February 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 70b58d: update pinned-requirements.txt
by GitHub 02 Feb '16

02 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 70b58d2bcff29ddb333dc7987d8ca1836554eaa1 https://github.com/galaxyproject/galaxy/commit/70b58d2bcff29ddb333dc7987d8c… Author: matthdsm <matthias.desmet(a)ugent.be> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- update pinned-requirements.txt Updated Bioblend versio 0.6.1 > 0.7.0 Commit: e863071309585eea5cfb03ff805e6249f946fb09 https://github.com/galaxyproject/galaxy/commit/e863071309585eea5cfb03ff805e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #1605 from matthdsm/patch-2 update pinned-requirements.txt Compare: https://github.com/galaxyproject/galaxy/compare/3e267124ad54...e86307130958

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[galaxyproject/usegalaxy-playbook] 4f1383: Forgot how XML comments work
by GitHub 02 Feb '16

02 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4f13837697316045c5b77c57fc34714532b0ecb1 https://github.com/galaxyproject/usegalaxy-playbook/commit/4f13837697316045… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 Log Message: ----------- Forgot how XML comments work

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[galaxyproject/galaxy] afc5f2: Fix: Use dependency resolvers if any config exists...
by GitHub 02 Feb '16

02 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: afc5f2a45399c474d86f1530a62afe280a0eb3be https://github.com/galaxyproject/galaxy/commit/afc5f2a45399c474d86f1530a62a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix: Use dependency resolvers if any config exists. This way resolvers like the Module resolver work even if tool_dependency_dir is not set. Commit: 916ddb575f40c445a47cf91a58aad00bf9360ae8 https://github.com/galaxyproject/galaxy/commit/916ddb575f40c445a47cf91a58aa… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #1648 from jmchilton/dependencies_conf [16.01] Fix use_tool_dependencies for non-default dependency_resolver_conf files. Compare: https://github.com/galaxyproject/galaxy/compare/e4e48941a617...916ddb575f40

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[galaxyproject/galaxy] 50ea46: Change python print() format to be backward compat...
by GitHub 02 Feb '16

02 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 50ea4694af82ac33eaac1ddc9ca8aee1e71e1f00 https://github.com/galaxyproject/galaxy/commit/50ea4694af82ac33eaac1ddc9ca8… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Change python print() format to be backward compatible with older versions In python versions prior to 3.1, the print("{}", .format(x)) form throws an error, use the more compatible print("{0}", .format(x)) form instead. Commit: e4e48941a6174a148cde06ef2218ef6480568716 https://github.com/galaxyproject/galaxy/commit/e4e48941a6174a148cde06ef2218… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Merge pull request #1651 from jmchilton/backport_print_fix [16.01] Backport print fix. Compare: https://github.com/galaxyproject/galaxy/compare/9170865dfbe0...e4e48941a617

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[galaxyproject/galaxy] e9d7d6: Export info required to re-run an exported workflo...
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e9d7d6f1be49aedd44b1ada0bf92e5ee7a14a638 https://github.com/galaxyproject/galaxy/commit/e9d7d6f1be49aedd44b1ada0bf92… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Export info required to re-run an exported workflow. Commit: 3e267124ad5454ac69c91aef59064d81b7e74140 https://github.com/galaxyproject/galaxy/commit/3e267124ad5454ac69c91aef5906… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1636 from mvdbeek/add_repo_info_to_wf_export Export toolshed repository information for workflow portability Compare: https://github.com/galaxyproject/galaxy/compare/f3b7dd56f766...3e267124ad54

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[galaxyproject/galaxy] 062711: Lint optional handling on conditional test paramet...
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0627116e112e2a250e5d3db9867224bdfc1fbed0 https://github.com/galaxyproject/galaxy/commit/0627116e112e2a250e5d3db98672… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/linters/inputs.py Log Message: ----------- Lint optional handling on conditional test parameters. Commit: f3b7dd56f766fdae9cdb8bd552fd29866d3ad81a https://github.com/galaxyproject/galaxy/commit/f3b7dd56f766fdae9cdb8bd552fd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/linters/inputs.py Log Message: ----------- Merge pull request #1639 from jmchilton/lint_test_params Lint optional handling on conditional test parameters. Compare: https://github.com/galaxyproject/galaxy/compare/c8d05e2fb704...f3b7dd56f766

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[galaxyproject/galaxy] a10a4a: attempt to fix suite outside of tool panel.
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a10a4a1b8478a3a89830fb9d61ebe721a33c13cd https://github.com/galaxyproject/galaxy/commit/a10a4a1b8478a3a89830fb9d61eb… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- attempt to fix suite outside of tool panel. Commit: cda1ee8be65db00d659809a4c383e7c614ca31dc https://github.com/galaxyproject/galaxy/commit/cda1ee8be65db00d659809a4c383… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- also save integrated tool panel Commit: c8d05e2fb7049a1938c403569ee01b0377d86733 https://github.com/galaxyproject/galaxy/commit/c8d05e2fb7049a1938c403569ee0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #1601 from mvdbeek/fix_outside_tool_panel Fix installation of repository suites outside of tool panel section Compare: https://github.com/galaxyproject/galaxy/compare/e0d0bcd4e4cb...c8d05e2fb704

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[galaxyproject/galaxy] 7ebc3e: Remove unnecessary variable and assignment of job ...
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ebc3eb0601f6a3f3509db586f28e65a85605740 https://github.com/galaxyproject/galaxy/commit/7ebc3eb0601f6a3f3509db586f28… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Remove unnecessary variable and assignment of job command Commit: e0d0bcd4e4cb00f84a998e5a29b98ba05982defe https://github.com/galaxyproject/galaxy/commit/e0d0bcd4e4cb00f84a998e5a29b9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #1616 from einon/job_code_tweaks Remove unnecessary variable and assignment of job command Compare: https://github.com/galaxyproject/galaxy/compare/41a3a1676245...e0d0bcd4e4cb

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[galaxyproject/galaxy] f05c95: Remove unvalidated values
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f05c9518be52ecaa9cb13885aeec3f57054e976a https://github.com/galaxyproject/galaxy/commit/f05c9518be52ecaa9cb13885aeec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Remove unvalidated values Commit: 89ba002475695d09542dbe85886c6d69e6f54307 https://github.com/galaxyproject/galaxy/commit/89ba002475695d09542dbe85886c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove late validation handling Commit: 49026134443e49c81d5b071817bb7a018357f945 https://github.com/galaxyproject/galaxy/commit/49026134443e49c81d5b071817bb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/dbkeys.py Log Message: ----------- Use bunch instead of trans Commit: 12f2571d975ca89548259e1322882e87dbb5b17e https://github.com/galaxyproject/galaxy/commit/12f2571d975ca89548259e132288… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Use self.app in tools Commit: 52b6881f017e38ea5969c5adb70b5c83d6753cd3 https://github.com/galaxyproject/galaxy/commit/52b6881f017e38ea5969c5adb70b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Revise history handling Commit: 34f46c98c7bdace6af9126b44534fd41c9121002 https://github.com/galaxyproject/galaxy/commit/34f46c98c7bdace6af9126b44534… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Remove comments Commit: 7eb6cc7b8247689d1bfef12c99a9514610bbd0bb https://github.com/galaxyproject/galaxy/commit/7eb6cc7b8247689d1bfef12c99a9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Revise validate signature Commit: a272bff066516019ca74ee0012b2ae6fe02c21bc https://github.com/galaxyproject/galaxy/commit/a272bff066516019ca74ee0012b2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use consistently other_values Commit: 550102915866ab4448a3e8a070437c80772320da https://github.com/galaxyproject/galaxy/commit/550102915866ab4448a3e8a07043… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Revise validate signature Commit: 4b6172299e2adc4edd117c505e5c7ddcde38c24b https://github.com/galaxyproject/galaxy/commit/4b6172299e2adc4edd117c505e5c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/work/context.py Log Message: ----------- Use workcontext Commit: eaf02029d43620db309e2860d4502e0f830bc2a9 https://github.com/galaxyproject/galaxy/commit/eaf02029d43620db309e2860d450… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix remaining self.app, use workcontext app Commit: 5a72480719055ac4a6d04ff690f69d5a118b5c81 https://github.com/galaxyproject/galaxy/commit/5a72480719055ac4a6d04ff690f6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix dataset selection Commit: 7cc505019d2b2af938b61efe0e00bd25a13af91b https://github.com/galaxyproject/galaxy/commit/7cc505019d2b2af938b61efe0e00… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/util/dbkeys.py Log Message: ----------- Use sa_session of workcontext Commit: b56574115fa9ae32f2d4703f0b257991ad2f4c26 https://github.com/galaxyproject/galaxy/commit/b56574115fa9ae32f2d4703f0b25… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/util/dbkeys.py Log Message: ----------- Fix trans usage Commit: 93dbf742b36b614bacbb7a806431532567203b70 https://github.com/galaxyproject/galaxy/commit/93dbf742b36b614bacbb7a806431… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Reinsert last validation Commit: 7c69227c8cde400df37f5e9390fdd88e51f64f2a https://github.com/galaxyproject/galaxy/commit/7c69227c8cde400df37f5e9390fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix db_builds Commit: 269ce36d3f5212b2d98315a67b25cc6db5a3429c https://github.com/galaxyproject/galaxy/commit/269ce36d3f5212b2d98315a67b25… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix check params Commit: 3acdee5143586d0224f896d2bfc5c085e3409349 https://github.com/galaxyproject/galaxy/commit/3acdee5143586d0224f896d2bfc5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Show validation error for workflow step preparation Commit: b38479c4a49efcf2c56e400b56d1da4f5eb4a02d https://github.com/galaxyproject/galaxy/commit/b38479c4a49efcf2c56e400b56d1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py Log Message: ----------- Remove unvalidated value handling in workflow extraction Commit: 6939c99f1bb06532e5c4cb4c2a4ef936075b4569 https://github.com/galaxyproject/galaxy/commit/6939c99f1bb06532e5c4cb4c2a4e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/extract.py Log Message: ----------- Remove more unvalidated value hacks Commit: 539ddd4d90bda5400c3006ab4c574bebd353d280 https://github.com/galaxyproject/galaxy/commit/539ddd4d90bda5400c3006ab4c57… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Remove optional parameter from request context initialization Commit: cc2cfe8d6adb264df41e18b4c33781712bb12cbb https://github.com/galaxyproject/galaxy/commit/cc2cfe8d6adb264df41e18b4c337… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use request context instead of trans in to_json Commit: a7117574268ab907fb27483a485d5d9e501b7e5e https://github.com/galaxyproject/galaxy/commit/a7117574268ab907fb27483a485d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Remove unused error handler, error is handled consistently through full validation Commit: 0ca9c7027b5ee3cd8ba433a4e8bc3e5ad57a5d7f https://github.com/galaxyproject/galaxy/commit/0ca9c7027b5ee3cd8ba433a4e8bc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.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/workflow/extract.py Log Message: ----------- Use request context in handle inputs Commit: 193c5293d9552d53a2358254fa2a25b236a31511 https://github.com/galaxyproject/galaxy/commit/193c5293d9552d53a2358254fa2a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M tools/data_source/upload.xml Log Message: ----------- Remove invalid validator from upload.xml Commit: 0fc8726414bfedcc234d7c4738ebff3a1b37e3d4 https://github.com/galaxyproject/galaxy/commit/0fc8726414bfedcc234d7c4738eb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix prefixed_label concatenation Commit: 0521644bb37336f31577c8bd73ac1fef6c936016 https://github.com/galaxyproject/galaxy/commit/0521644bb37336f31577c8bd73ac… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix select validator Commit: 8bd4cabdde922f23c06c64f95f50ea4d81caa940 https://github.com/galaxyproject/galaxy/commit/8bd4cabdde922f23c06c64f95f50… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/workflow/modules.py Log Message: ----------- Use request context for parameter helper Commit: b3f3f81a7d0d221e4a698dbd9a586a92cd6662af https://github.com/galaxyproject/galaxy/commit/b3f3f81a7d0d221e4a698dbd9a58… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Remove unused to_html helper Commit: 8b6e4c9f2584d5768926836ee08607aeae0bb501 https://github.com/galaxyproject/galaxy/commit/8b6e4c9f2584d5768926836ee086… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Remove unused filter value helper Commit: 27df773c5a8823fff2d0dd68a8bd162147336bed https://github.com/galaxyproject/galaxy/commit/27df773c5a8823fff2d0dd68a8bd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Always display discarded datasets on rerun Commit: f8e3fa51f4b2fbaab54becd869ede40e43c5067a https://github.com/galaxyproject/galaxy/commit/f8e3fa51f4b2fbaab54becd869ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/parameters/basic.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 Log Message: ----------- Apply suggested fixes, fix test cases Commit: 72370b251723eac746bd1720a85df539cd96e78a https://github.com/galaxyproject/galaxy/commit/72370b251723eac746bd1720a85d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix paused workflow step resubmission Commit: 41a3a1676245284fa01e9697bd91710244ddde83 https://github.com/galaxyproject/galaxy/commit/41a3a1676245284fa01e9697bd91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__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/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/work/context.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako 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 Log Message: ----------- Merge pull request #1572 from guerler/fix_unvalidated_008 Fix parameter validation Compare: https://github.com/galaxyproject/galaxy/compare/dacb91907af7...41a3a1676245

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[galaxyproject/galaxy] 30cceb: remove forgotten util.params that fails when POSTi...
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 30ccebfb0c8ef0809bbd3f1d2d64be5ac23bb3a2 https://github.com/galaxyproject/galaxy/commit/30ccebfb0c8ef0809bbd3f1d2d64… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- remove forgotten util.params that fails when POSTing a payload{} dict (because it cannot sanitize dict in dict) Commit: 9170865dfbe0f8588ec47449e683236e5ba92a39 https://github.com/galaxyproject/galaxy/commit/9170865dfbe0f8588ec47449e683… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1634 from martenson/remove-utilparams [16.01] libraries: remove forgotten util.params that fails when POSTing a payload {} Compare: https://github.com/galaxyproject/galaxy/compare/ee4f58ce7d6a...9170865dfbe0

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