John Chilton
28749c8c80
Merged in jmchilton/galaxy-central-fork-1 (pull request #342 )
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Refactor History Contents to Support Multiple Types
2014-03-04 07:25:07 -06:00
Daniel Blankenberg
e1750666e0
Delimit Biostar tags by commas.
2014-03-03 17:21:50 -05:00
Dave Bouvier
27cda094f6
Update setup_r_environment to work with the elimination of fabric.
2014-03-03 15:35:26 -05:00
Jeremy Goecks
ee7d642503
Extend TabularDataTableView to support full page view and an embedded view.
2014-03-03 14:04:09 -05:00
Enis Afgan
385b760b9d
Add kwd to get_dbkeys method signature to fix the API call that includes the actual API key in the request
2014-03-03 17:39:40 +01:00
Daniel Blankenberg
374eadfb62
Use qualified url for biostar_url_redirect due to javascript always prepending galaxy base prefix (e.g. usually /) unless url contains //
2014-03-03 10:09:19 -05:00
Daniel Blankenberg
38834dbe0f
Fixes for biostar show galaxy tag redirect
2014-03-03 09:57:31 -05:00
Daniel Blankenberg
6af8f4d88e
Update Biostar interaction to use new cookie-based method.
2014-03-03 09:11:38 -05:00
Jeremy Goecks
b1ead9cdb8
Automated merge
2014-02-28 17:03:52 -05:00
Jeremy Goecks
5c5ff9c085
Add header and line demarcation to tabular chunked data view.
2014-02-28 16:18:05 -05:00
John Chilton
be13bd26a7
Test cases for filtering tool parameters on other parameter values.
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Includes test case that is broken without JJ's contributions in pull request #343 .
2014-02-28 14:49:46 -06:00
Jeremy Goecks
388c8316d2
Trackster: replace custom config settings model and view with generic model/view from config.js. Improvements for generic config model/view. Whitespace fixes.
2014-02-28 15:27:59 -05:00
Daniel Blankenberg
5dca8912fa
UI fixes for Configure workflow menu.
2014-02-28 15:02:07 -05:00
John Chilton
fb9d65f76e
Add test cases for need_late_validation of select parameters.
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Two of these fail without JJ's work in pull request 336, additionally these verify 336 doesn't break GATK support for instance.
2014-02-28 12:42:30 -06:00
John Chilton
7d771ba629
Merge JJ's pull request #315 (with minor modifications discussed with JJ).
2014-02-28 10:08:26 -06:00
John Chilton
32d61e01f3
Modify jobs index to allow exact or inexact tool id filtering.
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Discussed this with JJ and Dannon. Formerly this was only inexact matchings, I was a little worried about API users expected exact tool id matches when using a parameter called tool_id. JJ's original intended behavior can be accessed using tool_id_like.
2014-02-28 10:02:29 -06:00
John Chilton
2754bcf995
Reduce a little code dup in api/jobs.py.
2014-02-28 09:57:53 -06:00
Greg Von Kuster
32a8bfe9e1
Minor fixes for installing tool dependencies and counting repositories processed during the tool shed's install and test runs.
2014-02-28 08:52:52 -05:00
John Chilton
e70cbcf372
Rework history_contents API to allow room for multiple 'type's of history contents.
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Downstream dataset collections are being added and can be associated with histories. They have hids, can be deleted, etc... many of the same properties as HDAs. This refactoring "makes room" for these in the history contents API by allowing type to be passed in.
Since HDAs and HDCAs can have the same id - the path history/{history_id}/contents/{contents_id} is somewhat ambigious - so this changeset adds the path history/{history_id}/contents/datasets/{history_dataset_id} while a matching resource path downstream history/{history_id}/contents/dataset_collections/{history_dataset_collection_id} has been added.
The vanilla contents path remains but should be considered deprecated IMO.
Adding type parameter to history/{history_id}/contents index route - this will always default to dataset for backward compatibility - but downstream can be specified as either dataset, dataset_collection, or "dataset,dataset_collection".
2014-02-27 18:06:36 -06:00
John Chilton
838ed82e31
Rework history.contents_iter to potentially support multiple types.
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This is utilized downstream in collections work to allow a similar API to be used for loading HistoryDatasetCollectionAssociations as HistoryDatasetAssociations.
2014-02-27 18:06:36 -06:00
John Chilton
77a0d8f277
Start rework of API test mixin TestsDataset into an plain object.
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Mirroring the newer WorkflowPopulator and LibraryPopulator.
2014-02-27 18:06:36 -06:00
John Chilton
347e4dd046
Infrastructure for library API testing.
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Doesn't really test libraries extensively, but adds enough infrastructure to enable a library dataset to history copy test via API.
2014-02-27 18:06:36 -06:00
John Chilton
00b0b6c442
Include LDDA state in library dataset to_dict.
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Needed to monitor library dataset uploads (in particular for API tests, but really any monitoring will benefit from this).
2014-02-27 18:06:36 -06:00
John Chilton
7f96eae91c
Include root folder id in output when creating library.
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This prevents the need to hit the API one more time to get the root folder ID before creating datasets/folders/etc... in the library.
2014-02-27 18:06:36 -06:00
John Chilton
a18dbc0a07
Initial work on test cases for history contents API.
2014-02-27 18:06:36 -06:00
Jeremy Goecks
c292039fe9
Automated merge
2014-02-27 16:56:25 -05:00
Jeremy Goecks
4e098ea2d5
Trackster: track mouse with vertical line to support visual alignment.
2014-02-27 16:56:03 -05:00
Dave Bouvier
601984107c
Eliminate the use of shell commands to perform functions that can be done internally with the elimination of fabric.local for tool dependency installation.
2014-02-27 15:46:03 -05:00
Greg Von Kuster
1c1e420bcb
Improve time management and process handling when installing repositories and tool dependencies from the tool shed and completely eliminate the tuse of fabric.local when installing tool dependencies.
2014-02-27 12:14:53 -05:00
Dave Bouvier
c2c5ffda35
Fix python 2.6 support.
2014-02-27 09:20:45 -05:00
Bjoern Gruening
071f8b22c1
change strip to rstrip as proposed by Nicola
2014-02-27 11:12:49 +01:00
Bjoern Gruening
a05617e5fe
strip trailing slashes in tool IDs
2014-02-27 09:40:35 +01:00
Dave Bouvier
cd8b4f7497
Merge stable.
2014-02-26 15:11:47 -05:00
Greg Von Kuster
73a12d096e
Fixes for handling complex repository dependency definitions in tool dependency recipes.
2014-02-26 15:09:43 -05:00
Greg Von Kuster
a88e1d324a
Fixes for handling complex repository dependency definitions in tool dependency recipes.
2014-02-26 15:09:43 -05:00
Jeremy Goecks
788f023ee9
Automated merge of stable to default.
2014-02-26 14:06:19 -05:00
Jeremy Goecks
7fdb6b2954
Trackster: location parsing/interpretation fix.
2014-02-26 14:05:50 -05:00
Aysam Guerler
3ef52ddb04
UI: Add click-event handler to tabs, Ui: Improve table wrapper, Charts: Hide tooltips on element hide, improve UI
2014-02-26 13:09:23 -05:00
John Chilton
8daf4c6e03
Merge latest stable.
2014-02-26 10:32:13 -06:00
John Chilton
6c5fcb9410
Merged in jmchilton/galaxy-central-fork-1/stable (pull request #333 )
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Disable rendering of user uploaded/tool generated SVG files.
2014-02-26 10:30:09 -06:00
Carl Eberhard
fa2732f347
merge
2014-02-26 10:53:13 -05:00
Carl Eberhard
c54cf5642b
Improve embedded item editing in pages: a) preserve empty paragraphs, b) when the cursor is in an embedded title and enter is pressed: create a new paragraph before the item, when the cursor is in an embedded content and enter is pressed: create a new paragraph after the item
2014-02-26 10:52:56 -05:00
Dave Bouvier
c5640993b6
Use log instead of print for tool dependency installation processes' stdout and stderr, since twill redirects those streams to a StringIO object.
2014-02-26 10:20:44 -05:00
Dave Bouvier
95ab78b847
Fix missing parenthesis.
2014-02-26 10:19:48 -05:00
Daniel Blankenberg
c5ab91e8f4
Fix for uninstalling a ToolShed tool repository revision with a tool with multiple versions installed not properly replacing with the still existing tool version in the tool panel.
2014-02-25 17:36:59 -05:00
Jeremy Goecks
f4b401aa7e
Automated merge of stable to default.
2014-02-25 16:43:51 -05:00
Jeremy Goecks
e6eeee639f
Trackster bug fixes: (a) ignore arrow keys in location textbox; (b) set title for location textbox; and (c) test low and high correctly when changing location. Pack scripts.
2014-02-25 16:43:18 -05:00
Greg Von Kuster
d6b5e3f4e2
More fixes for fabric.local elimination when installing tool dependencies.
2014-02-25 15:04:08 -05:00
Greg Von Kuster
de2507c00a
A bit of cleanup and some important fixes in re-engineered code for eliminating fabric.local when installing tool dependencies along with repositories from the tool shed.
2014-02-25 14:37:44 -05:00
Greg Von Kuster
9f9c962755
Make sure shlex receives a string when installing tool dependencies along with repositories intstalled from the tool shed.
2014-02-25 12:09:36 -05:00
John Chilton