Actionable mutation and dgidb issue

[robrollback]

Hi,

Seems to be a new issue regarding actionable mutation function and it's interaction with dgidb.

Any help would be much appreciated.

Using gemini 0.20.1 and tested on two separate clusters.

Error: Traceback (most recent call last): File "/cvmfs/soft.mugqic/CentOS6/software/gemini/shared/anaconda/bin/gemini", line 7, in gemini_main.main() File "/cvmfs/soft.mugqic/CentOS6/software/gemini/shared/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1232, in main args.func(parser, args) File "/cvmfs/soft.mugqic/CentOS6/software/gemini/shared/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1049, in get_actionable_mut_fn gemini_actionable_mutations.get_actionable_mutations(parser, args) File "/cvmfs/soft.mugqic/CentOS6/software/gemini/shared/anaconda/lib/python2.7/site-packages/gemini/gemini_actionable_mutations.py", line 35, in get_actionable_mutations dgidb_info = query_dgidb(genes) File "/cvmfs/soft.mugqic/CentOS6/software/gemini/shared/anaconda/lib/python2.7/site-packages/gemini/dgidb.py", line 34, in query_dgidb response = urlopen(query) File "/cvmfs/soft.mugqic/CentOS6/software/gemini/shared/anaconda/lib/python2.7/urllib2.py", line 154, in urlopen return opener.open(url, data, timeout) File "/cvmfs/soft.mugqic/CentOS6/software/gemini/shared/anaconda/lib/python2.7/urllib2.py", line 435, in open response = meth(req, response) File "/cvmfs/soft.mugqic/CentOS6/software/gemini/shared/anaconda/lib/python2.7/urllib2.py", line 548, in http_response 'http', request, response, code, msg, hdrs) File "/cvmfs/soft.mugqic/CentOS6/software/gemini/shared/anaconda/lib/python2.7/urllib2.py", line 473, in error return self._call_chain(args) File "/cvmfs/soft.mugqic/CentOS6/software/gemini/shared/anaconda/lib/python2.7/urllib2.py", line 407, in _call_chain result = func(args) File "/cvmfs/soft.mugqic/CentOS6/software/gemini/shared/anaconda/lib/python2.7/urllib2.py", line 556, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) urllib2.HTTPError: HTTP Error 308: Permanent Redirect

Best, Rob E.

[cailing20]

I think I have a related issue too:

Traceback (most recent call last): File "/cm/shared/apps/gemini/0.20.1/bin/gemini", line 4, in import('pkg_resources').run_script('gemini==0.20.1', 'gemini') File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 719, in run_script File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 1504, in run_script File "/cm/shared/apps/gemini/0.20.1/lib/python2.7/site-packages/gemini-0.20.1-py2.7.egg/EGG-INFO/scripts/gemini", line 7, in gemini_main.main() File "/cm/shared/apps/gemini/0.20.1/lib/python2.7/site-packages/gemini-0.20.1-py2.7.egg/gemini/gemini_main.py", line 1248, in main args.func(parser, args) File "/cm/shared/apps/gemini/0.20.1/lib/python2.7/site-packages/gemini-0.20.1-py2.7.egg/gemini/gemini_main.py", line 1065, in get_actionable_mut_fn gemini_actionable_mutations.get_actionable_mutations(parser, args) File "/cm/shared/apps/gemini/0.20.1/lib/python2.7/site-packages/gemini-0.20.1-py2.7.egg/gemini/gemini_actionable_mutations.py", line 35, in get_actionable_mutations dgidb_info = query_dgidb(genes) File "/cm/shared/apps/gemini/0.20.1/lib/python2.7/site-packages/gemini-0.20.1-py2.7.egg/gemini/dgidb.py", line 34, in query_dgidb response = urlopen(query) File "/cm/shared/apps/python/2.7.x-anaconda/lib/python2.7/urllib2.py", line 154, in urlopen return opener.open(url, data, timeout) File "/cm/shared/apps/python/2.7.x-anaconda/lib/python2.7/urllib2.py", line 435, in open response = meth(req, response) File "/cm/shared/apps/python/2.7.x-anaconda/lib/python2.7/urllib2.py", line 548, in http_response 'http', request, response, code, msg, hdrs) File "/cm/shared/apps/python/2.7.x-anaconda/lib/python2.7/urllib2.py", line 473, in error return self._call_chain(args) File "/cm/shared/apps/python/2.7.x-anaconda/lib/python2.7/urllib2.py", line 407, in _call_chain result = func(args) File "/cm/shared/apps/python/2.7.x-anaconda/lib/python2.7/urllib2.py", line 556, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) urllib2.HTTPError: HTTP Error 308: Permanent Redirect

[brentp]

The interface and URL for dgidb have changed. I'd accept a pull request to update to the new version.