March 2019 - galaxy-commits - lists.galaxyproject.org

The Galaxy-Commits List is going away
by Dave Clements 11 Mar '19

11 Mar '19

Hello all, This will be one of the last message posted to the Galaxy-Commits mailing list. This list was created almost 9 years ago as a way for the community to easily find out what was happening with the Galaxy code base. A lot has happened in 9 years, including 1) moving to GitHub <https://github.com/galaxyproject>, and 2) a proliferation of related repositories. A single "commits" list no longer makes sense and is no longer necessary, as it's easy to set up email alerts for commits in GitHub. To continue receiving email alerts about commits: 1) Log in to GitHub. 2) Navigate to the home page for the repo you are interested in, say https://github.com/galaxyproject/galaxy 3) Select "Watching" from the "Watch" pulldown menu at the top of the page. 4) Go to your account's settings -> Notifications page and tell GitHub how you want to get your notifications. Thanks and see you in GitHub, Dave C -- https://galaxyproject.org/ https://usegalaxy.org/

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[galaxyproject/galaxy] 88fd52: Test PJA actions
by Dannon 11 Mar '19

11 Mar '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 88fd52a4bb55641fe44a630ae5702adcc630f3a5 https://github.com/galaxyproject/galaxy/commit/88fd52a4bb55641fe44a630ae570… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test PJA actions The rename action works, the hide action fails. Building this to fix https://github.com/galaxyproject/galaxy/issues/7473. Commit: f26a1177b871c65dd14258024cc1ef65d4e7a8c9 https://github.com/galaxyproject/galaxy/commit/f26a1177b871c65dd14258024cc1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix delayed post jobs actions for DatabaseOperationTools Commit: dc232273781bc96a3cda8b4f83245ae7e603fa01 https://github.com/galaxyproject/galaxy/commit/dc232273781bc96a3cda8b4f8324… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M test/api/test_workflows.py M test/base/populators.py Log Message: ----------- Add tests for delete_intermediate and change_datatype PJAs `change_datatype` wasn't part of gxformat2, so this also requires a new release of gxformat2 with https://github.com/jmchilton/gxformat2/pull/7 Commit: 4cceb67d62dbae06dd6726b0db32e1d757505c3c https://github.com/galaxyproject/galaxy/commit/4cceb67d62dbae06dd6726b0db32… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Fix ChangeDatatype action for collection output Commit: 34725f61ac61dcf1366ec20de857fe7d67e9f0b3 https://github.com/galaxyproject/galaxy/commit/34725f61ac61dcf1366ec20de857… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Consolidate hiding HDAs in DatabaseOperation tools This fixes dataset being added to histories when the source HDA is visible. Commit: df8a4dcf16c60f323aa11001a31079345c4803f5 https://github.com/galaxyproject/galaxy/commit/df8a4dcf16c60f323aa11001a310… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py Log Message: ----------- Fix ChangeDatatypeAction for collections Commit: 5522360953f8d578792cf2fd681db007a97a8de5 https://github.com/galaxyproject/galaxy/commit/5522360953f8d578792cf2fd681d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update to gxformat2 with change_datatype action Commit: de7732f2777b63f02ac4cc31213831813421cc8b https://github.com/galaxyproject/galaxy/commit/de7732f2777b63f02ac4cc312138… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/populators.py Log Message: ----------- Merge pull request #7511 from mvdbeek/backport_pja_fixes [19.01] Backport Fix post job actions for Database Operation tools, implement change_datatype for collection output Compare: https://github.com/galaxyproject/galaxy/compare/aef53f6cde6f...de7732f2777b

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[galaxyproject/galaxy] 75ae68: remove biostar integrations
by Dannon 11 Mar '19

11 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 75ae68693fb1c0669de8a48df4ae64f9c45e0124 https://github.com/galaxyproject/galaxy/commit/75ae68693fb1c0669de8a48df4ae… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M config/error_report.yml.sample M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/tools/__init__.py R lib/galaxy/tools/error_reports/plugins/biostars.py R lib/galaxy/util/biostar.py M lib/galaxy/webapps/galaxy/config_schema.yml R lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/config.py R templates/webapps/galaxy/biostar/post_redirect.mako M templates/webapps/galaxy/galaxy.masthead.mako M test/functional/webhooks/masthead_test/config.yml Log Message: ----------- remove biostar integrations we stopped using it and this will lower our maintenance burden Commit: 5d90d78d2c2a57a62dd692849c4fc1847d4ac981 https://github.com/galaxyproject/galaxy/commit/5d90d78d2c2a57a62dd692849c4f… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M config/error_report.yml.sample M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/tools/__init__.py R lib/galaxy/tools/error_reports/plugins/biostars.py R lib/galaxy/util/biostar.py M lib/galaxy/webapps/galaxy/config_schema.yml R lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/config.py R templates/webapps/galaxy/biostar/post_redirect.mako M templates/webapps/galaxy/galaxy.masthead.mako M test/functional/webhooks/masthead_test/config.yml Log Message: ----------- Merge pull request #7510 from martenson/rip-biostar remove biostar integrations Compare: https://github.com/galaxyproject/galaxy/compare/cc62d06899b1...5d90d78d2c2a

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[galaxyproject/galaxy] 34dcc2: Test PJA actions
by John Chilton 11 Mar '19

11 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 34dcc2458ef5f1b6f51aae899d47b3708d5c5811 https://github.com/galaxyproject/galaxy/commit/34dcc2458ef5f1b6f51aae899d47… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test PJA actions The rename action works, the hide action fails. Building this to fix https://github.com/galaxyproject/galaxy/issues/7473. Commit: 0951324aef6935104e17a14f9e0fe21f3d29262b https://github.com/galaxyproject/galaxy/commit/0951324aef6935104e17a14f9e0f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix delayed post jobs actions for DatabaseOperationTools Commit: 62d8f2d5dfbee3b3092039902cced90b8d08ed40 https://github.com/galaxyproject/galaxy/commit/62d8f2d5dfbee3b3092039902cce… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M test/api/test_workflows.py M test/base/populators.py Log Message: ----------- Add tests for delete_intermediate and change_datatype PJAs `change_datatype` wasn't part of gxformat2, so this also requires a new release of gxformat2 with https://github.com/jmchilton/gxformat2/pull/7 Commit: 54adb6e73a193291dc27c9ed9a0dc24012c305ff https://github.com/galaxyproject/galaxy/commit/54adb6e73a193291dc27c9ed9a0d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Fix ChangeDatatype action for collection output Commit: 199468e920a409cb6a7dbb5ae40c3d7c3dd27028 https://github.com/galaxyproject/galaxy/commit/199468e920a409cb6a7dbb5ae40c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Consolidate hiding HDAs in DatabaseOperation tools This fixes dataset being added to histories when the source HDA is visible. Commit: 377bffd3aedd2a98c40a16b9ebbff95902cb19dc https://github.com/galaxyproject/galaxy/commit/377bffd3aedd2a98c40a16b9ebbf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py Log Message: ----------- Fix ChangeDatatypeAction for collections Commit: 48c303365c5d214cff823138a3ef510afe38350f https://github.com/galaxyproject/galaxy/commit/48c303365c5d214cff823138a3ef… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update to gxformat2 with change_datatype action Commit: cc62d06899b161645e7bf59a3ea3762ec6c2dfbb https://github.com/galaxyproject/galaxy/commit/cc62d06899b161645e7bf59a3ea3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/populators.py Log Message: ----------- Merge pull request #7480 from mvdbeek/fix_build_list_pjas Fix post job actions for Database Operation tools, implement change_datatype for collection output Compare: https://github.com/galaxyproject/galaxy/compare/8ae44cd8cb87...cc62d06899b1

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[galaxyproject/galaxy] c491b5: Add Globus config to PSA authnz backend.
by Martin Cech 11 Mar '19

11 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c491b5ea4e0d31ed19eed6f208c72bf1a7dc75f3 https://github.com/galaxyproject/galaxy/commit/c491b5ea4e0d31ed19eed6f208c7… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add Globus config to PSA authnz backend. Commit: 157c14088c28ac6ed0634de2a1355e6a983537b2 https://github.com/galaxyproject/galaxy/commit/157c14088c28ac6ed0634de2a135… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Make idp name matching generic, read from a dict of supported backends. Commit: c148606a4243d231bc1d0d69b7479f04122d8b72 https://github.com/galaxyproject/galaxy/commit/c148606a4243d231bc1d0d69b747… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Make idp setup generic. Commit: 686aa18a303c80b862331071c7824c7eb22e2acb https://github.com/galaxyproject/galaxy/commit/686aa18a303c80b862331071c782… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M config/oidc_backends_config.xml.sample Log Message: ----------- Add Globus to OIDC backends config file. Commit: c6afb31f2247d9f8cb188ccb241d3c900031d80f https://github.com/galaxyproject/galaxy/commit/c6afb31f2247d9f8cb188ccb241d… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M config/oidc_backends_config.xml.sample Log Message: ----------- Add a link to Globus documentaiton page on backend config example. Commit: 6a98f96b9018a99450f3692f92ccb5f47090e092 https://github.com/galaxyproject/galaxy/commit/6a98f96b9018a99450f3692f92cc… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M config/oidc_backends_config.xml.sample M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add Elixir backend. Commit: 38a0733b799dd60689ad3071b251196607cc0f2a https://github.com/galaxyproject/galaxy/commit/38a0733b799dd60689ad3071b251… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M config/oidc_backends_config.xml.sample M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add PixelPin backend. Commit: 61efb8c838c6c14535b73457e7e951b3a77ebf3f https://github.com/galaxyproject/galaxy/commit/61efb8c838c6c14535b73457e7e9… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt Log Message: ----------- Update PSA version to 3.1.0 and run `make update-dependencies`. Commit: e101d14230df11ae3acedc92c1a27775ae9cac8f https://github.com/galaxyproject/galaxy/commit/e101d14230df11ae3acedc92c1a2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- More dep updates Commit: 06dd2f8bae88230bddacff4318ff83a405352be8 https://github.com/galaxyproject/galaxy/commit/06dd2f8bae88230bddacff4318ff… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Revert sqlalchemy version increment, since it breaks all the tests. Commit: 8e56a53a7bfe5f93618c9d8e388de41f0640fb8a https://github.com/galaxyproject/galaxy/commit/8e56a53a7bfe5f93618c9d8e388d… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M config/oidc_backends_config.xml.sample M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Drop support to Elixir IdP per missing ID token in authn response. Commit: 81fbfdac4aba04a37c439eb373b0b62e38ca38e4 https://github.com/galaxyproject/galaxy/commit/81fbfdac4aba04a37c439eb373b0… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M config/oidc_backends_config.xml.sample M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Drop support for PixelPin IdP. Commit: 8ae44cd8cb87aa0b3d68c149472e76f7d07e750b https://github.com/galaxyproject/galaxy/commit/8ae44cd8cb87aa0b3d68c149472e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M config/oidc_backends_config.xml.sample M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt Log Message: ----------- Merge pull request #7463 from VJalili/upgrade_psa_2 Update to PSA 3.1 and support login with Globus identity Compare: https://github.com/galaxyproject/galaxy/compare/1ca256aaba84...8ae44cd8cb87

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[galaxyproject/usegalaxy-playbook] 0982f6: Standardize galaxy-bugs address format.
by Nate Coraor 11 Mar '19

11 Mar '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0982f6ceafdae5db7bbdf734e3ecf25e06f6f707 https://github.com/galaxyproject/usegalaxy-playbook/commit/0982f6ceafdae5db… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M env/common/files/galaxy/error/413/index.html M env/common/files/galaxy/error/502/index.shtml M env/main/group_vars/galaxyservers/vars.yml M env/test/group_vars/galaxyservers/vars.yml M env/test/group_vars/galaxywebservers.yml Log Message: ----------- Standardize galaxy-bugs address format.

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[galaxyproject/galaxy] 98a189: Fix warning message formatting in sharing controller
by Nicola Soranzo 11 Mar '19

11 Mar '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 98a189ceff8e0fd329acfbb4fdec585d85317e95 https://github.com/galaxyproject/galaxy/commit/98a189ceff8e0fd329acfbb4fdec… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Fix warning message formatting in sharing controller Reported by @erasche in https://github.com/galaxyproject/galaxy/issues/7503#issuecomment-471496500, broken in https://github.com/galaxyproject/galaxy/commit/e4399021520440a8f58e33dbae16… Commit: 7b316215f4d4653c11d5a421002255ed6f43d944 https://github.com/galaxyproject/galaxy/commit/7b316215f4d4653c11d5a4210022… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #7504 from mvdbeek/logging_fix [18.09] Fix warning message formatting in sharing controller Compare: https://github.com/galaxyproject/galaxy/compare/8e125b769879...7b316215f4d4

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[galaxyproject/galaxy] 1d0e4b: New, portable metadata generation.
by John Chilton 11 Mar '19

11 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1d0e4bcb2cd4eb47ef0a5c1d6027f25547292b06 https://github.com/galaxyproject/galaxy/commit/1d0e4bcb2cd4eb47ef0a5c1d6027… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/metadata/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy_ext/metadata/set_metadata.py M test/unit/tools/test_metadata.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- New, portable metadata generation. Variant of external metadata generation that doesn't use command-line arguments or absolute paths and simply takes operates on the current, job working directory and knows what to do. - Uses relative paths allowing the directory to be staged elsewhere via Pulsar, Condor, or Docker for instance. - Avoids DB objects for hard-coded paths making everything more robust. - Avoids huge command-lines which for huge collection reduction jobs might hit system limits for command-line length. - Uses JSON dicts to communicate parameters - meaning we can avoid awkward argument parsing as this evolves (see old max_metadata_value_size handling in set_metadata.py for instance). - Uses output names instead of database IDs to key files - so file naming is consistent and human readable. Commit: 17cb35bc25b2b7a9338d23d65d3cbaa8870c93bb https://github.com/galaxyproject/galaxy/commit/17cb35bc25b2b7a9338d23d65d3c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy/tools/provided_metadata.py A lib/galaxy_ext/metadata/_provided_metadata.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Use ToolProvidedMetadata abstraction in set_metadata. There is are somethings that happen in set_metadata.py that assume the old style galaxy.json. This sets the stage for proper external metadata collection of newer style galaxy.json files. Commit: 395380fc66c76dbbc49ef8f99792c17c23e5e3ba https://github.com/galaxyproject/galaxy/commit/395380fc66c76dbbc49ef8f99792… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy/tools/provided_metadata.py Log Message: ----------- Fix: Handle galaxy.json entries without dataset_id in galaxy.json. Commit: e7676868162497df4cdf35f86bc4afa31c2f8267 https://github.com/galaxyproject/galaxy/commit/e7676868162497df4cdf35f86bc4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy/metadata/__init__.py Log Message: ----------- Better I/O in metadata package. Commit: f0912eb4040185df5a11cff1c7e1865a6b18f33f https://github.com/galaxyproject/galaxy/commit/f0912eb4040185df5a11cff1c7e1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/metadata/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Fix set_metadata executing from wrong directory when using tool. Commit: 1ca256aaba84fb101f144c67447363435ec44622 https://github.com/galaxyproject/galaxy/commit/1ca256aaba84fb101f144c674473… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/config.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/jobs/__init__.py M lib/galaxy/metadata/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/provided_metadata.py A lib/galaxy_ext/metadata/_provided_metadata.py M lib/galaxy_ext/metadata/set_metadata.py M test/unit/tools/test_metadata.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #7470 from jmchilton/portable_metadata Implement portable metadata generation. Compare: https://github.com/galaxyproject/galaxy/compare/417292b5013b...1ca256aaba84

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[galaxyproject/galaxy] 1a636c: Fix HiddenParameter use
by Nicola Soranzo 10 Mar '19

10 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a636c376fe7fbdaa0ead866989ddfbf0ed7e943 https://github.com/galaxyproject/galaxy/commit/1a636c376fe7fbdaa0ead866989d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix HiddenParameter use Broken in https://github.com/galaxyproject/galaxy/commit/dd8d74f364770a1272555a3753f5… Fixes https://github.com/galaxyproject/galaxy/issues/7454 Commit: 76be1263cac3ed5f7954e451693352d7276e69a7 https://github.com/galaxyproject/galaxy/commit/76be1263cac3ed5f7954e4516933… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M test/api/test_workflows.py A test/functional/tools/hidden_param.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test that workflows with hidden params can be run Commit: b5bbdfd89fc64796a2049ffd2f3f4d568afbd7f3 https://github.com/galaxyproject/galaxy/commit/b5bbdfd89fc64796a2049ffd2f3f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M run_tests.sh Log Message: ----------- Also use correct image Commit: 9c711e7efabafbd13c0f35f6ec348a32c3a115dd https://github.com/galaxyproject/galaxy/commit/9c711e7efabafbd13c0f35f6ec34… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/workflow/modules.py M run_tests.sh M test/api/test_workflows.py A test/functional/tools/hidden_param.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #7458 from mvdbeek/fix_broken_hidden_parameter [19.01] Fix hidden parameter use in workflows Commit: c1a9095ad4fa37c5ca729b6f900d4aaca09496cc https://github.com/galaxyproject/galaxy/commit/c1a9095ad4fa37c5ca729b6f900d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restrict loading of JSON files on the server via the workflow API to Galaxy admins Fix https://github.com/galaxyproject/security/issues/29 Commit: 0ab05b3ce69e69f9ea865a9aae596ac5e36ebc71 https://github.com/galaxyproject/galaxy/commit/0ab05b3ce69e69f9ea865a9aae59… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #7499 from nsoranzo/release_18.05_fix_security_29 [18.05] Restrict loading of JSON files on the server via the workflow API to Galaxy admins Commit: 8e125b76987914ae48616cc1d8594b8e94a414cb https://github.com/galaxyproject/galaxy/commit/8e125b76987914ae48616cc1d859… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: aef53f6cde6feaea9443ea341304f966b7847a7e https://github.com/galaxyproject/galaxy/commit/aef53f6cde6feaea9443ea341304… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Commit: 417292b5013b3b6b4d57a15b3567d08288733f9f https://github.com/galaxyproject/galaxy/commit/417292b5013b3b6b4d57a15b3567… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py A test/functional/tools/hidden_param.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d4dadca145d9...417292b5013b

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[galaxyproject/galaxy] c1a909: Restrict loading of JSON files on the server via t...
by Nicola Soranzo 10 Mar '19

10 Mar '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: c1a9095ad4fa37c5ca729b6f900d4aaca09496cc https://github.com/galaxyproject/galaxy/commit/c1a9095ad4fa37c5ca729b6f900d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restrict loading of JSON files on the server via the workflow API to Galaxy admins Fix https://github.com/galaxyproject/security/issues/29 Commit: 0ab05b3ce69e69f9ea865a9aae596ac5e36ebc71 https://github.com/galaxyproject/galaxy/commit/0ab05b3ce69e69f9ea865a9aae59… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #7499 from nsoranzo/release_18.05_fix_security_29 [18.05] Restrict loading of JSON files on the server via the workflow API to Galaxy admins Commit: 8e125b76987914ae48616cc1d8594b8e94a414cb https://github.com/galaxyproject/galaxy/commit/8e125b76987914ae48616cc1d859… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: aef53f6cde6feaea9443ea341304f966b7847a7e https://github.com/galaxyproject/galaxy/commit/aef53f6cde6feaea9443ea341304… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Compare: https://github.com/galaxyproject/galaxy/compare/9c711e7efaba...aef53f6cde6f

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