{"action":"created","issue":{"url":"https://api.github.com/repos/greenelab/manubot/issues/71","repository_url":"https://api.github.com/repos/greenelab/manubot","labels_url":"https://api.github.com/repos/greenelab/manubot/issues/71/labels{/name}","comments_url":"https://api.github.com/repos/greenelab/manubot/issues/71/comments","events_url":"https://api.github.com/repos/greenelab/manubot/issues/71/events","html_url":"https://github.com/greenelab/manubot/issues/71","id":369506527,"node_id":"MDU6SXNzdWUzNjk1MDY1Mjc=","number":71,"title":"Passing PMCID to PMID citation parser","user":{"login":"agitter","id":3532898,"node_id":"MDQ6VXNlcjM1MzI4OTg=","avatar_url":"https://avatars0.githubusercontent.com/u/3532898?v=4","gravatar_id":"","url":"https://api.github.com/users/agitter","html_url":"https://github.com/agitter","followers_url":"https://api.github.com/users/agitter/followers","following_url":"https://api.github.com/users/agitter/following{/other_user}","gists_url":"https://api.github.com/users/agitter/gists{/gist_id}","starred_url":"https://api.github.com/users/agitter/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/agitter/subscriptions","organizations_url":"https://api.github.com/users/agitter/orgs","repos_url":"https://api.github.com/users/agitter/repos","events_url":"https://api.github.com/users/agitter/events{/privacy}","received_events_url":"https://api.github.com/users/agitter/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-10-12T11:11:19Z","updated_at":"2018-10-17T20:49:41Z","closed_at":null,"author_association":"COLLABORATOR","body":"I wanted to use Manubot to cite [PMCID PMC6063279 ](https://www.ncbi.nlm.nih.gov/pubmed/?term=PMC6063279) and instead received a citation for [PMID 6063279](https://www.ncbi.nlm.nih.gov/pubmed/?term=6063279).  I had accidentally written\r\n```\r\nmanubot cite pmid:PMC6063279\r\n```\r\n\r\nApparently the Entrez eutils takes the PMCID, strips `PMC`, and then returns the [XML](https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=PMC6063279&rettype=full) for that numeric PMID.  This seems like an error on the part of eutils.  Do we want to try to prevent this type of user error?  Or should we instead leave the Manubot behavior but notify the eutils maintainers?"},"comment":{"url":"https://api.github.com/repos/greenelab/manubot/issues/comments/430784708","html_url":"https://github.com/greenelab/manubot/issues/71#issuecomment-430784708","issue_url":"https://api.github.com/repos/greenelab/manubot/issues/71","id":430784708,"node_id":"MDEyOklzc3VlQ29tbWVudDQzMDc4NDcwOA==","user":{"login":"dhimmel","id":1117703,"node_id":"MDQ6VXNlcjExMTc3MDM=","avatar_url":"https://avatars1.githubusercontent.com/u/1117703?v=4","gravatar_id":"","url":"https://api.github.com/users/dhimmel","html_url":"https://github.com/dhimmel","followers_url":"https://api.github.com/users/dhimmel/followers","following_url":"https://api.github.com/users/dhimmel/following{/other_user}","gists_url":"https://api.github.com/users/dhimmel/gists{/gist_id}","starred_url":"https://api.github.com/users/dhimmel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dhimmel/subscriptions","organizations_url":"https://api.github.com/users/dhimmel/orgs","repos_url":"https://api.github.com/users/dhimmel/repos","events_url":"https://api.github.com/users/dhimmel/events{/privacy}","received_events_url":"https://api.github.com/users/dhimmel/received_events","type":"User","site_admin":false},"created_at":"2018-10-17T20:49:41Z","updated_at":"2018-10-17T20:49:41Z","author_association":"MEMBER","body":"We could warn and redirect, but I'm in favor of throwing the error such that the user is required to fix it. We want manubot manuscripts to adhere to good standards, especially say for future projects that analyze citation practices.\r\n\r\nI'm thinking we need better validation of all identifier types. If we know that a certain ID must adhere to a given format, we should do those checks for the user and provide good error messages, rather than the potentially more confusing error message provided by our retrieval functions."}}
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