Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 9d6a0e82f6f9634981ea96c37f0f48e38e9c5b12
https://github.com/galaxyproject/galaxy/commit/9d6a0e82f6f9634981ea96c37f0f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-02 (Wed, 02 Aug 2017)
Changed paths:
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Implement default_identifier_source for outputs
This allows tool authors to specify an input from which the element
identifier can be inherited. This applies only to non-collection output
when mapping a collection over an input, since collections have a
structured_like attribute.
Commit: 35c0a4770336ca82fda7dd3034fd029e3bd474b8
https://github.com/galaxyproject/galaxy/commit/35c0a4770336ca82fda7dd3034fd…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-02 (Wed, 02 Aug 2017)
Changed paths:
M test/api/test_tools.py
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Add test API test for default_identifier_source
Commit: 46fba6ec1c728125efa1339e7334202487a09e18
https://github.com/galaxyproject/galaxy/commit/46fba6ec1c728125efa1339e7334…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-02 (Wed, 02 Aug 2017)
Changed paths:
M lib/galaxy/dataset_collections/matching.py
Log Message:
-----------
Sort input keys by default, so the first matching input key will the source of the element identifiers
Commit: ea15f398e79771b6dd6ba5fdf0c8d96e10d39734
https://github.com/galaxyproject/galaxy/commit/ea15f398e79771b6dd6ba5fdf0c8…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-02 (Wed, 02 Aug 2017)
Changed paths:
M lib/galaxy/tools/execute.py
Log Message:
-----------
Fix failing API tests for explicit collection outputs
Commit: e92a15a18523e14c050d987b3c14be412fcaaddc
https://github.com/galaxyproject/galaxy/commit/e92a15a18523e14c050d987b3c14…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/xsd/galaxy.xsd
M test/api/test_tools.py
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #4368 from mvdbeek/tie_down_collection_matcher
Implement default_identifier_source for outputs and sort input keys by default
Compare: https://github.com/galaxyproject/galaxy/compare/68c7b0982bb1...e92a15a18523
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: b17091a3ec51a4836370f32b71ea72abfe4a966f
https://github.com/galaxyproject/galaxy/commit/b17091a3ec51a4836370f32b71ea…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/maps/galaxy.js.map
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/galaxy.js
M static/scripts/layout/menu.js
M static/scripts/mvc/user/user-preferences.js
M templates/galaxy_client_app.mako
M templates/user/login.mako
M templates/user/register.mako
M test/shed_functional/base/twilltestcase.py
Log Message:
-----------
CSRF protection for login, logout, and user registeration.
The approach is to use per-session CSRF tokens - this avoids many complications related to per-form tokens. We generate a sequence of hashes based on session IDs that doesn't follow the same pattern as normal database API IDs by supplying a "kind" parameter to encode_id (we use the same pattern for securing the job files API for Pulsar).
Commit: 4effd7d77ae75d577c5d04b34174464a43d075b8
https://github.com/galaxyproject/galaxy/commit/4effd7d77ae75d577c5d04b34174…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-08-05 (Sat, 05 Aug 2017)
Changed paths:
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/maps/galaxy.js.map
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/galaxy.js
M static/scripts/layout/menu.js
M static/scripts/mvc/user/user-preferences.js
M templates/galaxy_client_app.mako
M templates/user/login.mako
M templates/user/register.mako
M test/shed_functional/base/twilltestcase.py
Log Message:
-----------
Merge pull request #4365 from jmchilton/csrf
CSRF protection for login, logout, and user registration.
Compare: https://github.com/galaxyproject/galaxy/compare/575696dcc2cc...4effd7d77ae7
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8d5a315671b6fd1c475abc88f454a7c3bfb434f4
https://github.com/galaxyproject/galaxy/commit/8d5a315671b6fd1c475abc88f454…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-03 (Thu, 03 Aug 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Register tool lineage when loading tool via quick_load()
Commit: 51951a8850888d0d5538ef5f84327bb78ccbfba6
https://github.com/galaxyproject/galaxy/commit/51951a8850888d0d5538ef5f8432…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-03 (Thu, 03 Aug 2017)
Changed paths:
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/model/__init__.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M templates/webapps/galaxy/history/display_structured.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
Log Message:
-----------
Always use tool version to get tools from toolbox
This fixes a bug when getting parameters for jobs that were executed
with old tool versions.
Commit: faee2b65c29ee405d475d54a630d54c7b29a4159
https://github.com/galaxyproject/galaxy/commit/faee2b65c29ee405d475d54a630d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Use self.job instead of self.parent_job in Task
Noticed by @nsoranzo.
Commit: 7474474cc0ec8f98a0e23bfd7bf2906326938153
https://github.com/galaxyproject/galaxy/commit/7474474cc0ec8f98a0e23bfd7bf2…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Move tool lineage registration to toolbox.__add_tool()
Commit: ccad70c22c082b3801dec567600f054581e8044b
https://github.com/galaxyproject/galaxy/commit/ccad70c22c082b3801dec567600f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Add warnings if a tool lineage could not be retrieved
Commit: 575696dcc2cc775e72b58f5cda0612a79b62b87b
https://github.com/galaxyproject/galaxy/commit/575696dcc2cc775e72b58f5cda06…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M templates/webapps/galaxy/history/display_structured.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
Log Message:
-----------
Merge pull request #4375 from mvdbeek/tool_version_and_lineage_fixes
Tool version and lineage fixes
Compare: https://github.com/galaxyproject/galaxy/compare/dbd057f9d720...575696dcc2cc
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 32bd350fe9c06b9f506c21c9ba4eab97408c404d
https://github.com/galaxyproject/galaxy/commit/32bd350fe9c06b9f506c21c9ba4e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-03 (Thu, 03 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Fix URL for workflow editor 'Run' button
On the current dev this would point to api/workflows//download?style=run
and result in `Error occurred while loading the resource.`
Commit: dbd057f9d72036bff98d3217312e4de3148b3285
https://github.com/galaxyproject/galaxy/commit/dbd057f9d72036bff98d3217312e…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-03 (Thu, 03 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Merge pull request #4371 from mvdbeek/fix_run_from_workflow_editor
Fix URL for workflow editor 'Run' button
Compare: https://github.com/galaxyproject/galaxy/compare/fe3fdc82d239...dbd057f9d720
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 910e6fa035684fbdfc2b38e4675308e47e801083
https://github.com/galaxyproject/galaxy/commit/910e6fa035684fbdfc2b38e46753…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-02 (Wed, 02 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/managers/tags.py
M static/maps/mvc/workflow/workflow-forms.js.map
M static/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Allow removal of dataset tags in workflows
This adds a RemoveTagDatasetAction PJA, which removes user-specified
tags if they exist. Fixes
https://github.com/galaxyproject/galaxy/issues/4362
Commit: fe3fdc82d23978c4161d8f020c256576f663e10a
https://github.com/galaxyproject/galaxy/commit/fe3fdc82d23978c4161d8f020c25…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-03 (Thu, 03 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/managers/tags.py
M static/maps/mvc/workflow/workflow-forms.js.map
M static/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Merge pull request #4369 from mvdbeek/tag_removal
Allow removal of dataset tags in workflows
Compare: https://github.com/galaxyproject/galaxy/compare/6b2a2582002d...fe3fdc82d239