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11561 Commits
Author SHA1 Message Date
Dannon Baker 0dc57b08e8 Merge pull request #1974 from jmchilton/docker_fix 
Fix docker tool execution for #1688.
 2016-03-22 12:42:16 -04:00
Dannon Baker 45c1731888 Merge branch 'release_16.01' into dev 2016-03-22 09:18:55 -04:00
Björn Grüning 30750c32e4 Merge pull request #1880 from dannon/fix_migration_0131_mysql 
[16.01] Fixes to subworkflow migration 0131
 2016-03-22 14:14:43 +01:00
John Chilton c26788a267 Merge pull request #1971 from guerler/fix_nginx_upload_000 
Fix nginx-based file upload
 2016-03-22 07:51:33 -04:00
John Chilton 975937ec9d Fix docker tool execution for #1688. 
Thanks for @kellrott for the bug report.

\#minor
 2016-03-22 10:02:32 +00:00
guerler 4e3ca993f2 Fix nginx-based file upload 2016-03-21 20:44:22 -04:00
Dannon Baker 35e75d11ce Merge branch 'release_16.01' into dev. 
Rebuild client.
 2016-03-21 19:33:05 -04:00
Dannon Baker 566f556b07 Merge pull request #1952 from guerler/fix_tool_access_000 
[16.01] Fix tool access rights and forwarding
 2016-03-21 19:29:31 -04:00
Dannon Baker 8d37aeff50 Manual merge to resolve conflict 16.01->dev 2016-03-21 16:36:48 -04:00
Dannon Baker 377ccbe23b Merge pull request #1967 from jmchilton/fix_optional_numeric_params 
[16.01] Fix #1721.
 2016-03-21 16:18:27 -04:00
John Chilton 2efd9c2687 Fix #1721. 
TODO: write test...
 2016-03-21 13:51:26 +00:00
John Chilton 5df7830424 Do not use "is not" to compare strings. 
http://stackoverflow.com/questions/1504717/why-does-comparing-strings-in-python-using-either-or-is-sometimes-produce
 2016-03-21 12:06:35 +00:00
John Chilton 5ead8a95d1 Merge pull request #1941 from bgruening/chemical_datatypes 
add chemical datatypes
 2016-03-21 11:49:31 -04:00
John Chilton c8cb4280c1 Fix datatype sniff test to use sample and revert molecule registry hacks. 2016-03-21 09:53:21 +00:00
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
John Chilton 9e9dfdfd55 Fix workflow scheduler log message. 2016-03-21 00:51:18 +00:00
Bjoern Gruening 1e9b0e6dbd add molecule datatypes, like PDB and some cheminformatic ones 2016-03-20 18:06:14 +01:00
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
guerler 054fdf76f0 Parse user when filtering tools 2016-03-18 20:48:24 -04:00
guerler bd0439d9b7 Fix tool access rights and forwarding 2016-03-18 20:12:21 -04:00
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