Nate Coraor
97ad53f570
Merge remote-tracking branch 'upstream/dev' into smash_eggs
...
Conflicts:
eggs.ini
lib/galaxy/__init__.py
lib/galaxy/datatypes/binary.py
lib/galaxy/datatypes/converters/bgzip.py
lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
lib/galaxy/datatypes/converters/interval_to_bed_converter.py
lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
lib/galaxy/datatypes/converters/interval_to_coverage.py
lib/galaxy/datatypes/converters/interval_to_fli.py
lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
lib/galaxy/datatypes/converters/maf_to_interval_converter.py
lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
lib/galaxy/datatypes/coverage.py
lib/galaxy/eggs/__init__.py
lib/galaxy/eggs/dist.py
lib/galaxy/eggs/scramble.py
lib/galaxy/exceptions/__init__.py
lib/galaxy/jobs/runners/pbs.py
lib/galaxy/jobs/transfer_manager.py
lib/galaxy/model/__init__.py
lib/galaxy/model/migrate/check.py
lib/galaxy/model/orm/__init__.py
lib/galaxy/model/tool_shed_install/migrate/check.py
lib/galaxy/web/framework/__init__.py
lib/galaxy/web/framework/helpers/__init__.py
lib/galaxy/web/framework/middleware/sentry.py
lib/galaxy/web/framework/openid_manager.py
lib/galaxy/web/framework/webapp.py
lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
lib/galaxy/webapps/galaxy/controllers/dataset.py
lib/galaxy/webapps/galaxy/controllers/library_common.py
lib/galaxy/webapps/reports/controllers/workflows.py
lib/galaxy/webapps/tool_shed/controllers/repository.py
lib/galaxy/webapps/tool_shed/search/repo_search.py
lib/galaxy/webapps/tool_shed/search/tool_search.py
lib/galaxy_ext/metadata/set_metadata.py
lib/pulsar/client/config_util.py
lib/tool_shed/galaxy_install/install_manager.py
lib/tool_shed/galaxy_install/migrate/check.py
lib/tool_shed/grids/admin_grids.py
lib/tool_shed/grids/repository_grids.py
lib/tool_shed/repository_types/repository_suite_definition.py
lib/tool_shed/repository_types/tool_dependency_definition.py
lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
lib/tool_shed/scripts/check_repositories_for_functional_tests.py
lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py
lib/tool_shed/util/basic_util.py
lib/tool_shed/util/encoding_util.py
lib/tool_shed/util/hg_util.py
scripts/check_eggs.py
scripts/dist-scramble.py
scripts/fetch_eggs.py
scripts/make_egg_packager.py
scripts/scramble.py
scripts/scramble/lib/scramble_lib.py
scripts/scramble/scripts/DRMAA_python-macosx.py
scripts/scramble/scripts/DRMAA_python-solaris.py
scripts/scramble/scripts/DRMAA_python.py
scripts/scramble/scripts/MySQL_python-solaris.py
scripts/scramble/scripts/MySQL_python.py
scripts/scramble/scripts/PyRods.py
scripts/scramble/scripts/bx_python-solaris.py
scripts/scramble/scripts/generic.py
scripts/scramble/scripts/pbs_python.py
scripts/scramble/scripts/psycopg2-linux.py
scripts/scramble/scripts/psycopg2-macosx.py
scripts/scramble/scripts/psycopg2-solaris.py
scripts/scramble/scripts/psycopg2.py
scripts/scramble/scripts/pysam-solaris.py
scripts/scramble/scripts/pysqlite.py
scripts/test_dist_egg.py
2015-09-21 15:02:47 -04:00
John Chilton
57634f43ea
Fix lint problems from merge.
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How did that happen, those pieces of code were largely unrelated. Ekkk...
2015-09-14 11:21:04 +01:00
John Chilton
17d8e15e4e
Merge remote-tracking branch 'erasche/deduplication' into deduplication-merge
...
Conflicts:
lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
2015-09-14 11:14:42 +01:00
Nicola Soranzo
df808d0c1e
flake8 lib/tool_shed/ .
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Also:
- use sys.exit() instead of exit()
- fix sys.path manipulations.
2015-09-09 19:57:41 +01:00
Eric Rasche
1f3486cb51
Initialized variables
2015-09-07 12:10:12 -05:00
Eric Rasche
1aa7ef12ec
Refactor into a single method and flake
2015-09-03 15:30:49 -05:00
Martin Cech
ed54c343e6
Merge pull request #586 from davebx/ts_url_cleanup
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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
cc9b0bed85
Fix all E712 errors. Standardize sqlalchemy imports.
2015-07-14 20:49:34 +01:00
Nicola Soranzo
34d9388456
Use os.pardir everywhere instead of '..' .
2015-07-14 16:20:29 +01:00
Nate Coraor
033b1e88da
Remove all imports of galaxy.eggs and all calls to
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`{eggs,pkg_resources}.require`. Probably broke some stuff where we were
trying to be smart about whether a particular egg was available, but
Galaxy does at least start.
2015-07-13 15:37:59 -04:00
Dave B
97b19e422c
Manually cherry-pick ecf8973484248c37f8dc96670f14a5ecce1a0c18.
2015-06-25 11:23:10 -04:00
Dave B.
3eb203437c
Fix getting admin key when bootstrapping toolshed.
2015-06-23 16:00:55 -04:00
Nicola Soranzo
f8b364b9f5
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into pep8
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Conflicts:
lib/galaxy/tools/parameters/validation.py
2015-06-17 12:44:53 +01:00
Nicola Soranzo
3c40f32fa2
PEP-8 and pylint fixes.
2015-06-16 16:53:49 +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
Marius van den Beek
bf9f8cd283
Exclude curly braces from API-key to fix toolshed bootstrapping.
2015-06-01 16:19:14 +02:00
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
John Chilton
6f115a7d5c
PEP-8 fixes for install_and_test scripts.
2015-01-14 21:03:12 -05:00
Daniel Blankenberg
a187edba17
Fix toolshed bootstrapping for Macs.
2014-11-13 12:43:26 -05:00
Nate Coraor
c7acc3723f
Rename tool_shed_wsgi.ini.sample to tool_shed_wsgi.ini, fix static and other errors I created when moving it to config/ in the first place.
2014-09-16 14:55:38 -04:00
Dannon Baker
9be7118d6a
First pass removing to_json_string/from_json_string.
2014-09-08 16:41:53 -04:00
Dave Bouvier
a25cfad335
Improve fetching of api key for newly created user.
2014-07-28 12:17:47 -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
390d05bbd1
Eliminate the Tool Shed's td_common_util.py module by moving the functions to appropriate classes.
2014-05-28 15:49:02 -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
Dave Bouvier
4f2e506042
Enable running the create_users and create_categories scripts via run_tool_shed.sh
2014-05-22 10:59:18 -04:00
Greg Von Kuster
7238ba2304
Use the new hg_util.get_repo_for_repository() function to retrieve a mercurial repo for a repository.
2014-05-21 12:22:16 -04:00
Greg Von Kuster
9f05fec27c
I meant to make this file a .sample file.
2014-05-17 10:10:23 -04:00
Greg Von Kuster
60b2e731dc
Add a script for creating a new user and an associated API key to streamline the process of setting up a new local development tool shed.
2014-05-16 17:14:24 -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
Greg Von Kuster
c69b3f8065
Move some hg utility functions out of shed_util_common and into hg_util.
2014-04-24 15:45:55 -04:00
Greg Von Kuster
8b4e15423c
Add a new recipe manager to support tool dependency package installation. Create new classes for each recipe step where classes contain both a prepare_step() and an execute_step() function. This implementation breaks up the very large loops in install_util.py (where recipe steps are prepared) and fabric_util.py (where recipe steps are executed). The recipe manager currently loads all of the recipe step classes when it is instantiated - this approach could be tweaked if desired.
2014-04-24 10:46:56 -04:00
Dave Bouvier
5bdb75aa82
Correct usage of "it's" versus "its".
2014-04-17 15:49:32 -04:00
Greg Von Kuster
8bce650dda
Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.
2014-04-10 17:11:01 -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
Nate Coraor