{"action":"created","issue":{"url":"https://api.github.com/repos/biopython/biopython/issues/1801","repository_url":"https://api.github.com/repos/biopython/biopython","labels_url":"https://api.github.com/repos/biopython/biopython/issues/1801/labels{/name}","comments_url":"https://api.github.com/repos/biopython/biopython/issues/1801/comments","events_url":"https://api.github.com/repos/biopython/biopython/issues/1801/events","html_url":"https://github.com/biopython/biopython/issues/1801","id":363096880,"node_id":"MDU6SXNzdWUzNjMwOTY4ODA=","number":1801,"title":"entrez.read NotImplementedError","user":{"login":"nstfk","id":25326694,"node_id":"MDQ6VXNlcjI1MzI2Njk0","avatar_url":"https://avatars1.githubusercontent.com/u/25326694?v=4","gravatar_id":"","url":"https://api.github.com/users/nstfk","html_url":"https://github.com/nstfk","followers_url":"https://api.github.com/users/nstfk/followers","following_url":"https://api.github.com/users/nstfk/following{/other_user}","gists_url":"https://api.github.com/users/nstfk/gists{/gist_id}","starred_url":"https://api.github.com/users/nstfk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nstfk/subscriptions","organizations_url":"https://api.github.com/users/nstfk/orgs","repos_url":"https://api.github.com/users/nstfk/repos","events_url":"https://api.github.com/users/nstfk/events{/privacy}","received_events_url":"https://api.github.com/users/nstfk/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"mdehoon","id":136062,"node_id":"MDQ6VXNlcjEzNjA2Mg==","avatar_url":"https://avatars2.githubusercontent.com/u/136062?v=4","gravatar_id":"","url":"https://api.github.com/users/mdehoon","html_url":"https://github.com/mdehoon","followers_url":"https://api.github.com/users/mdehoon/followers","following_url":"https://api.github.com/users/mdehoon/following{/other_user}","gists_url":"https://api.github.com/users/mdehoon/gists{/gist_id}","starred_url":"https://api.github.com/users/mdehoon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mdehoon/subscriptions","organizations_url":"https://api.github.com/users/mdehoon/orgs","repos_url":"https://api.github.com/users/mdehoon/repos","events_url":"https://api.github.com/users/mdehoon/events{/privacy}","received_events_url":"https://api.github.com/users/mdehoon/received_events","type":"User","site_admin":false},"assignees":[{"login":"mdehoon","id":136062,"node_id":"MDQ6VXNlcjEzNjA2Mg==","avatar_url":"https://avatars2.githubusercontent.com/u/136062?v=4","gravatar_id":"","url":"https://api.github.com/users/mdehoon","html_url":"https://github.com/mdehoon","followers_url":"https://api.github.com/users/mdehoon/followers","following_url":"https://api.github.com/users/mdehoon/following{/other_user}","gists_url":"https://api.github.com/users/mdehoon/gists{/gist_id}","starred_url":"https://api.github.com/users/mdehoon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mdehoon/subscriptions","organizations_url":"https://api.github.com/users/mdehoon/orgs","repos_url":"https://api.github.com/users/mdehoon/repos","events_url":"https://api.github.com/users/mdehoon/events{/privacy}","received_events_url":"https://api.github.com/users/mdehoon/received_events","type":"User","site_admin":false}],"milestone":null,"comments":0,"created_at":"2018-09-24T10:55:50Z","updated_at":"2018-09-24T11:12:34Z","closed_at":null,"author_association":"NONE","body":"\r\nI am reporting a problem with Biopython version, Python version, and operating\r\nsystem as follows:\r\n\r\n```python\r\n3.5.2 (v3.5.2:4def2a2901a5, Jun 25 2016, 22:18:55) [MSC v.1900 64 bit (AMD64)]\r\nCPython\r\nWindows-10-10.0.17134-SP0\r\n1.72\r\n```\r\n\r\n### Expected behaviour\r\n\r\nfetching the articles\r\n\r\n### Actual behaviour\r\n\r\n`NotImplementedError:` The Bio.Entrez parser cannot handle XML data that make use of XML namespaces\r\n\r\n### Steps to reproduce\r\n    targetQ=\"personalized medicine\"\r\n    handle = Entrez.esearch(db=\"pubmed\", term=targetQ, RetMax=5000)\r\n    Rlist = Entrez.read(handle)\r\n    IDlist = Rlist[\"IdList\"]\r\n    fetch_handle = Entrez.efetch(db=\"pubmed\", id=IDlist, rettype=\"null\", retmode=\"xml\", parsed=True)\r\n                \r\n\r\n"},"comment":{"url":"https://api.github.com/repos/biopython/biopython/issues/comments/423941045","html_url":"https://github.com/biopython/biopython/issues/1801#issuecomment-423941045","issue_url":"https://api.github.com/repos/biopython/biopython/issues/1801","id":423941045,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMzk0MTA0NQ==","user":{"login":"peterjc","id":63959,"node_id":"MDQ6VXNlcjYzOTU5","avatar_url":"https://avatars2.githubusercontent.com/u/63959?v=4","gravatar_id":"","url":"https://api.github.com/users/peterjc","html_url":"https://github.com/peterjc","followers_url":"https://api.github.com/users/peterjc/followers","following_url":"https://api.github.com/users/peterjc/following{/other_user}","gists_url":"https://api.github.com/users/peterjc/gists{/gist_id}","starred_url":"https://api.github.com/users/peterjc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/peterjc/subscriptions","organizations_url":"https://api.github.com/users/peterjc/orgs","repos_url":"https://api.github.com/users/peterjc/repos","events_url":"https://api.github.com/users/peterjc/events{/privacy}","received_events_url":"https://api.github.com/users/peterjc/received_events","type":"User","site_admin":false},"created_at":"2018-09-24T11:12:34Z","updated_at":"2018-09-24T11:12:34Z","author_association":"MEMBER","body":"Most of the NCBI XML files use a DTD which is required for the ``Bio.Entrez`` parser. For the problem databases you might try ``ElementTree`` from the standard library. i.e. This is the expected behaviour for some NCBI databases' XML output, but that could be made more explicit in the message and also the documentation including the Tutorial: https://github.com/biopython/biopython/blob/master/Doc/Tutorial/chapter_entrez.tex\r\n\r\nI would investigate further but right now the NCBI is giving me ``HTTP Error 403: Forbidden`` for the\r\nhttp://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi call at the command line...\r\n\r\n```\r\n>>> try:\r\n...     fetch_handle = Entrez.efetch(db=\"pubmed\", id=IDlist, rettype=\"null\", retmode=\"xml\", parsed=True)\r\n... except Exception as e:\r\n...     print(e, e.url)\r\n... \r\nHTTP Error 403: Forbidden http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi\r\n```\r\n\r\nThis may be a temporary problem at the NCBI side, there are pubmed changes happening:\r\n\r\nhttps://www.ncbi.nlm.nih.gov/mailman/pipermail/utilities-announce/2018-August/000133.html\r\nhttps://www.ncbi.nlm.nih.gov/mailman/pipermail/utilities-announce/2018-September/000136.html"}}
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