studioevoque / python-dlp Goto Github PK

patch attached for remaining warnings -- looks as if most of them have already 
been fixed

See: http://www.w3.org/2000/10/swap/test/

I see you commited a relitive link 
/Users/chimezieogbuji/Projects/SemanticDB/SNOMED-CT/ManageSNOMED-CT.py

instead of ManageSNOMED-CT.py source

See: http://www.w3.org/2000/10/swap/test/

Man OWL rendering now uses capital letters for SOME, THAT, ONLY, etc. in order 
to distinguish them from the labels and 
identifiers of terms in the ontology being rendered

  Fixed here:

  http://code.google.com/p/fuxi/source/detail?r=134a4755c3bdc7545fc9666f5f6e6aa43020548a

[deleted issue]

source.getPublicID() should be source.getPublicId()

in:

def parse(self, source, publicID=None, format="xml", **args):
    """Parse source into Graph into it's own context (sub graph)

    Format defaults to xml (AKA rdf/xml). The publicID argument is for
    specifying the logical URI for the case that it's different from the
    physical source URI. Returns the context into which the source was
    parsed. In the case of n3 it returns the root context.
    """
    source = self.prepare_input_source(source, publicID)
    #id = self.context_id(self.absolutize(source.getPublicId()))
    context = Graph(store=self.store, identifier=
      publicID and URIRef(publicID) or source.getPublicID())
    context.remove((None, None, None))
    context.parse(source, publicID=publicID, format=format, **args)
    return context

If you use FuXi with --output=man-owl, for example, on an OWL file that has 
non-ascii unicode characters it will fail.  It should fail 'softly' via 
.encode('utf-8','ignore') instead.  Fixed here:

http://code.google.com/p/fuxi/source/detail?r=134a4755c3bdc7545fc9666f5f6e6aa430
20548a

I'm trying diligently to get up to speed on FuXi as part of an effort to 
demonstrate some basic 
semantic web inferencing via Python. In trying to wrap my head around all of 
this, I am running 
through the basic examples in the wiki and finding that one of them doesn't 
work. It appears 
that the actual output is quite different from what is expected as outlined in 
the wiki.

Is FuXi still in development or is this project not being actively developed 
anymore?

$ FuXi --ruleFacts --why="ASK { test:Ghent test:path test:Amsterdam }" --
ns=test=http://www.w3.org/2002/03owlt/TransitiveProperty/premises001# --dlp  --
output=conflict --debug  --method=both --strict=defaultDerived 
http://www.w3.org/2002/03owlt/TransitiveProperty/premises001
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Fu
Xi-
1.0_rc_II.dev-py2.6.egg/FuXi/Rete/AlphaNode.py:6: DeprecationWarning: the sets 
module is 
deprecated
  from sets import Set
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Fu
Xi-
1.0_rc_II.dev-py2.6.egg/FuXi/Rete/TopDown.py:12: DeprecationWarning: the md5 
module is 
deprecated; use hashlib instead
  import itertools, copy, md5
Time to build production rule (RDFLib): 7.5101852417e-05 seconds
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Fu
Xi-
1.0_rc_II.dev-py2.6.egg/FuXi/Rete/Magic.py:537: UserWarning: predicate symbol 
of test:path(?X 
?oEeWPnfn20) is in both IDB and EDB. Marking as derived
  "predicate symbol of %s is in both IDB and EDB. Marking as %s"%(term,mark))
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.6/bin/FuXi", line 8, in <module>
    load_entry_point('FuXi==1.0-rc-II.dev', 'console_scripts', 'FuXi')()
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/FuXi-
1.0_rc_II.dev-py2.6.egg/FuXi/Rete/CommandLine.py", line 404, in main
    defaultDerivedPreds))
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/FuXi-
1.0_rc_II.dev-py2.6.egg/FuXi/Rete/Magic.py", line 71, in SetupDDLAndAdornProgram
    return AdornProgram(factGraph,rules,GOALS,derivedPreds)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/FuXi-
1.0_rc_II.dev-py2.6.egg/FuXi/Rete/Magic.py", line 323, in AdornProgram
    adornedRule=AdornRule(derivedPreds,clause,term)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/FuXi-
1.0_rc_II.dev-py2.6.egg/FuXi/Rete/Magic.py", line 247, in AdornRule
    headArc = len(N)==1 and N[0] == GetOp(newHead)                
  File "build/bdist.macosx-10.3-fat/egg/rdflib/Collection.py", line 78, in __len__
AssertionError: There is a loop in the RDF list! 
(http://www.w3.org/2002/03owlt/TransitiveProperty/premises001#path has been 
processed 
before)

Build under python 2.6:

  File "/usr/local/lib/python2.6/dist-packages/FuXi-1.0_rc.dev_r310-
py2.6.egg/FuXi/Rete/CommandLine.py", line 182
    default=[],
SyntaxError: keyword argument repeated


The problem is easily fixed by removing that redundant line.

python-dlp/fuxi/lib/Syntax/__init__.py is missing @ revision 136.

I couldn't find a license for the library as a whole. The files in
lib/Rete/ have a Creative Commons license that does not allow commercial use. 

Could you please clarify the licensing of all the code, perhaps in a
'LICENSE' file at the top level?

Resulting OWL has significant redundancies with restrictions.  An example:

Class: sno:EntireHeartANDPericardium 
    ## Primitive Type (Entire heart AND pericardium) ##
    SNOMED-CT Code: 362010009 (a primitive concept)
    SubClassOf: ( ns1:part_of some Entire middle mediastinum )
                ( ro:part_of some Entire middle mediastinum )
                ( ro:part_of some Entire middle mediastinum )
                ( ro:part_of some Entire mediastinum )
                ( ro:part_of some Entire middle mediastinum )
                ( ro:part_of some Entire middle mediastinum )
                ( ro:part_of some Entire middle mediastinum )

/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/sha.py:8:
 DeprecationWarning: functions overriding warnings.showwarning() must support 
the 'line' argument
  DeprecationWarning, 2)
/Users/chimezieogbuji/Projects/python-dlp-devel/trunk/layercake-python/rdflib/st
ore/AbstractSQLStore.py:8: DeprecationWarning: the sha module is deprecated; 
use the hashlib module instead
  import sha,sys, weakref

What steps will reproduce the problem?
1. declare a unionOf class, eg: c = a | b
2. declare a property
3. declare a Restriction, eg: r = property |exactly| Literal(1)
4. serialize the graph in pretty-XML or XML format (no problem in n3 
format, I think)

What is the expected output? What do you see instead?
Expected output is a normal unionOf containing a and b. Sometimes (the 
way the graph is serialized makes the output result unstable), a or b is 
missing (see <issue.owl>, generated with <issue.py>).

What version of the product are you using? On what operating system?
Python 2.5.1, rdflib 2.4.0, FuXi 0.85b.dev_r196 on Ubuntu 7.10