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Author SHA1 Message Date
Kyle Ellrott e4f45e04e3 Adding script to generate UUIDs for datasets where the value is null. This is to backfill previously generated records (from now on UUID will be generated during creation) 2014-03-04 15:46:10 -08:00
Kyle Ellrott c9272740f9 Moving unique dataset id from dataset_id to uuid 2014-03-04 13:40:14 -08:00
Kyle Ellrott ea1cc72b6d Default merge 2014-03-04 13:04:28 -08:00
John Chilton 7e1ba0cefd Refactor out optional data selection handling. 
Reused a few times downstream for dataset collections.
 2014-03-04 11:49:35 -06:00
John Chilton 82e02eefa8 Eliminate code dup. in workflow editor for building input terminals. 2014-03-04 11:49:35 -06:00
John Chilton 14affd155a Eliminate code dup. in workflow editor for building connectors. 2014-03-04 11:49:35 -06:00
John Chilton 1f9667cc19 Fix node type being sent to prebuild_node in galaxy.workflow_editor.js. 2014-03-04 11:49:35 -06:00
Carl Eberhard a185504a92 JS utils: add ajax queue and named ajax queue to allow processing async calls in order and/or prevent duplicate async calls 2014-03-04 12:33:51 -05:00
Carl Eberhard 5cde6c8c14 History panel: allow override of toggle in toggle deleted/hidden, extract methods searchHdas and clearHdaSearch to allow js searching 2014-03-04 11:44:28 -05:00
Dave Bouvier 52b509b10c Fix for env.sh files being prematurely truncated in some environments. 2014-03-04 11:30:07 -05:00
Carl Eberhard b28d2db33e Return mode fn results when calling modebutton through interface; pack scripts 2014-03-04 11:26:16 -05:00
Carl Eberhard ef7fc31af1 Fix to tag_autocomplete_data when q is default (None) 2014-03-04 11:20:17 -05:00
John Chilton eaf077fcd6 Merge stable. 2014-03-04 07:48:28 -06:00
John Chilton 23e6521bea Fix Torque CLI runner to recognize complete ('C') state as 'ok'. 2014-03-04 07:47:58 -06:00
John Chilton bcaa8c6e49 Merged in nsoranzo/galaxy-central (pull request #341) 
Workflows API enhancements (pull request #337 corrected)
 2014-03-04 07:39:06 -06:00
John Chilton 28749c8c80 Merged in jmchilton/galaxy-central-fork-1 (pull request #342) 
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. 
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. 
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. 
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. 
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. 
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. 
Mirroring the newer WorkflowPopulator and LibraryPopulator.
 2014-02-27 18:06:36 -06:00
John Chilton 347e4dd046 Infrastructure for library API testing. 
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. 
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. 
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
Kyle Ellrott f969ad4e59 Patch to expose the actual dataset id in the LDDA and HDA to_dict calls (in addition to the instance id). 2014-02-26 14:28:40 -08:00
Dave Bouvier cd8b4f7497 Merge stable. 2014-02-26 15:11:47 -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