galaxy-commits January 2019

galaxy-commits@lists.galaxyproject.org

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136 discussions

[galaxyproject/galaxy] 63e466: Cleanup some log messages and one import
by Dannon 31 Jan '19

31 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 63e4663cc522d46f1749b08368c811108e73bb0d https://github.com/galaxyproject/galaxy/commit/63e4663cc522d46f1749b08368c8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-31 (Thu, 31 Jan 2019) Changed paths: M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Cleanup some log messages and one import Commit: 498eba2e290c6026e2f65929bc7c796bd730de42 https://github.com/galaxyproject/galaxy/commit/498eba2e290c6026e2f65929bc7c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-31 (Thu, 31 Jan 2019) Changed paths: 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 all dependencies with `make update-dependencies` using pipenv 2018.11.26 . Commit: d5a406cef70029e0e16b27e093ef8576dfe56322 https://github.com/galaxyproject/galaxy/commit/d5a406cef70029e0e16b27e093ef… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-31 (Thu, 31 Jan 2019) Changed paths: M cron/add_manual_builds.py M lib/galaxy/actions/library.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/jobs.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/util/hash_util.py M test/api/test_workflows.py M test/functional/test_toolbox.py M tools/maf/maf_to_bed.py M tools/phenotype_association/senatag.py M tools/stats/gsummary.py Log Message: ----------- Fix errors reported by new flake8 3.7.3 Commit: 8c2066f07ac7bb48c59cf8378e5a852e6fb82a4e https://github.com/galaxyproject/galaxy/commit/8c2066f07ac7bb48c59cf8378e5a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-31 (Thu, 31 Jan 2019) Changed paths: M cron/add_manual_builds.py M lib/galaxy/actions/library.py 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 M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/jobs.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/util/hash_util.py M test/api/test_workflows.py M test/functional/test_toolbox.py M tools/maf/maf_to_bed.py M tools/phenotype_association/senatag.py M tools/stats/gsummary.py Log Message: ----------- Merge pull request #7285 from nsoranzo/update_deps Update all dependencies Compare: https://github.com/galaxyproject/galaxy/compare/ed4f1290e84b...8c2066f07ac7

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[galaxyproject/galaxy] 7061f2: Fix installing tools via tool_id
by Nicola Soranzo 31 Jan '19

31 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7061f2a2af6ae7335b918dc4115ee8170efd7f67 https://github.com/galaxyproject/galaxy/commit/7061f2a2af6ae7335b918dc4115e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-28 (Mon, 28 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/toolshed.py Log Message: ----------- Fix installing tools via tool_id Commit: 6cdca798ef62a85d4fa1a4f402f58521e3c57249 https://github.com/galaxyproject/galaxy/commit/6cdca798ef62a85d4fa1a4f402f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-30 (Wed, 30 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/toolshed.py Log Message: ----------- Merge pull request #7277 from mvdbeek/fix_install_via_tool_id [19.01] Fix installing tools via tool_id Commit: ed4f1290e84b981f35a42ddbf254308ca10f4ad9 https://github.com/galaxyproject/galaxy/commit/ed4f1290e84b981f35a42ddbf254… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-31 (Thu, 31 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/toolshed.py Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6630e6bd1ced...ed4f1290e84b

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[galaxyproject/galaxy] 685af5: Handle subworkflows in view workflow mako
by John Chilton 30 Jan '19

30 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 685af5f7e49d02396c213f355d40f64d706a0691 https://github.com/galaxyproject/galaxy/commit/685af5f7e49d02396c213f355d40… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-28 (Mon, 28 Jan 2019) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Handle subworkflows in view workflow mako Otherwise displaying workflows with subworkflows via the "view" button errors with ``` File 'lib/galaxy/web/framework/middleware/error.py', line 154 in __call__ app_iter = self.application(environ, sr_checker) File '/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File 'lib/galaxy/web/framework/base.py', line 143 in __call__ return self.handle_request(environ, start_response) File 'lib/galaxy/web/framework/base.py', line 222 in handle_request body = method(trans, **kwargs) File 'lib/galaxy/webapps/galaxy/controllers/workflow.py', line 233 in display_by_username_and_slug return self._display(trans, stored_workflow) File 'lib/galaxy/webapps/galaxy/controllers/workflow.py', line 269 in _display user_item_rating=user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings) File 'lib/galaxy/web/framework/webapp.py', line 940 in fill_template_mako return template.render(**data) File '/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/mako/template.py', line 462 in render return runtime._render(self, self.callable_, args, data) File '/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/mako/runtime.py', line 838 in _render **_kwargs_for_callable(callable_, data)) File '/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/mako/runtime.py', line 873 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/mako/runtime.py', line 899 in _exec_template callable_(context, *args, **kwargs) File '/data/users/mvandenb/galaxy/database/template_cache/base/base_panels.mako.py', line 122 in render_body __M_writer(unicode(self.center_panel())) File '/data/users/mvandenb/galaxy/database/template_cache/display_base.mako.py', line 152 in render_center_panel __M_writer(unicode(self.render_content())) File '/data/users/mvandenb/galaxy/database/template_cache/display_base.mako.py', line 116 in render_render_content __M_writer(unicode(self.render_item( item, item_data ))) File '/data/users/mvandenb/galaxy/database/template_cache/workflow/display.mako.py', line 123 in render_render_item __M_writer(unicode(do_inputs( module.get_runtime_inputs(), step.state.inputs, "", step ))) File '/data/users/mvandenb/galaxy/database/template_cache/workflow/display.mako.py', line 78 in do_inputs return render_do_inputs(context,inputs,values,prefix,step,other_values) File '/data/users/mvandenb/galaxy/database/template_cache/workflow/display.mako.py', line 153 in render_do_inputs if input.type == "repeat": AttributeError: 'InputProxy' object has no attribute 'type' ``` Also allows displaying subworkflows as a nested table. Commit: 6630e6bd1ced92724808fbb5bf18069bd97fc0d8 https://github.com/galaxyproject/galaxy/commit/6630e6bd1ced92724808fbb5bf18… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-30 (Wed, 30 Jan 2019) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Merge pull request #7276 from mvdbeek/subworkflow_view Handle subworkflows in view workflow mako Compare: https://github.com/galaxyproject/galaxy/compare/1a61f31ec5fd...6630e6bd1ced

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[galaxyproject/galaxy] 7061f2: Fix installing tools via tool_id
by John Chilton 30 Jan '19

30 Jan '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 7061f2a2af6ae7335b918dc4115ee8170efd7f67 https://github.com/galaxyproject/galaxy/commit/7061f2a2af6ae7335b918dc4115e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-28 (Mon, 28 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/toolshed.py Log Message: ----------- Fix installing tools via tool_id Commit: 6cdca798ef62a85d4fa1a4f402f58521e3c57249 https://github.com/galaxyproject/galaxy/commit/6cdca798ef62a85d4fa1a4f402f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-30 (Wed, 30 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/toolshed.py Log Message: ----------- Merge pull request #7277 from mvdbeek/fix_install_via_tool_id [19.01] Fix installing tools via tool_id Compare: https://github.com/galaxyproject/galaxy/compare/152e0012c7c1...6cdca798ef62

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[galaxyproject/galaxy] 79fe78: Fixes for the cluster documentation
by Dannon 30 Jan '19

30 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 79fe78703705195e06620832053033a49c66e035 https://github.com/galaxyproject/galaxy/commit/79fe78703705195e066208320530… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-30 (Wed, 30 Jan 2019) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Fixes for the cluster documentation Fix https://github.com/galaxyproject/galaxy/issues/5319 Commit: 1a61f31ec5fd0bc25537c78065418361f377a029 https://github.com/galaxyproject/galaxy/commit/1a61f31ec5fd0bc25537c7806541… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-30 (Wed, 30 Jan 2019) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Merge pull request #7281 from nsoranzo/cluster_doc Fixes for the cluster documentation Compare: https://github.com/galaxyproject/galaxy/compare/064f25ed0b36...1a61f31ec5fd

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[galaxyproject/ansible-pulsar]
by erasche 30 Jan '19

30 Jan '19

Branch: refs/tags/0.4.4 Home: https://github.com/galaxyproject/ansible-pulsar

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[galaxyproject/galaxy] 53d2c3: Fix hotdata method access; this still needs a lot ...
by Nicola Soranzo 29 Jan '19

29 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 53d2c3490adb54c73afc4397768f04999184b723 https://github.com/galaxyproject/galaxy/commit/53d2c3490adb54c73afc4397768f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix hotdata method access; this still needs a lot of love/refactoring, but this makes it work again? Commit: 96a25fbe31781f36f4607b374b238adbb5ed11ee https://github.com/galaxyproject/galaxy/commit/96a25fbe31781f36f4607b374b23… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Prefer const, none of these are reassigned. Commit: f132f3ecbc416aeb24d96ff61a674fab7bb98bfa https://github.com/galaxyproject/galaxy/commit/f132f3ecbc416aeb24d96ff61a67… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Restored hotData to computed, but removed unnecessary side-effects Commit: 86eff98fc36f3897d1d201e708ddea89e376b600 https://github.com/galaxyproject/galaxy/commit/86eff98fc36f3897d1d201e708dd… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Removed slice method on non-array property Commit: 800e221c47044b02034a54727727ddadef700bef https://github.com/galaxyproject/galaxy/commit/800e221c47044b02034a54727727… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Removed commented code in RuleCollectionBuilder Commit: 064f25ed0b3676ee2498c2c3021ee2101dcf474f https://github.com/galaxyproject/galaxy/commit/064f25ed0b3676ee2498c2c3021e… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge pull request #7256 from dannon/fix_hotdata_access Fix hotdata method access; Compare: https://github.com/galaxyproject/galaxy/compare/acb256f54a4e...064f25ed0b36

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[galaxyproject/galaxy] f05a3f: Fix flakey history import metadata test
by Nicola Soranzo 29 Jan '19

29 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f05a3f9e5807a7b0a88232932cf29d40600aeb5a https://github.com/galaxyproject/galaxy/commit/f05a3f9e5807a7b0a88232932cf2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M test/api/test_histories.py Log Message: ----------- Fix flakey history import metadata test We need to wait for the BAM dataset to be final before we can export. (At least that solved it locally for me). Commit: acb256f54a4e14a4d1e00babd728588b9612ab79 https://github.com/galaxyproject/galaxy/commit/acb256f54a4e14a4d1e00babd728… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M test/api/test_histories.py Log Message: ----------- Merge pull request #7279 from mvdbeek/fix_history_import_test Fix flakey history import metadata test Compare: https://github.com/galaxyproject/galaxy/compare/d9dd2e3cf1ca...acb256f54a4e

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[galaxyproject/galaxy] 12128a: Fix _.escape typo in toolshed group detail view
by Nicola Soranzo 29 Jan '19

29 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 12128ad49d763ad725e5861ff0e1cd5aaeb5461e https://github.com/galaxyproject/galaxy/commit/12128ad49d763ad725e5861ff0e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M client/galaxy/scripts/toolshed/groups/group-detail-view.js Log Message: ----------- Fix _.escape typo in toolshed group detail view Commit: 8c93a914d86071968075a551ed307633ea68fbff https://github.com/galaxyproject/galaxy/commit/8c93a914d86071968075a551ed30… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M client/galaxy/scripts/toolshed/groups/group-detail-view.js Log Message: ----------- Merge pull request #7267 from dannon/toolshed-roup-detail-view-typo [19.01] Fix _.escape typo in toolshed group detail view Commit: d83db6a53796137c8ccc96efe3b40f3f3f88f694 https://github.com/galaxyproject/galaxy/commit/d83db6a53796137c8ccc96efe3b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-27 (Sun, 27 Jan 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Stop with tool migrations by default, they are not needed in modern Galaxies... ... and even problematic in some ways. Commit: c8b3d5e4c415514ef626b2009791476d51f9cf9b https://github.com/galaxyproject/galaxy/commit/c8b3d5e4c415514ef626b2009791… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #7275 from jmchilton/1901_migrate_tools [18.09] Stop tool migrations checking by default... Commit: 152e0012c7c1cb037894b1b32ee040b619642863 https://github.com/galaxyproject/galaxy/commit/152e0012c7c1cb037894b1b32ee0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Commit: d9dd2e3cf1ca8b50be1d17f0ee8218d9083555db https://github.com/galaxyproject/galaxy/commit/d9dd2e3cf1ca8b50be1d17f0ee82… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M client/galaxy/scripts/toolshed/groups/group-detail-view.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/884c7962ce48...d9dd2e3cf1ca

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[galaxyproject/galaxy] d83db6: Stop with tool migrations by default, they are not...
by Nicola Soranzo 29 Jan '19

29 Jan '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: d83db6a53796137c8ccc96efe3b40f3f3f88f694 https://github.com/galaxyproject/galaxy/commit/d83db6a53796137c8ccc96efe3b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-27 (Sun, 27 Jan 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Stop with tool migrations by default, they are not needed in modern Galaxies... ... and even problematic in some ways. Commit: c8b3d5e4c415514ef626b2009791476d51f9cf9b https://github.com/galaxyproject/galaxy/commit/c8b3d5e4c415514ef626b2009791… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #7275 from jmchilton/1901_migrate_tools [18.09] Stop tool migrations checking by default... Commit: 152e0012c7c1cb037894b1b32ee040b619642863 https://github.com/galaxyproject/galaxy/commit/152e0012c7c1cb037894b1b32ee0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Compare: https://github.com/galaxyproject/galaxy/compare/8c93a914d860...152e0012c7c1

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galaxy-commits January 2019