{"action":"created","issue":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/2","labels_url":"https://api.github.com/repos/cjfields/redmine-test/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/cjfields/redmine-test/issues/2/comments","events_url":"https://api.github.com/repos/cjfields/redmine-test/issues/2/events","html_url":"https://github.com/cjfields/redmine-test/issues/2","id":90556809,"number":2,"title":"Bio::ClusterIO::dbsnp breaks with new XML output","user":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Category:%20Core%20Components","name":"Category: Core Components","color":"ededed"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Component:%20URL","name":"Component: URL","color":"ededed"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Priority:%20Normal","name":"Priority: Normal","color":"ededed"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Status:%20New","name":"Status: New","color":"ededed"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Tracker:%20Bug","name":"Tracker: Bug","color":"ededed"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/cjfields/redmine-test/milestones/1","html_url":"https://github.com/cjfields/redmine-test/milestones/main-trunk","labels_url":"https://api.github.com/repos/cjfields/redmine-test/milestones/1/labels","id":1178599,"number":1,"title":"main-trunk","description":null,"creator":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"open_issues":2,"closed_issues":0,"state":"open","created_at":"2015-06-24T03:49:36Z","updated_at":"2015-06-24T03:49:59Z","due_on":null,"closed_at":null},"comments":2,"created_at":"2015-06-24T03:49:59Z","updated_at":"2015-06-24T03:50:00Z","closed_at":null,"body":"---\n\n\nAuthor Name: **Chris Fields** (Chris Fields)\nOriginal Redmine Issue: 2018, https://redmine.open-bio.org/issues/2018\nOriginal Date: 2006-06-07\nOriginal Assignee: Bioperl Guts\n\n---\n\nThe dbSNP XML schema at NCBI has changed recently (Oct. 2005) (no longer uses DTD).  Bio::ClusterIO::dbsnp breaks with new XML output from NCBI.\n\nUsing the old LittleChrY.dbsnp.xml (in t\\data in bioperl-live), everything works.  next_cluster returns a Bio::Variation::SNP object\n\nUsing the attached file (new XML) as input and using Data::Dumper as shown below, get undef returned (probably should throw something instead here).  \n\ntest script\n-----------------------------\n#! perl\nuse strict;\nuse warnings;\nuse Bio::ClusterIO;\nuse Data::Dumper;\nmy $cl_in = Bio::ClusterIO->new(-file => shift,\n                               -format => 'dbsnp');\n\nmy $cl_out = Bio::ClusterIO->new(-fh    => \\*STDOUT,\n                                -format => 'unigene');\nmy $cluster = $cl_in->next_cluster;\nprint Dumper($cl_in);\nprint Dumper($cluster);\n-----------------------------\n\n\n"},"comment":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/comments/114720333","html_url":"https://github.com/cjfields/redmine-test/issues/2#issuecomment-114720333","issue_url":"https://api.github.com/repos/cjfields/redmine-test/issues/2","id":114720333,"user":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"created_at":"2015-06-24T03:50:00Z","updated_at":"2015-06-24T03:50:00Z","body":"---\n\nOriginal Redmine Comment\nAuthor Name: **Heikki Lehvaslaiho** (Heikki Lehvaslaiho)\nOriginal Date: 2006-06-08T04:47:43Z\n\n---\n\nI've sort of fixed this but there are a lot of tags that are not recognised. The parser need more code.  The sample did not have heterozygosity values so those tests are commented out as the code is not fixed."}}