{"action":"created","issue":{"url":"https://api.github.com/repos/common-workflow-language/cwltool/issues/250","repository_url":"https://api.github.com/repos/common-workflow-language/cwltool","labels_url":"https://api.github.com/repos/common-workflow-language/cwltool/issues/250/labels{/name}","comments_url":"https://api.github.com/repos/common-workflow-language/cwltool/issues/250/comments","events_url":"https://api.github.com/repos/common-workflow-language/cwltool/issues/250/events","html_url":"https://github.com/common-workflow-language/cwltool/issues/250","id":194571581,"number":250,"title":"Error \"'HTTPResponse' object has no attribute 'chunked'\" when running cwltool","user":{"login":"muffato","id":623458,"avatar_url":"https://avatars.githubusercontent.com/u/623458?v=3","gravatar_id":"","url":"https://api.github.com/users/muffato","html_url":"https://github.com/muffato","followers_url":"https://api.github.com/users/muffato/followers","following_url":"https://api.github.com/users/muffato/following{/other_user}","gists_url":"https://api.github.com/users/muffato/gists{/gist_id}","starred_url":"https://api.github.com/users/muffato/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/muffato/subscriptions","organizations_url":"https://api.github.com/users/muffato/orgs","repos_url":"https://api.github.com/users/muffato/repos","events_url":"https://api.github.com/users/muffato/events{/privacy}","received_events_url":"https://api.github.com/users/muffato/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2016-12-09T11:16:03Z","updated_at":"2016-12-16T09:40:57Z","closed_at":null,"body":"Hi there,\r\nI got this error on a fresh install of cwltool + the workflows\r\n```\r\n$ cwltool --debug workflows/tools/picard-MergeSamFiles.cwl\r\n/home/matthieu/.local/bin/cwltool 1.0.20161207161158\r\nResolved 'workflows/tools/picard-MergeSamFiles.cwl' to 'file:///home/matthieu/workspace/hive/cwl/workflows/tools/picard-MergeSamFiles.cwl'\r\nTool definition failed initialization:\r\n('http://dublincore.org/2012/06/14/dcterms.rdf', AttributeError(\"'HTTPResponse' object has no attribute 'chunked'\",))\r\nTraceback (most recent call last):\r\n  File \"/home/matthieu/.local/lib/python2.7/site-packages/cwltool/main.py\", line 638, in main\r\n    fetcher_constructor=fetcher_constructor)\r\n  File \"/home/matthieu/.local/lib/python2.7/site-packages/cwltool/load_tool.py\", line 164, in validate_document\r\n    processobj, metadata = document_loader.resolve_all(workflowobj, fileuri)\r\n  File \"/home/matthieu/.local/lib/python2.7/site-packages/schema_salad/ref_resolver.py\", line 628, in resolve_all\r\n    newctx.add_schemas(document[u\"$schemas\"], file_base)\r\n  File \"/home/matthieu/.local/lib/python2.7/site-packages/schema_salad/ref_resolver.py\", line 269, in add_schemas\r\n    content = self.fetch_text(fetchurl)\r\n  File \"/home/matthieu/.local/lib/python2.7/site-packages/schema_salad/ref_resolver.py\", line 104, in fetch_text\r\n    raise RuntimeError(url, e)\r\nRuntimeError: ('http://dublincore.org/2012/06/14/dcterms.rdf', AttributeError(\"'HTTPResponse' object has no attribute 'chunked'\",))\r\n```\r\n\r\nI have a working internet connection and can download the file with `wget` but also from within python\r\n```\r\n$ python\r\nPython 2.7.6 (default, Oct 26 2016, 20:30:19) \r\n[GCC 4.8.4] on linux2\r\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\r\n>>> import urllib\r\n>>> h = urllib.urlopen('http://dublincore.org/2012/06/14/dcterms.rdf')\r\n>>> '<rdf' in h.read()\r\nTrue\r\n```"},"comment":{"url":"https://api.github.com/repos/common-workflow-language/cwltool/issues/comments/267555057","html_url":"https://github.com/common-workflow-language/cwltool/issues/250#issuecomment-267555057","issue_url":"https://api.github.com/repos/common-workflow-language/cwltool/issues/250","id":267555057,"user":{"login":"mr-c","id":1330696,"avatar_url":"https://avatars.githubusercontent.com/u/1330696?v=3","gravatar_id":"","url":"https://api.github.com/users/mr-c","html_url":"https://github.com/mr-c","followers_url":"https://api.github.com/users/mr-c/followers","following_url":"https://api.github.com/users/mr-c/following{/other_user}","gists_url":"https://api.github.com/users/mr-c/gists{/gist_id}","starred_url":"https://api.github.com/users/mr-c/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mr-c/subscriptions","organizations_url":"https://api.github.com/users/mr-c/orgs","repos_url":"https://api.github.com/users/mr-c/repos","events_url":"https://api.github.com/users/mr-c/events{/privacy}","received_events_url":"https://api.github.com/users/mr-c/received_events","type":"User","site_admin":false},"created_at":"2016-12-16T09:40:57Z","updated_at":"2016-12-16T09:40:57Z","body":"Thank you @muffato for the update -- I'm sorry this gave you such problems.\r\n\r\nFrom the requests release notes:\r\n\r\n\"Fixed regression from 2.12.2 where non-string types were rejected in the basic auth parameters. While support for this behaviour has been readded, the behaviour is deprecated and will be removed in the future.\"\r\n\r\n@tetron does this mean we need to change our usage?"}}
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