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Author SHA1 Message Date
Martin Cech 4b1b15aee8 libraries: provide select all/none options when importing 
improve UX by using autofocus in modals
fix a bug with selecting all folder items and deleting
 2016-03-21 17:26:01 -04:00
Dannon Baker 162f6d49af Merge pull request #1963 from jmchilton/str_comp 
Do not use "is not" to compare strings.
 2016-03-21 13:21:56 -04:00
John Chilton 058c644d88 Merge pull request #1954 from kellrott/dev 
Fixing error in run.sh script
 2016-03-21 12:55:25 -04:00
John Chilton c0f5ae88a7 Merge pull request #1962 from martenson/better-library-paging 
libraries: also show folder items paginator at the bottom of the items
 2016-03-21 12:54:38 -04:00
Martin Cech 50e5b08d7c libraries: also show folder items paginator at the bottom of the items 2016-03-21 12:09:14 -04:00
John Chilton 5ead8a95d1 Merge pull request #1941 from bgruening/chemical_datatypes 
add chemical datatypes
 2016-03-21 11:49:31 -04:00
Björn Grüning df719c83b6 Merge pull request #9 from jmchilton/chemical_datatypes 
Fix datatype sniff test to use sample and revert molecule registry ha…
 2016-03-21 15:57:53 +01:00
Martin Cech b71ab68862 Merge pull request #1961 from jmchilton/more_aggressive_retry 
Improve logging and retry  for another TS test...
 2016-03-21 10:22:14 -04:00
Martin Cech 901cab12cb Merge pull request #1956 from jmchilton/more_job_logging 
More job related timing logging.
 2016-03-21 09:37:39 -04:00
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 c8cb4280c1 Fix datatype sniff test to use sample and revert molecule registry hacks. 2016-03-21 09:53:21 +00:00
John Chilton d3c6dfc2d8 Improve logging and retry for another TS test... 
... I thought there was only one transiently failing tool shed test but there appears to be two.
 2016-03-21 08:46:28 +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
Kyle Ellrott d5c52cadfd Fixing error in run.sh script 2016-03-20 17:59:31 -07:00
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
Dannon Baker 53daf30dd2 Merge branch 'release_16.01' into dev 2016-03-18 15:41:14 -04:00
Daniel Blankenberg 19bf334c77 Merge pull request #1945 from dannon/fluent_logging_fix 
[16.01] Fix handling of time in fluent logger
 2016-03-18 10:14:42 -04:00
Aysam Guerler 6fff01c01c Merge pull request #1949 from blankenberg/history-list-new-hda 
Add "new" state to list of dataset states in saved history list.
 2016-03-17 20:28:53 -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
Jeremy Goecks 38d7bbb712 Merge pull request #3 from dannon/history-grid-state-optimization 
It's a function, not a true-y value :/
 2016-03-17 15:43:26 -04:00
Dannon Baker 78da8df812 Oops. 2016-03-17 15:20:27 -04:00
Jeremy Goecks 8c1defe60e Merge pull request #2 from dannon/history-grid-state-optimization 
Minor style tweaks to pass flake8
 2016-03-17 15:16:50 -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 c8e48bfacc Add fluentd configuration to galaxy.ini.sample 2016-03-17 13:03:04 -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
Björn Grüning 89b25edc31 Merge pull request #1942 from jmchilton/element_count_test 
Allow testing element counts in tool output collections.
 2016-03-17 15:02:15 +01:00
Dave Bouvier 80562acfe8 Fix API method broken in 6e13c3999. 2016-03-17 09:24:43 -04:00
Martin Cech 7fad23614b Merge pull request #1939 from jmchilton/transient_ts_test 
More debugging for transiently failing tool shed test.
 2016-03-17 09:16:16 -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
John Chilton 3e5aa68ccf More debugging for transiently failing tool test. 2016-03-16 18:59:42 +00:00
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 e86969b4cb Merge pull request #1934 from guerler/fix_icon_size_000 
Fix icon sizes
 2016-03-16 12:13:54 -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
guerler 4976945ab0 Fix icon sizes 2016-03-15 17:21:21 -04:00
Nate Coraor 00a7c3af05 Merge pull request #1890 from jmchilton/fix_virtualenvs 
[16.01] Fix virtual env handling broken with #1847.
 2016-03-15 16:52:52 -04:00