Merge pull request #197 from mpsonntag/picks

[1.3] Version handling, parser fixes, setup update

LGTM

Author: achilleas-k

.travis.yml

@@ -14,13 +14,10 @@ matrix:
         - python: "3.4"
         - python: "3.5"
 
-before_install:
-  - sudo apt-get -qq  update
-  - sudo apt-get install -y python-enum python-lxml
-
 install:
   - export PYVER=${TRAVIS_PYTHON_VERSION:0:1}
   - pip install --upgrade coveralls
+  - pip install lxml enum34 pyyaml
 
 script:
   - python setup.py build

odml/__init__.py

@@ -5,10 +5,10 @@
 from . import section
 from .dtypes import DType
 from .fileio import load, save, display
+from .info import VERSION
 from .tools.odmlparser import allowed_parsers as parsers
 
-
-__version__ = '1.3.2'
+__version__ = VERSION
 
 # the original property-function is overwritten
 # so get it back!

odml/fileio.py

@@ -1,18 +1,41 @@
-from .tools.odmlparser import ODMLReader, ODMLWriter
+from .tools.odmlparser import ODMLReader, ODMLWriter, allowed_parsers
 
-parsers = ["xml", "json", "yaml"]
+PARSERS = allowed_parsers
 
 
 def load(filename, backend="xml"):
+    """
+    Load an odML document from file.
+    :param filename: Path and filename from where the odML document
+                     is to be loaded and parsed.
+    :param backend: File format of the file containing the odML document.
+                    The default format is XML.
+    :return: The parsed odML document.
+    """
     reader = ODMLReader(backend)
     return reader.from_file(filename)
 
 
 def save(obj, filename, backend="xml"):
+    """
+    Save an open odML document to file of a specified format.
+    :param obj: odML document do be saved.
+    :param filename: Filename and path where the odML document
+                     should be saved.
+    :param backend: Format in which the odML document is to be saved.
+                    The default format is XML.
+    """
     writer = ODMLWriter(backend)
     return writer.write_file(obj, filename)
 
 
 def display(obj, backend="xml"):
+    """
+    Print an open odML document to the command line, formatted in the
+    specified format.
+    :param obj: odML document to be displayed.
+    :param backend: Format in which the odML document is to be displayed.
+                    The default format is XML.
+    """
     writer = ODMLWriter(backend)
     print(writer.to_string(obj))

odml/info.py

@@ -0,0 +1,15 @@
+VERSION = '1.3.3'
+FORMAT_VERSION = '1'
+AUTHOR = 'Hagen Fritsch, Christian Kellner, Jan Grewe, ' \
+          'Achilleas Koutsou, Michael Sonntag, Lyuba Zehl'
+COPYRIGHT = '(c) 2011-2017, German Neuroinformatics Node'
+CONTACT = '[email protected]'
+HOMEPAGE = 'https://github.com/G-Node/python-odml'
+CLASSIFIERS = [
+    'Programming Language :: Python :: 2',
+    'Programming Language :: Python :: 3',
+    'License :: OSI Approved :: BSD License',
+    'Development Status :: 5 - Production/Stable',
+    'Topic :: Scientific/Engineering',
+    'Intended Audience :: Science/Research'
+]

odml/section.py

@@ -25,12 +25,17 @@ class BaseSection(base.sectionable, mapping.mapableSection, Section):
 
     _format = format.Section
 
-    def __init__(self, name, type="undefined", parent=None, definition=None, mapping=None):
+    def __init__(self, name, type="undefined", parent=None, definition=None,
+                 mapping=None, reference=None, repository=None, link=None, include=None):
         self._parent = parent
         self._name = name
         self._props = base.SmartList()
         self._definition = definition
         self._mapping = mapping
+        self._reference = reference
+        self._repository = repository
+        self._link = link
+        self._include = include
         super(BaseSection, self).__init__()
         # this may fire a change event, so have the section setup then
         self.type = type

odml/tools/odmlparser.py

@@ -7,26 +7,28 @@
 
 """
 
-import yaml
 import json
+import yaml
+
 from .. import format
+from ..info import FORMAT_VERSION
 from . import xmlparser
 
-# FIX ME: Version should not be hardcoded here. Import from odML module after
-#         fixing the circular imports issue.
-odml_version = '1'
-
 allowed_parsers = ['ODML', 'XML', 'YAML', 'JSON']
 
 
+class ParserException(Exception):
+    pass
+
+
 class ODMLWriter:
-    '''
+    """
         A generic odML document writer, for XML, YAML and JSON.
 
         Usage:
             xml_writer = ODMLWriter(parser='XML')
             xml_writer.write_file(odml_document, filepath)
-    '''
+    """
 
     def __init__(self, parser='XML'):
         self.doc = None  # odML document
@@ -55,7 +57,6 @@ def to_dict(self, odml_document):
         self.parsed_doc = parsed_doc
 
     def get_sections(self, section_list):
-
         section_seq = []
 
         for section in section_list:
@@ -81,7 +82,6 @@ def get_sections(self, section_list):
         return section_seq
 
     def get_properties(self, props_list):
-
         props_seq = []
 
         for prop in props_list:
@@ -100,7 +100,7 @@ def get_properties(self, props_list):
                             prop_dict[attr] = t
 
             props_seq.append(prop_dict)
-        
+
         return props_seq
 
     def get_values(self, value_list):
@@ -122,6 +122,17 @@ def get_values(self, value_list):
         return value_seq
 
     def write_file(self, odml_document, filename):
+        # Write document only if it does not contain validation errors.
+        from ..validation import Validation  # disgusting import problems
+        validation = Validation(odml_document)
+        msg = ""
+        for e in validation.errors:
+            if e.is_error:
+                msg += "\n\t- %s %s: %s" % (e.obj, e.type, e.msg)
+        if msg != "":
+            msg = "Resolve document validation errors before saving %s" % msg
+            raise ParserException(msg)
+
         file = open(filename, 'w')
         file.write(self.to_string(odml_document))
         file.close()
@@ -135,7 +146,7 @@ def to_string(self, odml_document):
             self.to_dict(odml_document)
             odml_output = {}
             odml_output['Document'] = self.parsed_doc
-            odml_output['odml-version'] = odml_version
+            odml_output['odml-version'] = FORMAT_VERSION
 
             if self.parser == 'YAML':
                 string_doc = yaml.dump(odml_output, default_flow_style=False)
@@ -150,8 +161,8 @@ class ODMLReader:
     based on the given data exchange format, like XML, YAML or JSON.
 
     Usage:
-        yaml_odml_doc = ODMLReader(parser='YAML').fromFile(open("odml_doc.yaml"))
-        json_odml_doc = ODMLReader(parser='JSON').fromFile(open("odml_doc.json"))
+        yaml_odml_doc = ODMLReader(parser='YAML').from_file("odml_doc.yaml")
+        json_odml_doc = ODMLReader(parser='JSON').from_file("odml_doc.json")
     """
 
     def __init__(self, parser='XML'):
@@ -162,18 +173,29 @@ def __init__(self, parser='XML'):
         if parser not in allowed_parsers:
             raise NotImplementedError("'%s' odML parser does not exist!" % parser)
         self.parser = parser
+        self.warnings = []
 
     def is_valid_attribute(self, attr, fmt):
         if attr in fmt._args:
             return attr
         if fmt.revmap(attr):
             return attr
-        print("Invalid element <%s> inside <%s> tag" % (attr, fmt.__class__.__name__))
+        msg = "Invalid element <%s> inside <%s> tag" % (attr, fmt.__class__.__name__)
+        print(msg)
+        self.warnings.append(msg)
         return None
 
     def to_odml(self):
-
-        self.odml_version = self.parsed_doc.get('odml-version', odml_version)
+        # Parse only odML documents of supported format versions.
+        if 'odml-version' not in self.parsed_doc:
+            raise ParserException("Invalid odML document: Could not find odml-version.")
+        elif self.parsed_doc.get('odml-version') != FORMAT_VERSION:
+            msg = ("Cannot read file: invalid odML document format version '%s'. \n"
+                   "This package supports odML format versions: '%s'."
+                   % (self.parsed_doc.get('odml-version'), FORMAT_VERSION))
+            raise ParserException(msg)
+
+        self.odml_version = self.parsed_doc.get('odml-version')
         self.parsed_doc = self.parsed_doc['Document']
 
         doc_attrs = {}
@@ -193,7 +215,6 @@ def to_odml(self):
         return self.doc
 
     def parse_sections(self, section_list):
-        
         odml_sections = []
 
         for section in section_list:
@@ -218,7 +239,6 @@ def parse_sections(self, section_list):
 
         return odml_sections
 
-
     def parse_properties(self, props_list):
         odml_props = []
 
@@ -257,52 +277,54 @@ def parse_values(self, value_list):
 
         return odml_values
 
-
     def from_file(self, file):
 
         if self.parser == 'XML' or self.parser == 'ODML':
-            odml_doc = xmlparser.XMLReader().fromFile(file)
+            par = xmlparser.XMLReader(ignore_errors=True)
+            self.warnings = par.warnings
+            odml_doc = par.fromFile(file)
             self.doc = odml_doc
             return odml_doc
 
         elif self.parser == 'YAML':
-            try:
-                self.parsed_doc = yaml.load(file)
-            except yaml.parser.ParserError as e:
-                print(e)
-                return
-            finally:
-                file.close()
+            with open(file) as yaml_data:
+                try:
+                    self.parsed_doc = yaml.load(yaml_data)
+                except yaml.parser.ParserError as e:
+                    print(e)
+                    return
+
             return self.to_odml()
 
         elif self.parser == 'JSON':
-            try:
-                self.parsed_doc = json.load(file)
-            except json.decoder.JSONDecodeError as e:
-                print(e)
-                return
-            finally:
-                file.close()
-            return self.to_odml()
+            with open(file) as json_data:
+                try:
+                    self.parsed_doc = json.load(json_data)
+                except ValueError as e:  # Python 2 does not support JSONDecodeError
+                    print("JSON Decoder Error: %s" % e)
+                    return
 
+            return self.to_odml()
 
     def from_string(self, string):
 
         if self.parser == 'XML' or self.parser == 'ODML':
             odml_doc = xmlparser.XMLReader().fromString(string)
             self.doc = odml_doc
             return self.doc
+
         elif self.parser == 'YAML':
             try:
-                odml_doc = yaml.load(string)
+                self.parsed_doc = yaml.load(string)
             except yaml.parser.ParserError as e:
                 print(e)
                 return
             return self.to_odml()
+
         elif self.parser == 'JSON':
             try:
-                odml_doc = json.loads(string)
-            except json.decoder.JSONDecodeError as e:
-                print(e)
+                self.parsed_doc = json.loads(string)
+            except ValueError as e:  # Python 2 does not support JSONDecodeError
+                print("JSON Decoder Error: %s" % e)
                 return
             return self.to_odml()