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Commit 6f47fe03 authored by Piotr Gawron's avatar Piotr Gawron
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unit tests for parsing sbo terms into species type

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1 merge request!186Resolve "upload of sbml"
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converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
+ 4
− 1
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......@@ -4,12 +4,15 @@ import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParserTest;
@RunWith(Suite.class)
@SuiteClasses({ GenericSbmlParserTest.class, //
GenericSbmlToXmlParserTest.class, //
SbmlExporterTest.class, //
SbmlPareserForInvalidReactionTest.class, //
SbmlParserTest.class,//
SbmlParserTest.class, //
SbmlSpeciesParserTest.class,//
})
public class AllSbmlConverterTests {
......
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java 0 → 100644
+ 131
− 0
View file @ 6f47fe03
package lcsb.mapviewer.converter.model.sbml.species;
import static org.junit.Assert.assertTrue;
import java.io.FileNotFoundException;
import org.apache.log4j.Logger;
import org.junit.Test;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.sbml.SbmlParser;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Degraded;
import lcsb.mapviewer.model.map.species.Drug;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.model.map.species.IonChannelProtein;
import lcsb.mapviewer.model.map.species.Phenotype;
import lcsb.mapviewer.model.map.species.ReceptorProtein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.model.map.species.Unknown;
public class SbmlSpeciesParserTest {
Logger logger = Logger.getLogger(SbmlSpeciesParserTest.class);
SbmlParser parser = new SbmlParser();
@Test
public void testParseAntisenseRna() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/antisense_rna.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof AntisenseRna);
}
@Test
public void testParseComplex() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/complex.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof Complex);
}
@Test
public void testParseDegraded() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/degraded.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof Degraded);
}
@Test
public void testParseDrug() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/drug.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof Drug);
}
@Test
public void testParseGene() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/gene.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof Gene);
}
@Test
public void testParseGenericProtein() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/generic_protein.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof GenericProtein);
}
@Test
public void testParseIonChannel() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/ion_channel.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof IonChannelProtein);
}
@Test
public void testParseIon() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/ion.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof Ion);
}
@Test
public void testParsePhenotype() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/phenotype.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof Phenotype);
}
@Test
public void testParseReceptor() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/receptor.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof ReceptorProtein);
}
@Test
public void testParseRna() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/rna.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof Rna);
}
@Test
public void testParseSimpleMolecule() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/small_molecule.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof SimpleMolecule);
}
@Test
public void testParseSimpleMoleculeWithAlternativeSBOTerm() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/small_molecule2.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof SimpleMolecule);
}
@Test
public void testParseUnknown() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/unknown_species.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof Unknown);
}
}
converter-sbml/testFiles/small/antisense_rna.xml 0 → 100644
+ 26
− 0
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<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="cell" initialConcentration="1" id="s1" name="nm1" sboTerm="SBO:0000334">
<annotation/>
</species>
</listOfSpecies>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/complex.xml 0 → 100644
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− 0
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<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="cell" initialConcentration="1" id="s1" name="nm1" sboTerm="SBO:0000297">
<annotation/>
</species>
</listOfSpecies>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/degraded.xml 0 → 100644
+ 26
− 0
View file @ 6f47fe03
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="cell" initialConcentration="1" id="s1" name="nm1" sboTerm="SBO:0000291">
<annotation/>
</species>
</listOfSpecies>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/drug.xml 0 → 100644
+ 26
− 0
View file @ 6f47fe03
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="cell" initialConcentration="1" id="s1" name="nm1" sboTerm="SBO:0000298">
<annotation/>
</species>
</listOfSpecies>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/gene.xml 0 → 100644
+ 26
− 0
View file @ 6f47fe03
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="cell" initialConcentration="1" id="s1" name="nm1" sboTerm="SBO:0000243">
<annotation/>
</species>
</listOfSpecies>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/generic_protein.xml 0 → 100644
+ 26
− 0
View file @ 6f47fe03
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="cell" initialConcentration="1" id="s1" name="nm1" sboTerm="SBO:0000252">
<annotation/>
</species>
</listOfSpecies>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/ion.xml 0 → 100644
+ 26
− 0
View file @ 6f47fe03
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="cell" initialConcentration="1" id="s1" name="nm1" sboTerm="SBO:0000327">
<annotation/>
</species>
</listOfSpecies>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/ion_channel.xml 0 → 100644
+ 26
− 0
View file @ 6f47fe03
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="cell" initialConcentration="1" id="s1" name="nm1" sboTerm="SBO:0000284">
<annotation/>
</species>
</listOfSpecies>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/phenotype.xml 0 → 100644
+ 26
− 0
View file @ 6f47fe03
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="cell" initialConcentration="1" id="s1" name="nm1" sboTerm="SBO:0000358">
<annotation/>
</species>
</listOfSpecies>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/receptor.xml 0 → 100644
+ 26
− 0
View file @ 6f47fe03
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="cell" initialConcentration="1" id="s1" name="nm1" sboTerm="SBO:0000244">
<annotation/>
</species>
</listOfSpecies>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/rna.xml 0 → 100644
+ 26
− 0
View file @ 6f47fe03
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="cell" initialConcentration="1" id="s1" name="nm1" sboTerm="SBO:0000278">
<annotation/>
</species>
</listOfSpecies>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/small_molecule.xml 0 → 100644
+ 26
− 0
View file @ 6f47fe03
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="cell" initialConcentration="1" id="s1" name="nm1" sboTerm="SBO:0000247">
<annotation/>
</species>
</listOfSpecies>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/small_molecule2.xml 0 → 100644
+ 26
− 0
View file @ 6f47fe03
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="cell" initialConcentration="1" id="s1" name="nm1" sboTerm="SBO:0000299">
<annotation/>
</species>
</listOfSpecies>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/unknown_species.xml 0 → 100644
+ 26
− 0
View file @ 6f47fe03
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="cell" initialConcentration="1" id="s1" name="nm1" sboTerm="SBO:0000462">
<annotation/>
</species>
</listOfSpecies>
</model>
</sbml>
\ No newline at end of file
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