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Tests fail for a new installation of pyPPI. #2

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Aniket-Pradhan opened this issue Aug 31, 2018 · 2 comments
Open

Tests fail for a new installation of pyPPI. #2

Aniket-Pradhan opened this issue Aug 31, 2018 · 2 comments

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@Aniket-Pradhan
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Hey!

I was trying to use pyPPI on my PC. I followed the steps mentioned on the docs, and the tests always fail.

I built and installed the package in a virtual environment. After that, I downloaded the required data (It takes forever to download it). However, whenever I run python setup.py test it says test failed, giving an output as below.

running test
/home/major/.local/share/virtualenvs/pyPPI-nTZk3L3o/lib/python3.7/site-packages/scikit_learn-0.19.2-py3.7-linux-x86_64.egg/sklearn/feature_extraction/text.py:17: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
  from collections import Mapping, defaultdict
/home/major/.local/share/virtualenvs/pyPPI-nTZk3L3o/lib/python3.7/site-packages/scikit_learn-0.19.2-py3.7-linux-x86_64.egg/sklearn/ensemble/weight_boosting.py:29: DeprecationWarning: numpy.core.umath_tests is an internal NumPy module and should not be imported. It will be removed in a future NumPy release.
  from numpy.core.umath_tests import inner1d
........................................................................................................................................................................................................................................................................................2018-08-31 18:50:41 pyppi    WARNING  No protein for '"about:legacy-compat">' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for SYSTEM.
2018-08-31 18:50:41 pyppi    WARNING  Could not map SYSTEM.
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'xmlns="http://www.w3.org/1999/xhtml"' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for <html.
2018-08-31 18:50:41 pyppi    WARNING  Could not map <html.
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'xml:lang="en"><head><title>Retrieve/ID' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for lang="en".
2018-08-31 18:50:41 pyppi    WARNING  Could not map lang="en".
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'content="IE=edge"' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for mapping</title><meta.
2018-08-31 18:50:41 pyppi    WARNING  Could not map mapping</title><meta.
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'content="text/html;' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for http-equiv="X-UA-Compatible"/><meta.
2018-08-31 18:50:41 pyppi    WARNING  Could not map http-equiv="X-UA-Compatible"/><meta.
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'http-equiv="Content-Type"/><meta' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for charset=UTF-8".
2018-08-31 18:50:41 pyppi    WARNING  Could not map charset=UTF-8".
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'initial-scale=1"' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for content="width=device-width,.
2018-08-31 18:50:41 pyppi    WARNING  Could not map content="width=device-width,.
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'href="/"' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for name="viewport"/><link.
2018-08-31 18:50:41 pyppi    WARNING  Could not map name="viewport"/><link.
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'href="http://creativecommons.org/licenses/by-nd/3.0/"' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for rel="home"/><link.
2018-08-31 18:50:41 pyppi    WARNING  Could not map rel="home"/><link.
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'type="image/vnd.microsoft.icon"' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for rel="license"/><link.
2018-08-31 18:50:41 pyppi    WARNING  Could not map rel="license"/><link.
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'rel="shortcut' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for href="/favicon.ico".
2018-08-31 18:50:41 pyppi    WARNING  Could not map href="/favicon.ico".
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'href="/uniprot.min.css2018_07"' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for icon"/><link.
2018-08-31 18:50:41 pyppi    WARNING  Could not map icon"/><link.
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'rel="stylesheet"/><script' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for type="text/css".
2018-08-31 18:50:41 pyppi    WARNING  Could not map type="text/css".
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'var' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'uniprot.namespace' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'onRdyFn(uniprot.searchbar.init);' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'onRdyFn((new' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for type="text/javascript">.
2018-08-31 18:50:41 pyppi    WARNING  Could not map type="text/javascript">.
2018-08-31 18:50:41 pyppi    WARNING  No protein for '=' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No protein for '+' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for BASE.
2018-08-31 18:50:41 pyppi    WARNING  Could not map BASE.
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'var' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for '/';.
2018-08-31 18:50:41 pyppi    WARNING  Could not map '/';.
2018-08-31 18:50:41 pyppi    WARNING  No protein for '=' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for isInternal.
2018-08-31 18:50:41 pyppi    WARNING  Could not map isInternal.
2018-08-31 18:50:41 pyppi    WARNING  No protein for '</script><script' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for false;.
2018-08-31 18:50:41 pyppi    WARNING  Could not map false;.
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'type="text/javascript"></script><script' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:41 pyppi    WARNING  No reviewed acc found for src="/scripts/frontier/d3/d3.v3.min.js".
2018-08-31 18:50:41 pyppi    WARNING  Could not map src="/scripts/frontier/d3/d3.v3.min.js".
2018-08-31 18:50:41 pyppi    WARNING  No protein for 'type="text/javascript"></script><script' found in the database. Consider downloading the latest UniProt dat files and updating the database.

A little later after that, I got error messages like,

2018-08-31 18:50:42 pyppi    WARNING  No protein for 'id="help">Help</a></h3><p>Help' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:42 pyppi    WARNING  No protein for 'id="uniref">UniRef</a></h3><p>Sequence' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:42 pyppi    WARNING  No protein for 'id="saas">SAAS' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:42 pyppi    WARNING  No protein for 'id="taxonomy">Taxonomy</a></li><li><a' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:42 pyppi    WARNING  No protein for 'id="keywords">Keywords</a></li><li><a' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:42 pyppi    WARNING  No protein for 'id="locations">Subcellular' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:42 pyppi    WARNING  No protein for 'id="diseases">Human' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:42 pyppi    WARNING  No protein for 'class="closeBox"' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:42 pyppi    WARNING  No protein for 'class="icon' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:42 pyppi    WARNING  No reviewed acc found for href="#".
2018-08-31 18:50:42 pyppi    WARNING  Could not map href="#".
2018-08-31 18:50:42 pyppi    WARNING  No protein for 'class="fixedHeight_namespaces"><h3' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:42 pyppi    WARNING  No reviewed acc found for knowledgebase</p></li><li.
2018-08-31 18:50:42 pyppi    WARNING  Could not map knowledgebase</p></li><li.
2018-08-31 18:50:42 pyppi    WARNING  No protein for 'class="namespace-option' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:42 pyppi    WARNING  No reviewed acc found for class="namespace_uniparc"><a.
2018-08-31 18:50:42 pyppi    WARNING  Could not map class="namespace_uniparc"><a.
2018-08-31 18:50:42 pyppi    WARNING  No protein for 'href="#"' found in the database. Consider downloading the latest UniProt dat files and updating the database.
2018-08-31 18:50:42 pyppi    WARNING  No reviewed acc found for uniparc".
2018-08-31 18:50:42 pyppi    WARNING  Could not map uniparc".
2018-08-31 18:50:42 pyppi    WARNING  No protein for 'archive</p></li><li' found in the database. Consider downloading the latest UniProt dat files and updating the database.

In the end, I get a message saying that the test failed, and I got 3 fails, and 7 errors. I was unable to capture that output, but I got this message in the end.

My python version is:
Python 3.7.0

I have been using all of this in a virtual environment, so, I don't think my system files could've affected this. And, by seeing the output, I guess that it is also taking in the HTML code from the database as the Protein ID/Name.

Cheers.
@daniaki
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daniaki commented Sep 1, 2018

Thanks for letting me know! It definitely seems like it's trying to parse raw HTML. I'll look into this ASAP, but I suspect there might be an issue when interfacing with the biopython/bioservices UniProt APIs.

@Aniket-Pradhan
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Assuming that it was working earlier, I can only assume that BioPython Uniprot APIs have updated, or there's some change.

However, I can't find any such change over there.

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@daniaki @Aniket-Pradhan