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71 Commits
Author SHA1 Message Date
Nicola Soranzo d85db9daa6 Use __file__ when adding paths to sys.path instead of os.getcwd() . 
Also insert additional paths in position 1 unless strictly necessary.
 2016-02-18 15:45:15 +00:00
Nicola Soranzo 196d174716 Python 3 support for 3 files. 2016-02-18 15:45:15 +00:00
Nicola Soranzo 93348e7199 Fix the remaining 1334 flake8 errors in scripts/ . Close #391. 2016-02-18 15:45:15 +00:00
Nate Coraor 4a05d5ea12 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs 2015-10-20 18:59:06 -04:00
Eric Rasche 8a66701d4f Don't re-upload if already there 2015-10-15 16:02:05 -05:00
Eric Rasche 2cca823a78 Prepopulate memoization cache 2015-10-14 16:05:44 -05:00
Eric Rasche 6be301ca8a Support local/non local data and paths including root 2015-10-14 15:02:27 -05:00
Eric Rasche 33925747b8 Allow linking only 2015-10-14 14:50:35 -05:00
Eric Rasche aec9961407 Strip newlines 2015-10-14 14:43:08 -05:00
Eric Rasche decca0e96a Refactor to accept output of find 2015-10-14 14:37:21 -05:00
Eric Rasche 61f1cdf5d7 Added script to upload a directory to a data library 2015-10-14 14:16:45 -05:00
Nate Coraor 0469ed29e0 Remove egg cruft from scripts/ 2015-09-21 15:55:07 -04:00
Nicola Soranzo 34d9388456 Use os.pardir everywhere instead of '..' . 2015-07-14 16:20:29 +01:00
Martin Cech 508b685c70 fix common API scripts so they dont fail when response has no url param 2015-06-15 16:12:21 -04:00
Nate Coraor 8fadc6392b Rename universe_wsgi.ini -> galaxy.ini everywhere. 2014-09-15 16:43:51 -04:00
Greg Von Kuster 2d5c37a73f Enhance the galaxy API for the Tool Shed to retrieve the latest installable revision from the Tool Shed from an installed repository, specifying a name and owner. Enhance the ~/scripts/api/install_tool_shed_repositories.py script to allow the changeset_revision to be optional, and if not specified, the latest installable revision will be installed for the repository specified by the name and owner. 2014-05-14 18:13:33 -04:00
Daniel Blankenberg ea193ce2e6 Add a very simple example script that uses API to run data managers. 2014-02-10 11:59:58 -05:00
Dannon Baker e26d6e56c7 Tweaks to scripts/api/common.py to fix JSONDecodeError removal and clean up code. 2014-01-15 09:05:38 -05:00
Dannon Baker 559ecb4ec8 Remove dependency on simplejson; convert everything over to using the json module in the python standard library. 2014-01-10 07:29:05 -05:00
Greg Von Kuster a610d0d458 Enhance the Tool Shed and Galaxy APIs to support resetting metadata on repositories in the Tool Shed or installed into Galaxy respectively. When resetting repository metadata in the Tool Shed, if the API key is associated with an admin user, then setting the my_writable param value to True will restrict resetting metadata to only repositories that are writable by the user in addition to those repositories of type tool_dependency_definition. This param is ignored if the current user is not an admin user, in which case this same restriction is automatic. Also, when resetting metadata in the Tool Shed, repositories of type tool_dependency_definition are reset before repositories of type unrestricted. When setting metadata for installed repositories in Galaxy, neither repository types nor order are considered since these concepts are irrelevant in that environment. 2013-10-16 14:19:26 -04:00
Greg Von Kuster b5ecae6f3b Enhance the Galaxy API to display the list of exported workflows contained in an installed tool shed repository and to import one or more of those exported workflows into Galaxy. This change set is loosely based on John Chilton's pull request # 223 titled "Implement API methods for interfacing with an installed tool shed repository's workflows", but the implementation has been re-worked. All of John's contributed features should be available in this change set. 2013-09-24 12:05:17 -04:00
Greg Von Kuster cf96dccddb Add the ability to export a specified repository revision from the tool shed to a gzip compressed archive saved locally. The ability to import this archive to the same or another tool shed is not yet implemented, but coming soon. All of the repository's repository dependencies can optionally be exported into the same archive. The archive includes a manifest.xml file that contains the order in whcih the repositories in the archive must be imported. 
This feature is now available for any installable revision of a repository using the new "Export this revision" option in the Repository actions menu in the browser.  It is also available via the Tool Shed API using a command like the following:

export.py --url http://testtoolshed.g2.bx.psu.edu --name chemicaltoolbox --owner bgruening --revision 4133dbf7ff4d --export_repository_dependencies True --download_dir /tmp
 2013-08-02 19:30:03 -04:00
Greg Von Kuster 586c673338 Add support for repairing an installed tool shed repository and all of it's repository dependency hierarchy. Repairing a repository hierarchy will attempt to ensure all repositories in the hierarchy are correctly installed and all tool dependencies of each repository in the hierarchy are correctly installed. 
There is a new Repository Actions pop-up menu item for each repository labeled "Repair repository" that enables this in the browser.

This is also supported in the enhanced Galaxy API using a command like the following from the ~/scripts/api directory:

python ./repair_tool_shed_repository.py --api  <Galaxy admin API key> -l http://localhost:8763 --url http://localhost:9009/ -o test -r 1018e3cee313  --name chemicaltoolbox
 2013-06-26 21:17:00 -04:00
Carl Eberhard c86637486b scripts/api: Fixes to upload_to_history.py 2013-06-12 10:35:11 -04:00
Carl Eberhard 4512eeab3f API: libaray_contents.create: add support for copying an HDA; scripts/api: add copy_hda_to_library_folder.py, rename upload_to_history.py 2013-06-07 16:06:22 -04:00
Carl Eberhard be2bb18e83 Tools API: better error handling in create, encode ids returned; Scripts: add history_upload script to api 2013-05-29 17:28:47 -04:00
Greg Von Kuster a787646f92 Delete the original copy of the install_repository_tools.py Galaxy API script since it has been renamed to install_tool_shed_repositories.py 2013-05-22 14:36:08 -04:00
Dave Bouvier 9cf536f537 Rename install_repository_tools to install_tool_shed_repositories. Use shed_util_common.url_join to generate the API url. 2013-05-03 15:55:56 -04:00
Dannon Baker f51719aaa9 Fix install_repository_tools script to appropriately handle a trailing slash in the URL. 2013-05-03 15:46:53 -04:00
Greg Von Kuster c1f207b648 White space changes. 2013-04-16 10:38:58 -04:00
Greg Von Kuster 61f5eda689 Merged in BjoernGruening/galaxy-central-bgruening/tool-shed-api (pull request #153) 
merge install_repository_tool* scripts into one with a commandline interface
 2013-04-16 10:19:17 -04:00
Dannon Baker 78a4042517 Fixes for Search API. 2013-04-10 13:59:33 -04:00
Bjoern Gruening 045f94b651 merge install_repository_tool* scripts into one with a commandline interface 2013-04-06 20:54:40 +02:00
Greg Von Kuster 5d502906e5 Enhance and correct documentation in the new tool_shed_repositories Galaxy API controller as well as the documentation in the example API install scripts. Fix discovery of the tool_path setting in the selected shed-related tool panel config file in the tool_shed_repositories controller's install_repository_revision method. 2013-03-26 09:29:02 -04:00
Greg Von Kuster ed7248a819 Fix a few typos in my last commit. 2013-03-25 17:18:17 -04:00
Greg Von Kuster b9c6df9d91 Add baseline cupport for installing tool shed repositories from a specified tool shed into Galaxy via a combination of the tool shed API and the now enhanced Galaxy API. There are 3 new example scripts in ~/scripts/api that demonstrate how this works. The are named like: install_repository... 
In this implementation, all tools contained in repositories will be loaded into the Galaxy tool panel.

The user can specify the following when sending a POST to the new Galaxy API URL:
/api/tool_shed_repositories/new/install_repository_revision

1) an existing tool panel section id for loading tools or a new tool panel section label in which case a new ToolPanelSection will be created for containing the tools.
2) if they want tool dependencies installed along with the repository.
3) if they want repository dependencies installed along with the repository
4) which defined shed-related tool panel config file to use for installed tools
 2013-03-25 17:05:14 -04:00
Greg Von Kuster 9dee845318 Eliminate unnecessary resource mappers and api classes in the tool shed api, clean up the remaining tool shed api classes, and enhance the tool shed api by adding the ability to retrieve information about a specified repository and repository revision. 2013-03-22 10:43:58 -04:00
Kyle Ellrott 4aad0ad15e Enabling dataset UUID setting through library upload, upload1 tool, and galaxy.json file 2013-01-29 15:58:58 -08:00
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