Alexander Lenail
4dc8b7d803
clean things up a little...
2016-07-26 18:13:49 -04:00
Alexander Lenail
e349aafe04
fix bug.
2016-07-26 17:09:49 -04:00
Alexander Lenail
0b1730fe7f
trying this...
2016-07-26 16:48:22 -04:00
Alexander Lenail
0da66864e4
Merge pull request #2 from dannon/azure-blob-objectstore
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Fixes azure_blob detection for conditional dependency resolution
2016-07-26 16:32:08 -04:00
Dannon Baker
3199217448
Remove debug print
2016-07-26 08:08:55 -04:00
Dannon Baker
e59602fed1
Update check_azure_storage check, read the object store config to detect stores.
2016-07-26 08:06:53 -04:00
Alexander Lenail
d36162a389
fixes the lint error I think.
2016-07-22 13:29:41 -04:00
Alexander Lenail
7dcc6374cc
oops =)
2016-07-21 15:39:21 -04:00
Alexander Lenail
91081bf280
added dependency to azure
2016-07-21 15:36:37 -04:00
Alexander Lenail
ca79c905f8
oops again...
2016-07-21 14:08:23 -04:00
Alexander Lenail
4a8a14d8cf
Merge remote-tracking branch 'galaxyproject/dev' into azure-blob-objectstore
2016-07-21 13:26:02 -04:00
Alexander Lenail
d9d5492991
more consistent naming.
2016-07-21 13:25:53 -04:00
Nicola Soranzo
423e85fc81
Merge pull request #2630 from dannon/base_framework_string_handling
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Smart string handling on the wsgi response -- this fixes uwsgi blanki…
2016-07-21 18:07:38 +01:00
Alexander Lenail
ebe83e21bd
Merge pull request #1 from dannon/minor_azure_tweaks
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Address minor azure objblob lint issues, and one UndefinedObject issue.
2016-07-21 13:04:33 -04:00
Dannon Baker
a2c5e33d02
Address minor azure objblob lint issues, and one UndefinedObject issue.
2016-07-21 13:03:41 -04:00
Alexander Lenail
2405f558c8
Oops..
2016-07-21 13:00:19 -04:00
Alexander Lenail
4fa0c27bf1
Another lint pass.
2016-07-21 12:04:09 -04:00
Alexander Lenail
8bc8e38b36
typo
2016-07-21 11:25:59 -04:00
Alexander Lenail
c668baeea5
better naming
2016-07-21 11:24:26 -04:00
Alexander Lenail
cb44eb372e
Merge remote-tracking branch 'galaxyproject/dev' into azure-blob-objectstore
2016-07-21 11:18:11 -04:00
Alexander Lenail
3a3074134f
fixed most lint errors
2016-07-21 11:17:38 -04:00
John Chilton
f67d3cbe93
Merge pull request #2579 from phac-nml/add-dtd-to-galaxy
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Add DTD to Galaxy
2016-07-21 11:07:55 -04:00
Nicola Soranzo
47f25f1dc6
Merge pull request #2631 from jmchilton/output_filter_exception
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Add tool test for what happens when output filter throws exception.
2016-07-21 15:59:43 +01:00
John Chilton
274ec0f953
Fix typo spotted by @nsoranzo.
2016-07-21 08:55:35 -04:00
John Chilton
8d24fbe0fe
Merge pull request #2632 from guerler/fix_workflow_data_on_load
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Properly initialize datasets when workflow is loaded for execution
2016-07-21 08:52:32 -04:00
Dannon Baker
2b3a0334e0
Merge branch 'release_16.04' into dev
2016-07-21 08:36:15 -04:00
Dannon Baker
132bd4dd57
Merge branch 'backport_2613' into release_16.04
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(and rebuild client)
2016-07-21 08:33:47 -04:00
Dannon Baker
c6c22a977f
Merge pull request #2637 from nsoranzo/get_file_peek
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Optimize get_file_peek()
2016-07-21 08:30:22 -04:00
Eric Enns
a4c713bf64
Fix dict iteration in dtd default_destination parsing/validation
2016-07-20 16:22:08 -05:00
Eric Enns
5ae1058272
Updated tool_destinations.yml.sample to include a little more information
2016-07-20 16:04:46 -05:00
Eric Enns
43fccc9887
Moved dtd tests into a different folder
2016-07-20 15:52:04 -05:00
John Chilton
d87957e1a2
Ease configuration and add documentation for using DTD syntax for destinations.
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Moving rules also means it won't conflict with other peoples custom dynamic destinations and should prevent Galaxy from reloading the Python repeatedly.
2016-07-20 15:58:34 -04:00
John Chilton
ed48c6c28b
Use more traditional Galaxy config handling for DTD.
2016-07-20 15:46:57 -04:00
Dannon Baker
715441df84
Merge pull request #2639 from nturaga/typo_summary_stats_tool
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typo in summary statistics tool
2016-07-20 15:46:13 -04:00
nturaga
4fabf51f4b
typo in summary statistics tool
2016-07-20 15:27:24 -04:00
Dannon Baker
a5f9e5b9ef
Reverted the refactoring of flatten; generator wasn't unpacking (of
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course), and caused an infinite loop.
2016-07-20 13:39:12 -04:00
Nicola Soranzo
9b5f6d60c6
Fix smart_str doctest
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Docstrings should start with 'u"""' if containing Unicode characters (see
also PEP 257).
Backslashes should be doubled in docstrings (or raw strings should be used,
but the 'ur' prefix is not supported in Python3).
2016-07-20 18:17:30 +01:00
Nicola Soranzo
0303ec33ae
Optimize get_file_peek()
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last_line was always the empty string because line is read with readline()
and therefore '\n' is always its last character (if it is present).
Follow-up to #2556 .
2016-07-20 18:17:30 +01:00
Daniel Blankenberg
5fe4bea3ae
Merge pull request #2634 from jmchilton/list_list_list_problem
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Fix certain combos of dynamic deeply nested collections in workflows.
2016-07-20 13:12:24 -04:00
Dannon Baker
5ba7e5adae
Make sure yielded items from a flattened iterable are properly stringified.
2016-07-20 12:15:32 -04:00
Dannon Baker
01cdb9387e
Simplify flatten method
2016-07-20 12:09:09 -04:00
John Chilton
54b8ae00db
Rework test case that fails occasionally on Jenkins.
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Should be a little more robust now.
2016-07-20 12:08:18 -04:00
Dannon Baker
f36095a9fb
Merge branch 'release_16.04' into dev
2016-07-19 18:18:01 -04:00
Dannon Baker
95c64c0ba9
Rebuild as a part of merging from 16.01.
2016-07-19 18:14:15 -04:00
Dannon Baker
ac64c0162e
Merge branch 'release_16.01' into release_16.04
2016-07-19 18:12:47 -04:00
Dannon Baker
f4631d2e59
Merge pull request #2629 from carlfeberhard/fix.saved-copy
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[16.01] UI, history: replace copy dialog on grid refresh
2016-07-19 18:12:17 -04:00
John Chilton
85d7784b18
Fix concepts "populated" & "waiting_for_elements" for nested collections.
2016-07-19 16:20:55 -04:00
John Chilton
39c095aa6a
Improved logging and error message when mapping over an empty* collection.
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*actually empty or accidentally empty.
2016-07-19 16:20:55 -04:00
John Chilton
30fd1e0e64
Test case for dynamically creating list:list:lists.
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This could check the outputs ideally, but it was failing to simply execute the workflow so this does serve as check that some bugs are fixed.
2016-07-19 16:20:09 -04:00
Alexander Lenail
0a49f17411
Modified galaxy.objectstore.rst
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Not sure how RST works — would appreciate some guidance here.
2016-07-19 15:27:01 -04:00
Alexander Lenail