/**
* Copyright (C) 2012-2013 Selventa, Inc.
*
* This file is part of the OpenBEL Framework.
*
* This program is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* The OpenBEL Framework is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
* License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with the OpenBEL Framework. If not, see <http://www.gnu.org/licenses/>.
*
* Additional Terms under LGPL v3:
*
* This license does not authorize you and you are prohibited from using the
* name, trademarks, service marks, logos or similar indicia of Selventa, Inc.,
* or, in the discretion of other licensors or authors of the program, the
* name, trademarks, service marks, logos or similar indicia of such authors or
* licensors, in any marketing or advertising materials relating to your
* distribution of the program or any covered product. This restriction does
* not waive or limit your obligation to keep intact all copyright notices set
* forth in the program as delivered to you.
*
* If you distribute the program in whole or in part, or any modified version
* of the program, and you assume contractual liability to the recipient with
* respect to the program or modified version, then you will indemnify the
* authors and licensors of the program for any liabilities that these
* contractual assumptions directly impose on those licensors and authors.
*/
package org.openbel.framework.core.compiler;
import java.util.List;
import org.openbel.framework.common.enums.FunctionEnum;
import org.openbel.framework.common.enums.RelationshipType;
import org.openbel.framework.common.model.Document;
import org.openbel.framework.common.model.Statement;
import org.openbel.framework.common.model.Term;
/**
* Performs BEL semantic verification.
*/
public interface SemanticService {
/**
* Checks the provided parameterized term has the correct signature for its
* {@link Term#getFunctionEnum() function enum}.
* <p>
* This semantic check ensures the function signature matches what is
* provided by the function associated with the term {@code t}, a term with
* parameters.
* </p>
*
* @param t Term
* @throws SemanticWarning Thrown if the supplied term fails the semantic
* verification check or an error occurred during semantic verification
* @see org.openbel.framework.common.lang.Function BEL language
* functions
* @see org.openbel.framework.common.lang.Signature BEL function
* signatures
*/
public void checkParameterizedTerm(Term t) throws SemanticWarning;
/**
* Checks the non-parameterized term has the correct signature for its
* {@link Term#getFunctionEnum() function enum}.
* <p>
* This semantic check ensures the function signature matches what is
* provided by the function associated with the term {@code t}, a term
* without parameters.
* </p>
*
* @param t Term
* @throws SemanticWarning Thrown if the supplied term fails the semantic
* verification check or an error occurred during semantic verification
* @see org.openbel.framework.common.lang.Function BEL language
* functions
* @see org.openbel.framework.common.lang.Signature BEL function
* signatures
*/
public void checkTerm(Term t) throws SemanticWarning;
/**
* Checks the provided statement contains a relationship when necessary.
* <p>
* This semantic check ensures a statement provides a relationship when an
* object is present and does not provide a relationship when an object is
* absent. The attribute indicates the relationship between subject and
* object.
* </p>
*
* @param s Statement
* @throws SemanticWarning Thrown if the supplied statement fails the
* semantic verification check or an error occurred during semantic
* verification
* @see Statement
*/
public void checkRelationship(Statement s) throws SemanticWarning;
/**
* Checks the provided statement for improper use of {@link FunctionEnum#LIST LIST}.
* <p>
* This semantic check ensures that a statement that has an object using
* the {@link FunctionEnum#LIST LIST} function must have a
* relationship type of {@link RelationshipType#HAS_COMPONENTS HAS_COMPONENTS}
* or {@link RelationshipType#HAS_MEMBERS HAS_MEMBERS}. All statements using
* LIST without having a proper relationship type will be pruned from the
* document and a {@link SemanticWarning semantic warning} will be thrown.
* </p>
*
* @param s Statement
* @throws SemanticWarning Thrown if the supplied statement fails the
* semantic verification check or an error occurs during semantic
* verification
* @see Statement
*/
public void checkListUsage(Statement s, final Document doc)
throws SemanticWarning;
/**
* Checks the provided statement is constrained to the set of
* {@link RelationshipType#isCausal() causal} relationships, if and only if
* the statement {@link Statement#hasNestedStatement() is nested}.
*
* @param s Statement
* @throws SemanticWarning Thrown if the supplied statement fails the
* semantic verification check or an error occurred during semantic
* verification
* @see Statement
*/
public void checkNested(Statement s) throws SemanticWarning;
/**
* Checks that the provided {@link Statement statement }is only nested at
* most one time. If the {@link Statement statement} is nested more than
* once then it will be pruned from the {@link Document document} and a
* {@link SemanticWarning semantic warning} will be thrown.
*
* @param stmt the {@link Statement statement} to check for multi nesting
* @param doc the {@link Document document} containing the
* {@link Statement statement}
* @throws SemanticWarning Thrown if the {@link Statement statement}
* provided is nested more than once
*/
public void checkMultiNested(final Statement stmt, final Document doc)
throws SemanticWarning;
/**
* Checks the provided abundance term term is semantically valid. If the
* provided term is not one of:
* <ul>
* <li>{@link FunctionEnum#GENE_ABUNDANCE gene abundance}</li>
* <li>{@link FunctionEnum#PROTEIN_ABUNDANCE protein abundance}</li>
* <li>{@link FunctionEnum#RNA_ABUNDANCE RNA abundance}</li>
* </ul>
* this method returns immediately.
* <p>
* This check ensures valid function arguments are being used beyond the
* normal function and namespace value argument types. Refer to the BEL
* function specification for more information.
* </p>
*
* @param t Term
* @throws SemanticWarning Thrown if the supplied term fails the semantic
* verification check or an error occurred during semantic verification
* @see org.openbel.framework.common.lang.Function BEL language
* functions
* @see org.openbel.framework.common.lang.Signature BEL function
* signatures
*/
public List<SemanticWarning> checkAbundanceSubsets(Term t);
}