From 0307845f0707a9057d161d959376f1bf059b7d66 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 17 Dec 2018 10:04:37 +0100
Subject: [PATCH] throw proper exceptions
---
.../sbml/reaction/SbmlReactionParser.java | 8 ++++++++
.../model/sbml/species/SbmlSpeciesParser.java | 18 +++++++++++-------
.../mapviewer/model/map/reaction/Product.java | 6 +++++-
.../mapviewer/model/map/reaction/Reactant.java | 4 ++++
4 files changed, 28 insertions(+), 8 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
index be0d6950ae..2675a9451b 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
@@ -439,10 +439,18 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
for (SpeciesReference reactant : sbmlReaction.getListOfReactants()) {
Species element = minervaModel.getElementByElementId(reactant.getSpecies());
+ if (element == null) {
+ throw new InvalidInputDataExecption(
+ eu.getElementTag(reaction) + "Species with id " + reactant.getSpecies() + " cannot be found");
+ }
reaction.addReactant(new Reactant(element));
}
for (SpeciesReference product : sbmlReaction.getListOfProducts()) {
Species element = minervaModel.getElementByElementId(product.getSpecies());
+ if (element == null) {
+ throw new InvalidInputDataExecption(
+ eu.getElementTag(reaction) + "Species with id " + product.getSpecies() + " cannot be found");
+ }
reaction.addProduct(new Product(element));
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
index 53e3112ee5..fc85d01719 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
@@ -26,6 +26,9 @@ import lcsb.mapviewer.model.map.species.Unknown;
public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species> {
Logger logger = Logger.getLogger(SbmlSpeciesParser.class);
+ private static String ARTIFITIAL_SINK_ID = "sbml_artifitial_sink";
+ private static String ARTIFITIAL_SOURCE_ID = "sbml_artifitial_source";
+
public SbmlSpeciesParser(Layout layout, lcsb.mapviewer.model.map.model.Model minervaModel) {
super(layout, minervaModel);
}
@@ -70,7 +73,10 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
compartmentId = ((org.sbml.jsbml.Species) sbmlLayout.getSpeciesGlyph(element.getElementId())
.getSpeciesInstance()).getCompartment();
} else {
- compartmentId = sbmlModel.getSpecies(element.getElementId()).getCompartment();
+ if (!element.getElementId().equals(ARTIFITIAL_SINK_ID)
+ && !element.getElementId().equals(ARTIFITIAL_SOURCE_ID)) {
+ compartmentId = sbmlModel.getSpecies(element.getElementId()).getCompartment();
+ }
}
assignCompartment(element, compartmentId);
}
@@ -123,10 +129,9 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
}
public Species getArtifitialInput() {
- String artifitialId = "sbml_artifitial_source";
- Species result = minervaModel.getElementByElementId(artifitialId);
+ Species result = minervaModel.getElementByElementId(ARTIFITIAL_SOURCE_ID);
if (result == null) {
- result = new Unknown(artifitialId);
+ result = new Unknown(ARTIFITIAL_SOURCE_ID);
result.setName("Artifitial source");
minervaModel.addElement(result);
}
@@ -134,10 +139,9 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
}
public Species getArtifitialOutput() {
- String artifitialId = "sbml_artifitial_sink";
- Species result = minervaModel.getElementByElementId(artifitialId);
+ Species result = minervaModel.getElementByElementId(ARTIFITIAL_SINK_ID);
if (result == null) {
- result = new Degraded(artifitialId);
+ result = new Degraded(ARTIFITIAL_SINK_ID);
result.setName("Artifitial sink");
minervaModel.addElement(result);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Product.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Product.java
index 30a69c2fc0..110dcddb57 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Product.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Product.java
@@ -3,6 +3,7 @@ package lcsb.mapviewer.model.map.reaction;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
@@ -39,7 +40,10 @@ public class Product extends ReactionNode {
* element that represent this product
*/
public Product(Element element) {
- super(element);
+ super(element);
+ if (element==null) {
+ throw new InvalidArgumentException("Element cannot be null");
+ }
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reactant.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reactant.java
index a8d1910a64..aadfb454e2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reactant.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reactant.java
@@ -3,6 +3,7 @@ package lcsb.mapviewer.model.map.reaction;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
@@ -40,6 +41,9 @@ public class Reactant extends ReactionNode {
*/
public Reactant(Element element) {
super(element);
+ if (element==null) {
+ throw new InvalidArgumentException("Element cannot be null");
+ }
}
/**
--
GitLab