Parser and converter refactoring I

odml/__init__.py

@@ -6,7 +6,7 @@
 from .dtypes import DType
 from .fileio import load, save, display
 from .info import VERSION
-from .tools.odmlparser import allowed_parsers as parsers
+from .tools.parser_utils import SUPPORTED_PARSERS as PARSERS
 
 __version__ = VERSION
 

odml/base.py

@@ -4,8 +4,9 @@
 """
 
 import posixpath
-from odml import terminology
-from odml.tools.doc_inherit import inherit_docstring, allow_inherit_docstring
+
+from . import terminology
+from .tools.doc_inherit import inherit_docstring, allow_inherit_docstring
 
 
 class _baseobj(object):
@@ -15,6 +16,9 @@ class _baseobj(object):
 class baseobject(_baseobj):
     _format = None
 
+    def format(self):
+        return self._format
+
     @property
     def document(self):
         """ Returns the Document object in which this object is contained """

odml/doc.py

@@ -1,11 +1,11 @@
 # -*- coding: utf-8
 import uuid
 
-import odml.base as base
-import odml.dtypes as dtypes
-import odml.format as format
-import odml.terminology as terminology
-from odml.tools.doc_inherit import inherit_docstring, allow_inherit_docstring
+from . import base
+from . import dtypes
+from . import format
+from . import terminology
+from .tools.doc_inherit import inherit_docstring, allow_inherit_docstring
 
 
 class Document(base._baseobj):

odml/fileio.py

@@ -1,7 +1,5 @@
 import os
-from .tools.odmlparser import ODMLReader, ODMLWriter, allowed_parsers
-
-PARSERS = allowed_parsers
+from .tools.odmlparser import ODMLReader, ODMLWriter
 
 
 def load(filename, backend="xml"):

odml/format.py

@@ -11,20 +11,53 @@
 
 
 class Format(object):
+    _name = ""
+    _args = {}
     _map = {}
     _rev_map = None
     _rdf_map = {}
     _rdf_type = None
     _ns = Namespace("https://g-node.org/projects/odml-rdf#")
 
+    @property
+    def name(self):
+        """Returns the name of the current odML format"""
+        return self._name
+
+    @property
+    def arguments(self):
+        """Returns all items in the current odML format argument dict"""
+        return self._args.items()
+
+    @property
+    def arguments_keys(self):
+        """Returns all keys of the current odML format argument dict"""
+        return self._args.keys()
+
     def map(self, name):
         """ Maps an odml name to a python name """
         return self._map.get(name, name)
 
+    @property
+    def map_keys(self):
+        """Returns all keys of the current odML format map dict"""
+        return self._map.keys()
+
     def rdf_map(self, name):
         """ Maps a python name to a odml rdf namespace """
         return self._rdf_map.get(name, name)
 
+    @property
+    def rdf_map_keys(self):
+        """Returns all keys of the current odML format RDF map dict"""
+        return self._rdf_map.keys()
+
+    @property
+    def rdf_map_items(self):
+        """Returns all items of the current odML format RDF map dict"""
+        return self._rdf_map.items()
+
+    @property
     def rdf_type(self):
         """ Return rdf type of an object """
         return self._rdf_type

odml/property.py

@@ -2,10 +2,10 @@
 
 import uuid
 
-import odml.base as base
-import odml.dtypes as dtypes
-import odml.format as frmt
-from odml.tools.doc_inherit import inherit_docstring, allow_inherit_docstring
+from . import base
+from . import dtypes
+from . import format as frmt
+from .tools.doc_inherit import inherit_docstring, allow_inherit_docstring
 
 
 class Property(base._baseobj):
@@ -19,8 +19,8 @@ class BaseProperty(base.baseobject, Property):
 
     def __init__(self, name, value=None, parent=None, unit=None,
                  uncertainty=None, reference=None, definition=None,
-                 dependency=None, dependency_value=None, dtype=None, value_origin=None, id=None):
-        #TODO add description to :param value_origin
+                 dependency=None, dependency_value=None, dtype=None,
+                 value_origin=None, id=None):
         """
         Create a new Property with a single value. The method will try to infer
         the value's dtype from the type of the value if not explicitly stated.
@@ -46,7 +46,7 @@ def __init__(self, name, value=None, parent=None, unit=None,
         :param dependency_value: Dependency on a certain value.
         :param dtype: the data type of the values stored in the property,
                      if dtype is not given, the type is deduced from the values
-        :param value_origin:
+        :param value_origin: Reference where the value originated from e.g. a file name.
         """
         # TODO validate arguments
         try:
@@ -90,16 +90,19 @@ def __repr__(self):
     def dtype(self):
         """
         The data type of the value
-        If the data type is changed, it is tried, to convert the value to the
-        new type.
-        If this doesn't work, the change is refused.
-        This behaviour can be overridden by directly accessing the *_dtype*
-        attribute and adjusting the *data* attribute manually.
         """
         return self._dtype
 
     @dtype.setter
     def dtype(self, new_type):
+        """
+        If the data type of a property value is changed, it is tried
+        to convert the value to the new type.
+        If this doesn't work, the change is refused.
+
+        This behaviour can be overridden by directly accessing the *_dtype*
+        attribute and adjusting the *data* attribute manually.
+        """
         # check if this is a valid type
         if not dtypes.valid_type(new_type):
             raise AttributeError("'%s' is not a valid type." % new_type)
@@ -138,15 +141,15 @@ def parent(self, new_parent):
                 "odml.Property.parent: passed value is not of consistent type!"
                 "odml.Section expected")
 
-    def _validate_parent(self, new_parent):
+    @staticmethod
+    def _validate_parent(new_parent):
         from odml.section import BaseSection
         if isinstance(new_parent, BaseSection):
             return True
         return False
 
     @property
     def value(self):
-        # FIXME check the usage of value in the xmlwriter, jsonwriter
         return self._value
 
     def value_str(self, index=0):

odml/section.py

@@ -1,14 +1,14 @@
 # -*- coding: utf-8
 import uuid
 
-import odml.base as base
-import odml.format as format
-import odml.terminology as terminology
-from odml.doc import BaseDocument
+from . import base
+from . import format
+from . import terminology
+from .doc import BaseDocument
 # this is supposedly ok, as we only use it for an isinstance check
-from odml.property import Property
+from .property import Property
 # it MUST however not be used to create any Property objects
-from odml.tools.doc_inherit import inherit_docstring, allow_inherit_docstring
+from .tools.doc_inherit import inherit_docstring, allow_inherit_docstring
 
 
 class Section(base._baseobj):

odml/terminology.py

@@ -16,6 +16,8 @@
 except ImportError:
     import urllib2
 
+from .tools.parser_utils import ParserException
+
 
 REPOSITORY = 'http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml'
 
@@ -82,7 +84,7 @@ def _load(self, url):
             term = odml.tools.xmlparser.XMLReader(
                 filename=url, ignore_errors=True).from_file(fp)
             term.finalize()
-        except odml.tools.xmlparser.ParserException as e:
+        except ParserException as e:
             print("Failed to load %s due to parser errors" % url)
             print(' "%s"' % e)
             term = None

odml/tools/__init__.py

@@ -1,6 +1,5 @@
 from odml.tools import dumper
 from odml.tools import format_converter
-from odml.tools import jsonparser
 from odml.tools import odmlparser
 from odml.tools import rdf_converter
 from odml.tools import version_converter