diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
index 337bc2c992c2a3707b32d662824c273fd5a925cd..c6ec3e57c987a4b4f6d13e82db69f4a7a0ffc585 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
@@ -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 {
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..2a049eecec810853e37d1db9f6255c4989176cbc
--- /dev/null
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
@@ -0,0 +1,131 @@
+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);
+ }
+
+}
diff --git a/converter-sbml/testFiles/small/antisense_rna.xml b/converter-sbml/testFiles/small/antisense_rna.xml
new file mode 100644
index 0000000000000000000000000000000000000000..b665121932a52bf0801df98d65ae873d2019846a
--- /dev/null
+++ b/converter-sbml/testFiles/small/antisense_rna.xml
@@ -0,0 +1,26 @@
+<?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
diff --git a/converter-sbml/testFiles/small/complex.xml b/converter-sbml/testFiles/small/complex.xml
new file mode 100644
index 0000000000000000000000000000000000000000..f1670937cf9130c646cb216dd48447dcc1ed5072
--- /dev/null
+++ b/converter-sbml/testFiles/small/complex.xml
@@ -0,0 +1,26 @@
+<?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
diff --git a/converter-sbml/testFiles/small/degraded.xml b/converter-sbml/testFiles/small/degraded.xml
new file mode 100644
index 0000000000000000000000000000000000000000..44da559166368e0ec5be823cea338703c64e1be5
--- /dev/null
+++ b/converter-sbml/testFiles/small/degraded.xml
@@ -0,0 +1,26 @@
+<?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
diff --git a/converter-sbml/testFiles/small/drug.xml b/converter-sbml/testFiles/small/drug.xml
new file mode 100644
index 0000000000000000000000000000000000000000..11262cca4d4309a1c4164458b916979228195d64
--- /dev/null
+++ b/converter-sbml/testFiles/small/drug.xml
@@ -0,0 +1,26 @@
+<?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
diff --git a/converter-sbml/testFiles/small/gene.xml b/converter-sbml/testFiles/small/gene.xml
new file mode 100644
index 0000000000000000000000000000000000000000..5dcbce05b10d24ec416be06a62aba4c8e28a73aa
--- /dev/null
+++ b/converter-sbml/testFiles/small/gene.xml
@@ -0,0 +1,26 @@
+<?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
diff --git a/converter-sbml/testFiles/small/generic_protein.xml b/converter-sbml/testFiles/small/generic_protein.xml
new file mode 100644
index 0000000000000000000000000000000000000000..bf02fb868e8a728ec81e732c1833dafedc2763e0
--- /dev/null
+++ b/converter-sbml/testFiles/small/generic_protein.xml
@@ -0,0 +1,26 @@
+<?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
diff --git a/converter-sbml/testFiles/small/ion.xml b/converter-sbml/testFiles/small/ion.xml
new file mode 100644
index 0000000000000000000000000000000000000000..65da7f5f001c84097408809795cb61da56218dd1
--- /dev/null
+++ b/converter-sbml/testFiles/small/ion.xml
@@ -0,0 +1,26 @@
+<?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
diff --git a/converter-sbml/testFiles/small/ion_channel.xml b/converter-sbml/testFiles/small/ion_channel.xml
new file mode 100644
index 0000000000000000000000000000000000000000..d68d7c4f2d33b8b8e769c442a25707823cb64a24
--- /dev/null
+++ b/converter-sbml/testFiles/small/ion_channel.xml
@@ -0,0 +1,26 @@
+<?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
diff --git a/converter-sbml/testFiles/small/phenotype.xml b/converter-sbml/testFiles/small/phenotype.xml
new file mode 100644
index 0000000000000000000000000000000000000000..9cd80a6b2e8e9f126e07d2c99ee58e43379feee6
--- /dev/null
+++ b/converter-sbml/testFiles/small/phenotype.xml
@@ -0,0 +1,26 @@
+<?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
diff --git a/converter-sbml/testFiles/small/receptor.xml b/converter-sbml/testFiles/small/receptor.xml
new file mode 100644
index 0000000000000000000000000000000000000000..6dd46d743234c2b81dd7945ed0a9765633b13eed
--- /dev/null
+++ b/converter-sbml/testFiles/small/receptor.xml
@@ -0,0 +1,26 @@
+<?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
diff --git a/converter-sbml/testFiles/small/rna.xml b/converter-sbml/testFiles/small/rna.xml
new file mode 100644
index 0000000000000000000000000000000000000000..64293b1a8126452aac7281a81da0233cfe3776ed
--- /dev/null
+++ b/converter-sbml/testFiles/small/rna.xml
@@ -0,0 +1,26 @@
+<?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
diff --git a/converter-sbml/testFiles/small/small_molecule.xml b/converter-sbml/testFiles/small/small_molecule.xml
new file mode 100644
index 0000000000000000000000000000000000000000..1731df3a0774337946689e1c5318b82a6482d7df
--- /dev/null
+++ b/converter-sbml/testFiles/small/small_molecule.xml
@@ -0,0 +1,26 @@
+<?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
diff --git a/converter-sbml/testFiles/small/small_molecule2.xml b/converter-sbml/testFiles/small/small_molecule2.xml
new file mode 100644
index 0000000000000000000000000000000000000000..ea78913e5953326472ca1f8529b531407c0b1faf
--- /dev/null
+++ b/converter-sbml/testFiles/small/small_molecule2.xml
@@ -0,0 +1,26 @@
+<?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
diff --git a/converter-sbml/testFiles/small/unknown_species.xml b/converter-sbml/testFiles/small/unknown_species.xml
new file mode 100644
index 0000000000000000000000000000000000000000..fe21d6e802922002be13b8ae0ade69a2aee673ff
--- /dev/null
+++ b/converter-sbml/testFiles/small/unknown_species.xml
@@ -0,0 +1,26 @@
+<?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