Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 74d8faac9f07407ac9df344a78c9ecb06c178f93
https://github.com/galaxyproject/galaxy/commit/74d8faac9f07407ac9df344a78c9…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-11-21 (Mon, 21 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/history/options-menu.js
Log Message:
-----------
Change 'History Actions' to 'Current History' in history options menu.
as it was before 1cc57b1eb2c295dbd68837c864740b6ff079b83d.
Commit: ec08ec60bb4dadaf6f8759f9dce79f764f26c909
https://github.com/galaxyproject/galaxy/commit/ec08ec60bb4dadaf6f8759f9dce7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-21 (Mon, 21 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/history/options-menu.js
Log Message:
-----------
Merge pull request #3205 from blankenberg/history-current-options-name_16.10
[16.10] Change 'History Actions' to 'Current History' in history options menu.
Commit: a9dab631fb00252ac122ea297262e89f63887019
https://github.com/galaxyproject/galaxy/commit/a9dab631fb00252ac122ea297262…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-22 (Tue, 22 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M static/maps/mvc/form/form-section.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-section.js
Log Message:
-----------
Preserve custom event handler for form inputs
Commit: 0b2d0c1746c9b7d7cc5781fedc5c6a02af3bdfdb
https://github.com/galaxyproject/galaxy/commit/0b2d0c1746c9b7d7cc5781fedc5c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-22 (Tue, 22 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M static/maps/mvc/form/form-section.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-section.js
Log Message:
-----------
Merge pull request #3210 from guerler/fix_output_label_handler
[16.10] Preserve custom event handler for form inputs
Commit: 9a2bae7381b1ee8e2411681a76d75767b05ceffe
https://github.com/galaxyproject/galaxy/commit/9a2bae7381b1ee8e2411681a76d7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M templates/admin/tool_shed_repository/common.mako
Log Message:
-----------
simplify the UI of deps installation
by hiding the details under toggle button
Commit: 068ee6bd0ceb942ec67e634a7e6e434314cbe7fe
https://github.com/galaxyproject/galaxy/commit/068ee6bd0ceb942ec67e634a7e6e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
Log Message:
-----------
fix install repo test
Commit: 706bc3fbb118087cc057e6559e0262a6aca31127
https://github.com/galaxyproject/galaxy/commit/706bc3fbb118087cc057e6559e02…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
Log Message:
-----------
fix test and hide shed_conf select udner details
Commit: 73d010efa4236ed8ef0e46bb10d5e39233ae2d6b
https://github.com/galaxyproject/galaxy/commit/73d010efa4236ed8ef0e46bb10d5…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
Log Message:
-----------
fix another test
Commit: 4b794729b0cfd347d189a9a1e62273ab1788bc3e
https://github.com/galaxyproject/galaxy/commit/4b794729b0cfd347d189a9a1e622…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
Log Message:
-----------
fix a bug that renders conda dependency selection everytime
Commit: 94edc94b73e047612ae51ca2e075f17ac8e238bb
https://github.com/galaxyproject/galaxy/commit/94edc94b73e047612ae51ca2e075…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Add cached dependency manager
Similar to https://github.com/galaxyproject/galaxy/pull/2986, implement
a mechanism that allows tool dependencies to be cached.
If the `use_cached_dependency_manager` option is set to True in
galaxy.ini, we build a hash of the combination of a tools' requirements,
and store the resulting environment in a directory specified by the
`tool_dependency_cache_dir` option in galaxy.ini.
Commit: 0a9b6d8755dee530232ab893a3bad199407aa0bc
https://github.com/galaxyproject/galaxy/commit/0a9b6d8755dee530232ab893a3ba…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Better phrasing of cache options in galaxy.ini.sample (Thanks @nsoranzo)
Commit: 2b1765751b29008aecbd782f28269ac4e63db239
https://github.com/galaxyproject/galaxy/commit/2b1765751b29008aecbd782f2826…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Rework cached dependencies to be more robust
to updates or changes in depedencies, folder structure and resolver
configuration. Instead of hashing name, type and version of a
dependency, hash the json representation of the dependencies returned by
the dependency resolver, which include the path to the environment and
the depedency type. This is only applied to resolvers whose cacheable
attribute is set to True (conda-only, currently).
Commit: f919a98601252ab8f87bffff6e449105e770aadf
https://github.com/galaxyproject/galaxy/commit/f919a98601252ab8f87bffff6e44…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Build dependency cache at install time
and only activate cached environments if they exist.
Commit: 82f30e7645156b5f35c2b4cd77314e6275663979
https://github.com/galaxyproject/galaxy/commit/82f30e7645156b5f35c2b4cd7731…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/requirements.py
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Only attempt to build cache once per install
and override __eq__ for ToolRequirement, to simplify
checking if ToolRequirements are already installed/cached.
Commit: 64bc9241ed785d4d552c5fac21cd412558c54567
https://github.com/galaxyproject/galaxy/commit/64bc9241ed785d4d552c5fac21cd…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Fix NameError
Commit: cf769dd09deb73624b22628208fa103cc4f27150
https://github.com/galaxyproject/galaxy/commit/cf769dd09deb73624b22628208fa…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Add API to install resolver tool dependencies
and to build a tool dependency cache (if activated in galaxy.ini).
An example to install dependencies for the twobit converter:
```
import bioblend.galaxy
url = 'http://localhost:8080/'
api_key = 'admin_api_key'
tool_id = 'CONVERTER_fasta_to_2bit'
endpoint = "api/tools/%s/install_dependencies" % tool_id
gi = bioblend.galaxy.GalaxyInstance(url, api_key)
gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id})
```
If `use_cached_dependency_manager` is activated in the galaxy.ini,
a cached environment can be built like this:
```
endpoint = "api/tools/%s/build_dependency_cache" % tool_id
gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id})
```
Commit: cc7cd47ef54a09efbf8272d1e024f6f2ac92594b
https://github.com/galaxyproject/galaxy/commit/cc7cd47ef54a09efbf8272d1e024…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M test/integration/test_resolvers.py
Log Message:
-----------
Add integration test-case for install tool dependency API endpoint
Commit: f10fd793a68ed9413bec708daa48cef65769d09f
https://github.com/galaxyproject/galaxy/commit/f10fd793a68ed9413bec708daa48…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
Log Message:
-----------
Install the correct converter dependency
Commit: 045a2f0d471f7b4186aff625f3cea9abfa549fa2
https://github.com/galaxyproject/galaxy/commit/045a2f0d471f7b4186aff625f3ce…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/webapps/galaxy/api/tools.py
Log Message:
-----------
Add `force_rebuild` param to build_dependency_cache
This will remove a pre-existing cached dependency directory.
Commit: 16b49d9140edbf116f83b51b957cd61c4f2d91df
https://github.com/galaxyproject/galaxy/commit/16b49d9140edbf116f83b51b957c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/integration/test_resolvers.py
Log Message:
-----------
Add dependency_resolvers/clean endpoint
Commit: 1efd4d4b3b99ec40071aa4d6fb7cf4030c51e2e0
https://github.com/galaxyproject/galaxy/commit/1efd4d4b3b99ec40071aa4d6fb7c…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
add a conda clean function to remove downloaded tarballs after installation
Commit: 2a4ccac4039342c98d71bc72177aa951db6c4ba1
https://github.com/galaxyproject/galaxy/commit/2a4ccac4039342c98d71bc72177a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/integration/test_resolvers.py
Log Message:
-----------
Connect `clean` endpoint properly and add `-y` to exec_clean
Commit: e3f8b724648cee51636502959096adba88045e14
https://github.com/galaxyproject/galaxy/commit/e3f8b724648cee51636502959096…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M templates/admin/tool_shed_repository/common.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
Log Message:
-----------
Merge pull request #3226 from martenson/16-10-install-ux
[16.10] admin installation ux
Commit: d6f0e6b37c318a0202e0e266828e6325100cab19
https://github.com/galaxyproject/galaxy/commit/d6f0e6b37c318a0202e0e266828e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/tool_shed/galaxy_install/install_manager.py
M test/integration/test_resolvers.py
Log Message:
-----------
Merge pull request #3227 from mvdbeek/cached_deps_16.10
[16.10] Backport #3106 and #3222: Cached conda environments and API to manage them
Commit: a26568bdfaefc5748ff3b2385fa9424ece6c652c
https://github.com/galaxyproject/galaxy/commit/a26568bdfaefc5748ff3b2385fa9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-11-30 (Wed, 30 Nov 2016)
Changed paths:
M tox.ini
Log Message:
-----------
Pin flake8 and flake8-import-order
Do not pin when forward-merging to dev branch!
Commit: 888a8f91537e22dcbdea174a65eaecbced9ea8a8
https://github.com/galaxyproject/galaxy/commit/888a8f91537e22dcbdea174a65ea…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-30 (Wed, 30 Nov 2016)
Changed paths:
M tox.ini
Log Message:
-----------
Merge pull request #3232 from nsoranzo/release_16.10_pin_flake8
[16.10] Pin flake8 and flake8-import-order
Commit: 2d510fae981f0255f04b21272f99e995f0a16f0b
https://github.com/galaxyproject/galaxy/commit/2d510fae981f0255f04b21272f99…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-11-30 (Wed, 30 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/user/user-preferences.js
M static/style/blue/base.css
M templates/admin/tool_shed_repository/common.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
Log Message:
-----------
Merge branch 'release_16.10' into dev
Conflicts:
static/maps/mvc/form/form-section.js.map
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js
static/scripts/bundled/libs.bundled.js.map
static/scripts/bundled/login.bundled.js.map
static/scripts/mvc/form/form-section.js
Compare: https://github.com/galaxyproject/galaxy/compare/1bbab2d89d2c...2d510fae981f
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: b7055791257e51cf22a5d2dc9c0cf2af529a3a5e
https://github.com/galaxyproject/galaxy/commit/b7055791257e51cf22a5d2dc9c0c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/configuration.py
A test/api/test_configuration.py
R test/casperjs/api-configuration-tests.js
Log Message:
-----------
Fix configuration API admin checking and tests.
- Move CasperJS tests for configuration API into API test framework.
- Fix bug where configuration API wouldn't treat master API key as coming from an admin user.
Commit: 1bbab2d89d2c7af7b6d3d0ffd0b3ece2d153705f
https://github.com/galaxyproject/galaxy/commit/1bbab2d89d2c7af7b6d3d0ffd0b3…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-30 (Wed, 30 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/configuration.py
A test/api/test_configuration.py
R test/casperjs/api-configuration-tests.js
Log Message:
-----------
Merge pull request #3228 from jmchilton/configuration_test
Fix configuration API admin checking and tests.
Compare: https://github.com/galaxyproject/galaxy/compare/b165757288f0...1bbab2d89d2c
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: b8e2833b5bcb26242ef08967fe342a81c2811172
https://github.com/galaxyproject/galaxy/commit/b8e2833b5bcb26242ef08967fe34…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-07-30 (Sat, 30 Jul 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
A client/galaxy/scripts/mvc/user/manage-user-information.js
A client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/style/less/base.less
M static/maps/layout/menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/style/blue/base.css
Log Message:
-----------
Adding code for replacing mako for user preferences with simple features
Commit: 77f5655de1f606ae08f533ef27318d39097dbcd2
https://github.com/galaxyproject/galaxy/commit/77f5655de1f606ae08f533ef2731…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-07-30 (Sat, 30 Jul 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/user/manage-user-information.js
M client/galaxy/scripts/mvc/user/user-preferences.js
A lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Adding routes and api calls for user preferences
Commit: a63f63440ebe66715608907c809abeab59279166
https://github.com/galaxyproject/galaxy/commit/a63f63440ebe66715608907c809a…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-07-31 (Sun, 31 Jul 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/user/manage-user-information.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Adding login information section for manage user information feature
Commit: aaedf684f0e9693fc98f5867cde62170bbf35879
https://github.com/galaxyproject/galaxy/commit/aaedf684f0e9693fc98f5867cde6…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-08-01 (Mon, 01 Aug 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/user/manage-user-information.js
M client/galaxy/style/less/base.less
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/style/blue/base.css
Log Message:
-----------
Adding code for validating and saving email and username
Commit: 07409a89f86df86b86fc621fcc8b2f8533cf6116
https://github.com/galaxyproject/galaxy/commit/07409a89f86df86b86fc621fcc8b…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-08-01 (Mon, 01 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/manage-user-information.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Fixing a bug with multiple events firing
Commit: cc168ce95423c096bbd5ef198cb24c0549ef4c0e
https://github.com/galaxyproject/galaxy/commit/cc168ce95423c096bbd5ef198cb2…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-08-02 (Tue, 02 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/manage-user-information.js
M client/galaxy/style/less/base.less
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
Log Message:
-----------
Adding all the features for manage user info
Commit: 044eb9768362b7d341911a78446be6f3760746ac
https://github.com/galaxyproject/galaxy/commit/044eb9768362b7d341911a78446b…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-08-02 (Tue, 02 Aug 2016)
Changed paths:
M static/scripts/bundled/libs.bundled.js
Log Message:
-----------
adding the bundled file
Commit: 976e6e5ac6757db777db6d8248889f7053e2e776
https://github.com/galaxyproject/galaxy/commit/976e6e5ac6757db777db6d824888…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-08-02 (Tue, 02 Aug 2016)
Changed paths:
A client/galaxy/scripts/mvc/user/change-password.js
M client/galaxy/scripts/mvc/user/manage-user-information.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/style/less/base.less
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/style/blue/base.css
Log Message:
-----------
Adding change password feature
Commit: 0558225f5f98ececedbcef4f8232baec84620e70
https://github.com/galaxyproject/galaxy/commit/0558225f5f98ececedbcef4f8232…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-08-02 (Tue, 02 Aug 2016)
Changed paths:
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Adding missing files
Commit: ce1a478d8d073fbb5fda88834e4f4132bb5acfb3
https://github.com/galaxyproject/galaxy/commit/ce1a478d8d073fbb5fda88834e4f…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-08-08 (Mon, 08 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-password.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/style/less/base.less
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/style/blue/base.css
Log Message:
-----------
Adding Change Permissions on history feature
Commit: bbd020e8a7b84de184885428650bec488d102856
https://github.com/galaxyproject/galaxy/commit/bbd020e8a7b84de184885428650b…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-08-08 (Mon, 08 Aug 2016)
Changed paths:
A client/galaxy/scripts/mvc/user/change-permissions.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
adding missing files
Commit: 976729ad553ff34bff14f80eda94bfdbbf25491a
https://github.com/galaxyproject/galaxy/commit/976729ad553ff34bff14f80eda94…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-08-08 (Mon, 08 Aug 2016)
Changed paths:
A client/galaxy/scripts/mvc/user/api-keys.js
M client/galaxy/scripts/mvc/user/change-permissions.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
Log Message:
-----------
Adding Generate API key feature
Commit: 23744c36f28e1d3633363720236695a1f6113395
https://github.com/galaxyproject/galaxy/commit/23744c36f28e1d36333637202366…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-08-08 (Mon, 08 Aug 2016)
Changed paths:
M client/galaxy/style/less/base.less
Log Message:
-----------
adding missing file
Commit: cb79eac22ede7d9facc07b170d6b2c64bb217142
https://github.com/galaxyproject/galaxy/commit/cb79eac22ede7d9facc07b170d6b…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-08-14 (Sun, 14 Aug 2016)
Changed paths:
A client/galaxy/scripts/mvc/user/change-communication.js
A client/galaxy/scripts/mvc/user/toolbox-filter.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/style/less/base.less
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
Log Message:
-----------
Adding Manage toolbox filter and Change communication settings features
Commit: d7c6ca2bbd875a910e759acca015be40e5562064
https://github.com/galaxyproject/galaxy/commit/d7c6ca2bbd875a910e759acca015…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/user/change-password.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/style/less/ui.less
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/form/form-parameters.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/form/form-parameters.js
M static/style/blue/base.css
Log Message:
-----------
Use form view to build password change form
Commit: f11a87628f0c9571dc953976119f1a80d290460a
https://github.com/galaxyproject/galaxy/commit/f11a87628f0c9571dc953976119f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-password.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Connect main preference page with password change view without using global variables
Commit: 43054acb2e577f4928fb8a76931cb7825194888d
https://github.com/galaxyproject/galaxy/commit/43054acb2e577f4928fb8a76931c…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/user/change-password.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/style/less/ui.less
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/form/form-parameters.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/form/form-parameters.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #16 from guerler/remove_mako_user_pref_form_view
Use form view to build change password form
Commit: 4016b3e3037db64e04537b248f4d48f330b294db
https://github.com/galaxyproject/galaxy/commit/4016b3e3037db64e04537b248f4d…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-communication.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Change communication setting feature with form view
Commit: baae49f607480d98c2d63b6378f891c2eda4e154
https://github.com/galaxyproject/galaxy/commit/baae49f607480d98c2d63b6378f8…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-08-28 (Sun, 28 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/user/api-keys.js
M client/galaxy/scripts/mvc/user/change-communication.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Updating API key feature for user preferences with form view
Commit: 1adbcfc0ec1fcccd1987946f83118c496d9eb635
https://github.com/galaxyproject/galaxy/commit/1adbcfc0ec1fcccd1987946f8311…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-password.js
M client/galaxy/scripts/mvc/user/toolbox-filter.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Adding toolbox permissions feature using form view
Commit: e06d206eedf4ac36bfc03417d76fee6057fcae03
https://github.com/galaxyproject/galaxy/commit/e06d206eedf4ac36bfc03417d76f…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/manage-user-information.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Adding user login information using form view
Commit: 4addb9497299cd9c3ff0e65b0b30ecf7beb5aa41
https://github.com/galaxyproject/galaxy/commit/4addb9497299cd9c3ff0e65b0b30…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/user/manage-user-information.js
M client/galaxy/scripts/mvc/user/toolbox-filter.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/form/form-parameters.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-parameters.js
Log Message:
-----------
Extending the form view to have labels and buttons
Commit: 46cd30bb3523d182f319f9640d552a72dbae5ca5
https://github.com/galaxyproject/galaxy/commit/46cd30bb3523d182f319f9640d55…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-communication.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Updating the communication setting changes as reviewed/suggested by Aysam Guerler
Commit: 994eddfd5a15e85f37cb3ff0af734d31d276eb8a
https://github.com/galaxyproject/galaxy/commit/994eddfd5a15e85f37cb3ff0af73…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-communication.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Remove unused field value update, and api request parameters
Commit: 5d8bd3f72eb6f06c18bb5fc47a8fc2d269b1c1f7
https://github.com/galaxyproject/galaxy/commit/5d8bd3f72eb6f06c18bb5fc47a8f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-communication.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Fix spacing
Commit: 399f4ae9c06abc9a06240be158905b62085abd16
https://github.com/galaxyproject/galaxy/commit/399f4ae9c06abc9a06240be15890…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Change comment
Commit: 4b7324bab96cf5fea85b13216902589e6568b71c
https://github.com/galaxyproject/galaxy/commit/4b7324bab96cf5fea85b13216902…
Author: anup kumar <anup.rulez(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-communication.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Merge pull request #18 from guerler/fix_communication_settings
Remove unused field value update, and api request parameters
Commit: ebc1cc6ff3ac216ff54628e4ff5e66eca90d2f38
https://github.com/galaxyproject/galaxy/commit/ebc1cc6ff3ac216ff54628e4ff5e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/user/api-keys.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Revise api key generation form
Commit: 6a17e10d751b427ede173f40907d5fb5032201cb
https://github.com/galaxyproject/galaxy/commit/6a17e10d751b427ede173f40907d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/api-keys.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Fix info text
Commit: 14d045c54e0e91181689a2281115d17aee39561f
https://github.com/galaxyproject/galaxy/commit/14d045c54e0e91181689a2281115…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/api-keys.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Remove unused variable
Commit: e84251a7310005c7d16b6f87b423c178b0583065
https://github.com/galaxyproject/galaxy/commit/e84251a7310005c7d16b6f87b423…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/api-keys.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Fix request parameter
Commit: d59fa629cf269e7d118b38a48dbe85a8634dac60
https://github.com/galaxyproject/galaxy/commit/d59fa629cf269e7d118b38a48dbe…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/api-keys.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Remove unused variable
Commit: ab559072d22b8b98aa2fd001d79dd42f791ebb0a
https://github.com/galaxyproject/galaxy/commit/ab559072d22b8b98aa2fd001d79d…
Author: anup kumar <anup.rulez(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/user/api-keys.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Merge pull request #19 from guerler/fix_communication_settings
Revise api key generation form
Commit: 8f1156295989b11c127bba1d50438b516d7d80a8
https://github.com/galaxyproject/galaxy/commit/8f1156295989b11c127bba1d5043…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-09-10 (Sat, 10 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/toolbox-filter.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Updating toolbox filters
Commit: 222d1f2cac83adb0ebea0c24701ef2d01fcf6eb5
https://github.com/galaxyproject/galaxy/commit/222d1f2cac83adb0ebea0c24701e…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-09-10 (Sat, 10 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/toolbox-filter.js
Log Message:
-----------
Removing extra spaces
Commit: b4d0dfcc92ba9790f2975a557aaf0ecc6cb52af7
https://github.com/galaxyproject/galaxy/commit/b4d0dfcc92ba9790f2975a557aaf…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-09-11 (Sun, 11 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/user/manage-user-information.js
M static/maps/mvc/form/form-parameters.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-parameters.js
Log Message:
-----------
Adding user address filter feature using radiobuttons in manange user information
Commit: 9915ef7837fc75758b2329681fce96bf94c3be01
https://github.com/galaxyproject/galaxy/commit/9915ef7837fc75758b2329681fce…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-09-12 (Mon, 12 Sep 2016)
Changed paths:
A client/galaxy/scripts/mvc/user/add-edit-address.js
M client/galaxy/scripts/mvc/user/manage-user-information.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Adding add, edit, delete and undelete features for manage user information page
Commit: 961e01e700ecd775f4f7c2edd1aa4ac2a4efdc22
https://github.com/galaxyproject/galaxy/commit/961e01e700ecd775f4f7c2edd1aa…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/manage-user-information.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Replacing input building logic to server side for login form
Commit: 4bca99940f3f55425775b0f9cb4d9fcdfba8f08e
https://github.com/galaxyproject/galaxy/commit/4bca99940f3f55425775b0f9cb4d…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-09-17 (Sat, 17 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/manage-user-information.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Updating the display of user addresses
Commit: 123aa562c0878406eb0eaa16eb857661da63996c
https://github.com/galaxyproject/galaxy/commit/123aa562c0878406eb0eaa16eb85…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-09-17 (Sat, 17 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/user/manage-user-information.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/ui/ui-options.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/ui/ui-options.js
Log Message:
-----------
Adding edit, delete and undelete using radio button views and inputs built at server
Commit: 3b5905985de402c92051d1da97dfc26c43a94e41
https://github.com/galaxyproject/galaxy/commit/3b5905985de402c92051d1da97df…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-09-20 (Tue, 20 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/ui/ui-options.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/ui/ui-options.js
Log Message:
-----------
Removing the unchecked attribute from select
Commit: dc80c8962b31192929037448ffba1423819712f7
https://github.com/galaxyproject/galaxy/commit/dc80c8962b31192929037448ffba…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-09-20 (Tue, 20 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/add-edit-address.js
M client/galaxy/scripts/mvc/user/manage-user-information.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Merging the api calls for user info into one api call
Commit: 69800d41da8a131fcaee40ff1a6aa1194afe1427
https://github.com/galaxyproject/galaxy/commit/69800d41da8a131fcaee40ff1a6a…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/manage-user-information.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Adding user type form and address filters
Commit: 431fad09e06afe2a13ccd21e3ffff3ef826ee341
https://github.com/galaxyproject/galaxy/commit/431fad09e06afe2a13ccd21e3fff…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-09-24 (Sat, 24 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/user/change-permissions.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/form/form-parameters.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-parameters.js
Log Message:
-----------
Adding Change permissions view
Commit: c83fa12e56d221c162488225a6e61d632b46d7e0
https://github.com/galaxyproject/galaxy/commit/c83fa12e56d221c162488225a6e6…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-09-24 (Sat, 24 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/add-edit-address.js
M client/galaxy/scripts/mvc/user/api-keys.js
M client/galaxy/scripts/mvc/user/change-communication.js
M client/galaxy/scripts/mvc/user/change-password.js
M client/galaxy/scripts/mvc/user/change-permissions.js
M client/galaxy/scripts/mvc/user/manage-user-information.js
M client/galaxy/scripts/mvc/user/toolbox-filter.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Fixing styling and removing commented out code
Commit: 60d4570c54dcd58d69ff907c832881a2328b2545
https://github.com/galaxyproject/galaxy/commit/60d4570c54dcd58d69ff907c8328…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-09-24 (Sat, 24 Sep 2016)
Changed paths:
M .ci/first_startup.sh
M .ci/flake8_blacklist.txt
A .ci/flake8_lint_include_list.txt
A .ci/flake8_wrapper_imports.sh
M .ci/py3_sources.txt
A .ci/validate_test_tools.sh
M .gitignore
M .travis.yml
M CONTRIBUTORS.md
M LICENSE.txt
M Makefile
M client/bower.json
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/history-panel.js
A client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/layout/scratchbook.js
A client/galaxy/scripts/libs/bbi/bigwig.js
A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js
A client/galaxy/scripts/libs/bbi/jszlib.js
A client/galaxy/scripts/libs/bbi/spans.js
A client/galaxy/scripts/libs/jquery.complexify.js
M client/galaxy/scripts/libs/jquery/jquery.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/mvc/annotation.js
M client/galaxy/scripts/mvc/base-mvc.js
A client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/collection/collection-li-edit.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/copy-dialog.js
M client/galaxy/scripts/mvc/history/hda-li-edit.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hda-model.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
A client/galaxy/scripts/mvc/history/history-preferences.js
M client/galaxy/scripts/mvc/history/history-structure-view.js
M client/galaxy/scripts/mvc/history/history-view-annotated.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/list/list-item.js
M client/galaxy/scripts/mvc/list/list-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/error-modal.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-model.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/ui/search-input.js
M client/galaxy/scripts/utils/ajax-queue.js
M client/galaxy/scripts/utils/utils.js
A client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/base.less
A client/galaxy/style/less/collection.less
R client/galaxy/style/less/collections.less
A client/galaxy/style/less/dataset.less
A client/galaxy/style/less/flex.less
M client/galaxy/style/less/history.less
M client/galaxy/style/less/library.less
M client/galaxy/style/less/list-item.less
M client/galaxy/style/less/ui.less
A client/galaxy/style/less/ui/error-modal.less
M client/galaxy/style/less/ui/search-input.less
M client/galaxy/style/less/upload.less
M client/grunt-tasks/install-libs.js
M client/webpack.config.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/object_store_conf.xml.sample
A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample
A config/plugins/interactive_environments/neo/config/neo.ini.sample
A config/plugins/interactive_environments/neo/config/neo.xml
A config/plugins/interactive_environments/neo/static/js/neo.js
A config/plugins/interactive_environments/neo/templates/neo.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
M config/plugins/tours/core.scratchbook.yaml
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/forms/default.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
A config/plugins/visualizations/charts/static/charts/others/example/config.js
A config/plugins/visualizations/charts/static/charts/others/example/logo.png
A config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
A config/plugins/visualizations/charts/static/charts/overview.js
R config/plugins/visualizations/charts/static/charts/tools.js
M config/plugins/visualizations/charts/static/charts/types.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
A config/plugins/visualizations/charts/static/components/jobs.js
A config/plugins/visualizations/charts/static/components/model.js
A config/plugins/visualizations/charts/static/components/screenshot.js
A config/plugins/visualizations/charts/static/components/storage.js
R config/plugins/visualizations/charts/static/library/datasets.js
R config/plugins/visualizations/charts/static/library/jobs.js
R config/plugins/visualizations/charts/static/library/screenshot.js
R config/plugins/visualizations/charts/static/library/storage.js
R config/plugins/visualizations/charts/static/models/chart.js
R config/plugins/visualizations/charts/static/models/config.js
A config/plugins/visualizations/charts/static/views/description.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewer.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
M config/reports.ini.sample
M config/tool_shed.ini.sample
A doc/parse_gx_xsd.py
A doc/schema_template.md
A doc/source/admin/chat-0.png
A doc/source/admin/chat-1.png
A doc/source/admin/chat-2.png
A doc/source/admin/chat-3.png
A doc/source/admin/chat-4.png
A doc/source/admin/chat.rst
A doc/source/admin/communication_server.png
A doc/source/admin/communication_server_rooms.png
A doc/source/admin/conda_faq.rst
M doc/source/admin/index.rst
A doc/source/dev/build_a_job_runner.rst
M doc/source/lib/galaxy.objectstore.rst
A doc/source/releases/16.07.rst
M doc/source/releases/16.07_announce.rst
A doc/source/releases/16.10_announce.rst
M lib/galaxy/app.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/subcollections.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/msa.py
A lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/set_metadata_tool.xml
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/managers/annotatable.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/check.py
A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/objectstore/__init__.py
A lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/dockerfiles.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/toolbox/tags.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/verify/asserts/xml.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/wrappers.py
A lib/galaxy/tools/xsd/LICENSE
A lib/galaxy/tools/xsd/README.md
A lib/galaxy/tools/xsd/galaxy.jxb
A lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/checkers.py
A lib/galaxy/util/filelock.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/json.py
M lib/galaxy/util/lazy_process.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/util/permutations.py
A lib/galaxy/util/postfork.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/sockets.py
M lib/galaxy/util/sqlite.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/submodules.py
M lib/galaxy/util/template.py
M lib/galaxy/util/topsort.py
M lib/galaxy/util/validation.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/version.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/buildapp.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/__init__.py
A lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
R lib/galaxy/web/proxy/filelock.py
M lib/galaxy/web/proxy/js/lib/main.js
M lib/galaxy/web/proxy/js/lib/proxy.js
M lib/galaxy/web/proxy/js/package.json
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/mobile.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/buildapp.py
A lib/galaxy/webapps/reports/controllers/history.py
A lib/galaxy/webapps/reports/controllers/tools.py
M lib/galaxy/webapps/reports/controllers/users.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/hg.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
R lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/migrate/common.py
M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M lib/tool_shed/managers/repositories.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_types/registry.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_content_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/web_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M run.sh
M run_tests.sh
M scripts/bootstrap_history.py
M scripts/common_startup.sh
A scripts/communication/communication_server.py
A scripts/communication/template/communication.css
A scripts/communication/template/communication.html
A scripts/communication/template/communication.js
M scripts/nosetests.py
M scripts/tool_shed/api/common.py
M scripts/tool_shed/build_ts_whoosh_index.py
A scripts/validate_tools.sh
M setup.cfg
A static/maps/layout/generic-nav-view.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/maps/layout/panel.js.map
M static/maps/layout/scratchbook.js.map
A static/maps/libs/bbi/bigwig.js.map
A static/maps/libs/bbi/jquery-ajax-native.js.map
A static/maps/libs/bbi/jszlib.js.map
A static/maps/libs/bbi/spans.js.map
A static/maps/libs/jquery.complexify.js.map
M static/maps/libs/jquery/jquery.js.map
M static/maps/libs/raven.js.map
M static/maps/mvc/annotation.js.map
M static/maps/mvc/base-mvc.js.map
A static/maps/mvc/base/controlled-fetch-collection.js.map
M static/maps/mvc/collection/collection-li-edit.js.map
M static/maps/mvc/collection/collection-li.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/dataset/dataset-model.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/history/copy-dialog.js.map
M static/maps/mvc/history/hda-li-edit.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hda-model.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/hdca-model.js.map
M static/maps/mvc/history/history-content-model.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
A static/maps/mvc/history/history-preferences.js.map
M static/maps/mvc/history/history-structure-view.js.map
M static/maps/mvc/history/history-view-annotated.js.map
M static/maps/mvc/history/history-view-edit-current.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/list/list-item.js.map
M static/maps/mvc/list/list-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/error-modal.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/upload/upload-model.js.map
M static/maps/mvc/upload/upload-settings.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/ui/search-input.js.map
M static/maps/utils/ajax-queue.js.map
M static/maps/utils/utils.js.map
A static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
A static/scripts/layout/generic-nav-view.js
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
M static/scripts/layout/panel.js
M static/scripts/layout/scratchbook.js
A static/scripts/libs/bbi/bigwig.js
A static/scripts/libs/bbi/jquery-ajax-native.js
A static/scripts/libs/bbi/jszlib.js
A static/scripts/libs/bbi/spans.js
A static/scripts/libs/jquery.complexify.js
M static/scripts/libs/jquery/jquery.js
M static/scripts/libs/raven.js
M static/scripts/mvc/annotation.js
M static/scripts/mvc/base-mvc.js
A static/scripts/mvc/base/controlled-fetch-collection.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/dataset/dataset-model.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/copy-dialog.js
M static/scripts/mvc/history/hda-model.js
M static/scripts/mvc/history/hdca-model.js
M static/scripts/mvc/history/history-content-model.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
A static/scripts/mvc/history/history-preferences.js
M static/scripts/mvc/history/history-structure-view.js
M static/scripts/mvc/history/history-view-annotated.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/list/list-item.js
M static/scripts/mvc/list/list-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/error-modal.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-row.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/ui/search-input.js
M static/scripts/utils/ajax-queue.js
M static/scripts/utils/utils.js
A static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
A static/style/base.css
M static/style/blue/base.css
M static/style/blue/bootstrap-tour.css
M static/style/blue/jquery.rating.css
M static/style/blue/library.css
R static/style/blue/tool_menu.css
R templates/admin/tool_shed_repository/browse_categories.mako
A templates/admin/tool_shed_repository/browse_toolsheds.mako
M templates/admin/tool_shed_repository/common.mako
M templates/admin/tool_shed_repository/manage_repository.mako
R templates/admin/tool_shed_repository/preview_repository.mako
M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/base.mako
M templates/base/base_panels.mako
M templates/js-app.mako
M templates/show_params.mako
M templates/user/change_password.mako
A templates/user/communication_settings.mako
M templates/user/index.mako
M templates/user/info.mako
M templates/user/register.mako
M templates/user/username.mako
M templates/webapps/galaxy/admin/index.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/history/embed.mako
M templates/webapps/galaxy/history/view.mako
M templates/webapps/galaxy/history/view_multiple.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/galaxy/workflow/run.mako
A templates/webapps/reports/history_and_dataset_per_user.mako
A templates/webapps/reports/history_and_dataset_type.mako
A templates/webapps/reports/history_per_user.mako
M templates/webapps/reports/index.mako
A templates/webapps/reports/tool_error_messages.mako
A templates/webapps/reports/tool_execution_time.mako
A templates/webapps/reports/tool_execution_time_per_month.mako
A templates/webapps/reports/tools_and_job_state.mako
A templates/webapps/reports/tools_and_job_state_per_month.mako
M templates/webapps/tool_shed/admin/index.mako
M templates/webapps/tool_shed/group/index.mako
M templates/webapps/tool_shed/index.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/export_repository.mako
A test-data/neostore.zip
A test/api/test_api_batch.py
M test/base/driver_util.py
M test/base/interactor.py
M test/base/twilltestcase.py
A test/casperjs/api-batch-tests.js
M test/functional/tools/column_multi_param.xml
M test/functional/tools/column_param.xml
A test/functional/tools/dbkey_output_action.xml
M test/functional/tools/identifier_collection.xml
M test/functional/tools/identifier_multiple.xml
M test/functional/tools/identifier_single.xml
M test/functional/tools/inputs_as_json.xml
M test/functional/tools/multi_output.xml
M test/functional/tools/multi_output_assign_primary.xml
M test/functional/tools/multi_output_configured.xml
R test/functional/tools/multi_page.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/tool_directory.xml
A test/functional/tools/tool_provided_metadata_1.xml
A test/functional/tools/tool_provided_metadata_2.xml
A test/functional/tools/tool_provided_metadata_3.xml
M test/functional/tools/validation_repeat.xml
A test/integration/test_resolvers.py
M test/qunit/test-data/fakeserver.js
M test/qunit/tests/form_tests.js
M test/qunit/tests/history_contents_model_tests.js
M test/qunit/tests/upload_dialog_tests.js
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_0310_hg_api_features.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1400_review_migration_stages.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_objectstore.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
M tools/data_source/upload.xml
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tox.ini
Log Message:
-----------
Merging with dev
Commit: 5e0c346adbdb7be67a9e6a0bed8b4a6b34744022
https://github.com/galaxyproject/galaxy/commit/5e0c346adbdb7be67a9e6a0bed8b…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-09-24 (Sat, 24 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
dict creation
Commit: 2d6854cb5fe2153e9295e00807a9270f8456d357
https://github.com/galaxyproject/galaxy/commit/2d6854cb5fe2153e9295e00807a9…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-09-24 (Sat, 24 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
simplify code
Commit: eb4b58a76156a29020e339c81ab419c812677ccf
https://github.com/galaxyproject/galaxy/commit/eb4b58a76156a29020e339c81ab4…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-09-24 (Sat, 24 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
simplify code
Commit: 086e2d58700ec58f89f1e9446e4d1ec710073463
https://github.com/galaxyproject/galaxy/commit/086e2d58700ec58f89f1e9446e4d…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-09-24 (Sat, 24 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
some more fixes
Commit: 7e1a4a393d0b10e167341f8476a6bca069e6693f
https://github.com/galaxyproject/galaxy/commit/7e1a4a393d0b10e167341f8476a6…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-09-24 (Sat, 24 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
whitespace fixes
Commit: a34bdc4647ed58a4ce4d4c33ecd6f42811e1568f
https://github.com/galaxyproject/galaxy/commit/a34bdc4647ed58a4ce4d4c33ecd6…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-09-24 (Sat, 24 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
use enumerate
Commit: 30afad5cc5cb2514a9dcf6e8a354c1254274b3ed
https://github.com/galaxyproject/galaxy/commit/30afad5cc5cb2514a9dcf6e8a354…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-09-24 (Sat, 24 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
use enumerate
Commit: fb4a6d1c1ce69bb425226b7097cf79e3f7357ba3
https://github.com/galaxyproject/galaxy/commit/fb4a6d1c1ce69bb425226b7097cf…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-09-24 (Sat, 24 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
style
Commit: 55d94e9a2317de2a6fdd5626475e023d2a432e6e
https://github.com/galaxyproject/galaxy/commit/55d94e9a2317de2a6fdd5626475e…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-09-24 (Sat, 24 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge pull request #20 from bgruening/small_fixes
Small fixes
Commit: df38ca9fe809b9a1888386502643d85c5fbc1b9d
https://github.com/galaxyproject/galaxy/commit/df38ca9fe809b9a1888386502643…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-28 (Wed, 28 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Minor style fix
Commit: 597214a65f4681b8fa81e4b80f990d6da5849f76
https://github.com/galaxyproject/galaxy/commit/597214a65f4681b8fa81e4b80f99…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-28 (Wed, 28 Sep 2016)
Changed paths:
R client/galaxy/scripts/mvc/user/api-keys.js
M client/galaxy/scripts/mvc/user/change-communication.js
M client/galaxy/scripts/mvc/user/change-password.js
R client/galaxy/scripts/mvc/user/manage-user-information.js
R client/galaxy/scripts/mvc/user/toolbox-filter.js
M client/galaxy/scripts/mvc/user/user-preferences.js
A static/maps/mvc/user/change-api-key.js.map
A static/maps/mvc/user/change-communication.js.map
A static/maps/mvc/user/change-password.js.map
A static/maps/mvc/user/change-permissions.js.map
A static/maps/mvc/user/change-toolbox-filter.js.map
A static/maps/mvc/user/change-user-information.js.map
A static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/mvc/user/change-api-key.js
A static/scripts/mvc/user/change-communication.js
A static/scripts/mvc/user/change-password.js
A static/scripts/mvc/user/change-permissions.js
A static/scripts/mvc/user/change-toolbox-filter.js
A static/scripts/mvc/user/change-user-information.js
A static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Add packed files, use consistent file naming
Commit: 31867733173911de306ea45184ce62ba1eea63ea
https://github.com/galaxyproject/galaxy/commit/31867733173911de306ea45184ce…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-28 (Wed, 28 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/user/change-user-information.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Remove unused options for api index endpoint
Commit: faa7cb525b78ca53895ddf526c972eb4ef390c2d
https://github.com/galaxyproject/galaxy/commit/faa7cb525b78ca53895ddf526c97…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-28 (Wed, 28 Sep 2016)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Add to_dict functions to form_builder
Commit: 0c70b5bca27e51a84af1e9381f28ce3cd33e55b0
https://github.com/galaxyproject/galaxy/commit/0c70b5bca27e51a84af1e9381f28…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-29 (Thu, 29 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-section.js
A client/galaxy/scripts/mvc/user/change-api-key.js
A client/galaxy/scripts/mvc/user/change-toolbox-filter.js
A client/galaxy/scripts/mvc/user/change-user-information.js
M lib/galaxy/model/__init__.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/user/change-permissions.js.map
M static/maps/mvc/user/change-user-information.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/user/change-permissions.js
M static/scripts/mvc/user/change-user-information.js
Log Message:
-----------
Build address field dict
Commit: 60ed49a6acb48ed82fdbdca1d45c8184d25360d3
https://github.com/galaxyproject/galaxy/commit/60ed49a6acb48ed82fdbdca1d45c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Add user info form conditional builder
Commit: ed104067aa6504890dedfd54dd89a56952cafc9b
https://github.com/galaxyproject/galaxy/commit/ed104067aa6504890dedfd54dd89…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Fix
Commit: 8d9dc602d0d336872a08548fd1a27c59794477eb
https://github.com/galaxyproject/galaxy/commit/8d9dc602d0d336872a08548fd1a2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Add type form, untested
Commit: baa4676282d0acd85e721e8819910f3553bff1c1
https://github.com/galaxyproject/galaxy/commit/baa4676282d0acd85e721e881991…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Remove unused parsing
Commit: c7f21301ddc3b5d95e3085bffd3e39f0b14924f0
https://github.com/galaxyproject/galaxy/commit/c7f21301ddc3b5d95e3085bffd3e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Fix tabs
Commit: 15081cf00c5ff36d4e001c544ee2a523156be5be
https://github.com/galaxyproject/galaxy/commit/15081cf00c5ff36d4e001c544ee2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Validate custom fields
Commit: ee8a887dcdd228b2e3c9c8e2526d42ce69a8f777
https://github.com/galaxyproject/galaxy/commit/ee8a887dcdd228b2e3c9c8e2526d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Use single api endpoint to build user information form with addresses
Commit: bf3d447f0d9c26405344dcfe43763d0515df2efb
https://github.com/galaxyproject/galaxy/commit/bf3d447f0d9c26405344dcfe4376…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Remove user info handler
Commit: 6b9ab97f4aeadca9c2a637c8f346642facfbbdc2
https://github.com/galaxyproject/galaxy/commit/6b9ab97f4aeadca9c2a637c8f346…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Fix typo
Commit: b737a2c6d791399bf59a8ef645851709ad5ad0ce
https://github.com/galaxyproject/galaxy/commit/b737a2c6d791399bf59a8ef64585…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M lib/galaxy/web/form_builder.py
Log Message:
-----------
Fix password field type
Commit: eb5eb99b8415d00eac466b53550563dcbb241aa8
https://github.com/galaxyproject/galaxy/commit/eb5eb99b8415d00eac466b535505…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M lib/galaxy/web/form_builder.py
Log Message:
-----------
Add dictionary representation for checkboxes
Commit: da95fb95479d9e69efe95198b271e5d9eb232ff2
https://github.com/galaxyproject/galaxy/commit/da95fb95479d9e69efe95198b271…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M lib/galaxy/web/form_builder.py
Log Message:
-----------
Remove commas
Commit: ebaead0a890cfdcf3b17dc9be1f152045c16e74f
https://github.com/galaxyproject/galaxy/commit/ebaead0a890cfdcf3b17dc9be1f1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M lib/galaxy/web/form_builder.py
Log Message:
-----------
Add basic select field support for form builder
Commit: ef362ef3c3c557d31aa62268cb5135da1f1e6b33
https://github.com/galaxyproject/galaxy/commit/ef362ef3c3c557d31aa62268cb51…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Remove space
Commit: 57a93e70135f6f788d3a29620068a8b46ab10777
https://github.com/galaxyproject/galaxy/commit/57a93e70135f6f788d3a29620068…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Remove more spaces in widget handling
Commit: dc01a1a51a609bf1f66a046960f324c8e98713c2
https://github.com/galaxyproject/galaxy/commit/dc01a1a51a609bf1f66a046960f3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M lib/galaxy/web/form_builder.py
Log Message:
-----------
Fix field building style
Commit: b31ab08f092ac80a1df2e04d63194eca139c0e58
https://github.com/galaxyproject/galaxy/commit/b31ab08f092ac80a1df2e04d6319…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M lib/galaxy/web/form_builder.py
Log Message:
-----------
Remove unused ftp field from basic form builder
Commit: c5641cc87ac33b258849ead4b76a533947ad528e
https://github.com/galaxyproject/galaxy/commit/c5641cc87ac33b258849ead4b76a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/ui.less
M doc/schema_template.md
M doc/source/project/issues.rst
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/mapping.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M scripts/bootstrap_history.py
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
M templates/webapps/galaxy/library/common/common.mako
M templates/webapps/galaxy/workflow/run.mako
R templates/webapps/galaxy/workflow/run_complete.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M test/base/interactor.py
A test/functional/tools/metadata_column_names.xml
M test/functional/tools/samples_tool_conf.xml
M test/qunit/tests/form_tests.js
M test/unit/test_galaxy_mapping.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/unittest_utils/galaxy_mock.py
M tools/data_source/data_source.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import_code.py
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sff_extract.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ_code.py
Log Message:
-----------
Merge branch 'dev' into remove_mako_preferences_revision
Commit: eadc6f26d27eb87011813e0ab9575fb42950fd6c
https://github.com/galaxyproject/galaxy/commit/eadc6f26d27eb87011813e0ab957…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M lib/galaxy/web/form_builder.py
Log Message:
-----------
Remove unused drilldown element from basic form builder
Commit: 98d31d0adcf8e4a6c083a2d5edb8c5a7b756246e
https://github.com/galaxyproject/galaxy/commit/98d31d0adcf8e4a6c083a2d5edb8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M lib/galaxy/web/form_builder.py
Log Message:
-----------
Remove unused library parameter from basic form builder
Commit: 30a8c0a2451b98289cb063861d455387df2a0c5a
https://github.com/galaxyproject/galaxy/commit/30a8c0a2451b98289cb063861d45…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-user-information.js
M static/maps/mvc/user/change-user-information.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-user-information.js
Log Message:
-----------
Remove form customization patches
Commit: f353fe6e7ec3ad1390c6f9d42099733ad3b3ff84
https://github.com/galaxyproject/galaxy/commit/f353fe6e7ec3ad1390c6f9d42099…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
A .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/flake8_wrapper.sh
A .ci/flake8_wrapper_docstrings.sh
M .ci/py3_sources.txt
M .travis.yml
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/style/source_material/circle.py
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M doc/parse_gx_xsd.py
M doc/source/admin/conda_faq.rst
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/index.rst
A doc/source/admin/mulled_containers.rst
M doc/source/api/guidelines.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/formatting.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
M lib/galaxy/jobs/runners/__init__.py
A lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
A lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
A lib/galaxy/tools/deps/container_resolvers/__init__.py
A lib/galaxy/tools/deps/container_resolvers/explicit.py
A lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
A lib/galaxy/tools/deps/installable.py
A lib/galaxy/tools/deps/mulled/__init__.py
A lib/galaxy/tools/deps/mulled/_cli.py
A lib/galaxy/tools/deps/mulled/invfile.lua
A lib/galaxy/tools/deps/mulled/mulled_build.py
A lib/galaxy/tools/deps/mulled/mulled_build_channel.py
A lib/galaxy/tools/deps/mulled/mulled_build_files.py
A lib/galaxy/tools/deps/mulled/mulled_build_tool.py
A lib/galaxy/tools/deps/mulled/mulled_search.py
A lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/webapps/galaxy/api/genomes.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M scripts/bootstrap_history.py
M setup.cfg
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-modal.js
M test/api/helpers.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_history_contents.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
A test/api/test_workflow_batch.ga
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/base/api.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/test_logging.py
M test/base/twilltestcase.py
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
A test/functional/tools/color_param.xml
A test/functional/tools/mulled_example_multi_1.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/workflow.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional_tests.py
M test/unit/jobs/test_runner_local.py
M test/unit/workflows/test_run_parameters.py
M tox.ini
Log Message:
-----------
Merge branch 'dev' into remove_mako_preferences_revision
Commit: a06980c72fd5bf2ba2aa95ebd2dd81a56c361d9c
https://github.com/galaxyproject/galaxy/commit/a06980c72fd5bf2ba2aa95ebd2dd…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
A .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/flake8_wrapper.sh
A .ci/flake8_wrapper_docstrings.sh
M .ci/py3_sources.txt
M .travis.yml
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
R client/galaxy/scripts/mvc/user/api-keys.js
A client/galaxy/scripts/mvc/user/change-api-key.js
M client/galaxy/scripts/mvc/user/change-communication.js
M client/galaxy/scripts/mvc/user/change-password.js
A client/galaxy/scripts/mvc/user/change-toolbox-filter.js
A client/galaxy/scripts/mvc/user/change-user-information.js
R client/galaxy/scripts/mvc/user/manage-user-information.js
R client/galaxy/scripts/mvc/user/toolbox-filter.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/ui.less
M client/galaxy/style/source_material/circle.py
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M doc/parse_gx_xsd.py
M doc/schema_template.md
M doc/source/admin/conda_faq.rst
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/index.rst
A doc/source/admin/mulled_containers.rst
M doc/source/api/guidelines.rst
M doc/source/project/issues.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/formatting.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
M lib/galaxy/jobs/runners/__init__.py
A lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
A lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
A lib/galaxy/tools/deps/container_resolvers/__init__.py
A lib/galaxy/tools/deps/container_resolvers/explicit.py
A lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
A lib/galaxy/tools/deps/installable.py
A lib/galaxy/tools/deps/mulled/__init__.py
A lib/galaxy/tools/deps/mulled/_cli.py
A lib/galaxy/tools/deps/mulled/invfile.lua
A lib/galaxy/tools/deps/mulled/mulled_build.py
A lib/galaxy/tools/deps/mulled/mulled_build_channel.py
A lib/galaxy/tools/deps/mulled/mulled_build_files.py
A lib/galaxy/tools/deps/mulled/mulled_build_tool.py
A lib/galaxy/tools/deps/mulled/mulled_search.py
A lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/webapps/galaxy/api/genomes.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M scripts/bootstrap_history.py
M setup.cfg
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-portlet.js.map
A static/maps/mvc/user/change-api-key.js.map
A static/maps/mvc/user/change-communication.js.map
A static/maps/mvc/user/change-password.js.map
A static/maps/mvc/user/change-permissions.js.map
A static/maps/mvc/user/change-toolbox-filter.js.map
A static/maps/mvc/user/change-user-information.js.map
A static/maps/mvc/user/user-preferences.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
A static/scripts/mvc/user/change-api-key.js
A static/scripts/mvc/user/change-communication.js
A static/scripts/mvc/user/change-password.js
A static/scripts/mvc/user/change-permissions.js
A static/scripts/mvc/user/change-toolbox-filter.js
A static/scripts/mvc/user/change-user-information.js
A static/scripts/mvc/user/user-preferences.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
M templates/webapps/galaxy/library/common/common.mako
M templates/webapps/galaxy/workflow/run.mako
R templates/webapps/galaxy/workflow/run_complete.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M test/api/helpers.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_history_contents.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
A test/api/test_workflow_batch.ga
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/base/api.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/test_logging.py
M test/base/twilltestcase.py
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
A test/functional/tools/color_param.xml
A test/functional/tools/metadata_column_names.xml
A test/functional/tools/mulled_example_multi_1.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/workflow.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/qunit/tests/form_tests.js
M test/shed_functional/base/test_db_util.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional_tests.py
M test/unit/jobs/test_runner_local.py
M test/unit/test_galaxy_mapping.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/workflows/test_run_parameters.py
M tools/data_source/data_source.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import_code.py
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sff_extract.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ_code.py
M tox.ini
Log Message:
-----------
Merge pull request #22 from guerler/remove_mako_preferences_revision
Remove mako preferences revision
Commit: 42d4a677bfc5457219d47c3fc051b01e14a4b0c3
https://github.com/galaxyproject/galaxy/commit/42d4a677bfc5457219d47c3fc051…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-api-key.js
M client/galaxy/scripts/mvc/user/change-user-information.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/change-api-key.js.map
M static/maps/mvc/user/change-user-information.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-api-key.js
M static/scripts/mvc/user/change-user-information.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Fix inconsistent naming
Commit: 7273f43c0d211a6e11d8c0370bcb604b006e1026
https://github.com/galaxyproject/galaxy/commit/7273f43c0d211a6e11d8c0370bcb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-toolbox-filter.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/change-toolbox-filter.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/mvc/user/change-toolbox-filter.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Rename more endpoints and functions for consistency
Commit: 6005ce9fd7bfa224f59b00f705018c93c1bd2601
https://github.com/galaxyproject/galaxy/commit/6005ce9fd7bfa224f59b00f70501…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Fix naming
Commit: 35bca940bd35d8303df55a7e11c22107f95eb0a5
https://github.com/galaxyproject/galaxy/commit/35bca940bd35d8303df55a7e11c2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-user-information.js
M lib/galaxy/web/form_builder.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/user/change-user-information.js.map
M static/scripts/mvc/user/change-user-information.js
Log Message:
-----------
Ensure proper names for address fields
Commit: e5f729b40bfa7534e7b535d3c205fff56693fc8b
https://github.com/galaxyproject/galaxy/commit/e5f729b40bfa7534e7b535d3c205…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-user-information.js
M static/maps/mvc/user/change-user-information.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-user-information.js
Log Message:
-----------
Add save icon
Commit: f87047cc0c10e41c4ae7e892ecc4fa930f1f4d35
https://github.com/galaxyproject/galaxy/commit/f87047cc0c10e41c4ae7e892ecc4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
R client/galaxy/scripts/mvc/user/add-edit-address.js
M client/galaxy/scripts/mvc/user/change-api-key.js
M static/maps/mvc/user/change-api-key.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Remove unecessary view
Commit: 1eeb21f344020b52e44008364b83e4f46d0cdcd0
https://github.com/galaxyproject/galaxy/commit/1eeb21f344020b52e44008364b83…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-api-key.js
M client/galaxy/scripts/mvc/user/change-communication.js
M client/galaxy/scripts/mvc/user/change-password.js
M client/galaxy/scripts/mvc/user/change-permissions.js
M client/galaxy/scripts/mvc/user/change-toolbox-filter.js
M client/galaxy/scripts/mvc/user/change-user-information.js
M static/maps/mvc/user/change-api-key.js.map
M static/maps/mvc/user/change-communication.js.map
M static/maps/mvc/user/change-password.js.map
M static/maps/mvc/user/change-permissions.js.map
M static/maps/mvc/user/change-toolbox-filter.js.map
M static/maps/mvc/user/change-user-information.js.map
M static/scripts/mvc/user/change-api-key.js
M static/scripts/mvc/user/change-communication.js
M static/scripts/mvc/user/change-password.js
M static/scripts/mvc/user/change-permissions.js
M static/scripts/mvc/user/change-toolbox-filter.js
M static/scripts/mvc/user/change-user-information.js
Log Message:
-----------
Remove inconsistent function names
Commit: fdff89596eeae060b626e1f376eead7e79437180
https://github.com/galaxyproject/galaxy/commit/fdff89596eeae060b626e1f376ee…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Revise main view handling
Commit: e9a712c82d4ea007fea8ffbbbc9910a02e3c1714
https://github.com/galaxyproject/galaxy/commit/e9a712c82d4ea007fea8ffbbbc99…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Fix
Commit: 64b1bd1e613470117e6310ce4b8cd9710f4dbb1b
https://github.com/galaxyproject/galaxy/commit/64b1bd1e613470117e6310ce4b8c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-api-key.js
M client/galaxy/scripts/mvc/user/change-communication.js
M client/galaxy/scripts/mvc/user/change-password.js
M client/galaxy/scripts/mvc/user/change-toolbox-filter.js
M client/galaxy/scripts/mvc/user/change-user-information.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/change-api-key.js.map
M static/maps/mvc/user/change-communication.js.map
M static/maps/mvc/user/change-password.js.map
M static/maps/mvc/user/change-toolbox-filter.js.map
M static/maps/mvc/user/change-user-information.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-api-key.js
M static/scripts/mvc/user/change-communication.js
M static/scripts/mvc/user/change-password.js
M static/scripts/mvc/user/change-toolbox-filter.js
M static/scripts/mvc/user/change-user-information.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Remove redundant page loaders
Commit: 5f20a2b1181c0bb0584979f212f6866cc8aaf87b
https://github.com/galaxyproject/galaxy/commit/5f20a2b1181c0bb0584979f212f6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Add missing options
Commit: dd45dd6477963dd60067f31b20349885361c429b
https://github.com/galaxyproject/galaxy/commit/dd45dd6477963dd60067f31b2034…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Add footer, directly call template helper for links
Commit: 27216933f036fb603e65c2c1bf4dad0e30696836
https://github.com/galaxyproject/galaxy/commit/27216933f036fb603e65c2c1bf4d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Use void href
Commit: 783272416ed4416e57143843ad26eabf14c0cd35
https://github.com/galaxyproject/galaxy/commit/783272416ed4416e57143843ad26…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
R client/galaxy/scripts/mvc/user/add-edit-address.js
M client/galaxy/scripts/mvc/user/change-api-key.js
M client/galaxy/scripts/mvc/user/change-communication.js
M client/galaxy/scripts/mvc/user/change-password.js
M client/galaxy/scripts/mvc/user/change-permissions.js
M client/galaxy/scripts/mvc/user/change-toolbox-filter.js
M client/galaxy/scripts/mvc/user/change-user-information.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/web/form_builder.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/change-api-key.js.map
M static/maps/mvc/user/change-communication.js.map
M static/maps/mvc/user/change-password.js.map
M static/maps/mvc/user/change-permissions.js.map
M static/maps/mvc/user/change-toolbox-filter.js.map
M static/maps/mvc/user/change-user-information.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-api-key.js
M static/scripts/mvc/user/change-communication.js
M static/scripts/mvc/user/change-password.js
M static/scripts/mvc/user/change-permissions.js
M static/scripts/mvc/user/change-toolbox-filter.js
M static/scripts/mvc/user/change-user-information.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Merge pull request #23 from guerler/remove_mako_preferences_revision
More unifications and adjustments
Commit: b248acd5c26e7cb7a69cad69a45a87743021da40
https://github.com/galaxyproject/galaxy/commit/b248acd5c26e7cb7a69cad69a45a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-communication.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/change-communication.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-communication.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Iterate communications endpoint
Commit: 95e39bbc591a1d3d0e475b99add64953c3f2a920
https://github.com/galaxyproject/galaxy/commit/95e39bbc591a1d3d0e475b99add6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-api-key.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/change-api-key.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-api-key.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Fix api_key endpoint
Commit: a7df03710a8ee6254f7867b134f39984746c4ab2
https://github.com/galaxyproject/galaxy/commit/a7df03710a8ee6254f7867b134f3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-communication.js
M client/galaxy/scripts/mvc/user/change-password.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/auth/__init__.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/change-password.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-password.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Align password endpoint
Commit: ef6534285224e397772b91eb5aef9a0e70f2b387
https://github.com/galaxyproject/galaxy/commit/ef6534285224e397772b91eb5aef…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-19 (Wed, 19 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-api-key.js
M client/galaxy/scripts/mvc/user/change-communication.js
M client/galaxy/scripts/mvc/user/change-password.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/user/change-api-key.js.map
M static/maps/mvc/user/change-communication.js.map
M static/maps/mvc/user/change-password.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-api-key.js
M static/scripts/mvc/user/change-communication.js
M static/scripts/mvc/user/change-password.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Raise and display errors
Commit: b4b779dd04f1d7286a2014ce206a27abe832c55f
https://github.com/galaxyproject/galaxy/commit/b4b779dd04f1d7286a2014ce206a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-19 (Wed, 19 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-api-key.js
A client/galaxy/scripts/mvc/user/change-information.js
R client/galaxy/scripts/mvc/user/change-user-information.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/change-api-key.js.map
A static/maps/mvc/user/change-information.js.map
R static/maps/mvc/user/change-user-information.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-api-key.js
A static/scripts/mvc/user/change-information.js
R static/scripts/mvc/user/change-user-information.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Add packed files, fix general user information endpoints
Commit: f6ecb45040c4e39c83ab4493a9c392b26b825adb
https://github.com/galaxyproject/galaxy/commit/f6ecb45040c4e39c83ab4493a9c3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-19 (Wed, 19 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Prepare permissions and filter endpoints
Commit: d31998835ed543c4c528a11f8cdebebc3a67b098
https://github.com/galaxyproject/galaxy/commit/d31998835ed543c4c528a11f8cde…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-19 (Wed, 19 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-toolbox-filter.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/maps/mvc/user/change-toolbox-filter.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-toolbox-filter.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Revise toolbox filter ui and api endpoint
Commit: aa5ed9d2facc4a3549fd2eef55d19f0705b953cf
https://github.com/galaxyproject/galaxy/commit/aa5ed9d2facc4a3549fd2eef55d1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-19 (Wed, 19 Oct 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Fix filter handling if current label is missing?
Commit: 4fa9984eaa9b834fbf30209033e619dd28cddaf0
https://github.com/galaxyproject/galaxy/commit/4fa9984eaa9b834fbf30209033e6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-19 (Wed, 19 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-api-key.js
M client/galaxy/scripts/mvc/user/change-toolbox-filter.js
M static/maps/mvc/user/change-api-key.js.map
M static/maps/mvc/user/change-toolbox-filter.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-api-key.js
M static/scripts/mvc/user/change-toolbox-filter.js
Log Message:
-----------
Add icons for filter and api key forms
Commit: 1305b42b498e79940a81f0c3329238723369516b
https://github.com/galaxyproject/galaxy/commit/1305b42b498e79940a81f0c33292…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-19 (Wed, 19 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-api-key.js
M client/galaxy/scripts/mvc/user/change-communication.js
A client/galaxy/scripts/mvc/user/change-information.js
M client/galaxy/scripts/mvc/user/change-password.js
M client/galaxy/scripts/mvc/user/change-toolbox-filter.js
R client/galaxy/scripts/mvc/user/change-user-information.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/auth/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/maps/mvc/user/change-api-key.js.map
M static/maps/mvc/user/change-communication.js.map
A static/maps/mvc/user/change-information.js.map
M static/maps/mvc/user/change-password.js.map
M static/maps/mvc/user/change-toolbox-filter.js.map
R static/maps/mvc/user/change-user-information.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-api-key.js
M static/scripts/mvc/user/change-communication.js
A static/scripts/mvc/user/change-information.js
M static/scripts/mvc/user/change-password.js
M static/scripts/mvc/user/change-toolbox-filter.js
R static/scripts/mvc/user/change-user-information.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Merge pull request #24 from guerler/remove_mako_preferences_revision
Remove mako preferences revision
Commit: 3050e3db2ad39db7b9060ee167eb86775f66db64
https://github.com/galaxyproject/galaxy/commit/3050e3db2ad39db7b9060ee167eb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-20 (Thu, 20 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-permissions.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/user/change-permissions.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-permissions.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Permissions ui/endpoint revision
Commit: f4e5819c68b6e6705fd64fa102a2ef2ec7fbe16d
https://github.com/galaxyproject/galaxy/commit/f4e5819c68b6e6705fd64fa102a2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-20 (Thu, 20 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-permissions.js
M static/maps/mvc/user/change-permissions.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-permissions.js
Log Message:
-----------
Align permissions ui wrapper
Commit: 36e8f967dfd1b970c3f3f303e4387c0d7ca29ed7
https://github.com/galaxyproject/galaxy/commit/36e8f967dfd1b970c3f3f303e438…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-20 (Thu, 20 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-communication.js
M client/galaxy/scripts/mvc/user/change-information.js
M client/galaxy/scripts/mvc/user/change-password.js
M client/galaxy/scripts/mvc/user/change-permissions.js
M client/galaxy/scripts/mvc/user/change-toolbox-filter.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/user/change-communication.js.map
M static/maps/mvc/user/change-permissions.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-communication.js
M static/scripts/mvc/user/change-information.js
M static/scripts/mvc/user/change-password.js
M static/scripts/mvc/user/change-permissions.js
M static/scripts/mvc/user/change-toolbox-filter.js
Log Message:
-----------
Use select2 fields for permission assignment
Commit: 4dfb61033bad820a544500fc4ac6d9db7f2c5de9
https://github.com/galaxyproject/galaxy/commit/4dfb61033bad820a544500fc4ac6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-20 (Thu, 20 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-communication.js
M client/galaxy/scripts/mvc/user/change-password.js
M client/galaxy/scripts/mvc/user/change-permissions.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/user/change-communication.js.map
M static/maps/mvc/user/change-password.js.map
M static/maps/mvc/user/change-permissions.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-communication.js
M static/scripts/mvc/user/change-password.js
M static/scripts/mvc/user/change-permissions.js
Log Message:
-----------
Remove more unused code
Commit: 0d09e6e7bc73f0206401e77ca97d65602423a300
https://github.com/galaxyproject/galaxy/commit/0d09e6e7bc73f0206401e77ca97d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-20 (Thu, 20 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-password.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/user/change-password.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-password.js
Log Message:
-----------
Align password form, build input dictionaries in the backend
Commit: ee2b7c4159427f223fea0b9fd5b552bed5ce53ed
https://github.com/galaxyproject/galaxy/commit/ee2b7c4159427f223fea0b9fd5b5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-20 (Thu, 20 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/change-api-key.js
M client/galaxy/scripts/mvc/user/change-communication.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/user/change-api-key.js.map
M static/maps/mvc/user/change-communication.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/change-api-key.js
M static/scripts/mvc/user/change-communication.js
Log Message:
-----------
Build all input elements used for user preferences in backend
Commit: c408090c392f6fe4765a7e037ef3fe8cb1d58d08
https://github.com/galaxyproject/galaxy/commit/c408090c392f6fe4765a7e037ef3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-20 (Thu, 20 Oct 2016)
Changed paths:
R client/galaxy/scripts/mvc/user/change-api-key.js
R client/galaxy/scripts/mvc/user/change-communication.js
R client/galaxy/scripts/mvc/user/change-information.js
R client/galaxy/scripts/mvc/user/change-password.js
R client/galaxy/scripts/mvc/user/change-permissions.js
R client/galaxy/scripts/mvc/user/change-toolbox-filter.js
M client/galaxy/scripts/mvc/user/user-preferences.js
R static/maps/mvc/user/change-api-key.js.map
R static/maps/mvc/user/change-communication.js.map
R static/maps/mvc/user/change-information.js.map
R static/maps/mvc/user/change-password.js.map
R static/maps/mvc/user/change-permissions.js.map
R static/maps/mvc/user/change-toolbox-filter.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
R static/scripts/mvc/user/change-api-key.js
R static/scripts/mvc/user/change-communication.js
R static/scripts/mvc/user/change-information.js
R static/scripts/mvc/user/change-password.js
R static/scripts/mvc/user/change-permissions.js
R static/scripts/mvc/user/change-toolbox-filter.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Remove redundancies
Commit: fdd8099c342c9298a0669b18e763b0ab8abd63b5
https://github.com/galaxyproject/galaxy/commit/fdd8099c342c9298a0669b18e763…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-20 (Thu, 20 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Use generic form to view all preference forms
Commit: dd0951ecc39b577febaf75f3235af2b25fff53a7
https://github.com/galaxyproject/galaxy/commit/dd0951ecc39b577febaf75f3235a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-20 (Thu, 20 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Use traditional ajax submission for arrays
Commit: dfec446c4c6439bdd340ee38471e37a778503acf
https://github.com/galaxyproject/galaxy/commit/dfec446c4c6439bdd340ee38471e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-20 (Thu, 20 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Add auto save feature for communication settings
Commit: b6951841df274f455681cd4332f9bd64218fb9e6
https://github.com/galaxyproject/galaxy/commit/b6951841df274f455681cd4332f9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-20 (Thu, 20 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Fix messages
Commit: 3b164bd9f83c70ea798b1461ec0326f1149f6fa4
https://github.com/galaxyproject/galaxy/commit/3b164bd9f83c70ea798b1461ec03…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-20 (Thu, 20 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Fix password message
Commit: 30c2dcce923da2825f307faee9ccaecbbff16f71
https://github.com/galaxyproject/galaxy/commit/30c2dcce923da2825f307faee9cc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-21 (Fri, 21 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Fix permission api endpoint
Commit: d70f5a4ff46163330db07d3bebd75952b522b604
https://github.com/galaxyproject/galaxy/commit/d70f5a4ff46163330db07d3bebd7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-21 (Fri, 21 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Remove unnecessary line
Commit: b792a6feb49c3f5071506b689d32c96b64328473
https://github.com/galaxyproject/galaxy/commit/b792a6feb49c3f5071506b689d32…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-21 (Fri, 21 Oct 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M .gitignore
M Makefile
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/utils/utils.js
M config/galaxy.ini.sample
R config/plugins/visualizations/charts/Gruntfile.js
M config/plugins/visualizations/charts/config/charts.xml
M config/plugins/visualizations/charts/package.json
R config/plugins/visualizations/charts/sample.txt
R config/plugins/visualizations/charts/static/app.css
R config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/line/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/pie/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/example/config.js
R config/plugins/visualizations/charts/static/charts/others/example/logo.png
R config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/logo.png
R config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/logo.png
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
R config/plugins/visualizations/charts/static/charts/overview.js
R config/plugins/visualizations/charts/static/charts/types.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
A config/plugins/visualizations/charts/static/client/app.css
A config/plugins/visualizations/charts/static/client/app.js
A config/plugins/visualizations/charts/static/client/components/model.js
A config/plugins/visualizations/charts/static/client/components/screenshot.js
A config/plugins/visualizations/charts/static/client/views/description.js
A config/plugins/visualizations/charts/static/client/views/editor.js
A config/plugins/visualizations/charts/static/client/views/groups.js
A config/plugins/visualizations/charts/static/client/views/settings.js
A config/plugins/visualizations/charts/static/client/views/types.js
A config/plugins/visualizations/charts/static/client/views/viewer.js
A config/plugins/visualizations/charts/static/client/views/viewport.js
R config/plugins/visualizations/charts/static/components/jobs.js
R config/plugins/visualizations/charts/static/components/model.js
R config/plugins/visualizations/charts/static/components/screenshot.js
R config/plugins/visualizations/charts/static/components/storage.js
R config/plugins/visualizations/charts/static/plugins/canvg/canvg.js
R config/plugins/visualizations/charts/static/plugins/canvg/rgbcolor.js
R config/plugins/visualizations/charts/static/plugins/crossfilter/crossfilter.js
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.css
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.js
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.plugins.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.barRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.blockRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.boxplotRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisLabelRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisTickRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasOverlay.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasTextRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.categoryAxisRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.cursor.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.enhancedLegendRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.highlighter.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.ohlcRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css
R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js
A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js
A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map
A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js
A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map
A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js
A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map
A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_line.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_line.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_line.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_line.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js.map
A config/plugins/visualizations/charts/static/repository/build/others_example.js
A config/plugins/visualizations/charts/static/repository/build/others_example.js.map
A config/plugins/visualizations/charts/static/repository/build/others_heatmap.js
A config/plugins/visualizations/charts/static/repository/build/others_heatmap.js.map
A config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js
A config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js.map
A config/plugins/visualizations/charts/static/repository/build/pv_viewer.js
A config/plugins/visualizations/charts/static/repository/build/pv_viewer.js.map
A config/plugins/visualizations/charts/static/repository/build/registry.js
A config/plugins/visualizations/charts/static/repository/build/registry.js.map
A config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css
A config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/biojs.msa.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/drawrna.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/layout.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/base.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/connection.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/getnaview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/loop.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/naview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/radloop.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/region.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/radiate/getradiate.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
A config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js
A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css
A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js
A config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js
A config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/utilities/jobs.js
A config/plugins/visualizations/charts/static/repository/utilities/utils.js
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
R config/plugins/visualizations/charts/static/views/description.js
R config/plugins/visualizations/charts/static/views/editor.js
R config/plugins/visualizations/charts/static/views/groups.js
R config/plugins/visualizations/charts/static/views/settings.js
R config/plugins/visualizations/charts/static/views/types.js
R config/plugins/visualizations/charts/static/views/viewer.js
R config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
A config/plugins/visualizations/charts/webpack.config.js
M config/tool_conf.xml.sample
M doc/schema_template.md
M doc/source/conf.py
A doc/source/slideshow/architecture/galaxy_architecture.md
A doc/source/slideshow/architecture/images/backbone-model-view.svg
A doc/source/slideshow/architecture/images/cluster_support.svg
A doc/source/slideshow/architecture/images/data_managers.svg
A doc/source/slideshow/architecture/images/docker-chart.png
A doc/source/slideshow/architecture/images/family/team.png
A doc/source/slideshow/architecture/images/galaxy_schema.png
A doc/source/slideshow/architecture/images/hda.svg
A doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg
A doc/source/slideshow/architecture/images/hda_dataset.plantuml.txt
A doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg
A doc/source/slideshow/architecture/images/hda_hdca.plantuml.txt
A doc/source/slideshow/architecture/images/jsload.png
A doc/source/slideshow/architecture/images/libraries.svg
A doc/source/slideshow/architecture/images/library_permissions.svg
A doc/source/slideshow/architecture/images/objectstore.plantuml.svg
A doc/source/slideshow/architecture/images/objectstore.plantuml.txt
A doc/source/slideshow/architecture/images/objectstore_diagram.svg
A doc/source/slideshow/architecture/images/plantuml_options.txt
A doc/source/slideshow/architecture/images/sequence.json
A doc/source/slideshow/architecture/images/server_client.plantuml.svg
A doc/source/slideshow/architecture/images/server_client.plantuml.txt
A doc/source/slideshow/architecture/images/server_client_old.plantuml.svg
A doc/source/slideshow/architecture/images/server_client_old.plantuml.txt
A doc/source/slideshow/architecture/images/sqla_arch_small.png
A doc/source/slideshow/architecture/images/usegalaxy_webservers.svg
A doc/source/slideshow/architecture/images/usegalaxyorg.svg
A doc/source/slideshow/architecture/images/webapp.plantuml.svg
A doc/source/slideshow/architecture/images/webapp.plantuml.txt
A doc/source/slideshow/architecture/images/what-is-webpack.svg
A doc/source/slideshow/architecture/images/workflow_definition.svg
A doc/source/slideshow/architecture/images/workflow_run.svg
A doc/source/slideshow/architecture/images/wsgi_app.svg
A doc/source/slideshow/architecture/images/wsgi_request.svg
A doc/source/slideshow/architecture/remark-latest.min.js
A doc/source/slideshow/architecture/style.css
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
R lib/galaxy/datatypes/util/image_util.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/orm/now.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/mulled/_cli.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/mulled/mulled_build_files.py
M lib/galaxy/tools/deps/mulled/mulled_build_tool.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/exception_handling.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/loader_directory.py
A lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/checkers.py
A lib/galaxy/util/image_util.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/web/framework/middleware/static.py
M lib/galaxy/webapps/galaxy/api/tours.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/schedulers/core.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
A scripts/slideshow/__init__.py
A scripts/slideshow/build_slideshow.py
A scripts/slideshow/example.md
A scripts/slideshow/slideshow_template.html
A scripts/slideshow/style.sample.css
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/utils/utils.js
M test/api/test_histories.py
M test/api/test_libraries.py
M test/api/test_workflow_extraction.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/main.py
M test/base/driver_util.py
A test/functional/tools/multi_data_optional.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/version_command.py
A test/functional/tools/version_command_interpreter.xml
A test/functional/tools/version_command_plain.xml
A test/functional/tools/version_command_tool_dir.xml
M test/unit/jobs/test_job_wrapper.py
M test/unit/tools/test_tool_dependency_description.py
M test/unit/tools_support.py
M test/unit/unittest_utils/utility.py
M tools/data_source/upload.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/stats/filtering.py
Log Message:
-----------
Merge branch 'dev' into remove_mako_preferences_revision
Commit: f88b72f3474b98877417a0af7c128bdc8b18c8c6
https://github.com/galaxyproject/galaxy/commit/f88b72f3474b98877417a0af7c12…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-21 (Fri, 21 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Show icons in selection list
Commit: 88f6067364667c5a0ad7c3f1f9e20014be00d66c
https://github.com/galaxyproject/galaxy/commit/88f6067364667c5a0ad7c3f1f9e2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-21 (Fri, 21 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Prepare minor touch up of preference list rendering
Commit: 897137d94994121ea5f12d1b94a5346e8293eb09
https://github.com/galaxyproject/galaxy/commit/897137d94994121ea5f12d1b94a5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-21 (Fri, 21 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Change messages
Commit: fe1676af01b2a5317faa0e0e29e16c8b0cb3a85a
https://github.com/galaxyproject/galaxy/commit/fe1676af01b2a5317faa0e0e29e1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-21 (Fri, 21 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Improve preference ui
Commit: 02cf8326058ba920a676fb02b5d44fd35d5b4a69
https://github.com/galaxyproject/galaxy/commit/02cf8326058ba920a676fb02b5d4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-22 (Sat, 22 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Prepare logout and openid handling
Commit: 76f2287dbcf1ab553397bf3bf2170cc37c16b5ab
https://github.com/galaxyproject/galaxy/commit/76f2287dbcf1ab553397bf3bf217…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-22 (Sat, 22 Oct 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M .gitignore
M Makefile
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
R client/galaxy/scripts/mvc/user/change-api-key.js
R client/galaxy/scripts/mvc/user/change-communication.js
R client/galaxy/scripts/mvc/user/change-information.js
R client/galaxy/scripts/mvc/user/change-password.js
R client/galaxy/scripts/mvc/user/change-permissions.js
R client/galaxy/scripts/mvc/user/change-toolbox-filter.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/utils/utils.js
M config/galaxy.ini.sample
R config/plugins/visualizations/charts/Gruntfile.js
M config/plugins/visualizations/charts/config/charts.xml
M config/plugins/visualizations/charts/package.json
R config/plugins/visualizations/charts/sample.txt
R config/plugins/visualizations/charts/static/app.css
R config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/line/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/pie/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/example/config.js
R config/plugins/visualizations/charts/static/charts/others/example/logo.png
R config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/logo.png
R config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/logo.png
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
R config/plugins/visualizations/charts/static/charts/overview.js
R config/plugins/visualizations/charts/static/charts/types.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
A config/plugins/visualizations/charts/static/client/app.css
A config/plugins/visualizations/charts/static/client/app.js
A config/plugins/visualizations/charts/static/client/components/model.js
A config/plugins/visualizations/charts/static/client/components/screenshot.js
A config/plugins/visualizations/charts/static/client/views/description.js
A config/plugins/visualizations/charts/static/client/views/editor.js
A config/plugins/visualizations/charts/static/client/views/groups.js
A config/plugins/visualizations/charts/static/client/views/settings.js
A config/plugins/visualizations/charts/static/client/views/types.js
A config/plugins/visualizations/charts/static/client/views/viewer.js
A config/plugins/visualizations/charts/static/client/views/viewport.js
R config/plugins/visualizations/charts/static/components/jobs.js
R config/plugins/visualizations/charts/static/components/model.js
R config/plugins/visualizations/charts/static/components/screenshot.js
R config/plugins/visualizations/charts/static/components/storage.js
R config/plugins/visualizations/charts/static/plugins/canvg/canvg.js
R config/plugins/visualizations/charts/static/plugins/canvg/rgbcolor.js
R config/plugins/visualizations/charts/static/plugins/crossfilter/crossfilter.js
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.css
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.js
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.plugins.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.barRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.blockRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.boxplotRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisLabelRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisTickRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasOverlay.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasTextRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.categoryAxisRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.cursor.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.enhancedLegendRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.highlighter.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.ohlcRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css
R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js
A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js
A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map
A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js
A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map
A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js
A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map
A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_line.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_line.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_line.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_line.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js.map
A config/plugins/visualizations/charts/static/repository/build/others_example.js
A config/plugins/visualizations/charts/static/repository/build/others_example.js.map
A config/plugins/visualizations/charts/static/repository/build/others_heatmap.js
A config/plugins/visualizations/charts/static/repository/build/others_heatmap.js.map
A config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js
A config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js.map
A config/plugins/visualizations/charts/static/repository/build/pv_viewer.js
A config/plugins/visualizations/charts/static/repository/build/pv_viewer.js.map
A config/plugins/visualizations/charts/static/repository/build/registry.js
A config/plugins/visualizations/charts/static/repository/build/registry.js.map
A config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css
A config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/biojs.msa.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/drawrna.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/layout.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/base.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/connection.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/getnaview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/loop.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/naview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/radloop.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/region.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/radiate/getradiate.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
A config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js
A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css
A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js
A config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js
A config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/utilities/jobs.js
A config/plugins/visualizations/charts/static/repository/utilities/utils.js
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
R config/plugins/visualizations/charts/static/views/description.js
R config/plugins/visualizations/charts/static/views/editor.js
R config/plugins/visualizations/charts/static/views/groups.js
R config/plugins/visualizations/charts/static/views/settings.js
R config/plugins/visualizations/charts/static/views/types.js
R config/plugins/visualizations/charts/static/views/viewer.js
R config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
A config/plugins/visualizations/charts/webpack.config.js
M config/tool_conf.xml.sample
M doc/schema_template.md
M doc/source/conf.py
A doc/source/slideshow/architecture/galaxy_architecture.md
A doc/source/slideshow/architecture/images/backbone-model-view.svg
A doc/source/slideshow/architecture/images/cluster_support.svg
A doc/source/slideshow/architecture/images/data_managers.svg
A doc/source/slideshow/architecture/images/docker-chart.png
A doc/source/slideshow/architecture/images/family/team.png
A doc/source/slideshow/architecture/images/galaxy_schema.png
A doc/source/slideshow/architecture/images/hda.svg
A doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg
A doc/source/slideshow/architecture/images/hda_dataset.plantuml.txt
A doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg
A doc/source/slideshow/architecture/images/hda_hdca.plantuml.txt
A doc/source/slideshow/architecture/images/jsload.png
A doc/source/slideshow/architecture/images/libraries.svg
A doc/source/slideshow/architecture/images/library_permissions.svg
A doc/source/slideshow/architecture/images/objectstore.plantuml.svg
A doc/source/slideshow/architecture/images/objectstore.plantuml.txt
A doc/source/slideshow/architecture/images/objectstore_diagram.svg
A doc/source/slideshow/architecture/images/plantuml_options.txt
A doc/source/slideshow/architecture/images/sequence.json
A doc/source/slideshow/architecture/images/server_client.plantuml.svg
A doc/source/slideshow/architecture/images/server_client.plantuml.txt
A doc/source/slideshow/architecture/images/server_client_old.plantuml.svg
A doc/source/slideshow/architecture/images/server_client_old.plantuml.txt
A doc/source/slideshow/architecture/images/sqla_arch_small.png
A doc/source/slideshow/architecture/images/usegalaxy_webservers.svg
A doc/source/slideshow/architecture/images/usegalaxyorg.svg
A doc/source/slideshow/architecture/images/webapp.plantuml.svg
A doc/source/slideshow/architecture/images/webapp.plantuml.txt
A doc/source/slideshow/architecture/images/what-is-webpack.svg
A doc/source/slideshow/architecture/images/workflow_definition.svg
A doc/source/slideshow/architecture/images/workflow_run.svg
A doc/source/slideshow/architecture/images/wsgi_app.svg
A doc/source/slideshow/architecture/images/wsgi_request.svg
A doc/source/slideshow/architecture/remark-latest.min.js
A doc/source/slideshow/architecture/style.css
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
R lib/galaxy/datatypes/util/image_util.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/orm/now.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/mulled/_cli.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/mulled/mulled_build_files.py
M lib/galaxy/tools/deps/mulled/mulled_build_tool.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/exception_handling.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/loader_directory.py
A lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/checkers.py
A lib/galaxy/util/image_util.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/web/framework/middleware/static.py
M lib/galaxy/webapps/galaxy/api/tours.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/schedulers/core.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
A scripts/slideshow/__init__.py
A scripts/slideshow/build_slideshow.py
A scripts/slideshow/example.md
A scripts/slideshow/slideshow_template.html
A scripts/slideshow/style.sample.css
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-buttons.js.map
R static/maps/mvc/user/change-api-key.js.map
R static/maps/mvc/user/change-communication.js.map
R static/maps/mvc/user/change-information.js.map
R static/maps/mvc/user/change-password.js.map
R static/maps/mvc/user/change-permissions.js.map
R static/maps/mvc/user/change-toolbox-filter.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-buttons.js
R static/scripts/mvc/user/change-api-key.js
R static/scripts/mvc/user/change-communication.js
R static/scripts/mvc/user/change-information.js
R static/scripts/mvc/user/change-password.js
R static/scripts/mvc/user/change-permissions.js
R static/scripts/mvc/user/change-toolbox-filter.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/utils/utils.js
M test/api/test_histories.py
M test/api/test_libraries.py
M test/api/test_workflow_extraction.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/main.py
M test/base/driver_util.py
A test/functional/tools/multi_data_optional.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/version_command.py
A test/functional/tools/version_command_interpreter.xml
A test/functional/tools/version_command_plain.xml
A test/functional/tools/version_command_tool_dir.xml
M test/unit/jobs/test_job_wrapper.py
M test/unit/tools/test_tool_dependency_description.py
M test/unit/tools_support.py
M test/unit/unittest_utils/utility.py
M tools/data_source/upload.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/stats/filtering.py
Log Message:
-----------
Merge pull request #25 from guerler/remove_mako_preferences_revision
Remove unused code blocks, unify form handling, fix permissions endpoint
Commit: 4b14761f7ca94aba77495be7975267a066cf472a
https://github.com/galaxyproject/galaxy/commit/4b14761f7ca94aba77495be79752…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-22 (Sat, 22 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Add session logout feature
Commit: 7a0850116f6001f589e295b0279ef37d95a196eb
https://github.com/galaxyproject/galaxy/commit/7a0850116f6001f589e295b0279e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-22 (Sat, 22 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/style/less/ui.less
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
M static/style/blue/base.css
Log Message:
-----------
Move fixed css to styles, move footer to template
Commit: 97890f68e96d58698a4561ae8c678202ac7ffc5a
https://github.com/galaxyproject/galaxy/commit/97890f68e96d58698a4561ae8c67…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-22 (Sat, 22 Oct 2016)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Use margins instead of fixed width for icons
Commit: d8aea401bea1bfa8eced7b309a90647195aad296
https://github.com/galaxyproject/galaxy/commit/d8aea401bea1bfa8eced7b309a90…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-22 (Sat, 22 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Fix footer template
Commit: 8b66acaf9a405d83a557e1bf0a33a326d017868d
https://github.com/galaxyproject/galaxy/commit/8b66acaf9a405d83a557e1bf0a33…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-25 (Tue, 25 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Display mako based openid manager until grids have been revisited
Commit: 2a16b25e83883ea7e4086994d02bf0cdc238f8f0
https://github.com/galaxyproject/galaxy/commit/2a16b25e83883ea7e4086994d02b…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-25 (Tue, 25 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/style/less/ui.less
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #26 from guerler/remove_mako_preferences_revision
Add basic logout feature, link former openid manager page, remove inline styles
Commit: c89e415f2cfabd41743b460d0551423f2c547fe5
https://github.com/galaxyproject/galaxy/commit/c89e415f2cfabd41743b460d0551…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Adding insert address features to one point save user information api call
Commit: e0a38a5bed8555f6ea18a00c7d0d7d15619fb90a
https://github.com/galaxyproject/galaxy/commit/e0a38a5bed8555f6ea18a00c7d0d…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-10-28 (Fri, 28 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Updating add address feature for client side validations and adding delete address feature
Commit: 6e09d71ab04f5181a7fd1a65b6ba9303944611bf
https://github.com/galaxyproject/galaxy/commit/6e09d71ab04f5181a7fd1a65b6ba…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-10-28 (Fri, 28 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Adding edit feature for email and username along with client side validations for the Manage User Info form
Commit: f593ad6c70bc891f84cdee1d481c3ebd142da9b4
https://github.com/galaxyproject/galaxy/commit/f593ad6c70bc891f84cdee1d481c…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-10-30 (Sun, 30 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Fixing bug with numbers in postal code and phone number
Commit: c40be4f4c63ef99018ba899579e1776922f71662
https://github.com/galaxyproject/galaxy/commit/c40be4f4c63ef99018ba899579e1…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-10-30 (Sun, 30 Oct 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M Makefile
M client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
A client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
A config/plugins/webhooks/demo/history_test1/config/history_test1.yml
A config/plugins/webhooks/demo/history_test2/config/history_test2.yml
A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml
A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml
A config/plugins/webhooks/demo/phdcomics/helper/__init__.py
A config/plugins/webhooks/demo/phdcomics/static/script.js
A config/plugins/webhooks/demo/phdcomics/static/styles.css
A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml
A config/plugins/webhooks/demo/trans_object/helper/__init__.py
A config/plugins/webhooks/demo/xkcd/config/xkcd.yml
A config/plugins/webhooks/demo/xkcd/static/script.js
A config/plugins/webhooks/demo/xkcd/static/styles.css
M config/tool_data_table_conf.xml.sample
A doc/source/admin/images_webhooks/history-menu.png
A doc/source/admin/images_webhooks/masthead.png
A doc/source/admin/images_webhooks/masthead_trans_object.png
A doc/source/admin/images_webhooks/tool.png
A doc/source/admin/images_webhooks/workflow.png
A doc/source/admin/webhooks.rst
M doc/source/slideshow/architecture/images/galaxy_schema.png
M lib/galaxy/app.py
M lib/galaxy/auth/providers/alwaysreject.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/localdb.py
M lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/dataproviders/__init__.py
M lib/galaxy/datatypes/metadata.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/test.CEL
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/deferred/manual_data_transfer.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/jobs/runners/util/__init__.py
M lib/galaxy/jobs/runners/util/drmaa/__init__.py
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/json.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/topsort.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/buildapp.py
M lib/galaxy/web/framework/__init__.py
M lib/galaxy/web/framework/middleware/error.py
M lib/galaxy/web/framework/middleware/static.py
M lib/galaxy/webapps/galaxy/api/tours.py
A lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/__init__.py
M lib/galaxy/webapps/tool_shed/__init__.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
A lib/galaxy/webhooks/__init__.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
M scripts/db_shell.py
M static/maps/layout/menu.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form.js.map
A static/maps/mvc/tool/tool-webhooks.js.map
A static/maps/mvc/webhooks.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
A static/scripts/mvc/tool/tool-webhooks.js
A static/scripts/mvc/webhooks.js
M static/scripts/mvc/workflow/workflow-view.js
M templates/webapps/galaxy/workflow/editor.mako
R templates/webapps/galaxy/workflow/index.mako
R templates/webapps/galaxy/workflow/missing_tools.mako
R templates/webapps/galaxy/workflow/myexp_export_content.mako
R templates/webapps/galaxy/workflow/rename.mako
M test/api/test_histories.py
M test/api/test_libraries.py
M test/unit/tools/test_tool_dependency_description.py
Log Message:
-----------
Merge with dev
Commit: 14612f8a92560796bbfdb7fb35609169a00472b5
https://github.com/galaxyproject/galaxy/commit/14612f8a92560796bbfdb7fb3560…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-10-30 (Sun, 30 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
Log Message:
-----------
Updating conditions for communication settings for new user preferences
Commit: fb75c23f0d8d5a97eb49f8701da333d14a75ea36
https://github.com/galaxyproject/galaxy/commit/fb75c23f0d8d5a97eb49f8701da3…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-10-31 (Mon, 31 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
Log Message:
-----------
Adding more client side validations for Change password feature and code comments and a bit of code cleanup
Commit: 8a8ca4e5918b9e7f4a7a92562d8e6157013e760a
https://github.com/galaxyproject/galaxy/commit/8a8ca4e5918b9e7f4a7a92562d8e…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-11-01 (Tue, 01 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Updating the User information add and edit feature for Form Definitions
Commit: fd6bf953278f67cfebda46ffd3e04ad8b6026ecc
https://github.com/galaxyproject/galaxy/commit/fd6bf953278f67cfebda46ffd3e0…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-11-01 (Tue, 01 Nov 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
Log Message:
-----------
Adding config for enabling the new user preferences UI
Commit: c828ec65f8a927875d7194a49ac26b4d5348e69c
https://github.com/galaxyproject/galaxy/commit/c828ec65f8a927875d7194a49ac2…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-11-02 (Wed, 02 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Fixing styling errors
Commit: f04ea9f8db2dcfbe0f5c94fedcbc90b70aa237a4
https://github.com/galaxyproject/galaxy/commit/f04ea9f8db2dcfbe0f5c94fedcbc…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-11-02 (Wed, 02 Nov 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Changing the config variable name for toggling new user preferences
Commit: a22cd27ced212ae8343f3c43c765f57c1cb2dfb3
https://github.com/galaxyproject/galaxy/commit/a22cd27ced212ae8343f3c43c765…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-11-02 (Wed, 02 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Commenting variables in config file
Commit: 8f49202778c72389d567ef840df518e473b0e4f3
https://github.com/galaxyproject/galaxy/commit/8f49202778c72389d567ef840df5…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-11-02 (Wed, 02 Nov 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M .gitignore
M Makefile
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
A client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M client/galaxy/style/less/ui.less
M config/plugins/visualizations/charts/static/client/app.css
M config/plugins/visualizations/charts/static/client/views/editor.js
R config/plugins/visualizations/charts/static/client/views/types.js
M doc/Makefile
M doc/parse_gx_xsd.py
M doc/patch.py
M doc/schema_template.md
M doc/source/admin/conda_faq.rst
M doc/source/admin/interactive_environments.rst
R doc/source/admin/interactive_environments_success.png
M doc/source/admin/mulled_containers.rst
M doc/source/conf.py
M doc/source/dev/build_a_job_runner.rst
M doc/source/dev/index.rst
A doc/source/dev/inherit.png
A doc/source/dev/interactive_environments_success.png
A doc/source/dev/queue.png
A doc/source/dev/queue_b.png
A doc/source/dev/runner_diag.png
M doc/source/index.rst
M doc/source/lib/galaxy.datatypes.converters.rst
M doc/source/lib/galaxy.jobs.rst
M doc/source/lib/galaxy.rst
M doc/source/lib/galaxy.tools.linters.rst
M doc/source/lib/galaxy.tools.parameters.rst
R doc/source/lib/galaxy.util.backports.importlib.rst
M doc/source/lib/galaxy.util.backports.rst
M doc/source/lib/galaxy.util.rst
M doc/source/releases/16.04.rst
M doc/source/releases/16.04_announce.rst
M doc/source/releases/16.07.rst
M doc/source/releases/index.rst
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/__init__.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/decorators.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/managers/__init__.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/simplegraph.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M scripts/bootstrap_history.py
R scripts/bootstrap_history_announce_template.rst
M scripts/galaxy-main
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/ui/ui-tabs.js.map
A static/maps/mvc/ui/ui-thumbnails.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/ui/ui-tabs.js
A static/scripts/mvc/ui/ui-thumbnails.js
M static/style/blue/base.css
M templates/user/index.mako
M test/qunit/package.json
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Merge with dev
Commit: aece1f4870ea3468cf3d78a8234d8cb8c96b4f4a
https://github.com/galaxyproject/galaxy/commit/aece1f4870ea3468cf3d78a8234d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Remove unused submit field special case handling
Commit: caf8eb5d4c98333f6b1ef73586d2ae17b6fda5f0
https://github.com/galaxyproject/galaxy/commit/caf8eb5d4c98333f6b1ef73586d2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Fix spaces layout menu
Commit: 962e4f3130cd883af928bb168e7c11cacbfaaa24
https://github.com/galaxyproject/galaxy/commit/962e4f3130cd883af928bb168e7c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Use list to detect acceptable values for communication settings
Commit: 2ed916390162689900f79e8026ccca82c9a283d9
https://github.com/galaxyproject/galaxy/commit/2ed916390162689900f79e8026cc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
Log Message:
-----------
Undo new line in form input wrapper
Commit: eff7ba7b6d3c910faff79efe893b1d1fd0acae81
https://github.com/galaxyproject/galaxy/commit/eff7ba7b6d3c910faff79efe893b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
Log Message:
-----------
Undo new line in form parameter factory
Commit: 849d54f20e541e5bfdc8e9157204634ef7df6a56
https://github.com/galaxyproject/galaxy/commit/849d54f20e541e5bfdc8e9157204…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-section.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Remove new line form section wrapper, repack scripts
Commit: 5c83dbebc46a5726214e730014ba2b5e24ce48d5
https://github.com/galaxyproject/galaxy/commit/5c83dbebc46a5726214e730014ba…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M client/galaxy/style/less/base.less
M static/style/blue/base.css
Log Message:
-----------
These styles are not used
Commit: 6a4e175c03960393712167a6887c4e8f21d650a4
https://github.com/galaxyproject/galaxy/commit/6a4e175c03960393712167a6887c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Restore galaxy.ini.sample
Commit: a561368195e696de8239bcea4aba9472ef3965b2
https://github.com/galaxyproject/galaxy/commit/a561368195e696de8239bcea4aba…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Add new user preference activation flag to galaxy.ini.sample
Commit: 55d1fae34362dac33d6d42b49f192ca7b32cb2ff
https://github.com/galaxyproject/galaxy/commit/55d1fae34362dac33d6d42b49f19…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Remove unused backend routes
Commit: d2bbed967b81ff663414b505323222db673882eb
https://github.com/galaxyproject/galaxy/commit/d2bbed967b81ff663414b5053232…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Fix underscores for private functions in user_preferences api endpoints
Commit: bbc5c2afb501fec6bc43dfeca60a21ce8a1826e7
https://github.com/galaxyproject/galaxy/commit/bbc5c2afb501fec6bc43dfeca60a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Restore user preference api
Commit: 3a53ae41efdfa671689fe9071fda68084e67ee1a
https://github.com/galaxyproject/galaxy/commit/3a53ae41efdfa671689fe9071fda…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Move new private functions below parent caller, fix indent, remove spaces
Commit: 6e37b1f0fd84981555927bde0256a9e7c326d7d7
https://github.com/galaxyproject/galaxy/commit/6e37b1f0fd84981555927bde0256…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Remove unused variables and libraries, fix lint
Commit: 301c5ec637d8adb6cfa88bd9f728a623ccc06310
https://github.com/galaxyproject/galaxy/commit/301c5ec637d8adb6cfa88bd9f728…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Apply autopep8, fix lint
Commit: d5804d6ba7c555ea9d984dea2fb5b87f62c02311
https://github.com/galaxyproject/galaxy/commit/d5804d6ba7c555ea9d984dea2fb5…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/style/less/base.less
M config/galaxy.ini.sample
M lib/galaxy/model/__init__.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #28 from guerler/remove_mako_user_pref_000
Restore changes
Commit: eb178129c102b4645ba76071bd528a683a176242
https://github.com/galaxyproject/galaxy/commit/eb178129c102b4645ba76071bd52…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Fix add address caller name
Commit: 25a8edd66c6c999451c97535d2508b405764f7bb
https://github.com/galaxyproject/galaxy/commit/25a8edd66c6c999451c97535d250…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
Log Message:
-----------
Revise communication preference check
Commit: ec63866deeac2c4c5139078c2db6d8dca5312649
https://github.com/galaxyproject/galaxy/commit/ec63866deeac2c4c5139078c2db6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M doc/source/conf.py
M lib/galaxy/config.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/rods.py
M run_tool_shed.sh
Log Message:
-----------
Merge branch 'dev' into remove_mako_user_pref_000
Commit: f00cd6af2e53cbf56cc08dee26df72f40023338b
https://github.com/galaxyproject/galaxy/commit/f00cd6af2e53cbf56cc08dee26df…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Reinsert space to sample config
Commit: b37ac03cec65f479fd2d74678dacad0c92b914cc
https://github.com/galaxyproject/galaxy/commit/b37ac03cec65f479fd2d74678dac…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M static/maps/layout/menu.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/form/form-parameters.js
Log Message:
-----------
Fix parameter factory
Commit: 6b7936cbf4744c97034ecd5f96e082d6935e6c49
https://github.com/galaxyproject/galaxy/commit/6b7936cbf4744c97034ecd5f96e0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Get user in set information through same function like all other endpoints
Commit: 6f6cc9041143b96249df7d0a71e826ccdcfd0980
https://github.com/galaxyproject/galaxy/commit/6f6cc9041143b96249df7d0a71e8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Directly import MessageException into user preferences api
Commit: 17ae8cdcc0e9b7f7283fbbd7f5316259400a71ee
https://github.com/galaxyproject/galaxy/commit/17ae8cdcc0e9b7f7283fbbd7f531…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Add encoded user form id to dict, add to form select, resolve initial value
Commit: 2e97c7919d045717a922b6e97d68b24e1e3bb3c5
https://github.com/galaxyproject/galaxy/commit/2e97c7919d045717a922b6e97d68…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Fix user info form generation and stored value parsing
Commit: a9a0d8fab0002050f7e7a505f614f81eae5ae74b
https://github.com/galaxyproject/galaxy/commit/a9a0d8fab0002050f7e7a505f614…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/web/form_builder.py
Log Message:
-----------
Parse field label if available
Commit: 928611f4cf69c95c669e1aceaa0f4b9f114dd21d
https://github.com/galaxyproject/galaxy/commit/928611f4cf69c95c669e1aceaa0f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Validate and update username and email first, revise error handling
Commit: 6c8ff8ce30642dbc4015dc061e078441baa38d61
https://github.com/galaxyproject/galaxy/commit/6c8ff8ce30642dbc4015dc061e07…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Revise address handling, use regex, temporary disable validation and user info forms saving
Commit: d7d6c743e8dc8199a9f481d0ba046afee18723b7
https://github.com/galaxyproject/galaxy/commit/d7d6c743e8dc8199a9f481d0ba04…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Ensure storing address attributes as text value
Commit: be80dddf6cc680124cc964d981ebd27ffcca3540
https://github.com/galaxyproject/galaxy/commit/be80dddf6cc680124cc964d981eb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Delete previous addresses for now
Commit: 82703e35f6e936c977662483e122a613df8fd275
https://github.com/galaxyproject/galaxy/commit/82703e35f6e936c977662483e122…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Remove duplicate flush
Commit: 62d1fe750987f9044565e73b23e90713582b080e
https://github.com/galaxyproject/galaxy/commit/62d1fe750987f9044565e73b23e9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Revise user info form saving
Commit: ee54415e72ae74692cb1a07e1cd6fee7dd15cd05
https://github.com/galaxyproject/galaxy/commit/ee54415e72ae74692cb1a07e1cd6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Move prefix constant out of loop
Commit: bbec45c70652bb58919b12ebce96bbf7d54e645e
https://github.com/galaxyproject/galaxy/commit/bbec45c70652bb58919b12ebce96…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Properly update user information forms
Commit: eda1fe6fb73cc393fbf9353067181ec539e44222
https://github.com/galaxyproject/galaxy/commit/eda1fe6fb73cc393fbf935306718…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/web/form_builder.py
Log Message:
-----------
Fix boolean value handling in form builder
Commit: 0045e8cbc8fb2c488583a6fb27fba3a6186484c1
https://github.com/galaxyproject/galaxy/commit/0045e8cbc8fb2c488583a6fb27fb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Add whitespaces, fix imports
Commit: 363e136e8c37bae91b4eaac65d3c032360def7c9
https://github.com/galaxyproject/galaxy/commit/363e136e8c37bae91b4eaac65d3c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Update existing user addresses instead of recreating them
Commit: f52f953b01925ffc91a96b97f9b24b0428bfc371
https://github.com/galaxyproject/galaxy/commit/f52f953b01925ffc91a96b97f9b2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Rename short_desc to desc to align with stored address attribute
Commit: 0e25f118dd69febb9dcc4a6b5c7b91e7085d0284
https://github.com/galaxyproject/galaxy/commit/0e25f118dd69febb9dcc4a6b5c7b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Show preference return and save buttons as portlet operations
Commit: 0d7e074bcf47cdf95b17588e30f5fe7e556983ac
https://github.com/galaxyproject/galaxy/commit/0d7e074bcf47cdf95b17588e30f5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/web/form_builder.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Unify value handling for form parameters in form builder
Commit: f17e335407599f40b40fce97be0a9fcc57e91b65
https://github.com/galaxyproject/galaxy/commit/f17e335407599f40b40fce97be0a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Parse optional security encoder to field level
Commit: 22763844a67f332ae739ae536b8fe301ffb80b56
https://github.com/galaxyproject/galaxy/commit/22763844a67f332ae739ae536b8f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-05 (Sat, 05 Nov 2016)
Changed paths:
M lib/galaxy/web/form_builder.py
Log Message:
-----------
Handle help text and optional flags specified through form builder ui
Commit: b1da023f3205f8228170e6972373e657a6dda0c6
https://github.com/galaxyproject/galaxy/commit/b1da023f3205f8228170e6972373…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-05 (Sat, 05 Nov 2016)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Add default value handling for form field values not stored in user values
Commit: 021b4d6e7341e55d01a52da4d516d4e4d598422f
https://github.com/galaxyproject/galaxy/commit/021b4d6e7341e55d01a52da4d516…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Allow to distinguish between request methods within small api functions
Commit: e649bd01c94a10bedb2ea499e859f20b1f66231d
https://github.com/galaxyproject/galaxy/commit/e649bd01c94a10bedb2ea499e859…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Fix lint, rename info form
Commit: 29b5f33742c7ca0b09fe3690b8242217a257a525
https://github.com/galaxyproject/galaxy/commit/29b5f33742c7ca0b09fe3690b824…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M lib/galaxy/web/form_builder.py
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Insert basic address validation, reduce validation rules
Commit: 305f8d19639b6c344c01762dfe6c6a681e4c7d14
https://github.com/galaxyproject/galaxy/commit/305f8d19639b6c344c01762dfe6c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Use payload instead of kwd
Commit: f58ff7b1c6e28e73d16180fc80508f3f28e06c1f
https://github.com/galaxyproject/galaxy/commit/f58ff7b1c6e28e73d16180fc8050…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Specify json as request content type
Commit: 37fffc16674efa9c2ab123c6ebc6054d5b09b001
https://github.com/galaxyproject/galaxy/commit/37fffc16674efa9c2ab123c6ebc6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Remove debug statement
Commit: 0810cd26de20ad4932332a7676414db5531ffe12
https://github.com/galaxyproject/galaxy/commit/0810cd26de20ad4932332a767641…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Remove unused traditional flag from ajax put request
Commit: 5683edd76443987643dce013ce16c333548c7cf0
https://github.com/galaxyproject/galaxy/commit/5683edd76443987643dce013ce16…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Loop once through custom forms
Commit: 0b2ba5017b8ab731170909e601b17d8910030350
https://github.com/galaxyproject/galaxy/commit/0b2ba5017b8ab731170909e601b1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Remove unused custom address validation routine, validate through fields() instead
Commit: dee59fc8b59ad75fccb874a7d36f171f9ec4dd93
https://github.com/galaxyproject/galaxy/commit/dee59fc8b59ad75fccb874a7d36f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Remove unused import
Commit: 433ac08dafe4de7ee60940477a72f983be3158e7
https://github.com/galaxyproject/galaxy/commit/433ac08dafe4de7ee60940477a72…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/web/form_builder.py
Log Message:
-----------
Fix workflow and history selection fields
Commit: 7a6cd700597c873a6cae59b1021b0c85ae9acc8f
https://github.com/galaxyproject/galaxy/commit/7a6cd700597c873a6cae59b1021b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M lib/galaxy/web/form_builder.py
Log Message:
-----------
Remove redundant optional handling for history fields
Commit: 826f006b48aa07e4450779539ea5b042a3c837b4
https://github.com/galaxyproject/galaxy/commit/826f006b48aa07e4450779539ea5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M lib/galaxy/web/form_builder.py
Log Message:
-----------
Remove unused get_display_text caller
Commit: 56844f52bb76d8be4825f4368fd5e2bc66475745
https://github.com/galaxyproject/galaxy/commit/56844f52bb76d8be4825f4368fd5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Catch resource request errors when accessing form data
Commit: 44cd6ef738703454755044cd68abb2ac2a492023
https://github.com/galaxyproject/galaxy/commit/44cd6ef738703454755044cd68ab…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Show new preference form instead of old one if clicked on and active
Commit: 8004fea3fc7f5feb70d71431f43babfc7dae6cc8
https://github.com/galaxyproject/galaxy/commit/8004fea3fc7f5feb70d71431f43b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/user_preferences.py
Log Message:
-----------
Add dots to complete notification sentences for email and public name validation
Commit: e40c2554a5efcbe937f7e3b6d06733a002c4b32f
https://github.com/galaxyproject/galaxy/commit/e40c2554a5efcbe937f7e3b6d067…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
R lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Move preference handlers to users endpoint
Commit: 2675bc17d266a57abd80fdf85db4f0a2a36165a5
https://github.com/galaxyproject/galaxy/commit/2675bc17d266a57abd80fdf85db4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Adjust endpoint headers, merge api_key handler
Commit: 00ae244b6ab2bcad1b71bd40f8e43da750a6ba8a
https://github.com/galaxyproject/galaxy/commit/00ae244b6ab2bcad1b71bd40f8e4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/users.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Use regular show endpoint to access quota details
Commit: 5f6efbec861eb1b5ddf084d7a70b182148fbe042
https://github.com/galaxyproject/galaxy/commit/5f6efbec861eb1b5ddf084d7a70b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M lib/galaxy/managers/users.py
Log Message:
-----------
Fix quota helper
Commit: 38d2ab3cd5806edc1e053bbcc6d36e501bf74dd8
https://github.com/galaxyproject/galaxy/commit/38d2ab3cd5806edc1e053bbcc6d3…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M config/galaxy.ini.sample
M doc/source/conf.py
M lib/galaxy/config.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/webapp.py
R lib/galaxy/webapps/galaxy/api/user_preferences.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M run_tool_shed.sh
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Merge pull request #29 from guerler/remove_mako_user_pref_000
Fixes add address caller, parameter factory and revises preferences check
Commit: e4a97c88d04894110d03881316573367b183cba6
https://github.com/galaxyproject/galaxy/commit/e4a97c88d04894110d0388131657…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Remove unused dict values from get_information endpoint
Commit: 46acf5c7bd42d2d58d4494d8adcc0325e4e9e9d0
https://github.com/galaxyproject/galaxy/commit/46acf5c7bd42d2d58d4494d8adcc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Add missing sql component
Commit: 3b6bf1ab6094a177eea917edb98b53b6d64a060d
https://github.com/galaxyproject/galaxy/commit/3b6bf1ab6094a177eea917edb98b…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-11-09 (Wed, 09 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Merge pull request #30 from guerler/remove_mako_user_pref_000
Remove unused library, add missing sql component
Commit: eed7f2ce086460cc29b0f89def0986d727eec15a
https://github.com/galaxyproject/galaxy/commit/eed7f2ce086460cc29b0f89def09…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-10 (Thu, 10 Nov 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Rename to Preferences
Commit: af2b31e1fbc7ea2383e9f1ad3ea9d44db48bc41c
https://github.com/galaxyproject/galaxy/commit/af2b31e1fbc7ea2383e9f1ad3ea9…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-11-10 (Thu, 10 Nov 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Merge pull request #31 from guerler/remove_mako_user_pref_000
Restore menu item label
Commit: 9914130fb4d5bc33b70d9e241c08421dc0acc5c0
https://github.com/galaxyproject/galaxy/commit/9914130fb4d5bc33b70d9e241c08…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-17 (Thu, 17 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/users.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Remove logout endpoint from api, redirect to controller endpoint instead
Commit: d52f4fd52374def376367c3141f912a3e0303d94
https://github.com/galaxyproject/galaxy/commit/d52f4fd52374def376367c3141f9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-17 (Thu, 17 Nov 2016)
Changed paths:
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Use separate endpoints instead of identifying the request type
Commit: 364f57d06d0910d593a96d1748a26cc507d88e4b
https://github.com/galaxyproject/galaxy/commit/364f57d06d0910d593a96d1748a2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-17 (Thu, 17 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M CONTRIBUTORS.md
M Makefile
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/source_material/circle.py
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/tool_data_table_conf.xml.sample
M contrib/galaxy_config_merger.py
M contrib/nagios/check_galaxy.py
M cron/add_manual_builds.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M doc/Makefile
M doc/parse_gx_xsd.py
M doc/patch.py
M doc/source/admin/interactive_environments.rst
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/blast.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_len.py
M lib/galaxy/datatypes/converters/fasta_to_len.xml
M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_coverage.xml
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/len_to_linecount.xml
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/sam_to_bam.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml
M lib/galaxy/datatypes/triples.py
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/result_handlers/basic.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/queue_worker.py
M lib/galaxy/sample_tracking/data_transfer.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/sample_tracking/sample.py
M lib/galaxy/security/passwords.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/mulled/_cli.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/util/galaxyops/__init__.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/version.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/middleware/error.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/schedulers/core.py
M lib/galaxy_utils/sequence/fastq.py
M lib/galaxy_utils/sequence/vcf.py
M lib/mimeparse.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/workflow_util.py
M scripts/api/data_manager_example_execute.py
M scripts/api/example_watch_folder.py
M scripts/api/filter_failed_datasets_from_collection.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/install_tool_shed_repositories.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/reset_metadata_on_installed_repositories.py
M scripts/api/search.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_execute_parameters.py
M scripts/api/workflow_import.py
M scripts/auth/pam_auth_helper.py
M scripts/build_toolbox.py
M scripts/build_universe_config.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
M scripts/communication/communication_server.py
M scripts/create_db.py
M scripts/data_libraries/build_lucene_index.py
M scripts/data_libraries/build_whoosh_index.py
M scripts/drmaa_external_killer.py
M scripts/drmaa_external_runner.py
M scripts/external_chown_script.py
M scripts/extract_dataset_part.py
M scripts/extract_toolbox_sections.py
M scripts/functional_tests.py
M scripts/grt.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/manage_db.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/create_bacteria_loc_file.py
M scripts/microbes/create_bacteria_table.py
M scripts/microbes/get_builds_lengths.py
M scripts/microbes/harvest_bacteria.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/slideshow/build_slideshow.py
M scripts/summarize_timings.py
M scripts/sync_reports_config.py
M scripts/tool_shed/api/add_repository_registry_entry.py
M scripts/tool_shed/api/create_categories.py
M scripts/tool_shed/api/create_users.py
M scripts/tool_shed/api/export.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/api/import_capsule.py
M scripts/tool_shed/api/remove_repository_registry_entry.py
M scripts/tool_shed/api/reset_metadata_on_repositories.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/clean_up_tool_dependency_directory.py
M scripts/tool_shed/deprecate_repositories_without_metadata.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
M scripts/tools/maf/check_loc_file.py
M scripts/tools/re_escape_output.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/style/blue/base.css
M static/welcome.html.sample
M templates/webapps/galaxy/workflow/editor.mako
A test-data/bam_from_sam.bam
A test-data/sam_with_header.sam
M test/api/test_workflows.py
M test/api/workflows_format_2/main.py
M test/base/api.py
M test/base/api_asserts.py
M test/base/driver_util.py
M test/base/interactor.py
M test/base/twilltestcase.py
M test/functional/test_library_templates.py
A test/functional/tools/sam_to_bam.xml
M test/manual/workflows_scaling.py
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
M test/unit/dataset_collections/test_matching.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rule_helper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_fabric_util.py
M test/unit/shed_unit/test_td_common_util.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_transactions.py
M test/unit/test_routes.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_external_files.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_wrappers.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
A tool-data/blastdb.loc.sample
A tool-data/blastdb_d.loc.sample
A tool-data/blastdb_p.loc.sample
M tools/data_source/data_source.py
M tools/data_source/genbank.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_fasta.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/catWrapper.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
Log Message:
-----------
Merge branch 'dev' into remove_mako_user_pref
Commit: 51972a9916e8b113399bbcbb074802de8023d59f
https://github.com/galaxyproject/galaxy/commit/51972a9916e8b113399bbcbb0748…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-17 (Thu, 17 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Use inputs tag to indicate that the response is consistently for input handling
Commit: eabc648b9cda89df5d52071623613857b2d40f04
https://github.com/galaxyproject/galaxy/commit/eabc648b9cda89df5d5207162361…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-17 (Thu, 17 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Fix api_key and toolbox filter endpoints
Commit: 1f3f4be1caa56a2782a18c397c7cdb961065bd91
https://github.com/galaxyproject/galaxy/commit/1f3f4be1caa56a2782a18c397c7c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-17 (Thu, 17 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Fix lint
Commit: 9653d148a22f5bd537d7339ab1006afd99243765
https://github.com/galaxyproject/galaxy/commit/9653d148a22f5bd537d7339ab100…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-17 (Thu, 17 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Fix routing declaration style
Commit: b02eb9e7e0c2d5dfa35a72ee13e598dba74297fe
https://github.com/galaxyproject/galaxy/commit/b02eb9e7e0c2d5dfa35a72ee13e5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-17 (Thu, 17 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
M test/api/test_users.py
Log Message:
-----------
Add basic information test case, fix validation
Commit: 998fd3036d9887ece8aaa651c272d2360f5f9f85
https://github.com/galaxyproject/galaxy/commit/998fd3036d9887ece8aaa651c272…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-18 (Fri, 18 Nov 2016)
Changed paths:
M test/api/test_users.py
Log Message:
-----------
Add test case to add address to user information
Commit: 2cf91d4b1554b2fc22866e887cd6f3106d0e7230
https://github.com/galaxyproject/galaxy/commit/2cf91d4b1554b2fc22866e887cd6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-18 (Fri, 18 Nov 2016)
Changed paths:
M test/api/test_users.py
Log Message:
-----------
Add test case for communication server settings
Commit: daa19009296db8fba3337df76d6e2fba59b4ba06
https://github.com/galaxyproject/galaxy/commit/daa19009296db8fba3337df76d6e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-22 (Tue, 22 Nov 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Fix link to user preferences when library view is shown
Commit: 564a7236cacf06841a02d7ffdf607392ac52925c
https://github.com/galaxyproject/galaxy/commit/564a7236cacf06841a02d7ffdf60…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-22 (Tue, 22 Nov 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Remove api keys from user dropdown
Commit: a4ae3c953bf8b0778f32fe9b3cd36ead7db7a03d
https://github.com/galaxyproject/galaxy/commit/a4ae3c953bf8b0778f32fe9b3cd3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-22 (Tue, 22 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Only show communication settings if communication host has been specified
Commit: cfe0305f39d183952206b2f76da9ded322d946aa
https://github.com/galaxyproject/galaxy/commit/cfe0305f39d183952206b2f76da9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-22 (Tue, 22 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/webapps/galaxy/api/users.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Fix missing user tool filter handling
Commit: 15668f2ff37d1f25d665c60f01b18d39273d90d1
https://github.com/galaxyproject/galaxy/commit/15668f2ff37d1f25d665c60f01b1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-22 (Tue, 22 Nov 2016)
Changed paths:
M lib/galaxy/managers/configuration.py
Log Message:
-----------
Fix tabs in configuration handler
Commit: 5fe064d4c88d6657f65fc10feb06cf05f8515c3b
https://github.com/galaxyproject/galaxy/commit/5fe064d4c88d6657f65fc10feb06…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-22 (Tue, 22 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Mention history in permissions link
Commit: 2366eda8f3bebe9e0f71e5deea0e1f034e054796
https://github.com/galaxyproject/galaxy/commit/2366eda8f3bebe9e0f71e5deea0e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-22 (Tue, 22 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Use person icon for user information and chat bubbles for communication settings
Commit: 2108043ded3e631b929d2be585344062bbdbdd2f
https://github.com/galaxyproject/galaxy/commit/2108043ded3e631b929d2be58534…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-22 (Tue, 22 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Use current user icon for now, new user icon will be available in fa 4.7
Commit: f960be7b43e1b00b95f92218a7afc54e0ae48e68
https://github.com/galaxyproject/galaxy/commit/f960be7b43e1b00b95f92218a7af…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-22 (Tue, 22 Nov 2016)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/layout/menu.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Route user preferences analogous to tours
Commit: bb33e8959fca912912f7b7b988c949c3d83e2be1
https://github.com/galaxyproject/galaxy/commit/bb33e8959fca912912f7b7b988c9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-22 (Tue, 22 Nov 2016)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Align spacing, code style alignment
Commit: d4760ed2105d0f3743569458416cfd5e3ab41da3
https://github.com/galaxyproject/galaxy/commit/d4760ed2105d0f3743569458416c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-22 (Tue, 22 Nov 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M static/maps/layout/menu.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Enable new user preference ui by default
Commit: a40d5ebe69cbe79c8486a26e9a1ef99291f83b59
https://github.com/galaxyproject/galaxy/commit/a40d5ebe69cbe79c8486a26e9a1e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
R templates/webapps/galaxy/user/manage_info.mako
Log Message:
-----------
Remove manage info endpoint from controller
Commit: 14e635aaee2699cb395443d802dede15d6f25240
https://github.com/galaxyproject/galaxy/commit/14e635aaee2699cb395443d802de…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
R templates/user/change_password.mako
R templates/user/communication_settings.mako
R templates/user/edit_address.mako
R templates/user/new_address.mako
R templates/user/permissions.mako
R templates/user/toolbox_filters.mako
R templates/user/username.mako
A templates/webapps/tool_shed/user/change_password.mako
A templates/webapps/tool_shed/user/username.mako
Log Message:
-----------
Remove unused controller endpoints, move makos used by toolshed
Commit: 6cb1a2c39e40a752e756e355beb102bc398d692e
https://github.com/galaxyproject/galaxy/commit/6cb1a2c39e40a752e756e355beb1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
R templates/webapps/galaxy/user/api_keys.mako
A templates/webapps/tool_shed/user/api_keys.mako
Log Message:
-----------
Move api_keys mako and endpoint to toolshed
Commit: 98c5a59a182a2f64f6bb240863748144ad3e77bc
https://github.com/galaxyproject/galaxy/commit/98c5a59a182a2f64f6bb24086374…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tools.js
M config/galaxy.ini.sample
M config/plugins/tours/core.galaxy_ui.yaml
M lib/galaxy/config.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/tool_shed/galaxy_install/install_manager.py
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tools.js
M templates/webapps/galaxy/user/list_users.mako
Log Message:
-----------
Merge branch 'dev' into remove_mako_user_pref
Commit: 12623ac1a4a746d204320a649f2b5ebe673507f1
https://github.com/galaxyproject/galaxy/commit/12623ac1a4a746d204320a649f2b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
Log Message:
-----------
Fix lint
Commit: b38c6afefebd6d0a9bb99005efb1a78a5083a585
https://github.com/galaxyproject/galaxy/commit/b38c6afefebd6d0a9bb99005efb1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Merge branch 'dev' into remove_mako_user_pref
Commit: 20d45ee62c73d25b1757e9ab7a6cba5f122cfd88
https://github.com/galaxyproject/galaxy/commit/20d45ee62c73d25b1757e9ab7a6c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Temporary routing, not best practice
Commit: 16a60538d978ae196121f6fe474a97ae10520309
https://github.com/galaxyproject/galaxy/commit/16a60538d978ae196121f6fe474a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/layout/menu.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Fix history back, and forward
Commit: 416b94f1953f04147033bdd470b201c9e08114f8
https://github.com/galaxyproject/galaxy/commit/416b94f1953f04147033bdd470b2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Avoid using navigate, reload page until routing has been established
Commit: 6e1b26115ed6879294f011a12435a977d66e3e44
https://github.com/galaxyproject/galaxy/commit/6e1b26115ed6879294f011a12435…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/managers/configuration.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Hide communication server form if disabled
Commit: 7afc7ac6eb1eddd0a381042633ff848f43e2abdb
https://github.com/galaxyproject/galaxy/commit/7afc7ac6eb1eddd0a381042633ff…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
M templates/user/register.mako
Log Message:
-----------
Do not edit custom widgets when registering new user
Commit: 0f6013c7286ff73761577944e96a8d555e94962b
https://github.com/galaxyproject/galaxy/commit/0f6013c7286ff73761577944e96a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Advanced user preferences based on custom settings can be set after registration, using the new form
Commit: a4b70aaf92dfa560cd41aca876c95959763472f9
https://github.com/galaxyproject/galaxy/commit/a4b70aaf92dfa560cd41aca876c9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
Log Message:
-----------
Fix lint
Commit: e4222b9ae6676c80d22551dc61c3ba14ce2cb315
https://github.com/galaxyproject/galaxy/commit/e4222b9ae6676c80d22551dc61c3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Drop default tooltip
Commit: 57fb15984c9038427abd05d801d59e21e296dd6d
https://github.com/galaxyproject/galaxy/commit/57fb15984c9038427abd05d801d5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/security/__init__.py
Log Message:
-----------
Emphasize that users need certain permissions to access the history
Commit: f1e20b64f5c223e90a164cb0f4d07667f7aec340
https://github.com/galaxyproject/galaxy/commit/f1e20b64f5c223e90a164cb0f4d0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
A templates/webapps/tool_shed/user/index.mako
Log Message:
-----------
Move old user preference template to toolshed directory
Commit: 7f3c7b0e2342719526ca9fd4e4cb2d7b2889735f
https://github.com/galaxyproject/galaxy/commit/7f3c7b0e2342719526ca9fd4e4cb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/security/__init__.py
Log Message:
-----------
Undo history permission hint
Commit: e0a4171113c983fd9d6238a2d4922f69dd4cd8b8
https://github.com/galaxyproject/galaxy/commit/e0a4171113c983fd9d6238a2d492…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Attempt to rephrase user preference description for history permissions
Commit: e6c1e8e4e830f48203e0d26ed848a0d27860a7c9
https://github.com/galaxyproject/galaxy/commit/e6c1e8e4e830f48203e0d26ed848…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Rename label for history permissions
Commit: b165757288f0d8d277f8e246601eb83aea3c1c8a
https://github.com/galaxyproject/galaxy/commit/b165757288f0d8d277f8e246601e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-30 (Wed, 30 Nov 2016)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
A client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/ui.less
M config/galaxy.ini.sample
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M lib/galaxy/auth/__init__.py
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/ui/ui-misc.js.map
A static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/ui/ui-misc.js
A static/scripts/mvc/user/user-preferences.js
M static/style/blue/base.css
R templates/user/change_password.mako
R templates/user/communication_settings.mako
R templates/user/edit_address.mako
R templates/user/new_address.mako
R templates/user/permissions.mako
M templates/user/register.mako
R templates/user/toolbox_filters.mako
R templates/user/username.mako
R templates/webapps/galaxy/user/api_keys.mako
R templates/webapps/galaxy/user/manage_info.mako
A templates/webapps/tool_shed/user/api_keys.mako
A templates/webapps/tool_shed/user/change_password.mako
A templates/webapps/tool_shed/user/index.mako
A templates/webapps/tool_shed/user/username.mako
M test/api/test_users.py
Log Message:
-----------
Merge pull request #3118 from bgruening/remove_mako_user_pref
New User Preferences User Interface
Compare: https://github.com/galaxyproject/galaxy/compare/fd0a52a9a9ae...b165757288f0
Branch: refs/heads/release_16.10
Home: https://github.com/galaxyproject/galaxy
Commit: 94edc94b73e047612ae51ca2e075f17ac8e238bb
https://github.com/galaxyproject/galaxy/commit/94edc94b73e047612ae51ca2e075…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Add cached dependency manager
Similar to https://github.com/galaxyproject/galaxy/pull/2986, implement
a mechanism that allows tool dependencies to be cached.
If the `use_cached_dependency_manager` option is set to True in
galaxy.ini, we build a hash of the combination of a tools' requirements,
and store the resulting environment in a directory specified by the
`tool_dependency_cache_dir` option in galaxy.ini.
Commit: 0a9b6d8755dee530232ab893a3bad199407aa0bc
https://github.com/galaxyproject/galaxy/commit/0a9b6d8755dee530232ab893a3ba…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Better phrasing of cache options in galaxy.ini.sample (Thanks @nsoranzo)
Commit: 2b1765751b29008aecbd782f28269ac4e63db239
https://github.com/galaxyproject/galaxy/commit/2b1765751b29008aecbd782f2826…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Rework cached dependencies to be more robust
to updates or changes in depedencies, folder structure and resolver
configuration. Instead of hashing name, type and version of a
dependency, hash the json representation of the dependencies returned by
the dependency resolver, which include the path to the environment and
the depedency type. This is only applied to resolvers whose cacheable
attribute is set to True (conda-only, currently).
Commit: f919a98601252ab8f87bffff6e449105e770aadf
https://github.com/galaxyproject/galaxy/commit/f919a98601252ab8f87bffff6e44…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Build dependency cache at install time
and only activate cached environments if they exist.
Commit: 82f30e7645156b5f35c2b4cd77314e6275663979
https://github.com/galaxyproject/galaxy/commit/82f30e7645156b5f35c2b4cd7731…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/requirements.py
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Only attempt to build cache once per install
and override __eq__ for ToolRequirement, to simplify
checking if ToolRequirements are already installed/cached.
Commit: 64bc9241ed785d4d552c5fac21cd412558c54567
https://github.com/galaxyproject/galaxy/commit/64bc9241ed785d4d552c5fac21cd…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Fix NameError
Commit: cf769dd09deb73624b22628208fa103cc4f27150
https://github.com/galaxyproject/galaxy/commit/cf769dd09deb73624b22628208fa…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Add API to install resolver tool dependencies
and to build a tool dependency cache (if activated in galaxy.ini).
An example to install dependencies for the twobit converter:
```
import bioblend.galaxy
url = 'http://localhost:8080/'
api_key = 'admin_api_key'
tool_id = 'CONVERTER_fasta_to_2bit'
endpoint = "api/tools/%s/install_dependencies" % tool_id
gi = bioblend.galaxy.GalaxyInstance(url, api_key)
gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id})
```
If `use_cached_dependency_manager` is activated in the galaxy.ini,
a cached environment can be built like this:
```
endpoint = "api/tools/%s/build_dependency_cache" % tool_id
gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id})
```
Commit: cc7cd47ef54a09efbf8272d1e024f6f2ac92594b
https://github.com/galaxyproject/galaxy/commit/cc7cd47ef54a09efbf8272d1e024…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M test/integration/test_resolvers.py
Log Message:
-----------
Add integration test-case for install tool dependency API endpoint
Commit: f10fd793a68ed9413bec708daa48cef65769d09f
https://github.com/galaxyproject/galaxy/commit/f10fd793a68ed9413bec708daa48…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
Log Message:
-----------
Install the correct converter dependency
Commit: 045a2f0d471f7b4186aff625f3cea9abfa549fa2
https://github.com/galaxyproject/galaxy/commit/045a2f0d471f7b4186aff625f3ce…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/webapps/galaxy/api/tools.py
Log Message:
-----------
Add `force_rebuild` param to build_dependency_cache
This will remove a pre-existing cached dependency directory.
Commit: 16b49d9140edbf116f83b51b957cd61c4f2d91df
https://github.com/galaxyproject/galaxy/commit/16b49d9140edbf116f83b51b957c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/integration/test_resolvers.py
Log Message:
-----------
Add dependency_resolvers/clean endpoint
Commit: 1efd4d4b3b99ec40071aa4d6fb7cf4030c51e2e0
https://github.com/galaxyproject/galaxy/commit/1efd4d4b3b99ec40071aa4d6fb7c…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
add a conda clean function to remove downloaded tarballs after installation
Commit: 2a4ccac4039342c98d71bc72177aa951db6c4ba1
https://github.com/galaxyproject/galaxy/commit/2a4ccac4039342c98d71bc72177a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/integration/test_resolvers.py
Log Message:
-----------
Connect `clean` endpoint properly and add `-y` to exec_clean
Commit: d6f0e6b37c318a0202e0e266828e6325100cab19
https://github.com/galaxyproject/galaxy/commit/d6f0e6b37c318a0202e0e266828e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/tool_shed/galaxy_install/install_manager.py
M test/integration/test_resolvers.py
Log Message:
-----------
Merge pull request #3227 from mvdbeek/cached_deps_16.10
[16.10] Backport #3106 and #3222: Cached conda environments and API to manage them
Compare: https://github.com/galaxyproject/galaxy/compare/e3f8b724648c...d6f0e6b37c31
Branch: refs/heads/release_16.10
Home: https://github.com/galaxyproject/galaxy
Commit: 9a2bae7381b1ee8e2411681a76d75767b05ceffe
https://github.com/galaxyproject/galaxy/commit/9a2bae7381b1ee8e2411681a76d7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M templates/admin/tool_shed_repository/common.mako
Log Message:
-----------
simplify the UI of deps installation
by hiding the details under toggle button
Commit: 068ee6bd0ceb942ec67e634a7e6e434314cbe7fe
https://github.com/galaxyproject/galaxy/commit/068ee6bd0ceb942ec67e634a7e6e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
Log Message:
-----------
fix install repo test
Commit: 706bc3fbb118087cc057e6559e0262a6aca31127
https://github.com/galaxyproject/galaxy/commit/706bc3fbb118087cc057e6559e02…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
Log Message:
-----------
fix test and hide shed_conf select udner details
Commit: 73d010efa4236ed8ef0e46bb10d5e39233ae2d6b
https://github.com/galaxyproject/galaxy/commit/73d010efa4236ed8ef0e46bb10d5…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
Log Message:
-----------
fix another test
Commit: 4b794729b0cfd347d189a9a1e62273ab1788bc3e
https://github.com/galaxyproject/galaxy/commit/4b794729b0cfd347d189a9a1e622…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
Log Message:
-----------
fix a bug that renders conda dependency selection everytime
Commit: e3f8b724648cee51636502959096adba88045e14
https://github.com/galaxyproject/galaxy/commit/e3f8b724648cee51636502959096…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M templates/admin/tool_shed_repository/common.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
Log Message:
-----------
Merge pull request #3226 from martenson/16-10-install-ux
[16.10] admin installation ux
Compare: https://github.com/galaxyproject/galaxy/compare/0b2d0c1746c9...e3f8b724648c
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 40a95a300326bddeb0e78add288a47f4f23c087c
https://github.com/galaxyproject/galaxy/commit/40a95a300326bddeb0e78add288a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-27 (Sun, 27 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Add API to install resolver tool dependencies
and to build a tool dependency cache (if activated in galaxy.ini).
An example to install dependencies for the twobit converter:
```
import bioblend.galaxy
url = 'http://localhost:8080/'
api_key = 'admin_api_key'
tool_id = 'CONVERTER_fasta_to_2bit'
endpoint = "api/tools/%s/install_dependencies" % tool_id
gi = bioblend.galaxy.GalaxyInstance(url, api_key)
gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id})
```
If `use_cached_dependency_manager` is activated in the galaxy.ini,
a cached environment can be built like this:
```
endpoint = "api/tools/%s/build_dependency_cache" % tool_id
gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id})
```
Commit: e905b8baeb9081400ad775bcc20c2956808a11fd
https://github.com/galaxyproject/galaxy/commit/e905b8baeb9081400ad775bcc20c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-27 (Sun, 27 Nov 2016)
Changed paths:
M test/integration/test_resolvers.py
Log Message:
-----------
Add integration test-case for install tool dependency API endpoint
Commit: 3e48f3792bc10c081a8079cfa3d773531d6dad15
https://github.com/galaxyproject/galaxy/commit/3e48f3792bc10c081a8079cfa3d7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-27 (Sun, 27 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
Log Message:
-----------
Install the correct converter dependency
Commit: 8ff7ffa063c491b886bbeed1e1eb2e69fb6f3e68
https://github.com/galaxyproject/galaxy/commit/8ff7ffa063c491b886bbeed1e1eb…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-27 (Sun, 27 Nov 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/webapps/galaxy/api/tools.py
Log Message:
-----------
Add `force_rebuild` param to build_dependency_cache
This will remove a pre-existing cached dependency directory.
Commit: 3ebbb37c4dc09648ee08877eeb87a1db90a75d35
https://github.com/galaxyproject/galaxy/commit/3ebbb37c4dc09648ee08877eeb87…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-27 (Sun, 27 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/integration/test_resolvers.py
Log Message:
-----------
Add dependency_resolvers/clean endpoint
Commit: 23c6b1c6ff6b810fed69c05eec74166cd2d8fc5f
https://github.com/galaxyproject/galaxy/commit/23c6b1c6ff6b810fed69c05eec74…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-11-27 (Sun, 27 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
add a conda clean function to remove downloaded tarballs after installation
Commit: 00ca0a600a083bf05e2c8f90610851972e7e94ea
https://github.com/galaxyproject/galaxy/commit/00ca0a600a083bf05e2c8f906108…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/integration/test_resolvers.py
Log Message:
-----------
Connect `clean` endpoint properly and add `-y` to exec_clean
Commit: fd0a52a9a9aeba2e9ac5b555992c481a562b9162
https://github.com/galaxyproject/galaxy/commit/fd0a52a9a9aeba2e9ac5b555992c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/integration/test_resolvers.py
Log Message:
-----------
Merge pull request #3222 from mvdbeek/api_cache_env
Add API to install resolver tool dependencies
Compare: https://github.com/galaxyproject/galaxy/compare/c8ea393ccb13...fd0a52a9a9ae