- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] e0ee12: Fix problem with legacy workflows and duplicate ou...
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e0ee1203c6fc176ffb56ecd717540cc6b2f0b0e7 https://github.com/galaxyproject/galaxy/commit/e0ee1203c6fc176ffb56ecd71754… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Fix problem with legacy workflows and duplicate output labels. Fixes #1704 - many thanks to @tzk and @mvdbeek. Commit: ff29b263630614b96c617eb9468afcec9d04d72f https://github.com/galaxyproject/galaxy/commit/ff29b263630614b96c617eb9468a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #1718 from jmchilton/workflow_fixes [16.01] Fix problem with legacy workflows and duplicate output labels. Commit: 75a3797d0fa03fc80240326e6b7fdae40ee5d658 https://github.com/galaxyproject/galaxy/commit/75a3797d0fa03fc80240326e6b7f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-15 (Mon, 15 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Also fix legacy export. Commit: 00b739fc1451d7a529913ab626358bd968e75ee3 https://github.com/galaxyproject/galaxy/commit/00b739fc1451d7a529913ab62635… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-15 (Mon, 15 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1733 from mvdbeek/legacy_export [16.01] Also check for unique outputs on legacy workflow export Commit: 4a566b6db8ac69bf5f5619e9a9aa2640ce3bd9af https://github.com/galaxyproject/galaxy/commit/4a566b6db8ac69bf5f5619e9a9aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Improved debug message in workflow scheduling. Commit: 39ec09df48060e4e384d7af2669a6fe074b6d71a https://github.com/galaxyproject/galaxy/commit/39ec09df48060e4e384d7af2669a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #1741 from jmchilton/workflow_schedule_fixes [16.01] Improved debug message in workflow scheduling. Commit: 8e5aa4ac6774df0426d6f0ba458222dd061177e9 https://github.com/galaxyproject/galaxy/commit/8e5aa4ac6774df0426d6f0ba4582… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/3ee0594c692f...8e5aa4ac6774

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[galaxyproject/usegalaxy-playbook] f167a3: Bump Naive Variant Caller on Main to 64GB
by GitHub 16 Feb '16

16 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f167a34d0b4ff9105e76a5ab0c1ff0f07165ff58 https://github.com/galaxyproject/usegalaxy-playbook/commit/f167a34d0b4ff910… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Bump Naive Variant Caller on Main to 64GB

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[galaxyproject/galaxy] 4a566b: Improved debug message in workflow scheduling.
by GitHub 16 Feb '16

16 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 4a566b6db8ac69bf5f5619e9a9aa2640ce3bd9af https://github.com/galaxyproject/galaxy/commit/4a566b6db8ac69bf5f5619e9a9aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Improved debug message in workflow scheduling. Commit: 39ec09df48060e4e384d7af2669a6fe074b6d71a https://github.com/galaxyproject/galaxy/commit/39ec09df48060e4e384d7af2669a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #1741 from jmchilton/workflow_schedule_fixes [16.01] Improved debug message in workflow scheduling. Compare: https://github.com/galaxyproject/galaxy/compare/00b739fc1451...39ec09df4806

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[galaxyproject/galaxy] fad3e1: workaround for error message in case original tool...
by GitHub 16 Feb '16

16 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fad3e1fd73adad84ae9b723534ed16f95afcdfe3 https://github.com/galaxyproject/galaxy/commit/fad3e1fd73adad84ae9b723534ed… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- workaround for error message in case original toolshed had been disabled Commit: 3ee0594c692faac542ffa58f4339d79b9b8aefbd https://github.com/galaxyproject/galaxy/commit/3ee0594c692faac542ffa58f4339… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #1738 from mvdbeek/workflow_from_different_toolshed_fix workaround for error message on tool lookup in case original toolshed had been disabled Compare: https://github.com/galaxyproject/galaxy/compare/8fb3e461aca6...3ee0594c692f

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[galaxyproject/galaxy] 75a379: Also fix legacy export.
by GitHub 16 Feb '16

16 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 75a3797d0fa03fc80240326e6b7fdae40ee5d658 https://github.com/galaxyproject/galaxy/commit/75a3797d0fa03fc80240326e6b7f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-15 (Mon, 15 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Also fix legacy export. Commit: 00b739fc1451d7a529913ab626358bd968e75ee3 https://github.com/galaxyproject/galaxy/commit/00b739fc1451d7a529913ab62635… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-15 (Mon, 15 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1733 from mvdbeek/legacy_export [16.01] Also check for unique outputs on legacy workflow export Compare: https://github.com/galaxyproject/galaxy/compare/ff29b2636306...00b739fc1451

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[galaxyproject/galaxy] fb30e2: Update SnpEffDb and SnpSiftDbNSFP vor SnpEff v4.1
by GitHub 12 Feb '16

12 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fb30e2b06103f3fbfa3dd1238c1f4e707d04b633 https://github.com/galaxyproject/galaxy/commit/fb30e2b06103f3fbfa3dd1238c1f… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Update SnpEffDb and SnpSiftDbNSFP vor SnpEff v4.1 Commit: acef6ab3f99e5420602ea06b77ac647599f80e5a https://github.com/galaxyproject/galaxy/commit/acef6ab3f99e5420602ea06b77ac… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Fix style errors Commit: 8fb3e461aca6f0702f45b1a5d34392893fdd2cb5 https://github.com/galaxyproject/galaxy/commit/8fb3e461aca6f0702f45b1a5d343… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #1280 from jj-umn/patch-2 Update SnpEffDb and SnpSiftDbNSFP for SnpEff v4.1 Compare: https://github.com/galaxyproject/galaxy/compare/063c5ad0f87c...8fb3e461aca6

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[galaxyproject/galaxy] e0ee12: Fix problem with legacy workflows and duplicate ou...
by GitHub 12 Feb '16

12 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: e0ee1203c6fc176ffb56ecd717540cc6b2f0b0e7 https://github.com/galaxyproject/galaxy/commit/e0ee1203c6fc176ffb56ecd71754… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Fix problem with legacy workflows and duplicate output labels. Fixes #1704 - many thanks to @tzk and @mvdbeek. Commit: ff29b263630614b96c617eb9468afcec9d04d72f https://github.com/galaxyproject/galaxy/commit/ff29b263630614b96c617eb9468a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #1718 from jmchilton/workflow_fixes [16.01] Fix problem with legacy workflows and duplicate output labels. Compare: https://github.com/galaxyproject/galaxy/compare/65d9ec9cab2b...ff29b2636306

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[galaxyproject/galaxy] 3e3bc1: Wrap conditional test parameters
by GitHub 12 Feb '16

12 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3e3bc132d89d97fc9daac5115c63ce5c08eb0aef https://github.com/galaxyproject/galaxy/commit/3e3bc132d89d97fc9daac5115c63… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-11 (Thu, 11 Feb 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Wrap conditional test parameters Commit: 749fa90a4a67c4bd6b5b3ff24468f9b300dfb9fa https://github.com/galaxyproject/galaxy/commit/749fa90a4a67c4bd6b5b3ff24468… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-11 (Thu, 11 Feb 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Attempt to handle backward compatibility for previously unwrapped conditional test parameters Commit: 063c5ad0f87c6d7ef753608e715b64b1852745ad https://github.com/galaxyproject/galaxy/commit/063c5ad0f87c6d7ef753608e715b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #1714 from guerler/fix_conditional_wrapper_000 Wrap conditional test parameters Compare: https://github.com/galaxyproject/galaxy/compare/f8a6ee335407...063c5ad0f87c

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[galaxyproject/ansible-galaxy] 01b070: tags static setup
by GitHub 12 Feb '16

12 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 01b070656c76f3a6b425cf5c4c06d324db4e0791 https://github.com/galaxyproject/ansible-galaxy/commit/01b070656c76f3a6b425… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-11 (Thu, 11 Feb 2016) Changed paths: M tasks/main.yml Log Message: ----------- tags static setup Commit: 81856d319353f57642d3b74f3ea54a1baf9d3884 https://github.com/galaxyproject/ansible-galaxy/commit/81856d319353f57642d3… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M tasks/main.yml Log Message: ----------- Merge pull request #10 from mvdbeek/add_tag tag static_setup Compare: https://github.com/galaxyproject/ansible-galaxy/compare/6209af56b96b...8185…

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[galaxyproject/usegalaxy-playbook] 997e3a: commit Test mutable confs
by GitHub 11 Feb '16

11 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 997e3abfb0f0a9db4c5c1832f4bb1c8b47f2c201 https://github.com/galaxyproject/usegalaxy-playbook/commit/997e3abfb0f0a9db… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-11 (Thu, 11 Feb 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml Log Message: ----------- commit Test mutable confs uploaded the backup version from PB to Test because of accidental overwrite and playbook reordered it

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[galaxyproject/usegalaxy-playbook] 5f5599: update Main's mutable confs
by GitHub 11 Feb '16

11 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5f5599998c9d8a379f31e0dd5e39d49a62c060cb https://github.com/galaxyproject/usegalaxy-playbook/commit/5f5599998c9d8a37… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-11 (Thu, 11 Feb 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- update Main's mutable confs

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[galaxyproject/galaxy] 2ddf6e: Remove broken and hidden fix_errors tool.
by GitHub 10 Feb '16

10 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2ddf6eed639957369e3891d8766fa9f5c3d48c32 https://github.com/galaxyproject/galaxy/commit/2ddf6eed639957369e3891d8766f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M config/tool_conf.xml.sample R tools/validation/fix_errors.py R tools/validation/fix_errors.xml R tools/validation/fix_errors_code.py R tools/validation/validate.py Log Message: ----------- Remove broken and hidden fix_errors tool. Commit: 8703f3bd9ef595fb3b77a7021c85174f8502efa5 https://github.com/galaxyproject/galaxy/commit/8703f3bd9ef595fb3b77a7021c85… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: R tools/plotting/plot_filter.py R tools/plotting/plotter.py Log Message: ----------- Remove unused files. Commit: 39da6c327857a028d3540ec7e7c3b9aa101ff132 https://github.com/galaxyproject/galaxy/commit/39da6c327857a028d3540ec7e7c3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M .ci/flake8_blacklist.txt M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/sff_extract.py M tools/filters/sorter.py M 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/uniq.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.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/phenotype_association/pagetag.py M tools/phenotype_association/senatag.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/sr_mapping/srma_wrapper.xml M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py Log Message: ----------- Fix the remaining 2180 flake8 errors in tools/ . Commit: f8a6ee3354072d6edc8f7bf002d81e96285f17f0 https://github.com/galaxyproject/galaxy/commit/f8a6ee3354072d6edc8f7bf002d8… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M .ci/flake8_blacklist.txt M config/tool_conf.xml.sample M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/sff_extract.py M tools/filters/sorter.py M 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/uniq.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.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/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.py R tools/plotting/plot_filter.py R tools/plotting/plotter.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/sr_mapping/srma_wrapper.xml R tools/validation/fix_errors.py R tools/validation/fix_errors.xml R tools/validation/fix_errors_code.py R tools/validation/validate.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py Log Message: ----------- Merge pull request #1713 from nsoranzo/flake8_fixes Fix the remaining 2180 flake8 errors in tools/ . Compare: https://github.com/galaxyproject/galaxy/compare/1e46198becdb...f8a6ee335407

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[galaxyproject/galaxy] a4a104: API: allow filtering by date using string format Y...
by GitHub 10 Feb '16

10 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a4a104dcc2f020ed4100ed7edda75dd1d2857578 https://github.com/galaxyproject/galaxy/commit/a4a104dcc2f020ed4100ed7edda7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/history_contents.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- API: allow filtering by date using string format YYYY-MM-DDTHH:MM (by removing the 'T' from when parsing the filter), allow filtering by hybrid properties and not just columns; API, history contents: allow filtering, order, and limit/offset of contents (in the same format as histories) Commit: 1cb1c48975e915ab98a0776a6a37dca914c542d4 https://github.com/galaxyproject/galaxy/commit/1cb1c48975e915ab98a0776a6a37… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/managers/history_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Managers, history contents: use text fn to wrap history_content_type filters; API, history contents: correct default order Commit: d4374bd0617d162db1a7b2803f1cc42880e0a9c7 https://github.com/galaxyproject/galaxy/commit/d4374bd0617d162db1a7b2803f1c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/managers/history_contents.py Log Message: ----------- Managers, history contents: remove model_class column, remove content_type from allowed filters (does not work on postgres), general cleanup Commit: 31e252743e633ffb48c655a3a12f4640a90c155e https://github.com/galaxyproject/galaxy/commit/31e252743e633ffb48c655a3a12f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/history_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- API, history contents: provide support for deleted and visible filters as bare keywords (e.g. 'deleted=True') Commit: 81b4eb484d55c30b386cce0af3141d6e5d4ee565 https://github.com/galaxyproject/galaxy/commit/81b4eb484d55c30b386cce0af314… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- API, history contents: remove unreadable preceding binary operator, add blank line Commit: 120fef8cd09c4b158e5577833d89db60e7da3caf https://github.com/galaxyproject/galaxy/commit/120fef8cd09c4b158e5577833d89… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/managers/history_contents.py Log Message: ----------- API, History contents: allow filtering by state, history_content_type Commit: d95c7c9d2b25d8b27d342f94c28d5c967c4af47a https://github.com/galaxyproject/galaxy/commit/d95c7c9d2b25d8b27d342f94c28d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- API, history contents: split code path in index to prevent backwards incompatibility Commit: c423f1eaa5f17190bf79f5f97b4f8a41903f5e3b https://github.com/galaxyproject/galaxy/commit/c423f1eaa5f17190bf79f5f97b4f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py A lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py A test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- API, history_contents: allow filtering by update/create times, inclusion in type_id list; models: add type_id as sql property on HDCAs and HDAs; managers: allow count; testing Commit: 1561759919073caa77d25eec9930b0f2235a82a1 https://github.com/galaxyproject/galaxy/commit/1561759919073caa77d25eec9930… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: A .ci/first_startup.sh M .travis.yml M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.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-libraryrow-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.xml A config/plugins/interactive_environments/phinch/static/js/phinch.js A config/plugins/interactive_environments/phinch/templates/phinch.mako A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst M doc/source/project/issues.rst A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py A lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/sharable.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/objectstore/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/heartbeat.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/install_manager.py M scripts/binary_compatibility.py M scripts/bootstrap_history.py M scripts/common_startup.sh M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.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-libraryrow-view.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.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-libraryrow-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/onload.js M static/style/blue/base.css M static/style/blue/library.css M templates/admin/tool_shed_repository/manage_repository.mako M templates/user/info.mako M templates/user/username.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/common.mako M test-data/3.bam M test/api/test_workflows.py M test/api/workflows_format_2/converter.py A test/functional/tools/paths_as_file.xml M test/functional/tools/samples_tool_conf.xml M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.py M test/unit/tools_support.py M tools/data_source/upload.xml M tools/phenotype_association/linkToDavid.xml M tox.ini Log Message: ----------- (merge conflicts with dev) Commit: 1e46198becdba27f98f7ce93bb27f21ae59392a1 https://github.com/galaxyproject/galaxy/commit/1e46198becdba27f98f7ce93bb27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py A lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py A test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Merge pull request #1602 from carlfeberhard/history.contents API, history contents: allow filters, limit/offset, and ordering Compare: https://github.com/galaxyproject/galaxy/compare/6a5d2653a706...1e46198becdb

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[galaxyproject/galaxy] 167eb5: Modify show_param input walking to account for mul...
by GitHub 10 Feb '16

10 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 167eb50dd39cd362126ca6fecf2d1d20b111464b https://github.com/galaxyproject/galaxy/commit/167eb50dd39cd362126ca6fecf2d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Modify show_param input walking to account for multiple data parmaeters. xref https://github.com/galaxyproject/galaxy/pull/1561 fixes https://github.com/galaxyproject/galaxy/issues/1660 Commit: 6a5d2653a706fd82979d83f245ec4fbb89de71ff https://github.com/galaxyproject/galaxy/commit/6a5d2653a706fd82979d83f245ec… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #1670 from jmchilton/input_param_walking_fix Modify show_param input walking to account for multiple data parameters. Compare: https://github.com/galaxyproject/galaxy/compare/74c3ff0f5618...6a5d2653a706

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[galaxyproject/galaxy] bf4e73: Update david identifier types
by GitHub 09 Feb '16

09 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf4e736c3ca8e129ff8c75f8261c08f303c76080 https://github.com/galaxyproject/galaxy/commit/bf4e736c3ca8e129ff8c75f8261c… Author: pavanvidem <videmp(a)informatik.uni-freiburg.de> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M tools/phenotype_association/linkToDavid.xml Log Message: ----------- Update david identifier types David identifier types seem to be changed. Some of them are no more available on david web server. Commit: 776180ab80b352a60713fbf6576adbfc4934ed85 https://github.com/galaxyproject/galaxy/commit/776180ab80b352a60713fbf6576a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- show all available information for current library and the opened folder Commit: 65d9ec9cab2b6e46fa7a067948bba69e3255c1ff https://github.com/galaxyproject/galaxy/commit/65d9ec9cab2b6e46fa7a067948bb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #1705 from martenson/fix-location-info [16.01] libraries - fix location info Commit: db9c0b89ab56d5ba0b272bb7ddaa220ed3b48c14 https://github.com/galaxyproject/galaxy/commit/db9c0b89ab56d5ba0b272bb7ddaa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge release_16.01 into dev Commit: 22e84e4814b09a3fff4fcd8c44b7f83394ebc640 https://github.com/galaxyproject/galaxy/commit/22e84e4814b09a3fff4fcd8c44b7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- repack client after merge conflicts Commit: 74c3ff0f56184fa32f53fdde8928ce65bd079f1a https://github.com/galaxyproject/galaxy/commit/74c3ff0f56184fa32f53fdde8928… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #1708 from martenson/dev merge 16.01 into dev Compare: https://github.com/galaxyproject/galaxy/compare/5e7dd07db653...74c3ff0f5618

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[galaxyproject/galaxy] 8d6e9d: Sets mappable metadata as list (e.g. column_names)...
by GitHub 09 Feb '16

09 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d6e9d1d775c49148b2ecd0cecc49ad5a59372bd https://github.com/galaxyproject/galaxy/commit/8d6e9d1d775c49148b2ecd0cecc4… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/output.py Log Message: ----------- Sets mappable metadata as list (e.g. column_names) from a tool wrapper Commit: fbc4fa16781f91d1f3fdfd92062352c440eeac4b https://github.com/galaxyproject/galaxy/commit/fbc4fa16781f91d1f3fdfd920623… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/parameters/output.py Log Message: ----------- put old line back Commit: 5f9e1e67c239583d35d8a7e06ad515f5323c6cc4 https://github.com/galaxyproject/galaxy/commit/5f9e1e67c239583d35d8a7e06ad5… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Fixes flake8 error Commit: 134dd40fadcb8eab1c9e60d729f414166c74befe https://github.com/galaxyproject/galaxy/commit/134dd40fadcb8eab1c9e60d729f4… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Passing metadata through update Commit: 8ab40d502578597408686f0de7481554cc9d2ef4 https://github.com/galaxyproject/galaxy/commit/8ab40d502578597408686f0de748… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh A .ci/first_startup.sh M .ci/flake8_blacklist.txt A .ci/flake8_py3_wrapper.sh M .ci/flake8_wrapper.sh A .ci/py3_sources.txt M .gitignore M .travis.yml M CONTRIBUTING.md M CONTRIBUTORS.md A Makefile M README.rst A client/.docker-build.sh A client/Dockerfile M client/GruntFile.js M client/README.md M client/bower.json A client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/base.js R client/galaxy/scripts/galaxy-app-base.js R client/galaxy/scripts/galaxy.autocom_tagging.js R client/galaxy/scripts/galaxy.base.js R client/galaxy/scripts/galaxy.frame.js A client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js R client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.pages.js R client/galaxy/scripts/galaxy.panels.js R client/galaxy/scripts/galaxy.tools.js R client/galaxy/scripts/galaxy.ui.scrollPanel.js A client/galaxy/scripts/layout/masthead.js A client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/layout/modal.js A client/galaxy/scripts/layout/page.js A client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/IE/IE7.js R client/galaxy/scripts/libs/IE/IE8.js R client/galaxy/scripts/libs/IE/blank.gif R client/galaxy/scripts/libs/IE/excanvas.js R client/galaxy/scripts/libs/IE/ie7-recalc.js A client/galaxy/scripts/libs/backbone.js R client/galaxy/scripts/libs/backbone/backbone.js A client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/libs/d3.js R client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/libs/jquery/jquery.dynatree.js M client/galaxy/scripts/libs/jquery/select2.js A client/galaxy/scripts/mvc/annotation.js R client/galaxy/scripts/mvc/annotations.js R client/galaxy/scripts/mvc/app/app-analysis.js R client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M 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tools/data_source/upload.xml M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/catWrapper.py M tools/filters/cutWrapper.xml M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/lav_to_bed.py M tools/filters/secure_hash_message_digest.py M tools/filters/wig_to_bigwig.xml M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_importer.xml M tools/maf/interval2maf.py M tools/maf/interval2maf.xml 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/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/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 'upstream/dev' into metadata_list_fix Commit: 061828aac6cb663eb48767204c9e6c604c5ef14a https://github.com/galaxyproject/galaxy/commit/061828aac6cb663eb48767204c9e… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Passing metadata through update Commit: d370d3b012d9dc7e7976a94939506c6e8e7907a2 https://github.com/galaxyproject/galaxy/commit/d370d3b012d9dc7e7976a9493950… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- passing metadata through as list: revert value setting Commit: 5e7dd07db6532f54605c771aab706249511969a0 https://github.com/galaxyproject/galaxy/commit/5e7dd07db6532f54605c771aab70… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #961 from yhoogstrate/metadata_list_fix Sets mappable list-type metadata (e.g. column_names) from a tool wrapper Compare: https://github.com/galaxyproject/galaxy/compare/34376b1d8f25...5e7dd07db653

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[galaxyproject/galaxy] 83bb8c: Visualization plugins: add routes that more closel...
by GitHub 09 Feb '16

09 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 83bb8cbc11c242ebb0ee2c9338d284c2c0d306e3 https://github.com/galaxyproject/galaxy/commit/83bb8cbc11c242ebb0ee2c9338d2… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Visualization plugins: add routes that more closely match potential static assets in order to allow easier, relative hrefs (for both new and saved visualizations); Grids: allow operations to use named routes by adding kwarg '__route_name__' Commit: a89125cb76384462571275bbd68be77bfe6336f3 https://github.com/galaxyproject/galaxy/commit/a89125cb76384462571275bbd68b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Fix to 83bb8cb: remove debugging Commit: 683c49c185be37435bb7e4736799a2ccb3145f56 https://github.com/galaxyproject/galaxy/commit/683c49c185be37435bb7e4736799… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Visualization plugins: switch the registry to using the new urls, add similar url changes for interactive_environments urls Commit: 0718558a16b7f202818f698247fba5c1c21c32a9 https://github.com/galaxyproject/galaxy/commit/0718558a16b7f202818f698247fb… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Visualization plugins: remove print statement Commit: 34376b1d8f25ef51aba1f7ec0081a5b24eb8153a https://github.com/galaxyproject/galaxy/commit/34376b1d8f25ef51aba1f7ec0081… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Merge pull request #1615 from carlfeberhard/plugin-urls Visualization plugins: add routes that more closely match potential s… Compare: https://github.com/galaxyproject/galaxy/compare/db1bb2f19142...34376b1d8f25

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[galaxyproject/galaxy] 9e0b34: Remove deprecated symbolic link added in 15.03.
by GitHub 09 Feb '16

09 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9e0b348559211a0c6b26e37ccfa9bd9413516aae https://github.com/galaxyproject/galaxy/commit/9e0b348559211a0c6b26e37ccfa9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: R lib/galaxy/metadata Log Message: ----------- Remove deprecated symbolic link added in 15.03. Was added for running jobs - so this may break running jobs if people upgrade from 15.03 (or earlier) to 16.04 (or later) directly. Commit: f21cde984b866ca910d8b447be24a35c796b82cb https://github.com/galaxyproject/galaxy/commit/f21cde984b866ca910d8b447be24… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Style fix - use more Pythonic name than linePieces. Commit: 2d86e00a5af20420a31e67cea5c567e41997b0e2 https://github.com/galaxyproject/galaxy/commit/2d86e00a5af20420a31e67cea5c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py Log Message: ----------- Cleanup some relative imports in galaxy.datatypes. Commit: 3861cffdc5c1b385d848f91fdf49213f661432b6 https://github.com/galaxyproject/galaxy/commit/3861cffdc5c1b385d848f91fdf49… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Rename galaxy.model.datatypes_registry... ... to make it clear it shouldn't be accessed outside that module. Commit: ba0d06f6ba165f2fd3d5d2742b1ada152bcd73b0 https://github.com/galaxyproject/galaxy/commit/ba0d06f6ba165f2fd3d5d2742b1a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Eliminate more use of relative imports in datatypes modules. Commit: 3217bc78323271db4661e4aea308497d4f58fc81 https://github.com/galaxyproject/galaxy/commit/3217bc78323271db4661e4aea308… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py M test/unit/tools/test_column_parameters.py M test/unit/tools_support.py Log Message: ----------- Don't construct a DatatypesRegistry just for tests in galaxy.model. Construct the model in the tests, this should cause galaxy.model to import much faster. Commit: 1f4b32903270926389a9993b3938c169f105371d https://github.com/galaxyproject/galaxy/commit/1f4b32903270926389a9993b3938… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/tools/exception_handling.py A lib/galaxy/util/ucsc.py M tools/filters/wiggle_to_simple.py M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Refactor galaxy.tools.exception_handling... ... so datatype module doesn't need to import something from galaxy.tools - which causes a bunch of more things to be imported because galaxy.tools at the top-level has so many imports. Commit: 4d9498c4c6b181779439e8211fd20c20568c40cb https://github.com/galaxyproject/galaxy/commit/4d9498c4c6b181779439e8211fd2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Elimiante runtime sniff -> registry dependency. It only existed for testing, so only require it in tests. Commit: ae493bfde0d693ae8f1560319053230496cf932d https://github.com/galaxyproject/galaxy/commit/ae493bfde0d693ae8f1560319053… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Eliminate import of registry from galaxy.model. Commit: 5756f6059720d39a75e5786283b232787a60f14e https://github.com/galaxyproject/galaxy/commit/5756f6059720d39a75e5786283b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/model/__init__.py A lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/util/none_like.py Log Message: ----------- Relocate galaxy.datatypes.metadata to galaxy.model.metadata. This eliminates the last dependency in galaxy.model on galaxy.datatypes - establishing a strict ordering of dependencies (galaxy.datatypes depends on galaxy.model and not vice versa). The galaxy.datatypes.metadata interface needs to remain in place for tool shed datatypes and is perfectly reasonable to use from within the datatypes module - it now depends on galaxy.model.metadata and exports the same interfac. In the longer run, this is a better, more explict design and should eliminate certain classes of problems with circular dependencies. Fixes #1552 Commit: df5a3a6da7749b47e50a2faffb5c8f8a8a282230 https://github.com/galaxyproject/galaxy/commit/df5a3a6da7749b47e50a2faffb5c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: R scripts/set_metadata.py R set_metadata.sh Log Message: ----------- Eliminate legacy set metadata entry points. Commit: 499357e508035e7c9ffb5d711e0f355e960e1e05 https://github.com/galaxyproject/galaxy/commit/499357e508035e7c9ffb5d711e0f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M tools/data_source/data_source.py M tools/data_source/upload.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Remove unneeded galaxy.model import in upload.py... ... and document the ability to remove from other data sources. Commit: 448aee9f004befa8ebc02de2ca726dca8e4c22c9 https://github.com/galaxyproject/galaxy/commit/448aee9f004befa8ebc02de2ca72… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M tools/data_source/upload.py Log Message: ----------- Fix for multi-byte char problem in PR #1556... ... caught by @nsoranzo of course. Commit: db1bb2f19142e8a9a0a08ffeb9d4295a4f153fcb https://github.com/galaxyproject/galaxy/commit/db1bb2f19142e8a9a0a08ffeb9d4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py R lib/galaxy/metadata M lib/galaxy/model/__init__.py A lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/util/none_like.py A lib/galaxy/util/ucsc.py R scripts/set_metadata.py R set_metadata.sh M test/unit/tools/test_column_parameters.py M test/unit/tools_support.py M tools/data_source/data_source.py M tools/data_source/upload.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Merge pull request #1556 from jmchilton/datatype_imports Code design and legacy cleanup of datatypes and metadata. Compare: https://github.com/galaxyproject/galaxy/compare/e6dc96def3b9...db1bb2f19142

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[galaxyproject/galaxy] 776180: show all available information for current library...
by GitHub 09 Feb '16

09 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 776180ab80b352a60713fbf6576adbfc4934ed85 https://github.com/galaxyproject/galaxy/commit/776180ab80b352a60713fbf6576a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- show all available information for current library and the opened folder Commit: 65d9ec9cab2b6e46fa7a067948bba69e3255c1ff https://github.com/galaxyproject/galaxy/commit/65d9ec9cab2b6e46fa7a067948bb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #1705 from martenson/fix-location-info [16.01] libraries - fix location info Compare: https://github.com/galaxyproject/galaxy/compare/bf4e736c3ca8...65d9ec9cab2b

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[galaxyproject/galaxy] 539310: Copy over element_identifier to HDA.
by GitHub 09 Feb '16

09 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5393107a42fe6ef2a5942e56a870939026322b5c https://github.com/galaxyproject/galaxy/commit/5393107a42fe6ef2a5942e56a870… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Copy over element_identifier to HDA. Commit: 19efb1a99d5b46056392826324507fa952872591 https://github.com/galaxyproject/galaxy/commit/19efb1a99d5b4605639282632450… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Test if element_identifer is defined. Commit: e6dc96def3b91e76d6c772fedced0e4d455f8a52 https://github.com/galaxyproject/galaxy/commit/e6dc96def3b91e76d6c772fedced… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #1693 from mvdbeek/better_fix_for_missing_element_identifier Better fix for missing element identifier Compare: https://github.com/galaxyproject/galaxy/compare/f4c3177717c0...e6dc96def3b9

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[galaxyproject/galaxy] bf4e73: Update david identifier types
by GitHub 09 Feb '16

09 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: bf4e736c3ca8e129ff8c75f8261c08f303c76080 https://github.com/galaxyproject/galaxy/commit/bf4e736c3ca8e129ff8c75f8261c… Author: pavanvidem <videmp(a)informatik.uni-freiburg.de> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M tools/phenotype_association/linkToDavid.xml Log Message: ----------- Update david identifier types David identifier types seem to be changed. Some of them are no more available on david web server.

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[galaxyproject/galaxy] e468c9: Update david identifier types
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e468c9882f1a8ca85f303c1f1e878a042207b3b0 https://github.com/galaxyproject/galaxy/commit/e468c9882f1a8ca85f303c1f1e87… Author: pavanvidem <videmp(a)informatik.uni-freiburg.de> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M tools/phenotype_association/linkToDavid.xml Log Message: ----------- Update david identifier types David identifier types seem to be changed. Some of them are no more available on david web server. Commit: f4c3177717c0c673720fc40961467f9c0e45678a https://github.com/galaxyproject/galaxy/commit/f4c3177717c0c673720fc4096146… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M tools/phenotype_association/linkToDavid.xml Log Message: ----------- Merge pull request #1696 from pavanvidem/patch-1 Update david identifier types Compare: https://github.com/galaxyproject/galaxy/compare/d331b54b99cd...f4c3177717c0

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[galaxyproject/usegalaxy-playbook] be043f: update Test and mutable confs
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: be043f30573a4e205f3a0801307dcc674a38ffd3 https://github.com/galaxyproject/usegalaxy-playbook/commit/be043f30573a4e20… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version A stage/files/interactive_environments/plugins/phinch/config/phinch.ini.sample A stage/files/interactive_environments/plugins/phinch/config/phinch.xml A stage/files/interactive_environments/plugins/phinch/static/js/phinch.js A stage/files/interactive_environments/plugins/phinch/templates/phinch.mako M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version M stage/group_vars/all.yml Log Message: ----------- update Test and mutable confs

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[galaxyproject/galaxy] bf989f: correct typo in text datatype
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf989f6051303658c6bc537fc1e00c877c55c6e1 https://github.com/galaxyproject/galaxy/commit/bf989f6051303658c6bc537fc1e0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- correct typo in text datatype Commit: 04af1ae1c609c0b73afabaf2aeb58110043847e6 https://github.com/galaxyproject/galaxy/commit/04af1ae1c609c0b73afabaf2aeb5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Always use the python hashlib for verifying the virtualenv download in common_startup.sh rather than attempting to use sha256sum. Older versions of coreutils (such as in RHEL 6) did not include the --strict argument to sha256sum. Commit: 2641f0af9ac84f91ea0cf3e849b6e8348da8909d https://github.com/galaxyproject/galaxy/commit/2641f0af9ac84f91ea0cf3e849b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #1668 from natefoo/venv-checksum [16.01] Always use the python hashlib method for verifying the virtualenv download Commit: bb95a65b2201509ce950d6c3c578f8d417f83cc4 https://github.com/galaxyproject/galaxy/commit/bb95a65b2201509ce950d6c3c578… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #1666 from martenson/correct-datatype-typo [16.01] correct typo in text datatype Commit: 9551fc07b475b4095b7d002315cbc05bdf0925b5 https://github.com/galaxyproject/galaxy/commit/9551fc07b475b4095b7d002315cb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Add the `scientific` platform (Scientific Linux) as binary compatible with RHEL. Commit: 9ead68aeca6722f62d3d6fabae6484aa00246615 https://github.com/galaxyproject/galaxy/commit/9ead68aeca6722f62d3d6fabae64… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Merge pull request #1669 from natefoo/scientificlinux-tag-compat [16.01] Add the `scientific` platform (Scientific Linux) as binary compatible with RHEL Commit: 4b24d95f6f95124f357b72434a29113fa9bacf73 https://github.com/galaxyproject/galaxy/commit/4b24d95f6f95124f357b72434a29… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Improve documentation about binary-compatibility.cfg. Resolves #1672. Commit: ada39dea6ab68be543f53feb7a30e97167d96013 https://github.com/galaxyproject/galaxy/commit/ada39dea6ab68be543f53feb7a30… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- handle correctly application/json pased in POST Commit: 530501c682be85b595bd8115bc2fc0ebc53f57a0 https://github.com/galaxyproject/galaxy/commit/530501c682be85b595bd8115bc2f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- fix setting library permissions to accept JSON correctly Commit: 5dd839960e1ca5170b528c4c88ad8965eebde08b https://github.com/galaxyproject/galaxy/commit/5dd839960e1ca5170b528c4c88ad… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- unify api for library creation; support POST with url params Commit: edd8b222acac34cd2e35e768ab1cbd888b2fc824 https://github.com/galaxyproject/galaxy/commit/edd8b222acac34cd2e35e768ab1c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- catch value errors from id decoding Commit: 0398aafb1cf0aa0863d0867d20dd79a09bc2fb85 https://github.com/galaxyproject/galaxy/commit/0398aafb1cf0aa0863d0867d20dd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- fix updating library API to not require payload and to properly handle optional params Commit: 4b51be57d114d840112970baccb979ec1876663b https://github.com/galaxyproject/galaxy/commit/4b51be57d114d840112970baccb9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- allow specifying DELETE params in JSON Commit: c288b43627d3da925c5fe4b2fd0ebd5a7bc752b2 https://github.com/galaxyproject/galaxy/commit/c288b43627d3da925c5fe4b2fd0e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folders.py Log Message: ----------- allow creating folders with JSON payload Commit: 7867f3e0835a2cbd99658ad25debd9be278300f2 https://github.com/galaxyproject/galaxy/commit/7867f3e0835a2cbd99658ad25deb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M lib/galaxy/webapps/galaxy/api/folders.py M static/maps/mvc/library/library-folder-view.js.map M static/scripts/mvc/library/library-folder-view.js Log Message: ----------- accept json as input for setting permissions; fix inconsistency by leveraging role_manager Commit: a4c2098da010d79a70a9425e8ccb6c1e69807442 https://github.com/galaxyproject/galaxy/commit/a4c2098da010d79a70a9425e8ccb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folders.py Log Message: ----------- allow PATCHing with payload in urlparams Commit: b46636a53f579fc6ffa63fbca888196bb0ff99f6 https://github.com/galaxyproject/galaxy/commit/b46636a53f579fc6ffa63fbca888… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- remove deletion of the payload dict item it is not necessary and the key does not have to exist Commit: 170c83e6c283e97b1e399bc122ee94ddb8cb34b4 https://github.com/galaxyproject/galaxy/commit/170c83e6c283e97b1e399bc122ee… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- fix unused imports and unused vars Commit: 9c7c75b7661989b5fe6f2e4819b04ae6e7b901a1 https://github.com/galaxyproject/galaxy/commit/9c7c75b7661989b5fe6f2e4819b0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Typo Commit: c693b69b344461bd428a0ef314b3ec985e1a60d9 https://github.com/galaxyproject/galaxy/commit/c693b69b344461bd428a0ef314b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Merge pull request #1677 from natefoo/admin-docs [16.01] Improve documentation about binary-compatibility.cfg Commit: 134d792c1fcfba5d09e2937074c3263792bea991 https://github.com/galaxyproject/galaxy/commit/134d792c1fcfba5d09e2937074c3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- delete the 'payload' if it is in kwd so it is not supplied twice Commit: e7b6b4b13bd93a8520942c94d0ed28d110af261b https://github.com/galaxyproject/galaxy/commit/e7b6b4b13bd93a8520942c94d0ed… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- Revert "delete the 'payload' if it is in kwd so it is not supplied twice" This reverts commit 134d792c1fcfba5d09e2937074c3263792bea991. Commit: 5301269fbb54753e75969ecd446b8cb74c6093b6 https://github.com/galaxyproject/galaxy/commit/5301269fbb54753e75969ecd446b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- update docs of the data libraries API Commit: 5e77af198a9b81646dbe59a02b991d496b334967 https://github.com/galaxyproject/galaxy/commit/5e77af198a9b81646dbe59a02b99… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/style/less/base.less 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/style/blue/base.css Log Message: ----------- Update help text rST note/warning/error box styling for change in div class from toolHelpBody to ui-form-help. Commit: ef6bd90f20394f6fb74b1bdedbd0f94ecb752018 https://github.com/galaxyproject/galaxy/commit/ef6bd90f20394f6fb74b1bdedbd0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M static/maps/mvc/library/library-folder-view.js.map M static/scripts/mvc/library/library-folder-view.js Log Message: ----------- Merge pull request #1641 from martenson/libraries-load-handle-payload [16.01] libraries: handle correctly application/json pased in POST Commit: 054c04f490fe5e641c1dec8c4f8af53cf02daffd https://github.com/galaxyproject/galaxy/commit/054c04f490fe5e641c1dec8c4f8a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/style/less/base.less 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/style/blue/base.css Log Message: ----------- Merge pull request #1695 from natefoo/help-message-css [16.01] Update help text rST note/warning/error box styling for change in div class from toolHelpBody to ui-form-help. Commit: 308402235fe4d3d3bb85e350181ab5ab11df87f2 https://github.com/galaxyproject/galaxy/commit/308402235fe4d3d3bb85e350181a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/style/less/base.less M doc/source/admin/framework_dependencies.rst M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M scripts/binary_compatibility.py M scripts/common_startup.sh M static/maps/mvc/library/library-folder-view.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/mvc/library/library-folder-view.js M static/style/blue/base.css Log Message: ----------- Merge release_16.01 into dev Commit: 8acc7ebc048d58165d3a02b21446cc5674f6aefd https://github.com/galaxyproject/galaxy/commit/8acc7ebc048d58165d3a02b21446… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: 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/style/blue/base.css Log Message: ----------- repack client Commit: d331b54b99cdc9f07bf0e53f284adf1fa4398ce0 https://github.com/galaxyproject/galaxy/commit/d331b54b99cdc9f07bf0e53f284a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/style/less/base.less M doc/source/admin/framework_dependencies.rst M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M scripts/binary_compatibility.py M scripts/common_startup.sh M static/maps/mvc/library/library-folder-view.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-folder-view.js M static/style/blue/base.css Log Message: ----------- Merge pull request #1697 from martenson/merge-1601-dev merge 16.01 into dev Compare: https://github.com/galaxyproject/galaxy/compare/ae372ae33b67...d331b54b99cd

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[galaxyproject/galaxy] 055f18: Managers: fix sharable.list_published's incorrect ...
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 055f180d20bfe70c0edd7f550e0332b0a79e228f https://github.com/galaxyproject/galaxy/commit/055f180d20bfe70c0edd7f550e03… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/deletable.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/visualizations.py M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Managers: fix sharable.list_published's incorrect use of query, add manager getter to base serializer, deserializer, and filter parser; Managers, ratable: implement and attach to history Commit: de42737c44d93684f3b6e83b385beab2c0a5ea21 https://github.com/galaxyproject/galaxy/commit/de42737c44d93684f3b6e83b385b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/list/list-view.js M lib/galaxy/managers/base.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py A lib/galaxy/managers/history_contents.py M static/maps/mvc/list/list-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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/list/list-view.js M templates/show_params.mako M test/docker/base/run_test_wrapper.sh A test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into managers.ratable Commit: 4d75d1c6418a363f56700b2f3afd9c32c6d60516 https://github.com/galaxyproject/galaxy/commit/4d75d1c6418a363f56700b2f3afd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/ratable.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Managers, ratable: clean up, test, and fix Commit: 05a3d04b60bf9512a2fd9ebe07bc978a295e6865 https://github.com/galaxyproject/galaxy/commit/05a3d04b60bf9512a2fd9ebe07bc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/deletable.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/visualizations.py Log Message: ----------- Managers: extract manager() code and move into class with property accessor Commit: d07677bba16d535a67a2e4517f29ab28a8bb6c04 https://github.com/galaxyproject/galaxy/commit/d07677bba16d535a67a2e4517f29… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py Log Message: ----------- Managers: bit of cleanup for 05a3d04b Commit: 427909929296ccf5c24389aace39057225f4b2da https://github.com/galaxyproject/galaxy/commit/427909929296ccf5c24389aace39… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: A .ci/first_startup.sh M .travis.yml M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.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-libraryrow-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M client/galaxy/style/less/tour.less M config/galaxy.ini.sample M config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst M doc/source/project/issues.rst A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/special_tools.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/heartbeat.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/install_manager.py M scripts/bootstrap_history.py M scripts/common_startup.sh M static/maps/layout/menu.js.map M static/maps/layout/page.js.map R static/maps/libs/backbone/backbone.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-select-content.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-libraryrow-view.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/page.js R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-select-content.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-libraryrow-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/onload.js M static/style/blue/base.css M static/style/blue/library.css M templates/user/info.mako M templates/user/username.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M test-data/3.bam M test/api/test_workflows.py M test/api/workflows_format_2/converter.py A test/functional/tools/for_workflows/1.bam A test/functional/tools/for_workflows/mapper.xml A test/functional/tools/for_workflows/pileup.xml A test/functional/tools/paths_as_file.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.py M test/unit/tools_support.py M tools/data_source/upload.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into managers.ratable Commit: ae372ae33b67fb2b50d45f79dfed1e54452d60d0 https://github.com/galaxyproject/galaxy/commit/ae372ae33b67fb2b50d45f79dfed… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/webapps/galaxy/api/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #1618 from carlfeberhard/managers.ratable Implement the ratable mixin Compare: https://github.com/galaxyproject/galaxy/compare/eab2f1ff5c53...ae372ae33b67

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