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

[galaxyproject/galaxy] cc4cd5: Fix RStudio login
by GitHub 13 Jan '17

13 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: cc4cd55c1df0fd3ae78bdbff99ad70c2ed723def https://github.com/galaxyproject/galaxy/commit/cc4cd55c1df0fd3ae78bdbff99ad… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Fix RStudio login Thanks @shiltemann for reporting this Commit: c94ccb3f28cdf3acbfe863b386c5dcb58752fe50 https://github.com/galaxyproject/galaxy/commit/c94ccb3f28cdf3acbfe863b386c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Merge pull request #3414 from erasche/fix-rstudio-login [16.10] Fix RStudio login Compare: https://github.com/galaxyproject/galaxy/compare/2d69909218b2...c94ccb3f28cd

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[galaxyproject/galaxy] f9b9eb: Expose anyway if the user is an admin user
by GitHub 13 Jan '17

13 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f9b9ebdd38cf2ee1634bf7daab171a25a8cec953 https://github.com/galaxyproject/galaxy/commit/f9b9ebdd38cf2ee1634bf7daab17… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Expose anyway if the user is an admin user Commit: 7c02ed7a9d1ab2c5101fbc4753ae7ee35d770c14 https://github.com/galaxyproject/galaxy/commit/7c02ed7a9d1ab2c5101fbc4753ae… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M templates/webapps/galaxy/history/share.mako Log Message: ----------- Mirror change in #3250 Fixes #3372 Commit: 6fc538837bc541ea9ad46fefc3e54ca676526bc9 https://github.com/galaxyproject/galaxy/commit/6fc538837bc541ea9ad46fefc3e5… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M templates/webapps/galaxy/history/share.mako Log Message: ----------- Remove extraneous tag Commit: ec425007b11fd871b473a488e5321bb4450bccbf https://github.com/galaxyproject/galaxy/commit/ec425007b11fd871b473a488e532… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako Log Message: ----------- Merge pull request #3417 from erasche/fix-3372 Fix accidental email exposure Compare: https://github.com/galaxyproject/galaxy/compare/4946313fc9dc...ec425007b11f

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[galaxyproject/galaxy] 890107: Reversion of ui-misc messagebox changes.
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 890107334d25b80ee1fc02d00df011f2e7e9d88a https://github.com/galaxyproject/galaxy/commit/890107334d25b80ee1fc02d00df0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Reversion of ui-misc messagebox changes. Commit: 2d69909218b287f8085a599e0a2a1214480330c9 https://github.com/galaxyproject/galaxy/commit/2d69909218b287f8085a599e0a2a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Merge pull request #3415 from dannon/revert_uimisc [16.10]Reversion of ui-misc messagebox changes. Compare: https://github.com/galaxyproject/galaxy/compare/45a9d586b6e1...2d69909218b2

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[galaxyproject/galaxy] a5c445: Swap the client's ui-misc.Message to escape by def...
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: a5c445966ef3ea8385493ffd2ca6bf6dce8611aa https://github.com/galaxyproject/galaxy/commit/a5c445966ef3ea8385493ffd2ca6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js A static/maps/libs/showdown.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/libs/showdown.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Swap the client's ui-misc.Message to escape by default. Commit: e1083132b89f854e2ec824f97f187e925ba0abe6 https://github.com/galaxyproject/galaxy/commit/e1083132b89f854e2ec824f97f18… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Add UnescapedMessage, for when we actually need to display a message with html contents. Any users of this must escape contents on their own. Commit: 3060da4ee53e44c0814eebe2c468f2d3dc352233 https://github.com/galaxyproject/galaxy/commit/3060da4ee53e44c0814eebe2c468… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Export UnescapedMessage from ui-misc. Commit: 45a9d586b6e1db89bf0813aa93af5b3bbaf72efc https://github.com/galaxyproject/galaxy/commit/45a9d586b6e1db89bf0813aa93af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Formatting cleanup. Compare: https://github.com/galaxyproject/galaxy/compare/b0ac7daecdda...45a9d586b6e1

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[galaxyproject/galaxy]
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/revert-3399-markdown Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] e74ca2: Revert "Markdown datatype support."
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e74ca27dbfc8c9f6244ba7f786a9460bdf0af753 https://github.com/galaxyproject/galaxy/commit/e74ca27dbfc8c9f6244ba7f786a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py R static/maps/libs/showdown.js.map R static/scripts/libs/showdown.js R templates/webapps/galaxy/dataset/markdown.mako R test/functional/tools/creates_html.xml R test/functional/tools/creates_html_index.html R test/functional/tools/creates_markdown.xml R test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Revert "Markdown datatype support." Commit: 4946313fc9dc27d2bc2e3d0464682d8308b8702c https://github.com/galaxyproject/galaxy/commit/4946313fc9dc27d2bc2e3d046468… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py R static/maps/libs/showdown.js.map R static/scripts/libs/showdown.js R templates/webapps/galaxy/dataset/markdown.mako R test/functional/tools/creates_html.xml R test/functional/tools/creates_html_index.html R test/functional/tools/creates_markdown.xml R test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3408 from galaxyproject/revert-3399-markdown Revert "Markdown datatype support." Compare: https://github.com/galaxyproject/galaxy/compare/7bb8376490a2...4946313fc9dc

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[galaxyproject/galaxy] a60b7d: fix typo
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a60b7da85e2b9ef83aa86a0593dd5b810802ddf3 https://github.com/galaxyproject/galaxy/commit/a60b7da85e2b9ef83aa86a0593dd… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- fix typo Commit: 7bb8376490a251573252177ab4112caba64b4684 https://github.com/galaxyproject/galaxy/commit/7bb8376490a251573252177ab411… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Merge pull request #3409 from manabuishii/patch-4 fix typo Compare: https://github.com/galaxyproject/galaxy/compare/a87feb11ff61...7bb8376490a2

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[galaxyproject/galaxy] e74ca2: Revert "Markdown datatype support."
by GitHub 11 Jan '17

11 Jan '17

Branch: refs/heads/revert-3399-markdown Home: https://github.com/galaxyproject/galaxy Commit: e74ca27dbfc8c9f6244ba7f786a9460bdf0af753 https://github.com/galaxyproject/galaxy/commit/e74ca27dbfc8c9f6244ba7f786a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py R static/maps/libs/showdown.js.map R static/scripts/libs/showdown.js R templates/webapps/galaxy/dataset/markdown.mako R test/functional/tools/creates_html.xml R test/functional/tools/creates_html_index.html R test/functional/tools/creates_markdown.xml R test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Revert "Markdown datatype support."

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[galaxyproject/galaxy] 5ab4ae: Changes for Fastq Compression.
by GitHub 11 Jan '17

11 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ab4ae4f2f630ea12c8b4e82e90cd8dca2758a6f https://github.com/galaxyproject/galaxy/commit/5ab4ae4f2f630ea12c8b4e82e90c… Author: ashok <ashok(a)localhost.localdomain> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Changes for Fastq Compression. Commit: 7597da61e5de1796f0cf4ce2f6ea577cb390f311 https://github.com/galaxyproject/galaxy/commit/7597da61e5de1796f0cf4ce2f6ea… Author: ashok <ashok(a)localhost.localdomain> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- Updated sequence.py and datatypes_conf.xml Commit: aabfa4283d396ba01ea42b47ab0b8601122096bd https://github.com/galaxyproject/galaxy/commit/aabfa4283d396ba01ea42b47ab0b… Author: ashok <ashvark(a)gmail.com> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py M tools/data_source/upload.py Log Message: ----------- Changes to keep the compressed fastq file as it is with out decompressing. Commit: 7d4840ce6b46a2b51f0d5332d72e7b4d956ac808 https://github.com/galaxyproject/galaxy/commit/7d4840ce6b46a2b51f0d5332d72e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M tools/data_source/upload.py Log Message: ----------- For fastq.gz support inherit from Fastq and Binary and enhance FastQ format to be gzip aware. Commit: 10f1bb5459c4d27ca9142c0f4da1c8502ac9f1b2 https://github.com/galaxyproject/galaxy/commit/10f1bb5459c4d27ca9142c0f4da1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py A test-data/1.fastqsanger.gz A test/functional/tools/compressed_fastq_conversion.xml A test/functional/tools/compressed_fastq_no_conversion.xml Log Message: ----------- Create a BaseFastq class and add test tools Having a BaseFastq class allows Fastq and FastqGz classes to inherit from BaseFastq. FastqGz is therfor not a Fastq datatype and goes through the converter. Also add 2 tools to demonstrate that compressed fastq will be converted to uncompressed fastq if the tool specifies `format="fastq"`, while `format="fastq.gz"` leaves files compressed. The tool test can be run with: ``` planemo test --galaxy_root . test/functional/tools/compressed_fastq_no_conversion.xml planemo test --galaxy_root . test/functional/tools/compressed_fastq_conversion.xml ``` Note that fastq conversion appears to required a galaxy user session, and planemo testing fails. Interactive testing with `planemo serve` is not affected and works fine. Commit: b44a977e649e3c6ac7cfc0bc519c242139296789 https://github.com/galaxyproject/galaxy/commit/b44a977e649e3c6ac7cfc0bc519c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml M lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml M lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml M lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml M lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml Log Message: ----------- Quote paths in converters Commit: bcf08f630d40b45b852db56e4a59c362c3cfc2bf https://github.com/galaxyproject/galaxy/commit/bcf08f630d40b45b852db56e4a59… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Ensure closing of open files Commit: 304c05f3a3a99a9d450c06145bf3985f72f8b7db https://github.com/galaxyproject/galaxy/commit/304c05f3a3a99a9d450c06145bf3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml M lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml M lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml M lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml Log Message: ----------- Remove deprecated page attribute Commit: 99a037d5b92828cbef097ae8434e1d172df3c888 https://github.com/galaxyproject/galaxy/commit/99a037d5b92828cbef097ae8434e… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml M lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml M lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml M lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A test-data/1.fastqsanger.bz2 A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml R test/functional/tools/compressed_fastq_conversion.xml R test/functional/tools/compressed_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml Log Message: ----------- add fastq(*).bz2 datatypes and converters Commit: 833f2c3dbef2469fe7437e8939e329ddff8d2793 https://github.com/galaxyproject/galaxy/commit/833f2c3dbef2469fe7437e8939e3… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml M lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml M lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml M lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A test-data/1.fastqsanger.bz2 A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml R test/functional/tools/compressed_fastq_conversion.xml R test/functional/tools/compressed_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml Log Message: ----------- Merge pull request #1 from abretaud/bz2 Add fastq(*).bz2 datatypes and converters Commit: 500ed949e66cb0ddec757022cae8be230722d755 https://github.com/galaxyproject/galaxy/commit/500ed949e66cb0ddec757022cae8… Author: Anthony Bretaudeau <abretaud(a)irisa.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Fix indentation and import (#2) * fix indentation and import * import fix * refix indentation * better looking imports Commit: b327523c3011c81e164f12833ff010eb411d963e https://github.com/galaxyproject/galaxy/commit/b327523c3011c81e164f12833ff0… Author: Anthony Bretaudeau <abretaud(a)irisa.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- wrong import name (#3) Commit: 7d8bbd599a2528a3e0e9264d64d0da3e494b5016 https://github.com/galaxyproject/galaxy/commit/7d8bbd599a2528a3e0e9264d64d0… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- python lint Commit: 43abc55284fd4a1d7ea62535797d29f9977ef0af https://github.com/galaxyproject/galaxy/commit/43abc55284fd4a1d7ea62535797d… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- python lint Commit: 296889d0dfa767c3649c6331a911ba0fd904f9fd https://github.com/galaxyproject/galaxy/commit/296889d0dfa767c3649c6331a911… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-11-25 (Fri, 25 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- lint fix Commit: a87feb11ff61dc0a8ea2657c8afe99cd115d1eda https://github.com/galaxyproject/galaxy/commit/a87feb11ff61dc0a8ea2657c8afe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A test-data/1.fastqsanger.bz2 A test-data/1.fastqsanger.gz A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml Log Message: ----------- Merge pull request #3145 from mvdbeek/fastqgz Support for gzipped fastq formats Compare: https://github.com/galaxyproject/galaxy/compare/34458725b826...a87feb11ff61

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[galaxyproject/galaxy] 06cc5f: Fix implicit conversion for sessionless tool API c...
by GitHub 11 Jan '17

11 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 06cc5f58288fbd6e3762a91fdd8e76b715f7c4e6 https://github.com/galaxyproject/galaxy/commit/06cc5f58288fbd6e3762a91fdd8e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Fix implicit conversion for sessionless tool API calls. Also fixes it for backgrounded workflow invocations (fixes #3268 reported by @guerler). Includes a new test tool w/test definition that exercises this functionality. This tool fails without these changes. Commit: b6e9f4a6eefb53d2f3b8b415b80e1a674bd7cc8d https://github.com/galaxyproject/galaxy/commit/b6e9f4a6eefb53d2f3b8b415b80e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix workflow extraction of dataset/collections name. It works fine if multiple names are chosen, but if only one input is selected and named it doesn't work. This is a temporary workaround until that page is replaced by API calls with superior typing. Fixes #3247 reported by @peterjc. Commit: 41f5ff48ed848f4fe111f78c8f364e32abdfe405 https://github.com/galaxyproject/galaxy/commit/41f5ff48ed848f4fe111f78c8f36… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3375 from jmchilton/fix_3268 [16.10] Fix implicit conversion for sessionless tool API calls. Commit: 63e70f4f2f47f5b952bb7817e93b0e61c8614dd7 https://github.com/galaxyproject/galaxy/commit/63e70f4f2f47f5b952bb7817e93b… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #3376 from jmchilton/fix_3247 [16.10] Fix workflow extraction of dataset/collections name. Commit: 79752b5b4a0e80a6cd4b02aed8cfd93d8d61208a https://github.com/galaxyproject/galaxy/commit/79752b5b4a0e80a6cd4b02aed8cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Do not allow recursive replacements in PJA. May result in infinite loops in workflow scheduling threads. Commit: 24b250ab3369489b91361c22bdf51b1729861e85 https://github.com/galaxyproject/galaxy/commit/24b250ab3369489b91361c22bdf5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #3397 from jmchilton/backport_3395 [16.10] Backport #3395 Commit: 2d991bba073a9e1f40b18f6c927e4adf6ca1ddb9 https://github.com/galaxyproject/galaxy/commit/2d991bba073a9e1f40b18f6c927e… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Escapes some variables Commit: 535dd7a5f54617b12684eaa179066b4877965dd2 https://github.com/galaxyproject/galaxy/commit/535dd7a5f54617b12684eaa17906… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Merge pull request #3404 from dannon/backport_viz_escape [16.10] Backport of visualization hda.name escapes Commit: d49e014a63641db37814ab0b31b7aa4d1eded786 https://github.com/galaxyproject/galaxy/commit/d49e014a63641db37814ab0b31b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- The /user/logout endpoint is now used for both remote and internal users to handle logout logic, and should be accessible here. Commit: b0ac7daecdda4001f6bcd7d70a15bb30375216e5 https://github.com/galaxyproject/galaxy/commit/b0ac7daecdda4001f6bcd7d70a15… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #3405 from dannon/remoteuser_logout_fix [16.10] Remoteuser Logout Fix. Commit: be530a849428393ec2b16f5b0786cbe4fba148cd https://github.com/galaxyproject/galaxy/commit/be530a849428393ec2b16f5b0786… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into dev Commit: 34458725b826fb9cd8da2d245c094abd5041345c https://github.com/galaxyproject/galaxy/commit/34458725b826fb9cd8da2d245c09… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3406 from dannon/dev Merges 16.10 into dev Compare: https://github.com/galaxyproject/galaxy/compare/8041525223b2...34458725b826

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