{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/2204","repository_url":"https://api.github.com/repos/galaxyproject/tools-iuc","labels_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/2204/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/2204/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/2204/events","html_url":"https://github.com/galaxyproject/tools-iuc/pull/2204","id":388746032,"node_id":"MDExOlB1bGxSZXF1ZXN0MjM2OTQwMjIx","number":2204,"title":"[WIP] Fix the gemini data manager, data tables and wrapper tests","user":{"login":"wm75","id":4742081,"node_id":"MDQ6VXNlcjQ3NDIwODE=","avatar_url":"https://avatars0.githubusercontent.com/u/4742081?v=4","gravatar_id":"","url":"https://api.github.com/users/wm75","html_url":"https://github.com/wm75","followers_url":"https://api.github.com/users/wm75/followers","following_url":"https://api.github.com/users/wm75/following{/other_user}","gists_url":"https://api.github.com/users/wm75/gists{/gist_id}","starred_url":"https://api.github.com/users/wm75/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wm75/subscriptions","organizations_url":"https://api.github.com/users/wm75/orgs","repos_url":"https://api.github.com/users/wm75/repos","events_url":"https://api.github.com/users/wm75/events{/privacy}","received_events_url":"https://api.github.com/users/wm75/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-12-07T17:28:05Z","updated_at":"2018-12-14T15:45:15Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/2204","html_url":"https://github.com/galaxyproject/tools-iuc/pull/2204","diff_url":"https://github.com/galaxyproject/tools-iuc/pull/2204.diff","patch_url":"https://github.com/galaxyproject/tools-iuc/pull/2204.patch"},"body":"This changeset should make the gemini data manager fully functional\r\nand eliminate the need of any manual patching of the installed\r\ngemini data files.\r\nIt also introduces a new gemini_versioned_databases data table that\r\nallows gemini tool wrappers to filter the installed gemini\r\nannotation files for those they can actually work with.\r\n\r\nFOR CONTRIBUTOR:\r\n* [x] - I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the tools-iuc repo.\r\n* [ ] - License permits unrestricted use (educational + commercial)\r\n* [ ] - This PR adds a new tool or tool collection\r\n* [x] - This PR updates an existing tool or tool collection\r\n* [ ] - This PR does something else (explain below)\r\n\r\nFOR REVIEWER:\r\n* [ ] .shed.yml file ok\r\n    - [ ] Toolshed user `iuc` has access to associated toolshed repo(s)\r\n* [ ] Indentation is correct (4 spaces)\r\n* [ ] Tool version/build ok\r\n* [ ] `<command/>`\r\n  - [ ] Text parameters, input and output files `'single quoted'`\r\n  - [ ] Use of `<![CDATA[ ... ]]>` tags\r\n  - [ ] Parameters of type `text` or having `optional=\"true\"` attribute are checked with `if str($param)` before being used\r\n* [ ] Data parameters have a `format` attribute containing datatypes recognised by Galaxy\r\n* [ ] Tests\r\n  - [ ] Parameters are reasonably covered\r\n  - [ ] Test files are appropriate\r\n* [ ] Help\r\n  - [ ] Valid restructuredText and uses `<![CDATA[ ... ]]>` tags\r\n* [ ] Complies with other best practice in [Best Practices Doc](http://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html)\r\n"},"comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/comments/447363734","html_url":"https://github.com/galaxyproject/tools-iuc/pull/2204#issuecomment-447363734","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/2204","id":447363734,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0NzM2MzczNA==","user":{"login":"wm75","id":4742081,"node_id":"MDQ6VXNlcjQ3NDIwODE=","avatar_url":"https://avatars0.githubusercontent.com/u/4742081?v=4","gravatar_id":"","url":"https://api.github.com/users/wm75","html_url":"https://github.com/wm75","followers_url":"https://api.github.com/users/wm75/followers","following_url":"https://api.github.com/users/wm75/following{/other_user}","gists_url":"https://api.github.com/users/wm75/gists{/gist_id}","starred_url":"https://api.github.com/users/wm75/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wm75/subscriptions","organizations_url":"https://api.github.com/users/wm75/orgs","repos_url":"https://api.github.com/users/wm75/repos","events_url":"https://api.github.com/users/wm75/events{/privacy}","received_events_url":"https://api.github.com/users/wm75/received_events","type":"User","site_admin":false},"created_at":"2018-12-14T15:45:15Z","updated_at":"2018-12-14T15:45:15Z","author_association":"CONTRIBUTOR","body":"@bgruening I think that's how far I'd take this. The test coverage of the tools is still far from ideal, but, at least, gemini can now be tested at all.\r\nAfter this gets merged I can open a new PR that upgrades gemini to version 0.20.1. I'll add more tool tests there. "}}
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