Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 9c81089ed1c9d5c434ecb991be8fd542bbe3c75e https://github.com/galaxyproject/galaxy/commit/9c81089ed1c9d5c434ecb991be8fd... Author: Luca Pireddu <pireddu@crs4.it> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Catch IOErrors when the k8s runner tries to collect job logs This commit should fix cases where successful job can't be marked as done by Galaxy because the logs have gone missing. Commit: ac7c2d0473d09e8a3b4b39734527a383835478ab https://github.com/galaxyproject/galaxy/commit/ac7c2d0473d09e8a3b4b39734527a... Author: Luca Pireddu <pireddu@crs4.it> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Print full job object to the DEBUG log if k8s runner finds it in an unrecognized state Commit: cd6c4d4db8bcb72ae931797c216b9829313850cf https://github.com/galaxyproject/galaxy/commit/cd6c4d4db8bcb72ae931797c216b9... Author: Luca Pireddu <pireddu@crs4.it> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Add job id to missing k8s log text Commit: c434c271598d95130439ac86c8b9060f42455e9a https://github.com/galaxyproject/galaxy/commit/c434c271598d95130439ac86c8b90... Author: Luca Pireddu <pireddu@gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Improve k8s runner debug log message Commit: e235343f7674a5b74a707a693e94b80633d1ca2b https://github.com/galaxyproject/galaxy/commit/e235343f7674a5b74a707a693e94b... Author: Luca Pireddu <pireddu@crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Push k8s log IOError handling into `__produce_log_file` Handling the IOError within the function should result in other call sites within the kubernets.py module properly setting the job state even if the job directory has been removed. Commit: cf02c9812759505d61f284d6d33ee9ce2dc994e8 https://github.com/galaxyproject/galaxy/commit/cf02c9812759505d61f284d6d33ee... Author: Luca Pireddu <pireddu@crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Prefer `with open` syntax within kubernetes.py Commit: c13da94fd75d4b0010e4e3284649366c213a205d https://github.com/galaxyproject/galaxy/commit/c13da94fd75d4b0010e4e32846493... Author: Luca Pireddu <pireddu@crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Fix inverted log message arguments Thanks @pcm32! Commit: 1482cacee51a9fd91f65d54704c7bc36120f3a34 https://github.com/galaxyproject/galaxy/commit/1482cacee51a9fd91f65d54704c7b... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #6886 from ilveroluca/fix/k8s_error_handling Improve k8s job error handling Commit: 49d9409f007dfe6288de4d6a2c0e15a4b45af022 https://github.com/galaxyproject/galaxy/commit/49d9409f007dfe6288de4d6a2c0e1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Bam index is only available for coordinate sorted bam files Commit: 4c7ba6f0fe4a99c1324f70785d27b655ac8b5538 https://github.com/galaxyproject/galaxy/commit/4c7ba6f0fe4a99c1324f70785d27b... Author: John Chilton <jmchilton@gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #6946 from mvdbeek/bam_index_for_coordinate_sorted_only [18.09] Make Bam index only available for coordinate sorted bam files Commit: 717605af96bcb5fb9a5193295c9941d0d4632a93 https://github.com/galaxyproject/galaxy/commit/717605af96bcb5fb9a5193295c994... Author: M Bernt <m.bernt@ufz.de> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M test/functional/tools/output_filter.xml Log Message: ----------- added test Commit: 20cecd2a68527015d8b98a430367b8fcdf9a364d https://github.com/galaxyproject/galaxy/commit/20cecd2a68527015d8b98a430367b... Author: M Bernt <m.bernt@ufz.de> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- galaxy test needs to count data sets and collection outputs Commit: 30aaa296dd50471001323cc9895560219a33ce71 https://github.com/galaxyproject/galaxy/commit/30aaa296dd50471001323cc989556... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/1.qname_sorted.bam Log Message: ----------- Fix sniffing of readname sorted BAM files This fixes https://github.com/galaxyproject/galaxy/issues/6949. The problem is that `super` would fall back to the BamInputSorted sniffer, which prevents sniffing. Includes a test file for the new datatype upload testing framework. Commit: 4e098c5d5291209f4760010ff8bebd919ba19479 https://github.com/galaxyproject/galaxy/commit/4e098c5d5291209f4760010ff8beb... Author: M Bernt <m.bernt@ufz.de> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- tests: add parameter to output_filter Commit: 03eac8315d64e05df74f1f6fb286cff29e75f6b2 https://github.com/galaxyproject/galaxy/commit/03eac8315d64e05df74f1f6fb286c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix for workflow parameter collection in workflows view. Commit: 18644f91cf59265c1473d806845baffbf7a8132f https://github.com/galaxyproject/galaxy/commit/18644f91cf59265c1473d806845ba... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Avoid using var; let. Commit: 69b447169fb96048ea492a1d99d653585571c15b https://github.com/galaxyproject/galaxy/commit/69b447169fb96048ea492a1d99d65... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M lib/galaxy/datatypes/data.py Log Message: ----------- Allow deferring 'to_ext' extension to the server, implement for collections. Commit: 6b5f0a2ad1f21bbda92b06ff2700c961c34e84ea https://github.com/galaxyproject/galaxy/commit/6b5f0a2ad1f21bbda92b06ff2700c... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Allow upload for ``rdata.sce`` format Commit: 6da5157181a085d183c099645216893fe512a1f9 https://github.com/galaxyproject/galaxy/commit/6da5157181a085d183c0996452168... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6963 from nsoranzo/release_18.05_allow_rdata.sce_upload [18.05] Allow upload for ``rdata.sce`` format Commit: 357e2f39c77026c81c56ed30ffae9f1905d2d82a https://github.com/galaxyproject/galaxy/commit/357e2f39c77026c81c56ed30ffae9... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: 3d91738a697ff57047bc3cd505d5afc75de38f45 https://github.com/galaxyproject/galaxy/commit/3d91738a697ff57047bc3cd505d5a... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2018-11-04 (Sun, 04 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #6955 from dannon/wf_param_fix [18.09] Fix for workflow parameter collection in workflows view. Commit: 3be8d66d71bcdb3eccde2d1a37731442ed1aa63a https://github.com/galaxyproject/galaxy/commit/3be8d66d71bcdb3eccde2d1a37731... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py Log Message: ----------- Remove unncecessary implementations of display_data These were not updated to use `_download_filename`, and so this fixes the download name for collection elements to include the element identifier. Note that the Data class should handle composite data just fine. Commit: f8b160535c5f9363e85c6c1d041b69ce5c3e9cc2 https://github.com/galaxyproject/galaxy/commit/f8b160535c5f9363e85c6c1d041b6... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Some minor fixes for the blast datatype The signature for Data.display_data wasn't quite correct, and the description of display_data was also a little misleading. Commit: 9b42032098edaae076f5f88c48f135d8035a9ad6 https://github.com/galaxyproject/galaxy/commit/9b42032098edaae076f5f88c48f13... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fill in default state for test_optional_workflow_output Commit: 2deb302ae7be93924a8bdcaff17a43caa0b5e3b4 https://github.com/galaxyproject/galaxy/commit/2deb302ae7be93924a8bdcaff17a4... Author: Nicola Soranzo <nicola.soranzo@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/api/test_workflows.py M test/functional/tools/output_filter.xml Log Message: ----------- Merge pull request #6951 from bernt-matthias/topic/test-colouts-backport [18.09] Backport: tests need to count data sets and collections Commit: 61bda3d11a1d608ac8e1a731faf144ff989affc9 https://github.com/galaxyproject/galaxy/commit/61bda3d11a1d608ac8e1a731faf14... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py Log Message: ----------- Merge pull request #6960 from dannon/collection_ext_dl [18.09] Allow deferring 'to_ext' extension to the server Commit: dbf5ef33604aae1a7294abf7bd5303504e8a4d2a https://github.com/galaxyproject/galaxy/commit/dbf5ef33604aae1a7294abf7bd530... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Merge pull request #6974 from istevenshen/patch-2 Update locale.js Commit: fefa132cd741779a9c6a4bd03c44f473036a462a https://github.com/galaxyproject/galaxy/commit/fefa132cd741779a9c6a4bd03c44f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py A lib/galaxy/datatypes/test/1.qname_sorted.bam M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/tools/verify/interactor.py M test/api/test_workflows.py M test/functional/tools/output_filter.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' Compare: https://github.com/galaxyproject/galaxy/compare/315ca74305f1...fefa132cd741 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.