/22/2015
STAFF: lec
CHANGE: 
1) TR11932/daily/GO_gene_association.py

TAG: reports_db-5-2-1-17
TAG: reports_db-5-2-1-16
DATE: 04/17/2015
STAFF: lnh
CHANGE: TR11992
1) Added a new public report to run daily  daily/GO_gene_association.py
2) run_daily.csh: added code to copy the new report to ftp report directory

TAG: reports_db-5-2-1-15
DATE: 03/19/2015
STAFF: dbm
CHANGE: 
1) daily_sybase directory: renamed to daily
2) weekly_sybase, weekly_postgres directories: merged into weekly
3) Configuration.default: Removed DB_TYPE, KOMP_GENELIST and KOMP_TARGETLIST
                          and changed paths for daily and weekly directories
4) run_daily_sybase.csh: renamed to run_daily.csh
5) run_weekly_sybase.csh, run_weekly_postgres.csh: merged into run_weekly.csh
6) mgimarkerfeed/mgimarkerfeed_reports.csh: use gzip for compression
7) Install: change for daily and weekly directories

TAG: reports_db-5-2-1-14
DATE: 03/18/2015
STAFF: dbm
CHANGE: 
1) mgiMarkerFeed.py: Check DB_TYPE and fixed outer join a a genotype query

TAG: reports_db-5-2-1-13
TAG: reports_db-5-2-1-12
DATE: 03/17/2015
STAFF: dbm
CHANGE: 
1) Configuration.default: Remove SP2FASTA and PERLLIB
2) inparanoid/sp_to_fasta: Added
3) inparanoid/inparanoid.csh: Invoke new copy of sp_to_fasta
4) inparanoid/MGI_InParanoid_FASTA.py: Postgres support
5) run_daily_sybase.csh: Remove DB_TYPE -- moved to mgconfig
6) run_weekly_sybase.csh: Remove DB_TYPE -- moved to mgconfig
7) run_weekly_postgres.csh: Remove DB_TYPE -- moved to mgconfig

TAG: reports_db-5-2-1-11
DATE: 02/05/2015
STAFF: sc
CHANGE: TR11867, backed out change below

TAG: reports_db-5-2-1-10
TAG: reports_db-5-2-1-9
DATE: 02/02/2015
STAFF: sc
CHANGE: TR11867, add two new provider to goaload 
1) daily_sybase/GO_gene_association.py - special handkling for 
GO_Central --> GO Central

TAG: reports_db-5-2-1-8
DATE: 01/30/2015
STAFF: sc
CHANGE: TR11879 - Fix: non-protein coding genes in gp2protein file
1) weekly_postgres/GO_gp2protein.py - move RNA genes assoc with uniprot from
    protein to rna file

TAG: reports_db-5-2-1-7
DATE: 01/26/2015
STAFF: sc
CHANGES: TR11846 - NCBI Linkout changes
   bug fix in nucleotide marker URL

TAG: reports_db-5-2-1-6
DATE: 01/23/2015
STAFF: dbm
CHANGES: Infrastructure project cleanup
1) Configuration.default: Removed SUBPROCESSES setting
2) run_daily_sybase.csh: DB_TYPE and logging cleanup
3) run_weekly_sybase.csh: DB_TYPE and logging cleanup
4) run_weekly_postgres.csh: DB_TYPE and logging cleanup
5) runone_postgres_report.csh
6) runone_sybase_report.csh: New - replaces runone_report.csh
7) runone_report.csh: Removed
8) run_in_parallel.py: Removed
9) ncbilinkout/ncbilinkout.csh: DB_TYPE and logging cleanup

TAG: reports_db-5-2-1-5
DATE: 01/22/2015
STAFF: sc
CHANGES: TR11846 - NCBI Linkout changes
1) ncbilinkout.csh - updated the set of files ftp'd to the holding directory

TAG: reports_db-5-2-1-4
DATE: 01/15/2015
STAFF: sc 
CHANGES: TR11846 - NCBI Linkout changes
1) Configuration.default - updated NCBILINKOUT_ICON with new URL
2) ncbilinkout/nucleotide_linkout.py - updated to reflect current MGI marker URL
3) ncbilinkout/pubmed_linkout.py - update with URL to larger image, added 
    generation of a UID file, updated report to one link referencing the 
    UID file. Not certain the the report itself is correct because it 
    references &lo.id; which is not a defined ENTITY in the report. rmb and 
    drs decided to just put the report in production and check things after 
    they pick up the files as we have no way to test this.
4) MGI_OMIM.py - removed extraneous comma in a query that was inadvertently 
    committed on the trunk

TAG: reports_db-5-2-1-3
DATE: 01/09/2015
STAFF: jsb
CHANGES - updates to iPhone reports to use rolled-up MP and OMIM annotations

TAG: reports_db-5-2-1-2
TAG: reports_db-5-2-1-1
DATE: 12/18/2014
STAFF: kstone
CHANGES - removed IMSR database access by weekly_sybase reports, using Solr csv file instead

TAG: reports_db-5-2-0-3
DATE: 12/2/2014
STAFF: lnh 
CHANGES - added runone_postgres_report.csh to run single postgres report

TAG: reports_db-5-2-0-2
DATE: 11/27/2014
STAFF: sc
CHANGES TR11818 - chromosome positions missing from HOM_MouseHumanSequence.rpt

HOM_MouseHumanSequence.py
TAG: reports_db-5-2-0-1
DATE: 11/24/2014
STAFF: sc
CHANGES: TR11772/Modification of GAF file references

TAG: reports_db-5-2-0-?
DATE: 11/17/2014
STAFF: lec, kstone
CHANGES:
1) TR11750/postgres 
ALL_CRE : EBI is no longer using this report

TAG: reports_db-5-1-9-9
TAG: reports_db-5-1-9-8
TAG: reports_db-5-1-9-7
DATE: 10/27/2014
STAFF: lec
CHANGES:
1) TR11750/postgres 
2) TR11560/bug fix

TAG: reports_db-5-1-9-6
DATE: 09/11/2014
STAFF: lnh
CHANGES: TR11732
1)TR11732- weekly_postgres/MGI_iphone_app.py: 
  Got rid of extra the tab associated with each default field 
2)TR11774- weekly_postgres/MRK_Sequence.py: 
  Fixed Missing tab between RefSeqID and UniGeneID fields   

TAG: reports_db-5-1-9-5
DATE: 09/11/2014
STAFF: lnh
CHANGES: TR11732
1)weekly_postgres/MGI_iphone_app.py
Trim down iphone app reports - 
a.) iphone_app_snapshot_genes.rpt
b.) iphone_app_snapshot_mp.rpt
c.) iphone_app_snapshot_omim.rpt

TAG: reports_db-5-1-9-4
DATE: 08/19/2014
STAFF: dbm
CHANGES: TR11679
1) index.html.default: added mp.owl to A&P section
2) Configuration.default: added mp.owl to MPFILES setting

TAG: reports_db-5-1-9-3
DATE: 08/01/2014
STAFF: dbm
CHANGES: TR11662
1) index.html.default: added western clawed frog to HOM_AllOrganism.rpt
2) HOM_AllOrganism.py: added organism key 95

TAG: reports_db-5-1-9-2
DATE: 07/24/2014
STAFF: lnh
CHANGES: TR11725
1)weekly_postgres/MGI_iphone_app.py
Modified the init_report function to do the following to each report:
a.) Keep previous week report if exists
b.) create symbolic link labeled "old" to the previous week report

TAG: reports_db-5-1-9-1
DATE: 07/17/2014
STAFF: sc
CHANGES: TR11560
1) updated the following to exclude feature type 'mutation defined region
weekly_postgres/MGI_EntrezGene.py
weekly_postgres/MGI_GeneOMIM.py
weekly_postgres/MGI_OMIM.py
weekly_postgres/MRK_List.py
weekly_sybase/MRK_NomenUpdates.py

TAG: reports_db-5-1-8-5
DATE: 07/02/2014
STAFF: lec
CHANGES:
1) TR11693/GO_gene_association.py

TAG: reports_db-5-1-8-4
DATE: 07/01/2014
STAFF: lec
CHANGES:
1) TR11710/GO_gene_association.py

TAG: reports_db-5-1-8-3
DATE: 05/01/2014
STAFF: lec
CHANGES:
1) TR11660/MGI_GenePheno.py/add genotype ID
2) TR11669/weekly/MGI_CvDC.py moved to weekly_postgres

TAG: reports_db-5-1-8-2
DATE: 03/27/2014
STAFF: lec
CHANGES:
1) TR11615/MGI_IMSRKomp.py

TAG: reports_db-5-1-8-1
DATE: 03/06/2014
STAFF: lec
CHANGES:
1) merge to trunk : branch point for TR11515/allele stuff

TAG: reports_db-5-1-6-4
DATE: 01/14/2014
STAFF: lec
CHANGES:
1) TR11570/fix GO qualifier/use VOC_Term

TAG: reports_db-5-1-6-3
DATE: 01/02/2014
STAFF: lec
CHANGES:
1) TR11518/daily_sybase/GO_gene_association.py/new doCol16()

TAG: reports_db-tr11515-1
DATE: 12/31/2013, 03/06/2014
STAFF: lec
CHANGES:
1) changes to _Allele_Type_key
weekly_postgres/MGI_Mutations.py
weekly_postgres/MGI_OMIM.py
weekly_postgres/MGI_PhenotypicAllele.py
weekly_sybase/ALL_CellLine_Targeted.py 
weekly_sybase/MGI_Knockout.py : obsolete/removed
mgimarkerfeed/mgiMarkerFeed.py

TAG: reports_db-tr11515-BP
DATE: 12/31/2013
STAFF: lec
CHANGES:
1) branch point for TR11515/allele stuff

TAG: reports_db-5-1-6-2
TAG: reports_db-5-1-6-1
DATE: 12/05/2013, 12/19/2013
STAFF: lec
CHANGES: 
1) wrong version of daily_sybase/GO_gene_association.py
2) wrong Configuration.default

TAG: reports_db-5-1-5-8
DATE: 11/18/2013
STAFF: lec
CHANGES: 
1) TR11530/weekly_sybase/ALL_CellLine_GeneTrap.py
fix column 10/allele-type

TAG: reports_db-5-1-5-7
DATE: 11/05/2013
STAFF: lec
CHANGES: 
1) TR11510/weekly_postgres/GO_gp2protein.py
add feature type rules

TAG: reports_db-5-1-5-6
DATE: 11/1/2013
STAFF: sc	
CHANGES: MGI_PhenoGenoMP.rpt - Extra tab reported via user support

old:
fp.write(string.join(mpRef[refKey], ','))
new:
fp.write(string.join(mpRef[refKey], ',') + TAB)
old:
fp.write(TAB + string.join(mpMarker[genotype], ',') + CRT)
new:
fp.write(string.join(mpMarker[genotype], ',') + CRT)

TAG: reports_db-5-1-5-5
DATE: 10/16/2013
STAFF: dbm
CHANGES: 
1) TR11516/weekly_postgres/GO_gene_association_nonmouse.py: convert
   modification_date to YYYYMMDD format

TAG: reports_db-5-1-5-4
DATE: 10/09/2013
STAFF: lec
CHANGES: 
1) TR11502/weekly_postgres/MGI_MRK_Coord.py
add organism to version query

TAG: reports_db-5-1-5-3
DATE: 08/27/2013
STAFF: lec
CHANGES: 
1) TR11459/daily_sybase/GO_gene_association.py

TAG: reports_db-5-1-5-2
DATE: 08/24/2013
STAFF: dbm
CHANGES: 
1) run_daily_sybase.csh, run_weekly_sybase.csh, run_weekly_postgres.csh -
   logging fixes

TAG: reports-5-1-5-1
DATE: 08/23/2013
STAFF: sc	
CHANGES: Infrastructure I - merge tr11353 branch to trunk

TAG: reports-tr11353-6	
DATE: 08/19/2013
STAFF: dbm,sc
CHANGES: Issues running reports on prodapp1
1) inparanoid.csh - moved back to weekly_sybase as it uses wu-blast tools which
   are not available on linux
2) MGI_AllGenes.py  - moved back to weekly_sybase as it needs access to 
       lindon:${DATALOADSOUTPUT}/komp/kompreports/output/geneList.txt and 
       lindon:${DATALOADSOUTPUT}/komp/kompreports/output/geneListNoKo.txt
   added db.useOneConnection calls
3) MRK_NomenUpdates.py -  moved back to weekly_sybase as needs access to
   /usr/local/mgi/live/dbutils/mgidbutilities/text/jax_header which won't be
   installed on prodapp1
4) Install - modified to only make sym links to these directories when it is 
       being run on lindon since that's the only place where the files will 
       exist.
    ${DATALOADSOUTPUT}/mgi/vocload/runTimeMP
    ${DATALOADSOUTPUT}/mgi/vocload/runTimeMA
5) weekly_sybase/MGI_Knockout.py, MGI_Recombinase_Full.py, MRK_NomenUpdates.py -       added db.useOneConnection calls
6) weekly_postgres/MGI_CvDC.py - 'mgi:' -> 'MGI:'
7) inparanoid/MGI_InParanoid_FASTA.py - added db.useOneConnection calls
8) runone_report.csh - updated so it works for sybase as well as postgres
9) run_weekly_sybase.csh - added commented out inparanoid back into serially run
      section

TAG: reports-tr11353-5
DATE: 08/07/2013
STAFF: sc
CHANGES: US 133 - update to use new fewi allele detail URL 
1) ALL_OMIM.py
2) MGI_iphone_app.py

TAG: reports-tr11353-4
DATE: 08/07/2013
STAFF: sc
CHANGES: US 124 - update public reports to use new PG_PUB_* settings
1) Added:
    setenv PG_DBSERVER      ${PG_PUB_DBSERVER}
    setenv PG_DBNAME        ${PG_PUB_DBNAME}
    setenv PG_DBUSER        ${PG_PUB_DBUSER}
   To:
    * ondemand_reports.csh
    * run_weekly_postgres.csh
    * runone_report.csh
    * inparanoid/inparanoid.csh
2) bug in MGI_CvDC.py - converted to postgres

TAG: reports-tr11353-3
DATE: 07/12/2013
STAFF: sc
CHANGES: went back to parallel mode

TAG: reports-tr11353-2
TAG: reports-tr11353-1
DATE: 07/3/2013
STAFF: sc
CHANGES: 
1) added weekly_postgres, weekly_sybase, daily_sybase dirs and corresponding wrappers
2) removed daily and weekly dirs, reorganized into 1)
3) removed old daily and weekly wrappers
5) Install - updated for new directories in 1)
6) report scripts:
a) removed DB_TYPE from all report scripts; but not from Configuration as some
    library seems to be dependent on it
b) testing revealed 7 reports were including private data. Needed to remove private
   data from my sybase db to fully test.
	** EUCOMM_Allele.rpt
	** KOMP_Allele.rpt
	** MGI_ElsevierDOI.rp
	** MGI_GTRNA.gff
	** MGI_GTdbGSS_info.rpt
	** MGI_IKMC_DNA_GT_info.rpt 
	** MGI_IKMC_DNA_GT.gff
c) some reports needed case changes to run correctly in postgres e.g.
	** 'mgi:' --> 'MGI:'
	** 'Image' --> 'IMAGE'
d) MGI_IKMC_DNA_GT_info.rpt / MGI_IKMC_DNA_GT.rpt report not excluding RNA sequence
   tags properly - updated to use term keys instead of terms
e) MGI_CloneSet.py - ldb.name in never worked, missing quotes around ldbs:
   ('Image', 'NIA 15K,NIA 7.4K,NIA', 'RIKEN (FANTOM),RIKEN', 'RPCI-23', 'RPCI-24')
f) Configuration.defaults - added PUBDAILY, PUBWEEKLY_POSTGRES, PUBWEEKLY_SYBASE

TAG: reports-tr11353-BP
DATE: 06/19/2013
STAFF: sc
CHANGES: Infrastructure I project

TAG: reports_db-5-1-4-3
TAG: reports_db-5-1-4-2
DATE: 06/14/2013
STAFF: lec
1) MGI_InterProDomains.py/fix

TAG: reports_db-5-1-4-1
TAG: reports_db-5-1-3-7
DATE: 05/28/2013
STAFF: lec
CHANGES: TR11402
1) MRK_Sequence.py - added UniGene ID column (20)
2) index.html - added col 20 

TAG: reports_db-5-1-3-6
DATE: 05/28/2013
STAFF: lec
CHANGES:
TR11060/GO_gene_association.py/gene_association_pro.mgi
add all UniProtKB: and PR:

TAG: reports_db-5-1-3-5
DATE: 05/09/2013
STAFF: dbm
CHANGES: 
1) HOM_AllOrganism.py and HOM_MouseHumanSequence.py - allow for null strand

TAG: reports_db-5-1-3-4
DATE: 04/25/2013
STAFF: lec
CHANGES: 
1) TR11284/weekly/MRK_Reference.py

TAG: reports_db-5-1-3-3
DATE: 04/23/2013
STAFF: sc, jsb
CHANGES: N2MO
1) HMD_HumanPhenotype.py - updated to use MRK_Cluster* tables and deal w/N-M
2) index.html - added new column to HMD_HumanPhenotype.rpt
3) index.html - redefined MGI_OMIM report
4) MGI_OMIM.py - new addition (full rewrite of MGI_PhenoOMIM.py)
5) MGI_PhenoOMIM.py - removed; replaced by #4 above

TAG: reports_db-5-1-3-2
DATE: 04/18/2013
STAFF: sc
CHANGES: N2MO 
1) US142 - weekly/MGI_iphone_app.py, update to use MRK_Cluster*
2) US148 - weekly_reports.csh - US not finished (diff script not ready), 
    commented out code.

TAG: reports_db-5-1-3-1
DATE: 04/16/2013
STAFF: sc
CHANGES: N2MO merge tr6519  changes to trunk

TAG: reports_db-5-1-2-4
DATE: 04/02/2013
STAFF: lec
CHANGES:
1) TR11343 (scrum-dog TR11248)
mgimarkerfeed/mgiMarkerFeed.py:genotype_mpt.bcp

TAG: reports_db-5-1-2-3
DATE: 03/26/2013
STAFF: lec
CHANGES:
1) TR11330 (scrum-dog TR11248)
weekly/GO_gene_association_nonmouse.py

TAG: reports_db-tr6519-1
DATE: 04/04/2013
STAFF: sc
CHANGES: N2MO/TR6519
1) Jon's changes
2) MGI_ElsevierDOI.py - added GO annotation refs

TAG: reports_db-tr6519-BP
DATE: 02/25/2013
STAFF: jsb
CHANGES:
1) branch point for N-to-M orthologs release (n2mO)

TAG: reports_db-5-1-2-2
TAG: reports_db-5-1-2-1
DATE: 02/14/2013
STAFF: lec
CHANGES:
1) TR11112/GO_gene_association.py
2) TR11272/GO_gp2protein.py

TAG: reports_db-5-1-1-4
DATE: 01/15/2013
STAFF: sc
CHANGES: MGI_GTDNA.rpt contains RNA sequence tags - reported by Paul Hale
1) bug in MGI_GTDNA.py change: rnaMethods = '5'' RACE, 3'' RACE'
  to: rnaMethods = "5' RACE, 3' RACE"

TAG: reports_db-5-1-1-3
DATE: 12/19/2012
STAFF: lec
CHANGES:
1) TR11242/inclulde _Marker_Status_key in (1,3) only

TAG: reports_db-5-1-1-2
DATE: 11/12/2012
STAFF: jsb
CHANGES:
1) updated MGI_MRK_Coord.py to support null strands when looking up providers

TAG: reports_db-5-1-1-1
DATE: 11/07/2012
STAFF: dbm
CHANGES:
C4AM/B38 release

TAG: reports_db-5-0-0-29
DATE: 11/01/2012
STAFF: lec
CHANGES:
1) TR11164/MGI_PhenoGenoMP.py
while working on this TR, spotted a potential issue with this
report and fixed it

TAG: reports_db-5-0-0-28
DATE: 08/27/2012
STAFF: lec
CHANGES:
1) TR11149/mgimarkerfeed/mgiMarkerFeed.py
for Allele Notes: only select where MGI_NoteType.private = 0

TAG: reports_db-5-0-0-27
DATE: 08/14/2012
STAFF: lec
CHANGES:
1) TR11134/MGI_CvDC.py

TAG: reports_db-tr7106-BP
DATE: 07/25/2012
STAFF: jsb
CHANGES:
1) branch point for TR7106 -- coordinates for any marker

TAG: reports_db-5-0-0-26
DATE: 07/25/2012
STAFF: lec
CHANGES:
1) TR11046/MGI_iphone_app.py (updated)

TAG: reports_db-5-0-0-25
TAG: reports_db-5-0-0-24
DATE: 07/23/2012
STAFF: lec
CHANGES:
public_rpt_release.csh: remove iphone*[0-9]*

TAG: reports_db-5-0-0-23
DATE: 06/19/2012
STAFF: lec
CHANGES:
used by GBrowse:
SEQ_RepTransGenomic.rpt
MGI_ComprehensiveMarkerSequence.rpt
MRK_Sequence.rpt
MGI_PhenotypicAllele.rpt
MGI_Coordinate.rpt
MRK_ENSEMBL.rpt
MRK_VEGA.rpt
MRK_GeneTrap.rpt
MGI_GTGUP.rpt
MGI_GTDNA.gff
MGI_GTRNA.gff
MGI_QTL.gff
MGI_STS.gff
MGI_SNP.gff
build_37_chromosomes.gff

TAG: reports_db-5-0-0-22
TAG: reports_db-5-0-0-21
DATE: 06/07/2012
STAFF: lec
CHANGES:
1) TR11046/MGI_iphone_app.py (updated)

TAG: reports_db-5-0-0-20
DATE: 05/31/2012
STAFF: lec
CHANGES:
1) TR11046/MGI_iphone_app.py (new)
2) TR11034/GO_gp2protein.py
3) ALLCRE.py (use ansi standard)
4) TR11094/MGI_Recombinase_Full.py

TAG: reports_db-5-0-0-19
TAG: reports_db-5-0-0-18
DATE: 05/17/2012
DATE: 05/09/2012
STAFF: lec
CHANGES:
1) index.html.default: left-justify section names
2) TR11035/postgres cleanup
weekly/MRK_Sequence.py
3) turning off front-end translater:
	added db.setAutoTranslate(False)

TAG: reports_db-5-0-0-17
DATE: 05/08/2012
STAFF: lec
CHANGES:
TR11060/GO_gene_association.py/add subset report for Harold (hjd)
gene_association_pro.mgi

TAG: reports_db-5-0-0-16
DATE: 05/03/2012
STAFF: lec
CHANGES:
TR11035/postgres cleanup; bug fixes
re-installed:
MGI_MakerNames.py
GO_terms.py

TAG: reports_db-5-0-0-15
DATE: 05/01/2012
STAFF: sc
CHANGES: TR11057 - GO-gp2protein.py

TAG: reports_db-5-0-0-14
TAG: reports_db-5-0-0-13
TAG: reports_db-5-0-0-12
TAG: reports_db-5-0-0-11
TAG: reports_db-5-0-0-10
TAG: reports_db-5-0-0-9
TAG: reports_db-5-0-0-8
TAG: reports_db-5-0-0-7
TAG: reports_db-5-0-0-6
TAG: reports_db-5-0-0-5
TAG: reports_db-5-0-0-4
TAG: reports_db-5-0-0-3
DATE: 04/24/2012-04/30/2012
STAFF: lec
CHANGES:

TR11057/fix to gp2protein script (sc)
TR11035/Postgres Cleanup

added:
ondemand directory
ondemand_reports.csh

move to ondemand:
MGI_CloneSet.py
MAP_Mapping.py (removed sql versions)

add:
MRK_List.py

update:
MGI_EntrezGene.py
MRK_VEGA.py
MRK_ENSEMBL.py
MGI_Strain.py
MGI_CloneSet.py
ALL_CellLine_GeneTrap.py (reorganized/from 30 minutes to 8 minutes)

replace with MRK_List.py:
MRK_List1.py
MRK_List1.sql
MRK_List2.py
MRK_List2.sql
MRK_List3.py
MRK_List3.sql
MRK_List4.py
MRK_List4.sql
MRK_Synonym.py
MRK_Synonym.sql
MRK_Dump1.py
MRK_Dump2.py

remove:
MGI_RIKEN.py
MGI_MouseHumanSequence.py
HMD_OxfordGrid.py
MRK_GOHuman.py
GO_completedAnnotations.py
GO_refs.py
GO_refGenomeGenes.py
GO_terms.py
MRK_Ensembl_Pheno.py
PRB_CloneLibrary.py
PRB_CloneLibrarycDNA.py
PRB_TissueMouse.py
ncbilinkout/omim_linkout
MRK_InterPro.py

obsolete directories:
panelDocs
system_docs

TAG: reports_db-5-0-0-2
DATE: 04/12/2012
STAFF: lec
CHANGES:
TR11035/Postgres Cleanup
1) convert to using one db.sql() per sql command in preparation for postgres
2) re-order import statements in prep for postgres changes
3) convert 'create index idx' to unique index name
4) postgres options with "try/except" block added to all python reports
5) PRB_TissueMouse.sql moved to PRB_TissueMouse.py
6) MGI_InterProDomains.sql moved to MGI_InterProDomains.py
7) PRB_CloneLibrary.sql moved to PRB_CloneLibrary.py
8) MRK_NomenUpdates.py; first author needed to be increased

TAG: reports_db-5-0-0-1
DATE: 03/29/2012
STAFF: dbm
CHANGES:
1) public_rpt_release.csh: process control changes for 5.0 release

TAG: reports_db-5-0-0-?
DATE: 03/28/2012
STAFF: lec
CHANGES:
1)TR 11027
a) create_accession_anchor() for MGI 5.0 (see lib_py_reports_db)
b) MRK_NomenUpdates.py
c) MGI_Knockout.py
d) MGI_Recombinase_Full.py

TAG: reports_db-4-4-2-15
DATE: 03/27/2012
STAFF: sc
CHANGES: TR11021
1) MGI_GTdbGSS_info.py - added two additional columns
   parent cell line and strain

TAG: reports_db-4-4-2-14
DATE: 03/13/2012
STAFF: lec
CHANGES:
1) GO_gene_association.py: pubMed portion being called twice; add distinct

TAG: reports_db-4-4-2-13
DATE: 03/06/2012
STAFF: lec
CHANGES:
1) TR10998/add allele ids/MGI_GenePheno.py

TAG: reports_db-4-4-2-12
DATE: 03/05/2012
STAFF: lec
CHANGES:
1) TR10980/Elsevier DOI/weekly/MGI_ElsevierDOI.py

TAG: reports_db-4-4-2-11
DATE: 02/08/2012
STAFF: lec
CHANGES:
1) weekly/ALL_CRE.py
   marker may be null

TAG: reports_db-4-4-2-10
DATE: 01/11/2012
STAFF: lec
CHANGES:
1) TR10591/MGI_MarkerNames.py

TAG: reports_db-4-4-2-9
DATE: 01/04/2012
STAFF: dbm
CHANGES:
1) Added "-f" option to csh startup in wrapper scripts

TAG: reports_db-4-4-2-8
DATE: 12/28/2011
STAFF: lec
CHANGES:
1) change "*=" to left outer join
mgimarkerfeed/mgiMarkerFeed.py
weekly/ALL_CellLine_GeneTrap.py
weekly/ALL_CellLine_Targeted.py
weekly/ALL_CRE.py
weekly/GO_gene_association_nonmouse.py
weekly/HMD_Synonyms.py
weekly/MAP_Mapping.py

TAG: reports_db-4-4-2-7
DATE: 11/22/2011
STAFF: lec
CHANGES:
1) added -f to *csh, Configuration.default

TAG: reports_db-4-4-2-6
DATE: 11/08/2011
STAFF: lec
CHANGES: TR10899
1) add ma2ncit.obo to index.html.default

TAG: reports_db-4-4-2-5
DATE: 10/20/2011
STAFF: sc
CHANGES: TR9864
1) Fix to ALL_CellLine_Targeted.py and ALL_CellLine_Targeted.py

TAG: reports_db-4-4-2-3
TAG: reports_db-4-4-2-2
TAG: reports_db-4-4-2-1
DATE: 10/19/2011
STAFF: lec
CHANGES:
1) TR10885/weekly/MGI_EntrezGene.py/add rawbiotype/feature type
2) updated index.html.default

TAG: reports_db-4-4-1-31
DATE: 10/07/2011
STAFF: sc
CHANGES:
1) TR9864 added ALL_CellLine_GeneTrap.py ALL_CellLine_Targeted.py

TAG: reports_db-4-4-1-30
DATE: 08/24/2011
STAFF: lec
CHANGES: 
1) TR10829/MGI_PhenoGenoMP.py

TAG: reports_db-4-4-1-29
DATE: 08/22/2011
STAFF: lec
CHANGES: 
1) replace 're' with 'string'

TAG: reports_db-4-4-1-28
TAG: reports_db-4-4-1-27
TAG: reports_db-4-4-1-26
DATE: 08/16/2011
STAFF: lec
CHANGES: 
1) TR10591/monthly/MGI_MarkerNames.py
   fix bug in synonym-tabbing

TAG: reports_db-4-4-1-25
DATE: 07/20/2011
STAFF: lec
CHANGES:
1) MRK_Dump2.py; ansi standard; offset

TAG: reports_db-4-4-1-24
DATE: 07/12/2011
STAFF: lec
CHANGES:
1) mgimarkerfeed/mgiMarkerFeed.py

TAG: reports_db-4-4-1-23
DATE: 07/06/2011
STAFF: lec
CHANGES:
1) TR10770/remove MGI_PhenoOMIM.rpt from index page

TAG: reports_db-4-4-1-22
DATE: 07/06/2011
STAFF: lec
CHANGES:
1) TR10044/daily/GO_gene_association.py
2) weekly/GO_gene_association_nonmouse.py

TAG: reports_db-4-4-1-21
DATE: 07/05/2011
STAFF: lec
CHANGES:
1) replaced calls to VOC_Term_XXXX_View with direct call to table
this tag has *not* been installed and can go out with the next production tag

TAG: reports_db-4-4-1-20
DATE: 07/05/2011
STAFF: lec
CHANGES:
1) TR10770/weekly/MGI_PhenoOMIM.py

TAG: reports_db-4-4-1-18
DATE: 06/21/2011
STAFF: lec
CHANGES:
1) TR10753/weekly/MGI_GenePheno.py

TAG: reports_db-4-4-1-17
TAG: reports_db-4-4-1-16
DATE: 06/20/2011
STAFF: lec
CHANGES:
1) TR9308/daily/MGI_PhenoOMIM.py:removed;duplicate of weekly

TAG: reports_db-4-4-1-15
DATE: 05/12/2011
STAFF: lec
CHANGES:
1) TR9308/weekly/MGI_PhenoOMIM.py

TAG: reports_db-4-4-1-14
DATE: 04/26/2011
STAFF: sc
CHANGES: TR10336
1) weekly/MGI_BioTypeConflict.py, added additional column

TAG: reports_db-4-4-1-13
DATE: 04/18/2011
STAFF: dbm
CHANGES:
1) Merged tr10531 branch to the trunk

TAG: reports_db-tr10531-2
DATE: 04/18/2011
STAFF: dbm
CHANGES: TR10531 - move to weekly public release
1) weekly_reports.csh - uncomment *.sql reports (bug fix)

TAG: reports_db-tr10531-1
DATE: 04/14/2011
STAFF: dbm
CHANGES: TR10531 - move to weekly public release
1) Configuration.default - remove PUBMONTHLY setting
2) Install - remove step that create a link to GO_gene_association.py in the
             weekly directory
           - do not try to copy panel docs to the FTP site - unrelated to
             this TR, but the panel docs do not exist
3) daily reports - move mgiMarkerFeed.py to a new mgimarkerfeed directory
                 - move all other reports except GO_gene_association.py to
                   the weekly directory
4) monthly reports - move all reports to the weekly directory and remove
                     the monthly directory
5) mgimarkerfeed_report.csh - move to mgimarkerfeed directory and modify to
                              run the Python script from there
6) nightly_reports.csh - should only run *.py scripts which currently is only
                         GO_gene_association.py
                       - only copy the gene association file to FTP site
7) weekly_reports.csh - add logic to run all *.slq script, clone set reports
                        and NCBI linkout files
                      - do NOT copy any reports to the FTP site at this time
8) monthly_reports.csh - Remove
9) public_rpt_release.csh - New script to handle copying of reports to the
                            public FTP site in sync with public release

TAG: reports_db-tr10531-BP
DATE: 04/07/2011
STAFF: dbm
CHANGES:
1) branch point tag for TR10531 (weekly public release)

TAG: reports_db-4-4-1-12
DATE: 04/04/2011
STAFF: sc
CHANGES:TR10661
1) added weekly/MGI_GTDNA.py, MGI_GTRNA.py, MGI_GTdbGSS_info.py
2) Configuration.default - added gene trap report settings

TAG: reports_db-4-4-1-11
TAG: reports_db-4-4-1-10
DATE: 03/30/2011
STAFF: lec
CHANGES: 
1) TR10652
   GO_gene_association.py
   GO_gp2protein.py

TAG: reports_db-4-4-1-9
DATE: 03/21/2011
STAFF: lec
CHANGES: 
1) TR9962/add 'RefGenome' to column 15:GO_gene_association.py

TAG: reports_db-4-4-1-8
DATE: 03/16/2011
STAFF: lec
CHANGES: 
1) TR10633/Allow PRO ids (PR:) in column 17:GO_gene_association.py

TAG: reports_db-4-4-1-7
TAG: reports_db-4-4-1-6
TAG: reports_db-4-4-1-5
DATE: 03/02/2011
STAFF: lec
CHANGES: 
1) TR10616/weekly/MGI_GeneOMIM.py
   will *not* add to index.html at this time
2) TR10605/MGI_GenePheno.py
don't forget to edit index.html.default

TAG: reports_db-4-4-1-4
DATE: 02/23/2011
STAFF: lec
CHANGES: 
1) TR10591/monthly/MGI_MarkerNames.py
   will *not* add to index.html at this time

TAG: reports_db-4-4-1-3
DATE: 02/15/2011
STAFF: lec
CHANGES: 
1) TR10597/MGI_Coordinate.py

TAG: reports_db-4-4-1-2
DATE: 02/09/2011
STAFF: lec
CHANGES: TR10549
1) move MRK_ENSEMBL.py, MRK_Sequence.py to qcreports_db/weekly

TAG: reports_db-4-4-1-1
DATE: 02/02/2011
STAFF: sc
CHANGES: TR10549
Added daily/NorCOMM_Allele.py

TAG: reports_db-4-4-0-13
TAG: reports_db-4-4-0-12
TAG: reports_db-4-4-0-11
DATE: 12/07/2010
STAFF: sc
CHANGES: TR10470
Added weekly reports:
1) MGI_IKMC_DNA_GT.gff, MGI_IKMC_DNA_GT_info.rpt

TAG: reports_db-4-4-0-10
STAFF: lec
CHANGES: TR10308 biotype conflict revision
1) TR10460/add accession_allele_cellline.bcp
   daily/mgiMarkerFeed.py

TAG: reports_db-4-4-0-9
STAFF: sc
CHANGES: TR10308 biotype conflict revision
1) daily/MGI_BioTypeConflict.py -  updated to use marker feature type
	instead of marker type

TAG: reports_db-4-4-0-8
TAG: reports_db-4-4-0-7
DATE: 11/03/2010
STAFF: lec
CHANGES:
1) archived:
   MLD_BSSBSB.py
   MLD_RHData.py
2) these are not in the index.html but are in /logs/ftp/public/*/*/xferlog
   PRB_CloneLibrarycDNA.py
   PRB_CloneLibrary.sql

TAG: reports_db-4-4-0-6
DATE: 10/13/2010
STAFF: lec
CHANGES:
1) TR10393/GO_gene_association_nonmouse.py

TAG: reports_db-4-4-0-5
DATE: 09/30/2010
STAFF: dbm
CHANGES: TR8688
1) renamed nightly_reports.sh to nightly_reports.csh and fixed logging
2) renamed weekly_reports.sh to weekly_reports.csh and fixed logging
3) renamed monthly_reports.sh to monthly_reports.csh and fixed logging
4) renamed mgimarkerfeed_reports.sh to mgimarkerfeed_reports.cs and
   fixed logging
5) renamed inparanoid/inparanoid.sh to inparanoid.csh
6) renamed ncbilinkout/ncbilinkout.sh to ncbilinkout.csh
7) Configuration.defaults: added PUBDAILY, PUBWEEKLY and PUBMONTHLY
   settings and fixed spacing

TAG: reports_db-4-4-0-4
DATE: 09/14/2010
STAFF: lec
CHANGES:
1) TR10336/MGI_BioTypeConflict.py

TAG: reports_db-4-4-0-3
DATE: 09/02/2010
STAFF: lec
CHANGES:
1) fix index.html.default/MGI_GTGUP

TAG: reports_db-4-4-0-2
TAG: reports_db-4-4-0-1
DATE: 08/18/2010
STAFF: lec
CHANGES:
1) TR6839/merge tr6829 to trunk
2) TR10280/MGI_PhenotypicAllele.py/removed _AlleleType_key
   that was put in for testing

TAG: reports_db-4-3-4-16
DATE: 08/17/2010
STAFF: lec
CHANGES: 
1) TR10321/daily/GO_gp2protein.py

TAG: reports_db-tr6839-6
TAG: reports_db-tr6839-5
DATE: 08/17/2010
STAFF: lec
CHANGES: TR10321
1) daily/GO_gp2protein.py

TAG: reports_db-tr6839-4
TAG: reports_db-tr6839-3
TAG: reports_db-tr6839-2
DATE: 07/28/2010
STAFF: lec
CHANGES: TR6839
1) daily/MGI_GTGUP.py
   added Marker Features (MRK_MCV_Cache)

TAG: reports_db-tr6839-1
DATE: 07/13/2010
STAFF: lec
CHANGES: TR6839
1) GO_gene_association.py
2) GO_gp2protein.py
3) GXD_NonGeneMarkers.py

TAG: reports_db-tr6839-BP
DATE: 07/132010
STAFF: lec
CHANGES: 
1) branch point tag for TR6839

TAG: reports_db-4-3-4-15
DATE: 07/06/2010
STAFF: lec
CHANGES: 
1) TR10280/MGI_PhenotypicAllele.py

TAG: reports_db-4-3-4-14
TAG: reports_db-4-3-4-13
DATE: 06/22/2010
STAFF: lec
CHANGES: 
1) GO_gene_association.py; fix Vega/Ensembl prefix
2) GO_gene_association_nonmouse.py; TR10260

TAG: reports_db-4-3-4-12
TAG: reports_db-4-3-4-11
DATE: 06/10/2010
DATE: 06/15/2010
STAFF: lec
CHANGES: 
1) GO_gene_association.py; clean up hashes

TAG: reports_db-4-3-4-10
DATE: 06/03/2010
STAFF: lec
CHANGES: 
1) GO_gene_association.py; fix bug in column 15/TAB

TAG: reports_db-4-3-4-9
DATE: 05/25/2010
STAFF: lec
CHANGES: 
1) TR10049/daily/HMD_Synonyms.py
2) TR10178/MGI_Coordinate.py
3) TR10179/MGI_PhenoGenoMP.py

TAG: reports_db-4-3-4-8
DATE: 05/19/2010
STAFF: lec
CHANGES: daily/GO_gene_association.py

TAG: reports_db-4-3-4-7
DATE: 05/19/2010
STAFF: dbm
CHANGES: weekly/ALL_CRE.py: Changed PROD_MGI to PROD1_MGI (TR10039)

TAG: reports_db-4-3-4-6
DATE: 05/12/2010
STAFF: mhall
CHANGES: MAP_Mapping.py was creating a file called mapping.txt in error, this has been removed.

TAG: reports_db-4-3-4-5
TAG: reports_db-4-3-4-4
DATE: 05/07/2010
STAFF: mhall
CHANGES: Minor tweaks to the index page to fix some formatting issues.

TAG: reports_db-4-3-4-3
DATE: 05/06/2010
STAFF: lec
CHANGES: 
TR9777
1) daily/GO_gene_association.py; changed 'uniprotload' back to 'swissload' for 4..3.4 release

TAG: reports_db-4-3-4-2
DATE: 05/03/2010
STAFF: mhall
CHANGES:  Alpha build tag.

TAG: reports_db-4-3-3-13
DATE: 04/29/2010
STAFF: lec
CHANGES: 
TR10202
1) index.html.default

TAG: reports_db-4-3-3-12
DATE: 04/29/2010
STAFF: lec
CHANGES: 
TR9777
1) daily/GO_gene_association.py; changed 'swissload' to 'uniprotload'

TAG: reports_db-tr10173-1
TAG: reports_db-4-3-4-1
DATE: 04/28/2010
STAFF: mhall
CHANGES:  Initial Dev build tag.

TAG: reports_db-tr10173-BP
DATE: 04/20/2010
STAFF: mhall
CHANGES:

TAG: reports_db-4-3-3-11
DATE: 04/20/2010
STAFF: dbm
CHANGES: 
TR10163
1) weekly/ALL_CRE.py - Added by Joel (TR9848)

TAG: reports_db-4-3-3-10
DATE: 04/15/2010
STAFF: lec
CHANGES: 
TR10163
1) monthly/GO_gene_association_nonmouse.py

TAG: reports_db-4-3-3-9
TAG: reports_db-4-3-3-8
DATE: 04/01/2010
STAFF: dbm
CHANGES: TR10129 and TR10130
1) index.html.default: Affy report link changes

TAG: reports_db-4-3-3-7
DATE: 03/31/2010
STAFF: lec
CHANGES: TR10049/commented out this report
20. Human and Mouse Orthology with Synonyms
until further notice

TAG: reports_db-4-3-3-6
TAG: reports_db-4-3-3-5
DATE: 03/18/2010
STAFF: sc
CHANGES: MGI_BiotypeConflict.py - changed report header wording

TAG: reports_db-4-3-3-4
TAG: reports_db-4-3-3-3
DATE: 03/15/2010
STAFF: sc
CHANGES: TR9774

TAG: reports_db-4-3-3-2
TAG: reports_db-4-3-3-1
DATE: 03/02/2010,03/11/2010
STAFF: lec
CHANGES:
1) TR9239/added daily/MGI_BioTypeConflict.py

TAG: reports_db-4-3-2-4
DATE: 03/02/2010
STAFF: lec
CHANGES:
1) TR10035/GO_gene_association.py

TAG: reports_db-4-3-2-3
DATE: 02/02/2010
STAFF: mhall
CHANGES:
1) TR9901, Released column 16.

TAG: reports_db-4-3-2-2
DATE: 01/19/2010
STAFF: lec
CHANGES: 
1) TR10042;MGI_Recombinase_Full.py

TAG: reports_db-4-3-2-1
DATE: 01/07/2010
STAFF: lec
CHANGES: 
1) TR9683/MGI_QTLAllele.py

TAG: reports_db-4-3-1-11
TAG: reports_db-4-3-1-10
DATE: 10/28/2009
STAFF: lec
CHANGES: 
1) TR9892/HMD_OMIM.py; index.html.default

TAG: reports_db-4-3-1-9
DATE: 10/21/2009
STAFF: lec, sc
CHANGES: 
1) per Martin, can remove anatdict/ADinGOformat.py
2) KOMP_Allele.py - added ldbKey 126 KOMP-CSD-Project

TAG: reports_db-4-3-1-8
TAG: reports_db-4-3-1-7
TAG: reports_db-4-3-1-6
DATE: 10/20/2009
STAFF: lec
CHANGES: defect#26/MGI_Recombinase_Full.py

TAG: reports_db-4-3-1-5
TAG: reports_db-4-3-1-4
DATE: 10/13/2009,10/20/2009
STAFF: lec
CHANGES: TR9887/mgiMarkerFeed.py

TAG: reports_db-4-3-1-3
TAG: reports_db-4-3-1-2
TAG: reports_db-4-3-1-1
TAG: reports_db-4-3-0-8
DATE: 10/01/2009,10/13/2009
STAFF: lec
CHANGES: TR9807/Cre Allele report/MGI_Recombinase_Full.py

TAG: reports_db-4-3-0-7
DATE: 09/25/2009
STAFF: dbm
CHANGES: TR9711/ALL_OMIM.py; Tested and tagged for the new report that
         Joel converted from a custom SQL.

TAG: reports_db-4-3-0-6
DATE: 09/22/2009
STAFF: lec
CHANGES: TR9838/mgiMarkerFeed.py; more fixes...see code for details

TAG: reports_db-4-3-0-5
DATE: 09/10/2009
STAFF: lec
CHANGES: TR9831/mgiMarkerFeed.py; add status = Autoload to Alleles

TAG: reports_db-4-3-0-4
DATE: 08/21/2009
STAFF: mhall
CHANGES: Minor changes to the html file that the public reports uses.

TAG: reports_db-4-3-0-3
DATE: 08/20/2009
STAFF: mhall
CHANGES: Changes to the GO Gene Association report as per tr9919
Also merged branch tr9592 to the trunk

TAG: reports_db-4-3-0-2
DATE: 08/09/2009
STAFF: dbm
CHANGES: Remove MGI_UnassociatedGeneTraps.rpt from index file

TAG: reports_db-4-3-0-1
DATE: 07/14/2009
STAFF: lec
CHANGES: merge of TR7493 branch gene trap less filling

TAG: reports_db-tr7493-2
TAG: reports_db-tr7493-1
DATE: 5/27/2009, 07/14/2009
STAFF: lec
CHANGES: gene trap less filling

TAG: reports_db-tr7493-BP
DATE: 5/27/2009
STAFF: lec
CHANGES:
1) branch point tag for TR7493/gene trap less filling

TAG: reports_db-tr9592-BP
DATE: 4/16/2009
STAFF: mhall
CHANGES:
1) branch point tag for TR9199 Please note that the branch tag was incorrect for this one, but we decided to just live with it.

TAG: reports_db-4-2-1-4
DATE: 04/07/2009
STAFF: dbm
CHANGES:
1) Changed inparanoid.sh to use the sp_to_fasta tool instead of sp2fasta.
   The sp2fasta tool cannot handle new embl DE line format (TR9607).
2) Changed config file to include settings for sp_to_fasta and to override
   the common PERLLIB setting with the one needed by sp_to_fasta.
3) Added a note to the weekly version of MRK_ENSEMBL.py and MRK_Sequence.py
   to explain why they are needed when daily versions already exist.

TAG: reports_db-4-2-1-3
DATE: 04/02/2009
STAFF: dbm
CHANGES:
1) Renamed index.html to index.html.default
2) Changed Install to copy index.html.default to index.html and substitute
   the proper FTP URL

TAG: reports_db-4-2-1-2
DATE: 03/24/2009
STAFF: lec
CHANGES:
1) TR9569/monthly/GO_gene_association_nonmouse.py
2) TR9568/daily/MRK_GXDAssay.py

TAG: reports_db-4-2-1-1
DATE: 03/18/2009
STAFF: dbm
CHANGES:
1) Merged tr9440 branch to the trunk for 4.21 release
2) Added links to index.html for Microarray Annotation files

TAG: reports_db-4-2-0-4
TAG: reports_db-4-2-0-3
DATE: 3/11/2009
STAFF: lec
CHANGES:
1) TR9506/Chr missing from MGI_Coordinate.rpt
2) TR9517/problem running public/qc reports that join to IMSR
   moved MGI_Knockout.py from daily to weekly

TAG: reports_db-tr9440-2
TAG: reports_db-tr9440-1
DATE: 03/02/2008
STAFF: dbm
CHANGES:
1) Added microarray annotation files to index.html for 4.21 release

TAG: reports_db-tr9440-BP
DATE: 2/23/2009
STAFF: dbm
CHANGES:
1) branch point tag for TR9440 (4.21 release)

TAG: reports_db-4-2-0-2
DATE: 01/30/2009
STAFF: mhall
CHANGES:
1) TR 9449/GO_refGenomeGenes.py, GO_completedAnnotations.py

TAG: reports_db-4-2-0-1
DATE: 01/15/2009
STAFF: lec
CHANGES:
1) TR 9446/MRK_Synonym, MRK_List1, MRK_List2, MRK_List3, MRK_List4

TAG: reports_db-4-1-2-9
DATE: 10/22/2008
STAFF: lec
CHANGES:
1) TR 9325/GO_gp2protein.py

TAG: reports_db-4-1-2-9
DATE: 10/22/2008
STAFF: lec
CHANGES:
1) TR 9325/GO_gp2protein.py

TAG: reports_db-4-1-2-8
TAG: reports_db-4-1-2-7
TAG: reports_db-4-1-2-6
TAG: reports_db-4-1-2-5
TAG: reports_db-4-1-2-4
TAG: reports_db-4-1-2-3
TAG: reports_db-4-1-2-2
DATE: 10/07/2008
STAFF: lec
CHANGES:
1) TR 8776; add ncbilinkout directory

TAG: reports_db-4-1-2-1
DATE: 09/24/2008
STAFF: dbm
CHANGES:
1) TR 9270; Remove marker type restriction

TAG: reports_db-4-1-1-6
DATE: 09/16/2008
STAFF: dbm
CHANGES:
1) TR 9262/index.html

TAG: reports_db-4-1-1-5
DATE: 09/11/2008
STAFF: lec
CHANGES:
1) TR 9207/KOMP_Allele.py
2) TR 9152/MGI_Coordinate.py

TAG: reports_db-4-1-1-4
DATE: 08/11/2008
STAFF: dbm
CHANGES:
1) GO_gene_association_nonmouse.py - search for UniProtKB instead of UniProt
   in the inferredFrom field (per Harold)

TAG: reports_db-4-1-1-3
DATE: 07/30/2008
STAFF: lec
CHANGES:
1) TR9116/MGI_MouseHumanSequence.py; need to check _LogicalDB_key for Markers

TAG: reports_db-4-1-1-2
DATE: 07/25/2008
STAFF: jer
CHANGES:
1) TR9120: Added tab-delimited versions of MRK_List1, MRK_List2,
           MRK_List3, MRK_List4 and MRK_Synonym.

TAG: reports_db-4-1-1-1
DATE: 07/24/2008
STAFF: lec
CHANGES:
1) TR9134/GO_gene_association.py

TAG: reports_db-4-1-0-2
DATE: 6/23/2008
STAFF: dbm
CHANGES:
1) Fixed bug in index.html where FTP server was hardcoded to devftp

TAG: reports_db-4-1-0-1
DATE: 5/30/2008
STAFF: dbm
CHANGES:
1) Merged tr8528 branch to the trunk

TAG: reports_db-4-0-2-3
DATE: 05/27/2008
STAFF: lec
CHANGES:
1) fix to daily/mgiMarkerFeed.py after 4.02 release

TAG: reports_db-4-0-2-2
DATE: 5/19/2008
STAFF: dbm
CHANGES:
1) TR8994: change to GO_gp2protein.py to include with 4.02 release

TAG: reports_db-4-0-2-1
DATE: 5/13/2008
STAFF: lec
CHANGES:
1) Merged TR8747 branch to trunk

TAG: reports_db-tr8528-1
DATE: 5/9/2008
STAFF: dbm
CHANGES:
1) Modified MGI_Coordinate.py and index.html for Build 37

TAG: reports_db-4-0-1-3
DATE: 4/29/2008
STAFF: lec
CHANGES:
1) TR8963/HMD_HumanPhenotype

TAG: reports_db-4-0-1-2
DATE: 4/28/2008
STAFF: dbm
CHANGES:
1) Allow HMD_HGNC_Accession.rpt to display entire gene name (TR8960).

TAG: reports_db-tr8528-BP
DATE: 4/24/2008
STAFF: dbm
CHANGES:
1) branch point tag for TR8528 (Build 37)

TAG: reports_db-tr8747-3
TAG: reports_db-tr8747-2
TAG: reports_db-tr8747-1
DATE: 5/7/2008
DATE: 4/23/2008
STAFF: lec
CHANGES:
1) MRK_GXDAssay; exclude new assays
   mgiMarkerFeed: strain attribute replaces strain type
   PRB_Strain1.sql: removed
   PRB_Strain2.sql: removed
2) MGI_Strain.py (new)
3) MGI_StrainAllInbred (archive)

TAG: reports_db-tr8747-BP
DATE: 4/23/2008
STAFF: lec
CHANGES:
1) branch point tag for TR8747 (4.B)

TAG: reports_db-4-0-1-1
DATE: 4/4/2008
STAFF: dbm
CHANGES:
1) Modified GO_gene_association_nonmouse.py to include ISS, ISO, ISA and ISM
   evidence codes (TR 8900).

TAG: reports_db-4-0-0-2
DATE: 3/10/2008
STAFF: dbm
CHANGES:
1) Added build number next the file links for MGI_Coordinate.rpt,
   MGI_GTGUP.gff and MGI_MouseHumanSequence.rpt (TR 8837).

TAG: reports_db-4-0-0-1
DATE: 2/20/2008
STAFF: dbm
CHANGES:
1) Removed the general statistics section because the stats are provided
   in the WI as of the 4.0 release.

TAG: reports_db-3-5-4-12
DATE: 1/17/2008
STAFF: dbm
CHANGES:
1) Fixed bug in HMD_OxfordGrid.py where the temp table needed to drop between
   calls to processOrganism() method to avoid an SQL error.

TAG: reports_db-3-5-4-11
DATE: 1/7/2008
STAFF: dbm
CHANGES:
1) TR 8697; GO_gp2protein.py

TAG: reports_db-3-5-4-10
DATE: 12/20/2007
STAFF: dbm
CHANGES:
1) Changed GXD report title to contain "Literature Content Records" instead
   of "Literature Index Records" to prepare for 4.0, per Connie.

TAG: reports_db-3-5-4-9
DATE: 12/14/2007
STAFF: dbm
CHANGES:
1) Remove extra '|' characters from the InferredFrom field and use the GOA
   assignedBy value in the last column for GOA annotations (TR 8654)

TAG: reports_db-3-5-4-8
TAG: reports_db-3-5-4-7
TAG: reports_db-3-5-4-6
DATE: 11/16/2007
STAFF: dbm
CHANGES:
1) Modified MGI_InParanoid_FASTA.py to create an addition fasta file
   called "aaseq.10090.fasta" (TR 8630).
2) Modified weekly_reports.sh to copy the new file.

TAG: reports_db-3-5-4-5
DATE: 11/8/2007
STAFF: dbm
CHANGES:
1) Modified inparanoid/inparanoid.sh to use the "-c" option with gunzip
   to create the input file without overwriting the "gz" file.
2) Modified weekly_reports.sh to copy the inparanoid file to the
   FTP site (TR 8610).

TAG: reports_db-3-5-4-4
DATE: 11/7/2007
STAFF: dbm
CHANGES:
1) Modified MRK_NomenUpdates.py to create an additional tab-delimited
   version of the same report (TR 8601).
2) Modified index.html to have a link to the new report, updated the
   nomenclature report headings and fixed the FTP server URL so that the
   Install script can substitute the proper setting ("devftp" or "ftp").
3) Modified Install script to substitute FTPURL in index.html.

TAG: reports_db-3-5-4-3
DATE: 10/01/2007
STAFF: dbm
CHANGES:
1) Modified GO_gene_association.py to prefix MGI IDs in Inferred From
   column with an extra "MGI:" (TR 8504)

TAG: reports_db-3-5-4-2
DATE: 08/30/2007
STAFF: dbm
CHANGES:
1) Added HMD_HumanDisease.py (TR 8277)

TAG: reports_db-3-5-4-1
DATE: 08/27/2007
STAFF: jmason
CHANGES:
1) Renamed MGI_KOMP_AllGenes to MGI_AllGenes
2) Renamed MGI_KOMP_Mutations to MGI_Mutations
3) Changed header text appropriately

TAG: reports_db-3-5-3-5
DATE: 04/27/2007
STAFF: dbm
CHANGES:
1) Added J-Numbers and PubMed IDs to HMD_HumanSequence.py (TR 8277)

TAG: reports_db-3-5-3-4
DATE: 04/23/2007
STAFF: dbm
CHANGES:
1) Added VEGA coordinates to MGI_MouseHumanSequence.py (TR 8265)

TAG: reports_db-3-5-3-3
DATE: 04/20/2007
STAFF: dbm
CHANGES:
1) Added ES_CellLine.rpt to monthly and index.html (TR 8214)

TAG: reports_db-3-5-3-2
TAG: reports_db-3-5-3-1
DATE: 04/13/2007
STAFF: sc
CHANGES: Gene trap lite 
1) Added MGI_GeneTrap.rpt to monthly and index.html
2) Added MGI_UnassociatedGeneTraps.rpt to index.html
   (This is created and placed on ftp site by gtpipeline)

TAG: reports_db-3-5-1-46
DATE: 02/02/2007
STAFF: lec
CHANGES:
1) updated KOMP paths

TAG: reports_db-3-5-1-45
TAG: reports_db-3-5-1-44
DATE: 01/29/2007
STAFF: lec
CHANGES:
1) TR8120; MGI_GTGUP.py; moved from qcr reports

TAG: reports_db-3-5-1-43
DATE: 01/24/2007
STAFF: lec
CHANGES:
1) TR8122; GO_gene_association.py

TAG: reports_db-3-5-1-42
TAG: reports_db-3-5-1-41
TAG: reports_db-3-5-1-40
TAG: reports_db-3-5-1-39
DATE: 01/18/2007
STAFF: lec
CHANGES:
1) added VEGA columns to MGI_Coordinate.rpt

TAG: reports_db-3-5-1-38
TAG: reports_db-3-5-1-37
DATE: 01/10/2007
STAFF: lec
CHANGES:
1) added OMIM data

TAG: reports_db-3-5-1-36
DATE: 12/19/2006
STAFF: lec
CHANGES:
1) TR 8028/KOMP reports

TAG: reports_db-3-5-1-35
DATE: 12/14/2006
STAFF: lec
CHANGES:
1) inparanoid fix

TAG: reports_db-3-5-1-34
TAG: reports_db-3-5-1-33
DATE: 12/12/2006
STAFF: lec
CHANGES:
1) inparanoid fix

TAG: reports_db-3-5-1-32
TAG: reports_db-3-5-1-31
DATE: 12/07/2006
STAFF: lec
CHANGES:
1) TR8043

TAG: reports_db-3-5-1-30
DATE: 11/30/2006
STAFF: lec
CHANGES:
1) fixed index.html

TAG: reports_db-3-5-1-29
TAG: reports_db-3-5-1-28
TAG: reports_db-3-5-1-27
DATE: 11/15/2006
STAFF: lec
CHANGES:
1) TR8001; index.html
2) mgiconfig FTP

TAG: reports_db-3-5-1-26
DATE: 11/14/2006
STAFF: lec
CHANGES:
1) TR8001; index.html

TAG: reports_db-3-5-1-25
DATE: 11/6/2006
STAFF: lec
CHANGES:
1) fix monthtly/GO_gene_association_nonmouse.py; removed duplicate code

TAG: reports_db-3-5-1-24
TAG: reports_db-3-5-1-23
DATE: 11/3/2006
STAFF: lec
CHANGES:
1) fix rcp in nightly script
2) fix Configuration.default: goa

TAG: reports_db-3-5-1-22
DATE: 11/1/2006
STAFF: lec
CHANGES:
1) TR 7994

TAG: reports_db-3-5-1-21
DATE: 10/30/2006
STAFF: lec
CHANGES:
1) TR 7926/GO_gene_association.py

TAG: reports_db-3-5-1-20
TAG: reports_db-3-5-1-19
TAG: reports_db-3-5-1-18
DATE: 10/26/2006
STAFF: lec
CHANGES:
1) TR7492/HMD_Organism.py

TAG: reports_db-3-5-1-17
TAG: reports_db-3-5-1-16
DATE: 10/13/2006
STAFF: lec
CHANGES:
1) TR7967/goa.py;revisited

TAG: reports_db-3-5-1-15
TAG: reports_db-3-5-1-14
DATE: 10/12/2006
STAFF: lec
CHANGES:
1) TR7967/goa.py
2) TR 7968/MGI_Coordinate.py

TAG: reports_db-3-5-1-13
TAG: reports_db-3-5-1-12
DATE: 10/12/2006
STAFF: lec
CHANGES:
1) TR7943; removed trailer
2) TR7943; new header

TAG: reports_db-3-5-1-11
DATE: 10/10/2006
STAFF: lec
CHANGES:
1) TR7943; removed trailer
2) MRK_Sequence.py; only include markers with at least one sequence

TAG: reports_db-3-5-1-10
DATE: 10/06/2006
STAFF: lec
CHANGES:
1) TR7943; removed trailer

TAG: reports_db-3-5-1-9
TAG: reports_db-3-5-1-8
DATE: 10/04/2006
STAFF: lec
CHANGES:
1) TR7865; GO Unknowns
2) Converted HMD reports to use MRK_Homology_Cache

TAG: reports_db-3-5-1-7
DATE: 10/03/2006
STAFF: lec
CHANGES:
1) build36
2) HMD_Human.py, HMD_Rat.py; convert from regex to re

TAG: reports_db-3-5-1-6
DATE: 09/22/2006
STAFF: lec
CHANGES:
1) build36

TAG: reports_db-3-5-1-5
DATE: 09/19/2006
STAFF: lec
CHANGES:
1) build36
2) TR 7409/GOA

TAG: reports_db-3-5-1-4
TAG: reports_db-3-5-1-3
DATE: 09/14/2006
STAFF: lec
CHANGES:
1) build36
2) TR 7647
3) TR 7904

TAG: reports_db-3-5-1-2
DATE: 09/14/2006
STAFF: lec
CHANGES:
1) build36
2) TR 7647

TAG: reports_db-3-5-1-1
DATE: 09/06/2006
STAFF: lec
CHANGES:
1) build36; merge

TAG: reports_db-build36-1
DATE: 07/12/2006
STAFF: lec
CHANGES:
1) build36

TAG: reports_db-build36-BP
DATE: 07/12/2006
STAFF: lec
CHANGES:
1) branch point tag for build36

TAG: reports_db-3-5-0-11
TAG: reports_db-3-5-0-10
TAG: reports_db-3-5-0-9
DATE: 07/03/2006
STAFF: lec
CHANGES:
1) mgiconfig merge

TAG: reports_db-mgiconfig-3
DATE: 06/16/2006
STAFF: lec
CHANGES:
1) mgiconfig

TAG: reports_db-mgiconfig-2
TAG: reports_db-mgiconfig-1
DATE: 06/14/2006
STAFF: lec
CHANGES:
1) mgiconfig

TAG: reports_db-BP-mgiconfig
DATE: 06/14/2006
STAFF: lec
CHANGES:
1) branch point tag for mgiconfig

TAG: reports_db-3-5-0-8
DATE: 05/24/2006
STAFF: lec
CHANGES:
1) MGI 3.5

TAG: reports_db-3-5-0-7
TAG: reports_db-3-5-0-6
DATE: 05/17/2006
STAFF: lec
CHANGES:
1) MGI 3.5
2) TR 7685

TAG: reports_db-3-5-0-5
DATE: 05/11/2006
STAFF: lec
CHANGES:
1) MGI 3.5
2) mgiconfig

TAG: reports_db-3-5-0-4
TAG: reports_db-3-5-0-3
DATE: 05/10/2006
STAFF: lec
CHANGES:
1) MGI 3.5

TAG: reports_db-3-5-0-2
DATE: 04/27/2006
STAFF: lec
CHANGES:
1) MGI 3.5

TAG: reports_db-3-5-0-1
DATE: 04/24/2006
STAFF: lec
CHANGES:
1) merged MGI 3.5 tr7062 branch

TAG: reports_db-3-4-4-1
DATE: 04/24/2006
STAFF: lec
CHANGES:
1) TR 7617; added GO stats to MGD_Stats.sql

TAG: reports_db-3-4-0-15
DATE: 03/24/2006
STAFF: lec
CHANGES:
1) mgimarkerfeed_reports.sh; comment out of nightly_reports.sh

TAG: reports_db-3-4-0-14
DATE: 02/15/2006
STAFF: lec
CHANGES:
1) mgimarkerfeed.py; include all strain/marker associations 

TAG: reports_db-3-4-0-13
TAG: reports_db-3-4-0-12
TAG: reports_db-3-4-0-11
DATE: 02/15/2006
STAFF: lec
CHANGES:
1) TR 7418; daily/MGI_Knockout.py
2) GO_gene_association_nonmouse; changed file name

TAG: reports_db-3-4-0-10
TAG: reports_db-3-4-0-9
DATE: 02/10/2006
STAFF: lec
CHANGES:
1) TR 7418; daily/MGI_Knockout.py

TAG: reports_db-3-4-0-8
TAG: reports_db-3-4-0-7
DATE: 02/01/2006
STAFF: lec
CHANGES:
1) TR 7424; monthly/GO_gene_association_nonmouse.py; new format
2) TR 7418; daily/MGI_Knockout.py

TAG: reports_db-3-4-0-6
DATE: 01/20/2006
STAFF: lec
CHANGES:
1) mgiMarkerFeed; strain_marker.bcp

TAG: reports_db-3-4-0-5
DATE: 01/18/2006
STAFF: lec
CHANGES:
1) increased width of human chromosome in HMD reports

TAG: reports_db-3-4-0-4
DATE: 01/04/2006
STAFF: lec
CHANGES:
1) added RADAR_DBNAME to Configuration.default

TAG: reports_db-3-4-0-3
DATE: 11/18/2005
STAFF: lec
RELEASE: A
CHANGES:
1) PRB_CloneLibrarycDNA.py ; added clone ids

TAG: reports_db-3-4-0-2
DATE: 10/26/2005
STAFF: lec
RELEASE: A
CHANGES:
1) MGI 3.5

TAG: reports_db-3-4-0-1
DATE: 10/25/2005
STAFF: lec
RELEASE: A
CHANGES:
1) MGI 3.5

TAG: reports_db-3-3-0-9
TAG: reports_db-3-3-0-8
TAG: reports_db-3-3-0-7
TAG: reports_db-3-3-0-6
DATE: 10/25/2005
STAFF: lec
RELEASE: A
CHANGES:
1) TR 7173, GO_association.py; added PMID

TAG: reports_db-3-3-0-5
DATE: 10/19/2005
STAFF: lec
RELEASE: A
CHANGES:
1) TR 7173, GO_association.py; added PMID

TAG: reports_db-tr7062-6
DATE: 04/06/2006
STAFF: lec
CHANGES:
1) tag for MGI 3.5 (TR 7062)
2) converted regsub.gsub() to re.sub()

TAG: reports_db-tr7062-5
TAG: reports_db-tr7062-4
DATE: 03/23/2006
STAFF: lec
CHANGES:
1) tag for MGI 3.5 (TR 7062)

TAG: reports_db-tr7062-3
DATE: 12/08/2005
STAFF: lec
CHANGES:
1) tag for MGI 3.5 (TR 7062)

TAG: reports_db-tr7062-2
DATE: 12/05/2005
STAFF: lec
CHANGES:
1) tag for MGI 3.5 (TR 7062)

TAG: reports_db-tr7062-1
DATE: 11/22/2005
STAFF: lec
RELEASE: A
CHANGES:
1) tag for MGI 3.5 (TR 7062)

TAG: reports_db-BP-tr7062
DATE: 10/03/2005
STAFF: lec
RELEASE: A
CHANGES:
1) branch point for MGI 3.5 (TR 7062)

TAG: reports_db-3-3-0-4
DATE: 10/03/2005
STAFF: lec
RELEASE: A
CHANGES:
1) GO_association.py; replace SWALL w/ UniProt

TAG: reports_db-3-3-0-3
DATE: 09/20/2005
STAFF: lec
RELEASE: A
CHANGES:
1) TR 7131; PRB_CloneLibrarycDNA.py

TAG: reports_db-3-3-0-2
DATE: 08/25/2005
STAFF: lec
RELEASE: A
CHANGES:
1) OMIM
2) MGI_PhenoGenoMP.py fix

TAG: reports_db-3-3-0-1
DATE: 08/23/2005
STAFF: lec
RELEASE: A
CHANGES:
1) OMIM branch merge

TAG: reports_db-3-2-0-8
TAG: reports_db-3-2-0-7
DATE: 08/22/2005
STAFF: lec
RELEASE: A
CHANGES:
1) HMD_Human.py; fixed HMD_Human5.rpt
2) MRK_Sequence.py; exclude NP_, NR_ (TR 7033)
3) gene_association_nonmouse.py replaces GO_nonmouse.py

TAG: reports_db-3-2-0-6
DATE: 08/08/2005
STAFF: lec
RELEASE: A
CHANGES:
1) HMD_Human.py; added HMD_Human5.rpt

TAG: reports_db-3-2-0-5
DATE: 07/15/2005
STAFF: lec
RELEASE: A
CHANGES:
1) HMD_HGNC_Accession.py; added mouse EntrezGene ID

TAG: reports_db-omim-2
DATE: 08/10/2005
STAFF: lec
RELEASE: A
CHANGES:
1) OMIM

TAG: reports_db-omim-1
DATE: 08/09/2005
STAFF: lec
RELEASE: A
CHANGES:
1) OMIM

TAG: reports_db-BP-omim
DATE: 06/28/2005
STAFF: lec
RELEASE: A
CHANGES:
1) branch point for OMIM

TAG: reports_db-3-2-0-4
DATE: 06/03/2005
STAFF: lec
RELEASE: A
CHANGES:
1) MGI_PhenoGeno.py; (from customSQL 6820)

TAG: reports_db-3-2-0-3
DATE: 06/01/2005
STAFF: lec
RELEASE: A
CHANGES:
1) mgiMarkerFeed.py; added all markers (not just mouse) per csb.

TAG: reports_db-3-2-0-2
DATE: 05/10/2005
STAFF: lec
RELEASE: A
CHANGES:
1) TR 6782, MGI_PhenotypicAllele.py

TAG: reports_db-3-2-0-1
DATE: 04/22/2005
STAFF: lec
RELEASE: A
CHANGES:
1) MPR merge

TAG: reports_db-3-1-1-10
DATE: 03/18/2005
STAFF: lec
RELEASE: A
CHANGES: TR 6670, 6671
1) TR 6573/MGI_Coordinate.py

TAG: reports_db-mpr-4
DATE: 04/21/2005
STAFF: lec
RELEASE: A
CHANGES: 
1) MPR
2) Configuration.default

TAG: reports_db-mpr-3
DATE: 03/23/2005
STAFF: lec
RELEASE: A
CHANGES: 
1) MPR

TAG: reports_db-mpr-2
DATE: 03/22/2005
STAFF: lec
RELEASE: A
CHANGES: 
1) MPR

TAG: reports_db-mpr-1
DATE: 03/17/2005
STAFF: lec
RELEASE: A
CHANGES: 
1) MPR

TAG: reports_db-mpr-BP
DATE: 03/16/2005
STAFF: lec
RELEASE: A
CHANGES: 
1) branch point tag for MPR

TAG: reports_db-3-1-1-9
TAG: reports_db-3-1-1-8
DATE: 02/22/2005
STAFF: lec
RELEASE: A
CHANGES: MGI 3.11
1) TR 6573/MGI_Coordinate.py

TAG: reports_db-3-1-1-7
DATE: 02/09/2005
STAFF: lec
RELEASE: A
CHANGES: MGI 3.11
1) HMD_OMIM.py

TAG: reports_db-3-1-1-6
TAG: reports_db-3-1-1-5
DATE: 01/27/2005
STAFF: lec
RELEASE: A
CHANGES: MGI 3.11
1) TR 6500;inparanoid

TAG: reports_db-3-1-1-4
DATE: 01/27/2005
STAFF: lec
RELEASE: A
CHANGES: MGI 3.11
1) TR 6529;MRK_Sequence.py

TAG: reports_db-3-1-1-3
TAG: reports_db-3-1-1-2
TAG: reports_db-3-1-1-1
DATE: 01/26/2005
STAFF: lec
RELEASE: A
CHANGES: MGI 3.11
1) merge from maint6300 branch

TAG: reports_db-3-1-0-13
TAG: reports_db-3-1-0-12
DATE: 01/18/2005
STAFF: lec
RELEASE: A
CHANGES: MGI 3.1
1) TR6487; MRK_GXD.py, MRK_GXDAssay.py

TAG: reports_db-3-1-0-11
TAG: reports_db-3-1-0-10
TAG: reports_db-3-1-0-9
DATE: 01/13/2005
STAFF: lec
RELEASE: A
CHANGES: MGI 3.1
1) TR5939; EntrezGene conversion

TAG: reports_db-3-1-0-8
TAG: reports_db-3-1-0-7
TAG: reports_db-3-1-0-6
TAG: reports_db-3-1-0-5
DATE: 12/23/2004
STAFF: lec
RELEASE: A
CHANGES: MGI 3.1
1) TR6436; EntrezGene conversion (HMD_HumanSequence.py, HMD_OMIM.py)
2) new reportlib.py that sets db.useOneConnection and logging

TAG: reports_db-3-1-0-4
TAG: reports_db-3-1-0-3
DATE: 12/22/2004
STAFF: lec
RELEASE: A
CHANGES: MGI 3.1
1) TR6436; EntrezGene conversion (HMD_HumanSequence.py, HMD_OMIM.py)

TAG: reports_db-maint6300-4
TAG: reports_db-maint6300-3
TAG: reports_db-maint6300-2
DATE: 01/05/2005
STAFF: lec
RELEASE: A
CHANGES: 
1) TR 6300; TR 5686; MGI_Synonym
2) TR 5939

TAG: reports_db-maint6300-1
DATE: 12/22/2004
STAFF: lec
RELEASE: A
CHANGES: 
1) TR 6300; TR 5686; MGI_Synonym

TAG: reports_db-maint6300-BP
DATE: 12/21/2004
STAFF: lec
RELEASE: A
CHANGES: 
1) branch point tag for TR 6300 (MGI 3.11)

TAG: reports_db-3-1-0-2
TAG: reports_db-3-1-0-1
DATE: 12/16/2004
STAFF: lec
RELEASE: A
CHANGES: MGI 3.1
1) MRK_Dump2.py fix

TAG: reports_db-22-0-7
TAG: reports_db-22-0-6
DATE: 11/29/2004
STAFF: lec
RELEASE: A
CHANGES: MGI 3.1
1) MRK_Sequence.py

TAG: reports_db-22-0-5
TAG: reports_db-22-0-4
TAG: reports_db-22-0-3
DATE: 11/22/2004
STAFF: lec
RELEASE: A
CHANGES: MGI 3.1
1) TR 6284, GO_nonmouse.py (replaced GO_GOA.py)
2) TR 6103

TAG: reports_db-22-0-2
DATE: 11/16/2004
STAFF: lec
RELEASE: A
CHANGES: MGI 3.1
1) removed PRB_ESTMapped.py

TAG: reports_db-22-0-1
DATE: 11/08/2004
STAFF: lec
RELEASE: A
CHANGES: MGI 3.1
1) patch302 merge

TAG: reports_db-22-0-0
DATE: 10/08/2004
STAFF: lec
RELEASE: A
CHANGES: MGI 3.1
1) mgimarkerfeed

TAG: reports_db-21-0-10
DATE: 11/08/2004
STAFF: lec
RELEASE: A
CHANGES: MGI 3.02, TR 6284 (GO_GOA.py)

TAG: reports_db-21-0-9
DATE: 11/02/2004
STAFF: lec
RELEASE: A
CHANGES: MGI 3.02, TR 6284 (GO_GOA.py)

TAG: reports_db-21-0-8
DATE: 08/24/2004
STAFF: lec
RELEASE: A
CHANGES: TR 5996 fix

TAG: reports_db-21-0-7
DATE: 08/19/2004
STAFF: lec
RELEASE: A
CHANGES: TR 6039

TAG: reports_db-21-0-6
DATE: 08/16/2004
STAFF: lec
RELEASE: A
CHANGES: TR 6105

TAG: reports_db-21-0-5
TAG: reports_db-21-0-4
DATE: 07/29/2004
STAFF: lec
RELEASE: A
CHANGES: TR 5611, 5996, 5815

TAG: reports_db-21-0-3
DATE: 07/22/2004
STAFF: lec
RELEASE: A
CHANGES: MGI 3.01

TAG: reports_db-21-0-2
DATE: 07/07/2004
STAFF: lec
RELEASE: A
CHANGES: MGI 3.01, TR 6015

TAG: reports_db-21-0-1
DATE: 07/01/2004
STAFF: lec
RELEASE: A
CHANGES: MGI 3.01

TAG: reports_db-21-0-0
DATE: 06/29/2004
STAFF: lec
RELEASE: A
CHANGES: MGI 3.01

TAG: reports_db-20-0-7
DATE: 06/17/2004
STAFF: lec
RELEASE: A
CHANGES:
a) GO_gene_association.py
b) BIB_PubMed.py

TAG: reports_db-20-0-6
DATE: 05/19/2004
STAFF: lec
RELEASE: A
CHANGES:
a) convert ???_Acc_View to ACC_Accession
b) PRB_CloneSet*

TAG: reports_db-20-0-5
DATE: 05/14/2004
STAFF: lec
RELEASE: A
CHANGES:
a) TR 5818

TAG: reports_db-20-0-4
DATE: 05/04/2004
STAFF: lec
RELEASE: A
CHANGES:
a) TR 5637

TAG: reports_db-20-0-3
TAG: reports_db-20-0-2
DATE: 04/29/2004
STAFF: lec
RELEASE: A
CHANGES:
a) JSAM

TAG: reports_db-20-0-1
DATE: 04/07/2004
STAFF: lec
RELEASE: A
CHANGES:
a) JSAM

TAG: reports_db-20-0-0
DATE: 03/05/2004
STAFF: lec
RELEASE: A
CHANGES:
a) JSAM

TAG: reports_db-19-0-8-mgi298_BP
DATE: 02/09/2004
STAFF: lec
RELEASE: A
CHANGES:
a) branch point for MGI 2.98 production

TAG: reports_db-19-0-8
DATE: 02/09/2004
STAFF: lec
RELEASE: A
CHANGES:
a) fix MRK_List3.sql, MRK_List4.sql

TAG: reports_db-19-0-7
DATE: 02/06/2004
STAFF: lec
RELEASE: A
CHANGES:
a) review MRK_Reference.py to improve performance

TAG: reports_db-19-0-6
DATE: 02/04/2004
STAFF: lec
RELEASE: A
CHANGES:
a) TR 5539; HMD_RatHuman.py (new)

TAG: reports_db-19-0-5
DATE: 02/03/2004
STAFF: lec
RELEASE: A
CHANGES:
a) TR 5539; HMD_Rat.py replacing HMD_Rat*.sql per RGD

TAG: reports_db-19-0-4
DATE: 01/27/2004
STAFF: lec
RELEASE: A
CHANGES:
a) TR 5517; fixed weekly/MRK_NomenUpdates.py;Configuration.default

TAG: reports_db-19-0-3
TAG: reports_db-19-0-2
DATE: 01/20/2004
STAFF: lec
RELEASE: A
CHANGES:
a) TR 5485; MRK_Ensembl_Pheno.py

TAG: reports_db-19-0-1
DATE: 01/14/2004
STAFF: lec
RELEASE: A
CHANGES:
a) use "rcp" instead of "cp" to avoid using /net

TAG: reports_db-19-0-0
DATE: 12/19/2003
STAFF: lec
RELEASE: A
CHANGES:
a) TR 5327

TAG: reports_db-18-0-14
DATE: 12/18/2003
STAFF: lec
RELEASE: A
CHANGES:
a) TR 5440; MRK_Sequence.py; add Marker Type

TAG: no tag
DATE: 11/06/2003
STAFF: lec
RELEASE: A
CHANGES:
a) mgiMarkerFeed.py; use new Marker Status (official, interim)

TAG: reports_db-18-0-13
DATE: 10/27/2003
STAFF: lec
RELEASE: A
CHANGES:
a) TR 5252; MGI_RIKEN.py

TAG: reports_db-18-0-9
DATE: 10/10/2003
STAFF: lec
RELEASE: A
CHANGES:
a) MLD_BSSBSB.py

TAG: reports_db-18-0-8
DATE: 08/27/2003
STAFF: lec
TAG: reports_db-18-0-12
TAG: reports_db-18-0-11
TAG: reports_db-18-0-10
DATE: 10/23/2003
STAFF: lec
RELEASE: A
CHANGES:
a) fixed GO_gene_association.py
b) TR 4708 - MRK_List1.sql, MRK_List2.sql, MRK_List3.sql, MRK_List4.sql, MRK_Sequence.py, MRK_SwissProt.py

TAG: reports_db-18-0-9
DATE: 10/10/2003
STAFF: lec
RELEASE: A
CHANGES:
a) MLD_BSSBSB.py

TAG: reports_db-18-0-8
DATE: 08/27/2003
STAFF: lec
RELEASE: A
CHANGES:
a) TR 4708 - MRK_List2.sql, MRK_Sequence.py, MRK_SwissProt.py
b) TR 4970 - MRK_ENSEMBL.py
c) TR 5082 - HMD_HumanPhenotype.py

TAG: reports_db-18-0-7
DATE: 07/03/2003
STAFF: lec
RELEASE: A
CHANGES:
a) TR 4945; add LL IDs to HMD reports

TAG: reports_db-18-0-6
DATE: 06/06/2003
STAFF: lec
RELEASE: A
CHANGES:
a) TR 4877; GO_gp2protein.py

TAG: reports_db-18-0-5
DATE: 05/30/2003
STAFF: lec
RELEASE: A
CHANGES:
a) TR 4805; HMD_OxfordGrid.py

TAG: reports_db-18-0-4
DATE: 05/06/2003
STAFF: lec
RELEASE: A
CHANGES:
a) mgiMarkerFeed.py; added MMRRC strains

TAG: reports_db-18-0-3
DATE: 04/22/2003
STAFF: lec
RELEASE: A
CHANGES:
a) TR 2702; MRK_InterPro.py

TAG: reports_db-18-0-2
DATE: 04/18/2003
STAFF: lec
RELEASE: A
CHANGES:
a) TR 4729; provide link to MP vocabulary

TAG: reports_db-18-0-1
DATE: 04/15/2003
STAFF: lec
RELEASE: A
CHANGES:
a) added _Allele_key to mgimarkerfeed/strain_marker.bcp

TAG: reports_db-18-0-0
DATE: 03/26/2003
STAFF: lec
RELEASE: A
CHANGES:
a) TR 4270; added MRK_SwissProt_TrEMBL.py
b) TR 3702; added MGI_InterProDomains.sql

TAG: reports_db-17-0-2
DATE: 03/13/2003
STAFF: lec
RELEASE: A
CHANGES:
a) index.html

TAG: reports_db-17-0-1
TAG: reports_db-17-0-0
DATE: 02/20/2003
STAFF: lec
RELEASE: A
CHANGES:
a) TR 1892; mgiMarkerFeed.py (for LAF2)

TAG: reports_db-16-0-0
DATE: 02/12/2003
STAFF: dbm
RELEASE: A
CHANGES:
a) Added Primer Name to the report

TAG: reports_db-15-0-0
DATE: 02/11/2003
STAFF: dbm
RELEASE: A
CHANGES:
a) TR 4506; modified PRB_PrimerSeq.py

TAG: reports_db-14-0-0
DATE: 02/03/2003
STAFF: lec
RELEASE: A
CHANGES:
a) TR 4378; added MGI_Strain.py

TAG: reports_db-13-3-0
DATE: 01/29/2003
STAFF: lec
RELEASE: A
CHANGES:
a) TR 4384; added note to index page for Phenotypes

TAG: reports_db-13-2-0
DATE: 01/23/2003
STAFF: lec
RELEASE: A
CHANGES:
a) TR 4454; added MRK_Reference.py

TAG: reports_db-13-1-0
DATE: 12/31/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 4292; added MRK_InterPro.py

TAG: reports_db-13-0-9
DATE: 11/22/2002
STAFF: lec
RELEASE: A
CHANGES:
a) index.html; small revisions

TAG: reports_db-13-0-8
DATE: 11/19/2002
STAFF: lec
RELEASE: A
CHANGES:
a) index.html; small revisions

TAG: reports_db-13-0-7
DATE: 11/07/2002
STAFF: lec
RELEASE: A
CHANGES:
a) index.html; small revisions
b) TR 3655

TAG: reports_db-13-0-6
DATE: 11/04/2002
STAFF: lec
RELEASE: A
CHANGES:
a) index.html; removed duplicate PRB_TissueMouse.sql.rpt

TAG: reports_db-13-0-5
TAG: reports_db-13-0-4
DATE: 11/04/2002
STAFF: lec
RELEASE: A
CHANGES:
a) index.html; change "seq_dbs" to "seq_dbs.current"

TAG: reports_db-13-0-3
DATE: 10/29/2002
STAFF: pm
RELEASE: A
CHANGES:
a) index.html; change "Homology" to "Orthology" (wording only), change path to mouseBLAST per sc

TAG: reports_db-13-0-2
DATE: 10/23/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 2663; index.html

TAG: reports_db-13-0-1
DATE: 10/22/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 4180; added DoTS/TIGR 

TAG: reports_db-13-0-0
DATE: 10/16/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 2663; new index.html; removed tab-delimited.html; 
   Configuration.defaults, new FTP directory

TAG: reports_db-12-0-0
DATE: 08/30/2002
STAFF: lec
RELEASE: A
CHANGES:
a) Sybase 12.5

TAG: reports_db-11-0-18
DATE: 08/28/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 4027; added MRK_GXDAssay.py

TAG: reports_db-11-0-17
DATE: 07/26/2002
STAFF: lec
RELEASE: A
CHANGES:
a) added _LogicalDB_key

TAG: reports_db-11-0-16
DATE: 07/02/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 3855; GDB_Accession.py

TAG: reports_db-11-0-14, reports_db-11-0-15
DATE: 06/25/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 3827; MRK_NomenUpdates.py

TAG: reports_db-11-0-13
DATE: 06/20/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 3798; MRK_GXD.py

TAG: reports_db-11-0-12
DATE: 06/20/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 3807; index.html

TAG: reports_db-11-0-11
DATE: 06/18/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 3762; MRK_GOHuman.py
b) ; MRK_LocusLink.py

TAG: reports_db-11-0-9, reports_db-11-0-10
DATE: 06/10/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 3762; MRK_GOHuman.py
b) ; MRK_LocusLink.py

TAG: reports_db-11-0-8
DATE: 05/30/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 3736; MRK_Dump2.py; MRK_List*
b) ; MRK_LocusLink.py

TAG: reports_db-11-0-8
DATE: 05/30/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 3736; MRK_Dump2.py; MRK_List*

TAG: reports_db-11-0-7
DATE: 04/30/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 3522; added anatdict report
b) changed MGIFEEDFTPDIR to ftp/private/mgifeed

TAG: reports_db-11-0-5, reports_db-11-0-6
DATE: 04/25/2002
STAFF: lec
RELEASE: A
CHANGES:
a) modified GO reports to use fileExt
  and to trim the trailing spaces from the DAG column

TAG: reports_db-11-0-4
DATE: 04/25/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 3626/BIB_PubMed.py

TAG: reports_db-11-0-3
DATE: 04/24/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 3623/PhenoSlim reports

TAG: reports_db-11-0-2
DATE: 04/12/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 3554

TAG: reports_db-11-0-1
DATE: 04/09/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 3345

TAG: reports_db-11-0-0
DATE: 03/26/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 2986

TAG: reports_db-10-0-12
DATE: 03/21/2002
STAFF: lec
RELEASE: A
CHANGES:
a) TR 3469/GO_refs.py report

TAG: reports_db-10-0-11
DATE: 03/12/2002
STAFF: lec
RELEASE: A
CHANGES:
a) remove public strain report per jte

TAG: reports_db-10-0-10
DATE: 03/06/2002
STAFF: lec
RELEASE: A
CHANGES:
a) MGI 2.8/mgiMarkerFeed.py

TAG: reports_db-10-0-9
DATE: 03/04/2002
STAFF: lec
RELEASE: A
CHANGES:
a) MGI 2.8/GO_gene_association.py

TAG: reports_db-10-0-8
DATE: 02/22/2002
STAFF: lec
RELEASE: A
CHANGES:
a) MGI 2.8
b) mgimarkerfeed

TAG: reports_db-10-0-7
DATE: 02/20/2002
STAFF: lec
RELEASE: A
CHANGES:
a) MGI 2.8
b) mgimarkerfeed

TAG: reports_db-10-0-6
DATE: 02/13/2002
STAFF: lec
RELEASE: A
CHANGES:
a) MGI 2.8
b) mgimarkerfeed - add private to all strain bcp files

TAG: reports_db-10-0-5
DATE: 02/08/2002
STAFF: lec
RELEASE: A
CHANGES:
a) MGI 2.8
b) mgimarkerfeed - use date/time

TAG: reports_db-10-0-4
DATE: 02/08/2002
STAFF: lec
RELEASE: A
CHANGES:
a) MGI 2.8
b) fix tab-delimited.html

TAG: reports_db-10-0-3
DATE: 02/07/2002
STAFF: lec
RELEASE: A
CHANGES:
a) MGI 2.8
b) TR 3345 (mgimarkerfeed)

TAG: reports_db-10-0-1, reports_db-10-0-2
DATE: 01/30/2002
STAFF: lec
RELEASE: A
CHANGES:
a) MGI 2.8

TAG: reports_db-10-0-0
DATE: 12/21/2001
STAFF: lec
RELEASE: A
CHANGES:
a) MGI 2.8

TAG: reports_db-9-0-0
DATE: 11/28/2001
STAFF: lec
RELEASE: A
CHANGES:
a) TR 3137 - add MRK_Offset to MGI Marker Feed

TAG: reports_db-8-0-0
DATE: 11/01/2001
STAFF: lec
RELEASE: A
CHANGES:
a) TR 2714
	PRB_AltTranscripts.py
	PRB_TissueMouse.sql
b) use mgidbutilities/bin/reportisql.csh 
c) TR 2541
	PRB_Strain.py
	tab-delimited.html

TAG: reports_db-7-0-0
DATE: 09/18/2001
STAFF: lec
RELEASE: A
CHANGES:
1) TR 2943; added MGI_ProblemSequence.py

TAG: reports_db-6-0-1
DATE: 08/21/2001
STAFF: lec
RELEASE: A
CHANGES:
1) fix nightly_reports.sh

TAG: reports_db-6-0-0
DATE: 08/15/2001
STAFF: lec
RELEASE: A
CHANGES:
1) TR 2794; Marker Feed to M. Rosenstein

TAG: reports_db-5-0-7
DATE: 06/19/2001
STAFF: lec
RELEASE: A
CHANGES:
1) TR 2644; MRK_List1.sql, MRK_List3.sql

TAG: reports_db-5-0-6
DATE: 06/19/2001
STAFF: lec
RELEASE: A
CHANGES:
1) MRK_Nomen.py - TR 2613; added MGI IDs

TAG: reports_db-5-0-5
DATE: 05/23/2001
STAFF: jsb
RELEASE: A
CHANGES:
1) MRK_Sequence.py - added RefSeq IDs, per TR 2561

TAG: reports_db-5-0-4
DATE: 02/19/2001
STAFF: lec
RELEASE: A
CHANGES: 
1) MRK_NomenUpdates.py - Date argument

TAG: reports_db-5-0-3
DATE: 02/14/2001
STAFF: lec
RELEASE: A
CHANGES: 
1) MGD_Stats.sql; problem w/ polymorphism count

TAG: reports_db-5-0-2
DATE: 02/13/2001
STAFF: lec
RELEASE: A
CHANGES: 
1) MRK_NomenUpdates.py - fix sort order

TAG: reports_db-5-0-0, -1
DATE: 01/15/2001
STAFF: lec
RELEASE: A
CHANGES: 
1) new Install
2) bug fixes in monthly reports

TAG: reports_db-4-4-0
DATE: 10/30/2000
STAFF: lec
RELEASE: A
CHANGES: 
1) report MRK_Nomenclature.py not displaying entries w/out Seq IDs

TAG: reports_db-4-3-0
DATE: 10/20/2000
STAFF: lec
RELEASE: A
CHANGES: 
1) TR 2023; display J: as "J:#####" in Nomen report

TAG: reports_db-4-2-0
DATE: 10/12/2000
STAFF: lec
RELEASE: A
CHANGES: 
1) removed reference to Gbase from MGD_Stats

TAG: reports_db-4-1-0
DATE: 09/26/2000
STAFF: lec
RELEASE: A
CHANGES: 
1) TR 1970; MRK_List*; added cm Position

TAG: reports_db-4-0-0
DATE: 09/18/2000
STAFF: lec
RELEASE: A
CHANGES: 
1) renamed installapp to Install

TAG: reports_db-3-4-0
DATE: 09/11/2000
STAFF: lec
RELEASE: A
CHANGES: 
1) TR 1930; MRK_List?.sql were truncating Marker Names

TAG: reports_db-3-3-2
DATE: 07/18/2000
STAFF: lec
RELEASE: A
CHANGES: 
1) TR 1688; modified MRK_LocusLink.py to include LocusLink ID and Other Names

TAG: reports_db-3-3-1
DATE: 07/18/2000
STAFF: lec
RELEASE: A
CHANGES: 
1) revert to old MRK_LocusLink.py....install in July 24 instead

TAG: reports_db-3-3-0
DATE: 07/18/2000
STAFF: lec
RELEASE: A
CHANGES: 
1) TR 1806; added MGI Acc IDs to HMD_Human report (HMD_Human.py)

TAG: reports_db-3-2-0
DATE: 07/13/2000
STAFF: lec
RELEASE: A
CHANGES: 
1) TR 1688; modified MRK_LocusLink.py to include LocusLink ID and Other Names

TAG: reports_db-3-1-0
DATE: 07/12/2000
STAFF: lec
RELEASE: A
CHANGES: 
1) fixed MRK_SwissProt.py - logicaldb key should be 13

TAG: reports_db-3-0-5
DATE: 07/07/2000
STAFF: lec
RELEASE: A
CHANGES: 
1) TR 1627; fixed index.html

TAG: reports_db-3-0-4
DATE: 07/07/2000
STAFF: lec
RELEASE: A
CHANGES: 
1) TR 1627; removed MRK_Mutants1.sql MRK_Mutants2.sql MRK_Mutants3.sql

TAG: reports_db-3-0-3
DATE: 06/29/2000
STAFF: lec
RELEASE: A
CHANGES: 
1) TR 1734; added PRB_ESTMapped.rpt
2) added system_docs & README

TAG: reports_db-3-0-2
DATE: 06/27/2000
STAFF: lec
RELEASE: A
CHANGES: TR 1683; added DEPENDENCIES file

TAG: reports_db-3-0-1
DATE: 06/19/2000
STAFF: lec
RELEASE: A
CHANGES: TR 1604; montly_reports.sh

TAG: reports_db-3-0-0
DATE: 06/09/2000
STAFF: lec
RELEASE: A
CHANGES: created daily, weekly & monthly subdirs

TAG: reports_db-2-0-2
DATE: 06/08/2000
STAFF: lec
RELEASE: A
CHANGES: TR 1651; MRK_NomenUpdates.py

TAG: reports_db-2-0-1
DATE: 06/06/2000
STAFF: lec
RELEASE: A
CHANGES: removed MRK_NomenUpdates.py from executing in nighly_reports.sh script

TAG: reports_db-2-0-0
DATE: 05/30/2000
STAFF: lec
RELEASE: A
CHANGES: removed MRK_Recent.sql (TR 1627); revised MRK_Sequence.py (TR 1631)

TAG: reports_db-1-0-20
DATE: 05/19/2000
STAFF: lec
RELEASE: A
CHANGES: added Acc ID to MRK_List*

TAG: reports_db-1-0-19
DATE: 05/19/2000
STAFF: lec
RELEASE: A
CHANGES: removed reference to EI

TAG: reports_db-1-0-18
DATE: 05/19/2000
STAFF: lec
RELEASE: A
CHANGES: changes to MRK_List3.sql & MRK_List4.sql

TAG: reports_db-1-0-17
DATE: 05/16/2000
STAFF: lec
RELEASE: A
CHANGES: changes to HMD_Human.py sort

TAG: reports_db-1-0-16
DATE: 05/08/2000
STAFF: lec
RELEASE: A
CHANGES: fixed HMD_Human.py sort

TAG: reports_db-1-0-15
DATE: 05/03/2000
STAFF: lec
RELEASE: A
CHANGES: modify MRK_NomenUpdate.py

TAG: reports_db-1-0-14
DATE: 05/03/2000
STAFF: lec
RELEASE: A
CHANGES: use reportlib.create_accession_anchor

TAG: reports_db-1-0-13
DATE: 04/20/2000
STAFF: lec
RELEASE: A
CHANGES: removed MRK_MLC.rpt from tab-delimited.html

TAG: reports_db-1-0-12
DATE: 04/20/2000
STAFF: lec
RELEASE: A
CHANGES: added index.html and tab-delimited.html

TAG: reports_db-1-0-11
DATE: 04/20/2000
STAFF: lec
RELEASE: A
CHANGES: added HMD_Human.py; deleted old HMD_Human?.sql; TR 211

TAG: reports_db-1-0-10
DATE: 04/20/2000
STAFF: lec
RELEASE: A
CHANGES: added HMD_Human.py; deleted old HMD_Human?.sql; TR 211

TAG: reports_db-1-0-9
DATE: 04/20/2000
STAFF: lec
RELEASE: A
CHANGES: added Marker Type to MRK_LocusLink.py

TAG: reports_db-1-0-8
DATE: 04/12/2000
STAFF: lec
RELEASE: A
CHANGES: removed MRK_MLC.py per TR 1360

TAG: reports_db-1-0-7
DATE: 04/11/2000
STAFF: lec
RELEASE: A
CHANGES: MRK_Allele changed to ALL_Allele...

TAG: reports_db-1-0-6
DATE: 04/03/2000
STAFF: lec
RELEASE: A
CHANGES: replacing mgdlib with db

TAG: reports_db-1-0-5
DATE: 04/03/2000
STAFF: lec
RELEASE: A
CHANGES: fixed FTP dir

TAG: reports_db-1-0-4
DATE: 04/03/2000
STAFF: lec
RELEASE: A
CHANGES: permissions during installation

TAG: reports_db-1-0-3
DATE: 03/30/2000
STAFF: lec
RELEASE: A
CHANGES: updates

TAG: reports_db-1-0-2
DATE: 03/30/2000
STAFF: lec
RELEASE: A
CHANGES: updates

TAG: reports_db-1-0-1
DATE: 03/29/2000
STAFF: lec
RELEASE: A
CHANGES: updates

TAG: reports_db-1-0-0
DATE: 03/29/2000
STAFF: lec
RELEASE: A
CHANGES: New CVS repository