Greetings Everyone!
In the previous week, I had been working on constraint classes for ParametricObject class and the SpatialPoints class.
I did not encounter any major problems while implementing the two classes but did have to ask for some clarifications
from my mentors along the way.
The ParametricObject element has an attribute called pointIndex, which is written as values outside the XML tags as:
<spatial:parametricObject spatial:compression="uncompressed" spatial:dataType="double" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:name="someString" spatial:pointIndexLength="0" spatial:polygonType="triangle">
0 2 5; 0 6 2; 0 5 6; 2 6 5
</spatial:parametricObject>
I did not know how these values are being read. It turned out that there is a method processCharactersOf() in SpatialParser which reads these
values and calls the append() method of the ParametricObject class. The method appends the values to a string variable pointIndex one by one.
After this, the check on the values was fairly simple. I used StringTokenizer with an alternate constructor, passing a string of delimiters
" ;" as an argument. This argument helps the StringTokenizer to separate the string "0 2 5; 0 6 2; 0 5 6; 2 6 5" whenever it encounters a
space or a semicolon, thus returning the individual values.
For the SpatialPoints class, I still need to verify with a mentor of mine if the 'id' and 'name' attributes are a part of the new specification.
After that, necessary changes will be made either to the test files, or the existing class to incorporate the final decision.
Today I shall discuss checks on invalid and unknown attributes on an element.
1)
The value of the attribute <attribute_name> of a <spatial_element> object must be an array of values of type <datatype>.
OR
The value of the attribute <attribute_name> of a <spatial_element> object must conform to the syntax of SBML data type
<datakind_class> and may only take on the allowed values of <datakind_class> defined in SBML; that is, the value must
be one of the following: “value_1” or “value_2”.
For such rules, the first step is to modify the source class to handle invalid attributes whenever they are encountered.
In the readAttribute() method of the class, look for a branch condition on attributeName.equals() for the concerned attribute.
There must be an enclosed try-catch block inside the branched block of code. The try block sets the value of the attribute,
and the setting method throws an exception if the value is not syntactically correct. This is caught by the catch block, and
that is where we need to add the following line of code:
AbstractReaderWriter.processInvalidAttribute(attributeName, null, value, prefix, this);
This call handles the invalid attribute and adds it to the INVALID_XML object of the class.
Now the constraint is impemented by a single line as:
func = new InvalidAttributeValidationFunction<spatial_element>(SpatialConstants.<attribute_name>);
2)
A <spatial_element> object must have the required attributes <attribute_1> and <attribute_2>, and may have the optional
attributes <attribute_3>, <attribute_4> and <attribute_5>. No other attributes from the SBML Level 3 Spatial Processes
namespaces are permitted on a SpatialPoints object.
The helper class for such a rule is UnknownPackageAttributeValidationFunction. We need to override the check() method
to incorporate test on the must-required attributes. We call the pre-implemented check() method by a super call after
checking must-required attributes.
func = new UnknownPackageAttributeValidationFunction<element_name>(SpatialConstants.shortLabel) {
@Override
public boolean check(ValidationContext ctx, SpatialElement obj){
if(!obj.isSetAttribute1){
return false;
}
if(!obj.isSetAttribute2){
return false;
}
return super.check(ctx, obj);
}
};
