August 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 9d6a0e: Implement default_identifier_source for outputs
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d6a0e82f6f9634981ea96c37f0f48e38e9c5b12 https://github.com/galaxyproject/galaxy/commit/9d6a0e82f6f9634981ea96c37f0f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/tools/execute.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Implement default_identifier_source for outputs This allows tool authors to specify an input from which the element identifier can be inherited. This applies only to non-collection output when mapping a collection over an input, since collections have a structured_like attribute. Commit: 35c0a4770336ca82fda7dd3034fd029e3bd474b8 https://github.com/galaxyproject/galaxy/commit/35c0a4770336ca82fda7dd3034fd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M test/api/test_tools.py M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add test API test for default_identifier_source Commit: 46fba6ec1c728125efa1339e7334202487a09e18 https://github.com/galaxyproject/galaxy/commit/46fba6ec1c728125efa1339e7334… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/dataset_collections/matching.py Log Message: ----------- Sort input keys by default, so the first matching input key will the source of the element identifiers Commit: ea15f398e79771b6dd6ba5fdf0c8d96e10d39734 https://github.com/galaxyproject/galaxy/commit/ea15f398e79771b6dd6ba5fdf0c8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Fix failing API tests for explicit collection outputs Commit: e92a15a18523e14c050d987b3c14be412fcaaddc https://github.com/galaxyproject/galaxy/commit/e92a15a18523e14c050d987b3c14… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/dataset_collections/matching.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #4368 from mvdbeek/tie_down_collection_matcher Implement default_identifier_source for outputs and sort input keys by default Compare: https://github.com/galaxyproject/galaxy/compare/68c7b0982bb1...e92a15a18523

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[galaxyproject/galaxy] 9803dc: More updates to GRT
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9803dc600cb62235d9a1abad15e5b7b4877be2aa https://github.com/galaxyproject/galaxy/commit/9803dc600cb62235d9a1abad15e5… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M scripts/grt.py M scripts/grt.yml.sample Log Message: ----------- More updates to GRT Commit: 5abbf1102ed93b5d78bb126a571cef8e07a95b4e https://github.com/galaxyproject/galaxy/commit/5abbf1102ed93b5d78bb126a571c… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M scripts/grt.py Log Message: ----------- at loop time Commit: b0428352e07d444b58d428da2928608005647491 https://github.com/galaxyproject/galaxy/commit/b0428352e07d444b58d428da2928… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: A scripts/grt-submit.py M scripts/grt.py M scripts/grt.yml.sample Log Message: ----------- Split out the submission portion Commit: c14d37fbd6717a97ca700c5f4bb507444df570b9 https://github.com/galaxyproject/galaxy/commit/c14d37fbd6717a97ca700c5f4bb5… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M scripts/grt.py Log Message: ----------- timings Commit: 163127b4b2c513a810ece57d8deb1851123a9351 https://github.com/galaxyproject/galaxy/commit/163127b4b2c513a810ece57d8deb… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M scripts/grt.py Log Message: ----------- Also dump toolbox Commit: 2cd2c3967a74dacbdd3d920935fe141e65675043 https://github.com/galaxyproject/galaxy/commit/2cd2c3967a74dacbdd3d920935fe… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M scripts/grt.yml.sample Log Message: ----------- document GRT a bit more Commit: 11ac796f2df407ff2f547324842333591a543daa https://github.com/galaxyproject/galaxy/commit/11ac796f2df407ff2f5473248423… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M scripts/grt.py Log Message: ----------- Include hash for transport Commit: d453231226543face2eee1c7d652029450b056fd https://github.com/galaxyproject/galaxy/commit/d453231226543face2eee1c7d652… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M scripts/grt.py M scripts/grt.yml.sample Log Message: ----------- Various optimisations Commit: a0292a46c7f966d4f1c70a5cc19320f8255d64b1 https://github.com/galaxyproject/galaxy/commit/a0292a46c7f966d4f1c70a5cc193… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt-submit.py M scripts/grt.py M scripts/grt.yml.sample Log Message: ----------- Revert submission of instance metadata Commit: 93eac6dfcf8d2517381c0cff3b10429ae97aacad https://github.com/galaxyproject/galaxy/commit/93eac6dfcf8d2517381c0cff3b10… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- remove redundant code Commit: 50156d8e7be4cb7693cd3e92ccd5df682b4799a6 https://github.com/galaxyproject/galaxy/commit/50156d8e7be4cb7693cd3e92ccd5… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt-submit.py Log Message: ----------- import from grt Commit: df33d4f7080bd75a5d2e25ec20469ebc2ac54574 https://github.com/galaxyproject/galaxy/commit/df33d4f7080bd75a5d2e25ec2046… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- Super optimised GRT Commit: 07faeaa5ce2645be8e2ce9bfc61f1b8d8658505a https://github.com/galaxyproject/galaxy/commit/07faeaa5ce2645be8e2ce9bfc61f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- Batched sql queries, sanitization Commit: 94a8a9a841c4352c8dccfd42844f4fab2c97db7c https://github.com/galaxyproject/galaxy/commit/94a8a9a841c4352c8dccfd42844f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt.py M scripts/grt.yml.sample Log Message: ----------- default to sharing toolbox Commit: cf4dc28c5fa762c93dcc2fd51d42a7bb684f7ecb https://github.com/galaxyproject/galaxy/commit/cf4dc28c5fa762c93dcc2fd51d42… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt.py M scripts/grt.yml.sample Log Message: ----------- Disable sanitization by default Commit: cefa47c6986429ba37949f49b849e624d226a62e https://github.com/galaxyproject/galaxy/commit/cefa47c6986429ba37949f49b849… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt.yml.sample Log Message: ----------- remove keys from testing Commit: 6caded21251539c721907c281c8cd83b4797391e https://github.com/galaxyproject/galaxy/commit/6caded21251539c721907c281c8c… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- unused function Commit: 5e6d1cba409f082a3f2e7748d6eb1fa8010c4470 https://github.com/galaxyproject/galaxy/commit/5e6d1cba409f082a3f2e7748d6eb… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M scripts/grt.py M scripts/grt.yml.sample Log Message: ----------- Some simplification which should significantly speed up parsing Commit: 08aeea3e92158a45a3e88b5da5e8f3b31821e6ba https://github.com/galaxyproject/galaxy/commit/08aeea3e92158a45a3e88b5da5e8… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M scripts/grt.py M scripts/grt.yml.sample Log Message: ----------- add headers Commit: 058c4a74b83897ba36ec548b6be8162976a549c7 https://github.com/galaxyproject/galaxy/commit/058c4a74b83897ba36ec548b6be8… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- remove text metrics Commit: 16f17efe497e39bcd5fc1f493b7e5bb810a437b2 https://github.com/galaxyproject/galaxy/commit/16f17efe497e39bcd5fc1f493b7e… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- remove remenants of __any__ Commit: 70f4bc957e9a29b85f41e35cf8530122c8284356 https://github.com/galaxyproject/galaxy/commit/70f4bc957e9a29b85f41e35cf853… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M doc/source/admin/special_topics/grt.rst M scripts/grt.py Log Message: ----------- update documentation and fix blacklisting bug Commit: 5ed50dba1c4478ab58b9c96e1077652675fe9b2f https://github.com/galaxyproject/galaxy/commit/5ed50dba1c4478ab58b9c96e1077… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- Allow sending subsets Commit: 7deff206226ce90b68e2e306146a1ea59c745073 https://github.com/galaxyproject/galaxy/commit/7deff206226ce90b68e2e306146a… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- move up to fix print statement Commit: b381a90fcb2b4e169a133f3ff0667b4bf93375df https://github.com/galaxyproject/galaxy/commit/b381a90fcb2b4e169a133f3ff066… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M scripts/grt-submit.py M scripts/grt.py Log Message: ----------- flake8 Commit: d3b271761f4d2f998bea3a290e2b35389f968fe9 https://github.com/galaxyproject/galaxy/commit/d3b271761f4d2f998bea3a290e2b… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- remove a blank line Commit: e8b367bde3d429c991d223c3d8df76399d6cff81 https://github.com/galaxyproject/galaxy/commit/e8b367bde3d429c991d223c3d8df… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: R scripts/grt-submit.py R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/grt-submit.py A scripts/grt/grt.py A scripts/grt/grt.yml.sample Log Message: ----------- move to subdir Commit: 0ed3571f0d6285d5415eeffc0a8a8f97724aab77 https://github.com/galaxyproject/galaxy/commit/0ed3571f0d6285d5415eeffc0a8a… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M scripts/grt/grt-submit.py M scripts/grt/grt.py Log Message: ----------- Fix various logging statements Commit: 7e94cf20b0bd05e73c50976cb1f5196e776ebb1e https://github.com/galaxyproject/galaxy/commit/7e94cf20b0bd05e73c50976cb1f5… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M scripts/grt/grt.py Log Message: ----------- fix todo Commit: 1043ee5fd4e8eb559795e16c63f735dbbe9924a6 https://github.com/galaxyproject/galaxy/commit/1043ee5fd4e8eb559795e16c63f7… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M doc/source/admin/special_topics/grt.rst Log Message: ----------- update docs to reflect new locations Commit: ddcddecb4a3f049bc35fa7a6832339dc9f66bad9 https://github.com/galaxyproject/galaxy/commit/ddcddecb4a3f049bc35fa7a68323… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M doc/source/admin/special_topics/grt.rst A scripts/grt/export.py R scripts/grt/grt-submit.py R scripts/grt/grt.py A scripts/grt/upload.py Log Message: ----------- rename scripts Commit: 5b83c6c330f4bb8ccbe77031cd3d6db513a882f6 https://github.com/galaxyproject/galaxy/commit/5b83c6c330f4bb8ccbe77031cd3d… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge branch 'grt-update-2' of github.com:erasche/galaxy into grt-update-2 Commit: a6fcb95a15134e9ef42cd39663ebe70dfed37fd1 https://github.com/galaxyproject/galaxy/commit/a6fcb95a15134e9ef42cd39663eb… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M scripts/grt/grt.yml.sample Log Message: ----------- default false with expl Commit: 89887689b479e34e3d049dd689a5f8c8e3f47fc2 https://github.com/galaxyproject/galaxy/commit/89887689b479e34e3d049dd689a5… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M doc/source/admin/special_topics/grt.rst Log Message: ----------- correct some spelling errors Commit: 68c7b0982bb19c509cfdc87c58ac3578edf038db https://github.com/galaxyproject/galaxy/commit/68c7b0982bb19c509cfdc87c58ac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M doc/source/admin/special_topics/grt.rst R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/export.py A scripts/grt/grt.yml.sample A scripts/grt/upload.py Log Message: ----------- Merge pull request #4376 from erasche/grt-update-2 Galactic Radio Telescope Update Compare: https://github.com/galaxyproject/galaxy/compare/3f270e91afc3...68c7b0982bb1

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[galaxyproject/galaxy] 4b5247: Fix TypeError when uploading large files from ftp ...
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4b52476b24fd6cb196eac32295e6ae1a30228b2f https://github.com/galaxyproject/galaxy/commit/4b52476b24fd6cb196eac32295e6… Author: Jian-Long Huang <huang(a)jianlong.org> Date: 2017-07-14 (Fri, 14 Jul 2017) Changed paths: M lib/galaxy/objectstore/s3_multipart_upload.py Log Message: ----------- Fix TypeError when uploading large files from ftp to s3 Commit: 3f270e91afc3792233248c1f7cb9f6735b95b7f4 https://github.com/galaxyproject/galaxy/commit/3f270e91afc3792233248c1f7cb9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/objectstore/s3_multipart_upload.py Log Message: ----------- Merge pull request #4315 from jlhg/fix-s3mu-map-wrap Fix TypeError when uploading large files from ftp to s3 Compare: https://github.com/galaxyproject/galaxy/compare/4effd7d77ae7...3f270e91afc3

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[galaxyproject/galaxy] b17091: CSRF protection for login, logout, and user regist...
by GitHub 04 Aug '17

04 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b17091a3ec51a4836370f32b71ea72abfe4a966f https://github.com/galaxyproject/galaxy/commit/b17091a3ec51a4836370f32b71ea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/galaxy.js.map M static/maps/layout/menu.js.map M static/maps/mvc/user/user-preferences.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/galaxy.js M static/scripts/layout/menu.js M static/scripts/mvc/user/user-preferences.js M templates/galaxy_client_app.mako M templates/user/login.mako M templates/user/register.mako M test/shed_functional/base/twilltestcase.py Log Message: ----------- CSRF protection for login, logout, and user registeration. The approach is to use per-session CSRF tokens - this avoids many complications related to per-form tokens. We generate a sequence of hashes based on session IDs that doesn't follow the same pattern as normal database API IDs by supplying a "kind" parameter to encode_id (we use the same pattern for securing the job files API for Pulsar). Commit: 4effd7d77ae75d577c5d04b34174464a43d075b8 https://github.com/galaxyproject/galaxy/commit/4effd7d77ae75d577c5d04b34174… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-08-05 (Sat, 05 Aug 2017) Changed paths: M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/galaxy.js.map M static/maps/layout/menu.js.map M static/maps/mvc/user/user-preferences.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/galaxy.js M static/scripts/layout/menu.js M static/scripts/mvc/user/user-preferences.js M templates/galaxy_client_app.mako M templates/user/login.mako M templates/user/register.mako M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #4365 from jmchilton/csrf CSRF protection for login, logout, and user registration. Compare: https://github.com/galaxyproject/galaxy/compare/575696dcc2cc...4effd7d77ae7

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[galaxyproject/galaxy] 8d5a31: Register tool lineage when loading tool via quick_...
by GitHub 04 Aug '17

04 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d5a315671b6fd1c475abc88f454a7c3bfb434f4 https://github.com/galaxyproject/galaxy/commit/8d5a315671b6fd1c475abc88f454… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Register tool lineage when loading tool via quick_load() Commit: 51951a8850888d0d5538ef5f84327bb78ccbfba6 https://github.com/galaxyproject/galaxy/commit/51951a8850888d0d5538ef5f8432… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M lib/galaxy/jobs/rule_helper.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako Log Message: ----------- Always use tool version to get tools from toolbox This fixes a bug when getting parameters for jobs that were executed with old tool versions. Commit: faee2b65c29ee405d475d54a630d54c7b29a4159 https://github.com/galaxyproject/galaxy/commit/faee2b65c29ee405d475d54a630d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Use self.job instead of self.parent_job in Task Noticed by @nsoranzo. Commit: 7474474cc0ec8f98a0e23bfd7bf2906326938153 https://github.com/galaxyproject/galaxy/commit/7474474cc0ec8f98a0e23bfd7bf2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Move tool lineage registration to toolbox.__add_tool() Commit: ccad70c22c082b3801dec567600f054581e8044b https://github.com/galaxyproject/galaxy/commit/ccad70c22c082b3801dec567600f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Add warnings if a tool lineage could not be retrieved Commit: 575696dcc2cc775e72b58f5cda0612a79b62b87b https://github.com/galaxyproject/galaxy/commit/575696dcc2cc775e72b58f5cda06… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/jobs/rule_helper.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako Log Message: ----------- Merge pull request #4375 from mvdbeek/tool_version_and_lineage_fixes Tool version and lineage fixes Compare: https://github.com/galaxyproject/galaxy/compare/dbd057f9d720...575696dcc2cc

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[galaxyproject/galaxy] 32bd35: Fix URL for workflow editor 'Run' button
by GitHub 03 Aug '17

03 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 32bd350fe9c06b9f506c21c9ba4eab97408c404d https://github.com/galaxyproject/galaxy/commit/32bd350fe9c06b9f506c21c9ba4e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix URL for workflow editor 'Run' button On the current dev this would point to api/workflows//download?style=run and result in `Error occurred while loading the resource.` Commit: dbd057f9d72036bff98d3217312e4de3148b3285 https://github.com/galaxyproject/galaxy/commit/dbd057f9d72036bff98d3217312e… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #4371 from mvdbeek/fix_run_from_workflow_editor Fix URL for workflow editor 'Run' button Compare: https://github.com/galaxyproject/galaxy/compare/fe3fdc82d239...dbd057f9d720

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[galaxyproject/galaxy] 910e6f: Allow removal of dataset tags in workflows
by GitHub 03 Aug '17

03 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 910e6fa035684fbdfc2b38e4675308e47e801083 https://github.com/galaxyproject/galaxy/commit/910e6fa035684fbdfc2b38e46753… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Allow removal of dataset tags in workflows This adds a RemoveTagDatasetAction PJA, which removes user-specified tags if they exist. Fixes https://github.com/galaxyproject/galaxy/issues/4362 Commit: fe3fdc82d23978c4161d8f020c256576f663e10a https://github.com/galaxyproject/galaxy/commit/fe3fdc82d23978c4161d8f020c25… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Merge pull request #4369 from mvdbeek/tag_removal Allow removal of dataset tags in workflows Compare: https://github.com/galaxyproject/galaxy/compare/6b2a2582002d...fe3fdc82d239

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[galaxyproject/galaxy] 97c16d: Add ImzML composite defintion
by GitHub 03 Aug '17

03 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 97c16db8245570196b556854570b0c120abcb8b0 https://github.com/galaxyproject/galaxy/commit/97c16db8245570196b556854570b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Add ImzML composite defintion Commit: e2f69a9c5bc7d11274190e223493d6d12d33afb3 https://github.com/galaxyproject/galaxy/commit/e2f69a9c5bc7d11274190e223493… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add imzml to the datatypes conf file Commit: 1d609ca2caa158422adcdee0bbc65e73ce0527d2 https://github.com/galaxyproject/galaxy/commit/1d609ca2caa158422adcdee0bbc6… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- add edam format Commit: e768e77392471a60425984ae518fb4f34a0552ee https://github.com/galaxyproject/galaxy/commit/e768e77392471a60425984ae518f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- fix pep8 Commit: 6b2a2582002d38665b2f3def1245675d638e6c75 https://github.com/galaxyproject/galaxy/commit/6b2a2582002d38665b2f3def1245… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Merge pull request #4370 from bgruening/mzml Add imzML datatype Compare: https://github.com/galaxyproject/galaxy/compare/ade8844d11aa...6b2a2582002d

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[galaxyproject/galaxy] e88233: Preview feature for Bam datatype
by GitHub 02 Aug '17

02 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e88233af84d50822bc6328114e112165605e32fa https://github.com/galaxyproject/galaxy/commit/e88233af84d50822bc6328114e11… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Preview feature for Bam datatype Commit: 2005a9d685209789c95e5eb48d2a6c77d9703201 https://github.com/galaxyproject/galaxy/commit/2005a9d685209789c95e5eb48d2a… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Preview feature for Bam datatype. Final Changes Commit: bb67be81cd1c2043ecd1b1eb54942cbb5b52c828 https://github.com/galaxyproject/galaxy/commit/bb67be81cd1c2043ecd1b1eb5494… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Updated based on the changes requested Commit: 72c196f793aeb30ec00cf368e419bcdaecdbd514 https://github.com/galaxyproject/galaxy/commit/72c196f793aeb30ec00cf368e419… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Accessing Bam file via seek() and tell() Commit: c66298d62717c88cf4341ad1601176420b16f280 https://github.com/galaxyproject/galaxy/commit/c66298d62717c88cf4341ad16011… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- travis test correction Commit: 8c8aa8820fcc592c31693399660b87b04809b9da https://github.com/galaxyproject/galaxy/commit/8c8aa8820fcc592c31693399660b… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Preview feature for Bam datatype Commit: 3ddf819c83f881eee4b7ab19281926e1e64a58d3 https://github.com/galaxyproject/galaxy/commit/3ddf819c83f881eee4b7ab192819… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Preview feature for Bam datatype. Final Changes Commit: 9a8c8b8a61b1ec09509cc9b2b7738eae5238e036 https://github.com/galaxyproject/galaxy/commit/9a8c8b8a61b1ec09509cc9b2b773… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Updated based on the changes requested Commit: 731d1db4b23e2a75335f716a9c6f6d1b30938101 https://github.com/galaxyproject/galaxy/commit/731d1db4b23e2a75335f716a9c6f… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Accessing Bam file via seek() and tell() Commit: dac72950db3b64291c5c202b9db15fac3525de86 https://github.com/galaxyproject/galaxy/commit/dac72950db3b64291c5c202b9db1… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- travis test correction Commit: 635df817663ffc82fe26645512f880c16c251dd4 https://github.com/galaxyproject/galaxy/commit/635df817663ffc82fe26645512f8… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Log Message: ----------- resolving sniff.py conflict Commit: 253d0c2d4f435a9778a636ff3a162d0fe0717854 https://github.com/galaxyproject/galaxy/commit/253d0c2d4f435a9778a636ff3a16… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- reordering import statements Commit: 3ddd05d56985360c31bd62ea78027fbfc34bb796 https://github.com/galaxyproject/galaxy/commit/3ddd05d56985360c31bd62ea7802… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Removing the SAM datatype for class Bam and resetting changes with sniff.py Commit: c476090bdef84b7781458ff7445451d35e0af46b https://github.com/galaxyproject/galaxy/commit/c476090bdef84b7781458ff74454… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- setting default value for column_names, column_types and column Metadata Commit: 8b3e492bad9257bd0f4c9ba3e78f1a88cc64bfe6 https://github.com/galaxyproject/galaxy/commit/8b3e492bad9257bd0f4c9ba3e78f… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix for travis test Commit: 0cfdfbf275fda9072b521fa501ad1aaafdc87c8e https://github.com/galaxyproject/galaxy/commit/0cfdfbf275fda9072b521fa501ad… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- replaced last_read with offset variable Commit: 90a0ab0398860cccf84a78dd293f62b44bb0bf71 https://github.com/galaxyproject/galaxy/commit/90a0ab0398860cccf84a78dd293f… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-10 (Mon, 10 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Replace '\t' to ' ' in BAM headers Commit: b370a9cbaea3781d21c3d618cfa5521bdc5bea73 https://github.com/galaxyproject/galaxy/commit/b370a9cbaea3781d21c3d618cfa5… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-10 (Mon, 10 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- travis test fix Commit: ade8844d11aa90a1ccda20545d6283b5635befb5 https://github.com/galaxyproject/galaxy/commit/ade8844d11aa90a1ccda20545d62… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #4279 from ashvark/preview_bam Display preview feature for Bam datatype Compare: https://github.com/galaxyproject/galaxy/compare/14360d6737fb...ade8844d11aa

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[galaxyproject/usegalaxy-playbook] f0726c: drop ismb and gcc from carousel
by GitHub 02 Aug '17

02 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f0726c237e5c660b3f893111e0ef8e4768b9ebc4 https://github.com/galaxyproject/usegalaxy-playbook/commit/f0726c237e5c660b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- drop ismb and gcc from carousel

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