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
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
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
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."
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
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:
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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:
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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:
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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:
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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:
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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:
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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:
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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:
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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:
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Merge pull request #3406 from dannon/dev
Merges 16.10 into dev
Compare: https://github.com/galaxyproject/galaxy/compare/8041525223b2...34458725b826