From d6fad8c4c8033e9645792171330e7a97d216cb01 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 12 Jul 2018 13:20:49 +0200
Subject: [PATCH] unit tests fixed + subclasses use proper discrimantor
---
.../layout/ApplySimpleLayoutModelCommand.java | 6 +++--
.../mapviewer/commands/AllCommandsTests.java | 14 ++++++-----
.../map/species/field/BindingRegion.java | 2 +-
.../model/map/species/field/CodingRegion.java | 2 +-
.../species/field/ProteinBindingDomain.java | 2 +-
.../map/species/field/RegulatoryRegion.java | 2 +-
.../api/projects/drugs/DrugRestImpl.java | 24 ++-----------------
7 files changed, 18 insertions(+), 34 deletions(-)
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
index fc0c60226e..e9c3648829 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
@@ -120,7 +120,7 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
Set<Species> elementToAlign = new HashSet<>();
Map<Compartment, Set<Element>> elementsByStaticCompartment = new HashMap<>();
for (Element element : elements) {
- if (element.getWidth() == 0) {
+ if (element.getWidth() == null || element.getWidth() == 0) {
element.setWidth(SPECIES_WIDTH);
element.setHeight(SPECIES_HEIGHT);
@@ -360,7 +360,9 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
protected Dimension2D estimateDimension(Collection<BioEntity> bioEntites) {
double suggestedSize = Math.max(100 * bioEntites.size() / 4,
Math.sqrt((SPECIES_WIDTH + 10) * (SPECIES_HEIGHT + 10) * bioEntites.size()));
- suggestedSize = Math.max(suggestedSize, 2 * (SPECIES_WIDTH + 10));
+ if (bioEntites.size() > 0) {
+ suggestedSize = Math.max(suggestedSize, 2 * (SPECIES_WIDTH + 10));
+ }
return new DoubleDimension(suggestedSize, suggestedSize);
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java b/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java
index 8b883cd54a..71fece55e5 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.commands;
+import lcsb.mapviewer.commands.layout.AllLayoutTests;
import lcsb.mapviewer.commands.properties.AllPropertyCommandTests;
import org.junit.runner.RunWith;
@@ -7,12 +8,13 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AllPropertyCommandTests.class, //
- ColorModelCommandTest.class, //
- CopyCommandTest.class, //
- CreateHierarchyCommandTest.class, //
- MoveElementsCommandTest.class, //
- SubModelCommandTest.class,//
+@SuiteClasses({ AllLayoutTests.class, //
+ AllPropertyCommandTests.class, //
+ ColorModelCommandTest.class, //
+ CopyCommandTest.class, //
+ CreateHierarchyCommandTest.class, //
+ MoveElementsCommandTest.class, //
+ SubModelCommandTest.class,//
})
public class AllCommandsTests {
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/BindingRegion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/BindingRegion.java
index b334ee3191..daa42fe4e3 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/BindingRegion.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/BindingRegion.java
@@ -22,7 +22,7 @@ import lcsb.mapviewer.model.map.species.Species;
*
*/
@Entity
-@DiscriminatorValue("MODIFICATION_SITE")
+@DiscriminatorValue("BINDING_REGION")
public class BindingRegion extends AbstractRegionModification implements Serializable {
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/CodingRegion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/CodingRegion.java
index 0f8eac1c4b..4a10b40642 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/CodingRegion.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/CodingRegion.java
@@ -26,7 +26,7 @@ import lcsb.mapviewer.model.map.species.Species;
*
*/
@Entity
-@DiscriminatorValue("MODIFICATION_SITE")
+@DiscriminatorValue("CODING_REGION")
public class CodingRegion extends AbstractRegionModification implements Serializable {
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ProteinBindingDomain.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ProteinBindingDomain.java
index 1803b107ec..92d9ea58f2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ProteinBindingDomain.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ProteinBindingDomain.java
@@ -24,7 +24,7 @@ import lcsb.mapviewer.model.map.species.Species;
*
*/
@Entity
-@DiscriminatorValue("MODIFICATION_SITE")
+@DiscriminatorValue("PROTEIN_BINDING_DOMAIN")
public class ProteinBindingDomain extends AbstractRegionModification implements Serializable {
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/RegulatoryRegion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/RegulatoryRegion.java
index c2aa45c683..fd47c43c8b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/RegulatoryRegion.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/RegulatoryRegion.java
@@ -22,7 +22,7 @@ import lcsb.mapviewer.model.map.species.Species;
*
*/
@Entity
-@DiscriminatorValue("MODIFICATION_SITE")
+@DiscriminatorValue("REGULATORY_REGION")
public class RegulatoryRegion extends AbstractRegionModification implements Serializable {
/**
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
index f34f2cbe61..785e3def80 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
@@ -39,15 +39,12 @@ public class DrugRestImpl extends BaseRestImpl {
@Autowired
private IDrugService drugService;
- @Autowired
- private IModelService modelService;
-
@Autowired
private IUserService userService;
public List<Map<String, Object>> getDrugsByQuery(String token, String projectId, String columns, String query)
throws SecurityException, QueryException {
- Model model = modelService.getLastModelByProjectId(projectId, token);
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -87,23 +84,6 @@ public class DrugRestImpl extends BaseRestImpl {
this.userService = userService;
}
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
private Map<String, Object> prepareDrug(Drug drug, Set<String> columnsSet, List<Model> models) {
Map<String, Object> result = new TreeMap<>();
for (String string : columnsSet) {
@@ -171,7 +151,7 @@ public class DrugRestImpl extends BaseRestImpl {
public List<Map<String, Object>> getDrugsByTarget(String token, String projectId, String targetType, String targetId,
String columns) throws SecurityException, QueryException {
- Model model = modelService.getLastModelByProjectId(projectId, token);
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
--
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