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(edit) @1637:c141cb89aa45 [1637:c141cb89aa45] 11/20/08 16:15:39 Nate Coraor <nate@bx.psu.edu> Fix job recovery
(edit) @1636:8412e0cbe7f0 [1636:8412e0cbe7f0] 11/18/08 16:04:41 James Taylor <james@jamestaylor.org> bugfix to last commit
(edit) @1635:2302d3914843 [1635:2302d3914843] 11/18/08 15:47:13 James Taylor <james@jamestaylor.org> Always write keys in order when creating json strings. Also removed a …
(edit) @1634:ad26fd305881 [1634:ad26fd305881] 11/18/08 11:23:09 wychung (no commit message)
(edit) @1633:950a71339420 [1633:950a71339420] 11/14/08 13:21:02 wychung update poisson test tool for R warnings.
(edit) @1632:a5ec5ab6144b [1632:a5ec5ab6144b] 11/13/08 19:19:03 Nate Coraor <nate@bx.psu.edu> Some job runner fixes.
(edit) @1631:a39afe99b3bd [1631:a39afe99b3bd] 11/13/08 15:17:42 Greg Von Kuster <greg@bx.psu.edu> Missed translating the primaryTable data type from UCSC in my last commit.
(edit) @1630:311ee61dc989 [1630:311ee61dc989] 11/13/08 14:56:33 Greg Von Kuster <greg@bx.psu.edu> Add a new <data_type_translation> tag set to data_source tools that enable …
(edit) @1629:df23879dec70 [1629:df23879dec70] 11/12/08 15:42:46 Greg Von Kuster <greg@bx.psu.edu> Fix a bug I missed in my last commit.
(edit) @1628:54f12bb6cb29 [1628:54f12bb6cb29] 11/12/08 15:19:27 Greg Von Kuster <greg@bx.psu.edu> Fixes for the incorrect_gops_jobs script.
(edit) @1627:2cf304a0c1c6 [1627:2cf304a0c1c6] 11/12/08 10:16:04 guru Fixed an indentation bug in incorrect_gops_jobs script.
(edit) @1626:ddad87f713cc [1626:ddad87f713cc] 11/11/08 16:33:50 Nate Coraor <nate@bx.psu.edu> Change state to running before thread handoff.
(edit) @1625:82cf78640bc1 [1625:82cf78640bc1] 11/11/08 16:20:12 guru small modification to incorrect_gops_jobs script to include all HDAs …
(edit) @1624:bffe6becd372 [1624:bffe6becd372] 11/11/08 15:20:36 guru Script to fetch gops jobs that might have produced incorrect/empty oUtput …
(edit) @1623:41a4d178466d [1623:41a4d178466d] 11/11/08 14:54:24 Nate Coraor <nate@bx.psu.edu> Whoops, forgot to fix changed config param in the local runner.
(edit) @1622:fb44755b4c56 [1622:fb44755b4c56] 11/11/08 14:51:13 Nate Coraor <nate@bx.psu.edu> Start the job queue after the utils.
(edit) @1621:45067d8114eb [1621:45067d8114eb] 11/11/08 14:48:25 Nate Coraor <nate@bx.psu.edu> Add a thread pool for the PBS runner to use for queue/finish methods.
(edit) @1620:bc74a32f875e [1620:bc74a32f875e] 11/11/08 10:19:21 Nate Coraor <nate@bx.psu.edu> Add the "upload" job state to prevent job runner from grabbing upload jobs …
(edit) @1619:9ce784bcab86 [1619:9ce784bcab86] 11/11/08 09:52:20 Greg Von Kuster <greg@bx.psu.edu> Fixes for jobs reports.
(edit) @1618:e8f25fc7dde0 [1618:e8f25fc7dde0] 11/10/08 15:38:29 James Taylor <james@jamestaylor.org> Automated merge with ssh://scofield.bx.psu.edu//depot/projects/universe/hg
(edit) @1617:6d78c087e30f [1617:6d78c087e30f] 11/10/08 15:37:21 James Taylor <james@jamestaylor.org> imported patch workflow-bugfix-10Nov2008
(edit) @1616:330bf412f311 [1616:330bf412f311] 11/10/08 15:30:07 Greg Von Kuster <greg@bx.psu.edu> Fix for purging dataset - add check for pre-history_dataset_association …
(edit) @1615:2d7f872ddaf8 [1615:2d7f872ddaf8] 11/10/08 14:22:01 Greg Von Kuster <greg@bx.psu.edu> Add functioal test baseline support for the repeat construct, more work …
(edit) @1614:99b4d554afd1 [1614:99b4d554afd1] 11/10/08 12:41:29 Nate Coraor <nate@bx.psu.edu> A bug in recent job runner changes... nothing was ever actually sent to …
(edit) @1613:342e8ebf1305 [1613:342e8ebf1305] 11/07/08 16:27:07 Dan Blankenberg <dan@bx.psu.edu> Add a test for the sample analysis of retrieving genes flanked by DNAse …
(edit) @1612:3385fbd2af47 [1612:3385fbd2af47] 11/07/08 15:39:47 Dan Blankenberg <dan@bx.psu.edu> Fixes for testing framework to allow it to be run against an external …
(edit) @1611:c7bc4de93fbb [1611:c7bc4de93fbb] 11/06/08 09:44:19 Greg Von Kuster <greg@bx.psu.edu> Create a job_to_output_dataset for the upload tool job.
(edit) @1610:604b4b49e93f [1610:604b4b49e93f] 11/05/08 16:00:35 Greg Von Kuster <greg@bx.psu.edu> Monitor memory usage in the JobWrapper?.
(edit) @1609:af3fc2158202 [1609:af3fc2158202] 11/05/08 15:20:47 Dan Blankenberg <dan@bx.psu.edu> A better test to ensure that a MetadataCollection? is not stale.
(edit) @1608:53aa8d34c20a [1608:53aa8d34c20a] 11/05/08 11:43:22 Dan Blankenberg <dan@bx.psu.edu> Possible fix for the infinite metadata recursion issue.
(edit) @1607:4e2ad77de095 [1607:4e2ad77de095] 11/05/08 10:35:06 Greg Von Kuster <greg@bx.psu.edu> Fix jobs report to display jobs in deleted and waiting states.
(edit) @1606:72252f33edd1 [1606:72252f33edd1] 11/05/08 09:28:48 Greg Von Kuster <greg@bx.psu.edu> Make logging events a config setting.
(edit) @1605:f2e583f7cab9 [1605:f2e583f7cab9] 11/04/08 16:04:49 Greg Von Kuster <greg@bx.psu.edu> Add ability to track memory usage in code secments - requires config …
(edit) @1604:7a5d9759c702 [1604:7a5d9759c702] 11/04/08 14:00:30 Nate Coraor <nate@bx.psu.edu> Fix get_bool in config
(edit) @1603:85347b21a1b8 [1603:85347b21a1b8] 11/04/08 13:20:39 Greg Von Kuster <greg@bx.psu.edu> Fixes for upload tool job creation.
(edit) @1602:531be9ea2486 [1602:531be9ea2486] 11/04/08 11:56:09 Greg Von Kuster <greg@bx.psu.edu> Upload tool will now create a job record, no job queued though.
(edit) @1601:52e504c91cbc [1601:52e504c91cbc] 11/04/08 09:27:49 Greg Von Kuster <greg@bx.psu.edu> Apply James' faster_random patch from Nov 1.
(edit) @1600:7ae75e6d9d6a [1600:7ae75e6d9d6a] 11/03/08 15:31:38 Greg Von Kuster <greg@bx.psu.edu> Integrate "session_create_speed" and "faster_random" patches from James.
(edit) @1599:13cbdd1bbd19 [1599:13cbdd1bbd19] 11/03/08 15:21:03 Dan Blankenberg <dan@bx.psu.edu> A fix for the metadata reverting issue seen with PBS job runner.
(edit) @1598:ca640ce1abcf [1598:ca640ce1abcf] 11/03/08 15:15:22 Nate Coraor <nate@bx.psu.edu> Fix a bug: errored jobs weren't actually being deleted.
(edit) @1597:21f98b638868 [1597:21f98b638868] 11/03/08 15:07:22 Dan Blankenberg <dan@bx.psu.edu> Backed out changeset 36a297157114 Temporarilly rolling this change back…
(edit) @1596:36a297157114 [1596:36a297157114] 11/03/08 14:48:25 Dan Blankenberg <dan@bx.psu.edu> A fix for the metadata reverting issue seen with PBS job runner.
(edit) @1595:56bc2f789894 [1595:56bc2f789894] 11/01/08 15:30:13 Greg Von Kuster <greg@bx.psu.edu> Fix History.add_dataset() to be compatible with sqlalchemy 4.
(edit) @1594:881ac57dcc81 [1594:881ac57dcc81] 10/31/08 15:21:30 Dan Blankenberg <dan@bx.psu.edu> Fix for use of deprecated <display> tags in tool_form.mako.
(edit) @1593:cb3507efced7 [1593:cb3507efced7] 10/31/08 14:52:41 Dan Blankenberg <dan@bx.psu.edu> Small typo in one of the encode import tools.
(edit) @1592:6ddbf5c83efc [1592:6ddbf5c83efc] 10/31/08 11:00:50 Dan Blankenberg <dan@bx.psu.edu> Fixes for dealing with UnvalidatedValues? (i.e. when running workflows) and …
(edit) @1591:c4644668afff [1591:c4644668afff] 10/31/08 10:22:46 Nate Coraor <nate@bx.psu.edu> James' changes allowing the server to run w/o a job runner, …
(edit) @1590:7e94f40ee9e8 [1590:7e94f40ee9e8] 10/30/08 17:34:46 James Taylor <james@jamestaylor.org> Convert tool_form/tool_executed to mako (for performance)
(edit) @1589:1d113c5386da [1589:1d113c5386da] 10/30/08 16:17:46 Greg Von Kuster <greg@bx.psu.edu> Migrate central repo to alchemy 4.
(edit) @1588:ea92290c4e10 [1588:ea92290c4e10] 10/30/08 16:11:44 Nate Coraor <nate@bx.psu.edu> Use LD_RUN_PATH when building pbs_python
(edit) @1587:0da612f8a78e [1587:0da612f8a78e] 10/30/08 16:03:11 guru Added new functional tests to all gops tools using …
(edit) @1586:4e44d29377e3 [1586:4e44d29377e3] 10/30/08 14:46:57 Dan Blankenberg <dan@bx.psu.edu> Annotation profiler: Better handling of the case where regions extend …
(edit) @1585:6259ebdd0e99 [1585:6259ebdd0e99] 10/30/08 13:35:19 Dan Blankenberg <dan@bx.psu.edu> Fix typo on call to set_meta.
(edit) @1584:95bdb18ee62b [1584:95bdb18ee62b] 10/29/08 17:32:09 Nate Coraor <nate@bx.psu.edu> Update bx-python to r456.
(edit) @1583:bfb4189733db [1583:bfb4189733db] 10/29/08 17:20:54 Nate Coraor <nate@bx.psu.edu> Fix pbs_python to just use existing torque.
(edit) @1582:c9f19b8b21ba [1582:c9f19b8b21ba] 10/29/08 12:35:50 Nate Coraor <nate@bx.psu.edu> Re-add JOB_ERROR since some finish hooks use it (albeit improperly).
(edit) @1581:4841a9e393c7 [1581:4841a9e393c7] 10/28/08 14:31:02 Greg Von Kuster <greg@bx.psu.edu> Purge metadata files associated with a dataset when the dataset is purged. …
(edit) @1580:91f6455e19e4 [1580:91f6455e19e4] 10/28/08 12:57:39 Dan Blankenberg <dan@bx.psu.edu> Use a weakref in metadata to prevent a circular reference possibly …
(edit) @1579:778fcc385ab7 [1579:778fcc385ab7] 10/28/08 11:27:42 Greg Von Kuster <greg@bx.psu.edu> Add new EpiGRAPH tools that point to EpiGRAPH production server.
(edit) @1578:75312c1cab05 [1578:75312c1cab05] 10/28/08 10:55:39 Greg Von Kuster <greg@bx.psu.edu> Tweaks to my last commit - only persist job states defined in model, not …
(edit) @1577:0f4fd4c20cd6 [1577:0f4fd4c20cd6] 10/28/08 10:21:02 Greg Von Kuster <greg@bx.psu.edu> Improve job error messaging, some fixes for setting job state, job info, …
(edit) @1576:8eec48aaca6e [1576:8eec48aaca6e] 10/27/08 17:03:50 Nate Coraor <nate@bx.psu.edu> Add a memdump page to the admin controller, makes heapy output …
(edit) @1575:415cc6dc8e35 [1575:415cc6dc8e35] 10/27/08 16:03:43 Greg Von Kuster <greg@bx.psu.edu> Add a new URL_method attribute to data_source tool types whose value is …
(edit) @1574:36a7ff82faf0 [1574:36a7ff82faf0] 10/24/08 12:32:32 Nate Coraor <nate@bx.psu.edu> WebHelpers? imports simplejson. Import simplejson before …
(edit) @1573:c278ca8f9b73 [1573:c278ca8f9b73] 10/24/08 11:41:23 Dan Blankenberg <dan@bx.psu.edu> Add some missing 'url_for's.
(edit) @1572:f2ce31c74346 [1572:f2ce31c74346] 10/23/08 15:19:48 Nate Coraor <nate@bx.psu.edu> Fix a bug from the last commit, what I changed doesn't work right.
(edit) @1571:6e592c876f4d [1571:6e592c876f4d] 10/23/08 15:02:23 Nate Coraor <nate@bx.psu.edu> When creating display links, use url_for to add the proxy prefix, if any.
(edit) @1570:3e391f7192f6 [1570:3e391f7192f6] 10/22/08 14:37:28 Nate Coraor <nate@bx.psu.edu> Record a useful info message when a job fails to run because inputs …
(edit) @1569:df07d0c2830f [1569:df07d0c2830f] 10/22/08 14:27:57 Dan Blankenberg <dan@bx.psu.edu> Fix for mapping unit test. Testing of metadata elements requires a valid …
(edit) @1568:0b022adfdc34 [1568:0b022adfdc34] 10/22/08 13:49:22 Dan Blankenberg <dan@bx.psu.edu> Add a new metadata type of Metadata Files. These are now used to store …
(edit) @1567:b02b8d9196a8 [1567:b02b8d9196a8] 10/22/08 12:15:06 Nate Coraor <nate@bx.psu.edu> Like the local runner, if job preparation fails, catch and log.
(edit) @1566:510ff36caaf3 [1566:510ff36caaf3] 10/21/08 10:40:08 Nate Coraor <nate@bx.psu.edu> Add the guppy egg
(edit) @1565:4f9042e95e60 [1565:4f9042e95e60] 10/20/08 16:51:51 Dan Blankenberg <dan@bx.psu.edu> Fix for fix for unit tests.
(edit) @1564:eef0fd813076 [1564:eef0fd813076] 10/20/08 15:09:47 Nate Coraor <nate@bx.psu.edu> Add a Heapy-based memdump module. Send the Galaxy process SIGUSR1 …
(edit) @1563:98867708d5ae [1563:98867708d5ae] 10/20/08 14:16:38 Dan Blankenberg <dan@bx.psu.edu> Fix for unit test for DataTool? Parameter
(edit) @1562:26ae03082033 [1562:26ae03082033] 10/20/08 12:44:33 Dan Blankenberg <dan@bx.psu.edu> Fix for implicit conversion checking on multiple paged tools. Conversion …
(edit) @1561:d3a267ac124b [1561:d3a267ac124b] 10/20/08 09:25:38 Greg Von Kuster <greg@bx.psu.edu> Fix the use_heartbeat check in config.py
(edit) @1560:0a0045644219 [1560:0a0045644219] 10/17/08 13:31:17 Dan Blankenberg <dan@bx.psu.edu> Fix for optional datasets to work with metadata changes.
(edit) @1559:f802eb92a49a [1559:f802eb92a49a] 10/17/08 13:02:26 guru Added Validator to a bunch of tools..
(edit) @1558:f5b051c51295 [1558:f5b051c51295] 10/17/08 10:46:29 Greg Von Kuster <greg@bx.psu.edu> Fixes for data_source tools, data.name, data.info, data.dbkey, and …
(edit) @1557:a5831435c654 [1557:a5831435c654] 10/16/08 14:12:37 Dan Blankenberg <dan@bx.psu.edu> Refactor internals of metadata. Significantly reduce the number of …
(edit) @1556:97a8f6f5ba00 [1556:97a8f6f5ba00] 10/15/08 15:51:13 wychung update xml files for short reads mapping tools.
(edit) @1555:0adda80bcef4 [1555:0adda80bcef4] 10/14/08 10:58:43 guru Updating test-output for Extract Orthologous microsatellites tool, which …
(edit) @1554:e612b6609af9 [1554:e612b6609af9] 10/13/08 15:06:42 wychung add shrimp_color_space mapping tool with functional test data. add a new …
(edit) @1553:248627e7bd58 [1553:248627e7bd58] 10/13/08 14:55:13 Greg Von Kuster <greg@bx.psu.edu> Fix for data_source tool params sent in the post from the remote data …
(edit) @1552:4b9feffc3ce5 [1552:4b9feffc3ce5] 10/09/08 11:23:33 Dan Blankenberg <dan@bx.psu.edu> Maf stats will now use bitset instead of numpy.zerros.
(edit) @1551:fdbf15ea1f8a [1551:fdbf15ea1f8a] 10/08/08 12:00:16 Dan Blankenberg <dan@bx.psu.edu> Add ability to undelete histories.
(edit) @1550:64c0734ff262 [1550:64c0734ff262] 10/07/08 15:21:46 Greg Von Kuster <greg@bx.psu.edu> Use only 1 underlying executable ( data_source.py ) for data source tools. …
(edit) @1549:960820cccaaa [1549:960820cccaaa] 10/07/08 11:58:32 Dan Blankenberg <dan@bx.psu.edu> Users can copy datasets between their histories.
(edit) @1548:ae341e281c89 [1548:ae341e281c89] 10/06/08 13:34:51 Greg Von Kuster <greg@bx.psu.edu> Treat EpiGRAPH as a data source much like ucsc table browser.
(edit) @1547:684b78f79f8b [1547:684b78f79f8b] 10/06/08 11:48:35 Dan Blankenberg <dan@bx.psu.edu> Improve ajax deleting refreshing of dataset contents.
(edit) @1546:d93cf9d961bb [1546:d93cf9d961bb] 10/06/08 09:40:47 guru Updating "regional variation' section in tool_conf.xml.main.
(edit) @1545:cec03ea2d5aa [1545:cec03ea2d5aa] 10/06/08 09:33:52 guru Modified help message for indel rate tool.
(edit) @1544:7e2ec07716b8 [1544:7e2ec07716b8] 10/03/08 16:06:01 Dan Blankenberg <dan@bx.psu.edu> Add axaj async undelete ability. Fix redisplay of dataset when …
(edit) @1543:45033114f82d [1543:45033114f82d] 10/02/08 16:37:32 Dan Blankenberg <dan@bx.psu.edu> Add the ability to undelete deleted datasets from a history. A new …
(edit) @1542:20591fa0d05d [1542:20591fa0d05d] 10/02/08 15:51:17 Greg Von Kuster <greg@bx.psu.edu> Reverting to rev 1459.
(edit) @1541:993bed7b5e26 [1541:993bed7b5e26] 10/02/08 13:18:50 Greg Von Kuster <greg@bx.psu.edu> Remove a debug statement from root controller…
(edit) @1540:0041f2ba49ed [1540:0041f2ba49ed] 10/02/08 12:45:03 Greg Von Kuster <greg@bx.psu.edu> Fix all root controller methods so that history_dataset_association.id is …
(edit) @1539:dd58d5aeb274 [1539:dd58d5aeb274] 10/01/08 12:43:59 Greg Von Kuster <greg@bx.psu.edu> Fix for root/display() - history_dataset_association.dataset_id no longer …
(edit) @1538:f9431ad593b4 [1538:f9431ad593b4] 10/01/08 10:17:58 Greg Von Kuster <greg@bx.psu.edu> Fix for histogram tool when input dataset is empty.
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