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Serialized turtle file fails parsing #345

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brameshvt opened this issue Nov 20, 2013 · 1 comment
Closed

Serialized turtle file fails parsing #345

brameshvt opened this issue Nov 20, 2013 · 1 comment

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@brameshvt
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I am exploring migrating from rdflib-3.2.3 to rdflib-4.0.1 in our project. During the testing I noticed an issue where in if I serialize a graph into turtle format and then try to reload it will fail during the parsing stage. I figured this was because of auto generation of prefixes like "ns1", "ns2". I have a small test case that one can use to test this behavior in rdflib-4.0.1.

>>> import rdflib
>>> inp_data = """
... <http://www.example.com/foo/user.id?id=abcdefgh> a <http://www.example.com/foo#user.id>;
...     <http://www.example.com/bar#date.dob> "01/01/2001" ;
...     <http://www.example.com/bar#date.start> "10/10/2010" ;
...     <http://www.example.com/bar#date.end> "" ;
...     <http://www.example.com/bar#emp.room> "room 45";
...     <http://www.example.com/foo#type> "temp" .
... """
>>> g = rdflib.Graph().parse(data=inp_data, format="turtle")
>>> new_data = g.serialize(format="turtle")
>>> new_g = rdflib.Graph().parse(data=new_data, format="turtle")
Traceback (most recent call last):                                                                                                                                               
  File "<stdin>", line 1, in <module>                                                                                                                                            
  File "/home/bharath/rdflib-4.0.1/lib/python2.7/site-packages/rdflib/graph.py", line 1002, in parse                                                                             
    parser.parse(source, self, **args)                                                                                                                                           
  File "/home/bharath/rdflib-4.0.1/lib/python2.7/site-packages/rdflib/plugins/parsers/notation3.py", line 1739, in parse                                                         
    p.loadStream(source.getByteStream())                                                                                                                                         
  File "/home/bharath/rdflib-4.0.1/lib/python2.7/site-packages/rdflib/plugins/parsers/notation3.py", line 398, in loadStream                                                     
    return self.loadBuf(stream.read())    # Not ideal                                                                                                                            
  File "/home/bharath/rdflib-4.0.1/lib/python2.7/site-packages/rdflib/plugins/parsers/notation3.py", line 404, in loadBuf                                                        
    self.feed(buf)                                                                                                                                                               
  File "/home/bharath/rdflib-4.0.1/lib/python2.7/site-packages/rdflib/plugins/parsers/notation3.py", line 430, in feed                                                           
    i = self.directiveOrStatement(s, j)                                                                                                                                          
  File "/home/bharath/rdflib-4.0.1/lib/python2.7/site-packages/rdflib/plugins/parsers/notation3.py", line 447, in directiveOrStatement                                           
    j = self.statement(argstr, i)                                                                                                                                                
  File "/home/bharath/rdflib-4.0.1/lib/python2.7/site-packages/rdflib/plugins/parsers/notation3.py", line 608, in statement                                                      
    j = self.property_list(argstr, i, r[0])                                                                                                                                      
  File "/home/bharath/rdflib-4.0.1/lib/python2.7/site-packages/rdflib/plugins/parsers/notation3.py", line 975, in property_list                                                  
    i = self.objectList(argstr, j, objs)                                                                                                                                         
  File "/home/bharath/rdflib-4.0.1/lib/python2.7/site-packages/rdflib/plugins/parsers/notation3.py", line 1027, in objectList                                                    
    i = self.object(argstr, i, res)                                                                                                                                              
  File "/home/bharath/rdflib-4.0.1/lib/python2.7/site-packages/rdflib/plugins/parsers/notation3.py", line 1259, in object                                                        
    j = self.subject(argstr, i, res)                                                                                                                                             
  File "/home/bharath/rdflib-4.0.1/lib/python2.7/site-packages/rdflib/plugins/parsers/notation3.py", line 617, in subject                                                        
    return self.item(argstr, i, res)                                                                                                                                             
  File "/home/bharath/rdflib-4.0.1/lib/python2.7/site-packages/rdflib/plugins/parsers/notation3.py", line 703, in item                                                           
    return self.path(argstr, i, res)                                                                                                                                             
  File "/home/bharath/rdflib-4.0.1/lib/python2.7/site-packages/rdflib/plugins/parsers/notation3.py", line 733, in path                                                           
    "EOF found in middle of path syntax")
rdflib.plugins.parsers.notation3.BadSyntax: at line 8 of <>:
Bad syntax (EOF found in middle of path syntax) at ^ in:
"@prefix ns1: <http://www.example.com/foo#> .
@prefix ns2: <http://www.example.com/bar#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

<http://www.example.com/foo/user.id?id=abcdefgh> a ns1:user.id ;
    ns2:date.dob "01/01/2001" ;
    ns2:date.end "" ;
    ns2:date.start "10/10/2010" ;
    ns2:emp.room "room 45" ;
    ns1:type "temp" .
^..."
@gromgull
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It's a bug alright, but not in the serializer, amazingly, a dot (.) inside the localname of a qname is allowed:

PN_LOCAL    ::= (PN_CHARS_U | ':' | [0-9] | PLX) ((PN_CHARS | '.' | ':' | PLX)* (PN_CHARS | ':' | PLX))?

So it's the parser that is broken. I will code up a fix shortly.

mamash pushed a commit to TritonDataCenter/pkgsrc-wip that referenced this issue Feb 15, 2014
	2013/12/31 RELEASE 4.1
======================

This is a new minor version RDFLib, which includes a handful of new features:

* A TriG parser was added (we already had a serializer) - it is
  up-to-date wrt. to the newest spec from: http://www.w3.org/TR/trig/

* The Turtle parser was made up to date wrt. to the latest Turtle spec.

* Many more tests have been added - RDFLib now has over 2000
  (passing!) tests. This is mainly thanks to the NT, Turtle, TriG,
  NQuads and SPARQL test-suites from W3C. This also included many
  fixes to the nt and nquad parsers.

* ```ConjunctiveGraph``` and ```Dataset``` now support directly adding/removing
  quads with ```add/addN/remove``` methods.

* ```rdfpipe``` command now supports datasets, and reading/writing context
  sensitive formats.

* Optional graph-tracking was added to the Store interface, allowing
  empty graphs to be tracked for Datasets. The DataSet class also saw
  a general clean-up, see: RDFLib/rdflib#309

* After long deprecation, ```BackwardCompatibleGraph``` was removed.

Minor enhancements/bugs fixed:
------------------------------

* Many code samples in the documentation were fixed thanks to @PuckCh

* The new ```IOMemory``` store was optimised a bit

* ```SPARQL(Update)Store``` has been made more generic.

* MD5 sums were never reinitialized in ```rdflib.compare```

* Correct default value for empty prefix in N3
  [#312]RDFLib/rdflib#312

* Fixed tests when running in a non UTF-8 locale
  [#344]RDFLib/rdflib#344

* Prefix in the original turtle have an impact on SPARQL query
  resolution
  [#313]RDFLib/rdflib#313

* Duplicate BNode IDs from N3 Parser
  [#305]RDFLib/rdflib#305

* Use QNames for TriG graph names
  [#330]RDFLib/rdflib#330

* \uXXXX escapes in Turtle/N3 were fixed
  [#335]RDFLib/rdflib#335

* A way to limit the number of triples retrieved from the
  ```SPARQLStore``` was added
  [#346]RDFLib/rdflib#346

* Dots in localnames in Turtle
  [#345]RDFLib/rdflib#345
  [#336]RDFLib/rdflib#336

* ```BNode``` as Graph's public ID
  [#300]RDFLib/rdflib#300

* Introduced ordering of ```QuotedGraphs```
  [#291]RDFLib/rdflib#291

2013/05/22 RELEASE 4.0.1
========================

Following RDFLib tradition, some bugs snuck into the 4.0 release.
This is a bug-fixing release:

* the new URI validation caused lots of problems, but is
  nescessary to avoid ''RDF injection'' vulnerabilities. In the
  spirit of ''be liberal in what you accept, but conservative in
  what you produce", we moved validation to serialisation time.

* the   ```rdflib.tools```   package    was   missing   from   the
  ```setup.py```  script, and  was therefore  not included  in the
  PYPI tarballs.

* RDF parser choked on empty namespace URI
  [#288](RDFLib/rdflib#288)

* Parsing from ```sys.stdin``` was broken
  [#285](RDFLib/rdflib#285)

* The new IO store had problems with concurrent modifications if
  several graphs used the same store
  [#286](RDFLib/rdflib#286)

* Moved HTML5Lib dependency to the recently released 1.0b1 which
  support python3

2013/05/16 RELEASE 4.0
======================

This release includes several major changes:

* The new SPARQL 1.1 engine (rdflib-sparql) has been included in
  the core distribution. SPARQL 1.1 queries and updates should
  work out of the box.

  * SPARQL paths are exposed as operators on ```URIRefs```, these can
    then be be used with graph.triples and friends:

    ```py
    # List names of friends of Bob:
    g.triples(( bob, FOAF.knows/FOAF.name , None ))

    # All super-classes:
    g.triples(( cls, RDFS.subClassOf * '+', None ))
    ```

      * a new ```graph.update``` method will apply SPARQL update statements

* Several RDF 1.1 features are available:
  * A new ```DataSet``` class
  * ```XMLLiteral``` and ```HTMLLiterals```
  * ```BNode``` (de)skolemization is supported through ```BNode.skolemize```,
    ```URIRef.de_skolemize```, ```Graph.skolemize``` and ```Graph.de_skolemize```

* Handled of Literal equality was split into lexical comparison
  (for normal ```==``` operator) and value space (using new ```Node.eq```
  methods). This introduces some slight backwards incomaptible
  changes, but was necessary, as the old version had
  inconsisten hash and equality methods that could lead the
  literals not working correctly in dicts/sets.
  The new way is more in line with how SPARQL 1.1 works.
  For the full details, see:

  https://github.com/RDFLib/rdflib/wiki/Literal-reworking

* Iterating over ```QueryResults``` will generate ```ResultRow``` objects,
  these allow access to variable bindings as attributes or as a
  dict. I.e.

  ```py
  for row in graph.query('select ... ') :
     print row.age, row["name"]
  ```

* "Slicing" of Graphs and Resources as syntactic sugar:
  ([#271](RDFLib/rdflib#271))

  ```py
  graph[bob : FOAF.knows/FOAF.name]
            -> generator over the names of Bobs friends
  ```

* The ```SPARQLStore``` and ```SPARQLUpdateStore``` are now included
  in the RDFLib core

* The documentation has been given a major overhaul, and examples
  for most features have been added.


Minor Changes:
--------------

* String operations on URIRefs return new URIRefs: ([#258](RDFLib/rdflib#258))
  ```py
  >>> URIRef('http://example.org/')+'test
  rdflib.term.URIRef('http://example.org/test')
  ```

* Parser/Serializer plugins are also found by mime-type, not just
  by plugin name:  ([#277](RDFLib/rdflib#277))
* ```Namespace``` is no longer a subclass of ```URIRef```
* URIRefs and Literal language tags are validated on construction,
  avoiding some "RDF-injection" issues ([#266](RDFLib/rdflib#266))
* A new memory store needs much less memory when loading large
  graphs ([#268](RDFLib/rdflib#268))
* Turtle/N3 serializer now supports the base keyword correctly ([#248](RDFLib/rdflib#248))
* py2exe support was fixed ([#257](RDFLib/rdflib#257))
* Several bugs in the TriG serializer were fixed
* Several bugs in the NQuads parser were fixed
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