From f26a0e38ce8a2c977845deb4729f917755b7c345 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <p.gawron@atcomp.pl>
Date: Wed, 9 Apr 2025 10:13:23 +0200
Subject: [PATCH] fix problem with uploading data overlay
---
.../mapviewer/services/impl/FileService.java | 22 +++++++-----
.../services/interfaces/IFileService.java | 5 +--
.../project/overlay/NewDataOverlayDTO.java | 10 ++++++
.../project/overlay/NewOverlayController.java | 29 ++++++++++++++--
.../overlay/NewOverlayControllerTest.java | 34 +++++++++++++++++++
5 files changed, 86 insertions(+), 14 deletions(-)
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/FileService.java b/service/src/main/java/lcsb/mapviewer/services/impl/FileService.java
index c92d07d336..9344c78568 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/FileService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/FileService.java
@@ -1,25 +1,24 @@
package lcsb.mapviewer.services.impl;
-import java.io.FileNotFoundException;
-
-import org.hibernate.Hibernate;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Service;
-import org.springframework.transaction.annotation.Transactional;
-
import lcsb.mapviewer.annotation.cache.BigFileCache;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
import lcsb.mapviewer.services.interfaces.IFileService;
+import org.hibernate.Hibernate;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+
+import java.io.FileNotFoundException;
@Transactional
@Service
public class FileService implements IFileService {
- private UploadedFileEntryDao uploadedFileEntryDao;
+ private final UploadedFileEntryDao uploadedFileEntryDao;
- private BigFileCache bigFileCache;
+ private final BigFileCache bigFileCache;
@Autowired
public FileService(final UploadedFileEntryDao uploadedFileEntryDao, final BigFileCache bigFileCache) {
@@ -66,4 +65,9 @@ public class FileService implements IFileService {
uploadedFileEntryDao.delete(fileEntry);
}
+ @Override
+ public byte[] getContentById(final Integer fileId) {
+ return getById(fileId).getFileContent();
+ }
+
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IFileService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IFileService.java
index 505469a71e..c5638e49c9 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IFileService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IFileService.java
@@ -1,10 +1,10 @@
package lcsb.mapviewer.services.interfaces;
-import java.io.FileNotFoundException;
-
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.user.User;
+import java.io.FileNotFoundException;
+
public interface IFileService {
UploadedFileEntry getById(final Integer id);
@@ -19,4 +19,5 @@ public interface IFileService {
void delete(UploadedFileEntry fileEntry);
+ byte[] getContentById(Integer fileId);
}
diff --git a/web/src/main/java/lcsb/mapviewer/web/api/project/overlay/NewDataOverlayDTO.java b/web/src/main/java/lcsb/mapviewer/web/api/project/overlay/NewDataOverlayDTO.java
index 93b51ca8b2..cbfe920314 100644
--- a/web/src/main/java/lcsb/mapviewer/web/api/project/overlay/NewDataOverlayDTO.java
+++ b/web/src/main/java/lcsb/mapviewer/web/api/project/overlay/NewDataOverlayDTO.java
@@ -30,6 +30,8 @@ public class NewDataOverlayDTO extends AbstractDTO {
@Min(0)
private Integer orderIndex;
+ private Integer fileId;
+
@NotNull
private String description;
@@ -112,4 +114,12 @@ public class NewDataOverlayDTO extends AbstractDTO {
public void setGroup(final Integer group) {
this.group = group;
}
+
+ public Integer getFileId() {
+ return fileId;
+ }
+
+ public void setFileId(final Integer fileId) {
+ this.fileId = fileId;
+ }
}
diff --git a/web/src/main/java/lcsb/mapviewer/web/api/project/overlay/NewOverlayController.java b/web/src/main/java/lcsb/mapviewer/web/api/project/overlay/NewOverlayController.java
index af9b4188ba..ae5be3ee31 100644
--- a/web/src/main/java/lcsb/mapviewer/web/api/project/overlay/NewOverlayController.java
+++ b/web/src/main/java/lcsb/mapviewer/web/api/project/overlay/NewOverlayController.java
@@ -3,6 +3,9 @@ package lcsb.mapviewer.web.api.project.overlay;
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.TextFileUtils;
+import lcsb.mapviewer.converter.ColorSchemaReader;
+import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.BioEntity;
@@ -10,6 +13,7 @@ import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.overlay.DataOverlay;
import lcsb.mapviewer.model.overlay.DataOverlayEntry;
import lcsb.mapviewer.model.overlay.DataOverlayGroup;
+import lcsb.mapviewer.model.overlay.InvalidDataOverlayException;
import lcsb.mapviewer.model.security.PrivilegeType;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.map.DataOverlayGroupProperty;
@@ -45,8 +49,10 @@ import org.springframework.web.bind.annotation.RestController;
import javax.validation.Valid;
import javax.validation.constraints.NotNull;
+import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -134,7 +140,7 @@ public class NewOverlayController extends BaseController {
final @Valid @NotBlank @PathVariable(value = "projectId") String projectId,
final @Valid @RequestBody NewDataOverlayDTO data,
final Authentication authentication)
- throws QueryException, ObjectNotFoundException {
+ throws QueryException, ObjectNotFoundException, IOException, InvalidDataOverlayException {
final User user = userService.getUserByLogin(authentication.getName());
final Project project = projectService.getProjectByProjectId(projectId);
@@ -142,12 +148,29 @@ public class NewOverlayController extends BaseController {
throw new ObjectNotFoundException("Project with given projectId does not exist");
}
- final UploadedFileEntry entry = createEmptyFile(user);
-
final DataOverlay overlay = new DataOverlay();
data.saveToDataOverlay(overlay, getGroupIdToGroup(projectId, user.getLogin()));
overlay.setProject(project);
overlay.setCreator(user);
+
+ UploadedFileEntry entry;
+ if (data.getFileId() != null) {
+ entry = fileService.getById(data.getFileId());
+ byte[] content = fileService.getContentById(data.getFileId());
+
+ final ColorSchemaReader reader = new ColorSchemaReader();
+
+ final Map<String, String> parameters = TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(content));
+ final Collection<DataOverlayEntry> schemas = reader.readColorSchema(new ByteArrayInputStream(content), parameters);
+ overlay.addEntries(schemas);
+ String nonMatchingAlpha = parameters.get(ZipEntryFileFactory.NON_MATCHING_ALPHA);
+ if (nonMatchingAlpha != null) {
+ overlay.setNotMatchingAlpha(nonMatchingAlpha);
+ }
+ } else {
+ entry = createEmptyFile(user);
+ }
+
overlay.setInputData(entry);
dataOverlayService.add(overlay);
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/overlay/NewOverlayControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/overlay/NewOverlayControllerTest.java
index 0c8297e06c..b4aeab4eba 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/overlay/NewOverlayControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/overlay/NewOverlayControllerTest.java
@@ -2,13 +2,16 @@ package lcsb.mapviewer.web.api.project.overlay;
import com.fasterxml.jackson.core.type.TypeReference;
import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.overlay.DataOverlay;
+import lcsb.mapviewer.model.overlay.DataOverlayEntry;
import lcsb.mapviewer.model.overlay.DataOverlayGroup;
import lcsb.mapviewer.model.overlay.DataOverlayType;
import lcsb.mapviewer.model.security.PrivilegeType;
@@ -32,8 +35,10 @@ import org.springframework.test.web.servlet.RequestBuilder;
import javax.servlet.http.HttpServletResponse;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
@@ -530,4 +535,33 @@ public class NewOverlayControllerTest extends ControllerIntegrationTest {
mockMvc.perform(request)
.andExpect(status().isForbidden());
}
+
+ @Test
+ public void testCreateOverlayWithFile() throws Exception {
+ String content = "#" + ZipEntryFileFactory.NON_MATCHING_ALPHA + "=125\n" + createOverlayContentForAllEntities(map);
+ UploadedFileEntry file = createFile(content, admin);
+ final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
+
+ final NewDataOverlayDTO data = createDataOverlayDTO();
+ data.setFileId(file.getId());
+
+ final RequestBuilder request = post("/minerva/new_api/projects/{projectId}/overlays/", TEST_PROJECT)
+ .contentType(MediaType.APPLICATION_JSON)
+ .content(objectMapper.writeValueAsString(data))
+ .session(session);
+
+ final MockHttpServletResponse response = mockMvc.perform(request)
+ .andExpect(status().isCreated())
+ .andReturn().getResponse();
+ assertNotNull(response.getHeader("ETag"));
+ final Map<String, Object> result = objectMapper.readValue(response.getContentAsString(), new TypeReference<Map<String, Object>>() {
+ });
+
+ Set<DataOverlayEntry> entries = dataOverlayService.getDataOverlayEntriesById(TEST_PROJECT, (int) result.get("id"));
+
+ assertFalse(entries.isEmpty());
+
+ DataOverlay overlay = dataOverlayService.getDataOverlayById((int) result.get("id"));
+ assertEquals((Integer) 125, overlay.getNotMatchingAlpha());
+ }
}
--
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