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09a0e9395d159d51c017204eb64d63e207a1eea6
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11538 Commits
Author SHA1 Message Date
John Chilton 09a0e9395d More job related timing logging. 
- Log time of big flush statement.
 - Log time of adding datasets to history.
 - Log time for setting up job.

These log statements would make the output of the following gist (https://gist.github.com/blankenberg/43db2e0f61a566126c45) from #1831 a lot more informative.
 2016-03-21 01:03:25 +00:00
Martin Cech d0ceb29bd8 Merge pull request #1953 from mvdbeek/warn_if_user_inactive 
Warn if tool is executed and user account is inactive
 2016-03-20 11:40:52 -04:00
Marius van den Beek 34dedb3eb9 linting fixes 2016-03-20 12:04:33 +01:00
Marius van den Beek 3b71020dfc Account for anonymous user. 2016-03-20 11:49:21 +01:00
Marius van den Beek 9d362a2400 log warning if user account is not active 2016-03-20 10:24:37 +01:00
Dannon Baker 53daf30dd2 Merge branch 'release_16.01' into dev 2016-03-18 15:41:14 -04:00
Daniel Blankenberg 87bb98eed2 Add "new" state to list of dataset states in saved history list. 2016-03-17 16:37:20 -04:00
Dannon Baker 2bc3da6b49 Merge pull request #1948 from jgoecks/history-grid-state-optimization 
Use database query rather than dataset iteration to compute dataset c…
 2016-03-17 15:51:02 -04:00
Dannon Baker 78da8df812 Oops. 2016-03-17 15:20:27 -04:00
Dannon Baker 4520a619ab Minor style tweaks to pass flake8 2016-03-17 15:11:56 -04:00
jgoecks 6a123b12e9 Use database query rather than dataset iteration to compute dataset counts in saved histories grid. 2016-03-17 14:35:20 -04:00
Dannon Baker 98c65dcee0 Swap back to the first fix, update metrics api to use new signature. 2016-03-17 13:13:19 -04:00
Dannon Baker 87bcb5f5a1 Fix in a different way not requiring signature change; still not thrilled about overlapping kwarg names w/ stdlib module names. 2016-03-17 12:09:02 -04:00
Dannon Baker f277f99aed Fix handling of time in fluent logger. 2016-03-17 11:43:52 -04:00
Martin Cech c7d1f009a1 Merge pull request #1935 from guerler/fix_downloads_000 
Fix tool downloads in tool form
 2016-03-17 11:01:27 -04:00
Martin Cech cef58abb55 Merge pull request #1943 from davebx/ts_api_bug 
Fix API method broken in 6e13c3999.
 2016-03-17 11:00:39 -04:00
Dave Bouvier ad6edac562 Also prevent server error when repository is not found. 2016-03-17 10:19:31 -04:00
Dave Bouvier 381afd7576 Prevent server error if name or owner are missing. 2016-03-17 10:13:32 -04:00
Dave Bouvier 80562acfe8 Fix API method broken in 6e13c3999. 2016-03-17 09:24:43 -04:00
John Chilton 13f05d2d79 Allow testing element counts in tool output collections. 2016-03-17 07:39:57 +00:00
John Chilton 29b6d545cf Merge pull request #1926 from blankenberg/iobio-display 
Add iobio external display applications for BAM and VCF.
 2016-03-16 16:00:10 -04:00
Martin Cech aae2006079 Merge pull request #1912 from mvdbeek/relax_password_manager_matching 
Retrieve authentification also for long urls
 2016-03-16 14:19:47 -04:00
Martin Cech 46dc26eeda Merge pull request #1936 from mvdbeek/more_warnings_less_errors 
More warnings, less errors
 2016-03-16 12:11:24 -04:00
Marius van den Beek 5c45746e42 Metadata above max size should be a warning. 2016-03-16 11:51:28 +01:00
Marius van den Beek 18a4edc1ca FTP directory not existing should be a warning, not an exception 2016-03-16 11:44:49 +01:00
Dannon Baker 9a0f971596 Merge branch 'release_16.01' into dev 2016-03-15 16:24:17 -04:00
Dannon Baker 9a343efe8b Merge pull request #1930 from mvdbeek/more_bytestring_for_pysam 
[16.01] Ensure chrom, start, end as bytestring in BamDataProvider
 2016-03-15 16:16:22 -04:00
Marius van den Beek 18473a187e Ensure chrom, start, end as bytestring in BamDataProvider 2016-03-15 19:41:09 +01:00
Daniel Blankenberg 46728c5728 Add bam.iobio as a display application. 2016-03-15 12:56:54 -04:00
John Chilton ff0bcd3920 Merge pull request #1901 from guerler/fix_basic_000 
Use shared value serialization for tool model
 2016-03-14 10:48:39 -04:00
guerler 79a0972675 Improve empty dataset check, handle from_json inconsistency 2016-03-12 12:35:25 -05:00
Martin Cech 957a8ff885 Merge pull request #1910 from mvdbeek/fix_not_an_error_1 
do not assume toolshed to be on URL root
 2016-03-11 18:44:00 -05:00
Marius van den Beek 84865c893e Retrieve authentification also for long urls from shed_auth 2016-03-11 17:35:40 +01:00
Marius van den Beek 3476c7f928 Split the path on 'repos', so that toolsheds that are on a subdirectory do not show errors when loading tools if there is actually no error. 2016-03-11 16:42:10 +01:00
Nicola Soranzo 5a50a4691c Merge pull request #1909 from mvdbeek/backport_repository_for_dependency_relationship 
[16.01] Backport  PR #1868
 2016-03-11 14:49:06 +00:00
Dannon Baker 8423fe74df Merge branch 'release_16.01' into dev 2016-03-11 09:45:30 -05:00
Marius van den Beek d6e38c7d48 remove unused import 2016-03-11 13:10:08 +01:00
Marius van den Beek b3e9398c3a Replace get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision with get_repository_for_dependency_relationship 2016-03-11 13:10:02 +01:00
Martin Cech dd07156e11 Merge pull request #1900 from dannon/sentry_tool_errors 
Very basic tool error sentry reporting.
 2016-03-10 20:35:38 -05:00
Martin Cech 3abd2c213a Merge pull request #1898 from dannon/quota_api_fix_fabien 
[16.01] Quota API issue with serialization to JSON of Decimal
 2016-03-10 20:23:00 -05:00
guerler 3c402a3723 Remove __collection_reduce__ 2016-03-10 19:25:05 -05:00
Dannon Baker f46f1d5808 Add tool version to title for grouping, and include path to tool config file. 2016-03-10 15:46:41 -05:00
guerler b1a9823a3c Remove RuntimeValue arrays 2016-03-10 14:17:18 -05:00
guerler 773095d403 Unify json representation for regular datasets and collections 2016-03-10 11:58:58 -05:00
Dannon Baker effdc314da Merge branch 'history.updating' into dev 2016-03-10 09:38:24 -05:00
guerler b7b04ee920 Fix tool downloads 2016-03-10 03:01:02 -05:00
guerler 40c9e1af25 Use value_to_basic and to_json when populating the tool model 2016-03-10 02:54:43 -05:00
Dannon Baker 824c22942e Very basic tool error sentry reporting. 2016-03-09 15:17:03 -05:00
Dannon Baker a351c75687 Extra documentation for @mvdbeek 2016-03-09 11:31:18 -05:00
Dannon Baker f0b7a34dd3 Apply patch from Fabien Mareuil to resolve json serialization of Decimal error; for more see http://dev.list.galaxyproject.org/quota-api-error-td4669081.html 2016-03-09 11:07:12 -05:00