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33 Commits
Author SHA1 Message Date
Greg Von Kuster 4e91bb120e Enhancements to the tool shed api to enable the curretnly most important updates for repository_metadata records. 2013-02-22 14:35:34 -05:00
Kyle Ellrott 53e4dc4f6b Patch to make extended_metadata loader work better, and fixing library loader to catch non-ascii errors 2012-11-30 10:58:39 -08:00
Kyle Ellrott 4e8d938ff7 Adding the initial componenents of an extended metadata system for datasets. 
The idea behind an 'extended metadata' for datasets is to provide a mechanism to encode
and index user generated metadata and keep it attached to files. Users can provide a
JSON style data structure which will then be indexed and stored. Later this index can
be used to search and discover datasets via a pseudo-formal schema.

This patch introduces the tables, and makes it possible to inject user metadata into a file
load using the 'extended_metadata' field in the query.
 2012-10-28 00:28:42 -07:00
Scott McManus a0afee842e Re-commit new /api/folders section 2012-10-15 18:09:25 -04:00
Scott McManus 0148eabc72 Backout 2012-10-15 17:53:37 -04:00
Scott McManus 954e96fc34 Added /api/folders. The api_folders configuration variable controls access to it (and is False by default). 2012-10-15 17:29:29 -04:00
Richard Park 6839829211 Cleaned up codebase for attempting adding api additions to the galaxy main branch 2012-08-03 02:09:05 -04:00
Richard Park e6d5c55c89 Updated notes on how to run api/workflow_execute_parameters.py 2012-04-10 23:00:41 -04:00
Richard Park 412f779f76 Updated scripts for API workflow enhancements and changing workflow parameters programatically 2012-02-01 16:21:38 -05:00
Enis Afgan fa1959b579 Fix API history purge; a few documentation corrections 2012-06-18 14:53:02 +10:00
Jeremy Goecks 049891cc92 Remove enable_api flag; API is now enabled by default and cannot be disabled. 2012-04-11 14:45:44 -04:00
John Chilton 1c37cb28ca Augment workflow import api to allow add_to_menu argument which (when 
true) adds imported workflow to user's workflow menu. Augment api
example script to take in an optional fourth parameter --add_to_menu
to enable this.
 2012-03-19 12:13:59 -05:00
John Chilton 4bc926d9f0 Adding script to scripts/api directory for importing workflows from 
file paths.
 2012-03-08 09:03:27 -06:00
John Duddy a2c0328241 Merge 2011-10-07 13:25:19 -07:00
Nate Coraor e7180eed8f New API scripts to do POST/PUT/DELETE without any guidance. Use like: 
./update.py key url param1=val param2=val
 2011-09-14 14:40:38 -04:00
Nate Coraor 4fe140d6d6 Missing import in library_contents.py 2011-08-29 14:42:04 -04:00
Nate Coraor 1f744be77d API enhancements: Rename the 'contents' controller to 'library_contents', move (some) sanity and security checks to galaxy.web.api.util, add some enhancements to the histories code and some sample scripts for histories. 2011-08-26 13:55:08 -04:00
Dannon Baker 082bd83a5c Fix for example workflow api script failing when the requested library doesn't exist and an attempt is made to create it. 2011-03-15 15:39:35 -04:00
Dannon Baker 9655aa55f5 Set workflow scripts ugo+x, like the others in scripts/api. 2011-03-05 12:44:32 -05:00
Dannon Baker 159c25eb68 Example script that uses the API to watch a folder for inputs, upload (filepath upload) those to a data library, and then execute a specified workflow on them. 2011-03-05 12:28:16 -05:00
Dannon Baker e62494e2b0 Initial commit of workflows API. Supports simple execution, multiple input datasets. Does not support runtime tool parameter modification. 2011-03-05 11:47:12 -05:00
Ramkrishna Chakrabarty d4f484e9ae Moving sample state and dataset transfer status update api methods to the samples api controller. 2010-12-20 16:05:08 -05:00
Ramkrishna Chakrabarty 7858868650 First pass of the new sequencer_type & sequencer framework 
- sequencer table now populated with the unique sequencer in the request_type table
- sequencer_type is introduced which defines a sequencer
- support for sequencer (create, delete, edit)
- added support for a simple sequencer for backward compatibility
- added support for Solid sequencer
- tweaked the request_type api methods. removed the sequencer login info.
 2010-12-20 10:50:50 -05:00
Ramkrishna Chakrabarty 028137a54d added 'name' attribute to the sample xml form 2010-12-13 17:30:51 -05:00
Ramkrishna Chakrabarty b34ef29442 Adding a 'name' attribute in the field dict for form_definitions. In the 'form_values' 
table, the 'content' column is now a JSON dict instead of a list. Made appropriate code changes.
 2010-12-13 17:29:23 -05:00
Daniel Blankenberg 7b7453366f Initial pass on API for forms, request_type, users and roles. 
Additional effort is needed to abstract more previously existing functionality out of web controllers.

Add script that is able to create a sequencer configuration for the sample tracking system using API.
 2010-12-02 16:04:34 -05:00
Ramkrishna Chakrabarty 7d8a5c650a Improved error handling in api methods. 2010-11-07 22:18:22 -05:00
Ramkrishna Chakrabarty d5d27b67ad adding setup_rabbitmq.sh script. 
web api minor code fixes
 2010-10-27 12:36:56 -04:00
Ramkrishna Chakrabarty 6a9ab2813a sample_tracking: 
- added web api methods to update requests, samples using restful api
- removed the old ad-doc web api
- modified the data transfer code to use this api
- code cleanup
 2010-10-26 10:00:23 -04:00
Kanwei Li 0fbab45d14 trackster: Inline editing of configuration and removing of tracks, obsoleting the right editing panel. Improved appearance of overview box by adding a background for the scroll bar, and having a sliding window to indicate region shown. Added id numbers in front of API results for upcoming interactive script. 2010-09-23 20:00:58 -04:00
Nate Coraor cce1848d5e Use env for the API example scripts instead of directly referring to /usr/bin/python 2010-07-29 11:18:15 -04:00
Nate Coraor 7b93d1f53b API: Add library creation functionality. Note that no roles can be associated with libraries via the API at this time. 2010-06-23 14:44:37 -04:00
Nate Coraor 5eb9ca909f Initial implementation of the Galaxy Web API. Disabled unless 
'enable_api = True' in config file.  You should not enable the API on
production sites as this code is brand new and may contain serious bugs and
security flaws!  Implemented:

* Display libraries
* Display library info
* Display library contents
* Display library content info
* Create library folders
* Upload datasets to a library from a server directory or with a path paste.
* Basic example scripts in scripts/api/

Framework changes that were made to support this:

* API Key interface in User Preferences.
* New api_keys database table for storing users' API Keys.
* New API-specific route mapper in webapp.
* API controllers in galaxy.web.api
* Return handling in reused library_common methods.
* expose_api decorator for API controller methods validates key and ensures
  valid JSON format.
* UniverseWebTransaction renamed to GalaxyWebTransaction and subclassed for
  GalaxyWebUITransaction and GalaxyWebAPITransaction.

Things that need to be done next:

* Documentation!
* Refactor reused code from library_common and other controllers into an
  even-more-generic location and format.  The main changes are that the Web UI
  returns redirects and rendered templates, whereas the API returns various
  HTTP status codes and JSON.
* Implement more functionality.
* The request and response format should be considered alpha and are subject to
  change.  They will be standardized as the API matures.

Hints to get started can be found in scripts/api/README
 2010-06-22 13:10:28 -04:00