G-Node · achilleas-k · Aug 1, 2018 · Jul 30, 2018 · Jul 30, 2018 · Jul 30, 2018
diff --git a/odml/doc.py b/odml/doc.py
@@ -37,6 +37,10 @@ def __init__(self, author=None, date=None, version=None, repository=None, oid=No
         self._date = None
         self.date = date
 
+        # Enable setting of the file name from whence this document came.
+        # It is for knowing while processing and will not be serialized to a file.
+        self._origin_file_name = None
+
     def __repr__(self):
         return "<Doc %s by %s (%d sections)>" % (self._version, self._author,
                                                  len(self._sections))

diff --git a/odml/tools/odmlparser.py b/odml/tools/odmlparser.py
@@ -7,8 +7,11 @@
 
 import datetime
 import json
+import sys
 import yaml
 
+from os.path import basename
+
 from . import xmlparser
 from .dict_parser import DictWriter, DictReader
 from ..info import FORMAT_VERSION
@@ -17,6 +20,11 @@
 from .rdf_converter import RDFReader, RDFWriter
 from ..validation import Validation
 
+try:
+    unicode = unicode
+except NameError:
+    unicode = str
+
 
 class ODMLWriter:
     """
@@ -58,10 +66,10 @@ def to_string(self, odml_document):
         string_doc = ''
 
         if self.parser == 'XML':
-            string_doc = str(xmlparser.XMLWriter(odml_document))
+            string_doc = unicode(xmlparser.XMLWriter(odml_document))
         elif self.parser == "RDF":
             # Use turtle as default output format for now.
-            string_doc = RDFWriter(odml_document).get_rdf_str("turtle")
+            string_doc = RDFWriter(odml_document).get_rdf_str("xml")
         else:
             self.parsed_doc = DictWriter().to_dict(odml_document)
 
@@ -74,6 +82,9 @@ def to_string(self, odml_document):
                 string_doc = json.dumps(odml_output, indent=4,
                                         cls=JSONDateTimeSerializer)
 
+        if sys.version_info.major < 3:
+            string_doc = string_doc.encode("utf-8")
+
         return string_doc
 
 
@@ -122,6 +133,8 @@ def from_file(self, file, doc_format=None):
                     return
 
             self.doc = DictReader().to_odml(self.parsed_doc)
+            # Provide original file name via the in memory document
+            self.doc._origin_file_name = basename(file)
             return self.doc
 
         elif self.parser == 'JSON':
@@ -133,6 +146,8 @@ def from_file(self, file, doc_format=None):
                     return
 
             self.doc = DictReader().to_odml(self.parsed_doc)
+            # Provide original file name via the in memory document
+            self.doc._origin_file_name = basename(file)
             return self.doc
 
         elif self.parser == 'RDF':

diff --git a/odml/tools/rdf_converter.py b/odml/tools/rdf_converter.py
@@ -73,7 +73,7 @@ def save_element(self, e, node=None):
         fmt = e.format()
 
         if not node:
-            curr_node = URIRef(odmlns + str(e.id))
+            curr_node = URIRef(odmlns + unicode(e.id))
         else:
             curr_node = node
 
@@ -88,6 +88,11 @@ def save_element(self, e, node=None):
         if isinstance(fmt, Document.__class__):
             self.g.add((self.hub_root, odmlns.hasDocument, curr_node))
 
+            # If available add the documents filename to the document node
+            # so we can identify where the data came from.
+            if hasattr(e, "_origin_file_name"):
+                self.g.add((curr_node, odmlns.hasFileName, Literal(e._origin_file_name)))
+
         for k in fmt.rdf_map_keys:
             if k == 'id':
                 continue
@@ -101,7 +106,7 @@ def save_element(self, e, node=None):
                     self.g.add((curr_node, fmt.rdf_map(k), terminology_node))
                 else:
                     # adding terminology to the hub and to link with the doc
-                    node = URIRef(odmlns + str(uuid.uuid4()))
+                    node = URIRef(odmlns + unicode(uuid.uuid4()))
                     self.g.add((node, RDF.type, URIRef(terminology_url)))
                     self.g.add((self.hub_root, odmlns.hasTerminology, node))
                     self.g.add((curr_node, fmt.rdf_map(k), node))
@@ -111,20 +116,20 @@ def save_element(self, e, node=None):
                     k == 'sections' and len(getattr(e, k)) > 0:
                 sections = getattr(e, k)
                 for s in sections:
-                    node = URIRef(odmlns + str(s.id))
+                    node = URIRef(odmlns + unicode(s.id))
                     self.g.add((curr_node, fmt.rdf_map(k), node))
                     self.save_element(s, node)
             elif isinstance(fmt, Section.__class__) and \
                     k == 'properties' and len(getattr(e, k)) > 0:
                 properties = getattr(e, k)
                 for p in properties:
-                    node = URIRef(odmlns + str(p.id))
+                    node = URIRef(odmlns + unicode(p.id))
                     self.g.add((curr_node, fmt.rdf_map(k), node))
                     self.save_element(p, node)
             elif isinstance(fmt, Property.__class__) and \
                     k == 'value' and len(getattr(e, k)) > 0:
                 values = getattr(e, k)
-                seq = URIRef(odmlns + str(uuid.uuid4()))
+                seq = URIRef(odmlns + unicode(uuid.uuid4()))
                 self.g.add((seq, RDF.type, RDF.Seq))
                 self.g.add((curr_node, fmt.rdf_map(k), seq))
                 # rdflib so far does not respect RDF:li item order
@@ -133,15 +138,15 @@ def save_element(self, e, node=None):
                 # this should be reversed to RDF:li again!
                 # see https://github.com/RDFLib/rdflib/issues/280
                 # -- keep until supported
-                # bag = URIRef(odmlns + str(uuid.uuid4()))
+                # bag = URIRef(odmlns + unicode(uuid.uuid4()))
                 # self.g.add((bag, RDF.type, RDF.Bag))
                 # self.g.add((curr_node, fmt.rdf_map(k), bag))
                 # for v in values:
                 #     self.g.add((bag, RDF.li, Literal(v)))
 
                 counter = 1
                 for v in values:
-                    pred = "%s_%s" % (str(RDF), counter)
+                    pred = "%s_%s" % (unicode(RDF), counter)
                     self.g.add((seq, URIRef(pred), Literal(v)))
                     counter = counter + 1
 
@@ -222,7 +227,11 @@ def to_odml(self):
 
     def from_file(self, filename, doc_format):
         self.g = Graph().parse(source=filename, format=doc_format)
-        return self.to_odml()
+        docs = self.to_odml()
+        for d in docs:
+            # Provide original file name via the document
+            d._origin_file_name = os.path.basename(filename)
+        return docs
 
     def from_string(self, file, doc_format):
         self.g = Graph().parse(source=StringIO(file), format=doc_format)
@@ -242,7 +251,7 @@ def parse_document(self, doc_uri):
                 doc_attrs[attr[0]] = doc_uri.split("#", 1)[1]
             else:
                 if len(elems) > 0:
-                    doc_attrs[attr[0]] = str(elems[0].toPython())
+                    doc_attrs[attr[0]] = unicode(elems[0].toPython())
 
         return {'Document': doc_attrs, 'odml-version': FORMAT_VERSION}
 
@@ -264,7 +273,7 @@ def parse_section(self, sec_uri):
                 sec_attrs[attr[0]] = sec_uri.split("#", 1)[1]
             else:
                 if len(elems) > 0:
-                    sec_attrs[attr[0]] = str(elems[0].toPython())
+                    sec_attrs[attr[0]] = unicode(elems[0].toPython())
         self._check_mandatory_attrs(sec_attrs)
         return sec_attrs
 
@@ -293,7 +302,7 @@ def parse_property(self, prop_uri):
                 prop_attrs[attr[0]] = prop_uri.split("#", 1)[1]
             else:
                 if len(elems) > 0:
-                    prop_attrs[attr[0]] = str(elems[0].toPython())
+                    prop_attrs[attr[0]] = unicode(elems[0].toPython())
         self._check_mandatory_attrs(prop_attrs)
         return prop_attrs
 

diff --git a/odml/tools/version_converter.py b/odml/tools/version_converter.py
@@ -53,7 +53,8 @@ def _parse_xml(self):
                 doc = doc.replace(elem, val)
 
         # Make sure encoding is present for the xml parser
-        doc = doc.encode('utf-8')
+        if sys.version_info.major > 2:
+            doc = doc.encode('utf-8')
 
         # Make pretty print available by resetting format
         parser = ET.XMLParser(remove_blank_text=True)

diff --git a/odml/tools/xmlparser.py b/odml/tools/xmlparser.py
@@ -10,6 +10,7 @@
 from lxml.builder import E
 # this is needed for py2exe to include lxml completely
 from lxml import _elementpath as _dummy
+from os.path import basename
 
 try:
     from StringIO import StringIO
@@ -187,7 +188,12 @@ def from_file(self, xml_file):
             raise ParserException(e.msg)
 
         self._handle_version(root)
-        return self.parse_element(root)
+        doc = self.parse_element(root)
+
+        # Provide original file name via the in memory document
+        if isinstance(xml_file, unicode):
+            doc._origin_file_name = basename(xml_file)
+        return doc
 
     def from_string(self, string):
         try:

diff --git a/test/test_parser_odml.py b/test/test_parser_odml.py
@@ -83,7 +83,7 @@ def test_json_file(self):
 
     def test_rdf_file(self):
         self.rdf_writer.write_file(self.odml_doc, self.rdf_file)
-        rdf_doc = self.rdf_reader.from_file(self.rdf_file, "turtle")
+        rdf_doc = self.rdf_reader.from_file(self.rdf_file, "xml")
 
         self.assertEqual(self.odml_doc, rdf_doc[0])