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December 2017
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- 85 discussions
[galaxyproject/galaxy] 18221a: paster.pid/log to galaxy.pid/log reference update
by GitHub 15 Dec '17
by GitHub 15 Dec '17
15 Dec '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 18221ae931b22187a5978bd89222a8e84ed400f0
https://github.com/galaxyproject/galaxy/commit/18221ae931b22187a5978bd89222…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-12-15 (Fri, 15 Dec 2017)
Changed paths:
M .ci/first_startup.sh
M contrib/galaxy.fedora-init
M doc/source/admin/production.md
M scripts/summarize_timings.py
Log Message:
-----------
paster.pid/log to galaxy.pid/log reference update
Fix errors in `first_startup` jobs:
https://travis-ci.org/galaxyproject/galaxy/jobs/316342622#L1029
Introduced in https://github.com/galaxyproject/galaxy/pull/4475
Commit: 7e7dc249ab93e66e405abf830782bcf78c0788c5
https://github.com/galaxyproject/galaxy/commit/7e7dc249ab93e66e405abf830782…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-15 (Fri, 15 Dec 2017)
Changed paths:
M .ci/first_startup.sh
M contrib/galaxy.fedora-init
M doc/source/admin/production.md
M scripts/summarize_timings.py
Log Message:
-----------
Merge pull request #5226 from nsoranzo/fix_paster.log_pid
paster.pid/log to galaxy.pid/log reference update
Compare: https://github.com/galaxyproject/galaxy/compare/5b6eaac4a06c...7e7dc249ab93
1
0
15 Dec '17
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: 710177f3983d5e66b11c329f699079f67667329c
https://github.com/galaxyproject/galaxy/commit/710177f3983d5e66b11c329f6990…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M test/api/test_tools.py
Log Message:
-----------
Add API tests for history uploads from URL
Commit: a1f399c451715424dcd8d1bc9d9ec804e44de24d
https://github.com/galaxyproject/galaxy/commit/a1f399c451715424dcd8d1bc9d9e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Read in stderr form galaxy.json
before checking whether stderr and exit code combination should result in a
failed job. This should fix https://github.com/galaxyproject/galaxy/issues/5214.
Commit: 3d2adcd1f310b94d0d6f6e37e71d1ee74da2fb3d
https://github.com/galaxyproject/galaxy/commit/3d2adcd1f310b94d0d6f6e37e71d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Restrict reading tool provided metadata to tools that actually provide metadata
Commit: 62a3ff3562c5b9c534794c2d0bb6320de7747135
https://github.com/galaxyproject/galaxy/commit/62a3ff3562c5b9c534794c2d0bb6…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M test/integration/test_upload_configuration_options.py
Log Message:
-----------
Do not assert dataset state in test_gzipped_html_content_blocked_by_default test
Commit: 9ee2a7d4577a715137edcf33fd2b0a474a7a8b8d
https://github.com/galaxyproject/galaxy/commit/9ee2a7d4577a715137edcf33fd2b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-15 (Fri, 15 Dec 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Adjust stderr collection to (Legacy-)ToolProvidedMetadata
Commit: b39772011a717dc7c70f1e05dd581b427e33a521
https://github.com/galaxyproject/galaxy/commit/b39772011a717dc7c70f1e05dd58…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-15 (Fri, 15 Dec 2017)
Changed paths:
M test/base/populators.py
Log Message:
-----------
Optionally allow dataset populators to fail
Commit: 121285b40be5d7233af33b40045a9c2ffb5a9c46
https://github.com/galaxyproject/galaxy/commit/121285b40be5d7233af33b40045a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-15 (Fri, 15 Dec 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/parameters/output_collect.py
M tools/data_source/upload.py
Log Message:
-----------
Let ToolProvidedMetadata interface more directly decide if it has failed outputs.
I like this better for three reasons:
- Since usually it is scripts producing this JSON - we have the most control at that point for determining the failure and we don't have to deal with an artificial dependency between the tool's stdio and the output.
- At some point we could potentially allow some datasets to be ok now even though the job fails.
- It is a cleaner interface at the Python level between job finish and output collection IMO (no need for isinstance checking).
Commit: d52802d7962c3006b7fe91f43a9d21721187f27c
https://github.com/galaxyproject/galaxy/commit/d52802d7962c3006b7fe91f43a9d…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-12-15 (Fri, 15 Dec 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/parameters/output_collect.py
M tools/data_source/upload.py
Log Message:
-----------
Merge pull request #6 from jmchilton/fail_if_galaxy_json_tools_write_to_stderr
Let ToolProvidedMetadata interface more directly decide if it has failed outputs.
Commit: 3f6c45578e2c4e99fa725054c829e03a9c409a1b
https://github.com/galaxyproject/galaxy/commit/3f6c45578e2c4e99fa725054c829…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-15 (Fri, 15 Dec 2017)
Changed paths:
M test/api/test_tools.py
Log Message:
-----------
Fix dataset spelling (thx @nsoranzo)
Commit: 44635eae1dc1aeb511f3cf9c6006aff4219de841
https://github.com/galaxyproject/galaxy/commit/44635eae1dc1aeb511f3cf9c6006…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-15 (Fri, 15 Dec 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/parameters/output_collect.py
M test/api/test_tools.py
M test/base/populators.py
M test/integration/test_upload_configuration_options.py
M tools/data_source/upload.py
Log Message:
-----------
Merge pull request #5217 from mvdbeek/fail_if_galaxy_json_tools_write_to_stderr
[17.09] Fail job if tools that use galaxy.json write to stderr
Compare: https://github.com/galaxyproject/galaxy/compare/42c572f34469...44635eae1dc1
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6f722861cfd4c36f93348048fe6e6c83305fcc9f
https://github.com/galaxyproject/galaxy/commit/6f722861cfd4c36f93348048fe6e…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2017-12-15 (Fri, 15 Dec 2017)
Changed paths:
A .ci/check_py3_compatibility.sh
M contrib/nagios/check_galaxy.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/util/biostar.py
M test/base/driver_util.py
M test/functional/webhooks/phdcomics/helper/__init__.py
Log Message:
-----------
Python3: fix moved imports
Add `.ci/check_py3_compatibility.sh` script to find library modules
that have been moved in Python3. Fix errors found by the script.
Commit: 5b6eaac4a06cfcd714dd4b578cdbf3239868ca28
https://github.com/galaxyproject/galaxy/commit/5b6eaac4a06cfcd714dd4b578cdb…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-15 (Fri, 15 Dec 2017)
Changed paths:
A .ci/check_py3_compatibility.sh
M contrib/nagios/check_galaxy.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/util/biostar.py
M test/base/driver_util.py
M test/functional/webhooks/phdcomics/helper/__init__.py
Log Message:
-----------
Merge pull request #5221 from nsoranzo/python3
Python3: fix moved imports
Compare: https://github.com/galaxyproject/galaxy/compare/ad0459d81840...5b6eaac4a06c
1
0
[galaxyproject/galaxy] d1be0a: Allow shells with different parameters to co-exist
by GitHub 15 Dec '17
by GitHub 15 Dec '17
15 Dec '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d1be0a20eded8a31d5c514fcc7e370a96d0a01e9
https://github.com/galaxyproject/galaxy/commit/d1be0a20eded8a31d5c514fcc7e3…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-15 (Fri, 15 Dec 2017)
Changed paths:
M lib/galaxy/jobs/runners/util/cli/__init__.py
Log Message:
-----------
Allow shells with different parameters to co-exist
Commit: 86d9b64ec88a601f51607f09b4363cfe02388328
https://github.com/galaxyproject/galaxy/commit/86d9b64ec88a601f51607f09b436…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-15 (Fri, 15 Dec 2017)
Changed paths:
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
Log Message:
-----------
Use absolute import for Bunch
Commit: ad0459d81840464a03730f1cad90a860416e51c4
https://github.com/galaxyproject/galaxy/commit/ad0459d81840464a03730f1cad90…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-15 (Fri, 15 Dec 2017)
Changed paths:
M lib/galaxy/jobs/runners/util/cli/__init__.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
Log Message:
-----------
Merge pull request #5223 from mvdbeek/fix_second_submit_host
Allow shell plugins with different parameters to co-exist
Compare: https://github.com/galaxyproject/galaxy/compare/0d8520fe2df1...ad0459d81840
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: ab4db8925cc895e90972de8b22f1919d25423a12
https://github.com/galaxyproject/galaxy/commit/ab4db8925cc895e90972de8b22f1…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
A client/galaxy/scripts/components/admin/base-grid.vue
A client/galaxy/scripts/components/admin/data-manager-grid.vue
A client/galaxy/scripts/components/admin/data-tables-grid.vue
A client/galaxy/scripts/components/admin/data-tables.vue
A client/galaxy/scripts/components/message.vue
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
Log Message:
-----------
rewrite Admin/DataTables with Vue
Commit: 4516958e9d56ae78fbb606dbeb7664f57cf242b6
https://github.com/galaxyproject/galaxy/commit/4516958e9d56ae78fbb606dbeb76…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
Log Message:
-----------
Minor formatting.
Commit: 44a1c0bcbcf51dff72d3132f36e2ab106a121ad0
https://github.com/galaxyproject/galaxy/commit/44a1c0bcbcf51dff72d3132f36e2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
A client/galaxy/scripts/components/Message.vue
A client/galaxy/scripts/components/admin/BaseGrid.vue
A client/galaxy/scripts/components/admin/DataManagerGrid.vue
A client/galaxy/scripts/components/admin/DataTables.vue
A client/galaxy/scripts/components/admin/DataTablesGrid.vue
R client/galaxy/scripts/components/admin/base-grid.vue
R client/galaxy/scripts/components/admin/data-manager-grid.vue
R client/galaxy/scripts/components/admin/data-tables-grid.vue
R client/galaxy/scripts/components/admin/data-tables.vue
R client/galaxy/scripts/components/message.vue
Log Message:
-----------
Rename new .vue components.
Commit: fe8c009f48d9ed39bd8a7af41d26dc61b1219717
https://github.com/galaxyproject/galaxy/commit/fe8c009f48d9ed39bd8a7af41d26…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
R client/galaxy/scripts/components/UserAPIKeys.vue
A client/galaxy/scripts/components/admin/UserAPIKeys.vue
Log Message:
-----------
Move UserAPIKeys to components/admin
Commit: 0e13c14e9ebca17c385f09df977cb58653be424e
https://github.com/galaxyproject/galaxy/commit/0e13c14e9ebca17c385f09df977c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-11 (Mon, 11 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/panels/tool-panel.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/onload.js
M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample
M config/plugins/webhooks/demo/tour_generator/static/script.js
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/cram_to_bam.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/set_metadata_tool.xml
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/test/1.bam
A lib/galaxy/datatypes/test/1.vcf
A lib/galaxy/datatypes/test/1.vcf.gz
A lib/galaxy/datatypes/test/2.cram
A lib/galaxy/datatypes/test/2.shuffled.bam
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M static/scripts/bundled/adminToolshed.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/library.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/masthead.bundled.js
M static/scripts/bundled/viz.bundled.js
M static/scripts/bundled/workflow.bundled.js
A static/scripts/libs/bibtex.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/workflow/workflow-canvas.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/onload.js
M templates/webapps/galaxy/workflow/editor.mako
A test/integration/resubmission_dynamic_job_conf.xml
M test/integration/resubmission_rules/rules.py
M test/integration/test_job_resubmission.py
A test/unit/datatypes/converters/__init__.py
A test/unit/datatypes/converters/test_interval_to_tabix.py
A test/unit/datatypes/test_bam.py
A test/unit/datatypes/test_bcf.py
A test/unit/datatypes/test_cram.py
A test/unit/datatypes/test_vcf.py
A test/unit/datatypes/util.py
M tools/data_source/upload.xml
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into admin_data_tables_vue
Commit: 203630c509be0eca1fb150bfa680b8c0b152aa11
https://github.com/galaxyproject/galaxy/commit/203630c509be0eca1fb150bfa680…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
R .ci/py3_sources.txt
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/layout/modal.js
A client/galaxy/scripts/legacy/grid/grid-model.js
A client/galaxy/scripts/legacy/grid/grid-template.js
A client/galaxy/scripts/legacy/grid/grid-view.js
M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-shared.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
A client/galaxy/scripts/reports/run_stats.js
R client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/visualization.js
M client/gulpfile.js
M client/package.json
M client/webpack.config.js
M client/yarn.lock
M config/object_store_conf.xml.sample
M config/openid_conf.xml.sample
M config/plugins/webhooks/demo/tour_generator/helper/__init__.py
M lib/galaxy/config.py
M lib/galaxy/containers/docker_swarm_manager.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/runners/chronos.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/metadata.py
M lib/galaxy/objectstore/__init__.py
A lib/galaxy/objectstore/cloud.py
M lib/galaxy/openid/providers.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/util/permutations.py
M lib/galaxy/util/script.py
M lib/galaxy/visualization/data_providers/basic.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/form_builder.py
R lib/galaxy/web/framework/formbuilder.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/middleware/profile.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/security/__init__.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/web/stack/transport.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/authenticate.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/controllers/jobs.py
R lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/workflows.py
A lib/galaxy/webapps/reports/framework/__init__.py
A lib/galaxy/webapps/reports/framework/grids.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/tool_dependency_util.py
R openid/yahoo.xml
M scripts/build_universe_config.py
M scripts/data_libraries/build_lucene_index.py
M scripts/galaxy-main
M scripts/helper.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/microbes/create_bacteria_loc_file.py
M scripts/microbes/create_bacteria_table.py
M scripts/microbes/create_nib_seq_loc_file.py
M scripts/microbes/get_builds_lengths.py
M scripts/microbes/harvest_bacteria.py
M scripts/microbes/ncbi_to_ucsc.py
M scripts/microbes/util.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/paster.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/sync_reports_config.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/adminToolshed.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/galaxy.pages.js
A static/scripts/legacy/grid/grid-model.js
A static/scripts/legacy/grid/grid-template.js
A static/scripts/legacy/grid/grid-view.js
R static/scripts/libs/bibtex.js
R static/scripts/libs/vue.js
M static/scripts/mvc/grid/grid-model.js
M static/scripts/mvc/grid/grid-shared.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/history-list.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/user/user-preferences.js
A static/scripts/reports/run_stats.js
R static/scripts/reports_webapp/run_stats.js
M static/scripts/viz/trackster.js
M static/scripts/viz/visualization.js
M templates/admin/tool_shed_repository/common.mako
M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako
M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
R templates/common/select_template.mako
R templates/common/template_common.mako
M templates/display_common.mako
R templates/form.mako
R templates/grid_base.mako
R templates/grid_base_async.mako
A templates/legacy/grid_base.mako
A templates/legacy/grid_base_async.mako
R templates/panels.mako
M templates/user/index.mako
M templates/user/openid_manage.mako
M templates/user/register.mako
R templates/webapps/reports/grid.mako
M templates/webapps/reports/index.mako
R templates/webapps/reports/requests_per_month_all.mako
R templates/webapps/reports/requests_per_user.mako
R templates/webapps/reports/requests_user_per_month.mako
M templates/webapps/reports/run_stats.mako
M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako
M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako
M templates/webapps/tool_shed/category/grid.mako
M templates/webapps/tool_shed/category/valid_grid.mako
M templates/webapps/tool_shed/common/common.mako
M templates/webapps/tool_shed/common/grid_common.mako
M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/find_tools.mako
M templates/webapps/tool_shed/repository/find_workflows.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M templates/webapps/tool_shed/repository/view_repository.mako
M templates/webapps/tool_shed/repository_review/browse_review.mako
M templates/webapps/tool_shed/repository_review/edit_review.mako
M templates/webapps/tool_shed/repository_review/grid.mako
M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako
M templates/webapps/tool_shed/user/manage_email_alerts.mako
M test/selenium_tests/test_tool_form.py
M test/shed_functional/base/twilltestcase.py
M tools/data_source/upload.py
M tools/genomespace/genomespace_importer.py
M tools/stats/aggregate_scores_in_intervals.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into admin_data_tables_vue
Commit: f9d84f876f1c782b0d1580c23aea3b8465ed826c
https://github.com/galaxyproject/galaxy/commit/f9d84f876f1c782b0d1580c23aea…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/login.bundled.js
Log Message:
-----------
Build client.
Commit: 0d8520fe2df1c24c625d27ee8308b4daff0565dc
https://github.com/galaxyproject/galaxy/commit/0d8520fe2df1c24c625d27ee8308…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
A client/galaxy/scripts/components/Message.vue
R client/galaxy/scripts/components/UserAPIKeys.vue
A client/galaxy/scripts/components/admin/BaseGrid.vue
A client/galaxy/scripts/components/admin/DataManagerGrid.vue
A client/galaxy/scripts/components/admin/DataTables.vue
A client/galaxy/scripts/components/admin/DataTablesGrid.vue
A client/galaxy/scripts/components/admin/UserAPIKeys.vue
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/login.bundled.js
Log Message:
-----------
Merge pull request #5191 from dannon/admin_data_tables_vue
Admin data tables vue
Compare: https://github.com/galaxyproject/galaxy/compare/9aa596df8b68...0d8520fe2df1
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 12ce4e7266b2fb5985e8384eda62ff764930e60e
https://github.com/galaxyproject/galaxy/commit/12ce4e7266b2fb5985e8384eda62…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-09 (Sat, 09 Dec 2017)
Changed paths:
M lib/galaxy/security/__init__.py
Log Message:
-----------
Strip legacy request helpers
Commit: 67cf6944894f71a1408e0b596558039d00306f68
https://github.com/galaxyproject/galaxy/commit/67cf6944894f71a1408e0b596558…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-09 (Sat, 09 Dec 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
Log Message:
-----------
Remove field value helper
Commit: de5d29a6f2e66bf2792c4cde0a7eb2a56e018234
https://github.com/galaxyproject/galaxy/commit/de5d29a6f2e66bf2792c4cde0a7e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-09 (Sat, 09 Dec 2017)
Changed paths:
A lib/galaxy/webapps/reports/framework/grids.py
Log Message:
-----------
Move grid helper to reports
Commit: 7961dcc75ca8f9932b0c1f674347dbaf91190ce6
https://github.com/galaxyproject/galaxy/commit/7961dcc75ca8f9932b0c1f674347…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-09 (Sat, 09 Dec 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Strip mako support from galaxy grid helper
Commit: f600a1dd99998e9415215a045bafd3a47ffb4975
https://github.com/galaxyproject/galaxy/commit/f600a1dd99998e9415215a045baf…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-09 (Sat, 09 Dec 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/root.py
Log Message:
-----------
Remove comma from root controller config dict
Commit: 24cd0893e5f9ad5aab1befa2aa311ba9b597302a
https://github.com/galaxyproject/galaxy/commit/24cd0893e5f9ad5aab1befa2aa31…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-09 (Sat, 09 Dec 2017)
Changed paths:
M lib/galaxy/webapps/reports/controllers/jobs.py
Log Message:
-----------
Link jobs mako to legacy reports module
Commit: a8f59df445cbe36f9cdc281f2fe5aa91a809be5c
https://github.com/galaxyproject/galaxy/commit/a8f59df445cbe36f9cdc281f2fe5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-09 (Sat, 09 Dec 2017)
Changed paths:
M lib/galaxy/webapps/reports/controllers/workflows.py
Log Message:
-----------
Same for worflows grid in reports
Commit: 47578b641fadee5b9dd2d0e65fe06da1dfb5ccfd
https://github.com/galaxyproject/galaxy/commit/47578b641fadee5b9dd2d0e65fe0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-09 (Sat, 09 Dec 2017)
Changed paths:
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
Log Message:
-----------
Redirect for admin toolshed grids
Commit: b726cda3a7abbc49a0532b942fcf6923475d51df
https://github.com/galaxyproject/galaxy/commit/b726cda3a7abbc49a0532b942fcf…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-09 (Sat, 09 Dec 2017)
Changed paths:
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_review_grids.py
Log Message:
-----------
More redirects for toolshed grids
Commit: d4dda34f1214df3389d779e9b835d7557a7499c8
https://github.com/galaxyproject/galaxy/commit/d4dda34f1214df3389d779e9b835…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-09 (Sat, 09 Dec 2017)
Changed paths:
R templates/webapps/reports/grid.mako
Log Message:
-----------
Remove reports default grid mako
Commit: d930b114558814945bd0d5f054904318c2f83b35
https://github.com/galaxyproject/galaxy/commit/d930b114558814945bd0d5f05490…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-09 (Sat, 09 Dec 2017)
Changed paths:
R templates/grid_base.mako
R templates/grid_base_async.mako
A templates/webapps/reports/grid_base.mako
A templates/webapps/reports/grid_base_asyn.mako
Log Message:
-----------
Move grid makos from galaxy to reports app
Commit: 6c974dd81b0f6fb2dec6c65d1a0c3a98983cda5b
https://github.com/galaxyproject/galaxy/commit/6c974dd81b0f6fb2dec6c65d1a0c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-09 (Sat, 09 Dec 2017)
Changed paths:
M templates/webapps/reports/grid_base.mako
R templates/webapps/reports/grid_base_asyn.mako
A templates/webapps/reports/grid_base_async.mako
M templates/webapps/tool_shed/category/grid.mako
M templates/webapps/tool_shed/category/valid_grid.mako
M templates/webapps/tool_shed/common/grid_common.mako
M templates/webapps/tool_shed/repository_review/grid.mako
Log Message:
-----------
Redirect makos to new grid helper location in reports
Commit: d2752dc7b7977f6d887fe7b7c88f53141a2b46bf
https://github.com/galaxyproject/galaxy/commit/d2752dc7b7977f6d887fe7b7c88f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-09 (Sat, 09 Dec 2017)
Changed paths:
A lib/galaxy/webapps/reports/framework/__init__.py
Log Message:
-----------
Add init file to framework module
Commit: 96b9b151aea1236cc754bdabc9c1ebe29f23533c
https://github.com/galaxyproject/galaxy/commit/96b9b151aea1236cc754bdabc9c1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M lib/galaxy/webapps/reports/framework/grids.py
M lib/tool_shed/grids/repository_grids.py
Log Message:
-----------
Remove dict format from legacy grid helper
Commit: c9783de884db11c77c05303fbf36591fba84030a
https://github.com/galaxyproject/galaxy/commit/c9783de884db11c77c05303fbf36…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M lib/galaxy/config.py
R lib/galaxy/webapps/reports/controllers/sample_tracking.py
M templates/webapps/reports/index.mako
R templates/webapps/reports/requests_per_month_all.mako
R templates/webapps/reports/requests_per_user.mako
R templates/webapps/reports/requests_user_per_month.mako
Log Message:
-----------
Merge branch 'clear_sample_tracking' into remove_gridhelper
Commit: 1c8ed722c221de5baaf437085c0b3e84b1ee5689
https://github.com/galaxyproject/galaxy/commit/1c8ed722c221de5baaf437085c0b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
A client/galaxy/scripts/reports/run_stats.js
R client/galaxy/scripts/reports_webapp/run_stats.js
R static/scripts/reports_webapp/run_stats.js
M templates/webapps/reports/grid_base.mako
M templates/webapps/reports/run_stats.mako
Log Message:
-----------
Copy legacy grid code to reports app, redirect imports
Commit: f01a597480909c53ca3fadd3a1e01922ccf430b3
https://github.com/galaxyproject/galaxy/commit/f01a597480909c53ca3fadd3a1e0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M lib/galaxy/webapps/reports/framework/grids.py
M templates/webapps/reports/grid_base_async.mako
M templates/webapps/tool_shed/repository_review/grid.mako
Log Message:
-----------
Fix imports to new mako location
Commit: cbe7cab090398695431acc3b87b11e2c0e66a36b
https://github.com/galaxyproject/galaxy/commit/cbe7cab090398695431acc3b87b1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
Log Message:
-----------
Fix grids used within Galaxy's admin interface
Commit: f2d12a5d699b30532e5a73ea24a0f599ebe42481
https://github.com/galaxyproject/galaxy/commit/f2d12a5d699b30532e5a73ea24a0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Remove async attribute from grid helper
Commit: d12e65652e7eb001b9e274de5ccff2665276ec7c
https://github.com/galaxyproject/galaxy/commit/d12e65652e7eb001b9e274de5ccf…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Remove async attribute from grids
Commit: e32d965034f791756b3107cf6f6055ae0784ffab
https://github.com/galaxyproject/galaxy/commit/e32d965034f791756b3107cf6f60…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Remove async flag handling from grid client
Commit: 134b3cc47fd3f1f94fb896f8c7a4d5843d8f2280
https://github.com/galaxyproject/galaxy/commit/134b3cc47fd3f1f94fb896f8c7a4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/mvc/grid/grid-shared.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/visualization.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/mvc/grid/grid-model.js
M static/scripts/mvc/grid/grid-view.js
Log Message:
-----------
Remove dict format flag from grid client
Commit: efbd02743ed3be506c608662ae6e649f1695d675
https://github.com/galaxyproject/galaxy/commit/efbd02743ed3be506c608662ae6e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Remove dict format from controllers
Commit: 7624ce25ed1f224f3df1423fa30f88e02186012c
https://github.com/galaxyproject/galaxy/commit/7624ce25ed1f224f3df1423fa30f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/viz/trackster.js
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/galaxy.pages.js
M static/scripts/mvc/grid/grid-shared.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/history-list.js
M static/scripts/viz/trackster.js
M static/scripts/viz/visualization.js
Log Message:
-----------
Repack client
Commit: 0f7bc19e30d37acb3a2b7da14972ba6c046d4112
https://github.com/galaxyproject/galaxy/commit/0f7bc19e30d37acb3a2b7da14972…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/galaxy/webapps/reports/framework/grids.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
Log Message:
-----------
Remove unused preserve state attribute from grids
Commit: 1bb521b8ed693775e7e52322737f58c1867f9552
https://github.com/galaxyproject/galaxy/commit/1bb521b8ed693775e7e52322737f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
A client/galaxy/scripts/reports/grid/grid-model.js
A client/galaxy/scripts/reports/grid/grid-template.js
A client/galaxy/scripts/reports/grid/grid-view.js
A static/scripts/reports/grid/grid-model.js
A static/scripts/reports/grid/grid-template.js
A static/scripts/reports/grid/grid-view.js
Log Message:
-----------
Add separated grid client for reports and toolshed
Commit: 52ce746b64457d46ea8f6f7c72d90cb9b851243b
https://github.com/galaxyproject/galaxy/commit/52ce746b64457d46ea8f6f7c72d9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/reports/framework/grids.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
Log Message:
-----------
Remove unused imports, fix import order
Commit: 85fef66272014df1ad944117a017368253253b9f
https://github.com/galaxyproject/galaxy/commit/85fef66272014df1ad944117a017…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Remove unused expose attribute from grid helper
Commit: 73749b748276802c66a112cf181723036fcbef0f
https://github.com/galaxyproject/galaxy/commit/73749b748276802c66a112cf1817…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Remove unused pass_through_operations from grid helper
Commit: ced73c02e8acdebda9523ef6f3054eeea7845dd0
https://github.com/galaxyproject/galaxy/commit/ced73c02e8acdebda9523ef6f305…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M lib/galaxy/webapps/reports/framework/grids.py
Log Message:
-----------
Remove flags from legacy grid helper in reports
Commit: b703a4c525911dd9bf98a847b549417a589ad299
https://github.com/galaxyproject/galaxy/commit/b703a4c525911dd9bf98a847b549…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
R templates/panels.mako
Log Message:
-----------
Remove legacy panels mako for grids
Commit: 6586ce2b6dcab1ac866062e0e4c486daf489afc6
https://github.com/galaxyproject/galaxy/commit/6586ce2b6dcab1ac866062e0e4c4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Remove legacy comment
Commit: 644977c6a538db4829c33a0cd7d0827138a8f8e6
https://github.com/galaxyproject/galaxy/commit/644977c6a538db4829c33a0cd7d0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-11 (Mon, 11 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/cram_to_bam.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/set_metadata_tool.xml
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/test/1.bam
A lib/galaxy/datatypes/test/1.vcf
A lib/galaxy/datatypes/test/1.vcf.gz
A lib/galaxy/datatypes/test/2.cram
A lib/galaxy/datatypes/test/2.shuffled.bam
M lib/galaxy/visualization/data_providers/genome.py
M static/scripts/bundled/extended.bundled.js
M static/scripts/mvc/workflow/workflow-canvas.js
M static/scripts/mvc/workflow/workflow-view.js
A test/unit/datatypes/converters/__init__.py
A test/unit/datatypes/converters/test_interval_to_tabix.py
A test/unit/datatypes/test_bam.py
A test/unit/datatypes/test_bcf.py
A test/unit/datatypes/test_cram.py
A test/unit/datatypes/test_vcf.py
A test/unit/datatypes/util.py
M tools/data_source/upload.xml
Log Message:
-----------
Merge branch 'dev' into remove_gridhelper
Commit: 5c12a9a9bdbf6da453edf0259dcd1eb3400cbaed
https://github.com/galaxyproject/galaxy/commit/5c12a9a9bdbf6da453edf0259dcd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-11 (Mon, 11 Dec 2017)
Log Message:
-----------
Merge branch 'dev' into remove_gridhelper
Commit: 4411189f2589ca366098f93dfc48942b0d2cb7a9
https://github.com/galaxyproject/galaxy/commit/4411189f2589ca366098f93dfc48…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-11 (Mon, 11 Dec 2017)
Log Message:
-----------
Merge branch 'dev' into remove_gridhelper
Commit: 364804f40a176ab5bf2350c85a62bcb72a3cdddc
https://github.com/galaxyproject/galaxy/commit/364804f40a176ab5bf2350c85a62…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-12 (Tue, 12 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/mvc/user/user-preferences.js
M templates/user/openid_manage.mako
Log Message:
-----------
Use client side grid builder for openids table
Commit: 200d8a229a7f51cb7a1a3fbade94fca0412d492e
https://github.com/galaxyproject/galaxy/commit/200d8a229a7f51cb7a1a3fbade94…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-12 (Tue, 12 Dec 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Add error message if openids are disabled
Commit: 241de16c327c6e92d8127382770b8e1d9bdaf715
https://github.com/galaxyproject/galaxy/commit/241de16c327c6e92d8127382770b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-12 (Tue, 12 Dec 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Add delete operation to new openid controller
Commit: f2fd3b1626ee86d228102d9a5368f67b94ae6bbd
https://github.com/galaxyproject/galaxy/commit/f2fd3b1626ee86d228102d9a5368…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-12 (Tue, 12 Dec 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Remove previous delete operation caller
Commit: 7fd3bfb36566ad5d18814c081b136e0e13d688f9
https://github.com/galaxyproject/galaxy/commit/7fd3bfb36566ad5d18814c081b13…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-12 (Tue, 12 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/scripts/bundled/analysis.bundled.js
Log Message:
-----------
Prepare openid creation form
Commit: 8e4ab4012620fc4a28d6baa0eb2ca2bb186ba01b
https://github.com/galaxyproject/galaxy/commit/8e4ab4012620fc4a28d6baa0eb2c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-12 (Tue, 12 Dec 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
M templates/user/openid_manage.mako
Log Message:
-----------
Remove table view from manage mako
Commit: cf7cc197e7fd16bf6fb0619d08b449ca3f051d4c
https://github.com/galaxyproject/galaxy/commit/cf7cc197e7fd16bf6fb0619d08b4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-12 (Tue, 12 Dec 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M templates/user/openid_manage.mako
Log Message:
-----------
Use mako to display add account form
Commit: e942e4b3e2ccea0505dcfaef6d8a11444238485a
https://github.com/galaxyproject/galaxy/commit/e942e4b3e2ccea0505dcfaef6d8a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-12 (Tue, 12 Dec 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Show openid form in center panel
Commit: 87777cf52db6b811a99691a7bd2104decd7eecb5
https://github.com/galaxyproject/galaxy/commit/87777cf52db6b811a99691a7bd21…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-12 (Tue, 12 Dec 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
M templates/user/index.mako
Log Message:
-----------
Fix redirects to new client side route
Commit: 7bc92610a25db4d1480130a3022905eea8f27234
https://github.com/galaxyproject/galaxy/commit/7bc92610a25db4d1480130a30229…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-12 (Tue, 12 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/scripts/bundled/analysis.bundled.js
Log Message:
-----------
Fix delete operation, remove unused route to client form
Commit: 74d4ea8eef26cb83ede4a3f53be617cc9872b6e1
https://github.com/galaxyproject/galaxy/commit/74d4ea8eef26cb83ede4a3f53be6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-12 (Tue, 12 Dec 2017)
Changed paths:
M templates/user/openid_manage.mako
Log Message:
-----------
Remove unused mako properties
Commit: 1952e738a703afab2db0cffe615498536f74bb31
https://github.com/galaxyproject/galaxy/commit/1952e738a703afab2db0cffe6154…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-12 (Tue, 12 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/mvc/user/user-preferences.js
M templates/user/index.mako
M templates/user/openid_manage.mako
Log Message:
-----------
Merge branch 'replace_openid_table' into remove_gridhelper
Commit: d0a5a35dfd567ea8ce13fec38d1761fd44cd0ff2
https://github.com/galaxyproject/galaxy/commit/d0a5a35dfd567ea8ce13fec38d17…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-13 (Wed, 13 Dec 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Require only regular login to create openids
Commit: f239ef45465149964b30438b717cc30e7b2716ca
https://github.com/galaxyproject/galaxy/commit/f239ef45465149964b30438b717c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-13 (Wed, 13 Dec 2017)
Changed paths:
A client/galaxy/scripts/reports/run_stats.js
R client/galaxy/scripts/reports_webapp/run_stats.js
Log Message:
-----------
Move reports app to reports
Commit: 52cee726621e0281fde10c9ebb2820e8cc94a083
https://github.com/galaxyproject/galaxy/commit/52cee726621e0281fde10c9ebb28…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-13 (Wed, 13 Dec 2017)
Changed paths:
R client/galaxy/scripts/mvc/grid/grid-model.js
R client/galaxy/scripts/mvc/grid/grid-shared.js
R client/galaxy/scripts/mvc/grid/grid-template.js
R client/galaxy/scripts/mvc/grid/grid-view.js
A client/galaxy/scripts/reports/grid/grid-model.js
A client/galaxy/scripts/reports/grid/grid-shared.js
A client/galaxy/scripts/reports/grid/grid-template.js
A client/galaxy/scripts/reports/grid/grid-view.js
Log Message:
-----------
Move legacy grid client to reports
Commit: 5ed7b143eb457695bf230c5912e48dfabbfa7fb0
https://github.com/galaxyproject/galaxy/commit/5ed7b143eb457695bf230c5912e4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-13 (Wed, 13 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/reports/grid/grid-shared.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/visualization.js
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/workflows.py
A lib/galaxy/webapps/reports/framework/__init__.py
A lib/galaxy/webapps/reports/framework/grids.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/galaxy.pages.js
M static/scripts/mvc/grid/grid-model.js
M static/scripts/mvc/grid/grid-shared.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/history-list.js
M static/scripts/mvc/user/user-preferences.js
A static/scripts/reports/grid/grid-model.js
A static/scripts/reports/grid/grid-template.js
A static/scripts/reports/grid/grid-view.js
R static/scripts/reports_webapp/run_stats.js
M static/scripts/viz/trackster.js
M static/scripts/viz/visualization.js
R templates/grid_base.mako
R templates/grid_base_async.mako
R templates/panels.mako
M templates/user/index.mako
M templates/user/openid_manage.mako
R templates/webapps/reports/grid.mako
A templates/webapps/reports/grid_base.mako
A templates/webapps/reports/grid_base_async.mako
M templates/webapps/reports/run_stats.mako
M templates/webapps/tool_shed/category/grid.mako
M templates/webapps/tool_shed/category/valid_grid.mako
M templates/webapps/tool_shed/common/grid_common.mako
M templates/webapps/tool_shed/repository_review/grid.mako
Log Message:
-----------
Merge branch 'remove_gridhelper' into remove_gridhelper_001
Commit: 170b2431c9f61ea320a19ed04834e2f836f1c740
https://github.com/galaxyproject/galaxy/commit/170b2431c9f61ea320a19ed04834…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-13 (Wed, 13 Dec 2017)
Changed paths:
A client/galaxy/scripts/mvc/grid/grid-model.js
A client/galaxy/scripts/mvc/grid/grid-shared.js
A client/galaxy/scripts/mvc/grid/grid-template.js
A client/galaxy/scripts/mvc/grid/grid-view.js
Log Message:
-----------
Add grid modules
Commit: 6e8100f274648cb57fe5f2cda34dd22806b540ac
https://github.com/galaxyproject/galaxy/commit/6e8100f274648cb57fe5f2cda34d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-13 (Wed, 13 Dec 2017)
Changed paths:
A static/scripts/reports/grid/grid-shared.js
Log Message:
-----------
Pack client
Commit: c19ef1aacea869b33651fa3352970531150b0e07
https://github.com/galaxyproject/galaxy/commit/c19ef1aacea869b33651fa335297…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-13 (Wed, 13 Dec 2017)
Changed paths:
R client/galaxy/scripts/reports/grid/grid-shared.js
R static/scripts/reports/grid/grid-shared.js
Log Message:
-----------
Remove shared grid view
Commit: cbc4e55fda91dde884c9be474d7a95c62ccd98c7
https://github.com/galaxyproject/galaxy/commit/cbc4e55fda91dde884c9be474d7a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
Log Message:
-----------
Client format.
Commit: 85ba7c56e8ff0f2f6797a0e2b25f577ff7ee0071
https://github.com/galaxyproject/galaxy/commit/85ba7c56e8ff0f2f6797a0e2b25f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
A client/galaxy/scripts/legacy/grid/grid-model.js
A client/galaxy/scripts/legacy/grid/grid-template.js
A client/galaxy/scripts/legacy/grid/grid-view.js
R client/galaxy/scripts/reports/grid/grid-model.js
R client/galaxy/scripts/reports/grid/grid-template.js
R client/galaxy/scripts/reports/grid/grid-view.js
Log Message:
-----------
Relocate to legacy* templates to be very clear on the status of this code.
Commit: 8ecb6ecdfb6c7943b627bc63299d606fefe21c49
https://github.com/galaxyproject/galaxy/commit/8ecb6ecdfb6c7943b627bc63299d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M client/galaxy/scripts/legacy/grid/grid-view.js
Log Message:
-----------
Correct legacy grid* to point to the correct copied code (this was broken before the shift to legacy -- instead pointing back to the mvc version instead of the reports version
Commit: 8db84bea66615687d1ffba2f6b0af1fd770883b5
https://github.com/galaxyproject/galaxy/commit/8db84bea66615687d1ffba2f6b0a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M lib/galaxy/webapps/reports/framework/grids.py
A templates/legacy/grid_base.mako
A templates/legacy/grid_base_async.mako
R templates/webapps/reports/grid_base.mako
R templates/webapps/reports/grid_base_async.mako
M templates/webapps/tool_shed/category/grid.mako
M templates/webapps/tool_shed/category/valid_grid.mako
M templates/webapps/tool_shed/repository_review/grid.mako
Log Message:
-----------
Move templates (commonly used legacy grid code) from reports to legacy
Commit: 28653132bec89eab6bd3cdebebb334bd3fcb1345
https://github.com/galaxyproject/galaxy/commit/28653132bec89eab6bd3cdebebb3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
R .ci/py3_sources.txt
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/layout/modal.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/gulpfile.js
M client/package.json
M client/webpack.config.js
M client/yarn.lock
M config/plugins/webhooks/demo/tour_generator/helper/__init__.py
M lib/galaxy/containers/docker_swarm_manager.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/runners/chronos.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/openid/providers.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/util/permutations.py
M lib/galaxy/util/script.py
M lib/galaxy/visualization/data_providers/basic.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/authenticate.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M scripts/build_universe_config.py
M scripts/data_libraries/build_lucene_index.py
M scripts/galaxy-main
M scripts/helper.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/microbes/create_bacteria_loc_file.py
M scripts/microbes/create_bacteria_table.py
M scripts/microbes/create_nib_seq_loc_file.py
M scripts/microbes/get_builds_lengths.py
M scripts/microbes/harvest_bacteria.py
M scripts/microbes/ncbi_to_ucsc.py
M scripts/microbes/util.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/paster.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/sync_reports_config.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/libs.bundled.js
R static/scripts/libs/vue.js
M static/scripts/mvc/tool/tool-form-base.js
M test/selenium_tests/test_tool_form.py
M tools/data_source/upload.py
M tools/genomespace/genomespace_importer.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into remove_gridhelper_001
Commit: bb6e58b40dbc64b77dcf31291c28d1af7138e42a
https://github.com/galaxyproject/galaxy/commit/bb6e58b40dbc64b77dcf31291c28…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M client/galaxy/scripts/legacy/grid/grid-template.js
Log Message:
-----------
Formatting in grid-template
Commit: 985c65e677eb1dee5190685e85a429c8d1eab842
https://github.com/galaxyproject/galaxy/commit/985c65e677eb1dee5190685e85a4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M client/galaxy/scripts/legacy/grid/grid-model.js
M client/galaxy/scripts/legacy/grid/grid-template.js
Log Message:
-----------
Remove a little cruft in now-legacy grids.
Commit: e08a2839867b5214e830fe6a3df84dddca66521f
https://github.com/galaxyproject/galaxy/commit/e08a2839867b5214e830fe6a3df8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-template.js
Log Message:
-----------
Remove the same cruft from the mvc/grid/grid-template.
Commit: b832fec9e71694caf233627dd09c2f8921841534
https://github.com/galaxyproject/galaxy/commit/b832fec9e71694caf233627dd09c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M static/scripts/bundled/libs.bundled.js
A static/scripts/legacy/grid/grid-model.js
A static/scripts/legacy/grid/grid-template.js
A static/scripts/legacy/grid/grid-view.js
M static/scripts/mvc/grid/grid-template.js
R static/scripts/reports/grid/grid-model.js
R static/scripts/reports/grid/grid-template.js
R static/scripts/reports/grid/grid-view.js
A static/scripts/reports/run_stats.js
Log Message:
-----------
Build client
Commit: 609020da0fa8b2d3171e157bf609b30dd4b54067
https://github.com/galaxyproject/galaxy/commit/609020da0fa8b2d3171e157bf609…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
R .ci/py3_sources.txt
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/layout/modal.js
A client/galaxy/scripts/legacy/grid/grid-model.js
A client/galaxy/scripts/legacy/grid/grid-template.js
A client/galaxy/scripts/legacy/grid/grid-view.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
R client/galaxy/scripts/reports/grid/grid-model.js
R client/galaxy/scripts/reports/grid/grid-template.js
R client/galaxy/scripts/reports/grid/grid-view.js
M client/gulpfile.js
M client/package.json
M client/webpack.config.js
M client/yarn.lock
M config/plugins/webhooks/demo/tour_generator/helper/__init__.py
M lib/galaxy/containers/docker_swarm_manager.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/runners/chronos.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/openid/providers.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/util/permutations.py
M lib/galaxy/util/script.py
M lib/galaxy/visualization/data_providers/basic.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/authenticate.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/framework/grids.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M scripts/build_universe_config.py
M scripts/data_libraries/build_lucene_index.py
M scripts/galaxy-main
M scripts/helper.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/microbes/create_bacteria_loc_file.py
M scripts/microbes/create_bacteria_table.py
M scripts/microbes/create_nib_seq_loc_file.py
M scripts/microbes/get_builds_lengths.py
M scripts/microbes/harvest_bacteria.py
M scripts/microbes/ncbi_to_ucsc.py
M scripts/microbes/util.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/paster.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/sync_reports_config.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/libs.bundled.js
A static/scripts/legacy/grid/grid-model.js
A static/scripts/legacy/grid/grid-template.js
A static/scripts/legacy/grid/grid-view.js
R static/scripts/libs/vue.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/tool/tool-form-base.js
R static/scripts/reports/grid/grid-model.js
R static/scripts/reports/grid/grid-template.js
R static/scripts/reports/grid/grid-view.js
A static/scripts/reports/run_stats.js
A templates/legacy/grid_base.mako
A templates/legacy/grid_base_async.mako
R templates/webapps/reports/grid_base.mako
R templates/webapps/reports/grid_base_async.mako
M templates/webapps/tool_shed/category/grid.mako
M templates/webapps/tool_shed/category/valid_grid.mako
M templates/webapps/tool_shed/repository_review/grid.mako
M test/selenium_tests/test_tool_form.py
M tools/data_source/upload.py
M tools/genomespace/genomespace_importer.py
Log Message:
-----------
Merge pull request #23 from dannon/remove_gridhelper_001
Some fixes and cleanup, makes the merge clean.
Commit: 9aa596df8b6853bcf63635fdbd38790f634a0888
https://github.com/galaxyproject/galaxy/commit/9aa596df8b6853bcf63635fdbd38…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.pages.js
A client/galaxy/scripts/legacy/grid/grid-model.js
A client/galaxy/scripts/legacy/grid/grid-template.js
A client/galaxy/scripts/legacy/grid/grid-view.js
M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-shared.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/user/user-preferences.js
A client/galaxy/scripts/reports/run_stats.js
R client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/visualization.js
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/workflows.py
A lib/galaxy/webapps/reports/framework/__init__.py
A lib/galaxy/webapps/reports/framework/grids.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/galaxy.pages.js
A static/scripts/legacy/grid/grid-model.js
A static/scripts/legacy/grid/grid-template.js
A static/scripts/legacy/grid/grid-view.js
M static/scripts/mvc/grid/grid-model.js
M static/scripts/mvc/grid/grid-shared.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/history-list.js
M static/scripts/mvc/user/user-preferences.js
A static/scripts/reports/run_stats.js
R static/scripts/reports_webapp/run_stats.js
M static/scripts/viz/trackster.js
M static/scripts/viz/visualization.js
R templates/grid_base.mako
R templates/grid_base_async.mako
A templates/legacy/grid_base.mako
A templates/legacy/grid_base_async.mako
R templates/panels.mako
M templates/user/index.mako
M templates/user/openid_manage.mako
R templates/webapps/reports/grid.mako
M templates/webapps/reports/run_stats.mako
M templates/webapps/tool_shed/category/grid.mako
M templates/webapps/tool_shed/category/valid_grid.mako
M templates/webapps/tool_shed/common/grid_common.mako
M templates/webapps/tool_shed/repository_review/grid.mako
Log Message:
-----------
Merge pull request #5212 from guerler/remove_gridhelper_001
Remove html producing grid helpers
Compare: https://github.com/galaxyproject/galaxy/compare/b96c428cde5e...9aa596df8b68
1
0
[galaxyproject/galaxy] 504343: Selenium - little pause to let extension form in u...
by GitHub 14 Dec '17
by GitHub 14 Dec '17
14 Dec '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 5043439df2ca694254623887d351905be1d9b698
https://github.com/galaxyproject/galaxy/commit/5043439df2ca694254623887d351…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-13 (Wed, 13 Dec 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
Selenium - little pause to let extension form in upload dialog render.
xref https://github.com/galaxyproject/galaxy/issues/5169
Commit: 6fd6595238b5189e89f54ad01079b4d34fbcfea7
https://github.com/galaxyproject/galaxy/commit/6fd6595238b5189e89f54ad01079…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_tool_form.py
Log Message:
-----------
Another try to fix flakey tool form Selenium test.
Commit: b96c428cde5e9786376d0ecd5eba5f5233b6fec2
https://github.com/galaxyproject/galaxy/commit/b96c428cde5e9786376d0ecd5eba…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M test/selenium_tests/test_tool_form.py
Log Message:
-----------
Merge pull request #5211 from jmchilton/selenium_test_fixes
Mark transiently failing test_run_data as flakey.
Compare: https://github.com/galaxyproject/galaxy/compare/3b7f40198e96...b96c428cde5e
1
0
14 Dec '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 14259b11d9a5f6238153556ed5a28bf89468e2b4
https://github.com/galaxyproject/galaxy/commit/14259b11d9a5f6238153556ed5a2…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
R .ci/py3_sources.txt
M config/plugins/webhooks/demo/tour_generator/helper/__init__.py
M lib/galaxy/containers/docker_swarm_manager.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/runners/chronos.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/openid/providers.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/util/permutations.py
M lib/galaxy/util/script.py
M lib/galaxy/visualization/data_providers/basic.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/authenticate.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M scripts/build_universe_config.py
M scripts/data_libraries/build_lucene_index.py
M scripts/galaxy-main
M scripts/helper.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/microbes/create_bacteria_loc_file.py
M scripts/microbes/create_bacteria_table.py
M scripts/microbes/create_nib_seq_loc_file.py
M scripts/microbes/get_builds_lengths.py
M scripts/microbes/harvest_bacteria.py
M scripts/microbes/ncbi_to_ucsc.py
M scripts/microbes/util.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/paster.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/sync_reports_config.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M tools/genomespace/genomespace_importer.py
Log Message:
-----------
Python3: finish first pass on whole codebase
Commit: 820d1e259c625f2472f79ee46654bbf91b19dea4
https://github.com/galaxyproject/galaxy/commit/820d1e259c625f2472f79ee46654…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
Log Message:
-----------
Mercurial does not support Python3 yet
Commit: 3b7f40198e968d7c2bbda533551686688cfd8f48
https://github.com/galaxyproject/galaxy/commit/3b7f40198e968d7c2bbda5335516…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
R .ci/py3_sources.txt
M config/plugins/webhooks/demo/tour_generator/helper/__init__.py
M lib/galaxy/containers/docker_swarm_manager.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/runners/chronos.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/openid/providers.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/util/permutations.py
M lib/galaxy/util/script.py
M lib/galaxy/visualization/data_providers/basic.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/authenticate.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M scripts/build_universe_config.py
M scripts/data_libraries/build_lucene_index.py
M scripts/galaxy-main
M scripts/helper.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/microbes/create_bacteria_loc_file.py
M scripts/microbes/create_bacteria_table.py
M scripts/microbes/create_nib_seq_loc_file.py
M scripts/microbes/get_builds_lengths.py
M scripts/microbes/harvest_bacteria.py
M scripts/microbes/ncbi_to_ucsc.py
M scripts/microbes/util.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/paster.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/sync_reports_config.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M tools/genomespace/genomespace_importer.py
Log Message:
-----------
Merge pull request #5215 from nsoranzo/python3
Python3: finish first pass on whole codebase
Compare: https://github.com/galaxyproject/galaxy/compare/fd4f0e6aa6f7...3b7f40198e96
1
0
14 Dec '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: dda410da63ef26c7d86a40bd764adadb19cbbcd5
https://github.com/galaxyproject/galaxy/commit/dda410da63ef26c7d86a40bd764a…
Author: Peter Selten <peter.selten98(a)gmail.com>
Date: 2017-12-12 (Tue, 12 Dec 2017)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
Log Message:
-----------
#3002 update to newer version of virtualenv.
Commit: fd4f0e6aa6f7178639c3af556da86a0805460808
https://github.com/galaxyproject/galaxy/commit/fd4f0e6aa6f7178639c3af556da8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
Log Message:
-----------
Merge pull request #5202 from selten/dev
#3002 update to newer version of virtualenv.
Compare: https://github.com/galaxyproject/galaxy/compare/7b04c834e0ff...fd4f0e6aa6f7
1
0
14 Dec '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6eaa73e37ee5f795d8b96c9abe274403dfa62753
https://github.com/galaxyproject/galaxy/commit/6eaa73e37ee5f795d8b96c9abe27…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-11 (Mon, 11 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/gulpfile.js
M client/webpack.config.js
R static/scripts/libs/vue.js
Log Message:
-----------
Swap to vue via node_module; no staging.
Commit: 1a6065b0c3ee7178acbf96028672a33ee32bb195
https://github.com/galaxyproject/galaxy/commit/1a6065b0c3ee7178acbf96028672…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-11 (Mon, 11 Dec 2017)
Changed paths:
R static/scripts/libs/bibtex.js
Log Message:
-----------
Remove old bibtex.js cruft.
Commit: 662f35df490c66c2d9443f9815820c2041ee7fdd
https://github.com/galaxyproject/galaxy/commit/662f35df490c66c2d9443f981582…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-11 (Mon, 11 Dec 2017)
Changed paths:
M client/package.json
M client/yarn.lock
Log Message:
-----------
Upgrade vue.
Commit: 2ca7b90262a6ef5e833df0c65da4c3a5a45a6d9b
https://github.com/galaxyproject/galaxy/commit/2ca7b90262a6ef5e833df0c65da4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-11 (Mon, 11 Dec 2017)
Changed paths:
M client/package.json
M client/yarn.lock
Log Message:
-----------
Upgrade webpack to 3.10
Commit: 0a92f5b80bea2b593a9d37ab9d606e5ac97c2e71
https://github.com/galaxyproject/galaxy/commit/0a92f5b80bea2b593a9d37ab9d60…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-11 (Mon, 11 Dec 2017)
Changed paths:
M client/package.json
M client/yarn.lock
Log Message:
-----------
Update vue-template-compiler
Commit: 8cd62168d8eda3e5480ffcfb25e87c62b44163c6
https://github.com/galaxyproject/galaxy/commit/8cd62168d8eda3e5480ffcfb25e8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-11 (Mon, 11 Dec 2017)
Changed paths:
M client/package.json
M client/yarn.lock
Log Message:
-----------
Upgrade minor devDependencies.
Commit: 4dbe7c420e6f6c1515183bf44838a4f2ed3fa453
https://github.com/galaxyproject/galaxy/commit/4dbe7c420e6f6c1515183bf44838…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-11 (Mon, 11 Dec 2017)
Changed paths:
M client/package.json
M client/yarn.lock
Log Message:
-----------
Upgrade prettier 1.7->1.9
Commit: a363d81b7314bd41fba5ea15b2ff432a9bc83dad
https://github.com/galaxyproject/galaxy/commit/a363d81b7314bd41fba5ea15b2ff…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-11 (Mon, 11 Dec 2017)
Changed paths:
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/layout/modal.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Rerun new version of prettier.
Commit: c09643d57bac206bc101434f4623c0d63d75ca16
https://github.com/galaxyproject/galaxy/commit/c09643d57bac206bc101434f4623…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-11 (Mon, 11 Dec 2017)
Changed paths:
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Build client.
Commit: 7b04c834e0ff03eddedd81303ea0242d0e44fbc6
https://github.com/galaxyproject/galaxy/commit/7b04c834e0ff03eddedd81303ea0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-14 (Thu, 14 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/layout/modal.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/gulpfile.js
M client/package.json
M client/webpack.config.js
M client/yarn.lock
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/libs.bundled.js
R static/scripts/libs/vue.js
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Merge pull request #5190 from dannon/vue_dep_tweaks
Client dependency upgrades, changes.
Compare: https://github.com/galaxyproject/galaxy/compare/fce9f13eba7f...7b04c834e0ff
1
0