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

[galaxyproject/galaxy] 240ad3: Fix dataset access validation when attempting job ...
by GitHub 18 May '18

18 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 240ad36e20f34f1083b7d148340d4fadd72f8884 https://github.com/galaxyproject/galaxy/commit/240ad36e20f34f1083b7d148340d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Fix dataset access validation when attempting job reruns Commit: bd4f562005e26d56b5e4c9476748fb14f0fed242 https://github.com/galaxyproject/galaxy/commit/bd4f562005e26d56b5e4c9476748… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Merge pull request #6170 from mvdbeek/backport_6169 [18.01] Backport #6169 Fix dataset access validation when attempting job reruns Commit: 5489504e9794f31e26adc901f5612fcfb7d4a91d https://github.com/galaxyproject/galaxy/commit/5489504e9794f31e26adc901f561… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/5d6bc5721a25...5489504e9794 **NOTE:** This service 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] 240ad3: Fix dataset access validation when attempting job ...
by GitHub 18 May '18

18 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 240ad36e20f34f1083b7d148340d4fadd72f8884 https://github.com/galaxyproject/galaxy/commit/240ad36e20f34f1083b7d148340d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Fix dataset access validation when attempting job reruns Commit: bd4f562005e26d56b5e4c9476748fb14f0fed242 https://github.com/galaxyproject/galaxy/commit/bd4f562005e26d56b5e4c9476748… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Merge pull request #6170 from mvdbeek/backport_6169 [18.01] Backport #6169 Fix dataset access validation when attempting job reruns Compare: https://github.com/galaxyproject/galaxy/compare/3221afd8d49f...bd4f562005e2 **NOTE:** This service 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] 0c9fd0: Release notes for 18.05.
by GitHub 18 May '18

18 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0c9fd0e6de6d884dc5324288d74bdf049bc57e3d https://github.com/galaxyproject/galaxy/commit/0c9fd0e6de6d884dc5324288d74b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: A doc/source/releases/18.05.rst M doc/source/releases/18.05_announce.rst A doc/source/releases/18.05_new_viz.png A doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst Log Message: ----------- Release notes for 18.05. Commit: 276858e38e8126332c0952b581c09a2034b6a8d8 https://github.com/galaxyproject/galaxy/commit/276858e38e8126332c0952b581c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M doc/source/releases/18.05.rst M doc/source/releases/18.05_announce.rst Log Message: ----------- Fixes to the 18.05 release thanks to @nsoranzo's review. Commit: f3e49fb1e16ea063bd64de9f59914bf1ba2ada5c https://github.com/galaxyproject/galaxy/commit/f3e49fb1e16ea063bd64de9f5991… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- One more typo Commit: 11a31a1ae70be3ae41fb04b38852cab87ded1bd9 https://github.com/galaxyproject/galaxy/commit/11a31a1ae70be3ae41fb04b38852… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Update tool build API for implicit collection conversion. Commit: 63d4ea900b0fe8f1c3e653ebff33d7d9c3c25d05 https://github.com/galaxyproject/galaxy/commit/63d4ea900b0fe8f1c3e653ebff33… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/releases/18.05.rst M doc/source/releases/18.05_announce.rst R doc/source/releases/18.05_new_viz.png Log Message: ----------- add most important PRs added Commit: 5d6249ec6fb45db681ad727c63612d20cb40a013 https://github.com/galaxyproject/galaxy/commit/5d6249ec6fb45db681ad727c6361… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- add security and breaking changes to release notes Commit: 77e187ddd1d6571de72f4a67a4fc7eeb148ae14c https://github.com/galaxyproject/galaxy/commit/77e187ddd1d6571de72f4a67a4fc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- match styling with older RN Commit: d70aadd6d10337e0cc43df325f52a8ce2ec31376 https://github.com/galaxyproject/galaxy/commit/d70aadd6d10337e0cc43df325f52… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- add minor tinies Commit: c4f74c19f3d5b3f550fe384a94bd524d1e93acfc https://github.com/galaxyproject/galaxy/commit/c4f74c19f3d5b3f550fe384a94bd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- add more breaking changes Commit: 04d1536edff9d9d467a8158ca536fdffecf097bb https://github.com/galaxyproject/galaxy/commit/04d1536edff9d9d467a8158ca536… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M doc/source/releases/18.05.rst Log Message: ----------- Fix typos Commit: 82dce758f1ad7b6d9d517531eea5497e9ac5ed3f https://github.com/galaxyproject/galaxy/commit/82dce758f1ad7b6d9d517531eea5… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- Small fixes Commit: d2dc22d97f35ff1c4cc780ce03c3a6e41ded86cb https://github.com/galaxyproject/galaxy/commit/d2dc22d97f35ff1c4cc780ce03c3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Use RetryActionExecutor when executing commands via paramiko This should work around issues like ``` galaxy.jobs.runners ERROR 2018-05-16 10:15:55,522 [p:13768,w:0,m:1] [ShellRunner.work_thread-3] (34130) Unhandled exception calling queue_job Traceback (most recent call last): File "lib/galaxy/jobs/runners/__init__.py", line 112, in run_next method(arg) File "lib/galaxy/jobs/runners/cli.py", line 94, in queue_job chmod_out = shell.execute("chmod +x %s" % tool_script) File "lib/galaxy/jobs/runners/util/cli/shell/rsh.py", line 77, in execute self.connect() File "lib/galaxy/jobs/runners/util/cli/shell/rsh.py", line 69, in connect timeout=self.timeout) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paramiko/client.py", line 424, in connect passphrase, File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paramiko/client.py", line 714, in _auth raise saved_exception SSHException: not a valid OPENSSH private key file ``` that can intermittently occur with rapid submission of many small jobs. Commit: 206daec262d974bb8e50a091da91a102cb35c022 https://github.com/galaxyproject/galaxy/commit/206daec262d974bb8e50a091da91… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: A doc/source/releases/18.05.rst M doc/source/releases/18.05_announce.rst A doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #6006 from jmchilton/release_18.05_release_notes [18.05] Release notes for 18.05. Commit: fe37996de35ccf675f07dd5c7efbaa28b7d89da7 https://github.com/galaxyproject/galaxy/commit/fe37996de35ccf675f07dd5c7efb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M doc/source/releases/18.05_announce.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- rename the config option to enable_gdpr_beta to reflect the information that we do not guarantee compliance Commit: df6842a4054de142d6d5926354f81b52a6ec7530 https://github.com/galaxyproject/galaxy/commit/df6842a4054de142d6d5926354f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Remove the success green on dropdown click; the text already toggles to let you know you clicked, and this is much, much less jarring Commit: 4ed11c16b8c7a05eda2089ed528b7b1dca8d79e3 https://github.com/galaxyproject/galaxy/commit/4ed11c16b8c7a05eda2089ed528b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Use defined -dark instead of a flat black Commit: 5c455c4472f88cae48beab85864f970c49ea2544 https://github.com/galaxyproject/galaxy/commit/5c455c4472f88cae48beab85864f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Merge pull request #6144 from jmchilton/allow_implicit_conversion [18.05] Fix tool build API for implicit collection conversion. Commit: bfa69401ec869f83b8f52b1a1301145c6f551b03 https://github.com/galaxyproject/galaxy/commit/bfa69401ec869f83b8f52b1a1301… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Gold for active text click. Readable. Contrasts. Still indicates a click. Commit: 7029cb936a9f016a7f714dcbdc88709231ee8d5a https://github.com/galaxyproject/galaxy/commit/7029cb936a9f016a7f714dcbdc88… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Merge pull request #6149 from mvdbeek/fix_stuck_jobs_when_paramiko_fails [18.05] Use RetryActionExecutor when executing commands via paramiko Commit: a6df95508d5c9ea3bcd3be67d31cf91cc4bc281a https://github.com/galaxyproject/galaxy/commit/a6df95508d5c9ea3bcd3be67d31c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js Log Message: ----------- Backbone model url fixes (urlRoot isn't necessary in many of these situations, and only complicates (and breaks) some things Commit: 680948b1a5351b3819f6b7c55720f2bd2e68cadc https://github.com/galaxyproject/galaxy/commit/680948b1a5351b3819f6b7c55720… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js Log Message: ----------- Previous changes overstepped; this should be enough to fix the prefix serving at least in the multiview, and I'm not seeing errors elsewhere (yet). We should look at other urlRoot usage though; it likely has issues. This reverts commit 62811d0a40aafe5db8c5121ff857788c59880b56. Commit: b488c1d12b7742e64d95fba434bdb15aef57dd2c https://github.com/galaxyproject/galaxy/commit/b488c1d12b7742e64d95fba434bd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js Log Message: ----------- Merge pull request #6151 from dannon/urlroot_fixes [18.05] Backbone model url handling Commit: 10a2e68b82a3e175afe33f4686b9b015e7ac4ec4 https://github.com/galaxyproject/galaxy/commit/10a2e68b82a3e175afe33f4686b9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M doc/source/releases/18.05_announce.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #6152 from martenson/compliance-rename [18.05] rename the config option to enable_beta_gdpr Commit: 47950b1707b44b130355e3c2f98d3204be581fa1 https://github.com/galaxyproject/galaxy/commit/47950b1707b44b130355e3c2f98d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6155 from dannon/no-more-green [18.05] Dropdown active color tweaks Commit: 3208a685aab130477171c8638673aa77c99495bc https://github.com/galaxyproject/galaxy/commit/3208a685aab130477171c8638673… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/job-states-model.js Log Message: ----------- Fix fetching collection state for static histories. See comment in code. Commit: 6cfe5880e13e0f704782afb72ebafd7fac3d45d4 https://github.com/galaxyproject/galaxy/commit/6cfe5880e13e0f704782afb72eba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M lib/galaxy/tools/execute.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml R test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- [18.01] Fix structured_like unqualified references + test. Update tool XSD to encourage using fully qualified inputs. Reorganized the existing tests for consistency with other test tools I think. (Rebased with fixes, including XSD fixes from @nsoranzo.) Commit: 02fa00185aa704266cafa7a3fade90a800cada80 https://github.com/galaxyproject/galaxy/commit/02fa00185aa704266cafa7a3fade… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/job-states-model.js Log Message: ----------- Merge pull request #6165 from jmchilton/fix_history_view [18.05] Fix fetching collection state for static histories. Commit: 3aace5d60e0068fec34cb2ce51abb749fe4469a1 https://github.com/galaxyproject/galaxy/commit/3aace5d60e0068fec34cb2ce51ab… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Fix dataset access validation when attempting job reruns Commit: 3221afd8d49f9ba00c10448ac33b25e93c9c3c82 https://github.com/galaxyproject/galaxy/commit/3221afd8d49f9ba00c10448ac33b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/tools/execute.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml R test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6162 from jmchilton/structured_like_conditional [18.01] Fix structured_like unqualified references + test. Commit: 6f9a93bad11c189be1b26b6e11d1733c39b2f58d https://github.com/galaxyproject/galaxy/commit/6f9a93bad11c189be1b26b6e11d1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Merge pull request #6169 from guerler/rerun_no_admin [18.05] Fix job reruns for imported histories Commit: 5d6bc5721a25a76fa9e671d2e6c6fab9300b6001 https://github.com/galaxyproject/galaxy/commit/5d6bc5721a25a76fa9e671d2e6c6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/tools/execute.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml R test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 41e12f0b9d178641209f5d4c732c9d0bd6131184 https://github.com/galaxyproject/galaxy/commit/41e12f0b9d178641209f5d4c732c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst A doc/source/releases/18.05.rst M doc/source/releases/18.05_announce.rst A doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst M lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M static/style/blue/base.css M test/api/test_tools.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml R test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/24c32a3180b9...41e12f0b9d17 **NOTE:** This service 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] 6cfe58: [18.01] Fix structured_like unqualified references...
by GitHub 18 May '18

18 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 6cfe5880e13e0f704782afb72ebafd7fac3d45d4 https://github.com/galaxyproject/galaxy/commit/6cfe5880e13e0f704782afb72eba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M lib/galaxy/tools/execute.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml R test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- [18.01] Fix structured_like unqualified references + test. Update tool XSD to encourage using fully qualified inputs. Reorganized the existing tests for consistency with other test tools I think. (Rebased with fixes, including XSD fixes from @nsoranzo.) Commit: 3221afd8d49f9ba00c10448ac33b25e93c9c3c82 https://github.com/galaxyproject/galaxy/commit/3221afd8d49f9ba00c10448ac33b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/tools/execute.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml R test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6162 from jmchilton/structured_like_conditional [18.01] Fix structured_like unqualified references + test. Commit: 5d6bc5721a25a76fa9e671d2e6c6fab9300b6001 https://github.com/galaxyproject/galaxy/commit/5d6bc5721a25a76fa9e671d2e6c6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/tools/execute.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml R test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/6f9a93bad11c...5d6bc5721a25 **NOTE:** This service 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] 3aace5: Fix dataset access validation when attempting job ...
by GitHub 18 May '18

18 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 3aace5d60e0068fec34cb2ce51abb749fe4469a1 https://github.com/galaxyproject/galaxy/commit/3aace5d60e0068fec34cb2ce51ab… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Fix dataset access validation when attempting job reruns Commit: 6f9a93bad11c189be1b26b6e11d1733c39b2f58d https://github.com/galaxyproject/galaxy/commit/6f9a93bad11c189be1b26b6e11d1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Merge pull request #6169 from guerler/rerun_no_admin [18.05] Fix job reruns for imported histories Compare: https://github.com/galaxyproject/galaxy/compare/02fa00185aa7...6f9a93bad11c **NOTE:** This service 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] 6cfe58: [18.01] Fix structured_like unqualified references...
by GitHub 18 May '18

18 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 6cfe5880e13e0f704782afb72ebafd7fac3d45d4 https://github.com/galaxyproject/galaxy/commit/6cfe5880e13e0f704782afb72eba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M lib/galaxy/tools/execute.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml R test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- [18.01] Fix structured_like unqualified references + test. Update tool XSD to encourage using fully qualified inputs. Reorganized the existing tests for consistency with other test tools I think. (Rebased with fixes, including XSD fixes from @nsoranzo.) Commit: 3221afd8d49f9ba00c10448ac33b25e93c9c3c82 https://github.com/galaxyproject/galaxy/commit/3221afd8d49f9ba00c10448ac33b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/tools/execute.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml R test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6162 from jmchilton/structured_like_conditional [18.01] Fix structured_like unqualified references + test. Compare: https://github.com/galaxyproject/galaxy/compare/ec83035c2a4c...3221afd8d49f **NOTE:** This service 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] 504e03: WIP historyimport fixes
by GitHub 18 May '18

18 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 504e030291d3f7bfb49f62888551d68a43357318 https://github.com/galaxyproject/galaxy/commit/504e030291d3f7bfb49f62888551… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M test/selenium_tests/test_workflow_editor.py Log Message: ----------- WIP historyimport fixes Commit: 60a0e1b8cfac183caef799afbc9e6bb5ffcc6c16 https://github.com/galaxyproject/galaxy/commit/60a0e1b8cfac183caef799afbc9e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue Log Message: ----------- Fix history import form error display, also bs-vue it. Commit: 6bfc4edc6909c7d4b1949d1aeda657864b76d689 https://github.com/galaxyproject/galaxy/commit/6bfc4edc6909c7d4b1949d1aeda6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue Log Message: ----------- Use old-style message -- for now, argh. fix visibility, remove custom style and redundant placeholders. Commit: e920280692e02993e2bd1d5a8b3ec9bd0b351a5f https://github.com/galaxyproject/galaxy/commit/e920280692e02993e2bd1d5a8b3e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue Log Message: ----------- Re-enable commented out redir code from debugging Commit: c4ad8ab57c3d8c8e8c2453375292ca405baf2e6a https://github.com/galaxyproject/galaxy/commit/c4ad8ab57c3d8c8e8c2453375292… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue Log Message: ----------- Fix response message relay in history archive import; axios uses the response.data object here. Commit: e814b75dc27db739dcfe7d3b43f9c17b6510c1eb https://github.com/galaxyproject/galaxy/commit/e814b75dc27db739dcfe7d3b43f9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue Log Message: ----------- Floating this card approach for dialogs like this -- if we design components for display in cards, they'll be portable and usable everywhere. Commit: 24c32a3180b9214fa1bc55569a069dcbe5f7a4a3 https://github.com/galaxyproject/galaxy/commit/24c32a3180b9214fa1bc55569a06… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #6153 from dannon/history_import_safari_fix History import safari fix, overhaul Compare: https://github.com/galaxyproject/galaxy/compare/22774f4f2aa9...24c32a3180b9 **NOTE:** This service 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] 3208a6: Fix fetching collection state for static histories...
by GitHub 17 May '18

17 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 3208a685aab130477171c8638673aa77c99495bc https://github.com/galaxyproject/galaxy/commit/3208a685aab130477171c8638673… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/job-states-model.js Log Message: ----------- Fix fetching collection state for static histories. See comment in code. Commit: 02fa00185aa704266cafa7a3fade90a800cada80 https://github.com/galaxyproject/galaxy/commit/02fa00185aa704266cafa7a3fade… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/job-states-model.js Log Message: ----------- Merge pull request #6165 from jmchilton/fix_history_view [18.05] Fix fetching collection state for static histories. Compare: https://github.com/galaxyproject/galaxy/compare/47950b1707b4...02fa00185aa7 **NOTE:** This service 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] b70426: Cleanup in history contents while looking for hist...
by GitHub 17 May '18

17 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b70426cea47c8445efee96cc6bfc34f1cbc791ff https://github.com/galaxyproject/galaxy/commit/b70426cea47c8445efee96cc6bfc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Cleanup in history contents while looking for history name change bug Commit: 72c175bef2286192dee750daa7e8fefa6e7f0d62 https://github.com/galaxyproject/galaxy/commit/72c175bef2286192dee750daa7e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Minor refactoring, drop self usage in history-view-edit Commit: da0e5f637c2b4e31ca36cf11fbc4ec4cf2cf3123 https://github.com/galaxyproject/galaxy/commit/da0e5f637c2b4e31ca36cf11fbc4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M lib/galaxy/managers/histories.py Log Message: ----------- Bugfix: history serializer was not encoding user_id, which (other than leaking an unencoded uid) was causing ownership comparisons to always fail. Commit: 22774f4f2aa9ca06bd6dff7d7919581df6559313 https://github.com/galaxyproject/galaxy/commit/22774f4f2aa9ca06bd6dff7d7919… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M lib/galaxy/managers/histories.py Log Message: ----------- Merge pull request #6159 from dannon/history_rename_bugfix History click-to-rename bugfix Compare: https://github.com/galaxyproject/galaxy/compare/93d83c759d1a...22774f4f2aa9 **NOTE:** This service 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] df6842: Remove the success green on dropdown click; the te...
by GitHub 17 May '18

17 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: df6842a4054de142d6d5926354f81b52a6ec7530 https://github.com/galaxyproject/galaxy/commit/df6842a4054de142d6d5926354f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Remove the success green on dropdown click; the text already toggles to let you know you clicked, and this is much, much less jarring Commit: 4ed11c16b8c7a05eda2089ed528b7b1dca8d79e3 https://github.com/galaxyproject/galaxy/commit/4ed11c16b8c7a05eda2089ed528b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Use defined -dark instead of a flat black Commit: bfa69401ec869f83b8f52b1a1301145c6f551b03 https://github.com/galaxyproject/galaxy/commit/bfa69401ec869f83b8f52b1a1301… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Gold for active text click. Readable. Contrasts. Still indicates a click. Commit: 47950b1707b44b130355e3c2f98d3204be581fa1 https://github.com/galaxyproject/galaxy/commit/47950b1707b44b130355e3c2f98d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6155 from dannon/no-more-green [18.05] Dropdown active color tweaks Compare: https://github.com/galaxyproject/galaxy/compare/10a2e68b82a3...47950b1707b4 **NOTE:** This service 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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