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Error "'HTTPResponse' object has no attribute 'chunked'" when running cwltool

See original GitHub issue

Hi there, I got this error on a fresh install of cwltool + the workflows

$ cwltool --debug workflows/tools/picard-MergeSamFiles.cwl
/home/matthieu/.local/bin/cwltool 1.0.20161207161158
Resolved 'workflows/tools/picard-MergeSamFiles.cwl' to 'file:///home/matthieu/workspace/hive/cwl/workflows/tools/picard-MergeSamFiles.cwl'
Tool definition failed initialization:
('http://dublincore.org/2012/06/14/dcterms.rdf', AttributeError("'HTTPResponse' object has no attribute 'chunked'",))
Traceback (most recent call last):
  File "/home/matthieu/.local/lib/python2.7/site-packages/cwltool/main.py", line 638, in main
    fetcher_constructor=fetcher_constructor)
  File "/home/matthieu/.local/lib/python2.7/site-packages/cwltool/load_tool.py", line 164, in validate_document
    processobj, metadata = document_loader.resolve_all(workflowobj, fileuri)
  File "/home/matthieu/.local/lib/python2.7/site-packages/schema_salad/ref_resolver.py", line 628, in resolve_all
    newctx.add_schemas(document[u"$schemas"], file_base)
  File "/home/matthieu/.local/lib/python2.7/site-packages/schema_salad/ref_resolver.py", line 269, in add_schemas
    content = self.fetch_text(fetchurl)
  File "/home/matthieu/.local/lib/python2.7/site-packages/schema_salad/ref_resolver.py", line 104, in fetch_text
    raise RuntimeError(url, e)
RuntimeError: ('http://dublincore.org/2012/06/14/dcterms.rdf', AttributeError("'HTTPResponse' object has no attribute 'chunked'",))

I have a working internet connection and can download the file with wget but also from within python

$ python
Python 2.7.6 (default, Oct 26 2016, 20:30:19) 
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import urllib
>>> h = urllib.urlopen('http://dublincore.org/2012/06/14/dcterms.rdf')
>>> '<rdf' in h.read()
True

Issue Analytics

State:
Created 7 years ago
Comments:16 (11 by maintainers)

Top GitHub Comments

1reaction

tetroncommented, Aug 11, 2017

@kapilkd13 actually we have a build pipeline that’s blocked so I’m going to go ahead on it.

1reaction

nicocesarcommented, Aug 11, 2017

https://packages.ubuntu.com/search?keywords=python-requests https://packages.debian.org/jessie/python-requests

2.4.3 for debian8 2.9.1 for xenial (ubuntu16.04)

maybe on of those will work too? it will be great to have more distros supported rather than forcing the user to install outside the distro.

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