Commit 36a2e1a4 authored by Leo Gordon's avatar Leo Gordon
Browse files

added changelog for rel.66

parent ac793670
......@@ -13,6 +13,313 @@ Summary:
any program, algorithm, or parallel processing job control system. It is
not bound to any processing 'farm' system and can be adapted to any GRID.
Changelog:
---------------------[after EnsEMBL rel.66]----------------------------------------------------------------
2012-01-31 10:58 lg4
* sql/triggers.mysql: an optimization: do not touch analysis_stats
when job.status or job.analysis is not changing
2012-01-20 16:33 lg4
* modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm,
sql/tables.sql: changes for rel.66
2011-12-08 13:07 lg4
* modules/Bio/EnsEMBL/Hive/PipeConfig/LongMult_conf.pm: checked in
by mistake last time; took back the changes now
2011-12-08 12:08 lg4
* modules/Bio/EnsEMBL/Hive/AnalysisStats.pm,
modules/Bio/EnsEMBL/Hive/Meadow.pm,
modules/Bio/EnsEMBL/Hive/Queen.pm,
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisStatsAdaptor.pm,
modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm,
modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm,
modules/Bio/EnsEMBL/Hive/PipeConfig/LongMult_conf.pm,
scripts/beekeeper.pl, scripts/runWorker.pl,
sql/patch_2011-12-08.sql, sql/tables.sql, sql/tables.sqlite,
sql/triggers.mysql, sql/triggers.sqlite: Removed
maximise_concurrency and added analysis_stats.priority to guide
the scheduler; improved scheduler and LSF meadow
2011-11-29 17:49 lg4
* modules/Bio/EnsEMBL/Hive/AnalysisJob.pm,
modules/Bio/EnsEMBL/Hive/DataflowRule.pm,
modules/Bio/EnsEMBL/Hive/Worker.pm,
modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm,
modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm,
modules/Bio/EnsEMBL/Hive/PipeConfig/LongMult_conf.pm,
modules/Bio/EnsEMBL/Hive/Utils/Graph.pm,
sql/patch_2011-11-29.sql, sql/tables.sql, sql/tables.sqlite: An
extension to the dataflow-rule-driven semaphores ('2->A', '3->A'
and 'A->1' notation)
2011-11-29 12:59 lg4
* modules/Bio/EnsEMBL/Hive/RunnableDB/JobFactory.pm: removed
'sema_fan_branch_code' parameter since you can now set up a
semaphored group via PipeConfig' language
2011-11-28 09:57 lg4
* modules/Bio/EnsEMBL/Hive/Queen.pm: no need to check for
semaphores when state is already DONE or PASSED_ON
2011-11-28 09:57 lg4
* modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm: making sure
semaphores are correctly propagated through gc_dataflow and
PASSED_ON state
2011-11-25 10:22 lg4
* modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm: allow
more than one input_id_template per analysis
2011-11-24 20:12 lg4
* modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm: bugfix:
funnel_branch is no longer initialized to 1 when undef
2011-11-24 20:05 lg4
* modules/Bio/EnsEMBL/Hive/Queen.pm: bugfix: correct counting of
total_job_number in non-trigger mode
2011-11-24 12:37 lg4
* modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm: bugfix -
branch_name_2_code should return 1 on undef
2011-11-23 17:05 lg4
* modules/Bio/EnsEMBL/Hive/Utils/: Graph.pm, Graph/Config.pm: show
the dataflow-generated semaphores on the diagram
2011-11-23 15:52 lg4
* modules/Bio/EnsEMBL/Hive/DBSQL/: BaseAdaptor.pm,
ObjectAdaptor.pm: bugfix: object adaptor now correctly
reconstructs dbID
2011-11-23 12:23 lg4
* modules/Bio/EnsEMBL/Hive/: PipeConfig/LongMult_conf.pm,
PipeConfig/SemaLongMult_conf.pm, RunnableDB/LongMult/README,
RunnableDB/LongMult/SemaStart.pm: merge the two ways of running
the LongMult pipeline into one
2011-11-23 11:57 lg4
* modules/Bio/EnsEMBL/Hive/AnalysisJob.pm,
modules/Bio/EnsEMBL/Hive/DataflowRule.pm,
modules/Bio/EnsEMBL/Hive/Worker.pm,
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm,
modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm,
modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm,
modules/Bio/EnsEMBL/Hive/PipeConfig/LongMult_conf.pm,
sql/patch_2011-11-23.sql, sql/tables.sql, sql/tables.sqlite:
integrated semaphored fans/funnels into dataflow rules
2011-11-22 14:47 lg4
* modules/Bio/EnsEMBL/Hive/AnalysisStats.pm: this value was
returned but never used
2011-11-21 16:44 lg4
* modules/Bio/EnsEMBL/Hive/: AnalysisStats.pm, Queen.pm, Worker.pm,
DBSQL/AnalysisJobAdaptor.pm: remove the per-worker batch_size
method
2011-11-21 16:40 lg4
* scripts/: beekeeper.pl, runWorker.pl: remove the per-worker
batch_size flag from scripts
2011-11-17 14:56 lg4
* modules/Bio/EnsEMBL/Hive/Queen.pm,
modules/Bio/EnsEMBL/Hive/Worker.pm,
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisStatsAdaptor.pm,
sql/triggers.mysql, sql/triggers.sqlite: make num_running_workers
updatable by triggers + better updates during worker check-in
2011-11-10 14:30 lg4
* modules/Bio/EnsEMBL/Hive/: AnalysisStats.pm,
DBSQL/AnalysisStatsAdaptor.pm: these four methods were neither
used by Hive nor by Compara code
2011-11-04 12:05 lg4
* docs/eHive_install_usage.txt,
modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm: DBI with versions
older than 1.6 are not supported
2011-10-19 09:54 db8
* modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm, scripts/beekeeper.pl:
WGA/Projection used for CHIMP2.1.4
2011-10-15 10:20 lg4
* sql/: tables.sql, tables.sqlite: release 65
2011-09-23 11:53 lg4
*
modules/Bio/EnsEMBL/Hive/PipeConfig/RunListOfCommandsOnFarm_conf.pm:
An example pipeline that turns lines of a file into jobs and runs
them on the farm
2011-09-20 21:15 lg4
* modules/Bio/EnsEMBL/Hive/Process.pm: extend for other schema
types
2011-09-09 09:57 lg4
* sql/tables.sql: analysis_data may be overcrowded with inserts
during dataflow with input_id longer than 255 characters
2011-09-05 17:18 lg4
* docs/long_mult_example_pipeline.txt: couple of typos
2011-09-05 16:50 lg4
* docs/eHive_install_usage.txt: checkout seems to work better than
export
2011-09-01 16:12 lg4
* modules/Bio/EnsEMBL/Hive/: DependentOptions.pm,
PipeConfig/ApplyToDatabases_conf.pm,
PipeConfig/FailureTest_conf.pm,
PipeConfig/FileZipperUnzipper_conf.pm,
PipeConfig/HiveGeneric_conf.pm, PipeConfig/LongMult_conf.pm,
PipeConfig/SemaLongMult_conf.pm,
PipeConfig/TableDumperZipper_conf.pm: Incorporate ENV hash into
the tree of possible options in order to be able to "require" a
value. And a bit of config inheritance cleanup.
2011-08-25 20:37 lg4
* modules/Bio/EnsEMBL/Hive/: Process.pm, RunnableDB/JobFactory.pm,
RunnableDB/MySQLTransfer.pm, RunnableDB/SqlCmd.pm,
RunnableDB/SystemCmd.pm: Switching from DBI to DBConnection;
data_dbc() as the main focus point; standaloneJob.pl examples of
basic building blocks
2011-08-18 15:28 lg4
* modules/Bio/EnsEMBL/Hive/RunnableDB/: JobFactory.pm, SqlCmd.pm,
SystemCmd.pm: show query/cmd/filename when debug is on
2011-08-18 15:23 lg4
* modules/Bio/EnsEMBL/Hive/Utils/Graph.pm: sqlite databases do not
have a host name, so nothing to display here
2011-08-15 10:58 lg4
* sql/: tables.sql, tables.sqlite: the schema did not allow more
than one job_message per second from one attempt. This limitation
has been removed
2011-07-26 17:35 lg4
* modules/Bio/EnsEMBL/Hive/AnalysisJob.pm: allow standalone jobs to
emit warnings
2011-07-26 11:45 lg4
* sql/: tables.sql, tables.sqlite: for the production of rel.64
2011-07-20 19:40 lg4
* sql/: triggers.mysql, triggers.sqlite: bugfix: more foolproof
maths in triggers
2011-07-15 16:42 lg4
* modules/Bio/EnsEMBL/Hive/: Queen.pm, Worker.pm: moved Worker's
call to Queen->safe_synchronize_AnalysisStats into Worker.pm for
clarity
2011-07-15 15:13 lg4
* modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisStatsAdaptor.pm: now it
should properly refresh data in the existing object
2011-07-15 14:59 lg4
* modules/Bio/EnsEMBL/Hive/Queen.pm: do not update counters
unnecessarily
2011-07-15 14:23 lg4
* modules/Bio/EnsEMBL/Hive/: AnalysisStats.pm, Queen.pm: formatting
and cleanup
2011-07-15 14:21 lg4
* modules/Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm,
modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm,
sql/triggers.mysql, sql/triggers.sqlite: more flexible approach:
allows to add triggers later by simply by sourcing the triggers
file
2011-07-15 11:44 lg4
* modules/Bio/EnsEMBL/Hive/: Queen.pm,
DBSQL/AnalysisStatsAdaptor.pm: perform worker counting centrally
in the Queen
2011-07-15 11:14 lg4
* modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisStatsAdaptor.pm: do not
update these fields when triggers in place
2011-07-14 15:58 lg4
* modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm: added a
new beekeeper_extra_cmdline_options() interface method for
passing cmdline options to beekeeper.pl/runWorker.pl
2011-07-14 15:26 lg4
* modules/Bio/EnsEMBL/Hive/: Queen.pm, DBSQL/AnalysisJobAdaptor.pm,
DBSQL/AnalysisStatsAdaptor.pm, DBSQL/DBAdaptor.pm,
PipeConfig/HiveGeneric_conf.pm: optional (cmdline-controlled,
off-by-default) support of job-counting triggers
2011-07-14 12:52 lg4
* modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm,
sql/foreign_keys.mysql, sql/foreign_keys.sql,
sql/procedures.mysql, sql/procedures.sql: renamed procedures.sql
and foreign_keys.sql into .mysql equivalents
2011-07-14 12:47 lg4
* sql/: triggers.mysql, triggers.sqlite: experimental: do the job
counting immediately by SQL triggers rather than periodically by
Perl code
2011-07-13 17:24 lg4
* modules/Bio/EnsEMBL/Hive/Params.pm, scripts/standaloneJob.pl:
allow automatic dataflow into tables as well
--------------------------------------------------------------------------------------------------------
13.July, 2011 : Leo
......
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