Merge branch '1203-import-infinity-kinetic-parameter' into 'devel_14.0.x'

kinetic parameter with infinity can be parsed properly

See merge request !1096

CHANGELOG

@@ -5,6 +5,10 @@ minerva (14.0.11) stable; urgency=medium
     (#1198)
   * Bug fix: export to CellDesigner deal with CellDesigner issue that does not
     allow complex species alias to be shorter than 2 characters (#1204)
+  * Bug fix: kinetic parameters with INFINITY values could not be uploaded to
+    minerva (#1202)
+  * Bug fix: infinity value in kinetic parameter could not be parsed from
+    CellDesigner file minerva (#1203)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 30 Mar 2020 10:00:00 +0200
 

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserUtils.java

+package lcsb.mapviewer.converter.model.celldesigner;
+
+public class CellDesignerParserUtils {
+  public Double parseDouble(String input) {
+    if (input == null) {
+      return null;
+    }
+    if (input.equalsIgnoreCase("INF")) {
+      return Double.POSITIVE_INFINITY;
+    }
+    if (input.equalsIgnoreCase("-INF")) {
+      return Double.NEGATIVE_INFINITY;
+    }
+    return Double.parseDouble(input);
+  }
+}

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterXmlParser.java

@@ -6,6 +6,7 @@ import org.w3c.dom.Node;
 
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerParserUtils;
 import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
 import lcsb.mapviewer.model.map.model.Model;
 
@@ -27,7 +28,7 @@ public class ParameterXmlParser {
 
     SbmlParameter result = new SbmlParameter(parameterId);
     result.setName(XmlParser.getNodeAttr("name", unitNode));
-    result.setValue(Double.parseDouble(XmlParser.getNodeAttr("value", unitNode)));
+    result.setValue(new CellDesignerParserUtils().parseDouble(XmlParser.getNodeAttr("value", unitNode)));
     result.setUnits(model.getUnitsByUnitId(XmlParser.getNodeAttr("units", unitNode)));
     return result;
   }

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java

@@ -9,7 +9,7 @@ import lcsb.mapviewer.converter.model.celldesigner.annotation.AllAnnotationTests
 import lcsb.mapviewer.converter.model.celldesigner.compartment.AllCompartmentTests;
 import lcsb.mapviewer.converter.model.celldesigner.function.AllFunctionTests;
 import lcsb.mapviewer.converter.model.celldesigner.geometry.AllGeometryTests;
-import lcsb.mapviewer.converter.model.celldesigner.parameter.ParameterXmlParserTest;
+import lcsb.mapviewer.converter.model.celldesigner.parameter.AllParameterTests;
 import lcsb.mapviewer.converter.model.celldesigner.reaction.AllReactionTests;
 import lcsb.mapviewer.converter.model.celldesigner.species.AllSpeciesTests;
 import lcsb.mapviewer.converter.model.celldesigner.structure.AllStructureTests;
@@ -23,18 +23,19 @@ import lcsb.mapviewer.converter.model.celldesigner.unit.UnitXmlParserTest;
     AllCompartmentTests.class,
     AllFunctionTests.class,
     AllGeometryTests.class,
+    AllParameterTests.class,
     AllReactionTests.class,
     AllSpeciesTests.class,
     AllStructureTests.class,
     AllTypesTests.class,
     CellDesignerElementCollectionTest.class,
     CellDesignerXmlParserTest.class,
+    CellDesignerParserUtilsTest.class,
     ComplexParserTests.class,
     InvalidGroupExceptionTest.class,
     LayerXmlParserTest.class,
     NestedComplexParsingTests.class,
     ModificationTest.class,
-    ParameterXmlParserTest.class,
     ReconDataInCellDesignerXmlParserTest.class,
     SbmlValidationTests.class,
     UnitXmlParserTest.class,

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserUtilsTest.java

+package lcsb.mapviewer.converter.model.celldesigner;
+
+import static org.junit.Assert.*;
+
+import org.junit.Test;
+
+public class CellDesignerParserUtilsTest {
+
+  @Test
+  public void test() {
+    assertTrue(Double.isInfinite(new CellDesignerParserUtils().parseDouble("INF")));
+  }
+
+}

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/parameter/AllParameterTests.java

+package lcsb.mapviewer.converter.model.celldesigner.parameter;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ GenericParameterXmlParserTest.class, ParameterXmlParserTest.class })
+public class AllParameterTests {
+
+}

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/parameter/GenericParameterXmlParserTest.java

+package lcsb.mapviewer.converter.model.celldesigner.parameter;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.io.IOException;
+import java.nio.file.*;
+import java.util.*;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.model.map.kinetics.*;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+@RunWith(Parameterized.class)
+public class GenericParameterXmlParserTest extends CellDesignerTestFunctions {
+
+  private String filename;
+
+  public GenericParameterXmlParserTest(String filename) {
+    this.filename = filename;
+  }
+
+  @Parameters(name = "{0}")
+  public static Collection<Object[]> data() throws IOException {
+    List<Object[]> result = new ArrayList<>();
+    try (Stream<Path> walk = Files.walk(Paths.get("testFiles/parameter"))) {
+
+      List<String> filenames = walk.filter(Files::isRegularFile)
+          .map(x -> x.toString()).collect(Collectors.toList());
+      for (String string : filenames) {
+        result.add(new Object[] { string });
+      }
+      return result;
+    }
+  }
+
+  @Test
+  public void testSerialization() throws InvalidXmlSchemaException, IOException {
+    SbmlUnit volume = new SbmlUnit("volume");
+    Model model = new ModelFullIndexed(null);
+    model.addUnit(volume);
+    ParameterXmlParser parser = new ParameterXmlParser(model);
+    SbmlParameter parameter = parser
+        .parseParameter(super.getXmlDocumentFromFile(filename).getFirstChild());
+
+    assertNotNull(parameter);
+
+    String xml = parser.toXml(parameter);
+    SbmlParameter parameter2 = parser.parseParameter(super.getNodeFromXmlString(xml));
+    assertEquals(0, new SbmlParameterComparator().compare(parameter, parameter2));
+  }
+}

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterXmlParserTest.java

 package lcsb.mapviewer.converter.model.celldesigner.parameter;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.*;
 
 import java.io.IOException;
 
@@ -10,8 +9,7 @@ import org.junit.Test;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.kinetics.*;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 
@@ -23,14 +21,43 @@ public class ParameterXmlParserTest extends CellDesignerTestFunctions {
     Model model = new ModelFullIndexed(null);
     model.addUnit(volume);
     ParameterXmlParser parser = new ParameterXmlParser(model);
-    SbmlParameter unit = parser
+    SbmlParameter parameter = parser
         .parseParameter(super.getXmlDocumentFromFile("testFiles/parameter/simple.xml").getFirstChild());
 
-    assertNotNull(unit);
-    assertEquals(unit.getParameterId(), "param_id");
-    assertEquals(unit.getName(), "Parameter name");
-    assertEquals(unit.getValue(), 12.0, Configuration.EPSILON);
-    assertEquals(unit.getUnits(), volume);
+    assertNotNull(parameter);
+    assertEquals(parameter.getParameterId(), "param_id");
+    assertEquals(parameter.getName(), "Parameter name");
+    assertEquals(parameter.getValue(), 12.0, Configuration.EPSILON);
+    assertEquals(parameter.getUnits(), volume);
+  }
+
+  @Test
+  public void testParseInfinity() throws InvalidXmlSchemaException, IOException {
+    SbmlUnit volume = new SbmlUnit("volume");
+    Model model = new ModelFullIndexed(null);
+    model.addUnit(volume);
+    ParameterXmlParser parser = new ParameterXmlParser(model);
+    SbmlParameter parameter = parser
+        .parseParameter(super.getXmlDocumentFromFile("testFiles/parameter/infinity_parameter.xml").getFirstChild());
+
+    assertNotNull(parameter);
+    assertTrue(Double.isInfinite(parameter.getValue()));
+    assertTrue(parameter.getValue() > 0);
+  }
+
+  @Test
+  public void testParseNegativeInfinity() throws InvalidXmlSchemaException, IOException {
+    SbmlUnit volume = new SbmlUnit("volume");
+    Model model = new ModelFullIndexed(null);
+    model.addUnit(volume);
+    ParameterXmlParser parser = new ParameterXmlParser(model);
+    SbmlParameter parameter = parser
+        .parseParameter(
+            super.getXmlDocumentFromFile("testFiles/parameter/negative_infinity_parameter.xml").getFirstChild());
+
+    assertNotNull(parameter);
+    assertTrue(Double.isInfinite(parameter.getValue()));
+    assertTrue(parameter.getValue() < 0);
   }
 
 }

converter-CellDesigner/testFiles/parameter/infinity_parameter.xml

+<parameter metaid="param" id="param" name="infinity param" value="INF" units="substance"/>

converter-CellDesigner/testFiles/parameter/negative_infinity_parameter.xml

+<parameter metaid="param" id="param" name="infinity param" value="-INF" units="substance"/>

persist/src/main/resources/db/migration/14.0.11/V14.0.11.20200330__inifinity_kinetic_parameter.sql

+alter table sbml_parameter_table alter COLUMN value type double precision;