Confusing Error messages

[steven-albanese]

Just wanted to bring this up, but some of the error messages are difficult to interpret! I was running the following step of the pipeline:

ensembler gather_templates --gather_from uniprot --query 'domain:"Protein kinase" AND reviewed:yes' --uniprot_domain_regex '^Protein kinase(?!; truncated)(?!; inactive)'

and got the following error:

Traceback (most recent call last):
  File "/cbio/jclab/home/albaness/miniconda/bin/ensembler", line 6, in <module>
    sys.exit(main())
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/site-packages/ensembler/cli.py", line 40, in main
    command.dispatch(args)
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/site-packages/ensembler/cli_commands/gather_templates.py", line 116, in dispatch
    ensembler.initproject.gather_templates_from_uniprot(args['--query'], uniprot_domain_regex=args['--uniprot_domain_regex'], structure_dirs=structure_paths, loglevel=loglevel)
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/site-packages/ensembler/utils.py", line 37, in print_done
    fn(*args, **kwargs)
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/site-packages/ensembler/initproject.py", line 342, in gather_templates_from_uniprot
    uniprotxml = ensembler.uniprot.get_uniprot_xml(uniprot_query_string)
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/site-packages/ensembler/uniprot.py", line 43, in get_uniprot_xml
    uniprotxml = etree.fromstring(uniprotxmlstring, parser)
  File "src/lxml/lxml.etree.pyx", line 3213, in lxml.etree.fromstring (src/lxml/lxml.etree.c:82934)
  File "src/lxml/parser.pxi", line 1819, in lxml.etree._parseMemoryDocument (src/lxml/lxml.etree.c:124533)
  File "src/lxml/parser.pxi", line 1707, in lxml.etree._parseDoc (src/lxml/lxml.etree.c:123074)
  File "src/lxml/parser.pxi", line 1079, in lxml.etree._BaseParser._parseDoc (src/lxml/lxml.etree.c:117114)
  File "src/lxml/parser.pxi", line 573, in lxml.etree._ParserContext._handleParseResultDoc (src/lxml/lxml.etree.c:110510)
  File "src/lxml/parser.pxi", line 683, in lxml.etree._handleParseResult (src/lxml/lxml.etree.c:112276)
  File "src/lxml/parser.pxi", line 613, in lxml.etree._raiseParseError (src/lxml/lxml.etree.c:111124)
lxml.etree.XMLSyntaxError: AttValue: ' expected, line 2865323, column 15

It turned out that I was able to fix this by specifying taxonomy for --query. I then got the following error while running in an interactive session:

Traceback (most recent call last):
  File "/cbio/jclab/home/albaness/miniconda/bin/ensembler", line 6, in <module>
    sys.exit(main())
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/site-packages/ensembler/cli.py", line 40, in main
    command.dispatch(args)
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/site-packages/ensembler/cli_commands/gather_templates.py", line 116, in dispatch
    ensembler.initproject.gather_templates_from_uniprot(args['--query'], uniprot_domain_regex=args['--uniprot_domain_regex'], structure_dirs=structure_paths, loglevel=loglevel)
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/site-packages/ensembler/utils.py", line 37, in print_done
    fn(*args, **kwargs)
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/site-packages/ensembler/initproject.py", line 348, in gather_templates_from_uniprot
    get_structure_files(selected_pdbchains, structure_dirs)
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/site-packages/ensembler/initproject.py", line 474, in get_structure_files
    get_structure_files_for_single_pdbchain(pdbchain['pdbid'], structure_dirs)
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/site-packages/ensembler/initproject.py", line 493, in get_structure_files_for_single_pdbchain
    pdbid, project_structure_filepath, structure_type=structure_type
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/site-packages/ensembler/initproject.py", line 449, in download_structure_file
    download_pdb_file(pdbid, project_structure_filepath)
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/site-packages/ensembler/initproject.py", line 456, in download_pdb_file
    pdbgz_page = ensembler.pdb.retrieve_pdb(pdbid, compressed='yes')
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/site-packages/ensembler/pdb.py", line 103, in retrieve_pdb
    response = urlopen(url)
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/urllib2.py", line 154, in urlopen
    return opener.open(url, data, timeout)
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/urllib2.py", line 431, in open
    response = self._open(req, data)
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/urllib2.py", line 449, in _open
    '_open', req)
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/urllib2.py", line 409, in _call_chain
    result = func(*args)
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/urllib2.py", line 1227, in http_open
    return self.do_open(httplib.HTTPConnection, req)
  File "/cbio/jclab/home/albaness/miniconda/lib/python2.7/urllib2.py", line 1197, in do_open
    raise URLError(err)
urllib2.URLError: <urlopen error [Errno 110] Connection timed out>

Still looking into how to fix this