From 36a2e1a486a5d8e70a86d09794a2831607a3bd0c Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Fri, 10 Feb 2012 14:43:17 +0000
Subject: [PATCH] added changelog for rel.66
---
README | 307 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 307 insertions(+)
diff --git a/README b/README
index ed8e87b46..707f627bf 100644
--- a/README
+++ b/README
@@ -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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