fgcz / bfabricPy

API and commad line tools for b-fabric

Home Page:https://fgcz.github.io/bfabricPy/

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make `python3 -m unittest fgcz_maxquant_wrapper.py` pass

cpanse opened this issue · comments

cp@dhcp-wlan-eduroam-10-16-0-099:~/__checkouts/bfabricPy/bfabric/scripts  (bfabric9)> python3 -m unittest fgcz_maxquant_wrapper.py 
.../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/yaml/constructor.py:126: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
  if not isinstance(key, collections.Hashable):
no scratch dir '/scratch/MAXQUANT/WU181492'.
E
======================================================================
ERROR: test_xml (fgcz_maxquant_wrapper.TestFgczMaxQuantConfig)
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Traceback (most recent call last):
  File "/Users/cp/__checkouts/bfabricPy/bfabric/scripts/fgcz_maxquant_wrapper.py", line 670, in test_xml
    MQC.generate_mqpar("/tmp/output.xml", xml_template=mqpartree)
  File "/Users/cp/__checkouts/bfabricPy/bfabric/scripts/fgcz_maxquant_wrapper.py", line 89, in generate_mqpar
    element = xml_template.find(query)
  File "src/lxml/etree.pyx", line 1527, in lxml.etree._Element.find
  File "src/lxml/_elementpath.py", line 311, in lxml._elementpath.find
  File "src/lxml/_elementpath.py", line 300, in lxml._elementpath.iterfind
  File "src/lxml/_elementpath.py", line 269, in lxml._elementpath._build_path_iterator
  File "<string>", line None
SyntaxError: cannot use absolute path on element

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Ran 4 tests in 0.030s

FAILED (errors=1)