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
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[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
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Fix nginx-based file upload
2016-03-22 07:51:33 -04:00
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.
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Rebuild client.
2016-03-21 19:33:05 -04:00
Dannon Baker
566f556b07
Merge pull request #1952 from guerler/fix_tool_access_000
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[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
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[16.01] Fix #1721 .
2016-03-21 16:18:27 -04:00
John Chilton
2efd9c2687
Fix #1721 .
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TODO: write test...
2016-03-21 13:51:26 +00:00
John Chilton
5df7830424
Do not use "is not" to compare strings.
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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
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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.
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- 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
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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
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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
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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
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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
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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
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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
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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
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[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
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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
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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
Dannon Baker