Add class and test for convering network in attribute table

met4j-cytoscape/src/main/java/fr/inra/toulouse/metexplore/met4j_cytoscape/attributes/BioNetworkToAttributeTable.java

+/*******************************************************************************
+ * Copyright INRA
+ * 
+ *  Contact: ludovic.cottret@toulouse.inra.fr
+ * 
+ * 
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software.  You can  use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "http://www.cecill.info".
+ * 
+ * As a counterpart to the access to the source code and  rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty  and the software's author,  the holder of the
+ * economic rights,  and the successive licensors  have only  limited
+ * liability.
+ *  In this respect, the user's attention is drawn to the risks associated
+ * with loading,  using,  modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean  that it is complicated to manipulate,  and  that  also
+ * therefore means  that it is reserved for developers  and  experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and,  more generally, to use and operate it in the
+ * same conditions as regards security.
+ *  The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ ******************************************************************************/
+/**
+ * 10 juin 2011 
+ */
+package fr.inra.toulouse.metexplore.met4j_cytoscape.attributes;
+
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.TreeMap;
+
+import fr.inra.toulouse.metexplore.met4j_core.biodata.BioChemicalReaction;
+import fr.inra.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inra.toulouse.metexplore.met4j_core.biodata.BioPhysicalEntity;
+import fr.inra.toulouse.metexplore.met4j_core.utils.StringUtils;
+
+/**
+ * @author ludo 10 juin 2011
+ * 
+ * Complete refactoring 22/12/2016
+ * 
+ */
+public class BioNetworkToAttributeTable {
+
+	BioNetwork network;
+	String outputFile;
+
+	public BioNetworkToAttributeTable(BioNetwork bioNetwork, String outputFile) {
+
+		this.network = bioNetwork;
+		this.outputFile = outputFile;
+
+	}
+
+	public void writeAttributes(Boolean sbmlCoded) throws IOException {
+
+		FileWriter fw = new FileWriter(this.outputFile);
+
+		fw.write(
+				"id\tsbml type\tsbml name\tmass\tformula\tpathways\tec\trev\tcompartment\tgeneRules\tprotRules\tlb\tub\n");
+
+		/**
+		 * For ordering compounds in the file and thus making easy the tests
+		 */
+		TreeMap<String, BioPhysicalEntity> cpds = new TreeMap<String, BioPhysicalEntity>(
+				this.network.getPhysicalEntityList());
+
+		HashMap<String, String> cpdNames = (new NameAttributes(this.network, false, true)).getAttributes();
+		HashMap<String, String> cpdMasses = (new MassAttributes(this.network, false)).getAttributes();
+		HashMap<String, String> cpdFormulas = (new FormulaAttributes(this.network, false)).getAttributes();
+		HashMap<String, String> cpdPathways = (new PathwayAttributes(this.network, false, true)).getAttributes();
+		HashMap<String, String> cpdCompartments = (new CompartmentAttributes(this.network, false, true))
+				.getAttributes();
+
+		for (String cpdId : cpds.keySet()) {
+
+			String cpdName = cpdNames.get(cpdId);
+			String mass = cpdMasses.get(cpdId);
+			String formula = cpdFormulas.get(cpdId);
+			String pathways = cpdPathways.get(cpdId);
+			String compartmentName = cpdCompartments.get(cpdId);
+
+			if (sbmlCoded) {
+				cpdId = StringUtils.sbmlEncode(cpdId);
+			}
+			
+			fw.write(cpdId + "\tspecies\t" + cpdName + "\t" + mass + "\t" + formula + "\t" + pathways + "\tNA\tNA\t"
+					+ compartmentName + "\tNA\tNA\tNA\tNA\n");
+		}
+
+		/**
+		 * For ordering reactions in the file and thus making easy the tests
+		 */
+		TreeMap<String, BioChemicalReaction> reactions = new TreeMap<String, BioChemicalReaction>(
+				this.network.getBiochemicalReactionList());
+
+		HashMap<String, String> rxnNames = (new NameAttributes(this.network, false, false)).getAttributes();
+		HashMap<String, String> rxnFormulas = (new EquationAttributes(this.network, false)).getAttributes();
+		HashMap<String, String> rxnPathways = (new PathwayAttributes(this.network, false, false)).getAttributes();
+		HashMap<String, String> rxnEcs = (new ECAttributes(this.network, false)).getAttributes();
+		HashMap<String, String> rxnRev = (new ReversibilityAttributes(this.network, false)).getAttributes();
+		HashMap<String, String> rxnCpts = (new CompartmentAttributes(this.network, false, false)).getAttributes();
+		HashMap<String, String> rxnLb = (new FluxBoundAttributes(network, false, true)).getAttributes();
+		HashMap<String, String> rxnUb = (new FluxBoundAttributes(network, false, false)).getAttributes();
+		HashMap<String, String> rxnGenes = (new GPRAttributes(network, false, true)).getAttributes();
+		HashMap<String, String> rxnProteins = (new GPRAttributes(network, false, false)).getAttributes();
+		
+		for (String rxnId : reactions.keySet()) {
+
+			String rxnName = rxnNames.get(rxnId);
+			String rxnFormula = rxnFormulas.get(rxnId);
+			String pathwaysStr = rxnPathways.get(rxnId);
+			String ec = rxnEcs.get(rxnId);
+			String rev = rxnRev.get(rxnId);
+			String compartmentsStr = rxnCpts.get(rxnId);
+			String lb = rxnLb.get(rxnId);
+			String ub = rxnUb.get(rxnId);
+			String geneRules = rxnGenes.get(rxnId);
+			String proteinRules = rxnProteins.get(rxnId);
+			
+			if (sbmlCoded) {
+				rxnId = StringUtils.sbmlEncode(rxnId);
+			}
+
+			fw.write(rxnId + "\treaction\t" + rxnName + "\tNA\t" + rxnFormula + "\t" + pathwaysStr + "\t" + ec + "\t"
+					+ rev + "\t" + compartmentsStr + "\t" + geneRules + "\t" + proteinRules + "\t" + lb + "\t" + ub
+					+ "\n");
+
+		}
+
+		fw.close();
+
+	}
+
+}

met4j-cytoscape/src/test/java/fr/inra/toulouse/metexplore/met4j_cytoscape/attributes/BioNetworkToAttributeTableTest.java

+/*******************************************************************************
+ * Copyright INRA
+ * 
+ *  Contact: ludovic.cottret@toulouse.inra.fr
+ * 
+ * 
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software.  You can  use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "http://www.cecill.info".
+ * 
+ * As a counterpart to the access to the source code and  rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty  and the software's author,  the holder of the
+ * economic rights,  and the successive licensors  have only  limited
+ * liability.
+ *  In this respect, the user's attention is drawn to the risks associated
+ * with loading,  using,  modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean  that it is complicated to manipulate,  and  that  also
+ * therefore means  that it is reserved for developers  and  experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and,  more generally, to use and operate it in the
+ * same conditions as regards security.
+ *  The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ ******************************************************************************/
+/*******************************************************************************
+ * Copyright INRA
+ * 
+ *  Contact: ludovic.cottret@toulouse.inra.fr
+ * 
+ * 
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software.  You can  use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "http://www.cecill.info".
+ * 
+ * As a counterpart to the access to the source code and  rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty  and the software's author,  the holder of the
+ * economic rights,  and the successive licensors  have only  limited
+ * liability.
+ *  In this respect, the user's attention is drawn to the risks associated
+ * with loading,  using,  modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean  that it is complicated to manipulate,  and  that  also
+ * therefore means  that it is reserved for developers  and  experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and,  more generally, to use and operate it in the
+ * same conditions as regards security.
+ *  The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ ******************************************************************************/
+package fr.inra.toulouse.metexplore.met4j_cytoscape.attributes;
+
+import static org.junit.Assert.*;
+
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+
+import org.apache.commons.io.IOUtil;
+import org.junit.Test;
+
+import fr.inra.toulouse.metexplore.met4j_core.biodata.BioChemicalReaction;
+import fr.inra.toulouse.metexplore.met4j_core.biodata.BioCompartment;
+import fr.inra.toulouse.metexplore.met4j_core.biodata.BioGene;
+import fr.inra.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inra.toulouse.metexplore.met4j_core.biodata.BioPathway;
+import fr.inra.toulouse.metexplore.met4j_core.biodata.BioPhysicalEntity;
+import fr.inra.toulouse.metexplore.met4j_core.biodata.BioPhysicalEntityParticipant;
+import fr.inra.toulouse.metexplore.met4j_core.biodata.BioProtein;
+import fr.inra.toulouse.metexplore.met4j_core.biodata.BioUnitDefinition;
+import fr.inra.toulouse.metexplore.met4j_core.biodata.Flux;
+
+/**
+ * @author lcottret
+ *
+ */
+public class BioNetworkToAttributeTableTest {
+
+	/**
+	 * Test method for
+	 * {@link fr.inra.toulouse.metexplore.met4j_cytoscape.attributes.BioNetworkToAttributeTable#writeAttributes(java.lang.Boolean)}.
+	 * 
+	 * @throws IOException
+	 */
+	@Test
+	public void testWriteAttributes() throws IOException {
+
+		BioNetwork network = new BioNetwork();
+
+		BioCompartment cytosol = new BioCompartment("cytosol", "c");
+
+		BioCompartment periplasm = new BioCompartment("periplasm", "p");
+
+		BioChemicalReaction r1 = new BioChemicalReaction("r1-rxn", "R1");
+
+		BioUnitDefinition ud = new BioUnitDefinition();
+
+		BioProtein p = new BioProtein("p1", "P1");
+		BioGene g = new BioGene("g1", "gene1");
+		p.addGene(g);
+
+		BioPhysicalEntity a = new BioPhysicalEntity("A-cpd", "A';");
+		a.setMolecularWeight("10");
+		a.setChemicalFormula("formulaA");
+		a.setCompartment(cytosol);
+		BioPhysicalEntity b = new BioPhysicalEntity("B-cpd", "B");
+		b.setMolecularWeight("10d");
+		b.setChemicalFormula("formulaB");
+		b.setCompartment(periplasm);
+		BioPhysicalEntity c = new BioPhysicalEntity("C-cpd", "C");
+		c.setMolecularWeight("12.5");
+		c.setChemicalFormula("formulaC");
+		c.setCompartment(cytosol);
+		BioPhysicalEntity d = new BioPhysicalEntity("D-cpd", "D");
+
+		r1.addLeftParticipant(new BioPhysicalEntityParticipant(a));
+		r1.setEcNumber("1.1.1.1");
+		r1.setLowerBound(new Flux("-10000", ud));
+		r1.setUpperBound(new Flux("2", ud));
+		r1.addRightParticipant(new BioPhysicalEntityParticipant(c));
+
+		r1.addEnz(p);
+
+		BioChemicalReaction r2 = new BioChemicalReaction("r2-rxn", "R2<i>ase</i>");
+
+		r2.addRightParticipant(new BioPhysicalEntityParticipant(b));
+		r2.addLeftParticipant(new BioPhysicalEntityParticipant(d));
+
+		BioPathway p1 = new BioPathway("P-1", "pathway;");
+		BioPathway p2 = new BioPathway("P-2", "pathway--2;");
+		BioPathway p3 = new BioPathway("P-3", "pathway3;");
+		BioPathway p4 = new BioPathway("P-4", "pathway--4;");
+
+		r1.addPathway(p1);
+		r1.addPathway(p2);
+		r2.addPathway(p3);
+		r2.addPathway(p4);
+
+		network.addBiochemicalReaction(r1);
+		network.addBiochemicalReaction(r2);
+
+		String ref = "id\tsbml type\tsbml name\tmass\tformula\tpathways\tec\trev\tcompartment\tgeneRules\tprotRules\tlb\tub\n"
+
+				+ "A-cpd\t" + "species\t" + "A'\t" + "10\t" + "formulaA\t" + "(pathway::pathway--2)\t" + "NA\t" + "NA\t"
+				+ "cytosol\t" + "NA\t" + "NA\t" + "NA\t" + "NA\n"
+
+				+ "B-cpd\t" + "species\t" + "B\t" + "10d\t" + "formulaB\t" + "(pathway--4::pathway3)\t" + "NA\t"
+				+ "NA\t" + "periplasm\t" + "NA\t" + "NA\t" + "NA\t" + "NA\n"
+
+				+ "C-cpd\t" + "species\t" + "C\t" + "12.5\t" + "formulaC\t" + "(pathway::pathway--2)\t" + "NA\t"
+				+ "NA\t" + "cytosol\t" + "NA\t" + "NA\t" + "NA\t" + "NA\n"
+
+				+ "D-cpd\t" + "species\t" + "D\t" + "NA\t" + "NA\t" + "(pathway--4::pathway3)\t" + "NA\t" + "NA\t"
+				+ "NA\t" + "NA\t" + "NA\t" + "NA\t" + "NA\n"
+
+				+ "r1-rxn\t" + "reaction\t" + "R1\t" + "NA\t" + "A'[c] -> C[c]\t" + "(pathway::pathway--2)\t"
+				+ "1.1.1.1\t" + "false\t" + "(cytosol)\t" + "( gene1 )\t" + "( P1 )\t" + "-10000\t" + "2\n"
+
+				+ "r2-rxn\t" + "reaction\t" + "R2ase\t" + "NA\t" + "D[NA] -> B[p]\t" + "(pathway--4::pathway3)\t"
+				+ "\t" + "false\t" + "(NA::periplasm)\t" + "\t" + "\t" + "-99999\t" + "99999" + "\n";
+
+		
+		File testFile = File.createTempFile("testBioNetworkToAttributeTable", "txt");
+		testFile.deleteOnExit();
+
+		BioNetworkToAttributeTable converter = new BioNetworkToAttributeTable(network, testFile.getAbsolutePath());
+
+		converter.writeAttributes(false);
+
+		String test = IOUtil.toString(new FileReader(testFile));
+
+		assertEquals("Test and reference files are not equal", ref, test);
+		
+		ref = "id\tsbml type\tsbml name\tmass\tformula\tpathways\tec\trev\tcompartment\tgeneRules\tprotRules\tlb\tub\n"
+
+				+ "A__45__cpd\t" + "species\t" + "A'\t" + "10\t" + "formulaA\t" + "(pathway::pathway--2)\t" + "NA\t" + "NA\t"
+				+ "cytosol\t" + "NA\t" + "NA\t" + "NA\t" + "NA\n"
+
+				+ "B__45__cpd\t" + "species\t" + "B\t" + "10d\t" + "formulaB\t" + "(pathway--4::pathway3)\t" + "NA\t"
+				+ "NA\t" + "periplasm\t" + "NA\t" + "NA\t" + "NA\t" + "NA\n"
+
+				+ "C__45__cpd\t" + "species\t" + "C\t" + "12.5\t" + "formulaC\t" + "(pathway::pathway--2)\t" + "NA\t"
+				+ "NA\t" + "cytosol\t" + "NA\t" + "NA\t" + "NA\t" + "NA\n"
+
+				+ "D__45__cpd\t" + "species\t" + "D\t" + "NA\t" + "NA\t" + "(pathway--4::pathway3)\t" + "NA\t" + "NA\t"
+				+ "NA\t" + "NA\t" + "NA\t" + "NA\t" + "NA\n"
+
+				+ "r1__45__rxn\t" + "reaction\t" + "R1\t" + "NA\t" + "A'[c] -> C[c]\t" + "(pathway::pathway--2)\t"
+				+ "1.1.1.1\t" + "false\t" + "(cytosol)\t" + "( gene1 )\t" + "( P1 )\t" + "-10000\t" + "2\n"
+
+				+ "r2__45__rxn\t" + "reaction\t" + "R2ase\t" + "NA\t" + "D[NA] -> B[p]\t" + "(pathway--4::pathway3)\t"
+				+ "\t" + "false\t" + "(NA::periplasm)\t" + "\t" + "\t" + "-99999\t" + "99999" + "\n";
+
+		converter = new BioNetworkToAttributeTable(network, testFile.getAbsolutePath());
+
+		converter.writeAttributes(true);
+
+		test = IOUtil.toString(new FileReader(testFile));
+
+		assertEquals("Test and reference files are not equal (SBML coded)", ref, test);
+
+	}
+
+}