/**
* 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.protonetwork;
import static java.util.Arrays.asList;
import java.util.ArrayList;
import java.util.List;
import junit.framework.Assert;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.openbel.framework.common.enums.FunctionEnum;
import org.openbel.framework.common.enums.RelationshipType;
import org.openbel.framework.common.model.*;
import org.openbel.framework.common.protonetwork.model.ProtoNetwork;
import org.openbel.framework.common.protonetwork.model.ProtoNetworkError;
import org.openbel.framework.core.protonetwork.BinaryProtoNetworkDescriptor;
import org.openbel.framework.core.protonetwork.BinaryProtoNetworkExternalizer;
import org.openbel.framework.core.protonetwork.ProtoNetworkBuilder;
import org.openbel.framework.core.protonetwork.ProtoNetworkDescriptor;
import org.openbel.framework.core.protonetwork.ProtoNetworkExternalizer;
/**
* BinaryProtoNetworkIOTest tests the reading and writing of a binary
* {@link ProtoNetwork}.
*
* @author Anthony Bargnesi {@code <abargnesi@selventa.com>}
*/
public class BinaryProtoNetworkIOTest {
/**
* Define the test {@link ProtoNetwork}.
*/
private ProtoNetwork protoNetwork;
/**
* Define the test {@link ProtoNetworkDescriptor}.
*/
private ProtoNetworkDescriptor protoNetworkDescriptor;
/**
* Testcase - Test the roundtrip input/output of a binary
* {@link ProtoNetwork}.
*/
@Test
public void testProtoNetworkIO() {
ProtoNetworkExternalizer protoNetworkExternalizer =
new BinaryProtoNetworkExternalizer();
try {
// test write
protoNetworkDescriptor =
protoNetworkExternalizer.writeProtoNetwork(protoNetwork,
System.getProperty("user.dir"));
// test read
ProtoNetwork serializedProtoNetwork =
protoNetworkExternalizer
.readProtoNetwork(protoNetworkDescriptor);
Assert.assertEquals(protoNetwork, serializedProtoNetwork);
} catch (ProtoNetworkError e) {
e.printStackTrace();
Assert.fail("unexpected exception");
}
}
/**
* Setup - Set up a test BEL {@link Document}.
*/
@Before
public void setupTest() {
NamespaceGroup namespaceGroup = new NamespaceGroup();
Namespace entrezGeneNs =
new Namespace("EG", "http://www.belscript.org/ns/entrez-gene");
Namespace hgncNs =
new Namespace("HGNC", "http://www.belscript.org/ns/hgnc");
namespaceGroup.setNamespaces(asList(entrezGeneNs, hgncNs));
StatementGroup statementGroup = new StatementGroup();
AnnotationDefinition speciesDefinition =
new AnnotationDefinition("species", "Description", "Usage",
asList("9606"));
AnnotationDefinition tissueDefinition =
new AnnotationDefinition("tissue", "Description", "Usage",
asList("TH1", "TH2", "AB3"));
AnnotationGroup annotationGroup = new AnnotationGroup();
annotationGroup.setAnnotations(asList(
CommonModelFactory.getInstance().createAnnotation("9606",
speciesDefinition),
CommonModelFactory.getInstance().createAnnotation("TH1",
tissueDefinition)));
annotationGroup
.setEvidence(CommonModelFactory
.getInstance()
.createEvidence(
"the elevation of intracellular cAMP concentration that results from increased glucagon production also plays a role in the down-regulation process"));
statementGroup.setAnnotationGroup(annotationGroup);
FunctionEnum p = FunctionEnum.PROTEIN_ABUNDANCE;
List<BELObject> args = new ArrayList<BELObject>();
args.add(CommonModelFactory.getInstance().createParameter(hgncNs,
"NFKB"));
Term t = new Term(p, args);
FunctionEnum r = FunctionEnum.RNA_ABUNDANCE;
args = new ArrayList<BELObject>();
args.add(CommonModelFactory.getInstance()
.createParameter(hgncNs, "FAS"));
Term t2 = new Term(r, args);
Statement simpleIncrease = new Statement(t,
"", annotationGroup,
new org.openbel.framework.common.model.Statement.Object(t2),
RelationshipType.INCREASES);
statementGroup.setStatements(asList(simpleIncrease));
Header header = new Header("", asList("Unladen"), asList("Swallow"),
"", "", "", "", "");
Document document = new Document(header, statementGroup);
document.setDefinitions(asList(speciesDefinition, tissueDefinition));
document.setNamespaceGroup(namespaceGroup);
protoNetwork = new ProtoNetworkBuilder(document).buildProtoNetwork();
}
/**
* Teardown - Remove the file artifacts for the test {@link ProtoNetwork}.
*/
@After
public void teardownTest() {
boolean deleted =
((BinaryProtoNetworkDescriptor) protoNetworkDescriptor)
.getProtoNetwork().delete();
assert deleted;
}
}