John Chilton
1acda2715f
Introduce abstraction for updating ToolBox's shed configs.
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Hides some details of writing out integrated tool panel, reindexing, etc... from tool shed install code and reduces duplicatation in tool shed's tool_panel_manager.
Add unit tests.
2014-12-23 13:52:39 -05:00
John Chilton
540b6edacd
Introduce abstraction for reindexing tool search.
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Fixes re-indexing after tool shed modifications for 5c44ac1 and reduces duplication.
2014-12-23 13:52:39 -05:00
John Chilton
41628b3faf
PEP-8 fixes to tool_shed.galaxy_install.tools.tool_panel_manager.
2014-12-23 13:52:39 -05:00
John Chilton
d2081e1fea
Start work on unit tests for galaxy.tools.ToolBox.
2014-12-23 13:52:39 -05:00
John Chilton
82533c33e4
Update XML library use during tool parsing to elimiante FutureWarnings.
2014-12-23 13:52:39 -05:00
John Chilton
cc57715b15
Make use_tool_dependencies an optional attribute of config.
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This way the tool shed doesn't need to pointlessly configure this property to create a toolbox.
2014-12-23 13:52:39 -05:00
John Chilton
99a2c1950f
Make tool filters properties optional attributes of config.
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This way the tool shed doesn't need to pointlessly add them to its config object.
2014-12-23 13:52:39 -05:00
Carl Eberhard
2f7eec5d93
merge
2014-12-22 14:58:44 -05:00
Carl Eberhard
981954e107
UsesHistoryMixin, get_history: allow anon users to get their current history; update browser tests; remove unused selenium tests
2014-12-22 14:35:08 -05:00
John Chilton
8a10d14c32
Add comment to auto-generated integrated_tool_panel.xml.
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Someone more familiar with integrated_tool_panel.xml should feel free to make this comment sharper - but something is better nothing I think.
2014-12-22 13:16:30 -05:00
John Chilton
fb1e9fc5f4
Start decoupling Toolbox elements from XML (sections+labels).
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Just a small tweak and some tests to verify these things can indeed be created from dictionaries. Also slightly simplifies galaxy.tools.
2014-12-22 13:16:30 -05:00
John Chilton
dee0793e5a
Tweak completely broken DataTransfer._execute_workflow to respect toolbox abstraction.
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Least of the brokeness at this point I suppose - but I would like to not expose tools_by_id external to the Toolbox.
2014-12-22 13:16:28 -05:00
John Chilton
34e7ac89c5
Refactor tool tag handling out of toolbox.
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Pretty sure this had been broken (toolbox didn't have a self.sa_session). Anyway - this probably didn't fix that but at least now the big read tool tag loop is more readable (cyclomatic complexity of that method down from 18 to 12).
2014-12-22 13:16:28 -05:00
John Chilton
917175d237
Rework toolbox 'fix' tool tags when multiple configs are loaded.
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Looks like the tool tag stuff still assumed there was just one config file - that said toolbox doesn't have a self.sa_session so I think tool tags are broken and have been for some time.
2014-12-22 13:16:27 -05:00
John Chilton
92e6a8e4ff
Slightly rework lib/galaxy/workflow/modules.py for readability.
2014-12-22 13:16:27 -05:00
John Chilton
9d899a0654
Remove broken method fix_integrated_tool_panel_dict.
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As of 5f6c670 (Jan 10, 2014) this does nothing (``if section_value is None`` followed by ``if isinstance( section_value, Tool ):``) and nobody seemed to notice - so I assume it is unneeded. If still needed - someone needs to fix it :).
2014-12-22 13:16:26 -05:00
John Chilton
a23846839b
Small simplifications to lib/galaxy/tools/__init__.py.
2014-12-22 13:16:26 -05:00
John Chilton
7fa267ebcd
More PEP-8 style tweaks to lib/galaxy/tools/__init__.py.
2014-12-22 13:16:25 -05:00
John Chilton
ca370e3cfc
Remove some unused imports from lib/galaxy/tools/__init__.py.
2014-12-22 13:16:25 -05:00
John Chilton
285896dfe1
Increase consistency between job index and show.
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Add tests for new date range and history filtering as well as to ensure only admins get to see external_id and command_line and that users cannot see each other's jobs.
Always allow admins to views all jobs on index (instead of only when user_details is specified) and show. Add user_email and external_id to show (for admins) to bring it inline with index and add command_line to index (for admins) to bring it in line with show.
Show still allow more details including job standard error and output as well as job metrics.
2014-12-18 21:50:15 -05:00
John Chilton
92846d0ae8
PEP-8 fix for api/jobs.py.
2014-12-18 21:50:15 -05:00
John Chilton
675ba22e5c
Merge pull request #610 .
2014-12-18 21:49:03 -05:00
John Chilton
948b8d0375
Fix bug in 8d5089f2ba8183439a866026f3583c377f8bfa74.
2014-12-18 10:21:42 -05:00
John Chilton
6bb3958a55
Merged in jmchilton/galaxy-central-fork-1 (pull request #617 )
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Allow tool tests to assert properties about command, standard output, and standard error.
2014-12-17 15:47:54 -05:00
Dannon Baker
3b0e963015
Merge.
2014-12-17 15:41:21 -05:00
Dannon Baker
a02b5a5d33
Pointed out by Eric, Apache based remote_user_headers can possibly be (null)@domain.edu for some local configurations and this allows REMOTE_AUTH to work correctly in that situation as well as the usual (null) header.
2014-12-17 15:40:30 -05:00
John Chilton
8e060c77bc
Implement expect_failure and expect_exit_code on test tag of tools.
2014-12-17 14:22:08 -05:00
John Chilton
77ee2ace67
Allow tool tests to assert properties about command, standard output, and standard error.
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See test/functional/tools/job_properties.xml for example. Provides full access to assertion based XML tags - tabular and XML based assertions probably not so interesting so these include - has_text, has_line, not_has_text, has_text_matching, has_line_matching.
2014-12-17 12:34:39 -05:00
John Chilton
01d984624f
Remove old comment.
2014-12-17 12:32:50 -05:00
Dannon Baker
fe9e2be67d
Add thead element to tabular dataset view.
2014-12-17 12:06:23 -05:00
John Chilton
afba51fdc9
Merge.
2014-12-17 11:02:45 -05:00
John Chilton
0baffcb977
Fixed for botched automated merge 78597d2.
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Makes me worry about all the automated merges I have done lately. Also - I hate you mercurial.
2014-12-17 11:01:16 -05:00
Dannon Baker
00f80427fe
Delete *ancient* cron/cleanup_datsets.py content, but leave a nice deprecation warning and pointer for those who might actually be using it in cron jobs.
2014-12-17 11:00:29 -05:00
John Chilton
195eab61fb
Fix a74d320.
2014-12-17 10:57:44 -05:00
John Chilton
0a1a871fd0
Merge next-stable.
2014-12-17 09:41:26 -05:00
John Chilton
c4d29ad1b6
Fix gz/zip upload of files to test framework.
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With test case to ensure they don't break again. Problem was due to a small switch of an if to an elif in 7114d15a6d22 which had been sort of masking over an older bug.
Thanks to Peter Cock for reporting the issue.
2014-12-17 09:38:49 -05:00
Dannon Baker
9624b032ae
Merged in nitesh1989/galaxy-central3 (pull request #615 )
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"shed_tool_conf.xml.sample" is located inside config directory. Only seems logical that "shed_tool_conf.xml" should be in config also.
2014-12-16 15:48:44 -05:00
Dave Bouvier
5d3c362a3d
Merge next-stable into default.
2014-12-16 15:16:18 -05:00
Dave Bouvier
acad7fa8ee
Merge stable into next-stable.
2014-12-16 15:15:57 -05:00
Dave Bouvier
24012f7d65
Reduce minimum length of repository names from 4 characters to 2.
2014-12-16 15:00:50 -05:00
Aysam Guerler
61d34f4e95
ToolForm: Minor UI adjustments
2014-12-16 13:24:42 -05:00
Aysam Guerler
795b4c5068
ToolForm: Improve form update and job submission
2014-12-16 11:45:40 -05:00
Nitesh Turaga
020f393e8c
"shed_tool_conf.xml.sample" is located inside config directory. Only seems logical that "shed_tool_conf.xml" should be in config also.
2014-12-16 11:04:58 -05:00
Nate Coraor
75da622efe
Update tag latest_2014.10.06 for changeset 7086b87d83a9
2014-12-16 09:00:19 -05:00
Dannon Baker
4e191e3518
Merge.
2014-12-16 02:42:21 -05:00
Dannon Baker
1a9d041ab2
Merged in jjohnson/galaxy-central-8/jjohnson/use-a-select-statement-to-reliably-retri-1418411766371 (pull request #608 )
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Use a SELECT statement to reliably retrieve table column names.
2014-12-16 02:41:34 -05:00
Aysam Guerler
dd4d82b6db
Parameters: Add missing assertion
2014-12-16 02:11:07 -05:00
Dannon Baker
1f25f9bd28
Include packed script that was missed in b6f28aec
2014-12-16 02:03:12 -05:00
Dannon Baker
2896de69ff
Remove extraneous 'column' reference in exception message.
2014-12-16 01:54:45 -05:00
Dannon Baker
c7ebf7dacc
Merged in dan/galaxy-central-prs/stable (pull request #613 )
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[STABLE] Do not |h escape tool dependency error message, as it is escaped and formated by tool_shed.util.basic_util.to_html_string
2014-12-16 01:31:43 -05:00
John Chilton