From 045ff5d7db61b4a340f06b44eef2b58127415b98 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 23 Oct 2019 10:29:57 +0200
Subject: [PATCH] import/export of StructuralStat from sbgml uses new data
structure
---
.../model/sbgnml/SbgnmlXmlExporter.java | 35 ++++---
.../model/sbgnml/SbgnmlXmlParser.java | 27 +++++-
.../model/sbgnml/CellDesignerToSbgnTest.java | 5 +-
.../model/sbgnml/DbSerializationTest.java | 92 ++++++++-----------
.../model/sbgnml/SbgnmlXmlExporterTest.java | 23 +++--
.../insulin-like_growth_factor_signaling.sbgn | 0
.../mapk_cascade.sbgn | 0
.../neuronal_muscle_signalling.sbgn | 0
.../neuronal_muscle_signalling_color.sbgn | 0
.../states.sbgn | 0
.../submap.sbgn | 0
.../theWeirdOne.sbgn | 0
.../unitOfInformation.sbgn | 0
13 files changed, 97 insertions(+), 85 deletions(-)
rename converter-SBGNML/testFiles/{sbgnmlParserTestFiles/sbgnmlFiles => sbgnmlCellDesignerInompatible}/insulin-like_growth_factor_signaling.sbgn (100%)
rename converter-SBGNML/testFiles/{sbgnmlParserTestFiles/sbgnmlFiles => sbgnmlCellDesignerInompatible}/mapk_cascade.sbgn (100%)
rename converter-SBGNML/testFiles/{sbgnmlParserTestFiles/sbgnmlFiles => sbgnmlCellDesignerInompatible}/neuronal_muscle_signalling.sbgn (100%)
rename converter-SBGNML/testFiles/{sbgnmlParserTestFiles/sbgnmlFiles => sbgnmlCellDesignerInompatible}/neuronal_muscle_signalling_color.sbgn (100%)
rename converter-SBGNML/testFiles/{sbgnmlParserTestFiles/sbgnmlFiles => sbgnmlCellDesignerInompatible}/states.sbgn (100%)
rename converter-SBGNML/testFiles/{sbgnmlParserTestFiles/sbgnmlFiles => sbgnmlCellDesignerInompatible}/submap.sbgn (100%)
rename converter-SBGNML/testFiles/{sbgnmlParserTestFiles/sbgnmlFiles => sbgnmlCellDesignerInompatible}/theWeirdOne.sbgn (100%)
rename converter-SBGNML/testFiles/{sbgnmlParserTestFiles/sbgnmlFiles => sbgnmlCellDesignerInompatible}/unitOfInformation.sbgn (100%)
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
index c3cc9949f4..eb61780079 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
@@ -10,8 +10,8 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.sbgn.*;
import org.sbgn.bindings.*;
-import org.sbgn.bindings.Map;
import org.sbgn.bindings.Arc.*;
+import org.sbgn.bindings.Map;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -24,8 +24,7 @@ import lcsb.mapviewer.model.map.modifier.*;
import lcsb.mapviewer.model.map.reaction.*;
import lcsb.mapviewer.model.map.reaction.type.*;
import lcsb.mapviewer.model.map.species.*;
-import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.*;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -170,8 +169,8 @@ public class SbgnmlXmlExporter {
stateVariableGlyph.setId(newGlyph.getId().concat("-").concat(stateVariableGlyph.getId()));
newGlyph.getGlyph().add(stateVariableGlyph);
}
- if (protein.getStructuralState() != null && !protein.getStructuralState().isEmpty()) {
- newGlyph.getGlyph().add(createStateVariableForStructuralState(protein, protein.getStructuralState()));
+ if (protein.getStructuralState() != null && !protein.getStructuralState().getValue().isEmpty()) {
+ newGlyph.getGlyph().add(createStateVariableForStructuralState(protein.getStructuralState()));
}
}
@@ -186,8 +185,8 @@ public class SbgnmlXmlExporter {
Glyph childGlyph = elementToGlyph(child);
newGlyph.getGlyph().add(childGlyph);
}
- if (complex.getStructuralState() != null && !complex.getStructuralState().isEmpty()) {
- newGlyph.getGlyph().add(createStateVariableForStructuralState(complex, complex.getStructuralState()));
+ if (complex.getStructuralState() != null && !complex.getStructuralState().getValue().isEmpty()) {
+ newGlyph.getGlyph().add(createStateVariableForStructuralState(complex.getStructuralState()));
}
}
}
@@ -196,24 +195,24 @@ public class SbgnmlXmlExporter {
return newGlyph;
}
- private Glyph createStateVariableForStructuralState(Element element, String structuralState) {
+ private Glyph createStateVariableForStructuralState(StructuralState structuralState) {
Glyph glyph = new Glyph();
- glyph.setId(element.getElementId() + "-state");
+ glyph.setId(structuralState.getSpecies().getElementId() + "-state");
glyph.setClazz(GlyphClazz.STATE_VARIABLE.getClazz());
Glyph.State state = new Glyph.State();
- state.setValue(structuralState);
+ state.setValue(structuralState.getValue());
glyph.setState(state);
Bbox bbox = new Bbox();
-
- float width = (float) (element.getWidth() - 20);
- float height = 28.0f;
- bbox.setH(width);
- bbox.setW(height);
-
- bbox.setX((float) (element.getX() + 10));
- bbox.setY((float) (element.getY() - height / 2));
+
+ float width = structuralState.getWidth().floatValue();
+ float height = structuralState.getHeight().floatValue();
+ bbox.setH(height);
+ bbox.setW(width);
+
+ bbox.setX((float) structuralState.getPosition().getX());
+ bbox.setY((float) structuralState.getPosition().getY());
glyph.setBbox(bbox);
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
index 9423bb9f7c..fcc383be60 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.sbgnml;
-import java.awt.*;
+import java.awt.Color;
import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.io.File;
@@ -34,6 +34,7 @@ import lcsb.mapviewer.model.map.reaction.*;
import lcsb.mapviewer.model.map.reaction.type.*;
import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.species.field.*;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
* This class is a parser for SBGN-ML files.
@@ -590,13 +591,14 @@ public class SbgnmlXmlParser {
logger.warn(ex.getMessage());
}
} else {
- String structuralState = child.getState().getValue();
if (newSpecies instanceof Protein) {
Protein protein = (Protein) newSpecies;
- protein.setStructuralState(structuralState);
+ protein.setStructuralState(createStructuralState(child));
} else if (newSpecies instanceof Complex) {
Complex complex = (Complex) newSpecies;
- complex.setStructuralState(structuralState);
+ complex.setStructuralState(createStructuralState(child));
+ } else {
+ logger.warn(new ElementUtils().getElementTag(newSpecies) + "State is not supported");
}
}
}
@@ -608,6 +610,23 @@ public class SbgnmlXmlParser {
}
+ private StructuralState createStructuralState(Glyph glyph) {
+ StructuralState structuralState = new StructuralState();
+
+ double height = new Double(glyph.getBbox().getH());
+ double width = new Double(glyph.getBbox().getW());
+ double x = new Double(glyph.getBbox().getX());
+ double y = new Double(glyph.getBbox().getY());
+
+ structuralState.setFontSize(10);
+ structuralState.setValue(glyph.getState().getValue());
+ structuralState.setHeight(height);
+ structuralState.setWidth(width);
+ structuralState.setPosition(new Point2D.Double(x, y));
+
+ return structuralState;
+ }
+
/**
* {@link ModificationResidue} in element might have slightly off coordinates
* (due to different symbol shapes). For that we need to align them to match our
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
index 54da7290fb..f040b80617 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
@@ -18,6 +18,7 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.field.StructuralStateComparator;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class CellDesignerToSbgnTest extends SbgnmlTestFunctions {
@@ -108,7 +109,9 @@ public class CellDesignerToSbgnTest extends SbgnmlTestFunctions {
protein1 = model.getElementByElementId("sa2");
protein2 = model2.getElementByElementId("sa2");
- assertEquals(protein1.getStructuralState(), protein2.getStructuralState());
+ StructuralStateComparator comparator = new StructuralStateComparator();
+
+ assertEquals(0, comparator.compare(protein1.getStructuralState(), protein2.getStructuralState()));
}
}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
index 7f6000f2a5..c2a66df954 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
@@ -3,35 +3,61 @@ package lcsb.mapviewer.converter.model.sbgnml;
import static org.junit.Assert.assertEquals;
import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.junit.*;
import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.test.context.ContextConfiguration;
-import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.annotation.AnnotationConfigApplicationContext;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.model.map.model.*;
import lcsb.mapviewer.persist.DbUtils;
import lcsb.mapviewer.persist.dao.map.ModelDao;
-@Transactional
-@ContextConfiguration(classes = SpringSBGNMLConverterTestConfig.class)
-@RunWith(SpringJUnit4ClassRunner.class)
+@RunWith(Parameterized.class)
public class DbSerializationTest extends SbgnmlTestFunctions {
- @Autowired
- ModelDao modelDao;
- @Autowired
- DbUtils dbUtils;
+
+ static ApplicationContext applicationContext;
Logger logger = LogManager.getLogger(DbSerializationTest.class.getName());
- private void makeDbSerializationTest(String filePath) throws Exception {
+ private String fileName;
+
+ public DbSerializationTest(String filePath) {
+ this.fileName = filePath;
+ }
+
+ @Parameters(name = "{index} : {0}")
+ public static Collection<Object[]> data() throws IOException {
+ applicationContext = new AnnotationConfigApplicationContext(
+ SpringSBGNMLConverterTestConfig.class);
+
+ Collection<Object[]> data = new ArrayList<Object[]>();
+ data.add(new Object[] {"testFiles/sbgnmlParserTestFiles/sbgnmlFiles/VANTEDdiagram.sbgn"});
+ data.add(new Object[] {"testFiles/sbgnmlParserTestFiles/sbgnmlFiles/activated_stat1alpha_induction_of_the_irf1_gene.sbgn"});
+ data.add(new Object[] {"testFiles/sbgnmlParserTestFiles/sbgnmlFiles/adh.sbgn"});
+ data.add(new Object[] {"testFiles/sbgnmlParserTestFiles/sbgnmlFiles/clone-marker.sbgn"});
+ data.add(new Object[] {"testFiles/sbgnmlParserTestFiles/sbgnmlFiles/glycolysis.sbgn"});
+ data.add(new Object[] {"testFiles/sbgnmlCellDesignerInompatible/insulin-like_growth_factor_signaling.sbgn"});
+ data.add(new Object[] {"testFiles/sbgnmlCellDesignerInompatible/neuronal_muscle_signalling.sbgn"});
+ data.add(new Object[] {"testFiles/sbgnmlParserTestFiles/sbgnmlFiles/phenotypeTest.sbgn"});
+ return data;
+ }
+
+ @Test
+ @Transactional
+ public void dbSerializationTest() throws Exception {
+ ModelDao modelDao = applicationContext.getBean(ModelDao.class);
+
SbgnmlXmlParser parser = new SbgnmlXmlParser();
- String fileName = "testFiles/sbgnmlParserTestFiles/sbgnmlFiles/".concat(filePath);
Model model = parser.createModel(fileName, new File(fileName));
modelDao.add(model);
@@ -47,6 +73,7 @@ public class DbSerializationTest extends SbgnmlTestFunctions {
@Before
public void setUp() throws Exception {
+ DbUtils dbUtils = applicationContext.getBean(DbUtils.class);
// we use custom threads because in layoutservice there is commit method
// called, and because of that hibernate session injected by spring
// cannot
@@ -58,48 +85,9 @@ public class DbSerializationTest extends SbgnmlTestFunctions {
@After
public void tearDown() throws Exception {
+ DbUtils dbUtils = applicationContext.getBean(DbUtils.class);
// close session
dbUtils.closeSessionForCurrentThread();
}
- @Test
- public void VANTEDdiagramTest() throws Exception {
- makeDbSerializationTest("VANTEDdiagram.sbgn");
- }
-
- @Test
- public void activatedStat1AlphaTest() throws Exception {
- makeDbSerializationTest("activated_stat1alpha_induction_of_the_irf1_gene.sbgn");
- }
-
- @Test
- public void adhTest() throws Exception {
- makeDbSerializationTest("adh.sbgn");
- }
-
- @Test
- public void cloneMarkerTest() throws Exception {
- makeDbSerializationTest("clone-marker.sbgn");
- }
-
- @Test
- public void glycolysisTest() throws Exception {
- makeDbSerializationTest("glycolysis.sbgn");
- }
-
- @Test
- public void insulinLikeGrowthFactorSignalingTest() throws Exception {
- makeDbSerializationTest("insulin-like_growth_factor_signaling.sbgn");
- }
-
- @Test
- public void neuronalMuscleSignallingTest() throws Exception {
- makeDbSerializationTest("neuronal_muscle_signalling.sbgn");
- }
-
- @Test
- public void phenotypeTest() throws Exception {
- makeDbSerializationTest("phenotypeTest.sbgn");
- }
-
}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
index 6618aa6b87..e840c5e16d 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
@@ -2,8 +2,7 @@ package lcsb.mapviewer.converter.model.sbgnml;
import java.io.File;
import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Paths;
+import java.nio.file.*;
import java.util.ArrayList;
import java.util.Collection;
@@ -23,10 +22,10 @@ public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
Logger logger = LogManager.getLogger(SbgnmlXmlExporterTest.class.getName());
- private String testName;
+ private Path filePath;
- public SbgnmlXmlExporterTest(String testName) {
- this.testName = testName;
+ public SbgnmlXmlExporterTest(Path filePath) {
+ this.filePath = filePath;
}
@Parameters(name = "{index} : {0}")
@@ -34,25 +33,29 @@ public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
Collection<Object[]> data = new ArrayList<Object[]>();
Files.walk(Paths.get("testFiles/sbgnmlParserTestFiles/sbgnmlFiles")).forEach(fPath -> {
if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".sbgn")) {
- String tName = fPath.getFileName().toString().substring(0, fPath.getFileName().toString().indexOf(".sbgn"));
- data.add(new Object[] { tName });
+ data.add(new Object[] { fPath});
+ }
+ });
+ Files.walk(Paths.get("testFiles/sbgnmlCellDesignerInompatible")).forEach(fPath -> {
+ if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".sbgn")) {
+ data.add(new Object[] { fPath});
}
});
return data;
}
- private void parseAndExport(String testName) throws Exception {
+ private void parseAndExport(Path filePath) throws Exception {
Converter converter = new SbgnmlXmlConverter();
Model model = converter.createModel(new ConverterParams()
- .filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/".concat(testName).concat(".sbgn")));
+ .filename(filePath.toAbsolutePath().toString()));
converter.model2File(model, File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath());
}
@Test
public void test() throws Exception {
- parseAndExport(testName);
+ parseAndExport(filePath);
}
}
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/insulin-like_growth_factor_signaling.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/insulin-like_growth_factor_signaling.sbgn
similarity index 100%
rename from converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/insulin-like_growth_factor_signaling.sbgn
rename to converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/insulin-like_growth_factor_signaling.sbgn
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/mapk_cascade.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/mapk_cascade.sbgn
similarity index 100%
rename from converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/mapk_cascade.sbgn
rename to converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/mapk_cascade.sbgn
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/neuronal_muscle_signalling.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/neuronal_muscle_signalling.sbgn
similarity index 100%
rename from converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/neuronal_muscle_signalling.sbgn
rename to converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/neuronal_muscle_signalling.sbgn
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/neuronal_muscle_signalling_color.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/neuronal_muscle_signalling_color.sbgn
similarity index 100%
rename from converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/neuronal_muscle_signalling_color.sbgn
rename to converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/neuronal_muscle_signalling_color.sbgn
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/states.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/states.sbgn
similarity index 100%
rename from converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/states.sbgn
rename to converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/states.sbgn
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/submap.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/submap.sbgn
similarity index 100%
rename from converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/submap.sbgn
rename to converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/submap.sbgn
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/theWeirdOne.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/theWeirdOne.sbgn
similarity index 100%
rename from converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/theWeirdOne.sbgn
rename to converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/theWeirdOne.sbgn
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/unitOfInformation.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/unitOfInformation.sbgn
similarity index 100%
rename from converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/unitOfInformation.sbgn
rename to converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/unitOfInformation.sbgn
--
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