Merge pull request #389 from mpsonntag/refactorValid

Validation changes

LGTM

Author: achilleas-k

odml/doc.py

@@ -8,6 +8,7 @@
 from . import dtypes
 from . import format as fmt
 from . import terminology
+from . import validation
 from .tools.doc_inherit import inherit_docstring, allow_inherit_docstring
 
 
@@ -152,6 +153,14 @@ def finalize(self):
             if sec._include is not None:
                 sec.include = sec._include
 
+    def validate(self):
+        """
+        Runs a validation on itself and returns the Validation object.
+
+        :return: odml.Validation
+        """
+        return validation.Validation(self)
+
     @inherit_docstring
     def get_terminology_equivalent(self):
         if self.repository is None:

odml/property.py

@@ -213,6 +213,11 @@ def name(self, new_name):
         if self.name == new_name:
             return
 
+        # Make sure name cannot be set to None or empty
+        if not new_name:
+            self._name = self._id
+            return
+
         curr_parent = self.parent
         if hasattr(curr_parent, "properties") and new_name in curr_parent.properties:
 
@@ -569,11 +574,12 @@ def _values_cardinality_validation(self):
         is respected and prints a warning message otherwise.
         """
         valid = validation.Validation(self)
+        val_id = validation.IssueID.property_values_cardinality
 
         # Make sure to display only warnings of the current property
-        res = [curr for curr in valid.errors if self.id == curr.obj.id]
-        for err in res:
-            print("%s: %s" % (err.rank.capitalize(), err.msg))
+        for curr in valid.errors:
+            if curr.validation_id == val_id and self.id == curr.obj.id:
+                print("%s: %s" % (curr.rank.capitalize(), curr.msg))
 
     def set_values_cardinality(self, min_val=None, max_val=None):
         """

odml/section.py

@@ -171,6 +171,11 @@ def name(self, new_value):
         if self.name == new_value:
             return
 
+        # Make sure name cannot be set to None or empty
+        if not new_value:
+            self._name = self._id
+            return
+
         curr_parent = self.parent
         if hasattr(curr_parent, "sections") and new_value in curr_parent.sections:
             raise KeyError("Object with the same name already exists!")
@@ -416,10 +421,12 @@ def _sections_cardinality_validation(self):
         is respected and prints a warning message otherwise.
         """
         valid = validation.Validation(self)
+        val_id = validation.IssueID.section_sections_cardinality
+
         # Make sure to display only warnings of the current section
-        res = [curr for curr in valid.errors if self.id == curr.obj.id]
-        for err in res:
-            print("%s: %s" % (err.rank.capitalize(), err.msg))
+        for curr in valid.errors:
+            if curr.validation_id == val_id and self.id == curr.obj.id:
+                print("%s: %s" % (curr.rank.capitalize(), curr.msg))
 
     @property
     def prop_cardinality(self):
@@ -469,10 +476,12 @@ def _properties_cardinality_validation(self):
         is respected and prints a warning message otherwise.
         """
         valid = validation.Validation(self)
+        val_id = validation.IssueID.section_properties_cardinality
+
         # Make sure to display only warnings of the current section
-        res = [curr for curr in valid.errors if self.id == curr.obj.id]
-        for err in res:
-            print("%s: %s" % (err.rank.capitalize(), err.msg))
+        for curr in valid.errors:
+            if curr.validation_id == val_id and self.id == curr.obj.id:
+                print("%s: %s" % (curr.rank.capitalize(), curr.msg))
 
     @inherit_docstring
     def get_terminology_equivalent(self):

odml/tools/odmlparser.py

@@ -7,6 +7,7 @@
 import datetime
 import json
 import sys
+import warnings
 
 from os.path import basename
 
@@ -61,11 +62,18 @@ def write_file(self, odml_document, filename):
         msg = ""
         for err in validation.errors:
             if err.is_error:
-                msg += "\n\t- %s %s: %s" % (err.obj, err.rank, err.msg)
+                # msg += "\n\t- %s %s: %s" % (err.obj, err.rank, err.msg)
+                msg += "\n- %s" % err
         if msg != "":
             msg = "Resolve document validation errors before saving %s" % msg
             raise ParserException(msg)
 
+        report = validation.report()
+        if report:
+            msg += "The saved Document contains unresolved issues."
+            msg += " Run the Documents 'validate' method to access them.\n%s" % report
+            warnings.warn(msg)
+
         with open(filename, 'w') as file:
             # Add XML header to support odML stylesheets.
             if self.parser == 'XML':
@@ -153,6 +161,13 @@ def __init__(self, parser='XML', show_warnings=True):
         self.show_warnings = show_warnings
         self.warnings = []
 
+    def _validation_warning(self):
+        report = Validation(self.doc).report()
+        if report:
+            msg = "The loaded Document contains unresolved issues."
+            msg += " Run the Documents 'validate' method to access them.\n%s" % report
+            warnings.warn(msg)
+
     def from_file(self, file, doc_format=None):
         """
         Loads an odML document from a file. The ODMLReader.parser specifies the
@@ -171,6 +186,11 @@ def from_file(self, file, doc_format=None):
                                       show_warnings=self.show_warnings)
             self.warnings = par.warnings
             self.doc = par.from_file(file)
+
+            # Print validation warnings after parsing
+            if self.show_warnings:
+                self._validation_warning()
+
             return self.doc
 
         if self.parser == 'YAML':
@@ -188,6 +208,11 @@ def from_file(self, file, doc_format=None):
             self.doc = par.to_odml(self.parsed_doc)
             # Provide original file name via the in memory document
             self.doc.origin_file_name = basename(file)
+
+            # Print validation warnings after parsing
+            if self.show_warnings:
+                self._validation_warning()
+
             return self.doc
 
         if self.parser == 'JSON':
@@ -202,13 +227,27 @@ def from_file(self, file, doc_format=None):
             self.doc = par.to_odml(self.parsed_doc)
             # Provide original file name via the in memory document
             self.doc.origin_file_name = basename(file)
+
+            # Print validation warnings after parsing
+            if self.show_warnings:
+                self._validation_warning()
+
             return self.doc
 
         if self.parser == 'RDF':
             if not doc_format:
                 raise ValueError("Format of the rdf file was not specified")
 
+            # Importing from an RDF graph can return multiple documents
             self.doc = RDFReader().from_file(file, doc_format)
+
+            for doc in self.doc:
+                report = Validation(doc).report()
+                if report:
+                    msg = "The loaded Document contains unresolved issues."
+                    msg += " Run the Documents 'validate' method to access them.\n%s" % report
+                    warnings.warn(msg)
+
             return self.doc
 
     def from_string(self, string, doc_format=None):
@@ -227,6 +266,11 @@ def from_string(self, string, doc_format=None):
 
         if self.parser == 'XML':
             self.doc = xmlparser.XMLReader().from_string(string)
+
+            # Print validation warnings after parsing
+            if self.show_warnings:
+                self._validation_warning()
+
             return self.doc
 
         if self.parser == 'YAML':
@@ -237,6 +281,11 @@ def from_string(self, string, doc_format=None):
                 return
 
             self.doc = DictReader().to_odml(self.parsed_doc)
+
+            # Print validation warnings after parsing
+            if self.show_warnings:
+                self._validation_warning()
+
             return self.doc
 
         if self.parser == 'JSON':
@@ -247,13 +296,27 @@ def from_string(self, string, doc_format=None):
                 return
 
             self.doc = DictReader().to_odml(self.parsed_doc)
+
+            # Print validation warnings after parsing
+            if self.show_warnings:
+                self._validation_warning()
+
             return self.doc
 
         if self.parser == 'RDF':
             if not doc_format:
                 raise ValueError("Format of the rdf file was not specified")
 
+            # Importing from an RDF graph can return multiple documents
             self.doc = RDFReader().from_string(string, doc_format)
+
+            for doc in self.doc:
+                report = Validation(doc).report()
+                if report:
+                    msg = "The loaded Document contains unresolved issues."
+                    msg += " Run the Documents 'validate' method to access them.\n%s" % report
+                    warnings.warn(msg)
+
             return self.doc