cwltool: Error "'HTTPResponse' object has no attribute 'chunked'" when running cwltool
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
About this issue
- Original URL
- State: closed
- Created 8 years ago
- Comments: 16 (11 by maintainers)
Commits related to this issue
- Squashed 'cwltool/schemas/' changes from 0fbe804..3c40bd3 3c40bd3 Merge pull request #250 from common-workflow-language/draft-4-to-v1.0 b4de02d clarify cwlVersion requirement fad8810 move draft-4 to ... — committed to qiukunlong/cwltool by mr-c 8 years ago
- Merge pull request #250 from common-workflow-language/draft-4-to-v1.0 Draft 4 to v1.0 — committed to common-workflow-language/cwltool by mr-c 8 years ago
- changing requests min version to 2.12.4 — committed to arvados/cwltool by kapilkd13 7 years ago
@kapilkd13 actually we have a build pipeline that’s blocked so I’m going to go ahead on it.
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.
pip install --user --upgrade requestsfixed this for me too.