August 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] dd0a68: Fixes...
by GitHub 31 Aug '18

31 Aug '18

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.

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[galaxyproject/galaxy] 25ae4e: Fix get_fileobj() call in Eland.set_meta()
by GitHub 31 Aug '18

31 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 25ae4e6e26a27696fa47ea656fa36889f435e2f2 https://github.com/galaxyproject/galaxy/commit/25ae4e6e26a27696fa47ea656fa3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-30 (Thu, 30 Aug 2018) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fix get_fileobj() call in Eland.set_meta() Broken in commit 59f44cf2be48abd4bed0f7c6ddf7cc0aee5ad1f5 . Commit: 3a77b64aeb71c027d8f8d7ca56574b63ff83afb3 https://github.com/galaxyproject/galaxy/commit/3a77b64aeb71c027d8f8d7ca5657… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-31 (Fri, 31 Aug 2018) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #6659 from nsoranzo/fix_Eland_set_meta Fix get_fileobj() call in Eland.set_meta() Compare: https://github.com/galaxyproject/galaxy/compare/bb9545288272...3a77b64aeb71 **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.

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[galaxyproject/galaxy] feaaec: Strip API keys option from admin panel left side -...
by GitHub 29 Aug '18

29 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: feaaecf2199f78e42668418ab4eb5c8f68ff0e8d https://github.com/galaxyproject/galaxy/commit/feaaecf2199f78e42668418ab4eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Strip API keys option from admin panel left side -- this is all in the user management grid now. I don't know if this got added back in a bad merge or if it was erroneously left in. Commit: 223c3988083c5397626bd33908376bc007bc28bc https://github.com/galaxyproject/galaxy/commit/223c3988083c5397626bd3390837… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M test/galaxy_selenium/navigation.yml Log Message: ----------- drop admin api keys navigator from selenium configs (which may break other tests, we should wait to see) Commit: bb95452882726e4f6c3f26c76abfe7b22bafadb4 https://github.com/galaxyproject/galaxy/commit/bb95452882726e4f6c3f26c76abf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M test/galaxy_selenium/navigation.yml Log Message: ----------- Merge pull request #6651 from dannon/admin_apikeys_fixup Strip API keys option from admin panel left side Compare: https://github.com/galaxyproject/galaxy/compare/2adae6c4ca77...bb9545288272 **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.

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[galaxyproject/galaxy] 85751e: Add tag and group tag rule to history level rule b...
by GitHub 28 Aug '18

28 Aug '18

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.

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[galaxyproject/galaxy] 167ab6: Fix color of workflow panel background
by GitHub 28 Aug '18

28 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 167ab6b54eb330ad44b8c7900d52514a1c90d1cb https://github.com/galaxyproject/galaxy/commit/167ab6b54eb330ad44b8c7900d52… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix color of workflow panel background Commit: 3121d9f0a468d23f6619e3496cf46c627560d90c https://github.com/galaxyproject/galaxy/commit/3121d9f0a468d23f6619e3496cf4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6643 from guerler/fix_panel_background Fix color of workflow panel background Compare: https://github.com/galaxyproject/galaxy/compare/7fa539162791...3121d9f0a468 **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.

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[galaxyproject/galaxy] 982e87: Allow supplying name of pasted data, issue #4162
by GitHub 27 Aug '18

27 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 982e878f8e5903b42df291015522c6b3334f6035 https://github.com/galaxyproject/galaxy/commit/982e878f8e5903b42df291015522… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- Allow supplying name of pasted data, issue #4162 Commit: 163018c35177a9356a7e6f789ee719f3be5d861e https://github.com/galaxyproject/galaxy/commit/163018c35177a9356a7e6f789ee7… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- keep default Galaxy dataset name of pasted content to Pasted Entry Commit: 7fa539162791e5e1eca836616b31381f2ad62b05 https://github.com/galaxyproject/galaxy/commit/7fa539162791e5e1eca836616b31… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- Merge pull request #6415 from FredericBGA/supplying_name_pasted_data Allow supplying name of pasted data Compare: https://github.com/galaxyproject/galaxy/compare/660a51495b52...7fa539162791 **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.

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[galaxyproject/galaxy] 51c6e2: Add a step in PSA pipeline to determine if ID toke...
by GitHub 27 Aug '18

27 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51c6e2f6ba6b654b7f234c0440cfaa95ac2735b4 https://github.com/galaxyproject/galaxy/commit/51c6e2f6ba6b654b7f234c0440cf… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add a step in PSA pipeline to determine if ID token exists. Commit: 405a08522e8f54341478dde5c88868e33ed55ec7 https://github.com/galaxyproject/galaxy/commit/405a08522e8f54341478dde5c888… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- check for missing ID and refresh tokens. Commit: 0ed0bdf203c6d088487c24e42fd50951039f7e74 https://github.com/galaxyproject/galaxy/commit/0ed0bdf203c6d088487c24e42fd5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add some comments explaining when some OIDC-related errors can happen. Commit: 3e6fa40ec84206558aa11679170fd747ff2f20b3 https://github.com/galaxyproject/galaxy/commit/3e6fa40ec84206558aa11679170f… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Fix some lint issues in psa_authnz.py. Commit: b29311fdab1a08a70eee7fad69f77bc72d8e88bc https://github.com/galaxyproject/galaxy/commit/b29311fdab1a08a70eee7fad69f7… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Get ID token, if expired, refresh it. Commit: 27db877816bdba5f91ada327c63b7a7717341e18 https://github.com/galaxyproject/galaxy/commit/27db877816bdba5f91ada327c63b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove the `get_access_token` as it hides a base method. Commit: f0a8c541d8c83e6e6bbd7731ba4197cae549b47a https://github.com/galaxyproject/galaxy/commit/f0a8c541d8c83e6e6bbd7731ba41… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add a comment explaining a PSA pipeline step. Commit: 9d7f50c6c074a9d3e39763180d6e270f7290164f https://github.com/galaxyproject/galaxy/commit/9d7f50c6c074a9d3e39763180d6e… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add doc string for `contains_required_data` function. Commit: 660a51495b52cf886db31dbcc807e54c5b787469 https://github.com/galaxyproject/galaxy/commit/660a51495b52cf886db31dbcc807… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #6606 from VJalili/refresh_token Refresh an expired OIDC ID token Compare: https://github.com/galaxyproject/galaxy/compare/af99f49d82d9...660a51495b52 **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.

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[galaxyproject/galaxy] 296105: row ids that are all numeric become ints...
by GitHub 27 Aug '18

27 Aug '18

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 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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 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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.

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[galaxyproject/galaxy] 49eae7: Fix for workflow extraction cleanup routine.
by GitHub 27 Aug '18

27 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 49eae728916af02a6fbd3ce9d69599c08d4e58b9 https://github.com/galaxyproject/galaxy/commit/49eae728916af02a6fbd3ce9d695… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Fix for workflow extraction cleanup routine. Workflow extraction would be incorrect if you had parameters ordered and named as e.g. "somename" and "somename_2" in the input root. When these parameters are both dataset inputs, this would cause a server error. Commit: af99f49d82d917b681157ec8f5a4506c6a37cab6 https://github.com/galaxyproject/galaxy/commit/af99f49d82d917b681157ec8f5a4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Merge pull request #6636 from blankenberg/11yowffix Fix for workflow extraction cleanup routine. Compare: https://github.com/galaxyproject/galaxy/compare/0e69ca8bfbc3...af99f49d82d9 **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.

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[galaxyproject/galaxy] 6e8a7f: Fix empty handling rule.
by GitHub 26 Aug '18

26 Aug '18

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.

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