{"action":"created","comment":{"url":"https://api.github.com/repos/Ensembl/ensembl-xref/pulls/comments/242216103","pull_request_review_id":185676050,"id":242216103,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDI0MjIxNjEwMw==","diff_hunk":"@@ -37,6 +37,33 @@ my %source_name_for_section = (\n   'TrEMBL'     => 'Uniprot/SPTREMBL',\n );\n \n+# List of crossreference sources for which we want to create direct or\n+# dependent xrefs along with matching links. This includes both\n+# sources for crossreferences directly appearing in UniProt-KB files\n+# and special sources (at present, 'Uniprot_gn' and 'protein_id')\n+# xrefs for which are assembled in the transformer.","path":"modules/Bio/EnsEMBL/Xref/Parser/UniProtParser.pm","position":null,"original_position":8,"commit_id":"4ef336cda140ac6e9f9e533b3afae583a3477d38","original_commit_id":"b9a6b2b8d8025dec35955f676f18756782fcc222","user":{"login":"mkszuba","id":49689,"node_id":"MDQ6VXNlcjQ5Njg5","avatar_url":"https://avatars3.githubusercontent.com/u/49689?v=4","gravatar_id":"","url":"https://api.github.com/users/mkszuba","html_url":"https://github.com/mkszuba","followers_url":"https://api.github.com/users/mkszuba/followers","following_url":"https://api.github.com/users/mkszuba/following{/other_user}","gists_url":"https://api.github.com/users/mkszuba/gists{/gist_id}","starred_url":"https://api.github.com/users/mkszuba/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mkszuba/subscriptions","organizations_url":"https://api.github.com/users/mkszuba/orgs","repos_url":"https://api.github.com/users/mkszuba/repos","events_url":"https://api.github.com/users/mkszuba/events{/privacy}","received_events_url":"https://api.github.com/users/mkszuba/received_events","type":"User","site_admin":false},"body":"How about now?","created_at":"2018-12-17T16:24:18Z","updated_at":"2018-12-17T16:24:18Z","html_url":"https://github.com/Ensembl/ensembl-xref/pull/40#discussion_r242216103","pull_request_url":"https://api.github.com/repos/Ensembl/ensembl-xref/pulls/40","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/Ensembl/ensembl-xref/pulls/comments/242216103"},"html":{"href":"https://github.com/Ensembl/ensembl-xref/pull/40#discussion_r242216103"},"pull_request":{"href":"https://api.github.com/repos/Ensembl/ensembl-xref/pulls/40"}},"in_reply_to_id":242194563},"pull_request":{"url":"https://api.github.com/repos/Ensembl/ensembl-xref/pulls/40","id":239121667,"node_id":"MDExOlB1bGxSZXF1ZXN0MjM5MTIxNjY3","html_url":"https://github.com/Ensembl/ensembl-xref/pull/40","diff_url":"https://github.com/Ensembl/ensembl-xref/pull/40.diff","patch_url":"https://github.com/Ensembl/ensembl-xref/pull/40.patch","issue_url":"https://api.github.com/repos/Ensembl/ensembl-xref/issues/40","number":40,"state":"open","locked":false,"title":"miRBaseParser","user":{"login":"mkszuba","id":49689,"node_id":"MDQ6VXNlcjQ5Njg5","avatar_url":"https://avatars3.githubusercontent.com/u/49689?v=4","gravatar_id":"","url":"https://api.github.com/users/mkszuba","html_url":"https://github.com/mkszuba","followers_url":"https://api.github.com/users/mkszuba/followers","following_url":"https://api.github.com/users/mkszuba/following{/other_user}","gists_url":"https://api.github.com/users/mkszuba/gists{/gist_id}","starred_url":"https://api.github.com/users/mkszuba/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mkszuba/subscriptions","organizations_url":"https://api.github.com/users/mkszuba/orgs","repos_url":"https://api.github.com/users/mkszuba/repos","events_url":"https://api.github.com/users/mkszuba/events{/privacy}","received_events_url":"https://api.github.com/users/mkszuba/received_events","type":"User","site_admin":false},"body":"## Requirements\r\n\r\nNote that this PR depends on new code to be added by #28 . To make reviews easier I have set the merge base to the branch used by the latter PR, will switch it to master once it has been merged.\r\n\r\n## Description\r\n\r\nAdd miRBaseParser to the new xref repository. This is a full rewrite rather than a refactoring, albeit a minimal one because it mostly uses the new UniProtParser under the bonnet.\r\n\r\n## Use case\r\n\r\nTurns out the structure of miRBase data is virtually identical to that of UniProt-KB dat files. Moreover, although the old miRBaseParser is considerably less complicated than the old UniProtParser (for one thing, it doesn't have to mess with crossreferences because it only produces primary, sequence-matched xrefs) it is already incompatible with BaseParser changes made in _ensembl:feature/xref_sprint_ and I doubt it having morphed into BaseAdaptor as well as subsequent further cleanup would help matters.\r\n\r\nCompared the output of the new parser to that of the \"really old\" one (_i.e._ from _ensembl:master_) for human. No differences. Run time is similar.\r\n\r\n## Benefits\r\n\r\nWill be able to parse miRBase xrefs using the refactored xref pipeline.\r\n\r\n## Possible Drawbacks\r\n\r\nNone?\r\n\r\n## Testing\r\n\r\n_Have you added/modified unit tests to test the changes?_\r\n\r\nNot yet, this is a specialisation of the new UniProtParser so we should develop tests for the latter first.\r\n\r\n_If so, do the tests pass/fail?_\r\n\r\nN/A\r\n\r\n_Have you run the entire test suite and no regression was detected?_\r\n\r\nYes, no regression has been 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