Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51c586c264f2acd912060297804d61c2539f2483 https://github.com/galaxyproject/galaxy/commit/51c586c264f2acd912060297804d6... Author: mvdbeek m.vandenbeek@gmail.com Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py
Log Message: ----------- Fix tools placed outside of panel section
Occasionally tools were being installed outside of the selected too panel section. In the log one would find contradicting messages such as ```
tool_shed.util.repository_util DEBUG 2016-11-04 11:06:17,854 Adding new row for repository 'sra_tools' in the tool_shed_repository table, status set to 'New'. galaxy.tools.toolbox.base DEBUG 2016-11-04 11:06:17,886 Appending to tool panel section: NCBI SRA Tools 172.17.0.1 - - [04/Nov/2016:11:06:15 +0000] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 200 - "http://localhost/admin_toolshed/prepare_for_install?changeset_revisions=62e4..." " Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.71 Safari/537.36 nvalid tool_panel_section_key "ncbi_sra_tools" specified. Tools will be loaded outside of sections in the tool panel. ``` The intermittent POST is picked up by a different thread, that didn't have its toolbox updated with the new section. To circumvent this, we send the `create_panel_section` task to all threads.
Commit: 4365b907293e366d4ad48396bb5c9dc00f134611 https://github.com/galaxyproject/galaxy/commit/4365b907293e366d4ad48396bb5c9... Author: mvdbeek m.vandenbeek@gmail.com Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths: M test/unit/tools/test_toolbox.py
Log Message: ----------- Fix toolbox unittests
Commit: 202f96c73114fe9f05ed295505243ba17716b0e2 https://github.com/galaxyproject/galaxy/commit/202f96c73114fe9f05ed295505243... Author: Björn Grüning bjoern@gruenings.eu Date: 2016-11-06 (Sun, 06 Nov 2016)
Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_toolbox.py
Log Message: ----------- Merge pull request #3125 from mvdbeek/fix_invalid_section_key
Fix tools placed outside of panel section
Compare: https://github.com/galaxyproject/galaxy/compare/58b7b6cf15c5...202f96c73114