From f8a73b0ae648e06dbcd2055c7fae6239b1ca66b7 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 28 Aug 2019 19:39:48 +0200
Subject: [PATCH] ColorSchemaType is obligatory
---
.../converter/ComplexZipConverter.java | 14 +++++
.../services/impl/LayoutService.java | 16 ++++-
.../services/impl/ProjectService.java | 2 +
.../web/ControllerIntegrationTest.java | 2 +
.../web/OverlayControllerIntegrationTest.java | 63 +++++--------------
5 files changed, 47 insertions(+), 50 deletions(-)
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index e1a45aa32e..ed92ef5f76 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -12,10 +12,12 @@ import org.apache.commons.io.IOUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
+import lcsb.mapviewer.common.TextFileUtils;
import lcsb.mapviewer.common.exception.*;
import lcsb.mapviewer.common.exception.InvalidClassException;
import lcsb.mapviewer.converter.zip.*;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.map.layout.ColorSchemaType;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.model.*;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -310,6 +312,18 @@ public class ComplexZipConverter {
fileEntry.setFileContent(IOUtils.toByteArray(zipFile.getInputStream(entry)));
fileEntry.setOriginalFileName(entry.getName());
fileEntry.setLength(fileEntry.getFileContent().length);
+
+ Map<String, String> parameters = TextFileUtils.getHeaderParametersFromFile(zipFile.getInputStream(entry));
+ ColorSchemaType colorSchemaType = null;
+ String type = parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE);
+ if (type != null) {
+ colorSchemaType = ColorSchemaType.valueOf(type);
+ }
+ if (colorSchemaType == null) {
+ colorSchemaType = ColorSchemaType.GENERIC;
+ }
+
+ layout.setColorSchemaType(colorSchemaType);
layout.setInputData(fileEntry);
layout.setPublicLayout(true);
layout.setTitle(layoutEntry.getName());
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
index 3ae2367748..a17d871386 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -1,10 +1,9 @@
package lcsb.mapviewer.services.impl;
-import java.awt.*;
+import java.awt.Color;
import java.io.IOException;
import java.util.*;
import java.util.Comparator;
-import java.util.List;
import javax.mail.MessagingException;
@@ -153,6 +152,17 @@ public class LayoutService implements ILayoutService {
public Layout createLayout(final CreateLayoutParams params) throws IOException, InvalidColorSchemaException {
ColorSchemaReader reader = new ColorSchemaReader();
Map<String, String> parameters = TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream());
+ ColorSchemaType colorSchemaType = params.getColorSchemaType();
+ if (colorSchemaType == null) {
+ String type = parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE);
+ if (type != null) {
+ colorSchemaType = ColorSchemaType.valueOf(type);
+ }
+ }
+ if (colorSchemaType == null) {
+ colorSchemaType = ColorSchemaType.GENERIC;
+ }
+
if (parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE) == null && params.getColorSchemaType() != null) {
parameters.put(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE, params.getColorSchemaType().name());
}
@@ -171,7 +181,7 @@ public class LayoutService implements ILayoutService {
layoutDao.flush();
Layout topLayout = new Layout(params.getName(), false);
- topLayout.setColorSchemaType(params.getColorSchemaType());
+ topLayout.setColorSchemaType(colorSchemaType);
if (params.getUser() == null) {
topLayout.setPublicLayout(true);
} else {
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 3d1d1cc0d3..6a28bbb981 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -773,6 +773,7 @@ public class ProjectService implements IProjectService {
for (BuildInLayout buildInLayout : buildInLayouts) {
int submodelId = 0;
Layout topLayout = new Layout(buildInLayout.getTitle(), true);
+ topLayout.setColorSchemaType(ColorSchemaType.GENERIC);
topLayout.setStatus(LayoutStatus.NA);
topLayout.setProgress(0.0);
topLayout.setHierarchicalView(buildInLayout.isNested());
@@ -787,6 +788,7 @@ public class ProjectService implements IProjectService {
if (params.isSemanticZoomContainsMultipleLayouts() && buildInLayout == BuildInLayout.NESTED) {
for (int i = 0; i <= topModel.getZoomLevels(); i++) {
Layout semanticOverlay = new Layout(buildInLayout.getTitle() + "-" + i, true);
+ semanticOverlay.setColorSchemaType(ColorSchemaType.GENERIC);
String directory = params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + "-" + i + "-"
+ topModel.getId() + "/";
diff --git a/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
index 5f2aebf7e0..909799195d 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
@@ -31,6 +31,7 @@ import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.ProjectStatus;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.layout.ColorSchemaType;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.reaction.*;
@@ -302,6 +303,7 @@ abstract public class ControllerIntegrationTest {
file.setLength(content.getBytes().length);
Layout overlay = new Layout();
+ overlay.setColorSchemaType(ColorSchemaType.GENERIC);
overlay.setInputData(file);
overlay.setProject(project);
overlay.setCreator(admin);
diff --git a/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
index 31a1cbb489..0c0a3ea633 100644
--- a/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
@@ -83,15 +83,9 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
User user = createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD);
- Layout layout = new Layout();
- layout.setCreator(user);
- layout.setProject(project);
- layoutDao.add(layout);
+ createOverlay(project, user);
- Layout curatorLayout = new Layout();
- curatorLayout.setCreator(curator);
- curatorLayout.setProject(project);
- layoutDao.add(curatorLayout);
+ createOverlay(project, curator);
MockHttpSession session = createSession(TEST_ADMIN_LOGIN, TEST_ADMIN_PASSWORD);
@@ -112,8 +106,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
public void testListPublicOverlaysOverlaysWhenCreatorEmpty() throws Exception {
createAdmin(TEST_ADMIN_LOGIN, TEST_ADMIN_PASSWORD);
- Layout layout = new Layout();
- layout.setProject(project);
+ Layout layout= createOverlay(project, null);
layout.setPublicLayout(true);
layoutDao.add(layout);
@@ -136,8 +129,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
public void testListNonPublicOverlaysOverlaysWhenCreatorEmpty() throws Exception {
createAdmin(TEST_ADMIN_LOGIN, TEST_ADMIN_PASSWORD);
- Layout layout = new Layout();
- layout.setProject(project);
+ Layout layout= createOverlay(project, null);
layout.setPublicLayout(true);
layoutDao.add(layout);
@@ -164,15 +156,12 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD);
- Layout layout = new Layout();
- layout.setProject(project);
+ Layout layout = createOverlay(project, null);
layout.setPublicLayout(true);
layoutDao.add(layout);
- Layout curatorLayout = new Layout();
+ Layout curatorLayout = createOverlay(project, curator);
curatorLayout.setPublicLayout(false);
- curatorLayout.setCreator(curator);
- curatorLayout.setProject(project);
layoutDao.add(curatorLayout);
MockHttpSession session = createSession(TEST_ADMIN_LOGIN, TEST_ADMIN_PASSWORD);
@@ -197,15 +186,12 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
User user = createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD);
- Layout layout = new Layout();
- layout.setProject(project);
+ Layout layout = createOverlay(project, null);
layout.setPublicLayout(true);
layoutDao.add(layout);
- Layout userLayout = new Layout();
+ Layout userLayout = createOverlay(project, user);
userLayout.setPublicLayout(false);
- userLayout.setCreator(user);
- userLayout.setProject(project);
layoutDao.add(userLayout);
MockHttpSession session = createSession(TEST_CURATOR_LOGIN, TEST_CURATOR_PASSWORD);
@@ -227,20 +213,16 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
public void testUserShouldSeeAllPublicOverlaysAndOverlays() throws Exception {
User user = createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD, project);
- Layout layout = new Layout();
- layout.setProject(project);
+ Layout layout = createOverlay(project, null);
layout.setPublicLayout(true);
layoutDao.add(layout);
- Layout hiddenLayout = new Layout();
- hiddenLayout.setProject(project);
+ Layout hiddenLayout = createOverlay(project, null);
hiddenLayout.setPublicLayout(false);
layoutDao.add(hiddenLayout);
- Layout userLayout = new Layout();
+ Layout userLayout = createOverlay(project, user);
userLayout.setPublicLayout(false);
- userLayout.setCreator(user);
- userLayout.setProject(project);
layoutDao.add(userLayout);
MockHttpSession session = createSession(TEST_USER_LOGIN, TEST_USER_PASSWORD);
@@ -277,10 +259,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
User user = createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD, project);
createAdmin(TEST_ADMIN_LOGIN, TEST_ADMIN_PASSWORD);
- Layout overlay = new Layout();
- overlay.setProject(project);
- overlay.setCreator(user);
- layoutDao.add(overlay);
+ Layout overlay = createOverlay(project, user);
MockHttpSession session = createSession(TEST_ADMIN_LOGIN, TEST_ADMIN_PASSWORD);
@@ -298,10 +277,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
User curator = createCurator(TEST_CURATOR_LOGIN, TEST_CURATOR_PASSWORD);
userService.grantUserPrivilege(curator, PrivilegeType.READ_PROJECT, project.getProjectId());
- Layout overlay = new Layout();
- overlay.setProject(project);
- overlay.setCreator(user);
- layoutDao.add(overlay);
+ Layout overlay = createOverlay(project, user);
MockHttpSession session = createSession(TEST_CURATOR_LOGIN, TEST_CURATOR_PASSWORD);
@@ -317,10 +293,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
public void testUserCanAccessHisOwnOverlay() throws Exception {
User user = createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD, project);
- Layout overlay = new Layout();
- overlay.setProject(project);
- overlay.setCreator(user);
- layoutDao.add(overlay);
+ Layout overlay = createOverlay(project, user);
MockHttpSession session = createSession(TEST_USER_LOGIN, TEST_USER_PASSWORD);
@@ -337,10 +310,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD, project);
User admin = createAdmin(TEST_ADMIN_LOGIN, TEST_ADMIN_PASSWORD);
- Layout overlay = new Layout();
- overlay.setProject(project);
- overlay.setCreator(admin);
- layoutDao.add(overlay);
+ Layout overlay = createOverlay(project, admin);
MockHttpSession session = createSession(TEST_USER_LOGIN, TEST_USER_PASSWORD);
@@ -922,8 +892,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
public void testUserCanAccessPublicOverlay() throws Exception {
createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD, project);
- Layout overlay = new Layout();
- overlay.setProject(project);
+ Layout overlay = createOverlay(project, null);
overlay.setPublicLayout(true);
layoutDao.add(overlay);
--
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