Rework ucsc gather to use RDF models for gathering and storing track metadata.

[htsworkflow.git] / htsworkflow / util / rdfhelp.py

diff --git a/htsworkflow/util/rdfhelp.py b/htsworkflow/util/rdfhelp.py
index 7e9deda4e6497601abdaf130a795b860fee5b48d..8afa13255d0ae5d6d775681778796357db965dc7 100644 (file)
--- a/htsworkflow/util/rdfhelp.py
+++ b/htsworkflow/util/rdfhelp.py
@@ -1,17 +1,22 @@
 """Helper features for working with librdf
 """
-import RDF
+import os
 import types
 
+import RDF
+
 # standard ontology namespaces
+owlNS = RDF.NS('http://www.w3.org/2002/07/owl#')
 dublinCoreNS = RDF.NS("http://purl.org/dc/elements/1.1/")
 rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
 rdfsNS= RDF.NS("http://www.w3.org/2000/01/rdf-schema#")
 xsdNS = RDF.NS("http://www.w3.org/2001/XMLSchema#")
 
 # internal ontologies
-submitOntology = RDF.NS("http://jumpgate.caltech.edu/wiki/UCSCSubmissionOntology#")
+submissionOntology = RDF.NS("http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#")
+dafTermOntology = RDF.NS("http://jumpgate.caltech.edu/wiki/UcscDaf#")
 libraryOntology = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
+submissionLog = RDF.NS("http://jumpgate.caltech.edu/wiki/SubmissionsLog/")
 
 def blankOrUri(value=None):
     node = None
@@ -32,6 +37,12 @@ def toTypedNode(value):
             value = u'1'
         else:
             value = u'0'
+    elif type(value) in (types.IntType, types.LongType):
+        value_type = xsdNS['decimal'].uri
+        value = unicode(value)
+    elif type(value) == types.FloatType:
+        value_type = xsdNS['float'].uri
+        value = unicode(value)
     elif type(value) in types.StringTypes:
         value_type = xsdNS['string'].uri
     else:
@@ -39,4 +50,71 @@ def toTypedNode(value):
         value = unicode(value)
 
     return RDF.Node(literal=value, datatype=value_type)
+
+def fromTypedNode(node):
+    if node is None:
+        return None
+    
+    value_type = str(node.literal_value['datatype'])
+    # chop off xml schema declaration
+    value_type = value_type.replace(str(xsdNS[''].uri),'')
+    literal = node.literal_value['string']
+    literal_lower = literal.lower()
+
+    if value_type == 'boolean':
+        if literal_lower in ('1', 'yes', 'true'):
+            return True
+        elif literal_lower in ('0', 'no', 'false'):
+            return False
+        else:
+            raise ValueError("Unrecognized boolean %s" % (literal,))
+    elif value_type == 'decimal' and literal.find('.') == -1:
+        return int(literal)
+    elif value_type in ('decimal', 'float', 'double'):
+        return float(literal)
+    elif value_type in ('string'):
+        return literal
+    elif value_type in ('dateTime'):
+        raise NotImplemented('need to parse isoformat date-time')
+
+    return literal
+
+
+def get_model(model_name=None, directory=None):
+    if directory is None:
+        directory = os.getcwd()
+        
+    if model_name is None:
+        storage = RDF.MemoryStorage()
+    else:
+        storage = RDF.HashStorage(model_name,
+                      options="hash-type='bdb',dir='{0}'".format(directory))
+    model = RDF.Model(storage)
+    return model
+        
+
+def load_into_model(model, parser_name, filename, ns=None):
+    if not os.path.exists(filename):
+        raise IOError("Can't find {0}".format(filename))
     
+    data = open(filename, 'r').read()
+    rdf_parser = RDF.Parser(name=parser_name)
+    rdf_parser.parse_string_into_model(model, data, ns)
+
+
+def get_serializer(name='turtle'):
+    """Return a serializer with our standard prefixes loaded
+    """
+    writer = RDF.Serializer(name=name)
+    # really standard stuff
+    writer.set_namespace('owl', owlNS._prefix)
+    writer.set_namespace('rdf', rdfNS._prefix)
+    writer.set_namespace('rdfs', rdfsNS._prefix)
+    writer.set_namespace('xsd', xsdNS._prefix)
+
+    # should these be here, kind of specific to an application
+    writer.set_namespace('libraryOntology', libraryOntology._prefix)
+    writer.set_namespace('ucscSubmission', submissionOntology._prefix)
+    writer.set_namespace('ucscDaf', dafTermOntology._prefix)
+    return writer
+