/**
* 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 static junit.framework.Assert.fail;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.io.FileUtils;
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.core.protonetwork.ProtoNetworkBuilder;
import org.openbel.framework.core.protonetwork.ProtoNetworkDescriptor;
import org.openbel.framework.core.protonetwork.ProtoNetworkExternalizer;
import org.openbel.framework.core.protonetwork.TextProtoNetworkDescriptor;
import org.openbel.framework.core.protonetwork.TextProtoNetworkExternalizer;
/**
* TextProtoNetworkIOTest tests the reading and writing of a text table-based
* {@link ProtoNetwork}.
*
* @author Anthony Bargnesi {@code <abargnesi@selventa.com>}
*/
public class TextProtoNetworkIOTest {
/**
* Defines the test {@link ProtoNetwork}.
*/
private ProtoNetwork protoNetwork;
/**
* Defines the test {@link TextProtoNetworkDescriptor}. This must be cleaned
* up after each test runs.
*/
private TextProtoNetworkDescriptor protoNetworkDescriptor;
/**
* Testcase - Dummy test to see output of text table-based
* {@link ProtoNetwork}.
*/
@Test
public void testProtoNetworkIO() {
ProtoNetworkExternalizer protoNetworkExternalizer =
new TextProtoNetworkExternalizer();
try {
protoNetworkDescriptor =
(TextProtoNetworkDescriptor) protoNetworkExternalizer
.writeProtoNetwork(protoNetwork,
System.getProperty("user.dir"));
for (final File symt : protoNetworkDescriptor.getSymbolTables()) {
FileUtils.readFileToString(symt);
}
} catch (Exception e) {
e.printStackTrace();
fail("unexpected exception");
}
}
/**
* Setup - Set up the BEL {@link Document} and {@link ProtoNetwork} to test.
*/
@Before
public void setupTest() {
NamespaceGroup namespaceGroup = new NamespaceGroup();
Namespace hgncNs =
new Namespace("HGNC", "http://www.belscript.org/ns/hgnc");
namespaceGroup.setNamespaces(asList(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)));
annotationGroup
.setEvidence(CommonModelFactory
.getInstance()
.createEvidence(
"insulin activates the expression of SREBP-1c gene in primary hepatocytes whereas glucagon "
+ "and cAMP have the opposite effect suggests that SREBP could mediate some of the effects of insulin "
+ "on lipogenic gene expression in the liver, indirectly, by increasing glucose flux through glucokinase, "
+ "and/or directly, by activation of lipogenic gene expression"));
statementGroup.setAnnotationGroup(annotationGroup);
FunctionEnum fp = FunctionEnum.PROTEIN_ABUNDANCE;
List<BELObject> args = new ArrayList<BELObject>();
args.add(CommonModelFactory.getInstance().createParameter(hgncNs,
"TXNIP"));
Term t = new Term(fp, args);
FunctionEnum ft = FunctionEnum.TRANSCRIPTIONAL_ACTIVITY;
args = new ArrayList<BELObject>();
args.add(CommonModelFactory.getInstance().createParameter(hgncNs,
"IL3RA"));
Term t2 = new Term(ft, args);
FunctionEnum fr = FunctionEnum.RIBOSYLATION_ACTIVITY;
args = new ArrayList<BELObject>();
args.add(t2);
Term t3 = new Term(fr, args);
args = new ArrayList<BELObject>();
args.add(CommonModelFactory.getInstance().createParameter(hgncNs,
"ESR1"));
Term t4 = new Term(fp, args);
args = new ArrayList<BELObject>();
args.add(CommonModelFactory.getInstance().createParameter(hgncNs,
"BRCA1"));
Term t5 = new Term(fp, args);
args = new ArrayList<BELObject>();
args.add(t4);
Term t6 = new Term(ft, args);
FunctionEnum fg = FunctionEnum.GENE_ABUNDANCE;
args = new ArrayList<BELObject>();
args.add(CommonModelFactory.getInstance().createParameter(hgncNs,
"TXNIP"));
Term t7 = new Term(fg, args);
statementGroup
.setStatements(asList(
new Statement(
t,
"The first statement",
annotationGroup,
new org.openbel.framework.common.model.Statement.Object(
t3),
RelationshipType.DECREASES),
new Statement(
t5,
"The second statement",
annotationGroup,
new Statement.Object(
new Statement(
t6,
"The third statement",
annotationGroup,
new Statement.Object(t7),
RelationshipType.INCREASES)
),
RelationshipType.DECREASES)));
Header header = new Header("", asList("Another"),
asList("Shrubbery"), "", "", "", "", "");
Document document = new Document(header, statementGroup);
document.setDefinitions(asList(speciesDefinition, tissueDefinition));
document.setNamespaceGroup(namespaceGroup);
protoNetwork = new ProtoNetworkBuilder(document).buildProtoNetwork();
}
/**
* Teardown - Remove the {@link ProtoNetworkDescriptor} files written to
* disk.
*/
@After
public void teardownTest() {
boolean d = false;
for (final File symt : protoNetworkDescriptor.getSymbolTables()) {
d = symt.delete();
assert d;
}
d = new File("all.tbl").delete();
assert d;
}
}