E Rasche
2f8347d5bc
add clientside route
2017-08-10 17:53:01 +02:00
E Rasche
d7e400c96d
Per @jmchilton comment, rewrite as yml
2017-08-10 17:53:00 +02:00
E Rasche
46b621708a
Allow sentry to be verbose
2017-08-10 17:53:00 +02:00
E Rasche
181a72a6f3
flake8 import
2017-08-10 17:53:00 +02:00
E Rasche
9dd27dcc3d
flake8
2017-08-10 17:53:00 +02:00
E Rasche
70a64b304e
Refactor bug reporting into plugins
2017-08-10 17:53:00 +02:00
guerler
cfa3220d9f
Merge branch 'dev' into revise_page
2017-08-09 17:33:28 -04:00
Martin Cech
d52ac533da
fix indentation
2017-08-09 16:51:25 -04:00
Martin Cech
cff21d350d
Merge branch 'dev' into library_tags
2017-08-09 16:03:29 -04:00
guerler
8f056c2bbc
Merge branch 'dev' into revise_page
2017-08-09 12:32:30 -04:00
Nicola Soranzo
7ca5cd6585
Fix import order and Python3 compatibility for lib/galaxy/web/base/
2017-08-09 15:07:34 +01:00
Nicola Soranzo
c7d7b6c469
Merge pull request #4395 from jmchilton/parser_to_str_fix
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Bugfix: __str__ method on tool parsers would throw an Exception.
2017-08-09 11:20:47 +01:00
Marius van den Beek
a001145278
Merge pull request #4383 from jmchilton/split_conda
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Bugfix: Ensure task splitting handles before job resolution.
2017-08-09 07:47:22 +02:00
John Chilton
11365e9620
Bugfix: __str__ method on tool parsers would throw an Exception.
2017-08-08 22:53:08 -04:00
John Chilton
c03b29f485
Revise comment thanks to note from @mvdbeek.
2017-08-08 22:30:11 -04:00
John Chilton
bc23c26cf4
Merge pull request #4391 from mvdbeek/more_version_fixes
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Get tools with tool_version in more places
2017-08-08 22:25:44 -04:00
John Chilton
ff197fe915
Merge pull request #4386 from mvdbeek/display_minimum_required_galaxy_version
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Show minimum required galaxy version in tool shed and galaxy installation process
2017-08-08 13:59:19 -04:00
John Chilton
0da4768c35
Merge pull request #4388 from mvdbeek/iter_headers
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Replace list with generator when iterating headers
2017-08-08 13:55:02 -04:00
Eric Rasche
196a2bbcf5
Merge pull request #3383 from bgruening/extra_user_preferences
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Add extension point for user preferences
2017-08-08 18:42:09 +02:00
mvdbeek
43702ccacd
Process the first line when setting metdata for mother.otu files
2017-08-08 17:53:24 +02:00
mvdbeek
e6c238e234
Move iter_headers into try clause (thx @nsoranzo)
2017-08-08 17:35:04 +02:00
mvdbeek
a060690c3a
Get tools with tool_version in more places
2017-08-08 17:25:20 +02:00
Nicola Soranzo
4a35bd3532
Merge pull request #4390 from jmchilton/toollist
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Fix get_tool returning list when it shouldn't.
2017-08-08 15:40:33 +01:00
mvdbeek
fe2d607675
Replace list with generator when iterating headers
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This should be more memory-friendly. @blankenberg suggested doing this
in #4319 .
2017-08-08 15:10:39 +02:00
John Chilton
bf68966acc
Fix get_tool returning list when it shouldn't.
2017-08-08 08:36:46 -04:00
John Chilton
e811221042
Improve cohesion of interaction between ToolOutputCollectionStructure and ToolOutputCollection.
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Shield more of ToolOutputCollectionStructure internals from ToolOutputCollection.
2017-08-08 08:32:26 -04:00
John Chilton
ecad3996f1
Refactor ToolOutputCollectionStructure to allow it be more easily consumed.
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Make complex arguments optional.
2017-08-08 08:32:25 -04:00
mvdbeek
a77c4587fb
Shorten 'Minimum required Galaxy version' to 'Minimum Galaxy Version'
2017-08-08 13:09:56 +02:00
mvdbeek
20f90254bf
Show minimum required galaxy version in tool shed and galaxy installation process
2017-08-08 12:18:52 +02:00
Björn Grüning
eb8f7f0da3
remove debug statement
2017-08-08 11:39:34 +02:00
Björn Grüning
338fffad0b
Remove user_preferences_extra_conf.yml sample file from the default list
2017-08-08 10:32:12 +02:00
Björn Grüning
a06ec3e58d
change xml to yml
2017-08-08 10:10:39 +02:00
Martin Cech
d2394aa172
Merge pull request #4198 from fabio-cumbo/data-source-async
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Async update: support to collections
2017-08-07 17:52:58 -04:00
Björn Grüning
6e37bc05c1
Merge pull request #4382 from mvdbeek/enforce_tool_profiles
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Stop loading tools that require a newer galaxy
2017-08-07 22:24:48 +02:00
John Chilton
061eb25640
Add comment about fix for #4381 .
2017-08-07 15:36:37 -04:00
John Chilton
5be7768047
Merge pull request #4326 from mvdbeek/history_import_from_file
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Allow import of history archives via simple file upload
2017-08-07 15:21:17 -04:00
John Chilton
31f68edbba
Merge pull request #4358 from mvdbeek/paramiko_based_shell_runner
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Paramiko based shell runner
2017-08-07 15:15:42 -04:00
John Chilton
aa29b3a1a1
Fix job splitting so it happens before dependency resolution?
2017-08-07 15:02:06 -04:00
mvdbeek
b19640b81a
Stop loading tools that require a newer galaxy
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We look at a tools profile attribute, and if it is too new we will not
load the tool. This is a first step towards
https://github.com/galaxyproject/galaxy/issues/2086
2017-08-07 18:53:25 +02:00
Bjoern Gruening
03bbbe96a9
fix linting error
2017-08-07 18:17:04 +02:00
Bjoern Gruening
dc9c71f757
rename the config files from XML to YML
2017-08-07 15:57:01 +02:00
Bjoern Gruening
1ca8f2c927
use yml instead of XML and reorder the preference panels
2017-08-07 15:56:40 +02:00
Bjoern Gruening
4aa8d631d9
register user_preference config file
2017-08-07 15:14:45 +02:00
Bjoern Gruening
045039da95
merge with master, address Aysams comments
2017-08-07 14:52:32 +02:00
Bjoern Gruening
94b2184f89
merge with master
2017-08-07 14:52:27 +02:00
John Chilton
e92a15a185
Merge pull request #4368 from mvdbeek/tie_down_collection_matcher
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Implement default_identifier_source for outputs and sort input keys by default
2017-08-07 07:45:37 -04:00
John Chilton
3f270e91af
Merge pull request #4315 from jlhg/fix-s3mu-map-wrap
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Fix TypeError when uploading large files from ftp to s3
2017-08-07 07:35:01 -04:00
Eric Rasche
4effd7d77a
Merge pull request #4365 from jmchilton/csrf
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CSRF protection for login, logout, and user registration.
2017-08-05 08:27:57 +02:00
John Chilton
b17091a3ec
CSRF protection for login, logout, and user registeration.
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The approach is to use per-session CSRF tokens - this avoids many complications related to per-form tokens. We generate a sequence of hashes based on session IDs that doesn't follow the same pattern as normal database API IDs by supplying a "kind" parameter to encode_id (we use the same pattern for securing the job files API for Pulsar).
2017-08-04 11:52:13 -04:00
mvdbeek
ccad70c22c
Add warnings if a tool lineage could not be retrieved
2017-08-04 13:40:13 +02:00
E Rasche