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[galaxyproject/galaxy] 8ac38b: Move controller consistent workflow api endpoint t...
by GitHub 18 Jul '16

18 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8ac38bee15ee2a67908a09d8fc85951a79dc348f https://github.com/galaxyproject/galaxy/commit/8ac38bee15ee2a67908a09d8fc85… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Move controller consistent workflow api endpoint to internal api route Commit: 18f1593ead16544c523d0de4b03d87b215e064b4 https://github.com/galaxyproject/galaxy/commit/18f1593ead16544c523d0de4b03d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Rename 'internal_api' endpoint to 'api_internal' so that the base webapp transaction switching (and thus controller matching) works correctly. Commit: e77c3fd01a19ea01b748c22f5fe6174aad44c6aa https://github.com/galaxyproject/galaxy/commit/e77c3fd01a19ea01b748c22f5fe6… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #11 from dannon/internal_api Rename 'internal_api' endpoint to 'api_internal' so that the base web… Commit: 9e07774bb3b15dcc15c7c67d4710014f42790199 https://github.com/galaxyproject/galaxy/commit/9e07774bb3b15dcc15c7c67d4710… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix comment to indicate proper route Commit: d351121d126f84e4c3a5f0123fe1b96d333aef22 https://github.com/galaxyproject/galaxy/commit/d351121d126f84e4c3a5f0123fe1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #2622 from guerler/internal_api Reroute consistent workflow endpoint to internal api Compare: https://github.com/galaxyproject/galaxy/compare/e21a81fbf0c0...d351121d126f

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[galaxyproject/galaxy] aa6919: User API tests: add show
by GitHub 18 Jul '16

18 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa69199bd17c3bfa5602d06a9b118187c1b68e1c https://github.com/galaxyproject/galaxy/commit/aa69199bd17c3bfa5602d06a9b11… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M test/api/test_users.py Log Message: ----------- User API tests: add show Commit: 54e07906f51f58c1580b1bec64cdfc1c74ff8779 https://github.com/galaxyproject/galaxy/commit/54e07906f51f58c1580b1bec64cd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M test/api/test_users.py Log Message: ----------- User API tests: add update test Commit: 86a3531730dfffb81014302b2495c939ae4bd4ec https://github.com/galaxyproject/galaxy/commit/86a3531730dfffb81014302b2495… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/security/validate_user_input.py M test/unit/managers/test_UserManager.py Log Message: ----------- API, users: add deserializer to user manager - Adds deserialization method for usernames (note: still needs trans) - Adds tests for deserializer in test_UserManager.py Commit: f724e84fda22fb73042ea344ec00be86b3a7c564 https://github.com/galaxyproject/galaxy/commit/f724e84fda22fb73042ea344ec00… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/managers/users.py M test/api/test_users.py M test/unit/managers/test_UserManager.py Log Message: ----------- API, users: use default to assign username Commit: ad95cad99004f390dcd7937ac334fa655b48ac36 https://github.com/galaxyproject/galaxy/commit/ad95cad99004f390dcd7937ac334… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/managers/users.py M lib/galaxy/webapps/galaxy/api/users.py M test/api/test_users.py Log Message: ----------- API, users: implement users update - users and admin can now update usernames via the API - adds api tests to update Commit: e918d00cef31dca422b7348884db0e2055353bc4 https://github.com/galaxyproject/galaxy/commit/e918d00cef31dca422b7348884db… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- API, users: use api_inherit_admin in update Commit: 7ef9b2325e03c4a63023af39afb5ff5e742edc3b https://github.com/galaxyproject/galaxy/commit/7ef9b2325e03c4a63023af39afb5… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M test/api/test_users.py Log Message: ----------- API, users: remove log, change assertion style Commit: 09d10147f98793b97282aaec1c44efaff7c62585 https://github.com/galaxyproject/galaxy/commit/09d10147f98793b97282aaec1c44… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-11 (Mon, 11 Jul 2016) Changed paths: M test/unit/managers/test_UserManager.py Log Message: ----------- Tests, user: py3 exception and relative import fix Commit: e21a81fbf0c08dcaab2935211213c7afec56df7f https://github.com/galaxyproject/galaxy/commit/e21a81fbf0c08dcaab2935211213… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/webapps/galaxy/api/users.py M test/api/test_users.py M test/unit/managers/test_UserManager.py Log Message: ----------- Merge pull request #2595 from carlfeberhard/users.api-update Users API: add the update endpoint Compare: https://github.com/galaxyproject/galaxy/compare/47d154f979b2...e21a81fbf0c0

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[galaxyproject/galaxy] 888ee7: Graph visualization: add parsers, change datatypes
by GitHub 18 Jul '16

18 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 888ee700d7e8cb99d5e6c9674271c9da3b40ee74 https://github.com/galaxyproject/galaxy/commit/888ee700d7e8cb99d5e6c9674271… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-15 (Fri, 15 Jul 2016) Changed paths: M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/graphviz/static/js/graphVis.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/visualizations/graphviz/templates/graphviz.mako Log Message: ----------- Graph visualization: add parsers, change datatypes - Removes Data.Text and all subclasses from the applicable datatypes - Adds all datatypes that can provide node-edge data to be applicable (xgmll and sif) - Adds txt and json extensions as applicable - Minor clean up - Can use shift key to select multiple nodes Commit: 47d154f979b29a25fc2d9904583f677216a3b65d https://github.com/galaxyproject/galaxy/commit/47d154f979b29a25fc2d9904583f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/graphviz/static/js/graphVis.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/visualizations/graphviz/templates/graphviz.mako Log Message: ----------- Merge pull request #2620 from carlfeberhard/graphviz Graph visualization: add parsers, change datatypes Compare: https://github.com/galaxyproject/galaxy/compare/4bf21e624ece...47d154f979b2

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[galaxyproject/galaxy] 09b421: UI, history: implement list:list
by GitHub 18 Jul '16

18 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 09b42113c6b9fb1bcddbe66a86e299866431c9a4 https://github.com/galaxyproject/galaxy/commit/09b42113c6b9fb1bcddbe66a86e2… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: implement list:list Commit: 3646d08d7ff2303be21e9c12050a55039dc1219a https://github.com/galaxyproject/galaxy/commit/3646d08d7ff2303be21e9c12050a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: more feedback on bad collection type Commit: 510fe47ae19c170001eac652c83316d3fd2b181b https://github.com/galaxyproject/galaxy/commit/510fe47ae19c170001eac652c833… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- (bundle scripts) Commit: 4bf21e624ecea88ce67a9a802f6bd08b137e9a79 https://github.com/galaxyproject/galaxy/commit/4bf21e624ecea88ce67a9a802f6b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/util/__init__.py M lib/galaxy/web/framework/decorators.py M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M templates/ind_share_base.mako M tools/stats/gsummary.xml Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into HEAD Conflicts: static/maps/mvc/history/history-contents.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/history/history-contents.js Compare: https://github.com/galaxyproject/galaxy/compare/3b19a061cf89...4bf21e624ece

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[galaxyproject/galaxy] 9d3b30: UI, history: stringify contents copy params
by GitHub 18 Jul '16

18 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d3b304879959f9cea76cd2dd242b2eea6c1c478 https://github.com/galaxyproject/galaxy/commit/9d3b304879959f9cea76cd2dd242… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: stringify contents copy params Commit: 96cca7ccadba60c7aac970e656bf0932070b9d00 https://github.com/galaxyproject/galaxy/commit/96cca7ccadba60c7aac970e656bf… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/web/framework/decorators.py Log Message: ----------- Core, request body: handle hex vs. float better When parsing a non-json request body, params for a payload have been parsed individually using loads on a single value. This can cause a hex id in the (regex) form '\d+e\d+' to be parsed as a float. This commit: - adds a parse_non_hex_float function that refuses to parse scientific notation in the above form - and uses it *only* in the payload parsing method for non-json request bodies Commit: d157865857589ef73a164219dc4ed630a16520ca https://github.com/galaxyproject/galaxy/commit/d157865857589ef73a164219dc4e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-11 (Mon, 11 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/workflow/modules.py M scripts/common_startup.sh M static/maps/mvc/dataset/data.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-template.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/data.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-template.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into fix.hex-vs-float Commit: 3b19a061cf896ea1eed9933bf6bda549be7d8a06 https://github.com/galaxyproject/galaxy/commit/3b19a061cf896ea1eed9933bf6bd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M lib/galaxy/util/__init__.py M lib/galaxy/web/framework/decorators.py M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- Merge pull request #2597 from carlfeberhard/fix.hex-vs-float Fix hex vs float parsing in request body Compare: https://github.com/galaxyproject/galaxy/compare/389b2f4fbd2e...3b19a061cf89

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[galaxyproject/galaxy] c9291d: Merge pull request #6 from galaxyproject/dev
by GitHub 18 Jul '16

18 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c9291d0c949cb1469f62f53a3b4b370fd1b2f20f https://github.com/galaxyproject/galaxy/commit/c9291d0c949cb1469f62f53a3b4b… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M .ci/py3_sources.txt M Makefile M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/jupyter/config/jupyter.xml M lib/galaxy/config.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/managers/base.py M lib/galaxy/managers/context.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0030_history_slug_column.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py A lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/wrappers.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/genomes.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/modules.py M scripts/api/data_manager_example_execute.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/bootstrap_history.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/drmaa_external_runner.py M scripts/fetch_eggs.py M setup.cfg M static/maps/mvc/dataset/data.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-template.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/data.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-template.js M templates/admin/impersonate.mako M templates/user/change_password.mako M test/api/helpers.py M test/api/test_datasets.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py A test/functional/tools/identifier_collection.xml M test/functional/tools/samples_tool_conf.xml M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional_tests.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/managers/base.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_toolbox.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M tools/stats/aggregate_scores_in_intervals.py M tox.ini Log Message: ----------- Merge pull request #6 from galaxyproject/dev keeps up to date with galaxy:dev Commit: 4230a107373921c766d5dd6f19f405f54fafe1ab https://github.com/galaxyproject/galaxy/commit/4230a107373921c766d5dd6f19f4… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Reinstates workingDir setup for container on k8s. This was removed by mistake previously. Commit: 389b2f4fbd2e0f689f0e11ffc08f01f193e6026a https://github.com/galaxyproject/galaxy/commit/389b2f4fbd2e0f689f0e11ffc08f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #2616 from phnmnl/feature/missingWorkingDirK8sOption Kubernetes runner corrects working directory not passed to container Compare: https://github.com/galaxyproject/galaxy/compare/5b3a27c0b0e2...389b2f4fbd2e

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[galaxyproject/galaxy] d1ce99: Fix smart_str for Python 3. Add doctests
by GitHub 18 Jul '16

18 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d1ce991dd4acc2c50c18990b01571216f483907e https://github.com/galaxyproject/galaxy/commit/d1ce991dd4acc2c50c18990b0157… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix smart_str for Python 3. Add doctests Commit: 5b3a27c0b0e2c1e40e9f933dae139dfefd8be373 https://github.com/galaxyproject/galaxy/commit/5b3a27c0b0e2c1e40e9f933dae13… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #2608 from nsoranzo/smart_str Fix smart_str for Python 3. Add doctests Compare: https://github.com/galaxyproject/galaxy/compare/bb9907a81da4...5b3a27c0b0e2

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[galaxyproject/galaxy] 102bc2: Update to make the workflow share dropdown the sam...
by GitHub 18 Jul '16

18 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 102bc28011023ec22604c559a6c10ed98e535e3a https://github.com/galaxyproject/galaxy/commit/102bc28011023ec22604c559a6c1… Author: galaxy <galaxy(a)galaxy.development> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Update to make the workflow share dropdown the same width as the impersonate user dropdown. Commit: bb9907a81da44ea0f01190e1642796140dc59657 https://github.com/galaxyproject/galaxy/commit/bb9907a81da44ea0f01190e16427… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Merge pull request #2617 from sszakony/dev Update workflow share dropdown width Compare: https://github.com/galaxyproject/galaxy/compare/0480e5e5505e...bb9907a81da4

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[galaxyproject/galaxy] aa7ead: Strip whitespaces when processing <url_template> c...
by GitHub 15 Jul '16

15 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: aa7ead6dccd2c80152664c31bbf9b27f2f463799 https://github.com/galaxyproject/galaxy/commit/aa7ead6dccd2c80152664c31bbf9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Strip whitespaces when processing <url_template> content Otherwise download_binary action tries to save the file to an invalid filename. Reported by @remimarenco on IRC. Fix typo. Commit: 8c59d1c953c61b6d73d9bef5c4dda8a8056240b7 https://github.com/galaxyproject/galaxy/commit/8c59d1c953c61b6d73d9bef5c4dd… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-07-15 (Fri, 15 Jul 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #2618 from nsoranzo/release_16.04_fix_download_binary [16.04] Strip whitespaces when processing <url_template> content Compare: https://github.com/galaxyproject/galaxy/compare/05c063b13a3f...8c59d1c953c6

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[galaxyproject/galaxy] f7cbef: Update gsummary.xml
by GitHub 15 Jul '16

15 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f7cbefc1f3e1c4feb215cff26dbbf463b6d6e362 https://github.com/galaxyproject/galaxy/commit/f7cbefc1f3e1c4feb215cff26dbb… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Update gsummary.xml rpy seems not available within the Conda packages. So I add rpy2 in the requirements. It works for me! I :heart: Conda Commit: e86206733243f42ec414faab3148e32f76e004cb https://github.com/galaxyproject/galaxy/commit/e86206733243f42ec414faab3148… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Update gsummary.xml Commit: f951249c797f0e944133e8402b5602d83c600276 https://github.com/galaxyproject/galaxy/commit/f951249c797f0e944133e8402b56… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Update gsummary.xml Delete r and rpy deps Commit: 0480e5e5505e47709193b3e33d3068187ed0e6ac https://github.com/galaxyproject/galaxy/commit/0480e5e5505e47709193b3e33d30… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-15 (Fri, 15 Jul 2016) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Merge pull request #2590 from lecorguille/patch-1 Update gsummary.xml Compare: https://github.com/galaxyproject/galaxy/compare/7bbe0a217123...0480e5e5505e

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