Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: dd0a6884ba7b20788fdec5b38e3715596b2ac177
https://github.com/galaxyproject/galaxy/commit/dd0a6884ba7b20788fdec5b38e37…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-08-29 (Wed, 29 Aug 2018)
Changed paths:
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/history/history-contents.js
M lib/galaxy/managers/collections.py
M test/selenium_tests/test_collection_builders.py
Log Message:
-----------
Fixes...
Commit: 5d22d73f303298fdef98c5ab8c8e8e91bae65bb3
https://github.com/galaxyproject/galaxy/commit/5d22d73f303298fdef98c5ab8c8e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-08-29 (Wed, 29 Aug 2018)
Changed paths:
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/rules/rule-definitions.js
M client/galaxy/scripts/mvc/upload/upload-view.js
Log Message:
-----------
client-format
Commit: 410ec1927c34fbb4a61969e1fe188babd9a8f82b
https://github.com/galaxyproject/galaxy/commit/410ec1927c34fbb4a61969e1fe18…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-08-31 (Fri, 31 Aug 2018)
Changed paths:
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/rules/rule-definitions.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M lib/galaxy/managers/collections.py
M test/selenium_tests/test_collection_builders.py
Log Message:
-----------
Merge pull request #6656 from jmchilton/collect_builder_fixes
Assorted fixes for #6572
Compare: https://github.com/galaxyproject/galaxy/compare/3a77b64aeb71...410ec1927c34
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 85751ebb163eb5474d6ba18b7bf9d75097d53e15
https://github.com/galaxyproject/galaxy/commit/85751ebb163eb5474d6ba18b7bf9…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M client/galaxy/scripts/mvc/rules/rule-definitions.js
Log Message:
-----------
Add tag and group tag rule to history level rule builder
Commit: 1e7ce13b4773ffeaea169b03963a2a252187dfee
https://github.com/galaxyproject/galaxy/commit/1e7ce13b4773ffeaea169b03963a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M lib/galaxy/managers/hdas.py
M lib/galaxy/model/__init__.py
Log Message:
-----------
Reuse HDA copy method in HDAManager
Should benefit from smarter flush strategy in HDA.copy()
Commit: d1f9ab88e4637d00c6c5c3c2290f6a19dd369456
https://github.com/galaxyproject/galaxy/commit/d1f9ab88e4637d00c6c5c3c2290f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
Always copy HDAs when creating a new collection from exisitng datasets, and allow setting tags
Commit: 91438996df29caac56bb7a6fe8dc25e52815caf8
https://github.com/galaxyproject/galaxy/commit/91438996df29caac56bb7a6fe8dc…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M test/api/test_history_contents.py
Log Message:
-----------
Test creation of collection from existing dataset, with a new tag
Commit: eb4b878f3f5e9a898d5048c917ce2d379d7bf20f
https://github.com/galaxyproject/galaxy/commit/eb4b878f3f5e9a898d5048c917ce…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/hdas.py
Log Message:
-----------
Simplify hda manager usage
Commit: 5dd63dd6d077e9836f126d97a3c50b8a25ea66cc
https://github.com/galaxyproject/galaxy/commit/5dd63dd6d077e9836f126d97a3c5…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
Log Message:
-----------
Include tags in element_identifier when building collection from datasets
Commit: ce892a028cb9d65aa19f8a4333626b421a184ec9
https://github.com/galaxyproject/galaxy/commit/ce892a028cb9d65aa19f8a433362…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M lib/galaxy/managers/collections.py
Log Message:
-----------
Restore hiding of dataset instances
Commit: d4a80e61e13fbeeda43a65874910d85cfc1c8b29
https://github.com/galaxyproject/galaxy/commit/d4a80e61e13fbeeda43a65874910…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_HistoryContentsManager.py
Log Message:
-----------
Adapt unit tests to copying HDAs when creating collections
Commit: a9cb290754f09a1ea3073e8858df6f9a9e45b147
https://github.com/galaxyproject/galaxy/commit/a9cb290754f09a1ea3073e8858df…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M test/api/test_history_contents.py
M test/api/test_tools.py
M test/api/test_workflows.py
Log Message:
-----------
Adjust API tests to copying HDAs when creating collection
Commit: 711016ab9aac78c96fa65cd04f9421fbb6473b49
https://github.com/galaxyproject/galaxy/commit/711016ab9aac78c96fa65cd04f94…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
Treat LDDA as HDA when creating collection
This avoids copying the LDDA to HDA and then copying the HDA again.
Commit: 34cfdcac6a583c84c8641ac8e26243769d09598d
https://github.com/galaxyproject/galaxy/commit/34cfdcac6a583c84c8641ac8e262…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M test/api/test_history_contents.py
Log Message:
-----------
Test for proper 403 response
Coincidentally fixed by e013f2fbd1596b103ef195afcba8cbd787c49b33.
Commit: c00ae9f81b953df7909aa591e411ebd6298a6f7c
https://github.com/galaxyproject/galaxy/commit/c00ae9f81b953df7909aa591e411…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
Default to not copying source HDAs when creating new collections via API
Commit: 9409322a730d431344d4438e379e61559632812d
https://github.com/galaxyproject/galaxy/commit/9409322a730d431344d4438e379e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_HistoryContentsManager.py
Log Message:
-----------
Revert "Adapt unit tests to copying HDAs when creating collections"
This reverts commit 408a003f171be73e4b347579ee6f662a18fc1990.
Commit: b13cce0a1340a5f9b7a77ab7eda1ceb0930ed161
https://github.com/galaxyproject/galaxy/commit/b13cce0a1340a5f9b7a77ab7eda1…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M test/api/test_history_contents.py
M test/api/test_tools.py
M test/api/test_workflows.py
Log Message:
-----------
Revert "Adjust API tests to copying HDAs when creating collection"
This reverts commit f120390a63700ff0ec6c09185aad26b91ad8f842.
Commit: cfd8379917703ce03b631fd48b5a2bcecc30bbea
https://github.com/galaxyproject/galaxy/commit/cfd8379917703ce03b631fd48b5a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M test/api/test_history_contents.py
Log Message:
-----------
Send copy_elements=True in new create collection test
Commit: 43ee13a0ce43ae5b29ffa1e317df1db645cb93a8
https://github.com/galaxyproject/galaxy/commit/43ee13a0ce43ae5b29ffa1e317df…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
Log Message:
-----------
Default to copying HDAs when creating collections via the UI
Commit: 50a524496a4ed52184967ede53094e5c8243d93d
https://github.com/galaxyproject/galaxy/commit/50a524496a4ed52184967ede5309…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M test/unit/managers/test_HistoryContentsManager.py
Log Message:
-----------
Add unit test for copy_element option
Commit: ddb0c74b9bd9f534691a93911f10903da3609927
https://github.com/galaxyproject/galaxy/commit/ddb0c74b9bd9f534691a93911f10…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M lib/galaxy/managers/collections.py
Log Message:
-----------
Original HDA must be owned by user if hiding source elements
Commit: 366701cfb23d8de31eac3c4312c6accca2e74ef1
https://github.com/galaxyproject/galaxy/commit/366701cfb23d8de31eac3c4312c6…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M lib/galaxy/managers/tags.py
M lib/galaxy/util/__init__.py
A test/unit/managers/test_TagManager.py
Log Message:
-----------
Strip unicode control characters from tags
Leaving them in can trip up postgresql:
```
Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 283, in decorator
rval = func(self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy/api/history_contents.py", line 396, in create
return self.__create_dataset_collection(trans, history, payload, **kwd)
File "lib/galaxy/webapps/galaxy/api/history_contents.py", line 525, in __create_dataset_collection
**create_params
File "lib/galaxy/managers/collections.py", line 108, in create
copy_elements=copy_elements,
File "lib/galaxy/managers/collections.py", line 181, in create_dataset_collection
copy_elements=copy_elements)
File "lib/galaxy/managers/collections.py", line 217, in _element_identifiers_to_elements
copy_elements=copy_elements)
File "lib/galaxy/managers/collections.py", line 389, in __load_elements
copy_elements=copy_elements)
File "lib/galaxy/managers/collections.py", line 434, in __load_element
self.tag_manager.apply_item_tags(user=trans.user, item=element, tags_str=tag_str)
File "lib/galaxy/managers/tags.py", line 182, in apply_item_tags
self.apply_item_tag(user, item, name, value)
File "lib/galaxy/managers/tags.py", line 154, in apply_item_tag
tag = self._get_or_create_tag(lc_name)
File "lib/galaxy/managers/tags.py", line 233, in _get_or_create_tag
tag = self.get_tag_by_name(scrubbed_tag_str)
File "lib/galaxy/managers/tags.py", line 205, in get_tag_by_name
return self.sa_session.query(galaxy.model.Tag).filter_by(name=tag_name.lower()).first()
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2789, in first
ret = list(self[0:1])
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2581, in __getitem__
return list(res)
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2889, in __iter__
return self._execute_and_instances(context)
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2912, in _execute_and_instances
result = conn.execute(querycontext.statement, self._params)
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute
return meth(self, multiparams, params)
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 269, in _execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1060, in _execute_clauseelement
compiled_sql, distilled_params
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context
context)
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1416, in _handle_dbapi_exception
util.reraise(*exc_info)
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context
context)
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute
cursor.execute(statement, parameters)
ValueError: A string literal cannot contain NUL (0x00) characters.
```
Commit: 2adae6c4ca77067f2f45f3f101218d411fec7e25
https://github.com/galaxyproject/galaxy/commit/2adae6c4ca77067f2f45f3f10121…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-08-28 (Tue, 28 Aug 2018)
Changed paths:
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/rules/rule-definitions.js
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M test/api/test_history_contents.py
M test/unit/managers/test_HistoryContentsManager.py
A test/unit/managers/test_TagManager.py
Log Message:
-----------
Merge pull request #6572 from mvdbeek/add_group_tags_to_history_rule_builder
Add tagging rule to history level rule builder, copy HDAs when building collection
Compare: https://github.com/galaxyproject/galaxy/compare/3121d9f0a468...2adae6c4ca77
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/release_18.05
Home: https://github.com/galaxyproject/galaxy
Commit: 296105ee395194c48d962671a8c367469ea74907
https://github.com/galaxyproject/galaxy/commit/296105ee395194c48d962671a8c3…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
row ids that are all numeric become ints...
Since the "F" prefix is checked with substring, row_id must always be a string
Commit: 55d350d015f20afc1c350130caaa0aa9858b7aa0
https://github.com/galaxyproject/galaxy/commit/55d350d015f20afc1c350130caaa…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M static/scripts/admin.toolshed.js
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/chart.bundled.js
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/login.bundled.js
M static/scripts/galaxy.interactive_environments.js
M static/scripts/galaxy.js
M static/scripts/galaxy.library.js
M static/scripts/galaxy.pages.js
M static/scripts/i18n.js
M static/scripts/layout/communication-server-view.js
M static/scripts/layout/masthead.js
M static/scripts/layout/menu.js
M static/scripts/layout/modal.js
M static/scripts/layout/page.js
M static/scripts/layout/panel.js
M static/scripts/layout/router.js
M static/scripts/layout/scratchbook.js
M static/scripts/legacy/grid/grid-model.js
M static/scripts/legacy/grid/grid-template.js
M static/scripts/legacy/grid/grid-view.js
M static/scripts/mocha/test.js
M static/scripts/mocha/tests/rules_tests.js
M static/scripts/mvc/annotation.js
M static/scripts/mvc/base-mvc.js
M static/scripts/mvc/base/controlled-fetch-collection.js
M static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/collection-li-edit.js
M static/scripts/mvc/collection/collection-li.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/dataset/dataset-choice.js
M static/scripts/mvc/dataset/dataset-edit-attributes.js
M static/scripts/mvc/dataset/dataset-error.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/dataset/dataset-list.js
M static/scripts/mvc/dataset/dataset-model.js
M static/scripts/mvc/dataset/states.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/form/form-wrapper.js
M static/scripts/mvc/grid/grid-model.js
M static/scripts/mvc/grid/grid-shared.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/copy-dialog.js
M static/scripts/mvc/history/hda-li-edit.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hda-model.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/hdca-li.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-item-li.js
M static/scripts/mvc/history/history-list.js
M static/scripts/mvc/history/history-model.js
M 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/job-dag.js
M static/scripts/mvc/history/job-states-model.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/job/job-li.js
M static/scripts/mvc/job/job-model.js
M static/scripts/mvc/job/job-params.js
M static/scripts/mvc/lazy/lazy-limited.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-library-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-libraryrow-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/library/library-model.js
M static/scripts/mvc/library/library-util.js
M static/scripts/mvc/list/list-item.js
M static/scripts/mvc/list/list-view.js
M static/scripts/mvc/rules/rule-definitions.js
M static/scripts/mvc/tag.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/tool/tool-genomespace.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repo-queue-view.js
M static/scripts/mvc/toolshed/repo-status-view.js
M static/scripts/mvc/toolshed/repositories-view.js
M static/scripts/mvc/toolshed/repository-queue-view.js
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/shed-list-view.js
M static/scripts/mvc/toolshed/toolshed-model.js
M static/scripts/mvc/toolshed/util.js
M static/scripts/mvc/toolshed/workflows-view.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/ui/error-modal.js
M static/scripts/mvc/ui/icon-button.js
M static/scripts/mvc/ui/popup-menu.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-color-picker.js
M static/scripts/mvc/ui/ui-drilldown.js
M static/scripts/mvc/ui/ui-frames.js
M static/scripts/mvc/ui/ui-list.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-options.js
M static/scripts/mvc/ui/ui-popover.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-rules-edit.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-select-ftp.js
M static/scripts/mvc/ui/ui-select-genomespace.js
M static/scripts/mvc/ui/ui-select-library.js
M static/scripts/mvc/ui/ui-select.js
M static/scripts/mvc/ui/ui-slider.js
M static/scripts/mvc/ui/ui-table.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/mvc/ui/ui-thumbnails.js
M static/scripts/mvc/upload/collection/collection-row.js
M static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/collection/rules-input-view.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-button.js
M static/scripts/mvc/upload/upload-extension.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-model.js
M static/scripts/mvc/upload/upload-settings.js
M static/scripts/mvc/upload/upload-utils.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-model.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/user/user-quotameter.js
M static/scripts/mvc/visualization/chart/chart-client.js
M static/scripts/mvc/visualization/chart/components/model.js
M static/scripts/mvc/visualization/chart/components/screenshot.js
M static/scripts/mvc/visualization/chart/utilities/datasets.js
M static/scripts/mvc/visualization/chart/utilities/jobs.js
M static/scripts/mvc/visualization/chart/utilities/series.js
M static/scripts/mvc/visualization/chart/views/description.js
M static/scripts/mvc/visualization/chart/views/editor.js
M static/scripts/mvc/visualization/chart/views/groups.js
M static/scripts/mvc/visualization/chart/views/menu.js
M static/scripts/mvc/visualization/chart/views/settings.js
M static/scripts/mvc/visualization/chart/views/viewer.js
M static/scripts/mvc/visualization/visualization-model.js
M static/scripts/mvc/webhooks.js
M static/scripts/mvc/workflow/workflow-canvas.js
M static/scripts/mvc/workflow/workflow-connector.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-icons.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-model.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view-data.js
M static/scripts/mvc/workflow/workflow-view-node.js
M static/scripts/mvc/workflow/workflow-view-terminals.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/mvc/workflow/workflow.js
M static/scripts/nls/de/locale.js
M static/scripts/nls/es/locale.js
M static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/nls/zh/locale.js
M static/scripts/onload.js
M static/scripts/polyfills.js
M static/scripts/reports/run_stats.js
M static/scripts/toolshed/groups/group-detail-view.js
M static/scripts/toolshed/groups/group-list-view.js
M static/scripts/toolshed/groups/group-listrow-view.js
M static/scripts/toolshed/groups/group-model.js
M static/scripts/toolshed/toolshed.groups.js
M static/scripts/ui/autocom_tagging.js
M static/scripts/ui/editable-text.js
M static/scripts/ui/fa-icon-button.js
M static/scripts/ui/filter-control.js
M static/scripts/ui/hoverhighlight.js
M static/scripts/ui/loading-indicator.js
M static/scripts/ui/mode-button.js
M static/scripts/ui/pagination.js
M static/scripts/ui/peek-column-selector.js
M static/scripts/ui/popupmenu.js
M static/scripts/ui/scroll-panel.js
M static/scripts/ui/search-input.js
M static/scripts/utils/add-logging.js
M static/scripts/utils/ajax-queue.js
M static/scripts/utils/async-save-text.js
M static/scripts/utils/config.js
M static/scripts/utils/deferred.js
M static/scripts/utils/graph.js
M static/scripts/utils/levenshtein.js
M static/scripts/utils/localization.js
M static/scripts/utils/metrics-logger.js
M static/scripts/utils/natural-sort.js
M static/scripts/utils/query-string-parsing.js
M static/scripts/utils/uploadbox.js
M static/scripts/utils/utils.js
M static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/circster.js
M static/scripts/viz/phyloviz.js
M static/scripts/viz/sweepster.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/filters.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/slotting.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/trackster/util.js
M static/scripts/viz/visualization.js
M static/scripts/viz/viz_views.js
Log Message:
-----------
Add static for 2a148ff1ec37c68e280c431fceee88ee0510e017
Commit: 03c485ee45e96784b269896a23223d233c566b89
https://github.com/galaxyproject/galaxy/commit/03c485ee45e96784b269896a2322…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-08-27 (Mon, 27 Aug 2018)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/admin.toolshed.js
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/chart.bundled.js
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/login.bundled.js
M static/scripts/galaxy.interactive_environments.js
M static/scripts/galaxy.js
M static/scripts/galaxy.library.js
M static/scripts/galaxy.pages.js
M static/scripts/i18n.js
M static/scripts/layout/communication-server-view.js
M static/scripts/layout/masthead.js
M static/scripts/layout/menu.js
M static/scripts/layout/modal.js
M static/scripts/layout/page.js
M static/scripts/layout/panel.js
M static/scripts/layout/router.js
M static/scripts/layout/scratchbook.js
M static/scripts/legacy/grid/grid-model.js
M static/scripts/legacy/grid/grid-template.js
M static/scripts/legacy/grid/grid-view.js
M static/scripts/mocha/test.js
M static/scripts/mocha/tests/rules_tests.js
M static/scripts/mvc/annotation.js
M static/scripts/mvc/base-mvc.js
M static/scripts/mvc/base/controlled-fetch-collection.js
M static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/collection-li-edit.js
M static/scripts/mvc/collection/collection-li.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/dataset/dataset-choice.js
M static/scripts/mvc/dataset/dataset-edit-attributes.js
M static/scripts/mvc/dataset/dataset-error.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/dataset/dataset-list.js
M static/scripts/mvc/dataset/dataset-model.js
M static/scripts/mvc/dataset/states.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/form/form-wrapper.js
M static/scripts/mvc/grid/grid-model.js
M static/scripts/mvc/grid/grid-shared.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/copy-dialog.js
M static/scripts/mvc/history/hda-li-edit.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hda-model.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/hdca-li.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-item-li.js
M static/scripts/mvc/history/history-list.js
M static/scripts/mvc/history/history-model.js
M 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/job-dag.js
M static/scripts/mvc/history/job-states-model.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/job/job-li.js
M static/scripts/mvc/job/job-model.js
M static/scripts/mvc/job/job-params.js
M static/scripts/mvc/lazy/lazy-limited.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-library-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-libraryrow-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/library/library-model.js
M static/scripts/mvc/library/library-util.js
M static/scripts/mvc/list/list-item.js
M static/scripts/mvc/list/list-view.js
M static/scripts/mvc/rules/rule-definitions.js
M static/scripts/mvc/tag.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/tool/tool-genomespace.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repo-queue-view.js
M static/scripts/mvc/toolshed/repo-status-view.js
M static/scripts/mvc/toolshed/repositories-view.js
M static/scripts/mvc/toolshed/repository-queue-view.js
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/shed-list-view.js
M static/scripts/mvc/toolshed/toolshed-model.js
M static/scripts/mvc/toolshed/util.js
M static/scripts/mvc/toolshed/workflows-view.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/ui/error-modal.js
M static/scripts/mvc/ui/icon-button.js
M static/scripts/mvc/ui/popup-menu.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-color-picker.js
M static/scripts/mvc/ui/ui-drilldown.js
M static/scripts/mvc/ui/ui-frames.js
M static/scripts/mvc/ui/ui-list.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-options.js
M static/scripts/mvc/ui/ui-popover.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-rules-edit.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-select-ftp.js
M static/scripts/mvc/ui/ui-select-genomespace.js
M static/scripts/mvc/ui/ui-select-library.js
M static/scripts/mvc/ui/ui-select.js
M static/scripts/mvc/ui/ui-slider.js
M static/scripts/mvc/ui/ui-table.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/mvc/ui/ui-thumbnails.js
M static/scripts/mvc/upload/collection/collection-row.js
M static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/collection/rules-input-view.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-button.js
M static/scripts/mvc/upload/upload-extension.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-model.js
M static/scripts/mvc/upload/upload-settings.js
M static/scripts/mvc/upload/upload-utils.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-model.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/user/user-quotameter.js
M static/scripts/mvc/visualization/chart/chart-client.js
M static/scripts/mvc/visualization/chart/components/model.js
M static/scripts/mvc/visualization/chart/components/screenshot.js
M static/scripts/mvc/visualization/chart/utilities/datasets.js
M static/scripts/mvc/visualization/chart/utilities/jobs.js
M static/scripts/mvc/visualization/chart/utilities/series.js
M static/scripts/mvc/visualization/chart/views/description.js
M static/scripts/mvc/visualization/chart/views/editor.js
M static/scripts/mvc/visualization/chart/views/groups.js
M static/scripts/mvc/visualization/chart/views/menu.js
M static/scripts/mvc/visualization/chart/views/settings.js
M static/scripts/mvc/visualization/chart/views/viewer.js
M static/scripts/mvc/visualization/visualization-model.js
M static/scripts/mvc/webhooks.js
M static/scripts/mvc/workflow/workflow-canvas.js
M static/scripts/mvc/workflow/workflow-connector.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-icons.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-model.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view-data.js
M static/scripts/mvc/workflow/workflow-view-node.js
M static/scripts/mvc/workflow/workflow-view-terminals.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/mvc/workflow/workflow.js
M static/scripts/nls/de/locale.js
M static/scripts/nls/es/locale.js
M static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/nls/zh/locale.js
M static/scripts/onload.js
M static/scripts/polyfills.js
M static/scripts/reports/run_stats.js
M static/scripts/toolshed/groups/group-detail-view.js
M static/scripts/toolshed/groups/group-list-view.js
M static/scripts/toolshed/groups/group-listrow-view.js
M static/scripts/toolshed/groups/group-model.js
M static/scripts/toolshed/toolshed.groups.js
M static/scripts/ui/autocom_tagging.js
M static/scripts/ui/editable-text.js
M static/scripts/ui/fa-icon-button.js
M static/scripts/ui/filter-control.js
M static/scripts/ui/hoverhighlight.js
M static/scripts/ui/loading-indicator.js
M static/scripts/ui/mode-button.js
M static/scripts/ui/pagination.js
M static/scripts/ui/peek-column-selector.js
M static/scripts/ui/popupmenu.js
M static/scripts/ui/scroll-panel.js
M static/scripts/ui/search-input.js
M static/scripts/utils/add-logging.js
M static/scripts/utils/ajax-queue.js
M static/scripts/utils/async-save-text.js
M static/scripts/utils/config.js
M static/scripts/utils/deferred.js
M static/scripts/utils/graph.js
M static/scripts/utils/levenshtein.js
M static/scripts/utils/localization.js
M static/scripts/utils/metrics-logger.js
M static/scripts/utils/natural-sort.js
M static/scripts/utils/query-string-parsing.js
M static/scripts/utils/uploadbox.js
M static/scripts/utils/utils.js
M static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/circster.js
M static/scripts/viz/phyloviz.js
M static/scripts/viz/sweepster.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/filters.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/slotting.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/trackster/util.js
M static/scripts/viz/visualization.js
M static/scripts/viz/viz_views.js
Log Message:
-----------
Merge pull request #6639 from bwlang/patch-2
[18.05] row ids that are all numeric become ints...
Compare: https://github.com/galaxyproject/galaxy/compare/709e49f104e2...03c485ee45e9
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6e8a7fddb1727a7b6f4c3ae4817d38fe73f2079b
https://github.com/galaxyproject/galaxy/commit/6e8a7fddb1727a7b6f4c3ae4817d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-26 (Thu, 26 Jul 2018)
Changed paths:
M lib/galaxy/util/rules_dsl.py
M test/unit/test_rule_utils.py
Log Message:
-----------
Fix empty handling rule.
Commit: 42ddfbde4c429b6bd3a19f901f0f3bf7db1d85ba
https://github.com/galaxyproject/galaxy/commit/42ddfbde4c429b6bd3a19f901f0f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-26 (Thu, 26 Jul 2018)
Changed paths:
M client/galaxy/scripts/mvc/rules/rule-definitions.js
M test/base/data/rules_dsl_spec.yml
Log Message:
-----------
Fill out, polish the rule spec a little more.
Drop use of startsWith in favor of indexOf for PhantomJS testing.
Commit: 6cd8650b5a5530835e6d396e81d6f481ca6b141a
https://github.com/galaxyproject/galaxy/commit/6cd8650b5a5530835e6d396e81d6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-26 (Thu, 26 Jul 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Remove stray debug statement left in 18.05.
Commit: 4d83746cc2f83c1208abcefbce3e66a00f01076a
https://github.com/galaxyproject/galaxy/commit/4d83746cc2f83c1208abcefbce3e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-26 (Thu, 26 Jul 2018)
Changed paths:
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/mvc/rules/rule-definitions.js
M lib/galaxy/managers/collections.py
M lib/galaxy/util/rules_dsl.py
M test/base/data/rules_dsl_spec.yml
Log Message:
-----------
Allow loading tag metadata from existing objects in rule builder.
This should allow nesting and filtering from tags - including group tags.
Commit: 58072302539dd7c5283ee11c13512a19a9bf99fb
https://github.com/galaxyproject/galaxy/commit/58072302539dd7c5283ee11c1351…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-27 (Fri, 27 Jul 2018)
Changed paths:
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/mvc/rules/rule-definitions.js
M lib/galaxy/managers/collections.py
M lib/galaxy/util/rules_dsl.py
M test/api/test_tools.py
M test/base/data/rules_dsl_spec.yml
M test/base/populators.py
M test/base/rules_test_data.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/smart_components.py
M test/selenium_tests/test_tool_form.py
Log Message:
-----------
Implement rule builder rule to quickly grab group tag value.
Should make it a lot easier to nested and filter on group tag values.
Commit: 0e69ca8bfbc3c93bd18a22a32cd77494d55e915e
https://github.com/galaxyproject/galaxy/commit/0e69ca8bfbc3c93bd18a22a32cd7…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-08-26 (Sun, 26 Aug 2018)
Changed paths:
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/mvc/rules/rule-definitions.js
M lib/galaxy/managers/collections.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/util/rules_dsl.py
M test/api/test_tools.py
M test/base/data/rules_dsl_spec.yml
M test/base/populators.py
M test/base/rules_test_data.py
M test/selenium_tests/test_tool_form.py
Log Message:
-----------
Merge pull request #6545 from jmchilton/rule_builder_use_group_tags
Allow Consuming Tags in the Apply Rules Tool
Compare: https://github.com/galaxyproject/galaxy/compare/a3fc0b9f324f...0e69ca8bfbc3
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.