htsworkflow/util/rdfhelp.py

   1 """Helper features for working with librdf
   2 """
   3 import os
   4 import types
   5
   6 import RDF
   7
   8 # standard ontology namespaces
   9 owlNS = RDF.NS('http://www.w3.org/2002/07/owl#')
  10 dublinCoreNS = RDF.NS("http://purl.org/dc/elements/1.1/")
  11 rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
  12 rdfsNS= RDF.NS("http://www.w3.org/2000/01/rdf-schema#")
  13 xsdNS = RDF.NS("http://www.w3.org/2001/XMLSchema#")
  14
  15 # internal ontologies
  16 submissionOntology = RDF.NS("http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#")
  17 dafTermOntology = RDF.NS("http://jumpgate.caltech.edu/wiki/UcscDaf#")
  18 libraryOntology = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
  19 submissionLog = RDF.NS("http://jumpgate.caltech.edu/wiki/SubmissionsLog/")
  20
  21 def blankOrUri(value=None):
  22     node = None
  23     if value is None:
  24         node = RDF.Node()
  25     elif type(value) in types.StringTypes:
  26         node = RDF.Node(uri_string=value)
  27     elif isinstance(value, RDF.Node):
  28         node = value
  29
  30     return node
  31
  32
  33 def toTypedNode(value):
  34     if type(value) == types.BooleanType:
  35         value_type = xsdNS['boolean'].uri
  36         if value:
  37             value = u'1'
  38         else:
  39             value = u'0'
  40     elif type(value) in (types.IntType, types.LongType):
  41         value_type = xsdNS['decimal'].uri
  42         value = unicode(value)
  43     elif type(value) == types.FloatType:
  44         value_type = xsdNS['float'].uri
  45         value = unicode(value)
  46     elif type(value) in types.StringTypes:
  47         value_type = xsdNS['string'].uri
  48     else:
  49         value_type = None
  50         value = unicode(value)
  51
  52     return RDF.Node(literal=value, datatype=value_type)
  53
  54 def fromTypedNode(node):
  55     if node is None:
  56         return None
  57
  58     value_type = str(node.literal_value['datatype'])
  59     # chop off xml schema declaration
  60     value_type = value_type.replace(str(xsdNS[''].uri),'')
  61     literal = node.literal_value['string']
  62     literal_lower = literal.lower()
  63
  64     if value_type == 'boolean':
  65         if literal_lower in ('1', 'yes', 'true'):
  66             return True
  67         elif literal_lower in ('0', 'no', 'false'):
  68             return False
  69         else:
  70             raise ValueError("Unrecognized boolean %s" % (literal,))
  71     elif value_type == 'decimal' and literal.find('.') == -1:
  72         return int(literal)
  73     elif value_type in ('decimal', 'float', 'double'):
  74         return float(literal)
  75     elif value_type in ('string'):
  76         return literal
  77     elif value_type in ('dateTime'):
  78         raise NotImplemented('need to parse isoformat date-time')
  79
  80     return literal
  81
  82
  83 def get_model(model_name=None, directory=None):
  84     if directory is None:
  85         directory = os.getcwd()
  86
  87     if model_name is None:
  88         storage = RDF.MemoryStorage()
  89     else:
  90         storage = RDF.HashStorage(model_name,
  91                       options="hash-type='bdb',dir='{0}'".format(directory))
  92     model = RDF.Model(storage)
  93     return model
  94
  95
  96 def load_into_model(model, parser_name, filename, ns=None):
  97     if not os.path.exists(filename):
  98         raise IOError("Can't find {0}".format(filename))
  99
 100     data = open(filename, 'r').read()
 101     rdf_parser = RDF.Parser(name=parser_name)
 102     rdf_parser.parse_string_into_model(model, data, ns)
 103
 104
 105 def get_serializer(name='turtle'):
 106     """Return a serializer with our standard prefixes loaded
 107     """
 108     writer = RDF.Serializer(name=name)
 109     # really standard stuff
 110     writer.set_namespace('owl', owlNS._prefix)
 111     writer.set_namespace('rdf', rdfNS._prefix)
 112     writer.set_namespace('rdfs', rdfsNS._prefix)
 113     writer.set_namespace('xsd', xsdNS._prefix)
 114
 115     # should these be here, kind of specific to an application
 116     writer.set_namespace('libraryOntology', libraryOntology._prefix)
 117     writer.set_namespace('ucscSubmission', submissionOntology._prefix)
 118     writer.set_namespace('ucscDaf', dafTermOntology._prefix)
 119     return writer
 120