Nicola Soranzo
df808d0c1e
flake8 lib/tool_shed/ .
...
Also:
- use sys.exit() instead of exit()
- fix sys.path manipulations.
2015-09-09 19:57:41 +01:00
Martin Cech
ed54c343e6
Merge pull request #586 from davebx/ts_url_cleanup
...
Cleanup of the toolshed's url handling methods.
2015-08-16 20:14:01 -04:00
Dave B
7907136ffd
Code style cleanup.
2015-08-11 15:37:52 -04:00
Dave B
0f2e2152ee
Cleanup of the toolshed's url handling methods.
2015-08-10 15:48:30 -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
John Chilton
6d49f1ef51
Fix undefined variables in remote_repository_registry_entry.
2015-04-08 23:22:28 -04:00
John Chilton
dc256aebf2
Fix tool shed scripts that log without creating a log.
2015-04-08 23:22:28 -04:00
John Chilton
453dde829e
Fix unknown name self in tool_shed.scripts.api.export.
2015-04-08 23:22:28 -04:00
Dannon Baker
47e6f08982
Fix undefined vars in toolshed add_repository_entry API script
2015-03-03 19:24:45 -05:00
Dannon Baker
9be7118d6a
First pass removing to_json_string/from_json_string.
2014-09-08 16:41:53 -04:00
Greg Von Kuster
c2f089dcb0
Fixes in exception handlers in the Tool Shed's create_categories and create_users API modules.
2014-07-23 09:47:21 -04:00
Greg Von Kuster
bba63a24b0
Handle exporting and importing repository capsules with new ExportRepositoryManager and ImportRepositoryMnager classes respectively.
2014-06-24 13:11:24 -04:00
Dave Bouvier
64c1bc95c9
Fix the 3xx redirect handler in the tool shed's API methods to correctly handle PUT requests.
2014-06-11 16:05:46 -04:00
Dave Bouvier
dd82de6cd1
Additional fixes for urllib2's 3xx redirects not handling POST requests. This changeset handles httpd proxies that redirect to a secure port before delivering the request to Paste.
2014-06-10 11:11:32 -04:00
Greg Von Kuster
08702be139
Fixes for the Tool Shed API POST and PUT requests that were broken when attempting to handle urllib2 not handling 307 redirects. The initial attempt at handling the urllib2 weakness made a call to urllib2.get_url() which turns POST requests into GET requests as a side-effect.
2014-06-10 10:33:48 -04:00
Dannon Baker
ed94d528d8
Detail why the 307 redirect tracking attempt in tool_shed/scripts/api/common.py does not work.
2014-06-09 17:02:27 -04:00
Greg Von Kuster
5d56c27f9c
More fixes for handling 307 redirects not being handled nicely by urllib2.urlopen() when the urllib2.Request has data provided.
2014-06-08 08:45:16 -04:00
Greg Von Kuster
0285192a4c
Fix the exception handler in the Tool Shed APi submit() function so that an expected dict is returned instead of a string.
2014-06-04 09:21:18 -04:00
Greg Von Kuster
b2f3d6a551
Continued down-sizing of the Tool Shed's shed_util_common module by moving certain functions to more appropriate locations. Some fixes for adding and removing entries to the Tool Shed's repository registry.
2014-05-28 11:17:50 -04:00
Greg Von Kuster
f13d6fde70
Enhance the Tool Shed API as well as the Tool Shed's install and test framework in order to integrate the latter into the Tool Shed's new repository registry.
2014-05-23 13:18:06 -04:00
Greg Von Kuster
e18a0197d7
Tweaks to the recent Tool Shed API enhancements, making them more RESTful.
2014-05-01 16:44:44 -04:00
Greg Von Kuster
2028fb12fd
Enhance the Tool Shed API to provide information about users that is public (i.e., public username) and to include a function for creating a new user. Add a Tool Shed API script that retrieves all of the pubic information about users from a Tool Shed, automatically generates test email accounts and test passwords, and creates the list of users in another Tool Shed. This script streamlines the process of populating a development Tool Shed with users, enabling import of a repository capsule exportied from the specified Tool Shed. This simplifies the process of developing new repository hierarchies in a local development Tool Shed.
2014-05-01 16:07:48 -04:00
Greg Von Kuster
449e19eb2e
Add a Tool Shed API script that can be used to retrieve the current set of categories from a Tool Shed (e.g. the test Tool Shed) and create each of them in a local development Tool Shed. This script can be used to streamline the process of creating a new development Tool Shed, populating it with categories expected in a public Tool Shed, and creating a new repository hierarchy that can be exported into a capsule and imported into the public Tool Shed.
2014-04-29 15:11:46 -04:00
Dave Bouvier
5bdb75aa82
Correct usage of "it's" versus "its".
2014-04-17 15:49:32 -04:00
Greg Von Kuster
27e60943bf
The basis of this change set is to provide some fixes to certain Tool Shed functions for supporting changing HTTP protocols over time (ie.e, https <-> http). In doing this, I've refactored several functions and moved most of the Tool Shed <-> Galaxy URL munging functions to the Tool Shed's common_util.py module. Ive renamed the munging functions to clarify what each of them does. Several duplicate functions have been eliminated from the code as well.
2014-04-09 10:11:48 -04:00
Greg Von Kuster
e01cc26dd1
Fixes and code cleanup for the tool shed's install and test framework.
2014-01-20 11:48:05 -05:00
Dannon Baker
c1558e8205
One more simplejson/json fix that slipped through the merge.
2014-01-10 07:42:58 -05:00
Dannon Baker
a40457ab09
Merge.
2014-01-10 07:40:02 -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
3014265a07
Tool Shed API fixes and code cleanup.
2014-01-09 15:59:18 -05:00
Greg Von Kuster
00857760f0
Fixes for filtering repository revision to be tested by the Tool Shed's install and test framework, and a new Tool Shed API script to enable analyzing the the Tool Shed's install and test framework.
2013-12-03 15:16:14 -05:00
Greg Von Kuster
f96fdc565f
Fixes for the tool shed's install and test framework and enhancements to allow a configurable number of test runs to be stored and displayed.
2013-11-27 15:28:03 -05:00
Greg Von Kuster
6b431f44fc
Enhance the Tool Shed API to enable importing a repository capsule.
2013-11-08 16:51:25 -05:00
Greg Von Kuster
ba857229c9
Restrict diff file size to something reasonable when browsing changesets in the Tool shed, and add some additional logging and error handling when setting metadata on repositories in the tool shed and Galaxy.
2013-10-18 13:07:37 -04:00
Greg Von Kuster
8f2bdd7816
Allow for skipping specified repositories when setting metadata in the tool shed.
2013-10-17 11:18:05 -04:00
Greg Von Kuster
c90c0e503b
Enhance the Tool Shed API feature supporting resetting metadata on certain repositories to allow for individual repositories per request.
2013-10-16 16:29:00 -04:00
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
Dannon Baker
0f120bd92c
Strip trailing whitespace (and windows line endings) from all python files in lib
2013-08-29 23:39:52 -04:00
Greg Von Kuster
ba17fe567b
Enhance the generated name of the archive file created when exporting a tool shed repository.
2013-08-05 15:59:49 -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
97ec214602
Tool shed database migration script to alter the repository_metadata table by dropping the tool_test_errors column and adding columns tool_test_results, missing_test_components.
2013-04-25 09:36:52 -04:00
Greg Von Kuster
6267972180
Refactor several methods in Galaxy's admin_toolshed controller in preparation for supporting installing tool shed repositories via the tool shed and Galaxy APIs.
2013-03-23 10:44:46 -04:00
Greg Von Kuster
d791d11683
Move the tool_shed_repository_revision_update.py api example script to ~/lib/tool_shed/scripts/api
2013-03-21 10:58:11 -04:00
Nicola Soranzo