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- Sep 27, 2010
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Andy Yates authored
Incorrect passing of the DBConnection object to the execute update closure which meant we attempted to call out to attributes which did not exist on that object.
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Andy Yates authored
Cannot use the begin_work() command if we have turned off AutoCommit manually. We were doing the same thing
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- Sep 24, 2010
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Glenn Proctor authored
Many improvements to reduce memory usage. Now uses registry, so don't need to specify databases explicitly, just use e.g. -species human
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Andreas Kusalananda Kähäri authored
specified. Patch from Dan S.
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- Sep 21, 2010
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Steve Trevanion authored
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Andreas Kusalananda Kähäri authored
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- Sep 20, 2010
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Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
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Ian Longden authored
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Maurice Hendrix authored
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- Sep 17, 2010
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Ian Longden authored
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- Sep 16, 2010
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Andreas Kusalananda Kähäri authored
not needed and move declaration of a statment handle to aviod having to declare another one.
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Andreas Kusalananda Kähäri authored
Slice::dbID().
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- Sep 15, 2010
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Andreas Kusalananda Kähäri authored
attached slice.
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
allow user to set a list of sources that will not have the [Source:...] bit at the end of the gene description
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Ian Longden authored
MGI have added -ps to psuedo gene names but havana have not doen this yet so check for this when getting descriptions etc
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- Sep 13, 2010
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Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
push_master_tables.pl.
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Andreas Kusalananda Kähäri authored
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Andy Yates authored
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Andy Yates authored
Making sure if AutoCommit was off we issue a rollback to signal the start of a fresh block. This seems to be easier than using DBI's begin_work() since that will error if we have already begun a transaction
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Andreas Kusalananda Kähäri authored
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- Sep 10, 2010
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Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
for specifying inheritance.
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Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
line switches. This program takes the master tables from the production database and compares it to the corresponding tables on the given servers (by default, the staging servers). The program will display any discrepancies on the display while writing SQL to files in the current directory that will correct the discrepancies. Each SQL patch file will have the generic name "fix-DBNAME.sql" where "DBNAME" is the name of the database, e.g., "fix-oryctolagus_cuniculus_otherfeatures_60_3.sql". A discrepancy is patched by 1) Insertion into the master table in the production database in the case where a new entry has been added to a database without being added to the master table. 2) Insertion into the database table in the case where a new master entry is missing in the database. 3) Updating the database entry in the case where an entry (identified by its primary key only) differs in any of its fields. The SQL patch files may then be used to patch the databases: $ mysql -h server -u user -ppass < fix-DBNAME.sql BE SURE TO REVIEW THESE SQL PATCH FILES (along with the program output) WITH YOUR EYE AND BRAIN BEFORE APPLYING THEM
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Andreas Kusalananda Kähäri authored
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- Sep 09, 2010
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Nathan Johnson authored
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Andreas Kusalananda Kähäri authored
the wrong directory.
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Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
# This little script will bootstrap the master tables in the production # database (and nothing else). This means copying the relevant tables # from a known correct database (the "template database") into the # master_% tables in the production database. # # The template database needs to live on the same server as the # production database. # # The otuput of this script is SQL written to standard output. The SQL # needs to be run against the MySQL server manually. #
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Ian Longden authored
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- Sep 08, 2010
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Ian Longden authored
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Ian Longden authored
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