Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e8a1280f78e1fa19e2173f922f2221ea28279964 https://github.com/galaxyproject/galaxy/commit/e8a1280f78e1fa19e2173f922f222... Author: John Chilton <jmchilton@gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md Log Message: ----------- [17.09] Deployer doc fixes. Commit: 42c572f34469ec39a55588504a97f1466c59f332 https://github.com/galaxyproject/galaxy/commit/42c572f34469ec39a55588504a97f... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md Log Message: ----------- Merge pull request #5147 from jmchilton/1709_docs_fixes [17.09] Small deployer doc fixes. Commit: 710177f3983d5e66b11c329f699079f67667329c https://github.com/galaxyproject/galaxy/commit/710177f3983d5e66b11c329f69907... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M test/api/test_tools.py Log Message: ----------- Add API tests for history uploads from URL Commit: a1f399c451715424dcd8d1bc9d9ec804e44de24d https://github.com/galaxyproject/galaxy/commit/a1f399c451715424dcd8d1bc9d9ec... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Read in stderr form galaxy.json before checking whether stderr and exit code combination should result in a failed job. This should fix https://github.com/galaxyproject/galaxy/issues/5214. Commit: 3d2adcd1f310b94d0d6f6e37e71d1ee74da2fb3d https://github.com/galaxyproject/galaxy/commit/3d2adcd1f310b94d0d6f6e37e71d1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Restrict reading tool provided metadata to tools that actually provide metadata Commit: 62a3ff3562c5b9c534794c2d0bb6320de7747135 https://github.com/galaxyproject/galaxy/commit/62a3ff3562c5b9c534794c2d0bb63... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- Do not assert dataset state in test_gzipped_html_content_blocked_by_default test Commit: 9ee2a7d4577a715137edcf33fd2b0a474a7a8b8d https://github.com/galaxyproject/galaxy/commit/9ee2a7d4577a715137edcf33fd2b0... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Adjust stderr collection to (Legacy-)ToolProvidedMetadata Commit: b39772011a717dc7c70f1e05dd581b427e33a521 https://github.com/galaxyproject/galaxy/commit/b39772011a717dc7c70f1e05dd581... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M test/base/populators.py Log Message: ----------- Optionally allow dataset populators to fail Commit: 121285b40be5d7233af33b40045a9c2ffb5a9c46 https://github.com/galaxyproject/galaxy/commit/121285b40be5d7233af33b40045a9... Author: John Chilton <jmchilton@gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M tools/data_source/upload.py Log Message: ----------- Let ToolProvidedMetadata interface more directly decide if it has failed outputs. I like this better for three reasons: - Since usually it is scripts producing this JSON - we have the most control at that point for determining the failure and we don't have to deal with an artificial dependency between the tool's stdio and the output. - At some point we could potentially allow some datasets to be ok now even though the job fails. - It is a cleaner interface at the Python level between job finish and output collection IMO (no need for isinstance checking). Commit: d52802d7962c3006b7fe91f43a9d21721187f27c https://github.com/galaxyproject/galaxy/commit/d52802d7962c3006b7fe91f43a9d2... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #6 from jmchilton/fail_if_galaxy_json_tools_write_to_stderr Let ToolProvidedMetadata interface more directly decide if it has failed outputs. Commit: 3f6c45578e2c4e99fa725054c829e03a9c409a1b https://github.com/galaxyproject/galaxy/commit/3f6c45578e2c4e99fa725054c829e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix dataset spelling (thx @nsoranzo) Commit: 44635eae1dc1aeb511f3cf9c6006aff4219de841 https://github.com/galaxyproject/galaxy/commit/44635eae1dc1aeb511f3cf9c6006a... Author: John Chilton <jmchilton@gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5217 from mvdbeek/fail_if_galaxy_json_tools_write_to_stderr [17.09] Fail job if tools that use galaxy.json write to stderr Commit: 90ba35a9a49f583a1fe2a173c1239be86d71125a https://github.com/galaxyproject/galaxy/commit/90ba35a9a49f583a1fe2a173c1239... Author: John Chilton <jmchilton@gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools_upload.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_17.09' into merge_1709 Commit: 6d3eadedbd7093fc19553d7812152293960f3f14 https://github.com/galaxyproject/galaxy/commit/6d3eadedbd7093fc19553d7812152... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools_upload.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5227 from jmchilton/merge_1709 Merge 17.09. Compare: https://github.com/galaxyproject/galaxy/compare/717b5bbce9c5...6d3eadedbd70