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First attempt at sbol3-11704 and sbol3-11705 #25

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First attempt at sbol3-11704 and sbol3-11705 #25

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49 changes: 49 additions & 0 deletions libSBOLj3/src/main/java/org/sbolstandard/core3/entity/Constraint.java
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Original file line number Diff line number Diff line change
@@ -1,17 +1,20 @@
package org.sbolstandard.core3.entity;

import java.net.URI;
import java.util.ArrayList;
import java.util.List;

import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.Resource;
import org.sbolstandard.core3.util.Configuration;
import org.sbolstandard.core3.util.RDFUtil;
import org.sbolstandard.core3.util.SBOLGraphException;
import org.sbolstandard.core3.util.SBOLUtil;
import org.sbolstandard.core3.validation.IdentifiedValidator;
import org.sbolstandard.core3.validation.PropertyValidator;
import org.sbolstandard.core3.validation.ValidationMessage;
import org.sbolstandard.core3.vocabulary.DataModel;
import org.sbolstandard.core3.vocabulary.RestrictionType;

import jakarta.validation.constraints.NotNull;

Expand All @@ -33,10 +36,56 @@ protected Constraint(Resource resource) throws SBOLGraphException
@Override
public List<ValidationMessage> getValidationMessages() throws SBOLGraphException
{
ArrayList<URI> table8List = new ArrayList<URI>();
table8List.add(RestrictionType.Identity.verifyIdentical);
table8List.add(RestrictionType.Identity.differentFrom);
table8List.add(RestrictionType.Identity.replaces);
table8List.add(RestrictionType.Orientation.sameOrientationAs);
table8List.add(RestrictionType.Orientation.oppositeOrientationAs);

ArrayList<URI> table9List = new ArrayList<URI>();
table9List.add(RestrictionType.Topology.isDisjointFrom);
table9List.add(RestrictionType.Topology.strictlyContains);
table9List.add(RestrictionType.Topology.contains);
table9List.add(RestrictionType.Topology.equals);
table9List.add(RestrictionType.Topology.meets);
table9List.add(RestrictionType.Topology.covers);
table9List.add(RestrictionType.Topology.overlaps);

ArrayList<URI> table10List = new ArrayList<URI>();
table10List.add(RestrictionType.Sequential.precedes);
table10List.add(RestrictionType.Sequential.strictlyPrecedes);
table10List.add(RestrictionType.Sequential.meets);
table10List.add(RestrictionType.Sequential.overlaps);
table10List.add(RestrictionType.Sequential.contains);
table10List.add(RestrictionType.Sequential.strictlyContains);
table10List.add(RestrictionType.Sequential.equals);
table10List.add(RestrictionType.Sequential.finishes);
table10List.add(RestrictionType.Sequential.starts);

List<ValidationMessage> validationMessages=super.getValidationMessages();
validationMessages=IdentifiedValidator.assertNotEqual(this, validationMessages, this.getObject(), this.getSubject(), "{CONSTRAINT_OBJECT_AND_SUBJECT_ARE_NOT_EQUAL}", DataModel.Constraint.object);
validationMessages= IdentifiedValidator.assertEquals(this, DataModel.Constraint.subject, this.resource, this.getSubject(), validationMessages);
validationMessages= IdentifiedValidator.assertEquals(this, DataModel.Constraint.object, this.resource, this.getObject(), validationMessages);

URI restriction = this.getRestriction();
// CONSTRAINT_RESTRICTION_VALUE_FROM_TABLE_8_9_10_37
if (Configuration.getInstance().isValidateRecommendedRules()){
if(!table8List.contains(restriction) && !table9List.contains(restriction) && !table10List.contains(restriction)) {
validationMessages = addToValidations(validationMessages,new ValidationMessage("{CONSTRAINT_RESTRICTION_VALUE_FROM_TABLE_8_9_10_37}", DataModel.type));
}
}

// CONSTRAINT_RESTRICTION_TABLE8_MUST_MATCH_FEATURE
if(table8List.contains(restriction)) {
//If the restriction property of a Constraint is drawn from Table 8,
Feature subject = this.getSubject();
Feature object = this.getObject();
if(!restriction.equals(subject.getUri()) || !restriction.equals(object.getUri())) {
validationMessages = addToValidations(validationMessages,new ValidationMessage("{CONSTRAINT_RESTRICTION_TABLE8_MUST_MATCH_FEATURE}", DataModel.type));
}
}

return validationMessages;
}

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2 changes: 2 additions & 0 deletions libSBOLj3/src/main/resources/ValidationMessages.properties
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Expand Up @@ -18,6 +18,8 @@ CONSTRAINT_OBJECT_NOT_NULL = Constraint.object cannot be null.
CONSTRAINT_SUBJECT_MUST_REFER_TO_A_FEATURE_OF_THE_PARENT = sbol3-11701 - The Feature referenced by the subject property of a Constraint MUST be contained by the Component that contains the Constraint.
CONSTRAINT_OBJECT_MUST_REFER_TO_A_FEATURE_OF_THE_PARENT = sbol3-11702 - The Feature referenced by the object property of a Constraint MUST be contained by the Component that contains the Constraint.
CONSTRAINT_OBJECT_AND_SUBJECT_ARE_NOT_EQUAL= sbol3-11703 - The object property of a Constraint MUST NOT refer to the same SubComponent as the subject property of the Constraint.
CONSTRAINT_RESTRICTION_VALUE_FROM_TABLE_8_9_10_37 = sbol3-11704 - The value of the restriction property of a Constraint SHOULD be drawn from Table 8, 37 Table 9, or Table 10
CONSTRAINT_RESTRICTION_TABLE8_MUST_MATCH_FEATURE = sbol3-11705 - If the restriction property of a Constraint is drawn from Table 8, then the Feature objects referred to by the subject and object properties MUST comply with the relation specified in Table 8.
CUT_AT_NOT_NULL = Cut.at cannot be null.
CUT_AT_POSITIVE_OR_ZERO = sbol3-11501 - The value of the at property of a Cut MUST be greater than or equal to zero.
EXTERNALLYDEFINED_TYPE_IN_TABLE2 = sbol3-11104 - A ExternallyDefined SHOULD have a type property from Table 2.
Expand Down
24 changes: 21 additions & 3 deletions libSBOLj3/src/test/java/org/sbolstandard/core3/entity/test/ConstraintTest.java
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Expand Up @@ -51,15 +51,15 @@ public void testConstraintReference() throws SBOLGraphException, IOException, Ex
TestUtil.validateIdentified(constraint,doc,0);
TestUtil.validateProperty(constraint, "setRestriction", new Object[] {null}, URI.class);
constraint.setRestriction(null);
TestUtil.validateIdentified(constraint,doc,1);
TestUtil.validateIdentified(constraint,doc,2);

TestUtil.validateProperty(constraint, "setObject", new Object[] {null}, Feature.class);
constraint.setObject(null);
TestUtil.validateIdentified(constraint,doc,2);
TestUtil.validateIdentified(constraint,doc,3);

TestUtil.validateProperty(constraint, "setSubject", new Object[] {null}, Feature.class);
constraint.setSubject(null);
TestUtil.validateIdentified(constraint,doc,3);
TestUtil.validateIdentified(constraint,doc,4);

constraint.setRestriction(tempRestriction);
constraint.setSubject(tempSubject);
Expand Down Expand Up @@ -94,6 +94,24 @@ public void testConstraintReference() throws SBOLGraphException, IOException, Ex
constraint.setObject(tempObject);
TestUtil.validateIdentified(constraint,doc,0);

// CONSTRAINT_RESTRICTION_VALUE_FROM_TABLE_8_9_10_37
constraint.setRestriction(null);
TestUtil.validateIdentified(constraint,doc,2);
Configuration.getInstance().setValidateRecommendedRules(false);
TestUtil.validateIdentified(constraint,doc,1);
Configuration.getInstance().setValidateRecommendedRules(true);

constraint.setRestriction(tempRestriction);
TestUtil.validateIdentified(constraint,doc,0);

// CONSTRAINT_RESTRICTION_TABLE8_MUST_MATCH_FEATURE
constraint.setRestriction(RestrictionType.Identity.verifyIdentical);
TestUtil.validateIdentified(constraint,doc,1);

constraint.setRestriction(tempRestriction);
TestUtil.validateIdentified(constraint,doc,0);



}

Expand Down