Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dfccd902b00426c79670e77ef11696f381f5e10d https://github.com/galaxyproject/galaxy/commit/dfccd902b00426c79670e77ef1169... Author: John Chilton jmchilton@gmail.com Date: 2016-08-04 (Thu, 04 Aug 2016)

Changed paths: M lib/galaxy_ext/metadata/set_metadata.py

Log Message: ----------- Fix setting metadata in galaxy.json for working directory isolation change.

This has been broken since 16.04 I guess? Maybe retry internally means it hasn't been an issue?

Commit: af6bd40a57608464e3e70226c46490681d213446 https://github.com/galaxyproject/galaxy/commit/af6bd40a57608464e3e70226c4649... Author: John Chilton jmchilton@gmail.com Date: 2016-08-04 (Thu, 04 Aug 2016)

Changed paths: M lib/galaxy/tools/parameters/output_collect.py

Log Message: ----------- Fix setting dbkey in galaxy.json for discovered primary datasets.

Based on the change - I guess this must have been broken a long time ago - so maybe it isn't used? A subsequent change will add a test though - so hopefully there will be no regressions of this again.

Commit: e72201d2041a80db0042af9493b1f2f1512d68f7 https://github.com/galaxyproject/galaxy/commit/e72201d2041a80db0042af9493b1f... Author: John Chilton jmchilton@gmail.com Date: 2016-08-04 (Thu, 04 Aug 2016)

Changed paths: M lib/galaxy/jobs/__init__.py M test/base/interactor.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_1.xml

Log Message: ----------- Improvements for metadata specification w/galaxy.json of explicit outputs.

I call explicit outputs galaxy.json entries of type="dataset" (as opposed to type="new_primary_dataset" - which I call discovered datasets). Previously galaxy.json could set the name and extension of these datasets. I've added a test case to verify this and a small tweak to the tool test framework to allow easy testing of such metadata setting.

In order to bring explicit output metadata setting closer to parity with discovered dataset metadata setting, I've added the ability to define 'dbkey' and 'info' entries in galaxy.json for these outputs.

Commit: 1fab4dfaff3ebbb0f1c80c7b51f44125272b6cb9 https://github.com/galaxyproject/galaxy/commit/1fab4dfaff3ebbb0f1c80c7b51f44... Author: John Chilton jmchilton@gmail.com Date: 2016-08-04 (Thu, 04 Aug 2016)

Changed paths: M test/base/interactor.py M test/functional/tools/tool_provided_metadata_1.xml

Log Message: ----------- Add hack to test sleeping when verifying metadata.

Seems like a race condition but I can't determine why there would be one here - this check should help determine if it is a race condition or something else.

Commit: 76e84eb5e00e78e9e49667d39b2f3d91352f3d5a https://github.com/galaxyproject/galaxy/commit/76e84eb5e00e78e9e49667d39b2f3... Author: John Chilton jmchilton@gmail.com Date: 2016-08-04 (Thu, 04 Aug 2016)

Changed paths: M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_2.xml

Log Message: ----------- Add tool test for discovered dataset metadata from galaxy.json.

Commit: 41701aa6fe696e2ef1b26dec261f416686d02e20 https://github.com/galaxyproject/galaxy/commit/41701aa6fe696e2ef1b26dec261f4... Author: John Chilton jmchilton@gmail.com Date: 2016-08-04 (Thu, 04 Aug 2016)

Changed paths: M test/base/interactor.py

Log Message: ----------- Improved error message when testing metadata in tool tests.

Commit: 56bb42ad2536732c195c218c1b89cf174cd02b78 https://github.com/galaxyproject/galaxy/commit/56bb42ad2536732c195c218c1b89c... Author: John Chilton jmchilton@gmail.com Date: 2016-08-04 (Thu, 04 Aug 2016)

Changed paths: M lib/galaxy/tools/parser/xml.py M test/functional/tools/tool_provided_metadata_2.xml

Log Message: ----------- Fix allow tool to just test discovered datasets.

Previously some sort of test on the base file the primary datasets were keyed on was required.

Commit: 9ae333987b2cd713526ae68800ade5e0a73b1e08 https://github.com/galaxyproject/galaxy/commit/9ae333987b2cd713526ae68800ade... Author: John Chilton jmchilton@gmail.com Date: 2016-08-04 (Thu, 04 Aug 2016)

Changed paths: M test/base/interactor.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_3.xml

Log Message: ----------- Test tool demo-ing discovered dataset datatype metadata w/galaxy.json.

Also update the metadata test comparison to support non-textual values (e.g. floating point and integer metadata fields).

Commit: 1e8dd73b6def69aa8533f087e22d99d3423f94b3 https://github.com/galaxyproject/galaxy/commit/1e8dd73b6def69aa8533f087e22d9... Author: John Chilton jmchilton@gmail.com Date: 2016-08-16 (Tue, 16 Aug 2016)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Rework small for loop per @mvdbeek's suggestion...

... see https://github.com/galaxyproject/galaxy/pull/2697#discussion_r74939815 for context.

Commit: 5cc3613ff55537df7dbcfe7d6ba7ef4a679be935 https://github.com/galaxyproject/galaxy/commit/5cc3613ff55537df7dbcfe7d6ba7e... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-08-17 (Wed, 17 Aug 2016)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy_ext/metadata/set_metadata.py M test/base/interactor.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_1.xml A test/functional/tools/tool_provided_metadata_2.xml A test/functional/tools/tool_provided_metadata_3.xml

Log Message: ----------- Merge pull request #2697 from jmchilton/metadata_fixing

Fixes and improvements for galaxy.json.

Compare: https://github.com/galaxyproject/galaxy/compare/0210fb31b676...5cc3613ff555