From feb9892f1fed250c7d267a360c5dacae37ba6104 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 5 Nov 2019 11:41:47 +0100
Subject: [PATCH] import of structural state added
---
CHANGELOG | 2 +
.../model/sbgnml/SbgnmlXmlParser.java | 47 ++++++++++++++-----
.../model/sbgnml/SbgnmlXmlParserTest2.java | 14 +++++-
.../stateVariable.sbgn | 13 +++++
4 files changed, 62 insertions(+), 14 deletions(-)
create mode 100644 converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/stateVariable.sbgn
diff --git a/CHANGELOG b/CHANGELOG
index 494b81d535..463eb98d64 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,6 +1,8 @@
minerva (15.0.0~alpha.1) stable; urgency=medium
* Small improvement: sort order of tables in admin panel is preserved among
sessions (#836)
+ * Bug fix: structural states of proteins are imported properly from SBGNML PD
+ (#995)
minerva (15.0.0~alpha.0) stable; urgency=medium
* Improvement: logs provided for validation data model are structurized (#325)
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 eb83df8f67..598553d58c 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
@@ -585,10 +585,20 @@ public class SbgnmlXmlParser {
for (Glyph child : children) {
if (GlyphClazz.fromClazz(child.getClazz()).equals(GlyphClazz.STATE_VARIABLE)) {
if (child.getState() == null || child.getState().getVariable() != null) {
- try {
- parseStateVariable(child, newSpecies);
- } catch (Exception ex) {
- logger.warn(ex.getMessage());
+ Residue residue = stateVariableToResidue(child);
+ if (residue != null) {
+ if (newSpecies instanceof Protein) {
+ ((Protein) newSpecies).addResidue(residue);
+ } else {
+ logger.warn("Only macromolecule elements can have state variables.");
+ }
+ } else {
+ StructuralState state = stateVariableToStructuralState(child);
+ if (newSpecies instanceof Protein) {
+ ((Protein) newSpecies).setStructuralState(state);
+ } else {
+ logger.warn("Only macromolecule elements can have state.");
+ }
}
} else {
if (newSpecies instanceof Protein) {
@@ -610,6 +620,20 @@ public class SbgnmlXmlParser {
}
+ private StructuralState stateVariableToStructuralState(Glyph glyph) {
+ StructuralState state = new StructuralState();
+
+ state.setFontSize(10);
+ state.setPosition(new Point2D.Double(glyph.getBbox().getX(), glyph.getBbox().getY()));
+ state.setHeight((double) glyph.getBbox().getH());
+ state.setWidth((double) glyph.getBbox().getW());
+ if (glyph.getState() != null) {
+ state.setValue(glyph.getState().getValue());
+ }
+
+ return state;
+ }
+
private StructuralState createStructuralState(Glyph glyph) {
StructuralState structuralState = new StructuralState();
@@ -775,20 +799,19 @@ public class SbgnmlXmlParser {
*
* @param unitOfInformationGlyph
* unit of information glyph from sbgn-ml file
- * @param species
- * species that the unit of information considers
* @throws Exception
* Exception is thrown if state variable is parsed for species other
* than Protein
*/
- private void parseStateVariable(Glyph unitOfInformationGlyph, Species species) {
- if (!(species instanceof Protein)) {
- throw new InvalidArgumentException("Only macromolecule elements can have state variables.");
+ private Residue stateVariableToResidue(Glyph unitOfInformationGlyph) {
+ if (unitOfInformationGlyph.getState() != null && (unitOfInformationGlyph.getState().getVariable() == null
+ || unitOfInformationGlyph.getState().getVariable().trim().isEmpty())) {
+ return null;
+
}
- Protein protein = (Protein) species;
+
Residue mr = new Residue();
- mr.setSpecies(protein);
mr.setIdModificationResidue(unitOfInformationGlyph.getId());
if (unitOfInformationGlyph.getState() != null) {
// If State variable consists of value and variable
@@ -806,7 +829,7 @@ public class SbgnmlXmlParser {
mr.setPosition(new Point2D.Double(x, y));
- protein.addResidue(mr);
+ return mr;
}
/**
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
index b0168dd398..2d0019add6 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
@@ -14,8 +14,7 @@ import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.*;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.species.field.Residue;
public class SbgnmlXmlParserTest2 extends SbgnmlTestFunctions {
@@ -105,4 +104,15 @@ public class SbgnmlXmlParserTest2 extends SbgnmlTestFunctions {
assertEquals(p2.getLine().getBeginPoint(), outputOperator.getLine().getBeginPoint());
}
+ @Test
+ public void testProteinState() throws Exception {
+ Converter converter = new SbgnmlXmlConverter();
+ Model model = converter
+ .createModel(new ConverterParams().filename("testFiles/sbgnmlCellDesignerInompatible/stateVariable.sbgn"));
+
+ Protein protein = model.getElementByElementId("glyph_n20");
+ assertEquals("inactive", protein.getStructuralState().getValue());
+ assertEquals(0, protein.getModificationResidues().size());
+ }
+
}
diff --git a/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/stateVariable.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/stateVariable.sbgn
new file mode 100644
index 0000000000..c43a2b8f4e
--- /dev/null
+++ b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/stateVariable.sbgn
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
+ <map language="process description">
+ <glyph class="macromolecule" id="glyph_n20">
+ <label text="PKA"/>
+ <bbox w="80.0" h="40.0" x="662.7319" y="21.57837"/>
+ <glyph class="state variable" id="glyph_n20_4">
+ <state value="inactive" variable=""/>
+ <bbox w="50.0" h="18.0" x="677.7319" y="51.86792"/>
+ </glyph>
+ </glyph>
+ </map>
+</sbgn>
\ No newline at end of file
--
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