- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f56150: Rev subprocess32 dependency - that older version i...
by GitHub 21 May '18

21 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: f56150468984cc96e37fe52cefd33499e5f422b4 https://github.com/galaxyproject/galaxy/commit/f56150468984cc96e37fe52cefd3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Rev subprocess32 dependency - that older version is not compatible with manylinux. https://github.com/google/python-subprocess32/issues/12 Commit: 805854aa6b16eb2b68b6ab5f94b92e84342c2f9e https://github.com/galaxyproject/galaxy/commit/805854aa6b16eb2b68b6ab5f94b9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6183 from jmchilton/subprocess32_rev [18.05] Rev subprocess32 dependency - that older version is not compatible with manylinux. Compare: https://github.com/galaxyproject/galaxy/compare/92ebf285088c...805854aa6b16 **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/usegalaxy-playbook] e2dd20: Increase memory for collection column join
by GitHub 21 May '18

21 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e2dd20a092d32ecec553cfe25dc5e36f33c999aa https://github.com/galaxyproject/usegalaxy-playbook/commit/e2dd20a092d32ece… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Increase memory for collection column join **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/infrastructure-playbook] 98dd77: Switch galaxy06/stats.galaxyproject.org to use sta...
by GitHub 21 May '18

21 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 98dd777605efab54589964d1021e88ba42267b51 https://github.com/galaxyproject/infrastructure-playbook/commit/98dd777605e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M env/tacc/group_vars/statsservers/vars.yml Log Message: ----------- Switch galaxy06/stats.galaxyproject.org to use standard config/data/service layout for influxdb and grafana **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/usegalaxy-playbook] 7dcb6b: Update Main
by GitHub 21 May '18

21 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7dcb6bd67a7685fde19831a77bbdae1d04dcd70f https://github.com/galaxyproject/usegalaxy-playbook/commit/7dcb6bd67a7685fd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main **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] f07ba1: extraneous self
by GitHub 21 May '18

21 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: f07ba172418bdea209481b56b60980d2c9906823 https://github.com/galaxyproject/galaxy/commit/f07ba172418bdea209481b56b609… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- extraneous self Commit: 92ebf285088c744cef588a05b941ca6adf7848ee https://github.com/galaxyproject/galaxy/commit/92ebf285088c744cef588a05b941… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Merge pull request #6184 from erasche/gdpr [18.05] extraneous self causing bug reporter to fail Compare: https://github.com/galaxyproject/galaxy/compare/258c4a4d8fdd...92ebf285088c **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/infrastructure-playbook] 197a16: Add X11 runtime libs for Conda R
by GitHub 21 May '18

21 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 197a16c2ade835b66a0344783f7fd90de4393a63 https://github.com/galaxyproject/infrastructure-playbook/commit/197a16c2ade… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M env/tacc/group_vars/galaxynodes.yml Log Message: ----------- Add X11 runtime libs for Conda R **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/infrastructure-playbook] a49d14: Reenable UnkillableStepTimeout as disabling it was...
by GitHub 21 May '18

21 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a49d1483782a64e390c30f5b2977beccc4687171 https://github.com/galaxyproject/infrastructure-playbook/commit/a49d1483782… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M env/tacc/templates/slurm/slurm.conf.j2 Log Message: ----------- Reenable UnkillableStepTimeout as disabling it was causing lots of node drain **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] 872dbf: adding idat
by GitHub 21 May '18

21 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 872dbfb3c42ec36ffe3c452e164e0dcc2545c3cb https://github.com/galaxyproject/galaxy/commit/872dbfb3c42ec36ffe3c452e164e… Author: Ubuntu <ubuntu(a)ip-172-31-23-81.ec2.internal> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- adding idat Commit: 258c4a4d8fddacba64a5cc7ac634910a4839b371 https://github.com/galaxyproject/galaxy/commit/258c4a4d8fddacba64a5cc7ac634… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6179 from kpbioteam/idat [18.05] add idat datatype Compare: https://github.com/galaxyproject/galaxy/compare/f8fc8232a68d...258c4a4d8fdd **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] c25343: Fix append() for ANY_COLLECTION_TYPE type descript...
by GitHub 19 May '18

19 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: c253436b4a7c646910bdc1f8ce9c2f01fe43f1ff https://github.com/galaxyproject/galaxy/commit/c253436b4a7c646910bdc1f8ce9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Fix append() for ANY_COLLECTION_TYPE type description in WF editor. Append means take a collection type and extend it by the current type - so appending to list to paired -> list:paired for instance. ANY_COLLECTION_TYPE is a representation of incomplete information - it means this type description might be any kind of collection type (the way we use "input" to mean any kind of datatype in the editor). This is really a second order approximation of what a correct solution would be - a first order approximation would somehow represent the result of append being at least of "depth" specified (list:* or *:list instead of * for instance). A not approximation would be to do that but use ANY_COLLECTION_TYPE much less frequently by capturing type_source information and propagating it throughout the workflow properly. But these are harder things to do, this incorrect fix will allow many valid workflows to be editted that currently cannot be so I think it is good. "Fixes" #5205. Commit: f8fc8232a68dd1b0693ff9b007734cfa087cccdf https://github.com/galaxyproject/galaxy/commit/f8fc8232a68dd1b0693ff9b00773… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-19 (Sat, 19 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #6178 from jmchilton/fix_append_for_any_collection_Type [18.05] Fix append() for ANY_COLLECTION_TYPE type description in WF editor. Compare: https://github.com/galaxyproject/galaxy/compare/afc8d0abd81b...f8fc8232a68d **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/usegalaxy-playbook] f4e824: Updated lastz to version 1.3.2
by GitHub 18 May '18

18 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f4e8242ca584f37198ead277fd1fe92c5c50d128 https://github.com/galaxyproject/usegalaxy-playbook/commit/f4e8242ca584f371… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated lastz to version 1.3.2 **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] 2fef59: Fix upload file selector value resetting
by GitHub 18 May '18

18 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2fef59aa46c06aebe42c1f075c2d84a86fc11a30 https://github.com/galaxyproject/galaxy/commit/2fef59aa46c06aebe42c1f075c2d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix upload file selector value resetting Fix Commit: d0cb1d6f3c1c49d690a1b7279c7c1ef30df3593b https://github.com/galaxyproject/galaxy/commit/d0cb1d6f3c1c49d690a1b7279c7c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #6168 from guerler/fix_upload_selector [18.05] Fix upload file selector value resetting Compare: https://github.com/galaxyproject/galaxy/compare/d714dfb2fa36...d0cb1d6f3c1c **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/dev 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: c8ecb0b38dd172a73e0bd5ee86ce80fe83a1007e https://github.com/galaxyproject/galaxy/commit/c8ecb0b38dd172a73e0bd5ee86ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Add sample commentary to the stub in config manage, xref a88e19064a38415d867f4c118dd6938d8e368632 Commit: 6a30fe14f1ac018b424b38cba69827ddbfff186a https://github.com/galaxyproject/galaxy/commit/6a30fe14f1ac018b424b38cba698… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Config rebuild Commit: c6ce1342df0155fa848f551df41f01c016fcc98f https://github.com/galaxyproject/galaxy/commit/c6ce1342df0155fa848f551df41f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py Log Message: ----------- More standard spacing in additional config comments just added. 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 Commit: afc8d0abd81b56b0eb1797e9acca2e574976939b https://github.com/galaxyproject/galaxy/commit/afc8d0abd81b56b0eb1797e9acca… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py Log Message: ----------- Merge pull request #6172 from nsoranzo/release_18.05_backport_virtualenv_config [18.05] Restore config comment Commit: d714dfb2fa36c4ee9c067c85782eff4ae1d86f08 https://github.com/galaxyproject/galaxy/commit/d714dfb2fa36c4ee9c067c85782e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/41e12f0b9d17...d714dfb2fa36 **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] c8ecb0: Add sample commentary to the stub in config manage...
by GitHub 18 May '18

18 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: c8ecb0b38dd172a73e0bd5ee86ce80fe83a1007e https://github.com/galaxyproject/galaxy/commit/c8ecb0b38dd172a73e0bd5ee86ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Add sample commentary to the stub in config manage, xref a88e19064a38415d867f4c118dd6938d8e368632 Commit: 6a30fe14f1ac018b424b38cba69827ddbfff186a https://github.com/galaxyproject/galaxy/commit/6a30fe14f1ac018b424b38cba698… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Config rebuild Commit: c6ce1342df0155fa848f551df41f01c016fcc98f https://github.com/galaxyproject/galaxy/commit/c6ce1342df0155fa848f551df41f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py Log Message: ----------- More standard spacing in additional config comments just added. Commit: afc8d0abd81b56b0eb1797e9acca2e574976939b https://github.com/galaxyproject/galaxy/commit/afc8d0abd81b56b0eb1797e9acca… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py Log Message: ----------- Merge pull request #6172 from nsoranzo/release_18.05_backport_virtualenv_config [18.05] Restore config comment Compare: https://github.com/galaxyproject/galaxy/compare/5489504e9794...afc8d0abd81b **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_18.05 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.

1 0

[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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[galaxyproject/galaxy] fe3799: rename the config option to enable_gdpr_beta
by GitHub 17 May '18

17 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/b488c1d12b77...10a2e68b82a3 **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] a6df95: Backbone model url fixes (urlRoot isn't necessary ...
by GitHub 17 May '18

17 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/7029cb936a9f...b488c1d12b77 **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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