- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] a2fcc8: Update Main
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a2fcc8d915037f895985c1553eee651b51eb0198 https://github.com/galaxyproject/usegalaxy-playbook/commit/a2fcc8d915037f89… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main **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.

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[galaxyproject/galaxy] dc9128: Fix traceback when starting under Python3 with ``g...
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: dc9128213fbf4fd1d479fc94ace5b2416a5face5 https://github.com/galaxyproject/galaxy/commit/dc9128213fbf4fd1d479fc94ace5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Fix traceback when starting under Python3 with ``galaxy.ini`` Update `paste` requirement to 3.0.4 to include: https://github.com/cdent/paste/pull/14 to fix the following traceback: ``` Starting server in PID 6792. Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1055, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke exit_code = runner.run(args) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 226, in run result = self.command() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 676, in command serve() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 653, in serve server(app) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper **context.local_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call val = callable(*args, **kw) File "/opt/galaxy/.venv3/lib/python3.5/site-packages/paste/httpserver.py", line 1358, in server_runner for name, value in kwargs.items(): RuntimeError: dictionary changed size during iteration galaxy.app DEBUG 2018-11-05 13:38:00,059 Shutting down ``` Commit: 6487d52d513b6351bd3e3e44e74e79c8f949919a https://github.com/galaxyproject/galaxy/commit/6487d52d513b6351bd3e3e44e74e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6978 from nsoranzo/release_18.09_paste [18.09] Fix traceback when starting under Python3 with ``galaxy.ini`` Compare: https://github.com/galaxyproject/galaxy/compare/9029b95e6979...6487d52d513b **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.

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[galaxyproject/usegalaxy-playbook] 558335: Disable legacy late eager object store assignment ...
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5583358d1318a5cf9418cdb2a05962e3e3bb7e49 https://github.com/galaxyproject/usegalaxy-playbook/commit/5583358d1318a5cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Disable legacy late eager object store assignment on Main since bugs should be fixed **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.

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[galaxyproject/galaxy] ccb1e0: In enqueue, always set an object_store_id if one i...
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: ccb1e08000759184b2ebc4d26b8e88ebe9b4c9c4 https://github.com/galaxyproject/galaxy/commit/ccb1e08000759184b2ebc4d26b8e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- In enqueue, always set an object_store_id if one isn't set. Tool actions other than the regular tool action (such as the upload ones) might not set an object store id even in the legacy mode. Commit: 9029b95e69795992ecf67f3ffdfa6384b52e1f3a https://github.com/galaxyproject/galaxy/commit/9029b95e69795992ecf67f3ffdfa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #6969 from jmchilton/ensure_better [18.09] In enqueue, always set an object_store_id if one isn't set. Compare: https://github.com/galaxyproject/galaxy/compare/dbf5ef33604a...9029b95e6979 **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.

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[galaxyproject/galaxy] 9c8108: Catch IOErrors when the k8s runner tries to collec...
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 9c81089ed1c9d5c434ecb991be8fd542bbe3c75e https://github.com/galaxyproject/galaxy/commit/9c81089ed1c9d5c434ecb991be8f… Author: Luca Pireddu <pireddu(a)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/ac7c2d0473d09e8a3b4b39734527… Author: Luca Pireddu <pireddu(a)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/cd6c4d4db8bcb72ae931797c216b… Author: Luca Pireddu <pireddu(a)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/c434c271598d95130439ac86c8b9… Author: Luca Pireddu <pireddu(a)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/e235343f7674a5b74a707a693e94… Author: Luca Pireddu <pireddu(a)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/cf02c9812759505d61f284d6d33e… Author: Luca Pireddu <pireddu(a)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/c13da94fd75d4b0010e4e3284649… Author: Luca Pireddu <pireddu(a)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/1482cacee51a9fd91f65d54704c7… Author: Marius van den Beek <m.vandenbeek(a)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/49d9409f007dfe6288de4d6a2c0e… Author: mvdbeek <m.vandenbeek(a)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/4c7ba6f0fe4a99c1324f70785d27… Author: John Chilton <jmchilton(a)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/717605af96bcb5fb9a5193295c99… Author: M Bernt <m.bernt(a)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/20cecd2a68527015d8b98a430367… Author: M Bernt <m.bernt(a)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/30aaa296dd50471001323cc98955… Author: mvdbeek <m.vandenbeek(a)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/4e098c5d5291209f4760010ff8be… Author: M Bernt <m.bernt(a)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/03eac8315d64e05df74f1f6fb286… Author: Dannon Baker <dannon.baker(a)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/18644f91cf59265c1473d806845b… Author: Dannon Baker <dannon.baker(a)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/69b447169fb96048ea492a1d99d6… Author: Dannon Baker <dannon.baker(a)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/6b5f0a2ad1f21bbda92b06ff2700… Author: Nicola Soranzo <nicola.soranzo(a)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/6da5157181a085d183c099645216… Author: Martin Cech <marten(a)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/357e2f39c77026c81c56ed30ffae… Author: Nicola Soranzo <nicola.soranzo(a)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/3d91738a697ff57047bc3cd505d5… Author: Björn Grüning <bjoern(a)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/3be8d66d71bcdb3eccde2d1a3773… Author: mvdbeek <m.vandenbeek(a)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/f8b160535c5f9363e85c6c1d041b… Author: mvdbeek <m.vandenbeek(a)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/9b42032098edaae076f5f88c48f1… Author: mvdbeek <m.vandenbeek(a)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/2deb302ae7be93924a8bdcaff17a… Author: Nicola Soranzo <nicola.soranzo(a)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/61bda3d11a1d608ac8e1a731faf1… Author: Martin Cech <marten(a)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/dbf5ef33604aae1a7294abf7bd53… Author: Dannon Baker <dannon.baker(a)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/fefa132cd741779a9c6a4bd03c44… Author: Dannon Baker <dannon.baker(a)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.

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[galaxyproject/galaxy] 5d3d8f: Update locale.js
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 5d3d8f555901186bcbbd8885bb12da04ebc174a2 https://github.com/galaxyproject/galaxy/commit/5d3d8f555901186bcbbd8885bb12… Author: Steven Shen <ishenweiyan(a)qq.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Update locale.js Commit: dbf5ef33604aae1a7294abf7bd5303504e8a4d2a https://github.com/galaxyproject/galaxy/commit/dbf5ef33604aae1a7294abf7bd53… Author: Dannon Baker <dannon.baker(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/61bda3d11a1d...dbf5ef33604a **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.

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[galaxyproject/galaxy] 5d3d8f: Update locale.js
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 5d3d8f555901186bcbbd8885bb12da04ebc174a2 https://github.com/galaxyproject/galaxy/commit/5d3d8f555901186bcbbd8885bb12… Author: Steven Shen <ishenweiyan(a)qq.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Update locale.js Commit: 315ca74305f10c88c21bfc5b58805c698c0a5737 https://github.com/galaxyproject/galaxy/commit/315ca74305f10c88c21bfc5b5880… Author: Dannon <dannon.baker(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/cea9521b1a01...315ca74305f1 **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.

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[galaxyproject/galaxy] 734c39: added global monitor for window.Galaxy
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 734c39d4f58cfc96c637d9121b88b14398a9c4b2 https://github.com/galaxyproject/galaxy/commit/734c39d4f58cfc96c637d9121b88… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M .gitignore A client/galaxy/jsconfig.json M client/galaxy/scripts/galaxy.js A client/galaxy/scripts/galaxy.monitor.js R client/galaxy/scripts/onload.js A client/galaxy/scripts/onload/index.js A client/galaxy/scripts/onload/loadConfig.js A client/galaxy/scripts/utils/installMonitor.js A client/galaxy/scripts/utils/mock.js A client/galaxy/scripts/utils/serverPath.js M client/webpack.config.js M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- added global monitor for window.Galaxy Commit: 0cdf78956f29abf53e9e2233a6545dc1fba71f5c https://github.com/galaxyproject/galaxy/commit/0cdf78956f29abf53e9e2233a654… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M client/galaxy/scripts/onload/loadConfig.js M client/galaxy/scripts/utils/installMonitor.js Log Message: ----------- Corrected instructions, removed config function that is not used yet. Commit: 712aa6cb8742674777c4bc0ee36df9f361bfbeab https://github.com/galaxyproject/galaxy/commit/712aa6cb8742674777c4bc0ee36d… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M client/galaxy/scripts/utils/installMonitor.js Log Message: ----------- Removed debugger statements Commit: 4c13d204c454203b17194c6174177de642c0a2ae https://github.com/galaxyproject/galaxy/commit/4c13d204c454203b17194c617417… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M client/galaxy/scripts/utils/installMonitor.js Log Message: ----------- Corrected monitor value storage initialization Commit: ef5e01da82e532a819a343457ea31bf0cb16baa7 https://github.com/galaxyproject/galaxy/commit/ef5e01da82e532a819a343457ea3… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- White space awesomeness Commit: 3cf9dd85f4c20801807d0aef74b4628c26ca3f97 https://github.com/galaxyproject/galaxy/commit/3cf9dd85f4c20801807d0aef74b4… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M client/.babelrc M client/galaxy/scripts/polyfills.js M client/package.json M client/yarn.lock Log Message: ----------- Updating babel for proxy support with karma Commit: 04242c75034637f064173eca0c1e2f415343fe93 https://github.com/galaxyproject/galaxy/commit/04242c75034637f064173eca0c1e… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Renamed selenium utility function Commit: 66a7db94053763bfb1cc23ba5df1e537f0177219 https://github.com/galaxyproject/galaxy/commit/66a7db94053763bfb1cc23ba5df1… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M .gitignore M client/.babelrc R client/GruntFile.js A 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static/style/blue/warn_message_icon.png R static/style/blue/warn_small.png R static/style/blue/workflow_circle_drag.png R static/style/blue/workflow_circle_green.png R static/style/blue/workflow_circle_open.png R static/style/shared_images/data_running.gif R static/style/shared_images/error_large.png R static/style/shared_images/error_small.png R static/style/shared_images/info_large.png R static/style/shared_images/info_small.png R static/style/shared_images/ok_large.png R static/style/shared_images/ok_small.png R static/style/shared_images/wait_large.png R static/style/shared_images/wait_small.png R static/style/shared_images/warn_large.png R static/style/shared_images/warn_small.png M static/welcome.html.sample M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako M templates/galaxy_client_app.mako M templates/js-app.mako M templates/legacy/grid_base.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/gie.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/repository/browse_repository.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/rate_repository.mako M templates/webapps/tool_shed/repository/upload.mako M templates/webapps/tool_shed/repository/view_changelog.mako M templates/webapps/tool_shed/repository/view_changeset.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/repository_review/reviews_of_repository.mako M templates/webapps/tool_shed/repository_review/select_previous_review.mako M test/base/driver_util.py M test/base/populators.py A test/integration/test_datatype_upload.py M test/unit/datatypes/test_bam.py M test/unit/datatypes/test_vcf.py Log Message: ----------- Merged dev Commit: 294cfbf6716dbac554da36f0c410276669c1dce9 https://github.com/galaxyproject/galaxy/commit/294cfbf6716dbac554da36f0c410… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M client/webpack.config.js Log Message: ----------- Updated provide monitored proxy for Galaxy references Commit: d7d5e04f9276ba3c1cd9ef2c1a09ede1fc9f5ed0 https://github.com/galaxyproject/galaxy/commit/d7d5e04f9276ba3c1cd9ef2c1a09… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/utils/installMonitor.js Log Message: ----------- Changed toggle to installation toggle instead of logging toggle Commit: 5ffd438ebfef26c55b9b11da2f24abd6c2772b43 https://github.com/galaxyproject/galaxy/commit/5ffd438ebfef26c55b9b11da2f24… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/utils/installMonitor.js Log Message: ----------- Updated install console functions and instructions Commit: 11375a5692fe541e3df257f3ce2e36cd6f39a1f8 https://github.com/galaxyproject/galaxy/commit/11375a5692fe541e3df257f3ce2e… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M .travis.yml M Makefile M client/galaxy/scripts/qunit/test.js A client/galaxy/scripts/sample.test.js A client/galaxy/scripts/unitTestBundle.js M client/galaxy/style/scss/ui.scss R client/karma.config.js A client/karma/karma.config.base.js A client/karma/karma.config.mocha.js A client/karma/karma.config.qunit.js A client/karma/webpack.config.qunit.js A client/karma/webpack.config.unittest.js M client/package.json M client/yarn.lock M config/datatypes_conf.xml.sample M config/migrated_tools_conf.xml.sample M config/shed_tool_conf.xml.sample M doc/source/admin/tool_panel.rst M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/tar_to_directory.xml M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/test/diamond.rma6 M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/util/compression_utils.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/common_util.py M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/tool_sheds.mako M templates/webapps/galaxy/admin/view_display_applications.mako M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into window_monitor Commit: 38e9225aff0997efe3b023cf28ec869faa09d161 https://github.com/galaxyproject/galaxy/commit/38e9225aff0997efe3b023cf28ec… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/jsconfig.json M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/sample.test.js M client/galaxy/scripts/unitTestBundle.js M client/galaxy/scripts/utils/installMonitor.js M client/galaxy/scripts/utils/mock.js Log Message: ----------- Client format Commit: 4405d15fea61b2610045ecfe4a6a1a0922142df8 https://github.com/galaxyproject/galaxy/commit/4405d15fea61b2610045ecfe4a6a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M .gitignore A client/galaxy/jsconfig.json M client/galaxy/scripts/galaxy.js A client/galaxy/scripts/galaxy.monitor.js R client/galaxy/scripts/onload.js A client/galaxy/scripts/onload/index.js A client/galaxy/scripts/onload/loadConfig.js M client/galaxy/scripts/sample.test.js M client/galaxy/scripts/unitTestBundle.js A client/galaxy/scripts/utils/installMonitor.js A client/galaxy/scripts/utils/mock.js A client/galaxy/scripts/utils/serverPath.js M client/webpack.config.js M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge branch 'window_monitor' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e9f269393346...4405d15fea61 **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.

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[galaxyproject/ansible-galaxy] afc7c3: Fix syntax error in sample code (under Requirement...
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: afc7c33953fb4de4ab606997977bb7141150e08b https://github.com/galaxyproject/ansible-galaxy/commit/afc7c33953fb4de4ab60… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M README.md Log Message: ----------- Fix syntax error in sample code (under Requirements) Assignment vs. equality ('=' vs. '=='), see Jinja syntax. Commit: 1043f1c3931e185a2ba2b1ec367560885a1a7586 https://github.com/galaxyproject/ansible-galaxy/commit/1043f1c3931e185a2ba2… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M README.md Log Message: ----------- Merge pull request #40 from ic4f/master Fix syntax error in sample code (under Requirements) Compare: https://github.com/galaxyproject/ansible-galaxy/compare/1eed620a4a1f...1043… **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.

1 0

[galaxyproject/usegalaxy-playbook] 2fe7e5: Test mutable config for DM upgrades
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2fe7e55082bccb39d0d7042d40dd2ee0067be2cc https://github.com/galaxyproject/usegalaxy-playbook/commit/2fe7e55082bccb39… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M env/test/files/galaxy/var/shed_data_manager_conf.xml Log Message: ----------- Test mutable config for DM upgrades Commit: fb1d9545e605f1527537071560f0cccafcba289e https://github.com/galaxyproject/usegalaxy-playbook/commit/fb1d9545e605f152… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M env/common/templates/supervisor/galaxy_handler.j2 M env/test/files/galaxy/galaxy_version.yml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Update Test and increase its handler shutdown timeout. Commit: 86c430efbc9db6a2577f58ca577858b8c71c7e5f https://github.com/galaxyproject/usegalaxy-playbook/commit/86c430efbc9db6a2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml M env/testtoolshed/group_vars/toolshedservers/vars.yml M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/usegalaxy-playbook Commit: 00c9258264550ee6d460bdc2f0d5c849f5bd3118 https://github.com/galaxyproject/usegalaxy-playbook/commit/00c9258264550ee6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Test mutable configs Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/deafd85205f9...… **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.

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[galaxyproject/galaxy] d898b6: Vue rewrite of admin data manager (local data): in...
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d898b672adc6924395bbb8c282999e0183891b5a https://github.com/galaxyproject/galaxy/commit/d898b672adc6924395bbb8c28299… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/Alert.vue A client/galaxy/scripts/components/admin/DataManager/DataManager.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue M client/package.json M client/yarn.lock M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py R templates/webapps/galaxy/data_manager/index.mako M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py Log Message: ----------- Vue rewrite of admin data manager (local data): index page * Added Alert component: Light bootstrap-vue b-alert wrapper. - Hides automatically when given message is empty. - Translates galaxy state keywords into bootstrap ones. * Added vue-router integration: Display (future) Data Manager Jobs and Job components inside router-views. - Added router-view component DataManagerView. * Rewrite (old mako, new json interface, new vue component) - Index page (index.mako, data_managers_list, DataManager) * Added Selenium test for DataManager component (index page) Commit: 747e998d40b82117c21b80e86a347c96ff86353b https://github.com/galaxyproject/galaxy/commit/747e998d40b82117c21b80e86a34… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManager.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue M lib/galaxy/webapps/galaxy/controllers/data_manager.py R templates/webapps/galaxy/data_manager/manage_data_manager.mako M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py Log Message: ----------- Vue rewrite of admin data manager (local data): manager page * Rewrite (old mako, new json interface, new vue component) - Manager page (manage_data_manager.mako, jobs_list, DataManagerJobs) * Added Selenium test for DataManagerJobs component (manager page) Commit: 13b8098259c9fc7a53b2db51a07b530b1d748b76 https://github.com/galaxyproject/galaxy/commit/13b8098259c9fc7a53b2db51a07b… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: A client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue M lib/galaxy/webapps/galaxy/controllers/data_manager.py R templates/webapps/galaxy/data_manager/view_job.mako M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py Log Message: ----------- Vue rewrite of admin data manager (local data): view job page * Rewrite (old mako, new json interface, new vue component) - View job page (view_job.mako, job_info, DataManagerJob) * Added Selenium test for DataManagerJob component (view job page) Commit: 126c432bcf52279aea7ff952e771b0f4eefe012b https://github.com/galaxyproject/galaxy/commit/126c432bcf52279aea7ff952e771… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M .ci/jenkins/api-py3/run_tests.sh M .ci/jenkins/api/run_tests.sh M .ci/jenkins/framework-py3/run_tests.sh M .ci/jenkins/framework/run_tests.sh M .ci/jenkins/main-tools-py3/run_tests.sh M .ci/jenkins/main-tools/run_tests.sh M .ci/jenkins/selenium-py3/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .ci/jenkins/toolshed/run_tests.sh M .gitignore M client/README.md M client/galaxy/docs/bootstrap.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M 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templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/common/repository_actions_menu.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/role/role.mako M templates/webapps/tool_shed/user/username.mako A test-data/safetar_with_symlink.tar A test-data/testdir.tar A test-data/unsafe.tar A test-data/unsafe.zip A test-data/unsafe_relative_symlink.tar M test/api/test_api_batch.py M test/api/test_dataset_collections.py M test/api/test_histories.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/populators.py M test/base/workflow_fixtures.py R test/base/workflows_format_2/README.txt R test/base/workflows_format_2/__init__.py R test/base/workflows_format_2/converter.py R test/base/workflows_format_2/interface.py R test/base/workflows_format_2/main.py M test/functional/tools/disambiguate_cond.xml A test/functional/tools/identifier_in_conditional.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/selenium_tests/test_stock_tours.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py A test/unit/test_compression_util.py M test/unit/test_galaxy_mapping.py A test/unit/test_utils.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge branch 'dev' Commit: 2ef1aeef3c986938a3cd48e42758329e29792860 https://github.com/galaxyproject/galaxy/commit/2ef1aeef3c986938a3cd48e42758… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManager.vue Log Message: ----------- DataManager: delay rendering until server data is ready Commit: 8db26fe522f9cab6d29d3b03f41975b5354bcef3 https://github.com/galaxyproject/galaxy/commit/8db26fe522f9cab6d29d3b03f419… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue Log Message: ----------- DataManagerJobs: delay rendering until server data is ready Commit: d3b43da3f518a8d221f8ba71883ad97a95f610f9 https://github.com/galaxyproject/galaxy/commit/d3b43da3f518a8d221f8ba71883a… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue Log Message: ----------- DataManagerJob: delay rendering until server data is ready Commit: 8b7d203ec8ffe685ff56479d79243536f27d0252 https://github.com/galaxyproject/galaxy/commit/8b7d203ec8ffe685ff56479d7924… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManager.vue Log Message: ----------- DataManager: check for empty server data Commit: 3af83f4254a284e50e3a30ce6ed81dea82b2eabc https://github.com/galaxyproject/galaxy/commit/3af83f4254a284e50e3a30ce6ed8… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M lib/galaxy/webapps/galaxy/controllers/data_manager.py Log Message: ----------- DataManagerJobs: check for empty server data Fix jobs_list redirect in case data manager is non-existent with empty server response containing an error message and status. Commit: 877feae8bacd7104add9b31632843c7d3cbd2a39 https://github.com/galaxyproject/galaxy/commit/877feae8bacd7104add9b3163284… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue M lib/galaxy/webapps/galaxy/controllers/data_manager.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py Log Message: ----------- DataManagerJob: check for empty server data & refactoring * DataManagerJob - Check for empty server data & refactoring - Fix and numerate data-card ids * job_info - Fix error log in job_info. - Fix redirect in case job is non-existent with empty server response containing an error message and status. * Extend DataManagerJob test Commit: 53a505eaef3e8d91689ecfeb3b785928c54a8e42 https://github.com/galaxyproject/galaxy/commit/53a505eaef3e8d91689ecfeb3b78… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManager.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue M lib/galaxy/webapps/galaxy/controllers/data_manager.py R templates/webapps/galaxy/data_manager/manage_data_table.mako M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py Log Message: ----------- Vue rewrite of admin data manager (local data): manage data table * Rewrite (old mako, new json interface, new vue component) - Manage data table page (manage_data_table.mako, tool_data_table_info, DataManagerTable) * Added Selenium test for DataManagerTable component (Manage data table page) Commit: 6d2a755614239149193d87e8cb695c963c17dc71 https://github.com/galaxyproject/galaxy/commit/6d2a755614239149193d87e8cb69… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M client/README.md A 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templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/admin/tool_shed_repository/purge_repository_confirmation.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/admin/tool_shed_repository/view_workflow.mako M templates/message.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako M test/api/test_tools.py A test/base/ssh_util.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml M test/functional/tools/samples_tool_conf.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py M test/unit/test_remote_shell.py Log Message: ----------- Merge branch 'dev' into admin.data.manager.vue.steps Commit: 31b484492260f554020ed8eed1d1a20cd98089ef https://github.com/galaxyproject/galaxy/commit/31b484492260f554020ed8eed1d1… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/data_manager.py Log Message: ----------- Fix linting error by removing unused import markupsafe escape Commit: 8789713b9584c8ee58692b4dc02a282f32484502 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static/style/shared_images/wait_small.png R static/style/shared_images/warn_large.png R static/style/shared_images/warn_small.png M static/welcome.html.sample M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/ind_share_base.mako M templates/js-app.mako M templates/legacy/grid_base.mako M templates/message.mako M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/tool_sheds.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/share.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/visualization/gie.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/repository/browse_repository.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/rate_repository.mako M templates/webapps/tool_shed/repository/upload.mako M templates/webapps/tool_shed/repository/view_changelog.mako M templates/webapps/tool_shed/repository/view_changeset.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/repository_review/reviews_of_repository.mako M templates/webapps/tool_shed/repository_review/select_previous_review.mako A test-data/MTBLS6.zip M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/driver_util.py M test/base/populators.py M test/base/workflow_fixtures.py M test/functional/tools/output_filter.xml A test/functional/tools/remove_value.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/phdcomics/__init__.py M test/galaxy_selenium/navigation.yml A test/integration/test_datatype_upload.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_uploads.py M test/shed_functional/base/twilltestcase.py M test/unit/datatypes/test_bam.py M test/unit/datatypes/test_vcf.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/web/framework/test_webapp.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/extract/extract_genomic_dna.py M tools/filters/convert_characters.py M tools/filters/grep.py M tools/filters/uniq.py M tools/stats/filtering.py M tools/stats/gsummary.py Log Message: ----------- Merge branch 'dev' into admin.data.manager.vue.steps Commit: 91df3971be62419620c3cd08b0c9162ec6989856 https://github.com/galaxyproject/galaxy/commit/91df3971be62419620c3cd08b0c9… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-11-03 (Sat, 03 Nov 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/components/admin/DataManager/DataManager.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- DataManagerRouter, DataManager, DataManagerJobs: Fix routing problem * Forward path following the data manager url to DataManagerRouter * encode id in DataManager and DataManagerJobs Commit: 45d0f161c92c6fdac103ca3eecec421ac3fa3db3 https://github.com/galaxyproject/galaxy/commit/45d0f161c92c6fdac103ca3eecec… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-11-03 (Sat, 03 Nov 2018) Changed paths: M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1460_data_managers.py Log Message: ----------- Fix functional test case test_1460_data_managers Commit: 4b3606f1acd57064c3b4a2da6842a58d5d634a9b https://github.com/galaxyproject/galaxy/commit/4b3606f1acd57064c3b4a2da6842… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue Log Message: ----------- Target top with rerun to avoid nested Galaxy. Commit: e9f269393346175c2d88dd6e190d3d00547ef3c6 https://github.com/galaxyproject/galaxy/commit/e9f269393346175c2d88dd6e190d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/Alert.vue A client/galaxy/scripts/components/admin/DataManager/DataManager.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue M client/package.json M client/yarn.lock M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py R templates/webapps/galaxy/data_manager/index.mako R templates/webapps/galaxy/data_manager/manage_data_manager.mako R templates/webapps/galaxy/data_manager/manage_data_table.mako R templates/webapps/galaxy/data_manager/view_job.mako M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1460_data_managers.py Log Message: ----------- Merge pull request #6729 from scrathat/admin.data.manager.vue.steps Vue rewrite of admin data manager (local data) in steps Compare: https://github.com/galaxyproject/galaxy/compare/a53de291fefd...e9f269393346 **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.

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[galaxyproject/galaxy] e8a64a: Split qunit and mocha tests, clean up karma config...
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e8a64a862212af970690fcd1969ac8f5ebaaf407 https://github.com/galaxyproject/galaxy/commit/e8a64a862212af970690fcd1969a… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: A client/galaxy/scripts/apps/sample.test.js A client/galaxy/scripts/unitTestBundle.js A client/karma.config.base.js R client/karma.config.js A client/karma.config.mocha.js A client/karma.config.qunit.js M client/package.json A client/webpack.config.test.js M client/yarn.lock Log Message: ----------- Split qunit and mocha tests, clean up karma configs Commit: 1490b6ae839bd704af45b7a415ba70d7fc013df3 https://github.com/galaxyproject/galaxy/commit/1490b6ae839bd704af45b7a415ba… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M client/galaxy/style/scss/ui.scss M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako Log Message: ----------- Merge branch 'dev' into karma_chromeheadless Commit: b52b2d8c4817295f9dad56a057fe9d5a095d3a37 https://github.com/galaxyproject/galaxy/commit/b52b2d8c4817295f9dad56a057fe… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample M config/migrated_tools_conf.xml.sample M config/shed_tool_conf.xml.sample M doc/source/admin/tool_panel.rst A lib/galaxy/datatypes/converters/tar_to_directory.xml M lib/galaxy/datatypes/data.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/compression_utils.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/common_util.py M templates/webapps/galaxy/admin/tool_sheds.mako M test/api/test_tools.py M test/api/test_tools_upload.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into karma_chromeheadless Commit: 2cc0417530cb33dfa43cb0c0d64f2f807d5396d5 https://github.com/galaxyproject/galaxy/commit/2cc0417530cb33dfa43cb0c0d64f… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M .travis.yml M client/karma.config.base.js Log Message: ----------- Added chrome to qunit build, tried no sandbox flag on chrome Commit: b637c7575a6cdd17960b57e803cabcaa9fe5972c https://github.com/galaxyproject/galaxy/commit/b637c7575a6cdd17960b57e803ca… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M Makefile M client/karma.config.base.js M client/package.json Log Message: ----------- Modified test script calls Commit: 31d3c97e757fd9e9206c815d7b0c9b9d22d0d7a8 https://github.com/galaxyproject/galaxy/commit/31d3c97e757fd9e9206c815d7b0c… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/karma.config.qunit.js Log Message: ----------- Remove one failing test just to check build Commit: e92ce870928700917d69e9c3d939087d6d48eb56 https://github.com/galaxyproject/galaxy/commit/e92ce870928700917d69e9c3d939… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/galaxy/scripts/qunit/test.js M client/karma.config.qunit.js Log Message: ----------- Removed bad test just to test build Commit: b06957e90619b3b7c4cf1f7b989ae32242b55f83 https://github.com/galaxyproject/galaxy/commit/b06957e90619b3b7c4cf1f7b989a… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/karma.config.mocha.js Log Message: ----------- Added existing mocha tests back Commit: a7a73bcfcd32de2b89a6cd4119ba64db8be045ef https://github.com/galaxyproject/galaxy/commit/a7a73bcfcd32de2b89a6cd4119ba… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/karma.config.base.js M client/karma.config.mocha.js M client/karma.config.qunit.js M client/package.json A client/webpack.config.qunit.js R client/webpack.config.test.js A client/webpack.config.unittest.js M client/yarn.lock Log Message: ----------- Documented differences bretween different webpack configs, used cleaner tool and ignore-loader for true unit-tests Commit: c2f71c3a3ec31fd6af7479db9ae13f8b0975d584 https://github.com/galaxyproject/galaxy/commit/c2f71c3a3ec31fd6af7479db9ae1… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/webpack.config.qunit.js Log Message: ----------- Added missing settings on special qunit webpack config Commit: 19b2fdd73ba82d0eb3ae38141134915d8a745827 https://github.com/galaxyproject/galaxy/commit/19b2fdd73ba82d0eb3ae38141134… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-03 (Sat, 03 Nov 2018) Changed paths: R client/galaxy/scripts/apps/sample.test.js A client/galaxy/scripts/sample.test.js R client/karma.config.base.js R client/karma.config.mocha.js R client/karma.config.qunit.js A client/karma/karma.config.base.js A client/karma/karma.config.mocha.js A client/karma/karma.config.qunit.js A client/karma/webpack.config.qunit.js A client/karma/webpack.config.unittest.js M client/package.json R client/webpack.config.qunit.js R client/webpack.config.unittest.js Log Message: ----------- Reorganized config scripts, fleshed out comments and instructions Commit: a53de291fefd34ca9fcdf1a03bacd9739f768edf https://github.com/galaxyproject/galaxy/commit/a53de291fefd34ca9fcdf1a03bac… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M .travis.yml M Makefile M client/galaxy/scripts/qunit/test.js A client/galaxy/scripts/sample.test.js A client/galaxy/scripts/unitTestBundle.js R client/karma.config.js A client/karma/karma.config.base.js A client/karma/karma.config.mocha.js A client/karma/karma.config.qunit.js A client/karma/webpack.config.qunit.js A client/karma/webpack.config.unittest.js M client/package.json M client/yarn.lock Log Message: ----------- Merge pull request #6959 from Nerdinacan/karma_chromeheadless Switch from PhantomJS to Chrome Headless for unit tests Compare: https://github.com/galaxyproject/galaxy/compare/c3dc2392ce1a...a53de291fefd **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.

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[galaxyproject/galaxy] 69b447: Allow deferring 'to_ext' extension to the server, ...
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 69b447169fb96048ea492a1d99d653585571c15b https://github.com/galaxyproject/galaxy/commit/69b447169fb96048ea492a1d99d6… Author: Dannon Baker <dannon.baker(a)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: 3be8d66d71bcdb3eccde2d1a37731442ed1aa63a https://github.com/galaxyproject/galaxy/commit/3be8d66d71bcdb3eccde2d1a3773… Author: mvdbeek <m.vandenbeek(a)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/f8b160535c5f9363e85c6c1d041b… Author: mvdbeek <m.vandenbeek(a)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: 61bda3d11a1d608ac8e1a731faf144ff989affc9 https://github.com/galaxyproject/galaxy/commit/61bda3d11a1d608ac8e1a731faf1… Author: Martin Cech <marten(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/2deb302ae7be...61bda3d11a1d **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.

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[galaxyproject/galaxy] 717605: added test
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 717605af96bcb5fb9a5193295c9941d0d4632a93 https://github.com/galaxyproject/galaxy/commit/717605af96bcb5fb9a5193295c99… Author: M Bernt <m.bernt(a)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/20cecd2a68527015d8b98a430367… Author: M Bernt <m.bernt(a)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: 4e098c5d5291209f4760010ff8bebd919ba19479 https://github.com/galaxyproject/galaxy/commit/4e098c5d5291209f4760010ff8be… Author: M Bernt <m.bernt(a)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: 9b42032098edaae076f5f88c48f135d8035a9ad6 https://github.com/galaxyproject/galaxy/commit/9b42032098edaae076f5f88c48f1… Author: mvdbeek <m.vandenbeek(a)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/2deb302ae7be93924a8bdcaff17a… Author: Nicola Soranzo <nicola.soranzo(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/3d91738a697f...2deb302ae7be **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.

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[galaxyproject/galaxy] d4b6bf: Test for parameter replacement of GUI-style normal...
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d4b6bf28b5c834dc82591761a98a1aeefc0ed412 https://github.com/galaxyproject/galaxy/commit/d4b6bf28b5c834dc82591761a98a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test for parameter replacement of GUI-style normalized parameters. Commit: 06aea92eb8614faa06afdeaeffe91565e1390774 https://github.com/galaxyproject/galaxy/commit/06aea92eb8614faa06afdeaeffe9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- cleaner test test_run_subworkflow_runtime_parameters Commit: c3dc2392ce1a3c9ca91369caf63fa0b6008820d2 https://github.com/galaxyproject/galaxy/commit/c3dc2392ce1a3c9ca91369caf63f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #6954 from jmchilton/workflow_tests_2 Small API Workflow Test Improvements. Compare: https://github.com/galaxyproject/galaxy/compare/c1e4b0111a70...c3dc2392ce1a **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.

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[galaxyproject/galaxy] b1fe6f: Refactor collection mapping workflows toward indep...
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b1fe6fee9373f025341e25b248ffa003a10213b3 https://github.com/galaxyproject/galaxy/commit/b1fe6fee9373f025341e25b248ff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Refactor collection mapping workflows toward independence from tools. Refactor get_data_inputs into get_all_inputs and use the resulting dictionaries to reason about if collection mapping should occur during invocation of tools. Using these dictionaries instead of explicit tool input objects should allow reuse within other module types since they may produce the same interface. Commit: c1e4b0111a70e3bae63791f60a44e6b14b259a5c https://github.com/galaxyproject/galaxy/commit/c1e4b0111a70e3bae63791f60a44… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Merge pull request #6911 from jmchilton/workflow_mapping_refactor Refactor collection mapping workflows toward independence from tools. Compare: https://github.com/galaxyproject/galaxy/compare/a3f213e3c531...c1e4b0111a70 **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.

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[galaxyproject/galaxy] 0beac8: rma: add RMA6 data type (MEGAN6 read-match archive...
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0beac8fdf4835271ccafefd6a50f928afa055c2c https://github.com/galaxyproject/galaxy/commit/0beac8fdf4835271ccafefd6a50f… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/diamond.rma Log Message: ----------- rma: add RMA6 data type (MEGAN6 read-match archive) Commit: dcae06624a7561d082a7630917d095925795d30e https://github.com/galaxyproject/galaxy/commit/dcae06624a7561d082a7630917d0… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- rma: RMA->RMA6 Commit: 09de6fe4961adcfe09f8701989ac37b8f8df1930 https://github.com/galaxyproject/galaxy/commit/09de6fe4961adcfe09f8701989ac… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- rma: fix test Commit: ee0038a01f8ddd9f8b99d0612497fc6681a14acc https://github.com/galaxyproject/galaxy/commit/ee0038a01f8ddd9f8b99d0612497… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- rma: extension rma6 for consistency Commit: 562b10b7efc93c5ab15bd3a3d5918f32491d934d https://github.com/galaxyproject/galaxy/commit/562b10b7efc93c5ab15bd3a3d591… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/test/diamond.rma A lib/galaxy/datatypes/test/diamond.rma6 Log Message: ----------- rma: renamed test data to rma6 Commit: a3f213e3c5319bd8125e4856e0094fd3cd7ef737 https://github.com/galaxyproject/galaxy/commit/a3f213e3c5319bd8125e4856e009… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/diamond.rma6 Log Message: ----------- Merge pull request #6962 from bernt-matthias/topic/rma add RMA6 data type (MEGAN6 read-match archive) Compare: https://github.com/galaxyproject/galaxy/compare/0ede377925c4...a3f213e3c531 **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.

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[galaxyproject/ansible-galaxy] 89a26c: Update print statement syntax to support Python 3.
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 89a26cb0833845986893c08fadf7db4c57e4e14c https://github.com/galaxyproject/ansible-galaxy/commit/89a26cb0833845986893… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-11-04 (Sun, 04 Nov 2018) Changed paths: M files/makepyc.py M tasks/dependencies.yml Log Message: ----------- Update print statement syntax to support Python 3. Commit: 1eed620a4a1fe95c94169f5580722e088b58e2c1 https://github.com/galaxyproject/ansible-galaxy/commit/1eed620a4a1fe95c9416… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M files/makepyc.py M tasks/dependencies.yml Log Message: ----------- Merge pull request #39 from ic4f/master Update print statement syntax to support Python 3. Compare: https://github.com/galaxyproject/ansible-galaxy/compare/9ee412e2d63d...1eed… **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.

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[galaxyproject/galaxy] cc8e1c: fix empty loc file bug
by GitHub 04 Nov '18

04 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cc8e1c211ee5c7f6af3d358619b44b3a14ce4deb https://github.com/galaxyproject/galaxy/commit/cc8e1c211ee5c7f6af3d358619b4… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- fix empty loc file bug Commit: 13a4238510de2330bcf460519eac2198f66e0c33 https://github.com/galaxyproject/galaxy/commit/13a4238510de2330bcf460519eac… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- removed debug output Commit: 0ede377925c415cf5b7805de03d57d8d0bd2bca4 https://github.com/galaxyproject/galaxy/commit/0ede377925c415cf5b7805de03d5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-04 (Sun, 04 Nov 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #6957 from bernt-matthias/topic/empty-data-table Topic/empty data table Compare: https://github.com/galaxyproject/galaxy/compare/d6af6b7bd1ef...0ede377925c4 **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.

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[galaxyproject/galaxy] 03eac8: Fix for workflow parameter collection in workflows...
by GitHub 04 Nov '18

04 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 03eac8315d64e05df74f1f6fb286cff29e75f6b2 https://github.com/galaxyproject/galaxy/commit/03eac8315d64e05df74f1f6fb286… Author: Dannon Baker <dannon.baker(a)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/18644f91cf59265c1473d806845b… Author: Dannon Baker <dannon.baker(a)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: 3d91738a697ff57047bc3cd505d5afc75de38f45 https://github.com/galaxyproject/galaxy/commit/3d91738a697ff57047bc3cd505d5… Author: Björn Grüning <bjoern(a)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. Compare: https://github.com/galaxyproject/galaxy/compare/357e2f39c770...3d91738a697f **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.

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[galaxyproject/usegalaxy-playbook] deafd8: Update Test mutable configs
by GitHub 02 Nov '18

02 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: deafd85205f935de94d2acfb767f9522f660c2d6 https://github.com/galaxyproject/usegalaxy-playbook/commit/deafd85205f935de… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Update Test mutable configs **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.

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[galaxyproject/galaxy] 30aaa2: Fix sniffing of readname sorted BAM files
by GitHub 02 Nov '18

02 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 30aaa296dd50471001323cc9895560219a33ce71 https://github.com/galaxyproject/galaxy/commit/30aaa296dd50471001323cc98955… Author: mvdbeek <m.vandenbeek(a)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: 6b5f0a2ad1f21bbda92b06ff2700c961c34e84ea https://github.com/galaxyproject/galaxy/commit/6b5f0a2ad1f21bbda92b06ff2700… Author: Nicola Soranzo <nicola.soranzo(a)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/6da5157181a085d183c099645216… Author: Martin Cech <marten(a)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/357e2f39c77026c81c56ed30ffae… Author: Nicola Soranzo <nicola.soranzo(a)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: d6af6b7bd1ef9c9429d1362ac9473168be7ba471 https://github.com/galaxyproject/galaxy/commit/d6af6b7bd1ef9c9429d1362ac947… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f035d642ceb2...d6af6b7bd1ef **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.

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[galaxyproject/galaxy] 6b5f0a: Allow upload for ``rdata.sce`` format
by GitHub 02 Nov '18

02 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 6b5f0a2ad1f21bbda92b06ff2700c961c34e84ea https://github.com/galaxyproject/galaxy/commit/6b5f0a2ad1f21bbda92b06ff2700… Author: Nicola Soranzo <nicola.soranzo(a)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/6da5157181a085d183c099645216… Author: Martin Cech <marten(a)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/357e2f39c77026c81c56ed30ffae… Author: Nicola Soranzo <nicola.soranzo(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/30aaa296dd50...357e2f39c770 **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.

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[galaxyproject/galaxy] 6b5f0a: Allow upload for ``rdata.sce`` format
by GitHub 02 Nov '18

02 Nov '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 6b5f0a2ad1f21bbda92b06ff2700c961c34e84ea https://github.com/galaxyproject/galaxy/commit/6b5f0a2ad1f21bbda92b06ff2700… Author: Nicola Soranzo <nicola.soranzo(a)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/6da5157181a085d183c099645216… Author: Martin Cech <marten(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/3411852fedf3...6da5157181a0 **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.

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[galaxyproject/usegalaxy-playbook] d6d332: update fastqc, multiqc, trimgalore
by GitHub 01 Nov '18

01 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d6d3322f5eb0681a6425b6f2f00b545f38da5826 https://github.com/galaxyproject/usegalaxy-playbook/commit/d6d3322f5eb0681a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_data_manager_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- update fastqc, multiqc, trimgalore also add forgotten data_manager mutable confs **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.

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