From df38f8adb816951b83775bc3cd19516bfeddf017 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 28 Aug 2018 18:51:30 +0200
Subject: [PATCH] reactions that should be modifiers but are valid phenotype
reactions don't crash upload
---
.../resources/applicationContext-persist.xml | 7 +++++
.../persist/dao/map/ModelDaoTest.java | 28 +++++++++++++++++++
2 files changed, 35 insertions(+)
diff --git a/persist/src/main/resources/applicationContext-persist.xml b/persist/src/main/resources/applicationContext-persist.xml
index 94e3760435..87ddd6894e 100644
--- a/persist/src/main/resources/applicationContext-persist.xml
+++ b/persist/src/main/resources/applicationContext-persist.xml
@@ -55,9 +55,13 @@
<value>lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.DissociationReaction</value>
+ <value>lcsb.mapviewer.model.map.reaction.type.CatalysisReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction</value>
+ <value>lcsb.mapviewer.model.map.reaction.type.InhibitionReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction</value>
+ <value>lcsb.mapviewer.model.map.reaction.type.ModulationReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction</value>
+ <value>lcsb.mapviewer.model.map.reaction.type.PhysicalStimulationReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction</value>
@@ -66,7 +70,10 @@
<value>lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.TranslationReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.TransportReaction</value>
+ <value>lcsb.mapviewer.model.map.reaction.type.TriggerReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.TruncationReaction</value>
+ <value>lcsb.mapviewer.model.map.reaction.type.UnknownCatalysisReaction</value>
+ <value>lcsb.mapviewer.model.map.reaction.type.UnknownInhibitionReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction</value>
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
index 3a211e414a..b191c5e5a7 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
@@ -34,6 +34,7 @@ import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.ModulationReaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
@@ -205,6 +206,33 @@ public class ModelDaoTest extends PersistTestFunctions {
}
}
+ @Test
+ public void testModulationReaction() throws Exception {
+ try {
+ Model model = createModel();
+ Reaction reaction = new ModulationReaction();
+ reaction.addProduct(new Product(model.getElementByElementId("sa2")));
+ reaction.addReactant(new Reactant(model.getElementByElementId("sa1117")));
+ reaction.setIdReaction("re" + identifierCounter++);
+ model.addReaction(reaction);
+
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+ projectDao.evict(project);
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+
+ assertEquals(0, modelComparator.compare(model, new ModelFullIndexed(model2)));
+
+ project = projectDao.getById(project.getId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testModelWithParameters() throws Exception {
try {
--
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