Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 09b42113c6b9fb1bcddbe66a86e299866431c9a4
https://github.com/galaxyproject/galaxy/commit/09b42113c6b9fb1bcddbe66a86e2…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-07-14 (Thu, 14 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M static/maps/mvc/collection/collection-li.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/history/hdca-li-edit.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/hdca-model.js.map
M static/maps/mvc/history/history-contents.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/collection/collection-li.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/hdca-model.js
M static/scripts/mvc/history/history-contents.js
Log Message:
-----------
UI, history: implement list:list
Commit: 3646d08d7ff2303be21e9c12050a55039dc1219a
https://github.com/galaxyproject/galaxy/commit/3646d08d7ff2303be21e9c12050a…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-07-14 (Thu, 14 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
M static/maps/mvc/history/history-contents.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/history/history-contents.js
Log Message:
-----------
UI, history: more feedback on bad collection type
Commit: 510fe47ae19c170001eac652c83316d3fd2b181b
https://github.com/galaxyproject/galaxy/commit/510fe47ae19c170001eac652c833…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-07-14 (Thu, 14 Jul 2016)
Changed paths:
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:
-----------
(bundle scripts)
Commit: 4bf21e624ecea88ce67a9a802f6bd08b137e9a79
https://github.com/galaxyproject/galaxy/commit/4bf21e624ecea88ce67a9a802f6b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-07-18 (Mon, 18 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/util/__init__.py
M lib/galaxy/web/framework/decorators.py
M static/maps/mvc/history/history-contents.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/history/history-contents.js
M templates/ind_share_base.mako
M tools/stats/gsummary.xml
Log Message:
-----------
Merge remote-tracking branch 'galaxyproject/dev' into HEAD
Conflicts:
static/maps/mvc/history/history-contents.js.map
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
static/scripts/mvc/history/history-contents.js
Compare: https://github.com/galaxyproject/galaxy/compare/3b19a061cf89...4bf21e624ece
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 9d3b304879959f9cea76cd2dd242b2eea6c1c478
https://github.com/galaxyproject/galaxy/commit/9d3b304879959f9cea76cd2dd242…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-07-07 (Thu, 07 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
M static/maps/mvc/history/history-contents.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/history/history-contents.js
Log Message:
-----------
UI, history: stringify contents copy params
Commit: 96cca7ccadba60c7aac970e656bf0932070b9d00
https://github.com/galaxyproject/galaxy/commit/96cca7ccadba60c7aac970e656bf…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-07-07 (Thu, 07 Jul 2016)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/galaxy/web/framework/decorators.py
Log Message:
-----------
Core, request body: handle hex vs. float better
When parsing a non-json request body, params for a payload have
been parsed individually using loads on a single value. This can cause
a hex id in the (regex) form '\d+e\d+' to be parsed as a float.
This commit:
- adds a parse_non_hex_float function that refuses to parse scientific
notation in the above form
- and uses it *only* in the payload parsing method for non-json request
bodies
Commit: d157865857589ef73a164219dc4ed630a16520ca
https://github.com/galaxyproject/galaxy/commit/d157865857589ef73a164219dc4e…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-07-11 (Mon, 11 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/workflow/modules.py
M scripts/common_startup.sh
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-template.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/dataset/data.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-template.js
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into fix.hex-vs-float
Commit: 3b19a061cf896ea1eed9933bf6bda549be7d8a06
https://github.com/galaxyproject/galaxy/commit/3b19a061cf896ea1eed9933bf6bd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-18 (Mon, 18 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
M lib/galaxy/util/__init__.py
M lib/galaxy/web/framework/decorators.py
M static/maps/mvc/history/history-contents.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/history/history-contents.js
Log Message:
-----------
Merge pull request #2597 from carlfeberhard/fix.hex-vs-float
Fix hex vs float parsing in request body
Compare: https://github.com/galaxyproject/galaxy/compare/389b2f4fbd2e...3b19a061cf89
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c9291d0c949cb1469f62f53a3b4b370fd1b2f20f
https://github.com/galaxyproject/galaxy/commit/c9291d0c949cb1469f62f53a3b4b…
Author: Pablo Moreno <pcm32(a)users.noreply.github.com>
Date: 2016-07-14 (Thu, 14 Jul 2016)
Changed paths:
M .ci/py3_sources.txt
M Makefile
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/plugins/interactive_environments/jupyter/config/jupyter.xml
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/molecules.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/datatypes/util/gff_util.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/context.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
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
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
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
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0061_tasks.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
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/0076_fix_form_values_data_corruption.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
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
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
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
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
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
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
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
A lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/workflow/modules.py
M scripts/api/data_manager_example_execute.py
M scripts/api/example_watch_folder.py
M scripts/api/form_create_from_xml.py
M scripts/api/history_create_history.py
M scripts/api/history_delete_history.py
M scripts/api/import_library_dataset_to_history.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/library_create_folder.py
M scripts/api/library_create_library.py
M scripts/api/library_upload_from_import_dir.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/request_type_create_from_xml.py
M scripts/api/requests_update_state.py
M scripts/api/sample_dataset_update_status.py
M scripts/api/sample_update_state.py
M scripts/api/search.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/upload_to_history.py
M scripts/api/workflow_delete.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_import.py
M scripts/api/workflow_import_from_file_rpark.py
M scripts/bootstrap_history.py
M scripts/build_toolbox.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
M scripts/data_libraries/build_whoosh_index.py
M scripts/db_shell.py
M scripts/drmaa_external_runner.py
M scripts/fetch_eggs.py
M setup.cfg
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-template.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/dataset/data.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-template.js
M templates/admin/impersonate.mako
M templates/user/change_password.mako
M test/api/helpers.py
M test/api/test_datasets.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
A test/functional/tools/identifier_collection.xml
M test/functional/tools/samples_tool_conf.xml
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional_tests.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/managers/base.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/test_galaxy_mapping.py
M test/unit/tools/test_toolbox.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 tools/stats/aggregate_scores_in_intervals.py
M tox.ini
Log Message:
-----------
Merge pull request #6 from galaxyproject/dev
keeps up to date with galaxy:dev
Commit: 4230a107373921c766d5dd6f19f405f54fafe1ab
https://github.com/galaxyproject/galaxy/commit/4230a107373921c766d5dd6f19f4…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-07-14 (Thu, 14 Jul 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Reinstates workingDir setup for container on k8s. This was removed by mistake previously.
Commit: 389b2f4fbd2e0f689f0e11ffc08f01f193e6026a
https://github.com/galaxyproject/galaxy/commit/389b2f4fbd2e0f689f0e11ffc08f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-18 (Mon, 18 Jul 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Merge pull request #2616 from phnmnl/feature/missingWorkingDirK8sOption
Kubernetes runner corrects working directory not passed to container
Compare: https://github.com/galaxyproject/galaxy/compare/5b3a27c0b0e2...389b2f4fbd2e
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: ca82e6d746a685209b9585b3f69128a55198f801
https://github.com/galaxyproject/galaxy/commit/ca82e6d746a685209b9585b3f691…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-06-25 (Sat, 25 Jun 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Deletes existing jobs with same ID when re-submitting.
Commit: 01fd25b9f4b79b4f2868efc51ad76e19fc132b5d
https://github.com/galaxyproject/galaxy/commit/01fd25b9f4b79b4f2868efc51ad7…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-06-25 (Sat, 25 Jun 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Changes use of produce_unique_k8s_job_name to be able to use both job and job_wrappers.
Commit: 409eb373cd9233f7925c64e9c5716859a2363ba1
https://github.com/galaxyproject/galaxy/commit/409eb373cd9233f7925c64e9c571…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-06-25 (Sat, 25 Jun 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Fixes stop job method so that it correctly scales down the Kubernetes job.
Commit: 65a937965a22c46922f9b731475561e38809e588
https://github.com/galaxyproject/galaxy/commit/65a937965a22c46922f9b7314755…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-06-26 (Sun, 26 Jun 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Improves handling of Kubernetes logs
Commit: e8bf2df21fe7fb7405ea283a41eae22e6d58509f
https://github.com/galaxyproject/galaxy/commit/e8bf2df21fe7fb7405ea283a41ea…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-06-26 (Sun, 26 Jun 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Corrects usage of pods retrials parameters set in runner and container destinations.
Commit: 89b5f3f47f14fa82065b83326332313ec8cca629
https://github.com/galaxyproject/galaxy/commit/89b5f3f47f14fa82065b83326332…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-06-26 (Sun, 26 Jun 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Uses exception instead of pykube.exceptions.HTTPError to manage missing pod's log exception.
Commit: 9db3453e6559cb883af22793b741a84f3abd071c
https://github.com/galaxyproject/galaxy/commit/9db3453e6559cb883af22793b741…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-06-26 (Sun, 26 Jun 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Overrides parent fail_job to save stdout/stderr of pods when Kubernetes job fails (otherwise lost).
Commit: 5eb60b3448f2cdf8706aa2ab43e4d51dcfc0a0cb
https://github.com/galaxyproject/galaxy/commit/5eb60b3448f2cdf8706aa2ab43e4…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-06-28 (Tue, 28 Jun 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Adds missing whitespace to line in Kubernetes runner.
Commit: f3e9736ca3a592d9aed006ecfd072f67cebfa006
https://github.com/galaxyproject/galaxy/commit/f3e9736ca3a592d9aed006ecfd07…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-07-11 (Mon, 11 Jul 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Merge pull request #2559 from phnmnl/feature/failingPodsNotDetected
Kubernetes runner: improves handling of failed jobs
Compare: https://github.com/galaxyproject/galaxy/compare/a74a23764cc1...f3e9736ca3a5