{"action":"created","issue":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/9","labels_url":"https://api.github.com/repos/cjfields/redmine-test/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/cjfields/redmine-test/issues/9/comments","events_url":"https://api.github.com/repos/cjfields/redmine-test/issues/9/events","html_url":"https://github.com/cjfields/redmine-test/issues/9","id":95097695,"number":9,"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":"006699"},{"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":"666600"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Status:%20New","name":"Status: New","color":"FF6600"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Tracker:%20Bug","name":"Tracker: Bug","color":"FF0000"}],"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":1208465,"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":"2015-07-15T03:32:03Z","updated_at":"2015-07-15T03:34:27Z","due_on":null,"closed_at":null},"comments":15,"created_at":"2015-07-15T03:34:27Z","updated_at":"2015-07-15T03:34:30Z","closed_at":null,"body":"---\n\n\nAuthor Name: **Chris Fields** (@cjfields)\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/121476925","html_url":"https://github.com/cjfields/redmine-test/issues/9#issuecomment-121476925","issue_url":"https://api.github.com/repos/cjfields/redmine-test/issues/9","id":121476925,"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":"2015-07-15T03:34:30Z","updated_at":"2015-07-15T03:34:30Z","body":"---\n\nOriginal Redmine Comment\nAuthor Name: **Chris Fields** (@cjfields)\nOriginal Date: 2008-02-12T10:41:57Z\n\n---\n\nI don't see this getting fixed properly until the 1.7 release.  I would recommend (for now) using the XML returned from eutils instead."}}