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August 2015
- 1 participants
- 124 discussions
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 4dc92f5fb926f024865f004df3b48e760f4ea682
https://github.com/galaxyproject/galaxy/commit/4dc92f5fb926f024865f004df3b4…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-08-18 (Tue, 18 Aug 2015)
Changed paths:
A lib/galaxy/webapps/tool_shed/api/configuration.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
Log Message:
-----------
expose TS version through API
Commit: 5d0b2b5a87283dcd4149f780ed9093dca96c313f
https://github.com/galaxyproject/galaxy/commit/5d0b2b5a87283dcd4149f780ed90…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-08-18 (Tue, 18 Aug 2015)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/configuration.py
Log Message:
-----------
feed flake8
Commit: 5c263416de4f53129bba1ef4e9947694d474d7ef
https://github.com/galaxyproject/galaxy/commit/5c263416de4f53129bba1ef4e994…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-18 (Tue, 18 Aug 2015)
Changed paths:
A lib/galaxy/webapps/tool_shed/api/configuration.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
Log Message:
-----------
Merge pull request #613 from martenson/expose-api-ts-version
expose TS version through API
Compare: https://github.com/galaxyproject/galaxy/compare/b6e0ba29521b...5c263416de4f
1
0
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 8e818eade44799758a7db5d78bb6442279d59b28
https://github.com/galaxyproject/usegalaxy-playbook/commit/8e818eade4479975…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-08-18 (Tue, 18 Aug 2015)
Changed paths:
M stage/group_vars/toolshedservers.yml
Log Message:
-----------
update TTS
1
0

[galaxyproject/galaxy] a0cd5b: [WIP] Separate upload modal and default upload vie...
by GitHub 18 Aug '15
by GitHub 18 Aug '15
18 Aug '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a0cd5b7410c0136c874649bdc41f5c7e6a369e46
https://github.com/galaxyproject/galaxy/commit/a0cd5b7410c0136c874649bdc41f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-16 (Thu, 16 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/upload-button.js
A client/galaxy/scripts/mvc/upload/upload-view-default.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M static/maps/mvc/upload/upload-button.js.map
A static/maps/mvc/upload/upload-view-default.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/upload/upload-button.js
A static/scripts/mvc/upload/upload-view-default.js
M static/scripts/mvc/upload/upload-view.js
Log Message:
-----------
[WIP] Separate upload modal and default upload view, insert tabs
Commit: 85fc57696f0f92014780134ade8a1482dd61dca6
https://github.com/galaxyproject/galaxy/commit/85fc57696f0f92014780134ade8a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-17 (Fri, 17 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/mvc/upload/upload-view-default.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/style/less/upload.less
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/upload/upload-settings.js.map
M static/maps/mvc/upload/upload-view-default.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/upload/upload-settings.js
M static/scripts/mvc/upload/upload-view-default.js
M static/scripts/mvc/upload/upload-view.js
M static/style/blue/base.css
Log Message:
-----------
[WIP] Reinserting button panel
Commit: f42981810af88c46da482cba940b3c580ee3b193
https://github.com/galaxyproject/galaxy/commit/f42981810af88c46da482cba940b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-17 (Fri, 17 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/upload/upload-view-default.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/upload/upload-view-default.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/upload/upload-view-default.js
M static/scripts/mvc/upload/upload-view.js
Log Message:
-----------
[WIP] Fix button states
Commit: f36f7854568462bc9615fa7edd45425c49708410
https://github.com/galaxyproject/galaxy/commit/f36f7854568462bc9615fa7edd45…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-17 (Fri, 17 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/upload/upload-view-default.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/style/less/upload.less
M static/maps/mvc/upload/upload-view-default.js.map
M static/scripts/mvc/upload/upload-view-default.js
M static/scripts/mvc/upload/upload-view.js
M static/style/blue/base.css
Log Message:
-----------
[WIP] Adjust styles
Commit: ad661147e82e72641e5709dd3a131017d0227e13
https://github.com/galaxyproject/galaxy/commit/ad661147e82e72641e5709dd3a13…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-17 (Fri, 17 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/style/less/upload.less
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/upload/upload-view.js
M static/style/blue/base.css
Log Message:
-----------
[WIP] Style adjustments
Commit: 3678c111a6547cbcebc48101a39afa42601a481d
https://github.com/galaxyproject/galaxy/commit/3678c111a6547cbcebc48101a39a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-18 (Sat, 18 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/style/less/upload.less
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/upload/upload-view.js
M static/style/blue/base.css
Log Message:
-----------
Prepare composite tab
Commit: 04eadf4bfcec7b1848ad4c2e6d84607b40c4eb16
https://github.com/galaxyproject/galaxy/commit/04eadf4bfcec7b1848ad4c2e6d84…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-18 (Sat, 18 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/utils/uploadbox.js
M static/maps/utils/uploadbox.js.map
M static/scripts/mvc/upload/upload-view.js
M static/scripts/utils/uploadbox.js
Log Message:
-----------
Fix uploadbox trigger for local upload
Commit: dbc1bd50b425522cfc4cb22369e9efa59c5d3357
https://github.com/galaxyproject/galaxy/commit/dbc1bd50b425522cfc4cb22369e9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-18 (Sat, 18 Jul 2015)
Changed paths:
M client/galaxy/scripts/utils/uploadbox.js
M static/maps/utils/uploadbox.js.map
M static/scripts/utils/uploadbox.js
Log Message:
-----------
Code style adjustments for uploadbox code
Commit: 51dca28794f68ec07647854373d94b33aed19e6e
https://github.com/galaxyproject/galaxy/commit/51dca28794f68ec07647854373d9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-21 (Tue, 21 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/upload-view.js
M lib/galaxy/webapps/galaxy/api/datatypes.py
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/upload/upload-view.js
Log Message:
-----------
[WIP] Continue API integration
Commit: 64a7b9e197d1c029a8846a5cbd1485972ddcab6f
https://github.com/galaxyproject/galaxy/commit/64a7b9e197d1c029a8846a5cbd14…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-23 (Thu, 23 Jul 2015)
Changed paths:
M lib/galaxy/util/bunch.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
Log Message:
-----------
Add composite datatype details to datatypes api response
Commit: a022738cf2f70555f1f8dc67026e87200e5e87a3
https://github.com/galaxyproject/galaxy/commit/a022738cf2f70555f1f8dc67026e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-23 (Thu, 23 Jul 2015)
Changed paths:
M client/galaxy/scripts/utils/uploadbox.js
M static/maps/utils/uploadbox.js.map
M static/scripts/utils/uploadbox.js
Log Message:
-----------
Move uploadbox variables to local scope
Commit: 3c6a43148ab571a950b0009c1cdb43c6186841f0
https://github.com/galaxyproject/galaxy/commit/3c6a43148ab571a950b0009c1cdb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-23 (Thu, 23 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/upload-view-default.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M static/maps/mvc/upload/upload-view-default.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/upload/upload-view-default.js
M static/scripts/mvc/upload/upload-view.js
Log Message:
-----------
Parse composite file details to front-end, hide in regular upload view
Commit: 486bbb0bf5d7a866a7205aab03d8b63279f3b3de
https://github.com/galaxyproject/galaxy/commit/486bbb0bf5d7a866a7205aab03d8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-27 (Mon, 27 Jul 2015)
Changed paths:
R client/galaxy/scripts/mvc/upload/upload-row.js
R client/galaxy/scripts/mvc/upload/upload-view-default.js
M client/galaxy/scripts/mvc/upload/upload-view.js
R static/maps/mvc/upload/upload-row.js.map
R static/maps/mvc/upload/upload-view-default.js.map
M static/maps/mvc/upload/upload-view.js.map
R static/scripts/mvc/upload/upload-row.js
R static/scripts/mvc/upload/upload-view-default.js
M static/scripts/mvc/upload/upload-view.js
Log Message:
-----------
Separate regular and composite upload elements into directories
Commit: a390f071cc453d7d2895ba6e30ffd025414d63b3
https://github.com/galaxyproject/galaxy/commit/a390f071cc453d7d2895ba6e30ff…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-27 (Mon, 27 Jul 2015)
Changed paths:
A client/galaxy/scripts/mvc/upload/composite/composite-row.js
A client/galaxy/scripts/mvc/upload/composite/composite-view.js
A client/galaxy/scripts/mvc/upload/default/default-row.js
A client/galaxy/scripts/mvc/upload/default/default-view.js
A static/maps/mvc/upload/composite/composite-row.js.map
A static/maps/mvc/upload/composite/composite-view.js.map
A static/maps/mvc/upload/default/default-row.js.map
A static/maps/mvc/upload/default/default-view.js.map
A static/scripts/mvc/upload/composite/composite-row.js
A static/scripts/mvc/upload/composite/composite-view.js
A static/scripts/mvc/upload/default/default-row.js
A static/scripts/mvc/upload/default/default-view.js
Log Message:
-----------
Add separated files, repack
Commit: 3c372fce95c90ee1f1d5599155471f8bc16983b2
https://github.com/galaxyproject/galaxy/commit/3c372fce95c90ee1f1d559915547…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-27 (Mon, 27 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/style/less/upload.less
M static/maps/mvc/upload/composite/composite-view.js.map
M static/scripts/mvc/upload/composite/composite-view.js
M static/style/blue/base.css
Log Message:
-----------
Fix and adjust styles for composite upload view
Commit: 95ed2a2921110686a55afff909b466aa7bb7022b
https://github.com/galaxyproject/galaxy/commit/95ed2a2921110686a55afff909b4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-29 (Wed, 29 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-model.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/style/less/upload.less
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-model.js.map
M static/maps/mvc/upload/upload-settings.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-row.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-model.js
M static/scripts/mvc/upload/upload-settings.js
M static/style/blue/base.css
Log Message:
-----------
[WIP] Further customizations and adjustments of the upload ui
Commit: e5d61f3766588a4b9624a085035d20282bcd67a6
https://github.com/galaxyproject/galaxy/commit/e5d61f3766588a4b9624a085035d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-29 (Wed, 29 Jul 2015)
Changed paths:
A .ci/flake8_blacklist.txt
M .ci/flake8_wrapper.sh
R .ci/pep8_sources.txt
M client/GruntFile.js
M client/README.md
M client/bower.json
M client/galaxy/scripts/libs/handlebars.runtime.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/history/history-panel.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/list/list-panel.js
M client/galaxy/scripts/mvc/tools.js
M client/galaxy/scripts/mvc/ui/ui-slider.js
R client/galaxy/scripts/templates/compile_templates.py
M client/galaxy/scripts/templates/compiled/panel_section.js
M client/galaxy/scripts/templates/compiled/tool_form.js
M client/galaxy/scripts/templates/compiled/tool_link.js
M client/galaxy/scripts/templates/compiled/tool_search.js
M client/galaxy/scripts/utils/config.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/galaxy_bootstrap/variables.less
M client/galaxy/style/less/history.less
M client/galaxy/style/less/trackster.less
M client/galaxy/style/source_material/circle.py
M client/grunt-tasks/style.js
A client/grunt-tasks/templates.js
M client/package.json
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M contrib/nagios/check_galaxy.py
M cron/add_manual_builds.py
M cron/build_chrom_db.py
M cron/parse_builds_3_sites.py
M doc/patch.py
M lib/galaxy/__init__.py
A lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/subcollections.py
M lib/galaxy/dataset_collections/types/__init__.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/fasta_to_len.py
M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_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/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.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/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/__init__.py
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/dataproviders/chunk.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/decorators.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/metadata.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/registry.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/tracks.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/eggs/__init__.py
M lib/galaxy/eggs/dist.py
M lib/galaxy/eggs/scramble.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/result_handlers/__init__.py
M lib/galaxy/external_services/result_handlers/basic.py
M lib/galaxy/external_services/service.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/datasets.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/deferred/manual_data_transfer.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/metrics/formatting.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/lwr.py
M lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/state_handler_factory.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/jobs/splitters/basic.py
M lib/galaxy/jobs/splitters/multi.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/annotatable.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/containers.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/secured.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/taggable.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/visualizations.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.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/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/0018_ordered_tags_and_page_tags.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/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.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/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/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.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/0053_item_ratings.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/0058_history_import_export.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/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.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/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.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/0104_update_genome_downloader_job_parameters.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.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/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/orm/__init__.py
M lib/galaxy/model/orm/logging_connection_proxy.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/model/search.py
M lib/galaxy/model/tool_shed_install/mapping.py
M lib/galaxy/model/tool_shed_install/migrate/check.py
M lib/galaxy/objectstore/s3_multipart_upload.py
M lib/galaxy/openid/providers.py
M lib/galaxy/queue_worker.py
M lib/galaxy/quota/__init__.py
M lib/galaxy/sample_tracking/data_transfer.py
M lib/galaxy/sample_tracking/external_service_types.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/sample_tracking/sample.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/deps/__init__.py
A lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/aliaspickler.py
M lib/galaxy/util/backports/importlib/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/dbkeys.py
M lib/galaxy/util/debugging.py
M lib/galaxy/util/dictobj.py
M lib/galaxy/util/expressions.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/inflection.py
M lib/galaxy/util/jstree.py
M lib/galaxy/util/log/__init__.py
M lib/galaxy/util/log/fluent_log.py
M lib/galaxy/util/lrucache.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/odict.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/specs.py
M lib/galaxy/util/sqlite.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/template.py
M lib/galaxy/util/topsort.py
M lib/galaxy/util/validation.py
M lib/galaxy/visualization/data_providers/basic.py
M lib/galaxy/visualization/data_providers/cigar.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/phyloviz/__init__.py
M lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py
M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/web/buildapp.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/formbuilder.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/error.py
M lib/galaxy/web/framework/middleware/profile.py
M lib/galaxy/web/framework/middleware/request_id.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/middleware/static.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/params.py
M lib/galaxy/webapps/galaxy/api/annotations.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/extended_metadata.py
M lib/galaxy/webapps/galaxy/api/forms.py
M lib/galaxy/webapps/galaxy/api/genomes.py
M lib/galaxy/webapps/galaxy/api/group_roles.py
M lib/galaxy/webapps/galaxy/api/group_users.py
M lib/galaxy/webapps/galaxy/api/groups.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/item_tags.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/metrics.py
M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/request_types.py
M lib/galaxy/webapps/galaxy/api/requests.py
M lib/galaxy/webapps/galaxy/api/roles.py
M lib/galaxy/webapps/galaxy/api/samples.py
M lib/galaxy/webapps/galaxy/api/tool_data.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/biostar.py
M lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/error.py
M lib/galaxy/webapps/galaxy/controllers/external_service.py
M lib/galaxy/webapps/galaxy/controllers/external_services.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library.py
M lib/galaxy/webapps/galaxy/controllers/library_admin.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/mobile.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/request_type.py
M lib/galaxy/webapps/galaxy/controllers/requests.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.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
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/__init__.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/root.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/system.py
M lib/galaxy/webapps/reports/controllers/users.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/galaxy/webapps/tool_shed/__init__.py
M lib/galaxy/webapps/tool_shed/api/authenticate.py
M lib/galaxy/webapps/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/api/users.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/groups.py
M lib/galaxy/webapps/tool_shed/controllers/hg.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/galaxy/webapps/tool_shed/model/migrate/check.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
M lib/galaxy/webapps/tool_shed/search/repo_search.py
M lib/galaxy/webapps/tool_shed/search/tool_search.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/galaxy/webapps/tool_shed/util/ratings_util.py
M lib/galaxy/workflow/modules.py
M lib/galaxy_ext/metadata/__init__.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/log_tempfile.py
M lib/mimeparse.py
M lib/psyco_full.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M lib/tool_shed/managers/groups.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/scripts/api/common.py
M lib/tool_shed/scripts/check_repositories_for_functional_tests.py
M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/review_util.py
M lib/tool_shed/util/search_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_dependency_util.py
M scripts/api/common.py
A scripts/auth/pam_auth_helper.py
M scripts/bootstrap_history.py
M scripts/build_toolbox.py
M scripts/build_universe_config.py
M scripts/check_eggs.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/cleanup_datasets.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/db_shell.py
M scripts/dist-scramble.py
M scripts/drmaa_external_killer.py
M scripts/drmaa_external_runner.py
M scripts/edam_mapping.py
M scripts/egg_packager_template.py
M scripts/external_chown_script.py
M scripts/extract_dataset_part.py
M scripts/extract_toolbox_sections.py
M scripts/fetch_eggs.py
M scripts/functional_tests.py
M scripts/get_platforms.py
M scripts/helper.py
M scripts/make_egg_packager.py
M scripts/metagenomics/convert_title.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/create_bacteria_table.py
M scripts/migrate_tools/migrate_tools.py
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M scripts/paster.py
M scripts/runtime_stats.py
M scripts/scramble.py
M scripts/scramble/lib/scramble_lib.py
M scripts/scramble/scripts/DRMAA_python-macosx.py
M scripts/scramble/scripts/DRMAA_python-solaris.py
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M scripts/scramble/scripts/MySQL_python-solaris.py
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M scripts/scramble/scripts/PyRods.py
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M scripts/scramble/scripts/psycopg2-solaris.py
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M scripts/scramble/scripts/pysam-solaris.py
M scripts/scramble/scripts/pysqlite.py
M scripts/set_dataset_sizes.py
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M scripts/set_user_disk_usage.py
M scripts/summarize_timings.py
M scripts/sync_reports_config.py
M scripts/test_dist_egg.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M setup.cfg
M static/maps/libs/handlebars.runtime.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/history/history-panel.js.map
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/list/list-panel.js.map
M static/maps/mvc/tools.js.map
M static/maps/mvc/ui/ui-slider.js.map
M static/maps/templates/compiled/panel_section.js.map
M static/maps/templates/compiled/tool_form.js.map
M static/maps/templates/compiled/tool_link.js.map
M static/maps/templates/compiled/tool_search.js.map
M static/maps/utils/config.js.map
M static/maps/viz/sweepster.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/libs/handlebars.runtime.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/history/history-panel.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/list/list-panel.js
M static/scripts/mvc/tools.js
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M static/scripts/templates/compiled/tool_form.js
M static/scripts/templates/compiled/tool_link.js
M static/scripts/templates/compiled/tool_search.js
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R static/scripts/templates/tool_form.handlebars
R static/scripts/templates/tool_link.handlebars
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M static/scripts/utils/config.js
M static/scripts/viz/sweepster.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/autocomplete_tagging.css
M static/style/blue/base.css
M static/style/blue/circster.css
M static/style/blue/embed_item.css
M static/style/blue/iphone.css
M static/style/blue/library.css
M static/style/blue/masthead.css
M static/style/blue/sprite-fugue.png
M static/style/blue/sprite-history-buttons.png
M static/style/blue/sprite-history-states.png
M static/style/blue/trackster.css
A templates/page_base.mako
M templates/show_params.mako
M templates/sorting_base.mako
M templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/admin/sanitize_whitelist.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M test/api/test_dataset_collections.py
M test/api/test_datasets.py
M test/api/test_histories.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/yaml_to_workflow.py
M test/base/test_db_util.py
M test/base/twilltestcase.py
M test/casperjs/api-anon-history-permission-tests.js
M test/casperjs/api-history-permission-tests.js
M test/casperjs/hda-state-tests.js
M test/casperjs/modules/historypanel.js
M test/functional/test_admin_features.py
M test/functional/test_data_managers.py
M test/functional/test_data_security.py
M test/functional/test_get_data.py
M test/functional/test_library_features.py
M test/functional/test_library_security.py
M test/functional/test_library_templates.py
M test/functional/test_metadata_editing.py
M test/functional/test_sample_tracking.py
M test/functional/test_toolbox.py
M test/functional/test_ucsc_table_browser.py
M test/functional/test_user_info.py
A test/functional/tools/output_collection_filter.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/workflow.py
M test/install_and_test_tool_shed_repositories/base/test_db_util.py
M test/tool_shed/base/test_db_util.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_rules/20_instance.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_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_objectstore.py
M test/unit/test_routes.py
M test/unit/test_sockets.py
M test/unit/tool_shed_unit_tests/test_fabric_util.py
M test/unit/tool_shed_unit_tests/test_td_common_util.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/workflows/test_extract_summary.py
M tool_list.py
M tools/data_source/data_source.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/stats/grouping.py
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000
Conflicts:
static/style/blue/base.css
Commit: fb190f622f7a53d42e3244f47d3911043e9a6eb8
https://github.com/galaxyproject/galaxy/commit/fb190f622f7a53d42e3244f47d39…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-29 (Wed, 29 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M static/maps/mvc/upload/composite/composite-row.js.map
M static/scripts/mvc/upload/composite/composite-row.js
Log Message:
-----------
Remove mode icon from row
Commit: 6de2953c98cfc4ea32b8f6ae6bb6dc096c747d38
https://github.com/galaxyproject/galaxy/commit/6de2953c98cfc4ea32b8f6ae6bb6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-29 (Wed, 29 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/upload/upload-settings.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/upload/upload-view.js
Log Message:
-----------
Add 'hide_separator' attribute to modals
Commit: e5503824d1c6f691b58e9d790c1c596151285a5c
https://github.com/galaxyproject/galaxy/commit/e5503824d1c6f691b58e9d790c1c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-29 (Wed, 29 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/upload/upload-view.js
Log Message:
-----------
Rename property to 'title_separator'
Commit: bb7f9a8a51b9de8b48b15078de498f3f46515442
https://github.com/galaxyproject/galaxy/commit/bb7f9a8a51b9de8b48b15078de49…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-29 (Wed, 29 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/style/less/upload.less
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-row.js
M static/style/blue/base.css
Log Message:
-----------
[WIP] Further adjustments to styles and colors
Commit: a9274619afcbf2d114ef07ab7759e457411d8a46
https://github.com/galaxyproject/galaxy/commit/a9274619afcbf2d114ef07ab7759…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-29 (Wed, 29 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/style/less/upload.less
M static/maps/mvc/upload/composite/composite-row.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/style/blue/base.css
Log Message:
-----------
Adjust icon styles
Commit: 6a8fed5feed54263bac775dda908a046d9244c41
https://github.com/galaxyproject/galaxy/commit/6a8fed5feed54263bac775dda908…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-29 (Wed, 29 Jul 2015)
Changed paths:
M client/galaxy/style/less/upload.less
M static/style/blue/base.css
Log Message:
-----------
Fix ftp row label style
Commit: 5cdd511b7a528940090c01d4d306ccf153f2fc1f
https://github.com/galaxyproject/galaxy/commit/5cdd511b7a528940090c01d4d306…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-30 (Thu, 30 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/style/less/galaxy_bootstrap/variables.less
M lib/galaxy/managers/taggable.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/web_util.py
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/utils/uploadbox.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/utils/uploadbox.js
M static/style/blue/base.css
M static/style/blue/iphone.css
M static/style/blue/library.css
M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000
Conflicts:
static/style/blue/base.css
Commit: f83eaa8fe7a39f03c522a5b387961ac9154df9d8
https://github.com/galaxyproject/galaxy/commit/f83eaa8fe7a39f03c522a5b38796…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-30 (Thu, 30 Jul 2015)
Changed paths:
M client/galaxy/scripts/utils/uploadbox.js
M static/maps/utils/uploadbox.js.map
M static/scripts/utils/uploadbox.js
Log Message:
-----------
Uploadbox plugin touchup
Commit: 237a3d307d808d5be2e6e4d1a093a646f7d791a7
https://github.com/galaxyproject/galaxy/commit/237a3d307d808d5be2e6e4d1a093…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-30 (Thu, 30 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/style/less/upload.less
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/default/default-row.js
M static/style/blue/base.css
Log Message:
-----------
More touchup/cleanup for upload views
Commit: f753a6159e980df064d794c43b1440dd54a241dd
https://github.com/galaxyproject/galaxy/commit/f753a6159e980df064d794c43b14…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-07-31 (Fri, 31 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-model.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/utils/uploadbox.js
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/upload/upload-model.js.map
M static/maps/mvc/upload/upload-settings.js.map
M static/maps/utils/uploadbox.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/default/default-row.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-model.js
M static/scripts/mvc/upload/upload-settings.js
M static/scripts/utils/uploadbox.js
Log Message:
-----------
Fix for settings popup and more code cleanup
Commit: ecd38ef6dba00cfdb94365616210690091825651
https://github.com/galaxyproject/galaxy/commit/ecd38ef6dba00cfdb94365616210…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-02 (Sun, 02 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-button-menu.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M static/maps/mvc/ui/ui-button-menu.js.map
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/utils/uploadbox.js.map
M static/scripts/mvc/ui/ui-button-menu.js
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/utils/uploadbox.js
M static/style/blue/base.css
Log Message:
-----------
Enable drag-and-drop, use dropdown instead of select, style fix uploadbox.js
Commit: 1f9d5443fb5700fe47e3d57a0687f68db6508952
https://github.com/galaxyproject/galaxy/commit/1f9d5443fb5700fe47e3d57a0687…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-02 (Sun, 02 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/style/less/ui.less
M static/scripts/mvc/upload/upload-settings.js
M static/style/blue/base.css
Log Message:
-----------
Style margin fixes
Commit: ea26355761cd04512d4e392f821e7d63fbfc1b53
https://github.com/galaxyproject/galaxy/commit/ea26355761cd04512d4e392f821e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-03 (Mon, 03 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/composite/composite-view.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
Log Message:
-----------
More cleanup, fix model creation
Commit: 13389042883fe657c6b289ba6fb2db7630ffd86e
https://github.com/galaxyproject/galaxy/commit/13389042883fe657c6b289ba6fb2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-05 (Wed, 05 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/utils/uploadbox.js
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/utils/uploadbox.js.map
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/utils/uploadbox.js
Log Message:
-----------
Separate file submission from upload queue, augment and generalize send function
Commit: cc46b65d16275e8f73cfceb4c1546e795146bf35
https://github.com/galaxyproject/galaxy/commit/cc46b65d16275e8f73cfceb4c154…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-05 (Wed, 05 Aug 2015)
Changed paths:
M client/bower.json
M client/galaxy/scripts/libs/d3.js
M client/galaxy/scripts/libs/farbtastic.js
M client/galaxy/scripts/libs/jquery/jqtouch.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/libs/require.js
M client/galaxy/scripts/libs/tracekit.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-panel-edit.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/history.less
M client/grunt-tasks/install-libs.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/managers/histories.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M static/maps/libs/d3.js.map
M static/maps/libs/farbtastic.js.map
M static/maps/libs/jquery/jqtouch.js.map
M static/maps/libs/raven.js.map
M static/maps/libs/require.js.map
M static/maps/libs/tracekit.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-panel-edit.js.map
M static/maps/mvc/ui/ui-select-library.js.map
M static/maps/utils/utils.js.map
M static/scripts/libs/d3.js
M static/scripts/libs/farbtastic.js
M static/scripts/libs/jquery/jqtouch.js
M static/scripts/libs/raven.js
M static/scripts/libs/require.js
M static/scripts/libs/tracekit.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-panel-edit.js
M static/scripts/mvc/ui/ui-select-library.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
M templates/display_base.mako
M templates/search/index.mako
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/history/embed.mako
M templates/webapps/galaxy/history/structure.mako
M templates/webapps/galaxy/history/view.mako
M templates/webapps/galaxy/library/common/ldda_info.mako
M templates/webapps/galaxy/library/common/ldda_permissions.mako
M templates/webapps/galaxy/root/history.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M test/functional/test_toolbox.py
A test/functional/tool-data/fasta_indexes.loc
M test/functional/tool-data/sample_tool_data_tables.xml
A test/functional/tools/dbkey_filter_input.xml
A test/functional/tools/dbkey_filter_multi_input.xml
M test/functional/tools/samples_tool_conf.xml
M tools/extract/extract_genomic_dna.py
M tools/extract/extract_genomic_dna.xml
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000
Conflicts:
static/style/blue/base.css
Commit: 42c61535d6abdf5b30a4ad10396a42b4e22eb514
https://github.com/galaxyproject/galaxy/commit/42c61535d6abdf5b30a4ad10396a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-05 (Wed, 05 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/utils/uploadbox.js
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/utils/uploadbox.js.map
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/utils/uploadbox.js
Log Message:
-----------
Separate upload post function, remove some unnecessary functions
Commit: d85342d5097e66756900592bda86eb0bf4e5c363
https://github.com/galaxyproject/galaxy/commit/d85342d5097e66756900592bda86…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-05 (Wed, 05 Aug 2015)
Changed paths:
M client/galaxy/scripts/utils/uploadbox.js
Log Message:
-----------
Fix comment
Commit: 8e093847f9a718de63c7ac698adadebdffc076e7
https://github.com/galaxyproject/galaxy/commit/8e093847f9a718de63c7ac698ada…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-05 (Wed, 05 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/utils/uploadbox.js
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/utils/uploadbox.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/utils/uploadbox.js
Log Message:
-----------
Enable composite data submission
Commit: 8eca23e4b473824d1b75635e057d018d0825d767
https://github.com/galaxyproject/galaxy/commit/8eca23e4b473824d1b75635e057d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-05 (Wed, 05 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/utils/uploadbox.js
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/utils/uploadbox.js.map
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/utils/uploadbox.js
Log Message:
-----------
Attach success, error handlers for composite uploads, fixes
Commit: 960d9e5634826ea6ef1734f9adba25c3bb72a76b
https://github.com/galaxyproject/galaxy/commit/960d9e5634826ea6ef1734f9adba…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-07 (Fri, 07 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/style/blue/base.css
Log Message:
-----------
Fix ui behavior for restart, progress and result states
Commit: 2d332e9b71b4ff28d228ef57c8bd46b6c8b1d2c4
https://github.com/galaxyproject/galaxy/commit/2d332e9b71b4ff28d228ef57c8bd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-07 (Fri, 07 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M static/maps/mvc/upload/composite/composite-view.js.map
M static/scripts/mvc/upload/composite/composite-view.js
Log Message:
-----------
Disable restart button if upload completed
Commit: d76efc57523daa5cbb05200a2c6868e2eb9db228
https://github.com/galaxyproject/galaxy/commit/d76efc57523daa5cbb05200a2c68…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-07 (Fri, 07 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/composite/composite-view.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
Log Message:
-----------
Activate paste/fetch feature, improve behavior
Commit: b0c7b736d450121528c4518880a2c6f128a4ee7c
https://github.com/galaxyproject/galaxy/commit/b0c7b736d450121528c4518880a2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-07 (Fri, 07 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-view.js
Log Message:
-----------
Add green start button, fix text field
Commit: 1f3ee5f64806d41bc4166248370aab443c60c49e
https://github.com/galaxyproject/galaxy/commit/1f3ee5f64806d41bc4166248370a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-07 (Fri, 07 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/default/default-view.js
M static/maps/mvc/upload/default/default-view.js.map
M static/scripts/mvc/upload/default/default-view.js
Log Message:
-----------
Adjust start button location
Commit: 3fae23368b85682c99b82a855c8ddf0d28238e7b
https://github.com/galaxyproject/galaxy/commit/3fae23368b85682c99b82a855c8d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-07 (Fri, 07 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-view.js
Log Message:
-----------
Fix color to primary/blue
Commit: 17b84cb7b4bd67e4b0d9941b77cbed3c60201b43
https://github.com/galaxyproject/galaxy/commit/17b84cb7b4bd67e4b0d9941b77cb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-10 (Mon, 10 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/style/less/upload.less
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/default/default-row.js
M static/style/blue/base.css
Log Message:
-----------
Fix paste/fetch field style
Commit: 5e4c0bcf64666b4c30fe4519479d0d7e1aee9000
https://github.com/galaxyproject/galaxy/commit/5e4c0bcf64666b4c30fe4519479d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-10 (Mon, 10 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-view.js
Log Message:
-----------
Fix start button style
Commit: 92526c834049a4b8e16f479521400542eeb503c8
https://github.com/galaxyproject/galaxy/commit/92526c834049a4b8e16f47952140…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-10 (Mon, 10 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/default/default-view.js
Log Message:
-----------
Fix update screen calls
Commit: eaff25b6eb89bf1cd563b6a350f119e3a8371bc3
https://github.com/galaxyproject/galaxy/commit/eaff25b6eb89bf1cd563b6a350f1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-10 (Mon, 10 Aug 2015)
Changed paths:
A client/galaxy/scripts/libs/jquery.sparklines.js
M client/galaxy/scripts/mvc/form/form-select-content.js
M client/galaxy/scripts/mvc/upload/upload-view.js
A client/galaxy/scripts/reports_webapp/run_stats.js
A client/galaxy/scripts/utils/query-string-parsing.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/style/less/base.less
A client/galaxy/style/less/reports.less
M client/grunt-tasks/style.js
M config/datatypes_conf.xml.sample
M config/plugins/interactive_environments/ipython/config/ipython.ini.sample
M config/plugins/visualizations/trackster/config/trackster.xml
A doc/source/api/guidelines.rst
M doc/source/api_doc.rst
M doc/source/index.rst
M doc/source/releases/_header.rst
A doc/source/ts_api_doc.rst
M lib/galaxy/dataset_collections/builder.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/parameters/output.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
A lib/galaxy/webapps/reports/controllers/home.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/galaxy/webapps/tool_shed/search/tool_search.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/basic_util.py
M scripts/tool_shed/build_ts_whoosh_index.py
A static/images/reports_webapp/bases/home-icon-active.png
A static/images/reports_webapp/bases/home-icon-hov.png
A static/images/reports_webapp/bases/home-icon.png
A static/images/reports_webapp/home-icon-active.png
A static/images/reports_webapp/home-icon-hov.png
A static/images/reports_webapp/home-icon.png
A static/maps/libs/jquery.sparklines.js.map
M static/maps/mvc/form/form-select-content.js.map
M static/maps/mvc/upload/upload-view.js.map
A static/maps/reports_webapp/run_stats.js.map
A static/maps/utils/query-string-parsing.js.map
M static/maps/viz/trackster.js.map
A static/scripts/libs/jquery.sparklines.js
M static/scripts/mvc/form/form-select-content.js
A static/scripts/reports_webapp/run_stats.js
A static/scripts/utils/query-string-parsing.js
M static/scripts/viz/trackster.js
M static/style/blue/base.css
A static/style/blue/reports.css
M templates/base.mako
M templates/page_base.mako
M templates/sorting_base.mako
A templates/spark_base.mako
M templates/webapps/galaxy/cloud/index.mako
M templates/webapps/reports/base_panels.mako
M templates/webapps/reports/index.mako
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/jobs_tool_per_month.mako
M templates/webapps/reports/jobs_user_per_month.mako
M templates/webapps/reports/registered_users_per_month.mako
M templates/webapps/reports/registered_users_specified_month.mako
M templates/webapps/reports/requests_per_month_all.mako
M templates/webapps/reports/requests_per_user.mako
M templates/webapps/reports/requests_user_per_month.mako
A templates/webapps/reports/run_stats.mako
M templates/webapps/reports/users_last_access_date.mako
M templates/webapps/reports/users_user_disk_usage.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
A templates/webapps/reports/workflows_per_workflow.mako
M templates/webapps/reports/workflows_user_per_month.mako
R templates/webapps/tool_shed/message.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
M test/functional/test_toolbox.py
A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml
A test/functional/tools/collection_creates_dynamic_nested.xml
A test/functional/tools/collection_creates_list_of_pairs.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000
Conflicts:
client/galaxy/scripts/mvc/upload/upload-view.js
static/maps/mvc/upload/upload-view.js.map
static/scripts/mvc/upload/upload-view.js
static/style/blue/base.css
Commit: 4beeeecf4c3dda5ee18c4dc928fb416a7b56de79
https://github.com/galaxyproject/galaxy/commit/4beeeecf4c3dda5ee18c4dc928fb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-10 (Mon, 10 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/upload-model.js
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/mvc/upload/upload-model.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/upload-model.js
Log Message:
-----------
Fix file names and description
Commit: b3c0725d97a1cf5c4229f60a46a878710c41cab5
https://github.com/galaxyproject/galaxy/commit/b3c0725d97a1cf5c4229f60a46a8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M static/maps/mvc/ui/ui-popover.js.map
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/scripts/mvc/ui/ui-popover.js
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/default/default-row.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-ftp.js
M static/style/blue/base.css
Log Message:
-----------
Continue ftp popup integration
Commit: c7ad46099c1118a62936d0f2df4bdb2ff920895e
https://github.com/galaxyproject/galaxy/commit/c7ad46099c1118a62936d0f2df4b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-model.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/upload.less
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/upload/upload-model.js.map
M static/maps/utils/utils.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-model.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
Log Message:
-----------
Enable ftp file selection for composite uploads
Commit: a8def9a910ecae7fe5d3507ce38d235e20810038
https://github.com/galaxyproject/galaxy/commit/a8def9a910ecae7fe5d3507ce38d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/style/less/upload.less
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/upload-ftp.js
M static/style/blue/base.css
Log Message:
-----------
Style fixes, adjustments for ftp popover table
Commit: 80e45d230b1ea5a3bf8a77e573ed8a33a4263f4d
https://github.com/galaxyproject/galaxy/commit/80e45d230b1ea5a3bf8a77e573ed…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-ftp.js
Log Message:
-----------
Add icons to buttons in regular view
Commit: ab87393897b2948b306c86c692aaabd748abec31
https://github.com/galaxyproject/galaxy/commit/ab87393897b2948b306c86c692aa…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M lib/galaxy/datatypes/genetics.py
Log Message:
-----------
Place string split in make_html_table call into try block
Commit: 7695fec2fa217a056fa34a1cf78fcb41864549f2
https://github.com/galaxyproject/galaxy/commit/7695fec2fa217a056fa34a1cf78f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M client/galaxy/style/less/reports.less
M lib/galaxy/model/__init__.py
M lib/galaxy/webapps/galaxy/controllers/history.py
R static/help.css
R static/help.html
R static/help.rst
R static/images/SetAttr.png
R static/images/SetGenome.png
R static/images/brochure.pdf
R static/images/galaxy.png
R static/images/galaxyLogo_small.png
R static/images/lock.jpg
R static/images/qk/quickie1_small.png
R static/images/qk/quickie2_small.png
R static/images/qk/quickie3_small.png
R static/images/qk/quickie4_small.png
R static/images/qk/quickie5_small.png
R static/images/qk/quickie6_small.png
R static/images/qk/quickie7_small.png
R static/images/reports_webapp/bases/home-icon-active.png
R static/images/reports_webapp/bases/home-icon-hov.png
R static/images/reports_webapp/bases/home-icon.png
R static/images/reports_webapp/home-icon-active.png
R static/images/reports_webapp/home-icon-hov.png
R static/images/reports_webapp/home-icon.png
R static/images/screencast.png
R static/images/sequencer.png
R static/images/tools.gif
R static/images/toolsExpandingMenu.gif
R static/images/welcomePhoto.jpg
M static/style/blue/base.css
M static/style/blue/reports.css
R static/welcome.rst
M templates/webapps/reports/base_panels.mako
M templates/webapps/reports/index.mako
M tool-data/all_fasta.loc.sample
M tool-data/faseq.loc.sample
M tool-data/liftOver.loc.sample
M tool-data/mosaik_index.loc.sample
M tool-data/ngs_sim_fasta.loc.sample
M tool-data/perm_base_index.loc.sample
M tool-data/perm_color_index.loc.sample
M tool-data/picard_index.loc.sample
M tool-data/regions.loc.sample
M tool-data/srma_index.loc.sample
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000
Conflicts:
static/style/blue/base.css
Commit: 4da5f1370f8bad346e1a26b913f8fab0bd567f0d
https://github.com/galaxyproject/galaxy/commit/4da5f1370f8bad346e1a26b913f8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M lib/galaxy/webapps/galaxy/api/datatypes.py
M static/maps/mvc/upload/composite/composite-view.js.map
M static/scripts/mvc/upload/composite/composite-view.js
Log Message:
-----------
Fix corner cases ie missing datatype details
Commit: 82c732752f2c201ed223e46abb533ea262f9fe9e
https://github.com/galaxyproject/galaxy/commit/82c732752f2c201ed223e46abb53…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/upload-view.js
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/upload/upload-view.js
Log Message:
-----------
Fix unload message if queue is running/active
Commit: 1686109ae8d6ac615ffdb45d1a0a6e7b5f48c786
https://github.com/galaxyproject/galaxy/commit/1686109ae8d6ac615ffdb45d1a0a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/upload-view.js
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/upload/upload-view.js
Log Message:
-----------
Fix sorting for upper case extension
Commit: 71bcb8dc9d4b478c098e8ba2adf63e227eb3f658
https://github.com/galaxyproject/galaxy/commit/71bcb8dc9d4b478c098e8ba2adf6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/upload-view.js
M static/maps/mvc/upload/upload-view.js.map
Log Message:
-----------
Remove comments
Commit: 2bdbe8036f93409a8a2d5b7a9b75c205201bd448
https://github.com/galaxyproject/galaxy/commit/2bdbe8036f93409a8a2d5b7a9b75…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/upload-view.js
M static/maps/mvc/upload/upload-view.js.map
Log Message:
-----------
Remove comments
Commit: b07625b0c03045a4539b5f01a7115324f8905ff0
https://github.com/galaxyproject/galaxy/commit/b07625b0c03045a4539b5f01a711…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M static/maps/mvc/upload/upload-ftp.js.map
M static/scripts/mvc/upload/upload-ftp.js
Log Message:
-----------
Remove unnecessary if condition in ftp uploader
Commit: dd421d00076660ef368757c7871b5fa7c3ab80c9
https://github.com/galaxyproject/galaxy/commit/dd421d00076660ef368757c7871b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-12 (Wed, 12 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/upload/upload-view.js
Log Message:
-----------
Minor fixes
Commit: 304e693fd36fe5a84aeef0b1b1a2e3c909e1eb59
https://github.com/galaxyproject/galaxy/commit/304e693fd36fe5a84aeef0b1b1a2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-14 (Fri, 14 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-view.js
Log Message:
-----------
Allow safe switching between histories while queue is running
Commit: 704e031f6339f63103e24805369db1c28653fd58
https://github.com/galaxyproject/galaxy/commit/704e031f6339f63103e24805369d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-14 (Fri, 14 Aug 2015)
Changed paths:
M CONTRIBUTING.md
M client/galaxy/scripts/galaxy.menu.js
M config/galaxy.ini.sample
M doc/source/project/organization.rst
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/model/__init__.py
M lib/galaxy/quota/__init__.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/version.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/buildapp.py
R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/tool/tag_attribute_handler.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/scripts/api/common.py
M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M static/maps/galaxy.menu.js.map
M static/scripts/galaxy.menu.js
R templates/webapps/galaxy/cloud/index.mako
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000
Commit: 0c3fdd2d637255e61a08f4684f63bd6b097c02eb
https://github.com/galaxyproject/galaxy/commit/0c3fdd2d637255e61a08f4684f63…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-17 (Mon, 17 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/utils/utils.js
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/utils/utils.js.map
M static/scripts/mvc/ui/ui-color-picker.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/utils/utils.js
A test/qunit/test-app.js
M test/qunit/test-common.js
A test/qunit/test-data/bootstrapped.js
A test/qunit/test-data/fakeserver.js
A test/qunit/tests/upload_dialog_tests.html
A test/qunit/tests/upload_dialog_tests.js
M test/qunit/tests/workflow_editor_tests.js
Log Message:
-----------
Add test cases for uploader, add generic Galaxy environment to qunit
Commit: ed171e95190e651434927e05f67b5a65f1c84828
https://github.com/galaxyproject/galaxy/commit/ed171e95190e651434927e05f67b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-17 (Mon, 17 Aug 2015)
Changed paths:
M .ci/flake8_blacklist.txt
M CONTRIBUTING.md
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/style/less/reports.less
M client/grunt-tasks/scripts.js
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/tools/toolbox/lineages/stock.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy_utils/sequence/fasta.py
M lib/galaxy_utils/sequence/fastq.py
M lib/galaxy_utils/sequence/sequence.py
M lib/galaxy_utils/sequence/transform.py
M lib/galaxy_utils/sequence/vcf.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/scripts/api/common.py
M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/shed_util_common.py
M static/maps/galaxy.interactive_environments.js.map
M static/maps/libs/jquery/jqtouch.js.map
M static/maps/libs/raven.js.map
M static/maps/libs/toastr.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/data.js.map
M static/maps/mvc/dataset/dataset-choice.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-select-content.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/job/job-model.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/list/list-panel.js.map
M static/maps/mvc/tools/tools-form-base.js.map
M static/maps/mvc/tools/tools-form-workflow.js.map
M static/maps/mvc/tools/tools-jobs.js.map
M static/maps/mvc/ui/ui-frames.js.map
M static/maps/mvc/ui/ui-select.js.map
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/maps/utils/deferred.js.map
M static/maps/utils/graph.js.map
M static/maps/utils/metrics-logger.js.map
M static/maps/utils/utils.js.map
M static/maps/viz/trackster.js.map
M static/maps/viz/trackster/filters.js.map
M static/maps/viz/visualization.js.map
M static/scripts/galaxy.interactive_environments.js
M static/scripts/libs/jquery/jqtouch.js
M static/scripts/libs/raven.js
M static/scripts/libs/toastr.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/data.js
M static/scripts/mvc/dataset/dataset-choice.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-select-content.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/job/job-model.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/list/list-panel.js
M static/scripts/mvc/tools/tools-form-base.js
M static/scripts/mvc/tools/tools-form-workflow.js
M static/scripts/mvc/tools/tools-jobs.js
M static/scripts/mvc/ui/ui-frames.js
M static/scripts/mvc/ui/ui-select.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/utils/deferred.js
M static/scripts/utils/graph.js
M static/scripts/utils/metrics-logger.js
M static/scripts/utils/utils.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/filters.js
M static/scripts/viz/visualization.js
M static/style/blue/base.css
M static/style/blue/reports.css
M templates/page_base.mako
M templates/spark_base.mako
A templates/webapps/galaxy/history/as_xml.mako
M templates/webapps/galaxy/history/view.mako
R templates/webapps/galaxy/root/history.mako
R templates/webapps/galaxy/root/history_as_xml.mako
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_per_workflow.mako
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000
Conflicts:
static/maps/utils/utils.js.map
static/scripts/utils/utils.js
static/style/blue/base.css
Commit: 89801414bbdc18f5db98c32ca462ef92f97f5647
https://github.com/galaxyproject/galaxy/commit/89801414bbdc18f5db98c32ca462…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-17 (Mon, 17 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-view.js
Log Message:
-----------
Enhance FTP visibilty handling
Commit: e9e3dd62d2178d391f5ba9f0c677063800b0f3a3
https://github.com/galaxyproject/galaxy/commit/e9e3dd62d2178d391f5ba9f0c677…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-17 (Mon, 17 Aug 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/api/datatypes.py
Log Message:
-----------
Use list comprehension to build composite_files array
Commit: b6e0ba29521bbc382a9fe15493e55b2bbde1bfde
https://github.com/galaxyproject/galaxy/commit/b6e0ba29521bbc382a9fe15493e5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-18 (Tue, 18 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-button-menu.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
A client/galaxy/scripts/mvc/upload/composite/composite-row.js
A client/galaxy/scripts/mvc/upload/composite/composite-view.js
A client/galaxy/scripts/mvc/upload/default/default-row.js
A client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-model.js
R client/galaxy/scripts/mvc/upload/upload-row.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/util/bunch.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M static/maps/mvc/ui/ui-button-menu.js.map
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-popover.js.map
A static/maps/mvc/upload/composite/composite-row.js.map
A static/maps/mvc/upload/composite/composite-view.js.map
A static/maps/mvc/upload/default/default-row.js.map
A static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/upload/upload-model.js.map
R static/maps/mvc/upload/upload-row.js.map
M static/maps/mvc/upload/upload-settings.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/utils/uploadbox.js.map
M static/maps/utils/utils.js.map
M static/scripts/mvc/ui/ui-button-menu.js
M static/scripts/mvc/ui/ui-color-picker.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-popover.js
A static/scripts/mvc/upload/composite/composite-row.js
A static/scripts/mvc/upload/composite/composite-view.js
A static/scripts/mvc/upload/default/default-row.js
A static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-model.js
R static/scripts/mvc/upload/upload-row.js
M static/scripts/mvc/upload/upload-settings.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/utils/uploadbox.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
A test/qunit/test-app.js
M test/qunit/test-common.js
A test/qunit/test-data/bootstrapped.js
A test/qunit/test-data/fakeserver.js
A test/qunit/tests/upload_dialog_tests.html
A test/qunit/tests/upload_dialog_tests.js
M test/qunit/tests/workflow_editor_tests.js
Log Message:
-----------
Merge pull request #605 from guerler/upload_000
Add composite file uploader
Compare: https://github.com/galaxyproject/galaxy/compare/bb7795f63c47...b6e0ba29521b
1
0

18 Aug '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e1672f37b9bb0be4506b0df4610c14c3289df212
https://github.com/galaxyproject/galaxy/commit/e1672f37b9bb0be4506b0df4610c…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-18 (Tue, 18 Aug 2015)
Changed paths:
M client/galaxy/scripts/reports_webapp/run_stats.js
Log Message:
-----------
Changed refresh time on reports homepage
Commit: e7a753bb6f67082b2a70ec122a2113becebad046
https://github.com/galaxyproject/galaxy/commit/e7a753bb6f67082b2a70ec122a21…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-18 (Tue, 18 Aug 2015)
Changed paths:
M static/scripts/reports_webapp/run_stats.js
Log Message:
-----------
Ran grunt
Commit: 3ba118621d54b2b115281198a28576140507d7b0
https://github.com/galaxyproject/galaxy/commit/3ba118621d54b2b115281198a285…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-18 (Tue, 18 Aug 2015)
Changed paths:
M client/galaxy/scripts/reports_webapp/run_stats.js
M static/maps/reports_webapp/run_stats.js.map
Log Message:
-----------
Added documentation
Commit: bb7795f63c478c69e2671b2e5b4f2b12e1ff812a
https://github.com/galaxyproject/galaxy/commit/bb7795f63c478c69e2671b2e5b4f…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-08-18 (Tue, 18 Aug 2015)
Changed paths:
M client/galaxy/scripts/reports_webapp/run_stats.js
M static/maps/reports_webapp/run_stats.js.map
M static/scripts/reports_webapp/run_stats.js
Log Message:
-----------
Merge pull request #609 from Airistotal/dev
Changed refresh time on reports homepage
Compare: https://github.com/galaxyproject/galaxy/compare/9c8edf106bd6...bb7795f63c47
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: fe251e3c2de4d986b3654130b317fe5fe9b2cffb
https://github.com/galaxyproject/galaxy/commit/fe251e3c2de4d986b3654130b317…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-08-18 (Tue, 18 Aug 2015)
Changed paths:
M lib/tool_shed/capsule/capsule_manager.py
Log Message:
-----------
Ensure removal of temporary files.
Specifically, export_info.xml and manifest.xml were not being deleted after the capsule was created.
Commit: ed4bb86c3355cad578354696394dd6364b5a898d
https://github.com/galaxyproject/galaxy/commit/ed4bb86c3355cad578354696394d…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-08-18 (Tue, 18 Aug 2015)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
Log Message:
-----------
Also delete uploaded file data after processing.
API uploads, e.g. with planemo, would leave upload_file_data_XXXXXX lying around in the configured temporary directory. Forever.
Commit: 9c8edf106bd61851b0668ceb6047104784f2cb1a
https://github.com/galaxyproject/galaxy/commit/9c8edf106bd61851b0668ceb6047…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2015-08-18 (Tue, 18 Aug 2015)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/tool_shed/capsule/capsule_manager.py
Log Message:
-----------
Merge pull request #607 from davebx/ts_tempfiles
Ensure removal of temporary files.
Compare: https://github.com/galaxyproject/galaxy/compare/634799803ef3...9c8edf106bd6
1
0

17 Aug '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c938e66e98512d85120c1c06d485a13000ff82c1
https://github.com/galaxyproject/galaxy/commit/c938e66e98512d85120c1c06d485…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-13 (Thu, 13 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/scripts/mvc/workflow/workflow-terminals.js
Log Message:
-----------
Fix output collection terminal base class
Commit: 79dbff19674dbe667887b92d070165ade85ae834
https://github.com/galaxyproject/galaxy/commit/79dbff19674dbe667887b92d0701…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-13 (Thu, 13 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/scripts/mvc/workflow/workflow-terminals.js
Log Message:
-----------
Merge pull request #602 from guerler/fix_collections_000
[15.07] Fix output collection terminal base class
Commit: 4463676e2cf70989b4a036f155356418ef22b049
https://github.com/galaxyproject/galaxy/commit/4463676e2cf70989b4a036f15535…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-17 (Mon, 17 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/scripts/mvc/workflow/workflow-terminals.js
Log Message:
-----------
Merge branch 'release_15.07' into dev
Commit: 634799803ef36b9ea1a615bc980425f224d5d958
https://github.com/galaxyproject/galaxy/commit/634799803ef36b9ea1a615bc9804…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-17 (Mon, 17 Aug 2015)
Changed paths:
M static/maps/mvc/history/options-menu.js.map
M static/scripts/mvc/history/options-menu.js
Log Message:
-----------
Merge from release and rebuild.
Compare: https://github.com/galaxyproject/galaxy/compare/c0119de12eee...634799803ef3
1
0

[galaxyproject/galaxy] 646086: Add a --develop flag to grunt that is compatible w...
by GitHub 17 Aug '15
by GitHub 17 Aug '15
17 Aug '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 64608685393a235bad5c161421861af6c5609048
https://github.com/galaxyproject/galaxy/commit/64608685393a235bad5c16142186…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-13 (Thu, 13 Aug 2015)
Changed paths:
M client/grunt-tasks/scripts.js
Log Message:
-----------
Add a --develop flag to grunt that is compatible with both standard build *and* watch to allow for easier debugging instead of requiring the 'decompress' task -- though this still works. This makes it possible to drop in 'debugger' statements, etc., and should help when working on the client. Additionally enable drop_console for the compressor, since it's now much easier to use local development tweaks.
Commit: 63d6c37a39a53bae6806e3bb9267a1659313f878
https://github.com/galaxyproject/galaxy/commit/63d6c37a39a53bae6806e3bb9267…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-13 (Thu, 13 Aug 2015)
Changed paths:
M static/maps/galaxy.interactive_environments.js.map
M static/maps/libs/jquery/jqtouch.js.map
M static/maps/libs/raven.js.map
M static/maps/libs/toastr.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/data.js.map
M static/maps/mvc/dataset/dataset-choice.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-select-content.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/job/job-model.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/list/list-panel.js.map
M static/maps/mvc/tools/tools-form-base.js.map
M static/maps/mvc/tools/tools-form-workflow.js.map
M static/maps/mvc/tools/tools-jobs.js.map
M static/maps/mvc/ui/ui-frames.js.map
M static/maps/mvc/ui/ui-select.js.map
M static/maps/utils/deferred.js.map
M static/maps/utils/graph.js.map
M static/maps/utils/metrics-logger.js.map
M static/maps/utils/utils.js.map
M static/maps/viz/trackster.js.map
M static/maps/viz/trackster/filters.js.map
M static/maps/viz/visualization.js.map
M static/scripts/galaxy.interactive_environments.js
M static/scripts/libs/jquery/jqtouch.js
M static/scripts/libs/raven.js
M static/scripts/libs/toastr.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/data.js
M static/scripts/mvc/dataset/dataset-choice.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-select-content.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/job/job-model.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/list/list-panel.js
M static/scripts/mvc/tools/tools-form-base.js
M static/scripts/mvc/tools/tools-form-workflow.js
M static/scripts/mvc/tools/tools-jobs.js
M static/scripts/mvc/ui/ui-frames.js
M static/scripts/mvc/ui/ui-select.js
M static/scripts/utils/deferred.js
M static/scripts/utils/graph.js
M static/scripts/utils/metrics-logger.js
M static/scripts/utils/utils.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/filters.js
M static/scripts/viz/visualization.js
Log Message:
-----------
Rebuild client w/ new options.
Commit: 2666499da649fdbb3524d11ceab90b9af86205da
https://github.com/galaxyproject/galaxy/commit/2666499da649fdbb3524d11ceab9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-13 (Thu, 13 Aug 2015)
Changed paths:
M client/grunt-tasks/scripts.js
Log Message:
-----------
One minor styling issue
Commit: c0119de12eeeba5308c72b98811a2d140cdccbd4
https://github.com/galaxyproject/galaxy/commit/c0119de12eeeba5308c72b98811a…
Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com>
Date: 2015-08-17 (Mon, 17 Aug 2015)
Changed paths:
M client/grunt-tasks/scripts.js
M static/maps/galaxy.interactive_environments.js.map
M static/maps/libs/jquery/jqtouch.js.map
M static/maps/libs/raven.js.map
M static/maps/libs/toastr.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/data.js.map
M static/maps/mvc/dataset/dataset-choice.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-select-content.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/job/job-model.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/list/list-panel.js.map
M static/maps/mvc/tools/tools-form-base.js.map
M static/maps/mvc/tools/tools-form-workflow.js.map
M static/maps/mvc/tools/tools-jobs.js.map
M static/maps/mvc/ui/ui-frames.js.map
M static/maps/mvc/ui/ui-select.js.map
M static/maps/utils/deferred.js.map
M static/maps/utils/graph.js.map
M static/maps/utils/metrics-logger.js.map
M static/maps/utils/utils.js.map
M static/maps/viz/trackster.js.map
M static/maps/viz/trackster/filters.js.map
M static/maps/viz/visualization.js.map
M static/scripts/galaxy.interactive_environments.js
M static/scripts/libs/jquery/jqtouch.js
M static/scripts/libs/raven.js
M static/scripts/libs/toastr.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/data.js
M static/scripts/mvc/dataset/dataset-choice.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-select-content.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/job/job-model.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/list/list-panel.js
M static/scripts/mvc/tools/tools-form-base.js
M static/scripts/mvc/tools/tools-form-workflow.js
M static/scripts/mvc/tools/tools-jobs.js
M static/scripts/mvc/ui/ui-frames.js
M static/scripts/mvc/ui/ui-select.js
M static/scripts/utils/deferred.js
M static/scripts/utils/graph.js
M static/scripts/utils/metrics-logger.js
M static/scripts/utils/utils.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/filters.js
M static/scripts/viz/visualization.js
Log Message:
-----------
Merge pull request #601 from dannon/grunt_develop_mode
Grunt develop mode
Compare: https://github.com/galaxyproject/galaxy/compare/ed54c343e66d...c0119de12eee
1
0

16 Aug '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0f2e2152ee17532488a8231cf1220ed9ddddb3aa
https://github.com/galaxyproject/galaxy/commit/0f2e2152ee17532488a8231cf122…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-08-10 (Mon, 10 Aug 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/scripts/api/common.py
M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Cleanup of the toolshed's url handling methods.
Commit: 9f975e85067c1c5f695979f13d26ae4d132cb36f
https://github.com/galaxyproject/galaxy/commit/9f975e85067c1c5f695979f13d26…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-08-10 (Mon, 10 Aug 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Make travis happier.
Commit: 624cf19ba5bec88dfee58380722720fc47d68eb3
https://github.com/galaxyproject/galaxy/commit/624cf19ba5bec88dfee583807227…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-08-10 (Mon, 10 Aug 2015)
Changed paths:
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/util/common_util.py
Log Message:
-----------
More linting.
Commit: d7e6d627d0679a5cc95f30e71f5a9d30cc753802
https://github.com/galaxyproject/galaxy/commit/d7e6d627d0679a5cc95f30e71f5a…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
Log Message:
-----------
Correct errors found by Nicola.
Commit: 84329f8f3d7423106f197fb880fc12aee2d2b71d
https://github.com/galaxyproject/galaxy/commit/84329f8f3d7423106f197fb880fc…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M lib/tool_shed/util/common_util.py
Log Message:
-----------
Remove debug output.
Commit: 0efc866a07699067beb930dc0275aab7dfb40cd5
https://github.com/galaxyproject/galaxy/commit/0efc866a07699067beb930dc0275…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Correct additional errors discovered by Nicola.
Commit: 5ddd2c92a3caeb75bcb379f297f2967af26afc47
https://github.com/galaxyproject/galaxy/commit/5ddd2c92a3caeb75bcb379f297f2…
Author: Dave B. <dave(a)bx.psu.edu>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Fix missing parameter.
Commit: ed54c343e66d7dee79dd785da837f2ce55f69138
https://github.com/galaxyproject/galaxy/commit/ed54c343e66d7dee79dd785da837…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-08-16 (Sun, 16 Aug 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/scripts/api/common.py
M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Merge pull request #586 from davebx/ts_url_cleanup
Cleanup of the toolshed's url handling methods.
Compare: https://github.com/galaxyproject/galaxy/compare/2da0083cdfdf...ed54c343e66d
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d6ef0458309a9cfea12cb33b9d0931fd75eeb04a
https://github.com/galaxyproject/galaxy/commit/d6ef0458309a9cfea12cb33b9d09…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-07 (Fri, 07 Aug 2015)
Changed paths:
M lib/galaxy/webapps/reports/controllers/jobs.py
M templates/page_base.mako
M templates/spark_base.mako
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
Log Message:
-----------
Applied paging to all pages
Commit: 21ab4d2dbfa8576f89a13018d962cd8dc3738239
https://github.com/galaxyproject/galaxy/commit/21ab4d2dbfa8576f89a13018d962…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/upload-view.js
A client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/style/less/reports.less
M config/datatypes_conf.xml.sample
M config/plugins/interactive_environments/ipython/config/ipython.ini.sample
M lib/galaxy/dataset_collections/builder.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/parameters/output.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/webapps/galaxy/controllers/history.py
A lib/galaxy/webapps/reports/controllers/home.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/basic_util.py
R static/help.css
R static/help.html
R static/help.rst
R static/images/SetAttr.png
R static/images/SetGenome.png
R static/images/brochure.pdf
R static/images/galaxy.png
R static/images/galaxyLogo_small.png
R static/images/lock.jpg
R static/images/qk/quickie1_small.png
R static/images/qk/quickie2_small.png
R static/images/qk/quickie3_small.png
R static/images/qk/quickie4_small.png
R static/images/qk/quickie5_small.png
R static/images/qk/quickie6_small.png
R static/images/qk/quickie7_small.png
R static/images/screencast.png
R static/images/sequencer.png
R static/images/tools.gif
R static/images/toolsExpandingMenu.gif
R static/images/welcomePhoto.jpg
M static/maps/mvc/upload/upload-view.js.map
A static/maps/reports_webapp/run_stats.js.map
M static/scripts/mvc/upload/upload-view.js
A static/scripts/reports_webapp/run_stats.js
M static/style/blue/base.css
M static/style/blue/reports.css
R static/welcome.rst
M templates/base.mako
M templates/webapps/reports/base_panels.mako
M templates/webapps/reports/index.mako
A templates/webapps/reports/run_stats.mako
R templates/webapps/tool_shed/message.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
M test/functional/test_toolbox.py
A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml
A test/functional/tools/collection_creates_dynamic_nested.xml
A test/functional/tools/collection_creates_list_of_pairs.xml
M test/functional/tools/samples_tool_conf.xml
M tool-data/all_fasta.loc.sample
M tool-data/faseq.loc.sample
M tool-data/liftOver.loc.sample
M tool-data/mosaik_index.loc.sample
M tool-data/ngs_sim_fasta.loc.sample
M tool-data/perm_base_index.loc.sample
M tool-data/perm_color_index.loc.sample
M tool-data/picard_index.loc.sample
M tool-data/regions.loc.sample
M tool-data/srma_index.loc.sample
Log Message:
-----------
Merge branch 'dev' of https://github.com/Airistotal/galaxy into Reports_pages
Commit: dd51cfe6e0ae23e8faab7b43673f9f3bc6cc6dcf
https://github.com/galaxyproject/galaxy/commit/dd51cfe6e0ae23e8faab7b43673f…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M lib/galaxy/webapps/reports/controllers/workflows.py
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_per_workflow.mako
Log Message:
-----------
Added Paging to Workflows
Commit: a27ff9b2922aff5f863cf7d2e84094e236d8c6bb
https://github.com/galaxyproject/galaxy/commit/a27ff9b2922aff5f863cf7d2e840…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M client/galaxy/style/less/reports.less
M lib/galaxy/webapps/reports/controllers/workflows.py
M static/style/blue/base.css
M static/style/blue/reports.css
Log Message:
-----------
Added limits to queries (bug fix)
Changed homepage button location (small style change)
Changes for CI
Commit: 1d3e304644f0f5b7b3cb828a9016e2b679791f46
https://github.com/galaxyproject/galaxy/commit/1d3e304644f0f5b7b3cb828a9016…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-11 (Tue, 11 Aug 2015)
Changed paths:
M lib/galaxy/webapps/reports/controllers/jobs.py
M templates/webapps/reports/jobs_per_user.mako
Log Message:
-----------
Timing of the queries on the jobs per user page.
Commit: 266d96bcb0c34365b1f3ea136909abad7180a118
https://github.com/galaxyproject/galaxy/commit/266d96bcb0c34365b1f3ea136909…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-14 (Fri, 14 Aug 2015)
Changed paths:
M lib/galaxy/webapps/reports/controllers/jobs.py
M templates/webapps/reports/jobs_per_user.mako
Log Message:
-----------
Changed for CI, added total time for page load
Commit: 2da0083cdfdfc268229d730ef2a8f5432da781f1
https://github.com/galaxyproject/galaxy/commit/2da0083cdfdfc268229d730ef2a8…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-08-15 (Sat, 15 Aug 2015)
Changed paths:
M client/galaxy/style/less/reports.less
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M static/style/blue/base.css
M static/style/blue/reports.css
M templates/page_base.mako
M templates/spark_base.mako
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_per_workflow.mako
Log Message:
-----------
Merge pull request #576 from Airistotal/Reports_pages
Reports: Applied paging to all pages
Compare: https://github.com/galaxyproject/galaxy/compare/5b2e208b775f...2da0083cdfdf
1
0

[galaxyproject/galaxy] d9d86e: Update contact email address for security issues.
by GitHub 15 Aug '15
by GitHub 15 Aug '15
15 Aug '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d9d86ee8a749550d052ef4f7dc3ff4be51e00734
https://github.com/galaxyproject/galaxy/commit/d9d86ee8a749550d052ef4f7dc3f…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-08-07 (Fri, 07 Aug 2015)
Changed paths:
M CONTRIBUTING.md
Log Message:
-----------
Update contact email address for security issues.
Commit: 55e0f109fcebbee3da19e0d5a568ff5b4cedcddb
https://github.com/galaxyproject/galaxy/commit/55e0f109fcebbee3da19e0d5a568…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-08-07 (Fri, 07 Aug 2015)
Changed paths:
M CONTRIBUTING.md
Log Message:
-----------
Mention GitHub issues.
Commit: 86aa07d87e61a980b98cf6fa6e6360e7d649f5e5
https://github.com/galaxyproject/galaxy/commit/86aa07d87e61a980b98cf6fa6e63…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-08-07 (Fri, 07 Aug 2015)
Changed paths:
M CONTRIBUTING.md
Log Message:
-----------
Require PRs to pass the CI tests.
Commit: 3df58181cdf13f6a8e7e41fb813c49de4c5a6dd6
https://github.com/galaxyproject/galaxy/commit/3df58181cdf13f6a8e7e41fb813c…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-08-07 (Fri, 07 Aug 2015)
Changed paths:
M CONTRIBUTING.md
Log Message:
-----------
Small fixes for CONTRIBUTING.md .
Commit: 5b2e208b775f8284c651f67dad86fd55929456ac
https://github.com/galaxyproject/galaxy/commit/5b2e208b775f8284c651f67dad86…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-15 (Sat, 15 Aug 2015)
Changed paths:
M CONTRIBUTING.md
Log Message:
-----------
Merge pull request #574 from nsoranzo/dev
[PROCEDURES] GitHub issues, security email contact and CI testing
Compare: https://github.com/galaxyproject/galaxy/compare/cb1538588d8a...5b2e208b775f
1
0