- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 1e1c54: added missing parameter to function ensure_install...
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 1e1c549e695cf6541c4dcac5d554c852165e7b6a https://github.com/galaxyproject/galaxy/commit/1e1c549e695cf6541c4dcac5d554… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- added missing parameter to function ensure_installed Commit: a1b8a54ef8009ccf9ac64a699ed848cd56bba283 https://github.com/galaxyproject/galaxy/commit/a1b8a54ef8009ccf9ac64a699ed8… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- ensure_installed is now iterative instead of recursive Commit: 349c9c8f10f6f5eeac45c1a14e3b4a6c23cc373e https://github.com/galaxyproject/galaxy/commit/349c9c8f10f6f5eeac45c1a14e3b… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- version with no repetition at all Commit: a76547281f59b80acd27ddfa098c97e65a72d81a https://github.com/galaxyproject/galaxy/commit/a76547281f59b80acd27ddfa098c… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Set timeout for aquiring lock to 5min Commit: 748539a3a671552eea60e114a6c6e4dd7b48c7de https://github.com/galaxyproject/galaxy/commit/748539a3a671552eea60e114a6c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Merge pull request #4450 from mvdbeek/fix_file_lock_error [17.01] Fix file lock error handling Compare: https://github.com/galaxyproject/galaxy/compare/0f5ad34eaf6b...748539a3a671

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[galaxyproject/galaxy] df442e: Fix E201 errors (spaces in parens) in new memepsp ...
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: df442ea51a05541e83e304432ce4aac678a5b7a9 https://github.com/galaxyproject/galaxy/commit/df442ea51a05541e83e304432ce4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Fix E201 errors (spaces in parens) in new memepsp datatype Commit: 7ef099f6a6c97f0d9ac202860d6873c9a7aed66c https://github.com/galaxyproject/galaxy/commit/7ef099f6a6c97f0d9ac202860d68… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #4446 from dannon/memepsp_formatting Fix E201 errors (spaces in parens) in new memepsp datatype Compare: https://github.com/galaxyproject/galaxy/compare/cca1f9e9bcf4...7ef099f6a6c9

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[galaxyproject/galaxy] 5cebb0: Add support for the MEME psp format
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5cebb086b2849f92ac8da10d7e776e4334c28ff5 https://github.com/galaxyproject/galaxy/commit/5cebb086b2849f92ac8da10d7e77… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.psp Log Message: ----------- Add support for the MEME psp format Commit: 806370123b028eb0728e05fff2f9f9853c5cd6c5 https://github.com/galaxyproject/galaxy/commit/806370123b028eb0728e05fff2f9… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- fix XML error Commit: 7dae650fdbde77336250341832c928f604b41bab https://github.com/galaxyproject/galaxy/commit/7dae650fdbde77336250341832c9… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.memepsp R lib/galaxy/datatypes/test/1.psp Log Message: ----------- Change Psp to MemePsp and misc fixes per initial review Commit: 3026bf56c9662f47062fbd37904803156a4fe0db https://github.com/galaxyproject/galaxy/commit/3026bf56c9662f47062fbd379048… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Remove strange import - no idea from where it originated Commit: 2b94fa3b890a00bbe170ac1bec68d29e8d19c75a https://github.com/galaxyproject/galaxy/commit/2b94fa3b890a00bbe170ac1bec68… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix MemePsp sniff entry Commit: 5799fbc3d13ae6ec41ef5a17e55faf6f58059ae3 https://github.com/galaxyproject/galaxy/commit/5799fbc3d13ae6ec41ef5a17e55f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- change file_ext to be inline with memexml and co Commit: cca1f9e9bcf455b4b655fe9c54707bc34d3c6c32 https://github.com/galaxyproject/galaxy/commit/cca1f9e9bcf455b4b655fe9c5470… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.memepsp Log Message: ----------- Merge pull request #4430 from gregvonkuster/psp_format Add support for the MEME psp format Compare: https://github.com/galaxyproject/galaxy/compare/35ab7457b903...cca1f9e9bcf4

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[galaxyproject/galaxy] 03df49: Fix API tests broken in #4434
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 03df496540a6e2099aa4012fb2d46ec44be9bdbf https://github.com/galaxyproject/galaxy/commit/03df496540a6e2099aa4012fb2d4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fix API tests broken in #4434 Commit: 35ab7457b9039e9ac6e076ea16bf86dd828faaed https://github.com/galaxyproject/galaxy/commit/35ab7457b9039e9ac6e076ea16bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #4445 from nsoranzo/followup_on_4434 Fix API tests broken in #4434 Compare: https://github.com/galaxyproject/galaxy/compare/a85ee599ffc6...35ab7457b903

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[galaxyproject/galaxy] 21b44b: Fix all E201 and E202 style errors
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 21b44bf348ae10d170ab96a3b6f30bf9dbbd5a4a https://github.com/galaxyproject/galaxy/commit/21b44bf348ae10d170ab96a3b6f3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/style/source_material/circle.py M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M lib/galaxy/__init__.py M lib/galaxy/actions/admin.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.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/pbed_to_lped_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/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.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/exceptions.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/display_applications/util.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/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.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/triples.py M lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.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/basic.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.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/dynamic_tool_destination.py M lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/collectl/stats.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.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/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.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/stock_rules.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/api_keys.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.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/deletable.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/lddas.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/pages.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/tags.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/base.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0001_initial_tables.py M lib/galaxy/model/migrate/versions/0002_metadata_file_table.py M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.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 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tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py Log Message: ----------- Fix all E201 and E202 style errors using the following command: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 . ``` Commit: a353b2e88fc0693c8b9a60017cbc012448c4f4e0 https://github.com/galaxyproject/galaxy/commit/a353b2e88fc0693c8b9a60017cbc… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M contrib/nagios/check_galaxy.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.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/interval.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/external_services/actions.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.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/error_level.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/managers/base.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M 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test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional/test_1400_review_migration_stages.py M test/shed_functional/functional/test_1410_update_manager.py M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py M test/shed_functional/functional/test_1430_repair_installed_repository.py M test/shed_functional/functional/test_1440_missing_env_sh_files.py M test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py M test/shed_functional/functional/test_1460_data_managers.py M test/shed_functional/functional/test_1470_updating_installed_repositories.py M test/shed_functional/functional_tests.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_UserManager.py M tools/data_source/data_source.py M tools/data_source/upload.py M tools/filters/axt_to_lav.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Fix E127 errors introduced by previous commit using: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 . ``` Commit: a8d7b2df8bb0ccf49b2ca7247f2451b6123a5fd8 https://github.com/galaxyproject/galaxy/commit/a8d7b2df8bb0ccf49b2ca7247f24… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/model/__init__.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/folder_contents.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/library.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/microbes/BeautifulSoup.py M scripts/tool_shed/deprecate_repositories_without_metadata.py Log Message: ----------- Fix more indentation errors Commit: a85ee599ffc66ce3a5954ad819c864064bff838a https://github.com/galaxyproject/galaxy/commit/a85ee599ffc66ce3a5954ad819c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/style/source_material/circle.py M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M 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tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py Log Message: ----------- Merge pull request #4440 from nsoranzo/fix_E201_E202 Fix E201 and E202 style errors Compare: https://github.com/galaxyproject/galaxy/compare/008a1d849c4e...a85ee599ffc6

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[galaxyproject/galaxy] c72f43: Avoid adding `(imported from API)` to workflows
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c72f43dc5fb48e358d65caf6c59876ba0f15324e https://github.com/galaxyproject/galaxy/commit/c72f43dc5fb48e358d65caf6c598… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Avoid adding `(imported from API)` to workflows This should fail a few tests which I will fix with additional commits. Doing this from GitHub... Commit: 9ef13a1c724a2bb326bba3556019448ef69ae8fd https://github.com/galaxyproject/galaxy/commit/9ef13a1c724a2bb326bba3556019… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M test/api/test_search.py Log Message: ----------- Remove `(imported from API)` suffix from test Commit: 03a3d34f1e2326c99798299d53fc6b7026aadb09 https://github.com/galaxyproject/galaxy/commit/03a3d34f1e2326c99798299d53fc… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Remove `(imported from API)` suffix from test Commit: 008a1d849c4eb86ab52fd032ae611e4844c3cf09 https://github.com/galaxyproject/galaxy/commit/008a1d849c4eb86ab52fd032ae61… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py M test/api/test_search.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #4434 from chambm/patch-1 Avoid adding `(imported from API)` to workflows Compare: https://github.com/galaxyproject/galaxy/compare/1b69b9a5fedb...008a1d849c4e

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[galaxyproject/galaxy] 25bd71: Remove print of non-existent attribute 'content'
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 25bd7178c157f24523333caaf7f5a0a54f264abe https://github.com/galaxyproject/galaxy/commit/25bd7178c157f24523333caaf7f5… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M scripts/api/upload_to_history.py Log Message: ----------- Remove print of non-existent attribute 'content' Commit: 1b69b9a5fedbd232e76ef684734170e7b06fe3e9 https://github.com/galaxyproject/galaxy/commit/1b69b9a5fedbd232e76ef6847341… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M scripts/api/upload_to_history.py Log Message: ----------- Merge pull request #4439 from chambm/patch-2 Remove print of non-existent attribute 'content' Compare: https://github.com/galaxyproject/galaxy/compare/04583346a197...1b69b9a5fedb

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[galaxyproject/galaxy] 613f4f: Use dict format for admin tool versions grid
by GitHub 16 Aug '17

16 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 613f4fb1ced3c9a7e0d1417b8c9c14b681479bdd https://github.com/galaxyproject/galaxy/commit/613f4fb1ced3c9a7e0d1417b8c9c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use dict format for admin tool versions grid Commit: 381bf173d095ce51ba66d9cf19f5827c75c36dc8 https://github.com/galaxyproject/galaxy/commit/381bf173d095ce51ba66d9cf19f5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove message from tool versions Commit: cdfaebdaa4722226cf121454aa02b455d324d265 https://github.com/galaxyproject/galaxy/commit/cdfaebdaa4722226cf121454aa02… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Switch quotas grid to dict format Commit: 0e1b80b28f7558104c9a36bd1d224c60d91c2c70 https://github.com/galaxyproject/galaxy/commit/0e1b80b28f7558104c9a36bd1d22… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add async quota grid operations Commit: ad60f5a8ea4eaf574b4ffa1e51baa5bbe8282d47 https://github.com/galaxyproject/galaxy/commit/ad60f5a8ea4eaf574b4ffa1e51ba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/actions/admin.py Log Message: ----------- Allow empty params Commit: 83a48f8f336a4c73dd1faabe3c84ce8801fb181d https://github.com/galaxyproject/galaxy/commit/83a48f8f336a4c73dd1faabe3c84… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Build quota renaming form in admin panel using client side form builder Commit: 9dcc181f72d5f31b3d5feb45f673996714aca913 https://github.com/galaxyproject/galaxy/commit/9dcc181f72d5f31b3d5feb45f673… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix error message handling for quota operations, set default value for payloads to none Commit: 643f262ea913e8cc0f3bb5e39acf2af80194c71f https://github.com/galaxyproject/galaxy/commit/643f262ea913e8cc0f3bb5e39acf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use client form builder to render edit quota amount form Commit: ad2dc168307037070205db27d7bdb09fb82d549f https://github.com/galaxyproject/galaxy/commit/ad2dc168307037070205db27d7bd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix link to edit quota Commit: ae181d776fb9a565d7b51c18aa8edcae09018bc3 https://github.com/galaxyproject/galaxy/commit/ae181d776fb9a565d7b51c18aa8e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Provide async support for unsetting default quotas Commit: bd542000fa9ec420ba0f2e17d2b8f8047eb72f8c https://github.com/galaxyproject/galaxy/commit/bd542000fa9ec420ba0f2e17d2b8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Build set default quota forms using client form builder Commit: 17cd7d16c2db988581e26ad59a88a57302a202c9 https://github.com/galaxyproject/galaxy/commit/17cd7d16c2db988581e26ad59a88… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Add manage role support for quotas Commit: 9f580d0630026157f2727651cce2e8f444f78cdc https://github.com/galaxyproject/galaxy/commit/9f580d0630026157f2727651cce2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Use consistent naming for group and role parameters Commit: 0f84d8bd91722c4bd36d5a736d6ca02a57460cfc https://github.com/galaxyproject/galaxy/commit/0f84d8bd91722c4bd36d5a736d6c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add client side form to create new quota Commit: 5647dfe5dbb22b7d09b1b760e41a2e0cd96cd8c8 https://github.com/galaxyproject/galaxy/commit/5647dfe5dbb22b7d09b1b760e41a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: R templates/admin/quota/quota.mako R templates/admin/quota/quota_create.mako R templates/admin/quota/quota_edit.mako R templates/admin/quota/quota_rename.mako R templates/admin/quota/quota_set_default.mako Log Message: ----------- Remove unused quota makos Commit: 33acc1f8a337977eb85e9ba570f3404476411edc https://github.com/galaxyproject/galaxy/commit/33acc1f8a337977eb85e9ba570f3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/galaxy_bootstrap/overrides.less M config/datatypes_conf.xml.sample A config/error_report.yml.sample M config/tool_conf.xml.sample A config/user_preferences_extra_conf.yml.sample A doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py A lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/biostar.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/extract.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/grt/export.py M scripts/grt/upload.py A static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M templates/show_params.mako R templates/webapps/galaxy/dataset/errors.mako M templates/webapps/tool_shed/repository/common.mako A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml M test/unit/tools/test_parsing.py Log Message: ----------- Merge branch 'admin_grid_groups' into admin_grid_toolversion Commit: ef2c32ae84706897e70fa41808f46d95f1132ec9 https://github.com/galaxyproject/galaxy/commit/ef2c32ae84706897e70fa41808f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix lint Commit: b726c33c80b33ece878343b6208e65f3d983008f 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lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/checkers.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py A lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/reports/buildapp.py A lib/galaxy/webapps/reports/config_schema.yml A lib/galaxy/webapps/reports/uwsgi_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/config_schema.yml A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml A lib/galaxy/webapps/uwsgi_schema.yml M lib/galaxy/workflow/modules.py M openid/yahoo.xml M run.sh M run_reports.sh M run_tool_shed.sh A scripts/common_startup_functions.sh A scripts/config_sample_to_kwalify.py M scripts/manage_tools.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.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/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js A test-data/1.sam.gz A test-data/bad.html.gz A test-data/random-file M test/api/test_tools.py M test/api/test_workflows.py M test/base/api.py M test/base/interactor.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_upload_configuration_options.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'admin_grid_groups' into admin_grid_toolversion Commit: 9dfee375e9782f421832ecc44981a2cbdfc4f183 https://github.com/galaxyproject/galaxy/commit/9dfee375e9782f421832ecc44981… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Optionally allow to show or hide select all Commit: a1897bd32a112e68ce09b71fd6ad98e6b97f267b https://github.com/galaxyproject/galaxy/commit/a1897bd32a112e68ce09b71fd6ad… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Hide select all for role and group selectors Commit: d6f6a78ab8464bf1a10cbca74632873993744933 https://github.com/galaxyproject/galaxy/commit/d6f6a78ab8464bf1a10cbca74632… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M static/maps/mvc/form/form-wrapper.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Use 'Save' as default title for configuration forms Commit: 4688eef2a41e79b44e8cb19ad87d5f2fc9a3aaf1 https://github.com/galaxyproject/galaxy/commit/4688eef2a41e79b44e8cb19ad87d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix user id decoding, fix optional array handling Commit: 96cad03980b314a7a89a01a5e1d442b2855a22e8 https://github.com/galaxyproject/galaxy/commit/96cad03980b314a7a89a01a5e1d4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix label for default quotas Commit: 246489a7aa2b950d7a12bf2610faaaed26d90a55 https://github.com/galaxyproject/galaxy/commit/246489a7aa2b950d7a12bf2610fa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/actions/admin.py Log Message: ----------- Fix messages Commit: f9e889215021f7a99a4ccfe4612431caa963f63c https://github.com/galaxyproject/galaxy/commit/f9e889215021f7a99a4ccfe46124… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Catch user input error for auto created roles and groups Commit: bebc5ff56ae41a2660f884a2b04604b2a473dd11 https://github.com/galaxyproject/galaxy/commit/bebc5ff56ae41a2660f884a2b046… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Move decode id to correct location Commit: f1e13cef05759bc7782248c08d595043d03161fe https://github.com/galaxyproject/galaxy/commit/f1e13cef05759bc7782248c08d59… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/actions/admin.py Log Message: ----------- More messages to validate inputs Commit: 86cdaaf610011b2b0c43f1bd93d36d87907b30e7 https://github.com/galaxyproject/galaxy/commit/86cdaaf610011b2b0c43f1bd93d3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add validation messages if resource ids are not correct Commit: 2073151bf2f6b2c2427c10934b1feea967d010ff https://github.com/galaxyproject/galaxy/commit/2073151bf2f6b2c2427c10934b1f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Log Message: ----------- Merge branch 'dev' into admin_grid_toolversion Commit: fdcd46918d52c4ee8ab7c2c421fd3e559c9a1fdc https://github.com/galaxyproject/galaxy/commit/fdcd46918d52c4ee8ab7c2c421fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove unfilterable columns from group and quota search grids Commit: 2c4cf686f8fffd17bb7a248571fa7d502f52a046 https://github.com/galaxyproject/galaxy/commit/2c4cf686f8fffd17bb7a248571fa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.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/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/toolshed/scripts/mvc/groups/group-list-view.js M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/webhooks/demo/search/static/script.js M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/web/proxy/js/lib/proxy.js M scripts/communication/template/communication.js M static/maps/galaxy.pages.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.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/library/library-library-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/toolshed/categories-view.js.map M static/maps/mvc/toolshed/repo-status-view.js.map M static/maps/mvc/toolshed/repositories-view.js.map M static/maps/mvc/toolshed/repository-queue-view.js.map M static/maps/mvc/toolshed/repository-view.js.map M static/maps/mvc/toolshed/util.js.map M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/scroll-panel.js.map M static/maps/utils/graph.js.map M static/maps/utils/uploadbox.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.pages.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.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/library/library-library-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/scroll-panel.js M static/scripts/utils/graph.js M static/scripts/utils/uploadbox.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_execution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge branch 'dev' into admin_grid_toolversion and repack Commit: 04583346a1970f9bab4f0cd3b9e8693de4fedbf9 https://github.com/galaxyproject/galaxy/commit/04583346a1970f9bab4f0cd3b9e8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js R templates/admin/quota/quota.mako R templates/admin/quota/quota_create.mako R templates/admin/quota/quota_edit.mako R templates/admin/quota/quota_rename.mako R templates/admin/quota/quota_set_default.mako Log Message: ----------- Merge pull request #4411 from guerler/admin_grid_toolversion replace mako templates for tool lineage and quotas grids Compare: https://github.com/galaxyproject/galaxy/compare/1b7f25eeaec9...04583346a197

1 0

[galaxyproject/galaxy] 7ef9b4: Remove spurious null check.
by GitHub 16 Aug '17

16 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ef9b4cdafd0e2c6e68cba3729d9bd99645ef15f https://github.com/galaxyproject/galaxy/commit/7ef9b4cdafd0e2c6e68cba3729d9… Author: Max Schaefer <max(a)semmle.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/job/job-params.js Log Message: ----------- Remove spurious null check. Commit: 43ddd4732034ca2ee658ccd4ab0ae17d4a1bbe40 https://github.com/galaxyproject/galaxy/commit/43ddd4732034ca2ee658ccd4ab0a… Author: Max Schaefer <max(a)semmle.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.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/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/toolshed/scripts/mvc/groups/group-list-view.js M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/webhooks/demo/search/static/script.js M lib/galaxy/web/proxy/js/lib/proxy.js M scripts/communication/template/communication.js Log Message: ----------- Add missing `var` declarations. In all these cases, a variable was not declared to be a local using `var` (and hence was implicitly interpreted as a global variable), but all uses of that variable were preceded by a definition within the same function, suggesting that the variable was, in fact, meant to be local, not global. Commit: 48b835c35cd746c23c185ae69577ab6ae9fc4ee8 https://github.com/galaxyproject/galaxy/commit/48b835c35cd746c23c185ae69577… Author: Max Schaefer <max(a)semmle.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/viz/circster.js Log Message: ----------- Remove an unused variable. The result of the `_.map` call was never used, so I replaced it with `_.each`. Commit: 8950d4423ff7d02bcf95b417676b2ef1c311333a https://github.com/galaxyproject/galaxy/commit/8950d4423ff7d02bcf95b417676b… Author: Max Schaefer <max(a)semmle.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Move two variable definitions to combine them with their declarations. Commit: 57c6284269c3256529f9c55953279eccb07dfabf https://github.com/galaxyproject/galaxy/commit/57c6284269c3256529f9c5595327… Author: Max Schaefer <max(a)semmle.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M static/maps/galaxy.pages.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.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/library/library-library-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/toolshed/categories-view.js.map M static/maps/mvc/toolshed/repo-status-view.js.map M static/maps/mvc/toolshed/repositories-view.js.map M static/maps/mvc/toolshed/repository-queue-view.js.map M static/maps/mvc/toolshed/repository-view.js.map M static/maps/mvc/toolshed/util.js.map M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/scroll-panel.js.map M static/maps/utils/graph.js.map M static/maps/utils/uploadbox.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.pages.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.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/library/library-library-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/scroll-panel.js M static/scripts/utils/graph.js M static/scripts/utils/uploadbox.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Run `make client`. Commit: 1b7f25eeaec96ae8b6a5336090dca675076b07bd https://github.com/galaxyproject/galaxy/commit/1b7f25eeaec96ae8b6a5336090dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.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/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/toolshed/scripts/mvc/groups/group-list-view.js M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/webhooks/demo/search/static/script.js M lib/galaxy/web/proxy/js/lib/proxy.js M scripts/communication/template/communication.js M static/maps/galaxy.pages.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.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/library/library-library-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/toolshed/categories-view.js.map M static/maps/mvc/toolshed/repo-status-view.js.map M static/maps/mvc/toolshed/repositories-view.js.map M static/maps/mvc/toolshed/repository-queue-view.js.map M static/maps/mvc/toolshed/repository-view.js.map M static/maps/mvc/toolshed/util.js.map M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/scroll-panel.js.map M static/maps/utils/graph.js.map M static/maps/utils/uploadbox.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.pages.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.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/library/library-library-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/scroll-panel.js M static/scripts/utils/graph.js M static/scripts/utils/uploadbox.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Merge pull request #4421 from xiemaisi/fix-lgtm-alerts Fix lgtm alerts Compare: https://github.com/galaxyproject/galaxy/compare/c5a91491c646...1b7f25eeaec9

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[galaxyproject/galaxy] 522ca9: Fix private role validation
by GitHub 16 Aug '17

16 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 522ca9e5c2ebbf274af26b466c1bab5fb5bc5625 https://github.com/galaxyproject/galaxy/commit/522ca9e5c2ebbf274af26b466c1b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Fix private role validation Commit: c5a91491c64610ede9421af8b89ddf8389238be3 https://github.com/galaxyproject/galaxy/commit/c5a91491c64610ede9421af8b89d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Merge pull request #4432 from guerler/fix_role_association_check Fix private role validation Compare: https://github.com/galaxyproject/galaxy/compare/b6f0600e98b7...c5a91491c646

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[galaxyproject/galaxy] 210d3e: Refactor to clean up args in one method of galaxy....
by GitHub 16 Aug '17

16 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 210d3e31ab8bd71569ed6399cfc1894223e4ec36 https://github.com/galaxyproject/galaxy/commit/210d3e31ab8bd71569ed6399cfc1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Refactor to clean up args in one method of galaxy.tools. Commit: 997e7114be722e56e5633cd10b554d6d1428dfc8 https://github.com/galaxyproject/galaxy/commit/997e7114be722e56e5633cd10b55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py M test/unit/tools_support.py Log Message: ----------- More correct tool creation in tools_support. Now supports creating tool subclasses based on tool source. Commit: db91b29df96d354c8972f63513ed755b5dd4418d https://github.com/galaxyproject/galaxy/commit/db91b29df96d354c8972f63513ed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Have more tests use mock_galaxy's MockApp. Commit: a462afa0b7094a5fa439b0aa3b751e26cc18bd98 https://github.com/galaxyproject/galaxy/commit/a462afa0b7094a5fa439b0aa3b75… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_execution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Eliminate second unit test variant of MockApp. As well as my failed experiment in mocking out sqlalchemy - I think the in-memory database is more useful than mocking out sqlalchemy in retrospect. Commit: 7de7f3f63a438a9d2b2b452d61e3118a710826c7 https://github.com/galaxyproject/galaxy/commit/7de7f3f63a438a9d2b2b452d61e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M test/unit/tools_support.py Log Message: ----------- "Fix" import order of tools_support for Travis. Commit: b6f0600e98b74a301c2eb787263cd89e5ca487ca https://github.com/galaxyproject/galaxy/commit/b6f0600e98b74a301c2eb787263c… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_execution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #4387 from jmchilton/tool_unit_test_cleanup Cleanup of Unit Test Code for Loading Tools Compare: https://github.com/galaxyproject/galaxy/compare/8eb487e7c138...b6f0600e98b7

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[galaxyproject/galaxy] 09c4b1: Break connection in workflow editor if necessary
by GitHub 16 Aug '17

16 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 09c4b1037b0034093488ed679628b9f614849a5e https://github.com/galaxyproject/galaxy/commit/09c4b1037b0034093488ed679628… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/bundled/admin.bundled.js.map 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.map M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Break connection in workflow editor if necessary When switching tool versions in the workflow editor connections are maintained by default. If a tool changes the datatype one may end up with a connection between incompatible input/outputs. Therefore we update the datatypes and explicitly destroy invalid connections. Commit: 8eb487e7c1383cedd971de8128bb9ba143abaa41 https://github.com/galaxyproject/galaxy/commit/8eb487e7c1383cedd971de8128bb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/bundled/admin.bundled.js.map 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.map M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #4431 from mvdbeek/break_connections Break connection in workflow editor if necessary Compare: https://github.com/galaxyproject/galaxy/compare/4bddd617fe5d...8eb487e7c138

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[galaxyproject/galaxy] 71db6b: Fix lint
by GitHub 15 Aug '17

15 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 71db6b461da3d3b2e3c6880c9d2bf90bcd44098e https://github.com/galaxyproject/galaxy/commit/71db6b461da3d3b2e3c6880c9d2b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix lint Fix Commit: c72aca479729ddee6a8bf8e19431b41e98d39d89 https://github.com/galaxyproject/galaxy/commit/c72aca479729ddee6a8bf8e19431… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Revise admin groups endpoint Commit: 097cae67956b972cd609f1155890d122c5bb3742 https://github.com/galaxyproject/galaxy/commit/097cae67956b972cd609f1155890… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge branch 'admin_grid_roles' into admin_grid_groups Commit: 9822dede69c95796c24e87a1c60cd845788095d1 https://github.com/galaxyproject/galaxy/commit/9822dede69c95796c24e87a1c60c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add client route Commit: 1bf2d1782fca4c79708261ca98cabe92822e86cb https://github.com/galaxyproject/galaxy/commit/1bf2d1782fca4c79708261ca98ca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use client side formbuilder for rename group form Commit: 7a58fd113d32659c9ea6e0c4fdb830d5c1ca7a72 https://github.com/galaxyproject/galaxy/commit/7a58fd113d32659c9ea6e0c4fdb8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove self directed operation Commit: b2d54b377c6c78f016ccb730178afd3f7a70c0b3 https://github.com/galaxyproject/galaxy/commit/b2d54b377c6c78f016ccb730178a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add async support for group deleting Commit: afdfbf69ff8d1636c661c5758f52c636f9160220 https://github.com/galaxyproject/galaxy/commit/afdfbf69ff8d1636c661c5758f52… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add async support for undeleting groups Commit: 96557cd136730033c3a4b84e506b3cc5831d06af https://github.com/galaxyproject/galaxy/commit/96557cd136730033c3a4b84e506b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add async support for purging groups Commit: 037b7fa75754ae90917d0ee25b1565c9ab29cd03 https://github.com/galaxyproject/galaxy/commit/037b7fa75754ae90917d0ee25b15… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove exposure of async operation handlers, align naming Commit: 3840c6d61735fa674239be19a10af04d0d3647f9 https://github.com/galaxyproject/galaxy/commit/3840c6d61735fa674239be19a10a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix purge handler for groups Commit: 1e83a48c4635ba05576cdb8e42bbdf8f971b825a https://github.com/galaxyproject/galaxy/commit/1e83a48c4635ba05576cdb8e42bb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove exposure of user related operations Commit: 1795247bd849e3d7d1c034416d27d5c1672039e8 https://github.com/galaxyproject/galaxy/commit/1795247bd849e3d7d1c034416d27… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove new line Commit: e805db6896352042aa5eb8482febbd75af46b008 https://github.com/galaxyproject/galaxy/commit/e805db6896352042aa5eb8482feb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use client to build create groups form Commit: 5605f390fe36c8ab562d049b105db7164b8097c1 https://github.com/galaxyproject/galaxy/commit/5605f390fe36c8ab562d049b105d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Build manage users and roles for groups with client form builder Commit: c827bb0a867e2fcdf89417bb7ea912641e49cf8a https://github.com/galaxyproject/galaxy/commit/c827bb0a867e2fcdf89417bb7ea9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/tool_shed/util/admin_util.py R templates/admin/dataset_security/group/group.mako R templates/admin/dataset_security/group/group_create.mako R templates/admin/dataset_security/group/group_rename.mako A templates/webapps/tool_shed/admin/dataset_security/group/group.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako Log Message: ----------- Move unused mako templates to toolshed, adjust paths Commit: dbad2556d05dead2ac0991a7897d95f1eda16087 https://github.com/galaxyproject/galaxy/commit/dbad2556d05dead2ac0991a7897d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge branch 'admin_grid_roles' into admin_grid_groups Commit: c57c36b51465b1bfaefcf486b9814c32f7f92840 https://github.com/galaxyproject/galaxy/commit/c57c36b51465b1bfaefcf486b981… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove over indent Commit: 4a77956dc8756300825c3744ccfa3a4646be5775 https://github.com/galaxyproject/galaxy/commit/4a77956dc8756300825c3744ccfa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge branch 'admin_grid_roles' into admin_grid_groups Commit: b38ccbc10547ded7e3afec262a5819bd3d44613f 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lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py A lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/biostar.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/extract.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/grt/export.py M scripts/grt/upload.py A static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M templates/show_params.mako R templates/webapps/galaxy/dataset/errors.mako M templates/webapps/tool_shed/repository/common.mako A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml M test/unit/tools/test_parsing.py Log Message: ----------- Merge branch 'admin_grid_roles' into admin_grid_groups Commit: ad2f39c1e6475c65fcb1e300201c035701640f10 https://github.com/galaxyproject/galaxy/commit/ad2f39c1e6475c65fcb1e300201c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix lint Commit: eccdc8c248fabef6bc5a988cdb1889c1aa32ca7a https://github.com/galaxyproject/galaxy/commit/eccdc8c248fabef6bc5a988cdb18… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Removed unreached message line Commit: fd5f42dc17009cfdfbfc08583549ba608efb166a https://github.com/galaxyproject/galaxy/commit/fd5f42dc17009cfdfbfc08583549… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M Makefile M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample R config/reports.ini.sample A config/reports.yml.sample R config/tool_shed.ini.sample A config/tool_shed.yml.sample A doc/source/admin/reports.rst A doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.xls M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/checkers.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py A lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/reports/buildapp.py A lib/galaxy/webapps/reports/config_schema.yml A lib/galaxy/webapps/reports/uwsgi_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/config_schema.yml A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml A lib/galaxy/webapps/uwsgi_schema.yml M openid/yahoo.xml M run.sh M run_reports.sh M run_tool_shed.sh A scripts/common_startup_functions.sh A scripts/config_sample_to_kwalify.py M scripts/manage_tools.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js A test-data/1.sam.gz A test-data/bad.html.gz A test-data/random-file M test/api/test_tools.py M test/api/test_workflows.py M test/base/api.py M test/base/interactor.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_upload_configuration_options.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into admin_grid_groups Commit: e72948cb743e50b50a21bf7f778792ba36ec38bd https://github.com/galaxyproject/galaxy/commit/e72948cb743e50b50a21bf7f7787… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.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/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge branch 'dev' into admin_grid_groups Commit: 4bddd617fe5df41efcebacdda7a6bb1d280ac2ce https://github.com/galaxyproject/galaxy/commit/4bddd617fe5df41efcebacdda7a6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/util/admin_util.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R templates/admin/dataset_security/group/group.mako R templates/admin/dataset_security/group/group_create.mako R templates/admin/dataset_security/group/group_rename.mako A templates/webapps/tool_shed/admin/dataset_security/group/group.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako Log Message: ----------- Merge pull request #4405 from guerler/admin_grid_groups Admin grid groups revision Compare: https://github.com/galaxyproject/galaxy/compare/462b7def5d9b...4bddd617fe5d

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[galaxyproject/galaxy] d0b06a: Don't cast tool_version to string if tool_version ...
by GitHub 15 Aug '17

15 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d0b06a3b1da09ff3394e9ea036d788676817b58f https://github.com/galaxyproject/galaxy/commit/d0b06a3b1da09ff3394e9ea036d7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Don't cast tool_version to string if tool_version is None-type If a version is not specifically requested a wrong version (`None` cast to `'None'`) of a tool will be loaded in the workflow editor instead of the latest version. That should address @martenson's remark in https://github.com/galaxyproject/galaxy/pull/4373#issuecomment-321896674 (and maybe also https://github.com/galaxyproject/galaxy/issues/557#issuecomment-213498153) Commit: 6ad6fd9252bf5ec44beb00cb434876e170dc9548 https://github.com/galaxyproject/galaxy/commit/6ad6fd9252bf5ec44beb00cb4348… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Rebuild tool_version_cache on DetachedInstanceError Commit: 7f78ee7b18b83961b305cac19aa8949a4452710d https://github.com/galaxyproject/galaxy/commit/7f78ee7b18b83961b305cac19aa8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4420 from mvdbeek/fix_wrong_tool_version_cast [17.05] Don't cast tool_version to string if tool_version is None-type Commit: 07a30499994b33e27c0b1765df9f32c9bfcea0b2 https://github.com/galaxyproject/galaxy/commit/07a30499994b33e27c0b1765df9f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.05' into dev Conflicts: lib/galaxy/model/tool_shed_install/__init__.py Commit: 462b7def5d9b9298d50cea2e62cfbf89bd463d25 https://github.com/galaxyproject/galaxy/commit/462b7def5d9b9298d50cea2e62cf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4427 from nsoranzo/merge_release_17.05 Merge release_17.05 into dev Compare: https://github.com/galaxyproject/galaxy/compare/27be24963837...462b7def5d9b

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[galaxyproject/galaxy] 5f1b7d: Show verison button in workflow editor and trigger...
by GitHub 15 Aug '17

15 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5f1b7d5a5060c3c45601b499a953113e0b1b3125 https://github.com/galaxyproject/galaxy/commit/5f1b7d5a5060c3c45601b499a953… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Show verison button in workflow editor and trigger on_change Commit: 25e05b62c7b529b0379e3ff50fc75ccb5b8c28b6 https://github.com/galaxyproject/galaxy/commit/25e05b62c7b529b0379e3ff50fc7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Do postchange action only when modifiying tool versions in the workflow editor Commit: 5afe490822325d4aa6c9be726183175743dc88f6 https://github.com/galaxyproject/galaxy/commit/5afe490822325d4aa6c9be726183… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Fix qunit test Commit: 36ce9113f7ccb6372bc2d1f8e92e95a8aafdd066 https://github.com/galaxyproject/galaxy/commit/36ce9113f7ccb6372bc2d1f8e92e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Keep spacing consistent (thx @nsoranzo) Commit: 526e98e372e61747b1e3cd4b86a04603ca08959b https://github.com/galaxyproject/galaxy/commit/526e98e372e61747b1e3cd4b86a0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Reset outputs when changing tool versions in wf-editor Commit: db2ea853f699bf6b55b67cf7199ab355196910bc https://github.com/galaxyproject/galaxy/commit/db2ea853f699bf6b55b67cf7199a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Now thing are mostly working -- input and output connections are correctly altered ... but saving the workflow and reloading occasionally loads the wrong workflow Commit: ea1f4f866658e77465d1272b4d7f37bb85ee488b https://github.com/galaxyproject/galaxy/commit/ea1f4f866658e77465d1272b4d7f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Fix the occasional loading of the wrong workflow. Turns out that sometimes the tool_version is undefined (i.e) if the exact node had not been manipulated, but config_form.version is always up to date Commit: bc95f5e81b46a0bee54f6ffdd5c3a6615258af20 https://github.com/galaxyproject/galaxy/commit/bc95f5e81b46a0bee54f6ffdd5c3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Now adding/removing datasets and multiple version switches work fine, but PJA parameters are still problematic Commit: 92fedc0ae86127d670f3ff8e829d07ee657f30d7 https://github.com/galaxyproject/galaxy/commit/92fedc0ae86127d670f3ff8e829d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix logic for adding and removing outputs Commit: 1c286b158a8304380f499709b2f14c958b6fe203 https://github.com/galaxyproject/galaxy/commit/1c286b158a8304380f499709b2f1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Remove extra newlines Commit: 2e95026317e2e781163cf8bd4449bfd5ddfb894f https://github.com/galaxyproject/galaxy/commit/2e95026317e2e781163cf8bd4449… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Remove unused old_version variable Commit: 31c423a45a4186c41981f71d41a590177bad033d https://github.com/galaxyproject/galaxy/commit/31c423a45a4186c41981f71d41a5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Fix typo and remove leftover comment (thanks @nsoranzo) Commit: df91881c1f4dba06a9fb6a1720db68d059664041 https://github.com/galaxyproject/galaxy/commit/df91881c1f4dba06a9fb6a1720db… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Remove unused workflow outputs Commit: 73f4141d96ad54c25fdf7a3ffb458f2b1933e14e https://github.com/galaxyproject/galaxy/commit/73f4141d96ad54c25fdf7a3ffb45… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Add static JS Commit: aa7be28960a43802bd476be1d7d996c85134c055 https://github.com/galaxyproject/galaxy/commit/aa7be28960a43802bd476be1d7d9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/config.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/checkers.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map 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.map M static/scripts/mvc/library/library-foldertoolbar-view.js A test-data/1.sam.gz A test-data/bad.html.gz A test-data/random-file M test/api/test_tools.py M test/base/api.py M test/base/interactor.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_upload_configuration_options.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into switch_versions_in_workflows Commit: 27be24963837354af6cac1f429c1bc06e95626e1 https://github.com/galaxyproject/galaxy/commit/27be24963837354af6cac1f429c1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #4373 from mvdbeek/switch_versions_in_workflows Allow switching tool versions in workflow editor Compare: https://github.com/galaxyproject/galaxy/compare/44548f8f2fe2...27be24963837

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[galaxyproject/galaxy] 4dd503: Update conda channel order to sync with Bioconda
by GitHub 15 Aug '17

15 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4dd503046f59b13e925a76f88862882747dc6ad7 https://github.com/galaxyproject/galaxy/commit/4dd503046f59b13e925a76f88862… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Update conda channel order to sync with Bioconda Commit: 420e7a4f3408ec064403a4283ba22a134b65ece5 https://github.com/galaxyproject/galaxy/commit/420e7a4f3408ec064403a4283ba2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Remove _ensure_conda_context() function and make conda_context argument mandatory in functions/methods. This should help making sure the correct context (e.g. channels) is used for all Conda operations. Also remove unused is_target_available() function. Commit: cdbac056cb664e4c51f84c41c2519993d0412d74 https://github.com/galaxyproject/galaxy/commit/cdbac056cb664e4c51f84c41c251… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Override channel list on the command line instead of modifying condarc The way we were modifying condarc in the ensure_channels_configured() method was broken because we were appending the missing channels at the end, so the final order may not be the one specified in conda_ensure_channels . Also: - not modifying the user condarc is a much better approach - overriding the channel list on the command line will make debugging easier Commit: 44548f8f2fe258051ad2df45b153642586b85e00 https://github.com/galaxyproject/galaxy/commit/44548f8f2fe258051ad2df45b153… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #4409 from nsoranzo/fix_conda_channel_order Update conda channel order to sync with Bioconda Compare: https://github.com/galaxyproject/galaxy/compare/8721da8ca2e1...44548f8f2fe2

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[galaxyproject/galaxy] 68555f: some unicoding
by GitHub 15 Aug '17

15 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 68555f5571b5b872a39a34f8fa6035bfad67ea43 https://github.com/galaxyproject/galaxy/commit/68555f5571b5b872a39a34f8fa60… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- some unicoding Commit: 8721da8ca2e1f78a018baf4c43d8229327eb477f https://github.com/galaxyproject/galaxy/commit/8721da8ca2e1f78a018baf4c43d8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #4426 from erasche/local-runner-unicode some unicoding for local runner Compare: https://github.com/galaxyproject/galaxy/compare/9cbabef17e9a...8721da8ca2e1

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[galaxyproject/galaxy] d0b06a: Don't cast tool_version to string if tool_version ...
by GitHub 15 Aug '17

15 Aug '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: d0b06a3b1da09ff3394e9ea036d788676817b58f https://github.com/galaxyproject/galaxy/commit/d0b06a3b1da09ff3394e9ea036d7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Don't cast tool_version to string if tool_version is None-type If a version is not specifically requested a wrong version (`None` cast to `'None'`) of a tool will be loaded in the workflow editor instead of the latest version. That should address @martenson's remark in https://github.com/galaxyproject/galaxy/pull/4373#issuecomment-321896674 (and maybe also https://github.com/galaxyproject/galaxy/issues/557#issuecomment-213498153) Commit: 6ad6fd9252bf5ec44beb00cb434876e170dc9548 https://github.com/galaxyproject/galaxy/commit/6ad6fd9252bf5ec44beb00cb4348… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Rebuild tool_version_cache on DetachedInstanceError Commit: 7f78ee7b18b83961b305cac19aa8949a4452710d https://github.com/galaxyproject/galaxy/commit/7f78ee7b18b83961b305cac19aa8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4420 from mvdbeek/fix_wrong_tool_version_cast [17.05] Don't cast tool_version to string if tool_version is None-type Compare: https://github.com/galaxyproject/galaxy/compare/4faf496c9898...7f78ee7b18b8

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[galaxyproject/galaxy] 6c6c80: When a page is involved, the ID will be wrong
by GitHub 14 Aug '17

14 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c6c804ab63866c6239299f4221fa436dd4a9591 https://github.com/galaxyproject/galaxy/commit/6c6c804ab63866c6239299f4221f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- When a page is involved, the ID will be wrong Commit: 33a0c7fac3a0624d26efd8d08dabbca5f7e8c226 https://github.com/galaxyproject/galaxy/commit/33a0c7fac3a0624d26efd8d08dab… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Make client Commit: a2229783177b76786f581cc78040b059cbd2aab5 https://github.com/galaxyproject/galaxy/commit/a2229783177b76786f581cc78040… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4355 from erasche/patch-wrong-folder-id [release_17.05] Patch bug preventing creation of dataset library folders Commit: ecfb90ef9f8037575db2e62ae49d8bbb7e4e427b https://github.com/galaxyproject/galaxy/commit/ecfb90ef9f8037575db2e62ae49d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js R static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Revert "[release_17.05] Patch bug preventing creation of dataset library folders" Commit: 163e4ebbe1fbfc5f1f97b5aabc804621fdd426c9 https://github.com/galaxyproject/galaxy/commit/163e4ebbe1fbfc5f1f97b5aabc80… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js R static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4356 from galaxyproject/revert-4355-patch-wrong-folder-id Revert "[release_17.05] Patch bug preventing creation of dataset library folders" Commit: 12f0acba1dc1b81bb621ea130a75ec7dfac0fdaa https://github.com/galaxyproject/galaxy/commit/12f0acba1dc1b81bb621ea130a75… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Revert "Revert "[release_17.05] Patch bug preventing creation of dataset library folders"" Commit: 10efd7fac6e38c5ca07d94c351d10473811c7d6c https://github.com/galaxyproject/galaxy/commit/10efd7fac6e38c5ca07d94c351d1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4357 from galaxyproject/revert-4356-revert-4355-patch-wrong-folder-id [release_17.05] Patch bug preventing creation of dataset library folders Commit: ba3249acf07ca1a44a813e2c68a9d6074d2b7c4c https://github.com/galaxyproject/galaxy/commit/ba3249acf07ca1a44a813e2c68a9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py Log Message: ----------- Add missing chemical formats to datatypes_conf.xml.sample Commit: 61d172f18d8f7740585b038dd786e81178ca1831 https://github.com/galaxyproject/galaxy/commit/61d172f18d8f7740585b038dd786… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M setup.cfg M tox.ini Log Message: ----------- Update pin for flake8-docstrings Similar to commit 2586df45637d794c63252838573b2d1e6d692243 . Commit: a249dc01a5d0afa42474a6e4075ed2a3ad80400f https://github.com/galaxyproject/galaxy/commit/a249dc01a5d0afa42474a6e4075e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M .travis.yml Log Message: ----------- Use container-based infrastructure (sudo: false) in TravisCI Commit: 0f5ad34eaf6b65a2d258f308aa6fea8b4f39a52a https://github.com/galaxyproject/galaxy/commit/0f5ad34eaf6b65a2d258f308aa6f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M .travis.yml M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py M setup.cfg M tox.ini Log Message: ----------- Merge pull request #4413 from nsoranzo/release_17.01_really_add_datatypes [17.01] Add missing chemical formats to datatypes_conf.xml.sample Commit: 4faf496c9898786e8f504bd36b28dc70df4e3e26 https://github.com/galaxyproject/galaxy/commit/4faf496c9898786e8f504bd36b28… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Conflicts: tox.ini Commit: 9cbabef17e9afb4953324516d0883976edd51e87 https://github.com/galaxyproject/galaxy/commit/9cbabef17e9afb4953324516d088… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map 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.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge branch 'release_17.05' into dev Conflicts: static/maps/mvc/library/library-foldertoolbar-view.js.map static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/library/library-foldertoolbar-view.js Compare: https://github.com/galaxyproject/galaxy/compare/e594152de2dd...9cbabef17e9a

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[galaxyproject/galaxy] ba3249: Add missing chemical formats to datatypes_conf.xml...
by GitHub 14 Aug '17

14 Aug '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: ba3249acf07ca1a44a813e2c68a9d6074d2b7c4c https://github.com/galaxyproject/galaxy/commit/ba3249acf07ca1a44a813e2c68a9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py Log Message: ----------- Add missing chemical formats to datatypes_conf.xml.sample Commit: 61d172f18d8f7740585b038dd786e81178ca1831 https://github.com/galaxyproject/galaxy/commit/61d172f18d8f7740585b038dd786… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M setup.cfg M tox.ini Log Message: ----------- Update pin for flake8-docstrings Similar to commit 2586df45637d794c63252838573b2d1e6d692243 . Commit: a249dc01a5d0afa42474a6e4075ed2a3ad80400f https://github.com/galaxyproject/galaxy/commit/a249dc01a5d0afa42474a6e4075e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M .travis.yml Log Message: ----------- Use container-based infrastructure (sudo: false) in TravisCI Commit: 0f5ad34eaf6b65a2d258f308aa6fea8b4f39a52a https://github.com/galaxyproject/galaxy/commit/0f5ad34eaf6b65a2d258f308aa6f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M .travis.yml M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py M setup.cfg M tox.ini Log Message: ----------- Merge pull request #4413 from nsoranzo/release_17.01_really_add_datatypes [17.01] Add missing chemical formats to datatypes_conf.xml.sample Commit: 4faf496c9898786e8f504bd36b28dc70df4e3e26 https://github.com/galaxyproject/galaxy/commit/4faf496c9898786e8f504bd36b28… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Conflicts: tox.ini Compare: https://github.com/galaxyproject/galaxy/compare/10efd7fac6e3...4faf496c9898

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[galaxyproject/galaxy] ba3249: Add missing chemical formats to datatypes_conf.xml...
by GitHub 14 Aug '17

14 Aug '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: ba3249acf07ca1a44a813e2c68a9d6074d2b7c4c https://github.com/galaxyproject/galaxy/commit/ba3249acf07ca1a44a813e2c68a9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py Log Message: ----------- Add missing chemical formats to datatypes_conf.xml.sample Commit: 61d172f18d8f7740585b038dd786e81178ca1831 https://github.com/galaxyproject/galaxy/commit/61d172f18d8f7740585b038dd786… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M setup.cfg M tox.ini Log Message: ----------- Update pin for flake8-docstrings Similar to commit 2586df45637d794c63252838573b2d1e6d692243 . Commit: a249dc01a5d0afa42474a6e4075ed2a3ad80400f https://github.com/galaxyproject/galaxy/commit/a249dc01a5d0afa42474a6e4075e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M .travis.yml Log Message: ----------- Use container-based infrastructure (sudo: false) in TravisCI Commit: 0f5ad34eaf6b65a2d258f308aa6fea8b4f39a52a https://github.com/galaxyproject/galaxy/commit/0f5ad34eaf6b65a2d258f308aa6f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M .travis.yml M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py M setup.cfg M tox.ini Log Message: ----------- Merge pull request #4413 from nsoranzo/release_17.01_really_add_datatypes [17.01] Add missing chemical formats to datatypes_conf.xml.sample Compare: https://github.com/galaxyproject/galaxy/compare/bfb3ce6e7907...0f5ad34eaf6b

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[galaxyproject/galaxy] e901a0: Bugfix for loading subworkflows from workflow desc...
by GitHub 14 Aug '17

14 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e901a0c867cfa9af3420536c4725cbc001621cf8 https://github.com/galaxyproject/galaxy/commit/e901a0c867cfa9af3420536c4725… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Bugfix for loading subworkflows from workflow descriptions. Sometimes unrelated workflow steps can be flushed in a half complete state and violate integrity constraints when a subworkflow step causes a flush of during the load of a different step. This fixes that by preloading all subworkflows during workflow import. This PR doesn't include a test case but one will be included if the CWL branch is merged at a later date (xref https://github.com/common-workflow-language/common-workflow-language/pull/4…) Commit: e594152de2dd33dbdff2feb8e05f05ad5810ab27 https://github.com/galaxyproject/galaxy/commit/e594152de2dd33dbdff2feb8e05f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #4394 from jmchilton/subworkflow_loading_fix Bugfix for loading subworkflows from workflow descriptions. Compare: https://github.com/galaxyproject/galaxy/compare/8e192dbf4ca2...e594152de2dd

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[galaxyproject/galaxy] d39483: Revise summarize history errors to display more da...
by GitHub 14 Aug '17

14 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d39483bf0a88aa6c62cb69928abc8195e9082db7 https://github.com/galaxyproject/galaxy/commit/d39483bf0a88aa6c62cb69928abc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M test/base/interactor.py Log Message: ----------- Revise summarize history errors to display more data and outline collections. Commit: 67f9e34f530d1d505e12fcca9fef2648025d877e https://github.com/galaxyproject/galaxy/commit/67f9e34f530d1d505e12fcca9fef… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M test/api/test_tools.py M test/base/populators.py Log Message: ----------- Implement test lib history context. Commit: b7fe2fa2ecc44bde964be1c44e73e2ea11586bf5 https://github.com/galaxyproject/galaxy/commit/b7fe2fa2ecc44bde964be1c44e73… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M test/base/interactor.py M test/base/populators.py Log Message: ----------- Rework summarizing histories on errors to include all datasets. ``` -------------------- >> begin captured stdout << --------------------- Problem in history with id adb5f5c93f827949 - summary of datasets below. -------------------------------------- | 1 - Test Dataset (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 1 line | Dataset Info: | uploaded txt file | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>1 2 3</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 2 - Test Dataset (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 1 line | Dataset Info: | uploaded txt file | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>4 5 6</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 3 - multi_data_param on data 1 and data 2 (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 2 lines | Dataset Info: | *Dataset info is empty.* | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>1 2 3</td></tr><tr><td>4 5 6</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 4 - multi_data_param on data 1 and data 2 (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 2 lines | Dataset Info: | *Dataset info is empty.* | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>4 5 6</td></tr><tr><td>1 2 3</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- ``` Commit: 8e192dbf4ca2f7c6c0860430a4d8085de7732ab1 https://github.com/galaxyproject/galaxy/commit/8e192dbf4ca2f7c6c0860430a4d8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M test/api/test_tools.py M test/base/interactor.py M test/base/populators.py Log Message: ----------- Merge pull request #4397 from jmchilton/api_test_enhancement Better Error Summaries for API Tests Compare: https://github.com/galaxyproject/galaxy/compare/f849c7e6feaf...8e192dbf4ca2

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[galaxyproject/galaxy] 7a1fbd: Fix bug in upload HTML checker.
by GitHub 14 Aug '17

14 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7a1fbd37e9fb262432daed6eefc4e9c54ceff406 https://github.com/galaxyproject/galaxy/commit/7a1fbd37e9fb262432daed6eefc4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: M lib/galaxy/util/checkers.py Log Message: ----------- Fix bug in upload HTML checker. If a chunk was passed into the check_html function - e.g. it was read from a compressed file - it would search through each character in the string for certain HTML content instead of each line in the string. Commit: 59aa11864a795861484133dfc85212bf9150cf4a https://github.com/galaxyproject/galaxy/commit/59aa11864a795861484133dfc852… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/util/checkers.py M tools/data_source/upload.py Log Message: ----------- Add configuration option to disable upload content checking. Commit: 53b0b25456c170990ad3345021aab16f68e6e185 https://github.com/galaxyproject/galaxy/commit/53b0b25456c170990ad3345021aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: M test/base/populators.py Log Message: ----------- Better error reporting in test/base/populators.py. Commit: bee6af1e4117e7ff6f7caac0d9c84253ec1c4882 https://github.com/galaxyproject/galaxy/commit/bee6af1e4117e7ff6f7caac0d9c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: M test/base/api.py Log Message: ----------- Allow API tests to work with admin users (not just admin keys). Commit: fec1eab82dc6dea2d03711127ed08b3038ad5bf1 https://github.com/galaxyproject/galaxy/commit/fec1eab82dc6dea2d03711127ed0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M test/base/populators.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Add ability to arbitrarily not decompress files on upload via API. Commit: 06ca789f92ad2f4dfaffc36d3fa0bafb3c74920d https://github.com/galaxyproject/galaxy/commit/06ca789f92ad2f4dfaffc36d3fa0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: A test-data/1.sam.gz A test-data/bad.html.gz A test-data/random-file M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_upload_configuration_options.py Log Message: ----------- Configuration tests for the last few upload enhancements. Commit: f849c7e6feafabf905653bd008fde23dc1413a85 https://github.com/galaxyproject/galaxy/commit/f849c7e6feafabf905653bd008fd… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/checkers.py A test-data/1.sam.gz A test-data/bad.html.gz A test-data/random-file M test/base/api.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_upload_configuration_options.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge pull request #4417 from jmchilton/upload_enhance Fixes and enhancements for the upload API Compare: https://github.com/galaxyproject/galaxy/compare/fc861cdf38d1...f849c7e6feaf

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[galaxyproject/galaxy] 6d1397: Install tools and workflow
by GitHub 12 Aug '17

12 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d1397647fd6b185a639915a8f1ac929d78317d4 https://github.com/galaxyproject/galaxy/commit/6d1397647fd6b185a639915a8f1a… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Install tools and workflow import_tools is option and default is False. If import_tools is True, install tools in workflow. Commit: 30aa73e1974e1669984f0b6f242110451a8499ab https://github.com/galaxyproject/galaxy/commit/30aa73e1974e1669984f0b6f2421… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unused variable Commit: 02924dece4653d476a2838e9b91bd2664d8bf518 https://github.com/galaxyproject/galaxy/commit/02924dece4653d476a2838e9b91b… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix lint Commit: 23db89ba3ddf54420b40e881bd92edbfeff869c6 https://github.com/galaxyproject/galaxy/commit/23db89ba3ddf54420b40e881bd92… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper_docstrings.sh A 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client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js M client/galaxy/scripts/mvc/citation/citation-view.js A client/galaxy/scripts/mvc/collection/base-creator.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/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js A 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client/webpack.config.js A config/build_sites.yml.sample A config/containers_conf.yml.sample M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample A config/error_report.yml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/local_conda_mapping.yml.sample M config/openid_conf.xml.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js A 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config/tool_destinations.yml.sample M config/tool_shed.ini.sample A config/user_preferences_extra_conf.yml.sample M contrib/galaxy.debian-init M contrib/galaxy_config_merger.py M contrib/galaxy_supervisor.conf M contrib/nagios/check_galaxy M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M cron/updateucsc.sh.sample M display_applications/igv/bigwig.xml A display_applications/igv/genome_fasta.xml M doc/Makefile A doc/fix_schema_rst.sh M doc/parse_gx_xsd.py R doc/patch.py M doc/schema_template.md A doc/source/admin/authentication.md R doc/source/admin/chat-0.png R doc/source/admin/chat-1.png R doc/source/admin/chat-2.png R doc/source/admin/chat-3.png R doc/source/admin/chat-4.png R doc/source/admin/chat.rst R doc/source/admin/communication_server.png R doc/source/admin/communication_server_rooms.png M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M 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tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.py M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.py M tools/maf/vcf_to_maf_customtrack.xml M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/fastq_gen_conv.xml M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.xml M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into install_workflow_and_tools Conflicts: lib/galaxy/webapps/galaxy/api/workflows.py Commit: 7dd3ddccafee8f5cc185f1b0dd711056576a92ce https://github.com/galaxyproject/galaxy/commit/7dd3ddccafee8f5cc185f1b0dd71… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Require admin for new import_tools function in workflows API. Includes test case. Commit: fc861cdf38d1d20fd611e8bcb042328eb905b3c4 https://github.com/galaxyproject/galaxy/commit/fc861cdf38d1d20fd611e8bcb042… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #3064 from manabuishii/install_workflow_and_tools Install tools and workflow Compare: https://github.com/galaxyproject/galaxy/compare/331851b0495d...fc861cdf38d1

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