From d59443af63faefd0ae85621189f4547c9479711e Mon Sep 17 00:00:00 2001
From: Piotr Gawron <p.gawron@atcomp.pl>
Date: Tue, 8 Apr 2025 09:30:13 +0200
Subject: [PATCH] fix test issues
---
.../services/impl/ReactionService.java | 39 ++++++++++---------
.../lcsb/mapviewer/web/api/NewApiDocs.java | 12 ++++++
2 files changed, 33 insertions(+), 18 deletions(-)
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ReactionService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ReactionService.java
index 0865c6ff84..1d312720ef 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ReactionService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ReactionService.java
@@ -1,28 +1,28 @@
package lcsb.mapviewer.services.impl;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-
-import org.hibernate.Hibernate;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.data.domain.Page;
-import org.springframework.data.domain.Pageable;
-import org.springframework.stereotype.Service;
-import org.springframework.transaction.annotation.Transactional;
-
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
import lcsb.mapviewer.persist.dao.map.ReactionDao;
import lcsb.mapviewer.persist.dao.map.ReactionProperty;
import lcsb.mapviewer.services.ObjectNotFoundException;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IReactionService;
+import org.hibernate.Hibernate;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
+import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
@Transactional
@Service
@@ -43,8 +43,8 @@ public class ReactionService implements IReactionService {
public Reaction getReactionById(final String projectId, final int mapId, final int elementId) throws ObjectNotFoundException {
ModelData map = modelService.getModelByMapId(projectId, mapId);
Map<ReactionProperty, Object> filter = new HashMap<>();
- filter.put(ReactionProperty.MAP, Arrays.asList(map));
- filter.put(ReactionProperty.ID, Arrays.asList(elementId));
+ filter.put(ReactionProperty.MAP, Collections.singletonList(map));
+ filter.put(ReactionProperty.ID, Collections.singletonList(elementId));
Page<Reaction> page = reactionDao.getAll(filter, Pageable.unpaged());
if (page.getNumberOfElements() > 0) {
return page.getContent().get(0);
@@ -54,7 +54,7 @@ public class ReactionService implements IReactionService {
@Override
public List<Reaction> getReactionById(final String projectId, final String mapId, final Set<Integer> ids,
- final Set<Integer> participantIds) throws ObjectNotFoundException {
+ final Set<Integer> participantIds) throws ObjectNotFoundException {
List<ModelData> maps = modelService.getModelsByMapId(projectId, mapId);
Map<ReactionProperty, Object> filter = new HashMap<>();
filter.put(ReactionProperty.MAP, maps);
@@ -87,6 +87,9 @@ public class ReactionService implements IReactionService {
if (initializeLazy) {
for (final Reaction reaction : result) {
Hibernate.initialize(reaction.getModelData());
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ Hibernate.initialize(node.getElement());
+ }
}
}
return result;
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java b/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
index a0d15eec7c..e07f84d8f8 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
@@ -991,6 +991,10 @@ public class NewApiDocs {
.description("identifier of the element for this product")
.type(JsonFieldType.NUMBER)
.optional(),
+ fieldWithPath(prefix + "products[].elementId")
+ .description("element identifier of the element for this product")
+ .type(JsonFieldType.STRING)
+ .optional(),
fieldWithPath(prefix + "products[].stoichiometry")
.description("SBML stoichiometry")
.type(JsonFieldType.NUMBER)
@@ -1012,6 +1016,10 @@ public class NewApiDocs {
.description("identifier of the element for this reactant")
.type(JsonFieldType.NUMBER)
.optional(),
+ fieldWithPath(prefix + "reactants[].elementId")
+ .description("element identifier of the element for this reactant")
+ .type(JsonFieldType.STRING)
+ .optional(),
fieldWithPath(prefix + "reactants[].stoichiometry")
.description("SBML stoichiometry")
.type(JsonFieldType.NUMBER)
@@ -1033,6 +1041,10 @@ public class NewApiDocs {
.description("identifier of the element for this modifier")
.type(JsonFieldType.NUMBER)
.optional(),
+ fieldWithPath(prefix + "modifiers[].elementId")
+ .description("element identifier of the element for this modifier")
+ .type(JsonFieldType.STRING)
+ .optional(),
fieldWithPath(prefix + "modifiers[].stoichiometry")
.description("SBML stoichiometry")
.type(JsonFieldType.NUMBER)
--
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