Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6d1397647fd6b185a639915a8f1ac929d78317d4
https://github.com/galaxyproject/galaxy/commit/6d1397647fd6b185a639915a8f1a…
Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Install tools and workflow
import_tools is option and default is False.
If import_tools is True, install tools in workflow.
Commit: 30aa73e1974e1669984f0b6f242110451a8499ab
https://github.com/galaxyproject/galaxy/commit/30aa73e1974e1669984f0b6f2421…
Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Remove unused variable
Commit: 02924dece4653d476a2838e9b91bd2664d8bf518
https://github.com/galaxyproject/galaxy/commit/02924dece4653d476a2838e9b91b…
Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com>
Date: 2016-10-19 (Wed, 19 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Fix lint
Commit: 23db89ba3ddf54420b40e881bd92edbfeff869c6
https://github.com/galaxyproject/galaxy/commit/23db89ba3ddf54420b40e881bd92…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
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A .ci/jenkins/integration/run_tests.sh
A .ci/jenkins/selenium/Dockerfile
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A .ci/jenkins/selenium/galaxy.ini
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A .ci/jenkins/selenium/run_tests.sh
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M .gitignore
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M CITATION
M CONTRIBUTING.md
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M Makefile
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M client/galaxy/scripts/ui/autocom_tagging.js
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M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/visualization.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/dataset.less
M client/galaxy/style/less/galaxy_bootstrap/overrides.less
M client/galaxy/style/less/history.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/ui/paired-collection-creator.less
M client/galaxy/style/less/upload.less
M client/galaxy/style/source_material/circle.py
A client/package-lock.json
M client/package.json
M client/webpack.config.js
A config/build_sites.yml.sample
A config/containers_conf.yml.sample
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M config/dependency_resolvers_conf.xml.sample
A config/error_report.yml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/local_conda_mapping.yml.sample
M config/openid_conf.xml.sample
M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample
M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
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M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
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M contrib/galaxy.debian-init
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M contrib/galaxy_supervisor.conf
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M cron/add_manual_builds.py
M cron/build_chrom_db.py
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M lib/galaxy/jobs/runners/condor.py
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M lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/kubernetes.py
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M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
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M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/deletable.py
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M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/rbac_secured.py
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M lib/galaxy/managers/users.py
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M lib/galaxy/model/custom_types.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
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M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
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M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
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M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
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M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
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M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
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M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
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M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
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M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
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M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
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M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
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M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
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M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
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M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
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M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
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M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
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A lib/galaxy/webapps/galaxy/config_watchers.py
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M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/async.py
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A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
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M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/root.py
R lib/galaxy/webapps/galaxy/controllers/search.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
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M lib/galaxy/webapps/tool_shed/controllers/groups.py
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A scripts/slideshow/example.md
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A scripts/slideshow/style.sample.css
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A static/maps/app.js.map
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M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/visualization.js
M static/style/blue/base.css
M static/welcome.html.sample
M templates/admin/reload_tool.mako
R templates/admin/tool_shed_repository/browse_toolsheds.mako
M templates/admin/tool_shed_repository/common.mako
R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/admin/user/reset_password.mako
M templates/admin/user/user.mako
M templates/base.mako
M templates/base/base_panels.mako
M templates/display_base.mako
M templates/galaxy_client_app.mako
M templates/grid_base.mako
M templates/ind_share_base.mako
M templates/js-app.mako
M templates/sharing_base.mako
M templates/show_params.mako
R templates/user/change_password.mako
R templates/user/communication_settings.mako
R templates/user/dbkeys.mako
R templates/user/edit_address.mako
M templates/user/index.mako
M templates/user/login.mako
M templates/user/logout.mako
R templates/user/new_address.mako
R templates/user/permissions.mako
M templates/user/register.mako
R templates/user/toolbox_filters.mako
R templates/user/username.mako
M templates/webapps/galaxy/admin/center.mako
R templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/admin/manage_dependencies.mako
M templates/webapps/galaxy/base_panels.mako
M templates/webapps/galaxy/data_manager/index.mako
M templates/webapps/galaxy/dataset/display.mako
R templates/webapps/galaxy/dataset/edit_attributes.mako
R templates/webapps/galaxy/dataset/errors.mako
R templates/webapps/galaxy/dataset/grid.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/history/display_structured.mako
R templates/webapps/galaxy/history/grid.mako
R templates/webapps/galaxy/history/grid_js.mako
R templates/webapps/galaxy/history/list_published.mako
M templates/webapps/galaxy/history/share.mako
R templates/webapps/galaxy/history/shared_grid.mako
M templates/webapps/galaxy/mobile/form.mako
M templates/webapps/galaxy/mobile/index.mako
M templates/webapps/galaxy/page/editor.mako
R templates/webapps/galaxy/page/index.mako
R templates/webapps/galaxy/page/list_published.mako
R templates/webapps/galaxy/page/select_items_grid.mako
M templates/webapps/galaxy/requests/common/common.mako
M templates/webapps/galaxy/root/tool_runner.mako
R templates/webapps/galaxy/tracks/add_to_viz.mako
R templates/webapps/galaxy/tracks/add_tracks.mako
R templates/webapps/galaxy/tracks/history_datasets_select_grid.mako
R templates/webapps/galaxy/tracks/history_select_grid.mako
R templates/webapps/galaxy/tracks/library_datasets_select_grid.mako
R templates/webapps/galaxy/user/api_keys.mako
M templates/webapps/galaxy/user/list_users.mako
R templates/webapps/galaxy/user/manage_info.mako
R templates/webapps/galaxy/visualization/list.mako
R templates/webapps/galaxy/visualization/list_published.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
R templates/webapps/galaxy/workflow/configure_menu.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/galaxy/workflow/editor.mako
R templates/webapps/galaxy/workflow/editor_generic_form.mako
R templates/webapps/galaxy/workflow/editor_tool_form.mako
R templates/webapps/galaxy/workflow/import.mako
R templates/webapps/galaxy/workflow/index.mako
R templates/webapps/galaxy/workflow/list.mako
R templates/webapps/galaxy/workflow/list_for_run.mako
R templates/webapps/galaxy/workflow/list_published.mako
R templates/webapps/galaxy/workflow/missing_tools.mako
R templates/webapps/galaxy/workflow/myexp_export_content.mako
R templates/webapps/galaxy/workflow/rename.mako
R templates/webapps/galaxy/workflow/run.mako
M templates/webapps/reports/base_panels.mako
M templates/webapps/tool_shed/admin/center.mako
M templates/webapps/tool_shed/base_panels.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/tool_form.mako
A templates/webapps/tool_shed/user/api_keys.mako
A templates/webapps/tool_shed/user/change_password.mako
A templates/webapps/tool_shed/user/index.mako
A templates/webapps/tool_shed/user/username.mako
A test-data/1.fastqsanger.bz2
A test-data/1.fastqsanger.gz
A test-data/5_Ig-like.gff
A test-data/bam_from_sam.bam
A test-data/filter_labels_1.txt
A test-data/new_labels_1.txt
A test-data/new_labels_2.txt
A test-data/new_labels_bad_1.txt
A test-data/new_labels_bad_2.txt
A test-data/sam_with_header.sam
A test-data/simple.xml
A test-data/test.vcf.gz
M test/TESTING.md
R test/api/helpers.py
M test/api/test_api_batch.py
A test/api/test_configuration.py
M test/api/test_dataset_collections.py
M test/api/test_datasets.py
M test/api/test_datatypes.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_history_contents_provenance.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_search.py
M test/api/test_tools.py
M test/api/test_users.py
A test/api/test_visualizations.py
A test/api/test_webhooks.py
R test/api/test_workflow_1.ga
R test/api/test_workflow_2.ga
R test/api/test_workflow_batch.ga
M test/api/test_workflow_extraction.py
R test/api/test_workflow_map_reduce_pause.ga
R test/api/test_workflow_matching_lists.ga
R test/api/test_workflow_missing_tool.ga
R test/api/test_workflow_pause.ga
R test/api/test_workflow_topoambigouity.ga
R test/api/test_workflow_topoambigouity_auto_laidout.ga
R test/api/test_workflow_validation_1.ga
R test/api/test_workflow_with_runtime_input.ga
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
R test/api/workflows_format_2/README.txt
R test/api/workflows_format_2/__init__.py
R test/api/workflows_format_2/converter.py
R test/api/workflows_format_2/interface.py
R test/api/workflows_format_2/main.py
M test/base/api.py
M test/base/api_asserts.py
A test/base/data/test_workflow_1.ga
A test/base/data/test_workflow_2.ga
A test/base/data/test_workflow_batch.ga
A test/base/data/test_workflow_map_reduce_pause.ga
A test/base/data/test_workflow_matching_lists.ga
A test/base/data/test_workflow_missing_tool.ga
A test/base/data/test_workflow_pause.ga
A test/base/data/test_workflow_topoambigouity.ga
A test/base/data/test_workflow_topoambigouity_auto_laidout.ga
A test/base/data/test_workflow_validation_1.ga
A test/base/data/test_workflow_with_runtime_input.ga
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
A test/base/populators.py
M test/base/twilltestcase.py
A test/base/workflows_format_2/README.txt
A test/base/workflows_format_2/__init__.py
A test/base/workflows_format_2/converter.py
A test/base/workflows_format_2/interface.py
A test/base/workflows_format_2/main.py
R test/casperjs/anon-history-tests.js
R test/casperjs/api-batch-tests.js
R test/casperjs/api-configuration-tests.js
R test/casperjs/api-dataset-tests.js
R test/casperjs/api-history-tests.js
R test/casperjs/api-tool-tests.js
R test/casperjs/api-user-tests.js
R test/casperjs/api-visualizations-tests.js
R test/casperjs/hda-state-tests.js
R test/casperjs/history-options-tests.js
R test/casperjs/history-panel-tests.js
R test/casperjs/history-share-tests.js
R test/casperjs/login-tests.js
R test/casperjs/registration-tests.js
R test/casperjs/upload-tests.js
M test/docker/README.md
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/docker/base/run_test_wrapper.sh
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
M test/functional/tools/checksum.xml
A test/functional/tools/collection_creates_dynamic_nested_fail.xml
A test/functional/tools/collection_creates_list_fail.xml
M test/functional/tools/column_param.xml
A test/functional/tools/compressed_bz2_fastq_conversion.xml
A test/functional/tools/compressed_bz2_fastq_no_conversion.xml
A test/functional/tools/compressed_gz_fastq_conversion.xml
A test/functional/tools/compressed_gz_fastq_no_conversion.xml
M test/functional/tools/create_10.xml
A test/functional/tools/create_2.xml
A test/functional/tools/explicit_conversion.xml
A test/functional/tools/for_tours/filtering.py
A test/functional/tools/for_tours/filtering.xml
A test/functional/tools/for_workflows/mapper2.xml
A test/functional/tools/identifier_multiple_in_conditional.xml
A test/functional/tools/identifier_multiple_in_repeat.xml
A test/functional/tools/identifier_source.xml
A test/functional/tools/implicit_conversion.xml
A test/functional/tools/is_valid_xml.xml
A test/functional/tools/legacy_r.xml
M test/functional/tools/md5sum.xml
A test/functional/tools/mulled_example_conflict.xml
A test/functional/tools/mulled_example_multi_incomplete.xml
A test/functional/tools/mulled_example_multi_versionless.xml
A test/functional/tools/output_format_deprecated_when.xml
A test/functional/tools/paired_collection_map_over_structured_like.xml
A test/functional/tools/param_text_option.xml
A test/functional/tools/python_environment_problem.py
A test/functional/tools/python_environment_problem.xml
A test/functional/tools/sam_to_bam.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/vcf_bgzip.xml
A test/functional/webhooks/history_test1/config/history_test1.yml
A test/functional/webhooks/history_test2/config/history_test2.yml
A test/functional/webhooks/masthead_test/config/masthead_test.yml
A test/functional/webhooks/phdcomics/config/phdcomics.yaml
A test/functional/webhooks/phdcomics/helper/__init__.py
A test/functional/webhooks/phdcomics/static/script.js
A test/functional/webhooks/phdcomics/static/styles.css
A test/functional/webhooks/trans_object/config/trans_object.yaml
A test/functional/webhooks/trans_object/helper/__init__.py
A test/functional/webhooks/xkcd/config/xkcd.yml
A test/functional/webhooks/xkcd/static/script.js
A test/functional/webhooks/xkcd/static/styles.css
R test/functional/workflow.py
A test/galaxy_selenium/__init__.py
A test/galaxy_selenium/cli.py
A test/galaxy_selenium/data.py
A test/galaxy_selenium/driver_factory.py
A test/galaxy_selenium/has_driver.py
A test/galaxy_selenium/navigates_galaxy.py
A test/galaxy_selenium/navigation-data.yml
A test/galaxy_selenium/sizzle.py
A test/integration/resubmission_default_job_conf.xml
A test/integration/resubmission_job_conf.xml
A test/integration/resubmission_job_resource_parameters_conf.xml
A test/integration/resubmission_rules/__init__.py
A test/integration/resubmission_rules/rules.py
A test/integration/resubmission_runners.py
A test/integration/test_config_options_users.py
A test/integration/test_job_resubmission.py
A test/integration/test_maximum_worklfow_invocation_duration.py
M test/integration/test_resolvers.py
A test/integration/test_workflow_handler_configuration.py
A test/integration/workflow_handler_configuration_job_conf.xml
A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml
M test/manual/workflows_scaling.py
M test/qunit/package.json
M test/qunit/test-data/bootstrapped.js
M test/qunit/test-data/paired-collection-creator.data.js
M test/qunit/tests/form_tests.js
M test/qunit/tests/galaxy-app-base.js
M test/qunit/tests/page_tests.js
M test/qunit/tests/ui_tests.html
M test/qunit/tests/ui_tests.js
M test/qunit/tests/workflow_editor_tests.js
A test/selenium_tests/__init__.py
A test/selenium_tests/_workflow_fixtures.py
A test/selenium_tests/framework.py
A test/selenium_tests/test_anon_history.py
A test/selenium_tests/test_collection_builders.py
A test/selenium_tests/test_history_dataset_state.py
A test/selenium_tests/test_history_options.py
A test/selenium_tests/test_history_panel.py
A test/selenium_tests/test_history_sharing.py
A test/selenium_tests/test_login.py
A test/selenium_tests/test_registration.py
A test/selenium_tests/test_stock_tours.py
A test/selenium_tests/test_tool_form.py
A test/selenium_tests/test_uploads.py
A test/selenium_tests/test_workflow_editor.py
A test/selenium_tests/test_workflow_management.py
A test/selenium_tests/test_workflow_run.py
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1090_repository_dependency_handling.py
M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
M test/shed_functional/functional/test_1150_datatype_converters.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/unit/dataset_collections/test_matching.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
A test/unit/jobs/conditional_runners_job_conf.xml
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rule_helper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_fabric_util.py
A test/unit/shed_unit/test_installed_repository_manager.py
M test/unit/shed_unit/test_td_common_util.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_transactions.py
A test/unit/test_remote_shell.py
M test/unit/test_routes.py
M test/unit/test_sockets.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_dependency_description.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_external_files.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
A tool-data/blastdb.loc.sample
A tool-data/blastdb_d.loc.sample
A tool-data/blastdb_p.loc.sample
M tool-data/shared/ucsc/builds.txt.sample
M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/evolution/add_scores.xml
M tools/extract/extract_genomic_dna.py
M tools/extract/extract_genomic_dna.xml
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_fasta.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/catWrapper.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
R tools/filters/gff/sort_gtf.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/mergeCols.py
M tools/filters/pasteWrapper.xml
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/trimmer.xml
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wc_gnu.xml
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/genebed_maf_to_fasta.xml
M tools/maf/interval2maf.py
M tools/maf/interval2maf.xml
M tools/maf/interval2maf_pairwise.xml
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/interval_maf_to_merged_fasta.xml
M tools/maf/macros.xml
M tools/maf/maf_by_block_number.py
M tools/maf/maf_by_block_number.xml
M tools/maf/maf_filter.py
M tools/maf/maf_filter.xml
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_size.xml
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_limit_to_species.xml
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_reverse_complement.xml
M tools/maf/maf_split_by_species.py
M tools/maf/maf_split_by_species.xml
M tools/maf/maf_stats.py
M tools/maf/maf_stats.xml
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_thread_for_species.xml
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed.xml
M tools/maf/maf_to_fasta.xml
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/maf_to_interval.xml
M tools/maf/vcf_to_maf_customtrack.py
M tools/maf/vcf_to_maf_customtrack.xml
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.xml
M tools/metag_tools/shrimp_wrapper.xml
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/fastq_gen_conv.xml
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/plotting/bar_chart.xml
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_binned_scores_in_intervals.xml
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'jmchilton/dev' into install_workflow_and_tools
Conflicts:
lib/galaxy/webapps/galaxy/api/workflows.py
Commit: 7dd3ddccafee8f5cc185f1b0dd711056576a92ce
https://github.com/galaxyproject/galaxy/commit/7dd3ddccafee8f5cc185f1b0dd71…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
M test/api/test_workflows.py
Log Message:
-----------
Require admin for new import_tools function in workflows API.
Includes test case.
Commit: fc861cdf38d1d20fd611e8bcb042328eb905b3c4
https://github.com/galaxyproject/galaxy/commit/fc861cdf38d1d20fd611e8bcb042…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-12 (Sat, 12 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #3064 from manabuishii/install_workflow_and_tools
Install tools and workflow
Compare: https://github.com/galaxyproject/galaxy/compare/331851b0495d...fc861cdf38d1
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6a7cc34e1b1ade9580e464570fc6b83a488e941f
https://github.com/galaxyproject/galaxy/commit/6a7cc34e1b1ade9580e464570fc6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M run.sh
M run_reports.sh
M run_tool_shed.sh
A scripts/common_startup_functions.sh
Log Message:
-----------
Bring Galaxy, reports, and shed run scripts in sync.
- They now uniformly handle server option processing.
- Reports and Tool Shed now respect many new and important options such as --skip_venv.
- Reports and Tool Shed now do extra checking around Python version that Galaxy does.
In addition to improving the reports and tool shed startup scripts and reducing cognative load with respect to option handling, this is an important pre-condition to us being able us to switch on uwsgi by default for all three services simultaneously without a bunch of copy and pasting.
Commit: 72e5a00ba0ad9c1a8e56ad9544bec23c843d900d
https://github.com/galaxyproject/galaxy/commit/72e5a00ba0ad9c1a8e56ad9544be…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M run_reports.sh
M run_tool_shed.sh
M scripts/common_startup_functions.sh
Log Message:
-----------
Centralize launching server for reports and tool shed.
Initial outline of allowing launch via uwsgi.
Commit: 1bdb99bbd76d0827cd3a7e617d288564584863ea
https://github.com/galaxyproject/galaxy/commit/1bdb99bbd76d0827cd3a7e617d28…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/util/properties.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M scripts/manage_tools.py
Log Message:
-----------
Update galaxy.util.properties to allow YAML.
Commit: 8189a1f1e289e14d362fcb8871b9339c3355e8b2
https://github.com/galaxyproject/galaxy/commit/8189a1f1e289e14d362fcb8871b9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
A lib/galaxy/webapps/config_manage.py
A scripts/config_sample_to_kwalify.py
A test/unit/config/1607_root_filters/config/galaxy.ini
A test/unit/config/1607_root_filters/config/tool_shed.ini
A test/unit/config/1607_root_samples/config/galaxy.ini
A test/unit/config/1607_root_samples/config/reports.ini
A test/unit/config/1607_root_samples/config/tool_shed.ini
A test/unit/config/test_config_manage.py
Log Message:
-----------
Scripts to manage configuration infrastructure.
This has been rebased several times and includes a variety of fixes (some thanks to martenson).
Commit: 7973a914e0beef9680475d54947bd953c0b062cd
https://github.com/galaxyproject/galaxy/commit/7973a914e0beef9680475d54947b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
A lib/galaxy/webapps/uwsgi_schema.yml
Log Message:
-----------
Add uwsgi_schema.yml.
Commit: 90e899d68fbf21effad1cf309efbd786c54be556
https://github.com/galaxyproject/galaxy/commit/90e899d68fbf21effad1cf309efb…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
R config/tool_shed.ini.sample
A config/tool_shed.yml.sample
M lib/galaxy/webapps/tool_shed/buildapp.py
A lib/galaxy/webapps/tool_shed/config_schema.yml
A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml
M run_tool_shed.sh
Log Message:
-----------
Update tool shed to use newer configuration schema.
- Implement kwalify schema to validate/define the schema.
- Replace ini configuration with YAML (completely backward compatible).
- Rebuild a sample configuration from the schema (config/tool_shed.yml.sample).
Commit: 102566dd5e1c5903726057f1077a1d7fc614b815
https://github.com/galaxyproject/galaxy/commit/102566dd5e1c5903726057f1077a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
R config/reports.ini.sample
A config/reports.yml.sample
M lib/galaxy/webapps/reports/buildapp.py
A lib/galaxy/webapps/reports/config_schema.yml
A lib/galaxy/webapps/reports/uwsgi_schema.yml
M run_reports.sh
Log Message:
-----------
Update Galaxy Reports to use newer configuration schema.
- Implement kwalify schema to validate/define the schema.
- Replace ini configuration with YAML (completely backward compatible).
- Rebuild a sample configuration from the schema (config/reports.yml.sample).
Commit: 50d426ed2b9ae2aff8b243143478ce84c7731816
https://github.com/galaxyproject/galaxy/commit/50d426ed2b9ae2aff8b243143478…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
A doc/source/admin/reports.rst
A doc/source/admin/reports_options.rst
Log Message:
-----------
Add reports documentation to ``doc/``.
- Automatically generate RST docs from config schema.
- Describe older functionality as well as new YAML-based configuration.
- Replace https://wiki.galaxyproject.org/Admin/UsageReports.
Commit: 4945f55e4fe28842b58c025b37c4d6c96a07028f
https://github.com/galaxyproject/galaxy/commit/4945f55e4fe28842b58c025b37c4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M Makefile
Log Message:
-----------
Makefile shortcuts for configuration script.
Commit: ef46a60a829e3dae44d935f6f886feef39b873e3
https://github.com/galaxyproject/galaxy/commit/ef46a60a829e3dae44d935f6f886…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Add required dependency on uwsgi.
Required for the new out-of-the-box configuration of tool shed and reports.
Commit: 8191fd492819214b12c0aa28b35e5b6c4ea7bfa1
https://github.com/galaxyproject/galaxy/commit/8191fd492819214b12c0aa28b35e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Add pykwalify as dependency for the new config validation stuff.
xref https://github.com/galaxyproject/starforge/pull/110
Commit: ffe295e96dbd82615c987a2b9ba9bd15ea253826
https://github.com/galaxyproject/galaxy/commit/ffe295e96dbd82615c987a2b9ba9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M test/unit/config/test_config_manage.py
Log Message:
-----------
Fix Python 3 linting problem with test_config_manage.py.
Commit: 1ce93ccfdf7b54ec1efcf08b04c9f28b67ab0615
https://github.com/galaxyproject/galaxy/commit/1ce93ccfdf7b54ec1efcf08b04c9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Pin version of uWSGI to freshly released 2.0.15 available on wheels.galaxyproject.org.
Commit: 539a62f642ada1f2d832f1f88ab339cafe672c1f
https://github.com/galaxyproject/galaxy/commit/539a62f642ada1f2d832f1f88ab3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/util/properties.py
Log Message:
-----------
Fix ORM scripts for #3179.
Commit: 98ca8ce7a68d18533f3bf85097490c5b66e9f876
https://github.com/galaxyproject/galaxy/commit/98ca8ce7a68d18533f3bf8509749…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Update config overhaul branch for introduction of galaxy.web.stack package.
Commit: 331851b0495d429220450ceb3a540fbba900143a
https://github.com/galaxyproject/galaxy/commit/331851b0495d429220450ceb3a54…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-12 (Sat, 12 Aug 2017)
Changed paths:
M Makefile
R config/reports.ini.sample
A config/reports.yml.sample
R config/tool_shed.ini.sample
A config/tool_shed.yml.sample
A doc/source/admin/reports.rst
A doc/source/admin/reports_options.rst
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/util/properties.py
M lib/galaxy/web/framework/webapp.py
A lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/reports/buildapp.py
A lib/galaxy/webapps/reports/config_schema.yml
A lib/galaxy/webapps/reports/uwsgi_schema.yml
M lib/galaxy/webapps/tool_shed/buildapp.py
A lib/galaxy/webapps/tool_shed/config_schema.yml
A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml
A lib/galaxy/webapps/uwsgi_schema.yml
M run.sh
M run_reports.sh
M run_tool_shed.sh
A scripts/common_startup_functions.sh
A scripts/config_sample_to_kwalify.py
M scripts/manage_tools.py
A test/unit/config/1607_root_filters/config/galaxy.ini
A test/unit/config/1607_root_filters/config/tool_shed.ini
A test/unit/config/1607_root_samples/config/galaxy.ini
A test/unit/config/1607_root_samples/config/reports.ini
A test/unit/config/1607_root_samples/config/tool_shed.ini
A test/unit/config/test_config_manage.py
Log Message:
-----------
Merge pull request #3179 from jmchilton/web_config_overhaul_0
Configuration & Server Overhaul - Tool Shed and Reports
Compare: https://github.com/galaxyproject/galaxy/compare/c6e45e7b0720...331851b0495d
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e72f5e81a4baffcb4679d6e74837daedcfa65f67
https://github.com/galaxyproject/galaxy/commit/e72f5e81a4baffcb4679d6e74837…
Author: Frederic Sapet <frederic.sapet(a)biogemma.com>
Date: 2017-06-16 (Fri, 16 Jun 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
deals with .xls older file extension
Commit: 5fec6c87cba14dd7692d8239669a02d6b5586748
https://github.com/galaxyproject/galaxy/commit/5fec6c87cba14dd7692d8239669a…
Author: Frederic Sapet <frederic.sapet(a)biogemma.com>
Date: 2017-06-16 (Fri, 16 Jun 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
indentation for Travis
Commit: 9cd9c81279d1d7749af7d9c64f8329e8cfc7f6bf
https://github.com/galaxyproject/galaxy/commit/9cd9c81279d1d7749af7d9c64f83…
Author: Frederic Sapet <frederic.sapet(a)biogemma.com>
Date: 2017-06-16 (Fri, 16 Jun 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
deals with .xls older file extension
Commit: 93dadd6db491700de46cafa4d52a0efe74cd6e94
https://github.com/galaxyproject/galaxy/commit/93dadd6db491700de46cafa4d52a…
Author: Frederic Sapet <frederic.sapet(a)biogemma.com>
Date: 2017-06-16 (Fri, 16 Jun 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
use subprocess instead of os.popen
Commit: 83b19889314a922ba3cf906f26fe7d3a34926533
https://github.com/galaxyproject/galaxy/commit/83b19889314a922ba3cf906f26fe…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/1.xls
Log Message:
-----------
Refine new Excel XLS datatype.
- Call it excel.xls so we maintain backward compatiblity with older xls datatype.
- Add an example file with a sniff test.
- Correct variable name for Python styling.
- Quote paths when using file command-line trick to sniff for the new type.
- Switch file command-line flag to one that produces the Mimetype on both Linux and Mac OS X.
Commit: 10285b8ecbbc6891a4954b5067198df2839a2957
https://github.com/galaxyproject/galaxy/commit/10285b8ecbbc6891a4954b506719…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Tweak Excel format phrasing based on review from @nsoranzo.
Commit: fbde34f8c8e823badd0f565bce4922512448b532
https://github.com/galaxyproject/galaxy/commit/fbde34f8c8e823badd0f565bce49…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Add EDAM format for excel.xls datatype.
Commit: c6e45e7b0720376886626393ae355e3398561035
https://github.com/galaxyproject/galaxy/commit/c6e45e7b0720376886626393ae35…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/1.xls
Log Message:
-----------
Merge pull request #4410 from jmchilton/excel97
Add Excel97 Datatype
Compare: https://github.com/galaxyproject/galaxy/compare/cca00ea5d87f...c6e45e7b0720
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e49ba40d771dae0d7056ed089c99f3d53a81b933
https://github.com/galaxyproject/galaxy/commit/e49ba40d771dae0d7056ed089c99…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/parameters/grouping.py
Log Message:
-----------
Generalize allow_library_path_paste to allow_path_paste.
Enable pasting paths in the history upload GUI & general purpose tools API for admin users if enabled.
Commit: f97efa6f90f80ced8bd0c794841e450813238710
https://github.com/galaxyproject/galaxy/commit/f97efa6f90f80ced8bd0c794841e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/parameters/grouping.py
Log Message:
-----------
Remove unused dataset_info in parameters.grouping.
Commit: cca00ea5d87fb0baba3ceca715038158cf2ceba0
https://github.com/galaxyproject/galaxy/commit/cca00ea5d87fb0baba3ceca71503…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/parameters/grouping.py
Log Message:
-----------
Merge pull request #4404 from jmchilton/allow_path_paste
Generalize allow_library_path_paste to allow_path_paste.
Compare: https://github.com/galaxyproject/galaxy/compare/33c794d27327...cca00ea5d87f
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 37a6c488b0cb99450e2781656eee2462bf539900
https://github.com/galaxyproject/galaxy/commit/37a6c488b0cb99450e2781656eee…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-29 (Sat, 29 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Remove unused template
Commit: 4ccb3e3874e0548289d746fee03a96250df9f1e3
https://github.com/galaxyproject/galaxy/commit/4ccb3e3874e0548289d746fee03a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-29 (Sat, 29 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Return roles grid as dictionary
Commit: 6c91bc287ef0846869f1604d2ebfd684fb550df4
https://github.com/galaxyproject/galaxy/commit/6c91bc287ef0846869f1604d2ebf…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-29 (Sat, 29 Jul 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Add client side routes
Commit: b8396a961facd7dada8d8db837386b656855c3b1
https://github.com/galaxyproject/galaxy/commit/b8396a961facd7dada8d8db83738…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-30 (Sun, 30 Jul 2017)
Changed paths:
M client/galaxy/scripts/apps/panels/admin-panel.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Add admin role editing options
Commit: 00432345ff20bbcf5023995b6cfb54937eb4be9e
https://github.com/galaxyproject/galaxy/commit/00432345ff20bbcf5023995b6cfb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-31 (Mon, 31 Jul 2017)
Changed paths:
M lib/tool_shed/util/admin_util.py
M templates/admin/user/reset_password.mako
M templates/admin/user/user.mako
Log Message:
-----------
Merge branch 'revise_page' into admin_grid_roles
Commit: d7717cfa8b8562d82742ba285d54e7d7ab794d2d
https://github.com/galaxyproject/galaxy/commit/d7717cfa8b8562d82742ba285d54…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-31 (Mon, 31 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Remove unused galaxy role grid operations
Commit: 8ee4c29a0579b2a9156f0cd4a70139758ed58b60
https://github.com/galaxyproject/galaxy/commit/8ee4c29a0579b2a9156f0cd4a701…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-01 (Tue, 01 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/layout/router.js
A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/nls/fr/locale.js
M config/tool_shed.ini.sample
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/security/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/workflow/modules.py
M static/maps/galaxy.js.map
M static/maps/layout/router.js.map
A static/maps/mvc/dataset/dataset-edit-attributes.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/galaxy.js
M static/scripts/layout/router.js
A static/scripts/mvc/dataset/dataset-edit-attributes.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/nls/fr/locale.js
R templates/webapps/galaxy/dataset/edit_attributes.mako
Log Message:
-----------
Merge branch 'revise_page' into admin_grid_roles
Commit: f76f9515a3b243bfb510f89aaa50e95a4990465f
https://github.com/galaxyproject/galaxy/commit/f76f9515a3b243bfb510f89aaa50…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-01 (Tue, 01 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Parse url parameters for message handling
Commit: e32661301cef0815fdd36743d1ab9901d2576ef2
https://github.com/galaxyproject/galaxy/commit/e32661301cef0815fdd36743d1ab…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-02 (Wed, 02 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/user/user-preferences.js
R client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/style/less/base.less
M config/plugins/webhooks/demo/search/static/script.js
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/workflow/workflow.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/workflow/workflow.js
M static/style/blue/base.css
Log Message:
-----------
Merge branch 'dev' into admin_grid_roles
Commit: 77608ac4105ee90e3323d74e2273618fd2d06ca7
https://github.com/galaxyproject/galaxy/commit/77608ac4105ee90e3323d74e2273…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/form/form-view.js
A client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/utils/query-string-parsing.js
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/managers/tags.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/util/admin_util.py
M static/maps/layout/menu.js.map
M static/maps/mvc/form/form-view.js.map
A static/maps/mvc/form/form-wrapper.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/utils/query-string-parsing.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/form/form-view.js
A static/scripts/mvc/form/form-wrapper.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/utils/query-string-parsing.js
R templates/admin/dataset_security/group/grid.mako
R templates/admin/dataset_security/role/grid.mako
R templates/admin/quota/grid.mako
R templates/admin/tool_version/grid.mako
R templates/admin/user/grid.mako
R templates/admin/user/reset_password.mako
R templates/admin/user/user.mako
A templates/webapps/tool_shed/admin/user/reset_password.mako
A templates/webapps/tool_shed/admin/user/user.mako
R templates/webapps/tool_shed/repository/grid.mako
Log Message:
-----------
Merge branch 'revise_grid_forms' into admin_grid_roles
Commit: b46f4e4c84f042a3b668020d6767b6777e2babb4
https://github.com/galaxyproject/galaxy/commit/b46f4e4c84f042a3b668020d6767…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Remove unused routing message handler
Commit: 44a339546b1849131b9c9f993aee332171217709
https://github.com/galaxyproject/galaxy/commit/44a339546b1849131b9c9f993aee…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/panels/admin-panel.js
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Fix menu link
Commit: ffe3ac294d8a21a10546f45518e4d2c52e1bc966
https://github.com/galaxyproject/galaxy/commit/ffe3ac294d8a21a10546f45518e4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Do not parse empty messages
Commit: 246e94ae8470e1ef78f1b136bcdc117f45e036ef
https://github.com/galaxyproject/galaxy/commit/246e94ae8470e1ef78f1b136bcdc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Build role renaming in client
Commit: 20ce574e3304af6cb09d98b9d8e17a7ff7c3c628
https://github.com/galaxyproject/galaxy/commit/20ce574e3304af6cb09d98b9d8e1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Add role renaming feature to revised endpoint
Commit: 99bf6809bebb621a33050164f2c7e2a2f203ae40
https://github.com/galaxyproject/galaxy/commit/99bf6809bebb621a33050164f2c7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Repack scripts
Commit: 5ab9ea4ffdb7c5359d32a0653f6ac59d9fc37d21
https://github.com/galaxyproject/galaxy/commit/5ab9ea4ffdb7c5359d32a0653f6a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-wrapper.js
M static/maps/mvc/form/form-wrapper.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/form/form-wrapper.js
Log Message:
-----------
Use primary button
Commit: 4d542820e70d02c0809d3bd8482746b90e68642d
https://github.com/galaxyproject/galaxy/commit/4d542820e70d02c0809d3bd84827…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-wrapper.js
M lib/galaxy/webapps/galaxy/api/users.py
M static/maps/mvc/form/form-wrapper.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/form/form-wrapper.js
Log Message:
-----------
Remove unused messages, set default message status
Commit: 502b2a068c06e190484fda2adcdc43ffef7d07e2
https://github.com/galaxyproject/galaxy/commit/502b2a068c06e190484fda2adcdc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/form/form-wrapper.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/form/form-wrapper.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Use redirect option for user preferences
Commit: b908e98e37de20aff2b18acd6b93b79b9020f4a8
https://github.com/galaxyproject/galaxy/commit/b908e98e37de20aff2b18acd6b93…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-wrapper.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-wrapper.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-buttons.js
M static/style/blue/base.css
Log Message:
-----------
Fix button and operations floating handling
Commit: bf6e2d26bd128e773ae3c604216e7b939abf8c01
https://github.com/galaxyproject/galaxy/commit/bf6e2d26bd128e773ae3c604216e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Fix floating for custom build form button
Commit: afa6964994fb6aa6acad44d03f4123f2f7726839
https://github.com/galaxyproject/galaxy/commit/afa6964994fb6aa6acad44d03f41…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-list.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-list.js
M static/style/blue/base.css
Log Message:
-----------
Fix style for list parameter
Commit: d11fc568a41a3dba540457f9d861182acfbae117
https://github.com/galaxyproject/galaxy/commit/d11fc568a41a3dba540457f9d861…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/grids/repository_grids.py
R templates/admin/tool_shed_repository/grid.mako
Log Message:
-----------
Merge branch 'revise_grid_forms' into admin_grid_roles
Commit: 9d8bdc6f304d676157f8c0e5a76f6c49dd9e5d4b
https://github.com/galaxyproject/galaxy/commit/9d8bdc6f304d676157f8c0e5a76f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-05 (Sat, 05 Aug 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
M static/maps/galaxy.js.map
M static/scripts/galaxy.js
Log Message:
-----------
Repack scripts
Commit: 1675b9cca2cc1c5aa8a4e495e23c0877a781cf39
https://github.com/galaxyproject/galaxy/commit/1675b9cca2cc1c5aa8a4e495e23c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-05 (Sat, 05 Aug 2017)
Changed paths:
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/maps/galaxy.js.map
M static/maps/layout/menu.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/galaxy.js
M static/scripts/layout/menu.js
M static/scripts/mvc/user/user-preferences.js
M templates/galaxy_client_app.mako
M templates/user/login.mako
M templates/user/register.mako
M templates/webapps/galaxy/history/display_structured.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M test/shed_functional/base/twilltestcase.py
Log Message:
-----------
Merge branch 'revise_grid_forms' into admin_grid_roles
Commit: d698d32ceb043fdb9820b68615748ca13e0825c8
https://github.com/galaxyproject/galaxy/commit/d698d32ceb043fdb9820b6861574…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Manage users and groups for role
Commit: 9ee062bd4622481165d4cb1e783454a49fcdd704
https://github.com/galaxyproject/galaxy/commit/9ee062bd4622481165d4cb1e7834…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Show current name and description when renaming roles
Commit: 183176a05c95e063a710ff469a368c463e18db2f
https://github.com/galaxyproject/galaxy/commit/183176a05c95e063a710ff469a36…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Add create role form
Commit: 663c6c13975b01cf0472a083a68164d9bd010871
https://github.com/galaxyproject/galaxy/commit/663c6c13975b01cf0472a083a681…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
R templates/admin/dataset_security/role/role.mako
R templates/admin/dataset_security/role/role_create.mako
R templates/admin/dataset_security/role/role_rename.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role_rename.mako
Log Message:
-----------
Fix boolean title, and move unused role makos to toolshed
Commit: e77fd47b034e6af5b19756bd778f5081332e7c85
https://github.com/galaxyproject/galaxy/commit/e77fd47b034e6af5b19756bd778f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix boolean handling
Commit: 419f3db64fb3614d5a70ed9a9eea8a260b6f5865
https://github.com/galaxyproject/galaxy/commit/419f3db64fb3614d5a70ed9a9eea…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/tool_shed/util/admin_util.py
Log Message:
-----------
Remove unused information feature for toolshed
Commit: 733e225ec96b058dd159dda4e18ba1f7572573fd
https://github.com/galaxyproject/galaxy/commit/733e225ec96b058dd159dda4e18b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M client/galaxy/scripts/utils/query-string-parsing.js
M static/maps/utils/query-string-parsing.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/utils/query-string-parsing.js
Log Message:
-----------
Fix message handling in user preference main view
Commit: a5d7c0fa84d8fe24fc94ac814b9f7502283de7c2
https://github.com/galaxyproject/galaxy/commit/a5d7c0fa84d8fe24fc94ac814b9f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-wrapper.js
M static/maps/mvc/form/form-wrapper.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-wrapper.js
Log Message:
-----------
Scroll to highlight message
Commit: 4b2eca373e936308b0550b9fabfc6494228b837a
https://github.com/galaxyproject/galaxy/commit/4b2eca373e936308b0550b9fabfc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Remove duplicate roles from selection list
Commit: 5a8adbf8b77dc985353803a724fc4344dcbbdc79
https://github.com/galaxyproject/galaxy/commit/5a8adbf8b77dc985353803a724fc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M doc/source/admin/special_topics/grt.rst
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/runners/util/cli/__init__.py
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/objectstore/s3_multipart_upload.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/history.py
R scripts/grt.py
R scripts/grt.yml.sample
A scripts/grt/export.py
A scripts/grt/grt.yml.sample
A scripts/grt/upload.py
M test/api/test_tools.py
A test/functional/tools/identifier_source.xml
M test/functional/tools/samples_tool_conf.xml
A test/unit/test_remote_shell.py
M test/unit/tools/test_toolbox.py
M test/unit/tools_support.py
M tox.ini
Log Message:
-----------
Merge branch 'remove_duplicates' into admin_grid_roles
Commit: a7c6c69cbf6a6eeffdf53815144e623576c47b13
https://github.com/galaxyproject/galaxy/commit/a7c6c69cbf6a6eeffdf53815144e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix lint
Commit: d3b8889c04ef22d740f8b668a8212c728ba5832c
https://github.com/galaxyproject/galaxy/commit/d3b8889c04ef22d740f8b668a821…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/panels/admin-panel.js
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Fix second role link in admin panel
Commit: c01023b5adc402a6a8662e9f319afcd9e4f5fc6e
https://github.com/galaxyproject/galaxy/commit/c01023b5adc402a6a8662e9f319a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix indention
Commit: d32a3a58a50bdbdbe6144a265ef3424a2f011ae2
https://github.com/galaxyproject/galaxy/commit/d32a3a58a50bdbdbe6144a265ef3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M config/datatypes_conf.xml.sample
A config/user_preferences_extra_conf.yml.sample
M lib/galaxy/config.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M templates/webapps/tool_shed/repository/common.mako
M test/unit/tools/test_parsing.py
Log Message:
-----------
Merge branch 'revise_page' into admin_grid_roles
Commit: 938bf525f46c8d3c7568d9b2a97edfa958ba900f
https://github.com/galaxyproject/galaxy/commit/938bf525f46c8d3c7568d9b2a97e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0135_add_library_tags.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Merge branch 'revise_grid_forms' into admin_grid_roles
Commit: be19b36ecaab43dd9cbf2fd5f80995e7ac9ff507
https://github.com/galaxyproject/galaxy/commit/be19b36ecaab43dd9cbf2fd5f809…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
A client/galaxy/scripts/mvc/job/job-params.js
M client/galaxy/style/less/galaxy_bootstrap/overrides.less
M config/datatypes_conf.xml.sample
A config/error_report.yml.sample
M config/tool_conf.xml.sample
A doc/source/admin/special_topics/bug_reports.rst
M doc/source/admin/special_topics/index.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/error_reports/__init__.py
A lib/galaxy/tools/error_reports/plugins/__init__.py
A lib/galaxy/tools/error_reports/plugins/biostars.py
A lib/galaxy/tools/error_reports/plugins/email.py
A lib/galaxy/tools/error_reports/plugins/json.py
A lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/errors.py
A lib/galaxy/tools/sort_collection_list.xml
M lib/galaxy/util/biostar.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M scripts/grt/export.py
M scripts/grt/upload.py
A static/maps/mvc/dataset/dataset-error.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
A static/maps/mvc/job/job-params.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/mvc/dataset/dataset-error.js
M static/scripts/mvc/dataset/dataset-li-edit.js
A static/scripts/mvc/job/job-params.js
M static/scripts/mvc/user/user-preferences.js
M static/style/blue/base.css
M templates/show_params.mako
R templates/webapps/galaxy/dataset/errors.mako
A test-data/test.vcf.gz
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/vcf_bgzip.xml
Log Message:
-----------
Merge branch 'revise_grid_forms' into admin_grid_roles
Commit: 33c794d273271b14732fb8037c2ea8105a3c688e
https://github.com/galaxyproject/galaxy/commit/33c794d273271b14732fb8037c2e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/utils/query-string-parsing.js
M client/galaxy/style/less/ui.less
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/tool_shed/util/admin_util.py
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-wrapper.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/mvc/ui/ui-list.js.map
M static/maps/mvc/user/user-custom-builds.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/utils/query-string-parsing.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-wrapper.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-list.js
M static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/utils/query-string-parsing.js
M static/style/blue/base.css
R templates/admin/dataset_security/role/role.mako
R templates/admin/dataset_security/role/role_create.mako
R templates/admin/dataset_security/role/role_rename.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role_rename.mako
Log Message:
-----------
Merge pull request #4385 from guerler/admin_grid_roles
Admin grid roles revision
Compare: https://github.com/galaxyproject/galaxy/compare/600b0aad7ce1...33c794d27327
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a7885e0b6e195ecc1beaab6f526ce52e927053c2
https://github.com/galaxyproject/galaxy/commit/a7885e0b6e195ecc1beaab6f526c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-03 (Thu, 03 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/user/user-preferences.js
A static/maps/mvc/form/form-wrapper.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/mvc/form/form-wrapper.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Generalize how user preferences build forms
Commit: ddcace7527d6fc20ce93c983d795ff3b35117191
https://github.com/galaxyproject/galaxy/commit/ddcace7527d6fc20ce93c983d795…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-03 (Thu, 03 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-wrapper.js
M static/maps/mvc/form/form-wrapper.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-wrapper.js
Log Message:
-----------
Remove unused options parsing
Commit: 6c11ffbe84f2e279607a5dd16f6d0532d26dc1f9
https://github.com/galaxyproject/galaxy/commit/6c11ffbe84f2e279607a5dd16f6d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-03 (Thu, 03 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
User generic form wrapper to reset password
Commit: cd8314808e67dc8a880c0bb16a1faf4e5a571456
https://github.com/galaxyproject/galaxy/commit/cd8314808e67dc8a880c0bb16a1f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-03 (Thu, 03 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/utils/query-string-parsing.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/maps/utils/query-string-parsing.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/utils/query-string-parsing.js
Log Message:
-----------
Allow array parsing through url
Commit: 06b5be23ddec4298cd78503e6e07f2949d882a6e
https://github.com/galaxyproject/galaxy/commit/06b5be23ddec4298cd78503e6e07…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-03 (Thu, 03 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Specify password reset form
Commit: e0ccec46b3f4f4d8f13091fa2f5dcafd987c7b51
https://github.com/galaxyproject/galaxy/commit/e0ccec46b3f4f4d8f13091fa2f5d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-03 (Thu, 03 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Move help info
Commit: c6dee98c55a46b23e9373ea53c4fa22e545978a3
https://github.com/galaxyproject/galaxy/commit/c6dee98c55a46b23e9373ea53c4f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Fix input types, repack scripts
Commit: 23b141a2ec3e5ff865a8ea0718d41b9845e79d64
https://github.com/galaxyproject/galaxy/commit/23b141a2ec3e5ff865a8ea0718d4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Complete new controller endpoint to reset passwords
Commit: 8312b07e60ee945fdde6ecc29eadcac9423ab3d5
https://github.com/galaxyproject/galaxy/commit/8312b07e60ee945fdde6ecc29ead…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M static/maps/mvc/form/form-wrapper.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-wrapper.js
M static/scripts/mvc/grid/grid-template.js
Log Message:
-----------
Allow form redirect to grid view
Commit: 4e050282652ea3c3cbf20998653acb9a34a85415
https://github.com/galaxyproject/galaxy/commit/4e050282652ea3c3cbf20998653a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Create dictionary for form definitions
Commit: f50e0ba5bba5fe6605bcbcc446ddb10f58ae898b
https://github.com/galaxyproject/galaxy/commit/f50e0ba5bba5fe6605bcbcc446dd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/form/form-wrapper.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/form/form-wrapper.js
Log Message:
-----------
Revise endpoint to manage user roles and groups, add initial message support to form wrapper
Commit: 7e1c40799efa67f43fe13b589ef2432b05fdebc3
https://github.com/galaxyproject/galaxy/commit/7e1c40799efa67f43fe13b589ef2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-wrapper.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/maps/mvc/form/form-wrapper.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-wrapper.js
Log Message:
-----------
Use initial method parsing for reset password info
Commit: 63ebee1a415a9433b01164ef72e90e08c177fc18
https://github.com/galaxyproject/galaxy/commit/63ebee1a415a9433b01164ef72e9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Add put handling to revised manage_roles_and_groups_for_user controller endpoint
Commit: e791ac29bb310cefcbcc8afd762c7c7ddec54586
https://github.com/galaxyproject/galaxy/commit/e791ac29bb310cefcbcc8afd762c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/util/admin_util.py
R templates/admin/user/grid.mako
R templates/admin/user/reset_password.mako
R templates/admin/user/user.mako
A templates/webapps/tool_shed/admin/user/reset_password.mako
A templates/webapps/tool_shed/admin/user/user.mako
Log Message:
-----------
Move user form grid makos to toolshed
Commit: 3007122bd9c9e111ef8d0010707ddac51bff6387
https://github.com/galaxyproject/galaxy/commit/3007122bd9c9e111ef8d0010707d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M templates/webapps/tool_shed/admin/user/reset_password.mako
M templates/webapps/tool_shed/admin/user/user.mako
Log Message:
-----------
Remove custom case handling for galaxy app from makos, restoring previous state
Commit: 146dd82f043c9adaa8f2891f03ab31f76b16af2e
https://github.com/galaxyproject/galaxy/commit/146dd82f043c9adaa8f2891f03ab…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/tool_shed/grids/admin_grids.py
R templates/admin/dataset_security/group/grid.mako
R templates/admin/dataset_security/role/grid.mako
R templates/admin/quota/grid.mako
R templates/admin/tool_version/grid.mako
R templates/webapps/tool_shed/repository/grid.mako
Log Message:
-----------
Remove unnecessary grid makos
Commit: c2b98bce78366b4daf33b76c7a1fe2d465212274
https://github.com/galaxyproject/galaxy/commit/c2b98bce78366b4daf33b76c7a1f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M lib/tool_shed/grids/repository_grids.py
Log Message:
-----------
Remove unused grid makos
Commit: 010a7dfb9ce1e0002c2ea81d7ff88dbe3c1ecb38
https://github.com/galaxyproject/galaxy/commit/010a7dfb9ce1e0002c2ea81d7ff8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
R templates/admin/tool_shed_repository/grid.mako
Log Message:
-----------
Remove unused toolshed grid mako
Commit: 96cc67a2caf6470c235d871878a86e6ebaca3b1c
https://github.com/galaxyproject/galaxy/commit/96cc67a2caf6470c235d871878a8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix lint
Commit: 9dc5ace31a5ec847e408baeaccb9dbd7433f02b7
https://github.com/galaxyproject/galaxy/commit/9dc5ace31a5ec847e408baeaccb9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-04 (Fri, 04 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Remove lines
Commit: d2d250b847f22934a2f1d3c1d2256b40c52abc55
https://github.com/galaxyproject/galaxy/commit/d2d250b847f22934a2f1d3c1d225…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-05 (Sat, 05 Aug 2017)
Changed paths:
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/maps/galaxy.js.map
M static/maps/layout/menu.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/galaxy.js
M static/scripts/layout/menu.js
M static/scripts/mvc/user/user-preferences.js
M templates/galaxy_client_app.mako
M templates/user/login.mako
M templates/user/register.mako
M templates/webapps/galaxy/history/display_structured.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M test/shed_functional/base/twilltestcase.py
Log Message:
-----------
Merge branch 'dev' into revise_grid_forms
Commit: f531d2c0c9810b2d0ee8f0482cb12e163bbc0de2
https://github.com/galaxyproject/galaxy/commit/f531d2c0c9810b2d0ee8f0482cb1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-05 (Sat, 05 Aug 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
M static/maps/galaxy.js.map
M static/maps/layout/menu.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/galaxy.js
M static/scripts/layout/menu.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Repack scripts
Commit: c49e749534f76c8bb2d0ea8bb629a6ee236ff5cc
https://github.com/galaxyproject/galaxy/commit/c49e749534f76c8bb2d0ea8bb629…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/tool_shed/util/admin_util.py
Log Message:
-----------
Fix user info link for toolshed
Commit: e477cce9b68d90a313d1534c3ad156f9eb8cc6ec
https://github.com/galaxyproject/galaxy/commit/e477cce9b68d90a313d1534c3ad1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M config/datatypes_conf.xml.sample
A config/user_preferences_extra_conf.yml.sample
M doc/source/admin/special_topics/grt.rst
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/util/cli/__init__.py
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0135_add_library_tags.py
M lib/galaxy/objectstore/s3_multipart_upload.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
R scripts/grt.py
R scripts/grt.yml.sample
A scripts/grt/export.py
A scripts/grt/grt.yml.sample
A scripts/grt/upload.py
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M templates/webapps/tool_shed/repository/common.mako
M test/api/test_tools.py
A test/functional/tools/identifier_source.xml
M test/functional/tools/samples_tool_conf.xml
A test/unit/test_remote_shell.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_toolbox.py
M test/unit/tools_support.py
M tox.ini
Log Message:
-----------
Merge branch 'revise_page' into revise_grid_forms
Commit: b8c05ede4dd188dce24c914912f8fa35963d9562
https://github.com/galaxyproject/galaxy/commit/b8c05ede4dd188dce24c914912f8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Log Message:
-----------
Merge branch 'dev' into revise_grid_forms
Commit: 583765c7c087c77c6d1f2756e4233ce97a71240f
https://github.com/galaxyproject/galaxy/commit/583765c7c087c77c6d1f2756e423…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
A client/galaxy/scripts/mvc/job/job-params.js
M client/galaxy/style/less/galaxy_bootstrap/overrides.less
M config/datatypes_conf.xml.sample
A config/error_report.yml.sample
M config/tool_conf.xml.sample
A doc/source/admin/special_topics/bug_reports.rst
M doc/source/admin/special_topics/index.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/error_reports/__init__.py
A lib/galaxy/tools/error_reports/plugins/__init__.py
A lib/galaxy/tools/error_reports/plugins/biostars.py
A lib/galaxy/tools/error_reports/plugins/email.py
A lib/galaxy/tools/error_reports/plugins/json.py
A lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/errors.py
A lib/galaxy/tools/sort_collection_list.xml
M lib/galaxy/util/biostar.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M scripts/grt/export.py
M scripts/grt/upload.py
A static/maps/mvc/dataset/dataset-error.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
A static/maps/mvc/job/job-params.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/mvc/dataset/dataset-error.js
M static/scripts/mvc/dataset/dataset-li-edit.js
A static/scripts/mvc/job/job-params.js
M static/style/blue/base.css
M templates/show_params.mako
R templates/webapps/galaxy/dataset/errors.mako
A test-data/test.vcf.gz
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/vcf_bgzip.xml
Log Message:
-----------
Merge branch 'dev' into revise_grid_forms
Commit: 600b0aad7ce10c1e427513684c4cd7423f5b52aa
https://github.com/galaxyproject/galaxy/commit/600b0aad7ce10c1e427513684c4c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/form/form-view.js
A client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/utils/query-string-parsing.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.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/util/admin_util.py
M static/maps/mvc/form/form-view.js.map
A static/maps/mvc/form/form-wrapper.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/utils/query-string-parsing.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/form/form-view.js
A static/scripts/mvc/form/form-wrapper.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/utils/query-string-parsing.js
R templates/admin/dataset_security/group/grid.mako
R templates/admin/dataset_security/role/grid.mako
R templates/admin/quota/grid.mako
R templates/admin/tool_shed_repository/grid.mako
R templates/admin/tool_version/grid.mako
R templates/admin/user/grid.mako
R templates/admin/user/reset_password.mako
R templates/admin/user/user.mako
A templates/webapps/tool_shed/admin/user/reset_password.mako
A templates/webapps/tool_shed/admin/user/user.mako
R templates/webapps/tool_shed/repository/grid.mako
Log Message:
-----------
Merge pull request #4377 from guerler/revise_grid_forms
Remove makos of admin user grid forms
Compare: https://github.com/galaxyproject/galaxy/compare/6353704e4b44...600b0aad7ce1
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: aa1ce50689dd464c5c1e8b8b333397031914afb5
https://github.com/galaxyproject/galaxy/commit/aa1ce50689dd464c5c1e8b8b3333…
Author: Vahid <VJalili(a)users.noreply.github.com>
Date: 2017-05-05 (Fri, 05 May 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Updated missing parameters check for OpenID
When you have the OpenID URL, you don't need to recreate the provider. Only create the provider, if its not already created.
Commit: dedc8eb1dc80804c7f43e08f8022f74edc2c91b3
https://github.com/galaxyproject/galaxy/commit/dedc8eb1dc80804c7f43e08f8022…
Author: Vahid <VJalili(a)users.noreply.github.com>
Date: 2017-05-12 (Fri, 12 May 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Inform that the default provider is being used.
Commit: a0e863f5706bfb7706e8dcb9e023a0f3c32a7629
https://github.com/galaxyproject/galaxy/commit/a0e863f5706bfb7706e8dcb9e023…
Author: Vahid <VJalili(a)users.noreply.github.com>
Date: 2017-05-12 (Fri, 12 May 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Updated all `openid_url` and `openid_provider` checks
Commit: a3c2ddff2b10a05eca6dfb460f8d539f2f595f19
https://github.com/galaxyproject/galaxy/commit/a3c2ddff2b10a05eca6dfb460f8d…
Author: Vahid <VJalili(a)users.noreply.github.com>
Date: 2017-05-12 (Fri, 12 May 2017)
Changed paths:
M openid/yahoo.xml
Log Message:
-----------
Corrected Yahoo OpenID endpoint
At the time of making this change, Yahoo OpenID endpoint has issues--It's not accessible.
This should be checked again later.
Commit: 6353704e4b44e9eded6571b467f52a6dd288387d
https://github.com/galaxyproject/galaxy/commit/6353704e4b44e9eded6571b467f5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
M openid/yahoo.xml
Log Message:
-----------
Merge pull request #4039 from VJalili/patch-11
Updated parameters check for OpenID
Compare: https://github.com/galaxyproject/galaxy/compare/bcdf2c84f6df...6353704e4b44
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 63865e11935724a02ae641857d802f8650a7f97d
https://github.com/galaxyproject/galaxy/commit/63865e11935724a02ae641857d80…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-07-07 (Fri, 07 Jul 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Add VcfGz datatype
This adds support for uploading VcfGz files in the upload box. When a
user does this, the file will not be uncompressed. Also adds
uncompressed preview.
TODO:
- Move Vcf class to BaseVcf
- Vcf and VcfGz should both inherit from BaseVcf
- Add a metadata element for VcfGz indexes (vzf.gz.tbi)
- Create index (in set_meta method of VcfGz class)
- Write test tools
This is a kcikstart to @ffinfo GCC hack project.
Commit: 83f1e82e84a79673b2913f9f4a6c63dc6d6526f4
https://github.com/galaxyproject/galaxy/commit/83f1e82e84a79673b2913f9f4a6c…
Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl>
Date: 2017-07-07 (Fri, 07 Jul 2017)
Changed paths:
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Added index job to vcf.gz files
Commit: f4e02700f5c27dfffab0034f2201b208533e42ba
https://github.com/galaxyproject/galaxy/commit/f4e02700f5c27dfffab0034f2201…
Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl>
Date: 2017-07-07 (Fri, 07 Jul 2017)
Changed paths:
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Fixed some spacings
Commit: e9daa0d74464534a490129476f027455dbf26a69
https://github.com/galaxyproject/galaxy/commit/e9daa0d74464534a490129476f02…
Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl>
Date: 2017-07-07 (Fri, 07 Jul 2017)
Changed paths:
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Fixed import order
Commit: b96b5076cec2624cc1700bfcec43fd7745d0c0e5
https://github.com/galaxyproject/galaxy/commit/b96b5076cec2624cc1700bfcec43…
Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl>
Date: 2017-07-07 (Fri, 07 Jul 2017)
Changed paths:
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Fixed import order (again ;) )
Commit: 986379fd0d65c0e5d2d6bdcf1428ba5182713ae7
https://github.com/galaxyproject/galaxy/commit/986379fd0d65c0e5d2d6bdcf1428…
Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl>
Date: 2017-07-07 (Fri, 07 Jul 2017)
Changed paths:
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Fixed import order (again ;) )
Commit: 9d98f10767d7c43e979720ba8a9badee86501c78
https://github.com/galaxyproject/galaxy/commit/9d98f10767d7c43e979720ba8a9b…
Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl>
Date: 2017-07-07 (Fri, 07 Jul 2017)
Changed paths:
M lib/galaxy/datatypes/tabular.py
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/vcf_bgzip.xml
Log Message:
-----------
Adding test tool
Commit: 99703469c0a30348683190a894a0fc682f92ff68
https://github.com/galaxyproject/galaxy/commit/99703469c0a30348683190a894a0…
Author: pjvan_thof <pjrvanthof(a)gmail.com>
Date: 2017-07-07 (Fri, 07 Jul 2017)
Changed paths:
A test-data/test.vcf.gz
Log Message:
-----------
Added test file
Commit: e29611f52dba5e44924b39009ee28c933f4ba7fd
https://github.com/galaxyproject/galaxy/commit/e29611f52dba5e44924b39009ee2…
Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl>
Date: 2017-07-07 (Fri, 07 Jul 2017)
Changed paths:
M test/functional/tools/vcf_bgzip.xml
Log Message:
-----------
Fixing formats in test
Commit: ed2e71a8383698543d97f339bd2b1175a5c07986
https://github.com/galaxyproject/galaxy/commit/ed2e71a8383698543d97f339bd2b…
Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl>
Date: 2017-07-07 (Fri, 07 Jul 2017)
Changed paths:
M test/functional/tools/vcf_bgzip.xml
Log Message:
-----------
Fixing tool format
Commit: 77b948678d69769c3d6c117a4dc718b3b3cb8388
https://github.com/galaxyproject/galaxy/commit/77b948678d69769c3d6c117a4dc7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-07-07 (Fri, 07 Jul 2017)
Changed paths:
M test/functional/tools/sample_datatypes_conf.xml
Log Message:
-----------
Add vcf_bgzip and dependent datatypes to test/functional/tools/sample_datatypes_conf.xml
Commit: 5cc71d2e3c009841c96657d2c359dbe5182548b8
https://github.com/galaxyproject/galaxy/commit/5cc71d2e3c009841c96657d2c359…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-07-07 (Fri, 07 Jul 2017)
Changed paths:
M lib/galaxy/datatypes/tabular.py
M test/functional/tools/vcf_bgzip.xml
Log Message:
-----------
Simplify vcf_bgzip.xml test wrapper and fix index file access
Commit: ed67b117517920affeb71982f08bc355ed0a6cda
https://github.com/galaxyproject/galaxy/commit/ed67b117517920affeb71982f08b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Use with statement in VcfGz class
Commit: bcdf2c84f6df020e81c8868b10bcf337e2d72630
https://github.com/galaxyproject/galaxy/commit/bcdf2c84f6df020e81c8868b10bc…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/tabular.py
A test-data/test.vcf.gz
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/vcf_bgzip.xml
Log Message:
-----------
Merge pull request #4254 from ffinfo/vcf_gz_datatype
Vcf gz datatype
Compare: https://github.com/galaxyproject/galaxy/compare/e3de5e250d02...bcdf2c84f6df
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e0d8db05b8707b01a42a7be3e46df627bbdf0307
https://github.com/galaxyproject/galaxy/commit/e0d8db05b8707b01a42a7be3e46d…
Author: Jorrit Boekel <jorrit.boekel(a)scilifelab.se>
Date: 2017-07-21 (Fri, 21 Jul 2017)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/sort_collection_list.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Created alphabetic and numerical sort tool for collection operations
Commit: e3de5e250d02d105aff4265a0caf13553e3c3ade
https://github.com/galaxyproject/galaxy/commit/e3de5e250d02d105aff4265a0caf…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/sort_collection_list.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #4329 from glormph/collection_list_sort
Created alphabetic and numerical sort tool for collection operations
Compare: https://github.com/galaxyproject/galaxy/compare/fcd06a96d613...e3de5e250d02