From d54fa3dc8193e11b97076d44391fd68e455d32c6 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 21 Aug 2023 11:46:20 +0200
Subject: [PATCH] move clipboard to celldesigner plugin module (it cannot be
 used on server side)

---
 .gitlab-ci.yml                                             | 7 +------
 .../java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java | 1 -
 .../lcsb/mapviewer/cdplugin/copypaste/PasteAction.java     | 1 -
 .../mapviewer/cdplugin/copypaste}/SystemClipboard.java     | 2 +-
 .../mapviewer/cdplugin/copypaste/AllCopyPasteTests.java    | 1 +
 .../lcsb/mapviewer/cdplugin/copypaste/CopyActionTest.java  | 1 -
 .../mapviewer/cdplugin/copypaste/CopyPastePluginTest.java  | 1 -
 .../lcsb/mapviewer/cdplugin/copypaste/PasteActionTest.java | 1 -
 .../mapviewer/cdplugin/copypaste}/SystemClipboardTest.java | 6 ++++--
 .../test/java/lcsb/mapviewer/common/AllCommonTests.java    | 1 -
 10 files changed, 7 insertions(+), 15 deletions(-)
 rename {commons/src/main/java/lcsb/mapviewer/common => CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste}/SystemClipboard.java (97%)
 rename {commons/src/test/java/lcsb/mapviewer/common => CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste}/SystemClipboardTest.java (92%)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 2d6c98f81d..365a2ae03d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -31,7 +31,7 @@ test:frontend:
     - npm test
 
 .jdk_8_template: &jdk_8_definition
-  image: maven:3.6.0-jdk-8
+  image: maven:3.8.6-jdk-8
   services:
     - postgres:9.6
   stage: test
@@ -61,11 +61,6 @@ test:frontend:
 .test_backend_commons_template:
   script: &test_backend_commons_definition
 #xvfb is for X11 connection used by some parts of the java code: https://stackoverflow.com/a/47575851/1127920
-    - apt-get update
-    - DEBIAN_FRONTEND=noninteractive apt-get install -y xvfb
-    - Xvfb :99 &
-    - export DISPLAY=:99
-
     - mvn -DskipTests=true clean install -pl commons -am
     - mvn test -pl commons
     - awk -F"," '{ instructions += $4 + $5; covered += $5 } END { print covered, "/", instructions, "instructions covered"; print 100*covered/instructions,"% covered" }' commons/target/site/jacoco/jacoco.csv
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java
index e9bfd56389..afdd178afc 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java
@@ -8,7 +8,6 @@ import jp.sbi.celldesigner.plugin.PluginReaction;
 import jp.sbi.celldesigner.plugin.PluginSBase;
 import jp.sbi.celldesigner.plugin.PluginSpecies;
 import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
-import lcsb.mapviewer.common.SystemClipboard;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 
 /**
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java
index b66d6f632f..7d0ba23e86 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java
@@ -11,7 +11,6 @@ import jp.sbi.celldesigner.plugin.PluginSBase;
 import jp.sbi.celldesigner.plugin.PluginSpecies;
 import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
 import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.SystemClipboard;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.model.map.MiriamData;
 
diff --git a/commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/SystemClipboard.java
similarity index 97%
rename from commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java
rename to CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/SystemClipboard.java
index 6dd2325541..8d441767ba 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/SystemClipboard.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.common;
+package lcsb.mapviewer.cdplugin.copypaste;
 
 import java.awt.Toolkit;
 import java.awt.datatransfer.Clipboard;
diff --git a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/AllCopyPasteTests.java b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/AllCopyPasteTests.java
index 4592dfdabc..f1b5e83224 100644
--- a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/AllCopyPasteTests.java
+++ b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/AllCopyPasteTests.java
@@ -9,6 +9,7 @@ import org.junit.runners.Suite.SuiteClasses;
     CopyPasteAbstractActionTest.class,
     CopyPastePluginTest.class,
     PasteActionTest.class,
+    SystemClipboardTest.class,
 })
 public class AllCopyPasteTests {
 
diff --git a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyActionTest.java b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyActionTest.java
index aaa2f38c86..9ec7685706 100644
--- a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyActionTest.java
+++ b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyActionTest.java
@@ -8,7 +8,6 @@ import org.mockito.Mockito;
 
 import jp.sbi.celldesigner.plugin.PluginListOf;
 import lcsb.mapviewer.cdplugin.CdPluginFunctions;
-import lcsb.mapviewer.common.SystemClipboard;
 
 public class CopyActionTest extends CdPluginFunctions {
 
diff --git a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePluginTest.java b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePluginTest.java
index cc4c5f0c11..868e4ac368 100644
--- a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePluginTest.java
+++ b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePluginTest.java
@@ -11,7 +11,6 @@ import org.mockito.Mockito;
 
 import jp.sbi.celldesigner.plugin.PluginListOf;
 import lcsb.mapviewer.cdplugin.CdPluginFunctions;
-import lcsb.mapviewer.common.SystemClipboard;
 
 public class CopyPastePluginTest extends CdPluginFunctions {
 
diff --git a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/PasteActionTest.java b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/PasteActionTest.java
index eea9c0781d..25d47b4b26 100644
--- a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/PasteActionTest.java
+++ b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/PasteActionTest.java
@@ -13,7 +13,6 @@ import jp.sbi.celldesigner.plugin.PluginReaction;
 import jp.sbi.celldesigner.plugin.PluginSpecies;
 import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
 import lcsb.mapviewer.cdplugin.CdPluginFunctions;
-import lcsb.mapviewer.common.SystemClipboard;
 
 public class PasteActionTest extends CdPluginFunctions {
 
diff --git a/commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/SystemClipboardTest.java
similarity index 92%
rename from commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java
rename to CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/SystemClipboardTest.java
index cae5f61666..2a0225108f 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java
+++ b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/SystemClipboardTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.common;
+package lcsb.mapviewer.cdplugin.copypaste;
 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNull;
@@ -14,7 +14,9 @@ import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
 
-public class SystemClipboardTest extends CommonTestFunctions {
+import lcsb.mapviewer.cdplugin.CdPluginFunctions;
+
+public class SystemClipboardTest extends CdPluginFunctions {
 
   @Before
   public void setUp() throws Exception {
diff --git a/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java b/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
index b09bf968af..e9aee332cc 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
@@ -17,7 +17,6 @@ import lcsb.mapviewer.common.geometry.AllGeometryTests;
     MimeTypeTest.class,
     ObjectUtilsTest.class,
     PairTest.class,
-    SystemClipboardTest.class,
     TextFileUtilsTest.class,
     XmlParserTest.class,
 })
-- 
GitLab