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92 Commits
Author SHA1 Message Date
Nicola Soranzo ad02c53154 Fix many links 2018-09-03 14:34:13 +01:00
Nicola Soranzo d66a63012a Replace unmaintained pycrypto dependency with pycryptodome 
Minimum secret key length for Blowfish was increased from 4 to 5 bytes.

First argument to Blowfish.new() must be a bytestring, and the `mode`
argument is no more optional.

Remove unused `encode_id` function from `scripts/api/common.py` .

Documentation updated, then rebuilt with `make config-rebuild` .
 2018-06-13 03:07:04 +01:00
John Chilton 1c6cc02415 Hierarchical upload API optimized for folders & collections. 
Allows describing hierarchical data in JSON or inferring structure from archives or directories.

Datasets or archive sources can be specified via uploads, URLs, paths (if admin && allow_path_paste), library_import_dir/user_library_import_dir, and/or FTP imports. Unlike existing API endpoints, a mix of these on a per file basis is allowed and they work seemlessly between libraries and histories.

Supported "archives" include gzip, zip, bagit directories, bagit achives (with fetching and validations of downloads).

The existing upload API endpoint is quite rough to work with both in terms of adding parameters (e.g. the file type and dbkey hanlding in 4563 was difficult to implement, terribly hacky, and should seemingly have been trivial) and in terms of building requests (one needs to build a tool form - not describe sensible inputs in JSON). This API is built to be intelligable from an API standpoint instead of being constrained to the older style tool form. Additionally it built with hierarchical data in mind in a way that would not be easy at all enhancing the tool form components we don't even render.

This implements 5159 though much simpler YAML descriptions of data libraries should be possible basically as the API descriptions. We can replace the data library script in Ephemeris https://github.com/galaxyproject/ephemeris/blob/master/ephemeris/setup_data_libraries.py with one that converts a simple YAML file into an API call and allows many new options for free.

In future PRs I'll add filtering options to this and it will serve as the backend to 4733.
 2018-03-08 10:33:36 -05:00
John Chilton f9969ee97a Remove API scripts for axed APIs. 2017-12-15 16:02:18 -05:00
Nicola Soranzo 48aca7dce8 Update to flake8-import-order 0.16 2017-12-01 11:09:57 +00:00
Nicola Soranzo d1bc98dfcb Python3: fix remaining print statements 
Remove some debugging prints.
Fix import order.
Consolidate exception logging in ToolShed database migrations.
 2017-10-12 18:34:29 +01:00
Nicola Soranzo 9b1832abb1 Fix import order for cron/, scripts/ and test/ 2017-09-25 23:44:39 +01:00
Nicola Soranzo a353b2e88f Fix E127 errors introduced by previous commit 
using:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 .
```
 2017-08-17 11:35:39 +01:00
Nicola Soranzo 21b44bf348 Fix all E201 and E202 style errors 
using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
 2017-08-17 11:35:39 +01:00
Matt Chambers 25bd7178c1 Remove print of non-existent attribute 'content' 2017-08-16 14:44:51 -05:00
Frederic Sapet 3384e13744 correction of a typo leading to incomplete format string 2017-06-16 14:29:34 +02:00
Martin Cech 0602712a35 deduplicate obsolete API readme 2017-03-20 10:57:06 -04:00
Nicola Soranzo 3d57c22b63 Fix I201 errors from flake8-import-order 
Also fix Python3 compatibility.
Remove unused method
galaxy.tools.parameters.sanitize.ToolParameterSanitizer.restore_param() .
 2016-11-23 18:31:04 +00:00
Nicola Soranzo 1d17a29c79 Fixes for pycodestyle 2.2.0 2016-11-15 16:56:50 +00:00
Nicola Soranzo 9c37c6df89 Fixes for flake8-import-order 0.11 
Also fix Python3 compatibility.
 2016-11-11 15:09:34 +00:00
Junzhou Wang e45f8abb54 Python3:script/api/ 2016-06-25 20:49:06 -04:00
Junzhou Wang a04f6589ea Python3: test/shed_functional/ and test/unit/ 2016-06-25 20:00:42 -04:00
Nicola Soranzo 6ba6f798ec Fix more E203 flake8 errors 2016-05-17 23:53:16 +01:00
Nicola Soranzo 8a43b2b492 Python 3: use "as" instead of comma in except clause 2016-05-17 23:53:16 +01:00
Matt Chambers 384bdbfe70 Fix flaky "errors" 2016-05-13 11:38:48 -05:00
chambm 3a708a0089 Add filter_failed_datasets_from_collection.py script 2016-05-13 10:53:56 -05:00
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