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Merge branch '2.4.x' of git://github.com/bioclipse/bioclipse.core int…

…o 2.4.x
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commit 3f9ee5ebe55ba48947162056321ec15e73cb24c5 2 parents 0fd648d + 0747cb2
@jonalv jonalv authored
Showing with 888 additions and 950 deletions.
  1. +0 −1  features/net.bioclipse.birt_feature/build.properties
  2. +0 −590 features/net.bioclipse.birt_feature/feature.xml
  3. +1 −1  features/{net.bioclipse.birt_feature → net.bioclipse.core.tests_feature}/.project
  4. +40 −0 features/net.bioclipse.core.tests_feature/AllCorePluginTestsSuit.launch
  5. +5 −0 features/net.bioclipse.core.tests_feature/build.properties
  6. +103 −0 features/net.bioclipse.core.tests_feature/feature.xml
  7. +7 −0 features/net.bioclipse.core_feature/feature.xml
  8. BIN  net.bioclipse.target.platform/libs/commons-lang-2.5-javadoc.jar
  9. BIN  net.bioclipse.target.platform/libs/commons-lang-2.5-sources.jar
  10. BIN  net.bioclipse.target.platform/libs/commons-lang-2.5.jar
  11. +0 −3  net.bioclipse.target.platform/target-platform.target
  12. +0 −7 plugins/net.bioclipse.birt/.classpath
  13. +0 −18 plugins/net.bioclipse.birt/META-INF/MANIFEST.MF
  14. +0 −11 plugins/net.bioclipse.birt/about.ini
  15. +0 −1  plugins/net.bioclipse.birt/about.mappings
  16. +0 −23 plugins/net.bioclipse.birt/about.properties
  17. +0 −10 plugins/net.bioclipse.birt/build.properties
  18. BIN  plugins/net.bioclipse.birt/icons/report32.png
  19. +0 −9 plugins/net.bioclipse.birt/plugin.xml
  20. +0 −46 plugins/net.bioclipse.birt/reports/empty.rptdesign
  21. +0 −60 plugins/net.bioclipse.birt/src/net/bioclipse/birt/Activator.java
  22. +0 −103 plugins/net.bioclipse.birt/src/net/bioclipse/birt/Startup.java
  23. +8 −7 plugins/net.bioclipse.core.tests/META-INF/MANIFEST.MF
  24. +0 −2  plugins/net.bioclipse.core.tests/build.properties
  25. +0 −55 plugins/net.bioclipse.core.tests/src/net/bioclipse/core/tests/Activator.java
  26. +32 −0 plugins/net.bioclipse.core/src/net/bioclipse/core/util/FileUtil.java
  27. +124 −0 plugins/net.bioclipse.core/src/net/bioclipse/core/util/ImageUtils.java
  28. +36 −0 plugins/net.bioclipse.jasper/.classpath
  29. +1 −1  plugins/{net.bioclipse.birt → net.bioclipse.jasper}/.project
  30. +52 −0 plugins/net.bioclipse.jasper/META-INF/MANIFEST.MF
  31. +37 −0 plugins/net.bioclipse.jasper/build.properties
  32. BIN  plugins/net.bioclipse.jasper/icons/lastd.gif
  33. BIN  plugins/net.bioclipse.jasper/lib/batik-anim.jar
  34. BIN  plugins/net.bioclipse.jasper/lib/batik-awt-util.jar
  35. BIN  plugins/net.bioclipse.jasper/lib/batik-bridge.jar
  36. BIN  plugins/net.bioclipse.jasper/lib/batik-css.jar
  37. BIN  plugins/net.bioclipse.jasper/lib/batik-dom.jar
  38. BIN  plugins/net.bioclipse.jasper/lib/batik-ext.jar
  39. BIN  plugins/net.bioclipse.jasper/lib/batik-gvt.jar
  40. BIN  plugins/net.bioclipse.jasper/lib/batik-parser.jar
  41. BIN  plugins/net.bioclipse.jasper/lib/batik-script.jar
  42. BIN  plugins/net.bioclipse.jasper/lib/batik-svg-dom.jar
  43. BIN  plugins/net.bioclipse.jasper/lib/batik-svggen.jar
  44. BIN  plugins/net.bioclipse.jasper/lib/batik-util.jar
  45. BIN  plugins/net.bioclipse.jasper/lib/batik-xml.jar
  46. BIN  plugins/net.bioclipse.jasper/lib/bsh-2.0b4.jar
  47. BIN  plugins/net.bioclipse.jasper/lib/commons-beanutils-1.8.0.jar
  48. BIN  plugins/net.bioclipse.jasper/lib/commons-collections-2.1.1.jar
  49. BIN  plugins/net.bioclipse.jasper/lib/commons-digester-1.7.jar
  50. BIN  plugins/net.bioclipse.jasper/lib/groovy-all-1.5.5.jar
  51. BIN  plugins/net.bioclipse.jasper/lib/iText-2.1.7.jar
  52. BIN  plugins/net.bioclipse.jasper/lib/jasperreports-3.7.3.jar
  53. BIN  plugins/net.bioclipse.jasper/lib/jasperreports-fonts-3.7.3.jar
  54. BIN  plugins/net.bioclipse.jasper/lib/jaxen-1.1.1.jar
  55. BIN  plugins/net.bioclipse.jasper/lib/jcommon-1.0.0.jar
  56. BIN  plugins/net.bioclipse.jasper/lib/jcommon-1.0.15.jar
  57. BIN  plugins/net.bioclipse.jasper/lib/jfreechart-1.0.0.jar
  58. BIN  plugins/net.bioclipse.jasper/lib/jfreechart-1.0.12.jar
  59. BIN  plugins/net.bioclipse.jasper/lib/jpa.jar
  60. BIN  plugins/net.bioclipse.jasper/lib/jxl-2.6.jar
  61. BIN  plugins/net.bioclipse.jasper/lib/png-encoder-1.5.jar
  62. BIN  plugins/net.bioclipse.jasper/lib/poi-3.5-FINAL-20090928.jar
  63. BIN  plugins/net.bioclipse.jasper/lib/swtjasperviewer-1.2.0.jar
  64. +16 −0 plugins/net.bioclipse.jasper/plugin.xml
  65. +2 −2 ...tests/src/net/bioclipse/managers/tests → net.bioclipse.jasper/src/net/bioclipse/jasper}/Activator.java
  66. +52 −0 plugins/net.bioclipse.jasper/src/net/bioclipse/jasper/charCustomizers/DoseResponseChartCustomizer.java
  67. +343 −0 plugins/net.bioclipse.jasper/src/net/bioclipse/jasper/editor/ReportEditor.java
  68. +1 −0  plugins/net.bioclipse.logback/src/logback.xml
  69. +28 −0 plugins/net.bioclipse.logger/.project
View
1  features/net.bioclipse.birt_feature/build.properties
@@ -1 +0,0 @@
-bin.includes = feature.xml
View
590 features/net.bioclipse.birt_feature/feature.xml
@@ -1,590 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<feature
- id="net.bioclipse.birt_feature"
- label="Bioclipse BIRT"
- version="2.4.0.20100709"
- provider-name="The Bioclipse Team"
- plugin="net.bioclipse.birt">
-
- <description>
- Provides the core for producing reports with Eclipse Business Intelligence and Reporting Toolkit (BIRT).
- </description>
-
- <copyright>
- (C) Copyright, 2009, the Bioclipse developers.
-All rights reserved.
- </copyright>
-
- <license url="http://www.eclipse.org/legal/epl-v10.html">
- This feature and the accompanying materials are made available
-under the terms of the Eclipse Public License v1.0 + exception,
-putting no constraints on choice of backend and/or license for
-creating plugins for Bioclipse; it is totally open for both open
-source plugins as well as commercial. The exception allows GPL
-plugins to be written and run in any combination with EPL licensed
-plugins, addressing incompatibility between the EPL and the GPL
-v.2.
-The Eclipse Public License accompanies this distribution, and
-is available at http://www.eclipse.org/legal/epl-v10.html
- </license>
-
- <plugin
- id="net.bioclipse.birt"
- download-size="0"
- install-size="0"
- version="0.0.0"
- unpack="false"/>
-
- <plugin
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View
2  features/net.bioclipse.birt_feature/.project → ...net.bioclipse.core.tests_feature/.project
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
- <name>net.bioclipse.birt_feature</name>
+ <name>net.bioclipse.core.tests_feature</name>
<comment></comment>
<projects>
</projects>
View
40 features/net.bioclipse.core.tests_feature/AllCorePluginTestsSuit.launch
@@ -0,0 +1,40 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.pde.ui.JunitLaunchConfig">
+<booleanAttribute key="append.args" value="true"/>
+<booleanAttribute key="askclear" value="false"/>
+<booleanAttribute key="automaticAdd" value="true"/>
+<booleanAttribute key="automaticValidate" value="false"/>
+<stringAttribute key="bootstrap" value=""/>
+<stringAttribute key="checked" value="[NONE]"/>
+<booleanAttribute key="clearConfig" value="true"/>
+<booleanAttribute key="clearws" value="true"/>
+<booleanAttribute key="clearwslog" value="false"/>
+<stringAttribute key="configLocation" value="${workspace_loc}/.metadata/.plugins/org.eclipse.pde.core/pde-junit"/>
+<booleanAttribute key="default" value="true"/>
+<booleanAttribute key="default_auto_start" value="true"/>
+<booleanAttribute key="includeOptional" value="true"/>
+<stringAttribute key="location" value="${workspace_loc}/../junit-workspace"/>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+<listEntry value="/net.bioclipse.core.tests/src/net/bioclipse/AllCorePluginTestsSuit.java"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="1"/>
+</listAttribute>
+<stringAttribute key="org.eclipse.jdt.junit.CONTAINER" value=""/>
+<booleanAttribute key="org.eclipse.jdt.junit.KEEPRUNNING_ATTR" value="false"/>
+<stringAttribute key="org.eclipse.jdt.junit.TESTNAME" value=""/>
+<stringAttribute key="org.eclipse.jdt.junit.TEST_KIND" value="org.eclipse.jdt.junit.loader.junit4"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="net.bioclipse.AllCorePluginTestsSuit"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROGRAM_ARGUMENTS" value="-os ${target.os} -ws ${target.ws} -arch ${target.arch} -nl ${target.nl}"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="net.bioclipse.core.tests"/>
+<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.pde.ui.workbenchClasspathProvider"/>
+<stringAttribute key="pde.version" value="3.3"/>
+<stringAttribute key="product" value="net.bioclipse.ui.product"/>
+<booleanAttribute key="run_in_ui_thread" value="true"/>
+<booleanAttribute key="show_selected_only" value="false"/>
+<stringAttribute key="testApplication" value="net.bioclipse.ui.application"/>
+<booleanAttribute key="tracing" value="false"/>
+<booleanAttribute key="useDefaultConfig" value="true"/>
+<booleanAttribute key="useDefaultConfigArea" value="false"/>
+<booleanAttribute key="useProduct" value="true"/>
+</launchConfiguration>
View
5 features/net.bioclipse.core.tests_feature/build.properties
@@ -0,0 +1,5 @@
+bin.includes = feature.xml
+
+category.id.net.bioclipse.core.tests=Core Test Feature
+category.members.net.bioclipse.core.tests=net.bioclipse.core.tests_feature
+category.description.net.bioclipse.core.tests=Collections of tests for the core repository.
View
103 features/net.bioclipse.core.tests_feature/feature.xml
@@ -0,0 +1,103 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<feature
+ id="net.bioclipse.core.tests_feature"
+ label="Tests feature for core"
+ version="1.0.0.qualifier">
+
+ <description url="http://www.example.com/description">
+ [Enter Feature Description here.]
+ </description>
+
+ <copyright url="http://www.example.com/copyright">
+ [Enter Copyright Description here.]
+ </copyright>
+
+ <license url="http://www.example.com/license">
+ [Enter License Description here.]
+ </license>
+
+ <plugin
+ id="net.bioclipse.browser.tests"
+ download-size="0"
+ install-size="0"
+ version="0.0.0"
+ unpack="false"/>
+
+ <plugin
+ id="net.bioclipse.business.test"
+ download-size="0"
+ install-size="0"
+ version="0.0.0"
+ unpack="false"/>
+
+ <plugin
+ id="net.bioclipse.core.tests"
+ download-size="0"
+ install-size="0"
+ version="0.0.0"
+ unpack="false"/>
+
+ <plugin
+ id="net.bioclipse.encryption.tests"
+ download-size="0"
+ install-size="0"
+ version="0.0.0"
+ unpack="false"/>
+
+ <plugin
+ id="net.bioclipse.gist.test"
+ download-size="0"
+ install-size="0"
+ version="0.0.0"
+ unpack="false"/>
+
+ <plugin
+ id="net.bioclipse.scripting.tests"
+ download-size="0"
+ install-size="0"
+ version="0.0.0"
+ unpack="false"/>
+
+ <plugin
+ id="net.bioclipse.scripting.ui.tests"
+ download-size="0"
+ install-size="0"
+ version="0.0.0"
+ unpack="false"/>
+
+ <plugin
+ id="net.bioclipse.ui.business.tests"
+ download-size="0"
+ install-size="0"
+ version="0.0.0"
+ unpack="false"/>
+
+ <plugin
+ id="net.bioclipse.ui.tests"
+ download-size="0"
+ install-size="0"
+ version="0.0.0"
+ unpack="false"/>
+
+ <plugin
+ id="net.bioclipse.usermanager.tests"
+ download-size="0"
+ install-size="0"
+ version="0.0.0"
+ unpack="false"/>
+
+ <plugin
+ id="net.bioclipse.webservices.tests"
+ download-size="0"
+ install-size="0"
+ version="0.0.0"
+ unpack="false"/>
+
+ <plugin
+ id="net.bioclipse.xml.test"
+ download-size="0"
+ install-size="0"
+ version="0.0.0"
+ unpack="false"/>
+
+</feature>
View
7 features/net.bioclipse.core_feature/feature.xml
@@ -941,4 +941,11 @@ The Eclipse Public License accompanies this distribution, and is available at ht
fragment="true"
unpack="false"/>
+ <plugin
+ id="net.bioclipse.jasper"
+ download-size="0"
+ install-size="0"
+ version="0.0.0"
+ unpack="false"/>
+
</feature>
View
BIN  net.bioclipse.target.platform/libs/commons-lang-2.5-javadoc.jar
Binary file not shown
View
BIN  net.bioclipse.target.platform/libs/commons-lang-2.5-sources.jar
Binary file not shown
View
BIN  net.bioclipse.target.platform/libs/commons-lang-2.5.jar
Binary file not shown
View
3  net.bioclipse.target.platform/target-platform.target
@@ -7,7 +7,6 @@
<unit id="org.eclipse.zest.feature.group" version="1.1.2.v20100111-1352-6618yD6DH8G6N59OM53B2A"/>
<repository location="http://download.eclipse.org/tools/gef/updates/releases/"/>
</location>
-<location id="org.eclipse.mylyn_feature" path="${eclipse_home}" type="Feature"/>
<location includeAllPlatforms="true" includeMode="slicer" type="InstallableUnit">
<unit id="nu.psnet.quickimage.feature.group" version="1.0.3.2"/>
<repository location="http://psnet.nu/eclipse/updates"/>
@@ -17,8 +16,6 @@
<location path="${project_loc:net.bioclipse.target.platform}/spring-osgi-1.0.2/lib" type="Directory"/>
<location path="${project_loc:/net.bioclipse.target.platform}/logging" type="Directory"/>
<location includeAllPlatforms="true" includeMode="slicer" type="InstallableUnit">
-<unit id="org.eclipse.birt.osgi.runtime.sdk.feature.group" version="2.5.2.v20090925-579385tF0KMS-Eb6SPBIO0qaQNgB"/>
-<unit id="org.eclipse.birt.feature.group" version="2.5.2.v20090925-9dE-9CGJexwJPcfpfqGkK_4lg9Ti"/>
<unit id="org.eclipse.datatools.connectivity.feature.feature.group" version="1.7.2.v200909251450-7B7OANEn1Xi4gycmhPC6njFVDz0q"/>
<unit id="org.eclipse.platform.sdk" version="3.5.2.M20100211-1343"/>
<unit id="org.eclipse.sdk.feature.group" version="3.5.2.R35x_v20100119-7Q7bARBPWUHM_CSjz-8bF1f7_n8rLSyWHoiKoyxBQSGT4"/>
View
7 plugins/net.bioclipse.birt/.classpath
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5"/>
- <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
- <classpathentry kind="src" path="src"/>
- <classpathentry kind="output" path="bin"/>
-</classpath>
View
18 plugins/net.bioclipse.birt/META-INF/MANIFEST.MF
@@ -1,18 +0,0 @@
-Manifest-Version: 1.0
-Bundle-ManifestVersion: 2
-Bundle-Name: Bioclipse Birt
-Bundle-SymbolicName: net.bioclipse.birt;singleton:=true
-Bundle-Version: 2.4.0.20100709
-Bundle-Activator: net.bioclipse.birt.Activator
-Bundle-Vendor: The Bioclipse Team
-Require-Bundle: org.eclipse.ui,
- org.eclipse.core.runtime,
- org.eclipse.birt.report.viewer,
- org.eclipse.ui.browser,
- org.eclipse.ui.editors,
- org.eclipse.ui.ide,
- org.eclipse.core.resources,
- org.eclipse.birt.report.engine,
- org.eclipse.birt.report.engine.script.javascript;bundle-version="2.5.1"
-Bundle-RequiredExecutionEnvironment: J2SE-1.5
-Bundle-ActivationPolicy: lazy
View
11 plugins/net.bioclipse.birt/about.ini
@@ -1,11 +0,0 @@
-# about.ini
-# contains information about a feature
-# java.io.Properties file (ISO 8859-1 with "\" escapes)
-# "%key" are externalized strings defined in about.properties
-# This file does not need to be translated.
-
-# Property "aboutText" contains blurb for "About" dialog (translated)
-aboutText=%blurb
-
-# Property "featureImage" contains path to feature image (32x32)
-featureImage=icons/report32.png
View
1  plugins/net.bioclipse.birt/about.mappings
@@ -1 +0,0 @@
-0=2.1.1.v20091002
View
23 plugins/net.bioclipse.birt/about.properties
@@ -1,23 +0,0 @@
-###############################################################################
-# Copyright (c) 2005-2007 Bioclipse Project
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the Eclipse Public License v1.0
-# (which accompanies this distribution, and is available at
-# http://www.eclipse.org/legal/epl-v10.html) + exception, putting
-# no constraints on choice of backend and/or license for creating
-# plugins for Bioclipse; it is totally open for both open source
-# plugins as well as commercial. The exception allows GPL plugins
-# to be written and run in any combination with EPL licensed plugins,
-# addressing incompatibility between the EPL and the GPL v.2.
-#
-# More information is available at: http://bioclipse.net/license.html
-###############################################################################
-
-blurb=MetaPrint2D\n\
-\n\
-Version: {featureVersion}\n\
-\n\
-Reporting tools for Bioclipse based on BIRT.\
-\n\
-(c) Copyright 2010 The Bioclipse Project. All rights reserved.\n\
-Visit http://www.bioclipse.net
View
10 plugins/net.bioclipse.birt/build.properties
@@ -1,10 +0,0 @@
-source.. = src/
-output.. = bin/
-bin.includes = META-INF/,\
- .,\
- plugin.xml,\
- reports/,\
- icons/,\
- about.ini,\
- about.mappings,\
- about.properties
View
BIN  plugins/net.bioclipse.birt/icons/report32.png
Deleted file not rendered
View
9 plugins/net.bioclipse.birt/plugin.xml
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<?eclipse version="3.4"?>
-<plugin>
-
- <extension point="org.eclipse.ui.startup">
- <startup class="net.bioclipse.birt.Startup"/>
- </extension>
-
-</plugin>
View
46 plugins/net.bioclipse.birt/reports/empty.rptdesign
@@ -1,46 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<report xmlns="http://www.eclipse.org/birt/2005/design" version="3.2.17" id="1">
- <property name="units">in</property>
- <property name="iconFile">/templates/blank_report.gif</property>
- <property name="bidiLayoutOrientation">ltr</property>
- <styles>
- <style name="crosstab" id="4">
- <property name="borderBottomColor">#CCCCCC</property>
- <property name="borderBottomStyle">solid</property>
- <property name="borderBottomWidth">1pt</property>
- <property name="borderLeftColor">#CCCCCC</property>
- <property name="borderLeftStyle">solid</property>
- <property name="borderLeftWidth">1pt</property>
- <property name="borderRightColor">#CCCCCC</property>
- <property name="borderRightStyle">solid</property>
- <property name="borderRightWidth">1pt</property>
- <property name="borderTopColor">#CCCCCC</property>
- <property name="borderTopStyle">solid</property>
- <property name="borderTopWidth">1pt</property>
- </style>
- <style name="crosstab-cell" id="5">
- <property name="borderBottomColor">#CCCCCC</property>
- <property name="borderBottomStyle">solid</property>
- <property name="borderBottomWidth">1pt</property>
- <property name="borderLeftColor">#CCCCCC</property>
- <property name="borderLeftStyle">solid</property>
- <property name="borderLeftWidth">1pt</property>
- <property name="borderRightColor">#CCCCCC</property>
- <property name="borderRightStyle">solid</property>
- <property name="borderRightWidth">1pt</property>
- <property name="borderTopColor">#CCCCCC</property>
- <property name="borderTopStyle">solid</property>
- <property name="borderTopWidth">1pt</property>
- </style>
- </styles>
- <page-setup>
- <simple-master-page name="Simple MasterPage" id="2">
- <page-footer>
- <text id="3">
- <property name="contentType">html</property>
- <text-property name="content"><![CDATA[<value-of>new Date()</value-of>]]></text-property>
- </text>
- </page-footer>
- </simple-master-page>
- </page-setup>
-</report>
View
60 plugins/net.bioclipse.birt/src/net/bioclipse/birt/Activator.java
@@ -1,60 +0,0 @@
-/* *****************************************************************************
- * Copyright (c) 2009 Ola Spjuth.
- * All rights reserved. This program and the accompanying materials
- * are made available under the terms of the Eclipse Public License v1.0
- * which accompanies this distribution, and is available at
- * http://www.eclipse.org/legal/epl-v10.html
- *
- * Contributors:
- * Ola Spjuth - initial API and implementation
- ******************************************************************************/
-package net.bioclipse.birt;
-
-import org.eclipse.ui.plugin.AbstractUIPlugin;
-import org.osgi.framework.BundleContext;
-
-/**
- * The activator class controls the plug-in life cycle
- */
-public class Activator extends AbstractUIPlugin {
-
- // The plug-in ID
- public static final String PLUGIN_ID = "net.bioclipse.birt";
-
- // The shared instance
- private static Activator plugin;
-
- /**
- * The constructor
- */
- public Activator() {
- }
-
- /*
- * (non-Javadoc)
- * @see org.eclipse.ui.plugin.AbstractUIPlugin#start(org.osgi.framework.BundleContext)
- */
- public void start(BundleContext context) throws Exception {
- super.start(context);
- plugin = this;
- }
-
- /*
- * (non-Javadoc)
- * @see org.eclipse.ui.plugin.AbstractUIPlugin#stop(org.osgi.framework.BundleContext)
- */
- public void stop(BundleContext context) throws Exception {
- plugin = null;
- super.stop(context);
- }
-
- /**
- * Returns the shared instance
- *
- * @return the shared instance
- */
- public static Activator getDefault() {
- return plugin;
- }
-
-}
View
103 plugins/net.bioclipse.birt/src/net/bioclipse/birt/Startup.java
@@ -1,103 +0,0 @@
-/* *****************************************************************************
- * Copyright (c) 2009 Ola Spjuth.
- * All rights reserved. This program and the accompanying materials
- * are made available under the terms of the Eclipse Public License v1.0
- * which accompanies this distribution, and is available at
- * http://www.eclipse.org/legal/epl-v10.html
- *
- * Contributors:
- * Ola Spjuth - initial API and implementation
- ******************************************************************************/
-package net.bioclipse.birt;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.net.URL;
-import java.util.HashMap;
-
-import org.eclipse.birt.report.viewer.utilities.WebViewer;
-import org.eclipse.core.runtime.FileLocator;
-import org.eclipse.core.runtime.IProgressMonitor;
-import org.eclipse.core.runtime.IStatus;
-import org.eclipse.core.runtime.Path;
-import org.eclipse.core.runtime.Status;
-import org.eclipse.core.runtime.jobs.Job;
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.browser.Browser;
-import org.eclipse.swt.widgets.Display;
-import org.eclipse.swt.widgets.Shell;
-import org.eclipse.ui.IStartup;
-import org.osgi.framework.Bundle;
-
-/**
- *
- * @author ola
- *
- */
-public class Startup implements IStartup {
-
- Browser browser;
-
- public void earlyStartup() {
-
- Display.getDefault().syncExec( new Runnable(){
-
- public void run() {
- final Shell shell = new Shell(Display.getDefault());
- browser=new Browser(shell, SWT.NONE);
- }} );
-
-
-
-
- //Start up a background job for starting BIRT
- Job loadBirtJob=new Job("Starting BIRT engine"){
-
- @Override
- protected IStatus run( IProgressMonitor monitor ) {
-
- monitor.beginTask( "Initializing BIRT ", 3 );
- monitor.worked( 1 );
-
- WebViewer.startup();
-
- Bundle bundle = org.eclipse.core.runtime.Platform.getBundle(
- Activator.PLUGIN_ID);
- URL url = FileLocator.find(bundle,
- new Path("/reports/empty.rptdesign"),
- null);
- final String rpt;
- try {
- rpt = FileLocator.toFileURL(url).getPath();
-
- //Do new viewer
-// ViewerPlugin.getDefault( ).getPluginPreferences( ).setValue("APPCONTEXT_EXTENSION_KEY", "MyAppContext");
-
- final HashMap myparms = new HashMap();
- myparms.put("SERVLET_NAME_KEY", "frameset");
- myparms.put("FORMAT_KEY", "html");
-
- monitor.worked( 1 );
-
- Display.getDefault().syncExec( new Runnable(){
-
- public void run() {
- WebViewer.display(rpt, browser, myparms);
- }} );
-
-
- } catch ( IOException e ) {
- e.printStackTrace();
- }
-
- monitor.done();
- return Status.OK_STATUS;
- }
-
- };
- loadBirtJob.setUser( false );
- loadBirtJob.schedule();
-
-
- }
-
-}
View
15 plugins/net.bioclipse.core.tests/META-INF/MANIFEST.MF
@@ -5,15 +5,15 @@ Bundle-SymbolicName: net.bioclipse.core.tests
Bundle-Version: 2.4.0.20100709
Require-Bundle: org.eclipse.ui,
org.eclipse.core.runtime,
- net.bioclipse.core,
- org.junit4,
org.eclipse.core.resources,
- net.bioclipse.ui;bundle-version="2.0.0",
- org.springframework.osgi.aopalliance.osgi;bundle-version="1.0.0"
-Eclipse-LazyStart: true
+ org.springframework.osgi.aopalliance.osgi;bundle-version="1.0.0",
+ net.bioclipse.core,
+ net.bioclipse.ui,
+ org.eclipse.jdt.junit4.runtime;bundle-version="1.1.0",
+ org.junit4;bundle-version="4.5.0"
+Bundle-ActivationPolicy: lazy
Bundle-Vendor: The Bioclipse project
-Bundle-ClassPath: junit.jar,
- .
+Bundle-ClassPath: .
Export-Package: net.bioclipse,
net.bioclipse.core,
net.bioclipse.core.domain,
@@ -23,3 +23,4 @@ Export-Package: net.bioclipse,
net.bioclipse.recording
Import-Package: nu.xom;version="1.1.0",
org.apache.log4j
+Bundle-RequiredExecutionEnvironment: JavaSE-1.6
View
2  plugins/net.bioclipse.core.tests/build.properties
@@ -2,6 +2,4 @@ source.. = src/
output.. = bin/
bin.includes = META-INF/,\
.,\
- junit.jar,\
src/log4j.properties
-source.junit.jar = src/
View
55 plugins/net.bioclipse.core.tests/src/net/bioclipse/core/tests/Activator.java
@@ -1,55 +0,0 @@
- /* *****************************************************************************
- * Copyright (c) 2008 The Bioclipse Project and others.
- * All rights reserved. This program and the accompanying materials
- * are made available under the terms of the Eclipse Public License v1.0
- * which accompanies this distribution, and is available at
- * http://www.eclipse.org/legal/epl-v10.html
- *
- * Ola Spjuth
- * Jonathan Alvarsson
- *
- ******************************************************************************/
-package net.bioclipse.core.tests;
-
-import net.bioclipse.core.util.LogUtils;
-
-import org.apache.log4j.Logger;
-import org.eclipse.ui.plugin.AbstractUIPlugin;
-import org.osgi.framework.BundleContext;
-import org.osgi.util.tracker.ServiceTracker;
-
-/**
- * The activator class controls the plug-in life cycle
- */
-public class Activator extends AbstractUIPlugin {
-
- private static final Logger logger = Logger.getLogger(Activator.class);
-
- // The shared instance
- private static Activator plugin;
-
- /**
- * The constructor
- */
- public Activator() {
- }
-
- public void start(BundleContext context) throws Exception {
- super.start(context);
- plugin = this;
- }
-
- public void stop(BundleContext context) throws Exception {
- plugin = null;
- super.stop(context);
- }
-
- /**
- * Returns the shared instance
- *
- * @return the shared instance
- */
- public static Activator getDefault() {
- return plugin;
- }
-}
View
32 plugins/net.bioclipse.core/src/net/bioclipse/core/util/FileUtil.java
@@ -10,17 +10,24 @@
******************************************************************************/
package net.bioclipse.core.util;
+import java.io.File;
+import java.io.IOException;
+import java.net.URL;
import java.util.Random;
+import net.bioclipse.core.business.BioclipseException;
+
import org.eclipse.core.resources.IFile;
import org.eclipse.core.resources.IProject;
import org.eclipse.core.resources.IResource;
import org.eclipse.core.resources.IWorkspace;
import org.eclipse.core.resources.ResourcesPlugin;
import org.eclipse.core.runtime.CoreException;
+import org.eclipse.core.runtime.FileLocator;
import org.eclipse.core.runtime.IPath;
import org.eclipse.core.runtime.NullProgressMonitor;
import org.eclipse.core.runtime.Path;
+import org.eclipse.core.runtime.Platform;
/**
* Utility methods to manipulate files in Bioclipse
@@ -87,4 +94,29 @@ public static void deleteLinkedProject() throws CoreException{
project.delete( true, new NullProgressMonitor() );
}
+ /**
+ * Get the absolute path from a file with plugin-relative path
+ * @return absolute path to file.
+ * @throws IOException
+ */
+ public static String getFilePath(String pluginRelativePath, String pluginID)
+ throws IllegalArgumentException, IOException {
+
+ if (pluginRelativePath==null || pluginRelativePath.isEmpty())
+ throw new IllegalArgumentException("pluginRelativePath must " +
+ "not be empty");
+
+ if (pluginID==null || pluginID.isEmpty())
+ throw new IllegalArgumentException("pluginID must " +
+ "not be empty");
+
+ URL url = FileLocator.toFileURL(Platform.getBundle(pluginID)
+ .getEntry(pluginRelativePath));
+ File file=new File(url.getFile());
+ if (!file.exists())
+ throw new IOException("File: " + pluginRelativePath
+ + " does not exist in plugin: " + pluginID);
+
+ return url.getFile();
+ }
}
View
124 plugins/net.bioclipse.core/src/net/bioclipse/core/util/ImageUtils.java
@@ -0,0 +1,124 @@
+package net.bioclipse.core.util;
+import java.awt.image.BufferedImage;
+import java.awt.image.ColorModel;
+import java.awt.image.DirectColorModel;
+import java.awt.image.IndexColorModel;
+import java.awt.image.WritableRaster;
+
+import org.eclipse.swt.graphics.ImageData;
+import org.eclipse.swt.graphics.PaletteData;
+import org.eclipse.swt.graphics.RGB;
+
+
+public class ImageUtils {
+
+ public static BufferedImage convertToAWT(ImageData data) {
+ ColorModel colorModel = null;
+ PaletteData palette = data.palette;
+ if (palette.isDirect) {
+ colorModel = new DirectColorModel(data.depth, palette.redMask,
+ palette.greenMask, palette.blueMask);
+ BufferedImage bufferedImage = new BufferedImage(colorModel,
+ colorModel.createCompatibleWritableRaster(data.width,
+ data.height), false, null);
+ WritableRaster raster = bufferedImage.getRaster();
+ int[] pixelArray = new int[3];
+ for (int y = 0; y < data.height; y++) {
+ for (int x = 0; x < data.width; x++) {
+ int pixel = data.getPixel(x, y);
+ RGB rgb = palette.getRGB(pixel);
+ pixelArray[0] = rgb.red;
+ pixelArray[1] = rgb.green;
+ pixelArray[2] = rgb.blue;
+ raster.setPixels(x, y, 1, 1, pixelArray);
+ }
+ }
+ return bufferedImage;
+ } else {
+ RGB[] rgbs = palette.getRGBs();
+ byte[] red = new byte[rgbs.length];
+ byte[] green = new byte[rgbs.length];
+ byte[] blue = new byte[rgbs.length];
+ for (int i = 0; i < rgbs.length; i++) {
+ RGB rgb = rgbs[i];
+ red[i] = (byte) rgb.red;
+ green[i] = (byte) rgb.green;
+ blue[i] = (byte) rgb.blue;
+ }
+ if (data.transparentPixel != -1) {
+ colorModel = new IndexColorModel(data.depth, rgbs.length, red,
+ green, blue, data.transparentPixel);
+ } else {
+ colorModel = new IndexColorModel(data.depth, rgbs.length, red,
+ green, blue);
+ }
+ BufferedImage bufferedImage = new BufferedImage(colorModel,
+ colorModel.createCompatibleWritableRaster(data.width,
+ data.height), false, null);
+ WritableRaster raster = bufferedImage.getRaster();
+ int[] pixelArray = new int[1];
+ for (int y = 0; y < data.height; y++) {
+ for (int x = 0; x < data.width; x++) {
+ int pixel = data.getPixel(x, y);
+ pixelArray[0] = pixel;
+ raster.setPixel(x, y, pixelArray);
+ }
+ }
+ return bufferedImage;
+ }
+ }
+
+ public static ImageData convertToSWT(BufferedImage bufferedImage) {
+ if (bufferedImage.getColorModel() instanceof DirectColorModel) {
+ DirectColorModel colorModel = (DirectColorModel) bufferedImage
+ .getColorModel();
+ PaletteData palette = new PaletteData(colorModel.getRedMask(),
+ colorModel.getGreenMask(), colorModel.getBlueMask());
+ ImageData data = new ImageData(bufferedImage.getWidth(),
+ bufferedImage.getHeight(), colorModel.getPixelSize(),
+ palette);
+ WritableRaster raster = bufferedImage.getRaster();
+ int[] pixelArray = new int[3];
+ for (int y = 0; y < data.height; y++) {
+ for (int x = 0; x < data.width; x++) {
+ raster.getPixel(x, y, pixelArray);
+ int pixel = palette.getPixel(new RGB(pixelArray[0],
+ pixelArray[1], pixelArray[2]));
+ data.setPixel(x, y, pixel);
+ }
+ }
+ return data;
+ } else if (bufferedImage.getColorModel() instanceof IndexColorModel) {
+ IndexColorModel colorModel = (IndexColorModel) bufferedImage
+ .getColorModel();
+ int size = colorModel.getMapSize();
+ byte[] reds = new byte[size];
+ byte[] greens = new byte[size];
+ byte[] blues = new byte[size];
+ colorModel.getReds(reds);
+ colorModel.getGreens(greens);
+ colorModel.getBlues(blues);
+ RGB[] rgbs = new RGB[size];
+ for (int i = 0; i < rgbs.length; i++) {
+ rgbs[i] = new RGB(reds[i] & 0xFF, greens[i] & 0xFF,
+ blues[i] & 0xFF);
+ }
+ PaletteData palette = new PaletteData(rgbs);
+ ImageData data = new ImageData(bufferedImage.getWidth(),
+ bufferedImage.getHeight(), colorModel.getPixelSize(),
+ palette);
+ data.transparentPixel = colorModel.getTransparentPixel();
+ WritableRaster raster = bufferedImage.getRaster();
+ int[] pixelArray = new int[1];
+ for (int y = 0; y < data.height; y++) {
+ for (int x = 0; x < data.width; x++) {
+ raster.getPixel(x, y, pixelArray);
+ data.setPixel(x, y, pixelArray[0]);
+ }
+ }
+ return data;
+ }
+ return null;
+ }
+
+}
View
36 plugins/net.bioclipse.jasper/.classpath
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry exported="true" kind="lib" path="lib/jcommon-1.0.15.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/jfreechart-1.0.12.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/iText-2.1.7.jar"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+ <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
+ <classpathentry kind="src" path="src"/>
+ <classpathentry exported="true" kind="lib" path="lib/batik-anim.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/batik-awt-util.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/batik-bridge.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/batik-css.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/batik-dom.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/batik-ext.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/batik-gvt.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/batik-parser.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/batik-script.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/batik-svg-dom.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/batik-svggen.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/batik-util.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/batik-xml.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/bsh-2.0b4.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/commons-beanutils-1.8.0.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/commons-collections-2.1.1.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/commons-digester-1.7.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/groovy-all-1.5.5.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/jasperreports-3.7.3.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/jasperreports-fonts-3.7.3.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/jaxen-1.1.1.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/jpa.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/jxl-2.6.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/png-encoder-1.5.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/poi-3.5-FINAL-20090928.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/swtjasperviewer-1.2.0.jar"/>
+ <classpathentry kind="output" path="bin"/>
+</classpath>
View
2  plugins/net.bioclipse.birt/.project → plugins/net.bioclipse.jasper/.project
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
- <name>net.bioclipse.birt</name>
+ <name>net.bioclipse.jasper</name>
<comment></comment>
<projects>
</projects>
View
52 plugins/net.bioclipse.jasper/META-INF/MANIFEST.MF
@@ -0,0 +1,52 @@
+Manifest-Version: 1.0
+Bundle-ManifestVersion: 2
+Bundle-Name: Jasper Reports for Bioclipse
+Bundle-SymbolicName: net.bioclipse.jasper;singleton:=true
+Bundle-Version: 1.2.0
+Bundle-Activator: net.bioclipse.jasper.Activator
+Bundle-Vendor: The Bioclipse Team
+Require-Bundle: org.eclipse.ui,
+ org.eclipse.core.runtime,
+ net.bioclipse.core,
+ net.bioclipse.ui,
+ org.eclipse.core.resources
+Bundle-RequiredExecutionEnvironment: JavaSE-1.6
+Bundle-ActivationPolicy: lazy
+Bundle-ClassPath: .,
+ lib/batik-anim.jar,
+ lib/batik-awt-util.jar,
+ lib/batik-bridge.jar,
+ lib/batik-css.jar,
+ lib/batik-dom.jar,
+ lib/batik-ext.jar,
+ lib/batik-gvt.jar,
+ lib/batik-parser.jar,
+ lib/batik-script.jar,
+ lib/batik-svg-dom.jar,
+ lib/batik-svggen.jar,
+ lib/batik-util.jar,
+ lib/batik-xml.jar,
+ lib/bsh-2.0b4.jar,
+ lib/commons-beanutils-1.8.0.jar,
+ lib/commons-collections-2.1.1.jar,
+ lib/commons-digester-1.7.jar,
+ lib/groovy-all-1.5.5.jar,
+ lib/jasperreports-3.7.3.jar,
+ lib/jasperreports-fonts-3.7.3.jar,
+ lib/jaxen-1.1.1.jar,
+ lib/jpa.jar,
+ lib/jxl-2.6.jar,
+ lib/png-encoder-1.5.jar,
+ lib/poi-3.5-FINAL-20090928.jar,
+ lib/swtjasperviewer-1.2.0.jar,
+ lib/iText-2.1.7.jar,
+ lib/jcommon-1.0.15.jar,
+ lib/jfreechart-1.0.12.jar
+Import-Package: org.apache.commons.logging,
+ org.apache.log4j
+Export-Package: net.bioclipse.jasper,
+ net.bioclipse.jasper.editor,
+ net.sf.jasperreports.engine,
+ org.jfree.chart,
+ org.jfree.chart.axis,
+ org.jfree.chart.plot
View
37 plugins/net.bioclipse.jasper/build.properties
@@ -0,0 +1,37 @@
+source.. = src/
+output.. = bin/
+bin.includes = .,\
+ plugin.xml,\
+ icons/,\
+ lib/batik-anim.jar,\
+ lib/batik-awt-util.jar,\
+ lib/batik-bridge.jar,\
+ lib/batik-css.jar,\
+ lib/batik-dom.jar,\
+ lib/batik-ext.jar,\
+ lib/batik-gvt.jar,\
+ lib/batik-parser.jar,\
+ lib/batik-script.jar,\
+ lib/batik-svg-dom.jar,\
+ lib/batik-svggen.jar,\
+ lib/batik-util.jar,\
+ lib/batik-xml.jar,\
+ lib/bsh-2.0b4.jar,\
+ lib/commons-beanutils-1.8.0.jar,\
+ lib/commons-collections-2.1.1.jar,\
+ lib/commons-digester-1.7.jar,\
+ lib/groovy-all-1.5.5.jar,\
+ lib/jasperreports-3.7.3.jar,\
+ lib/jasperreports-fonts-3.7.3.jar,\
+ lib/jaxen-1.1.1.jar,\
+ lib/jpa.jar,\
+ lib/jxl-2.6.jar,\
+ lib/png-encoder-1.5.jar,\
+ lib/poi-3.5-FINAL-20090928.jar,\
+ lib/swtjasperviewer-1.2.0.jar,\
+ lib/iText-2.1.7.jar,\
+ META-INF/,\
+ lib/jcommon-1.0.15.jar,\
+ lib/jfreechart-1.0.12.jar
+source.. = src/
+jars.compile.order = .
View
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16 plugins/net.bioclipse.jasper/plugin.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?eclipse version="3.4"?>
+<plugin>
+ <extension
+ point="org.eclipse.ui.editors">
+ <editor
+ class="net.bioclipse.jasper.editor.ReportEditor"
+ default="false"
+ id="net.bioclipse.jasper.report.editor"
+ extensions="bogus"
+ icon="icons/lastd.gif"
+ name="Report Editor">
+ </editor>
+ </extension>
+
+</plugin>
View
4 ...t/bioclipse/managers/tests/Activator.java → ...r/src/net/bioclipse/jasper/Activator.java
@@ -1,4 +1,4 @@
-package net.bioclipse.managers.tests;
+package net.bioclipse.jasper;
import org.eclipse.ui.plugin.AbstractUIPlugin;
import org.osgi.framework.BundleContext;
@@ -9,7 +9,7 @@
public class Activator extends AbstractUIPlugin {
// The plug-in ID
- public static final String PLUGIN_ID = "net.bioclipse.managers.tests";
+ public static final String PLUGIN_ID = "net.bioclipse.jasper";
// The shared instance
private static Activator plugin;
View
52 ...ioclipse.jasper/src/net/bioclipse/jasper/charCustomizers/DoseResponseChartCustomizer.java
@@ -0,0 +1,52 @@
+/*
+ * Copyright (c) 2010 Jonathan Alvarsson <jonalv@users.sourceforge.net>
+ *
+ * All rights reserved. This program and the accompanying materials are made
+ * available under the terms of the Eclipse Public License v1.0 which
+ * accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ */
+package net.bioclipse.jasper.charCustomizers;
+
+import java.awt.Font;
+import java.awt.geom.Ellipse2D;
+
+import org.jfree.chart.JFreeChart;
+import org.jfree.chart.axis.LogarithmicAxis;
+import org.jfree.chart.axis.NumberAxis;
+import org.jfree.chart.axis.ValueAxis;
+
+import net.sf.jasperreports.engine.JRChart;
+import net.sf.jasperreports.engine.JRChartCustomizer;
+
+
+/**
+ * @author jonalv
+ *
+ */
+public class DoseResponseChartCustomizer implements JRChartCustomizer {
+
+
+ private static final Font normalsize
+ = new Font( "SansSerif", Font.PLAIN, 4 );
+ private static final Font small
+ = new Font( "SansSerif", Font.PLAIN, 2 );
+
+ @Override
+ public void customize( JFreeChart chart, JRChart jasperchart ) {
+ ValueAxis domainAxis = new LogarithmicAxis("Concentration");
+ ValueAxis rangeAxis = new NumberAxis("SI%");
+ domainAxis.setTickLabelFont( small );
+ rangeAxis.setTickLabelFont( small );
+ domainAxis.setLabelFont( normalsize );
+ rangeAxis.setLabelFont( normalsize );
+ rangeAxis.setRange( 0, 110 );
+ chart.getXYPlot().setDomainAxis( domainAxis );
+ chart.getXYPlot().setRangeAxis( rangeAxis );
+ chart.getXYPlot().setDomainGridlinesVisible( false );
+ chart.getXYPlot()
+ .getRenderer()
+ .setSeriesShape( 0, new Ellipse2D.Double(-1, -1, 2, 2) );
+ }
+}
View
343 plugins/net.bioclipse.jasper/src/net/bioclipse/jasper/editor/ReportEditor.java
@@ -0,0 +1,343 @@
+package net.bioclipse.jasper.editor;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.util.Collection;
+import java.util.Map;
+
+import net.bioclipse.core.business.BioclipseException;
+import net.sf.jasperreports.engine.JRDataSource;
+import net.sf.jasperreports.engine.JasperFillManager;
+import net.sf.jasperreports.engine.JasperPrint;
+import net.sf.jasperreports.engine.data.JRBeanCollectionDataSource;
+
+
+import org.apache.log4j.Logger;
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.jface.action.GroupMarker;
+import org.eclipse.jface.action.IAction;
+import org.eclipse.jface.action.IToolBarManager;
+import org.eclipse.jface.action.MenuManager;
+import org.eclipse.jface.action.Separator;
+import org.eclipse.jface.viewers.ISelection;
+import org.eclipse.jface.viewers.ISelectionChangedListener;
+import org.eclipse.jface.viewers.ISelectionProvider;
+import org.eclipse.jface.viewers.StructuredSelection;
+import org.eclipse.swt.SWT;
+import org.eclipse.swt.layout.GridData;
+import org.eclipse.swt.layout.GridLayout;
+import org.eclipse.swt.widgets.Composite;
+import org.eclipse.swt.widgets.Control;
+import org.eclipse.ui.IEditorInput;
+import org.eclipse.ui.IEditorSite;
+import org.eclipse.ui.IWorkbenchActionConstants;
+import org.eclipse.ui.PartInitException;
+import org.eclipse.ui.part.EditorPart;
+
+import com.jasperassistant.designer.viewer.DefaultHyperlinkHandler;
+import com.jasperassistant.designer.viewer.IReportViewer;
+import com.jasperassistant.designer.viewer.ReportViewer;
+import com.jasperassistant.designer.viewer.StatusBar;
+import com.jasperassistant.designer.viewer.actions.ExportAsCsvAction;
+import com.jasperassistant.designer.viewer.actions.ExportAsHtmlAction;
+import com.jasperassistant.designer.viewer.actions.ExportAsJasperReportsAction;
+import com.jasperassistant.designer.viewer.actions.ExportAsMultiXlsAction;
+import com.jasperassistant.designer.viewer.actions.ExportAsPdfAction;
+import com.jasperassistant.designer.viewer.actions.ExportAsRtfAction;
+import com.jasperassistant.designer.viewer.actions.ExportAsSingleXlsAction;
+import com.jasperassistant.designer.viewer.actions.ExportAsXmlAction;
+import com.jasperassistant.designer.viewer.actions.ExportAsXmlWithImagesAction;
+import com.jasperassistant.designer.viewer.actions.ExportMenuAction;
+import com.jasperassistant.designer.viewer.actions.FirstPageAction;
+import com.jasperassistant.designer.viewer.actions.LastPageAction;
+import com.jasperassistant.designer.viewer.actions.NextPageAction;
+import com.jasperassistant.designer.viewer.actions.PageNumberContributionItem;
+import com.jasperassistant.designer.viewer.actions.PreviousPageAction;
+import com.jasperassistant.designer.viewer.actions.PrintAction;
+import com.jasperassistant.designer.viewer.actions.ReloadAction;
+import com.jasperassistant.designer.viewer.actions.ZoomActualSizeAction;
+import com.jasperassistant.designer.viewer.actions.ZoomComboContributionItem;
+import com.jasperassistant.designer.viewer.actions.ZoomFitPageAction;
+import com.jasperassistant.designer.viewer.actions.ZoomFitPageWidthAction;
+import com.jasperassistant.designer.viewer.actions.ZoomInAction;
+import com.jasperassistant.designer.viewer.actions.ZoomOutAction;
+
+/**
+ * An editor wrappping a Jasper ReportViewer.
+ *
+ * @author ola
+ *
+ */
+public class ReportEditor extends EditorPart implements ISelectionProvider{
+
+ private ReportViewer reportViewer = new ReportViewer(SWT.BORDER);
+
+ private static final Logger logger = Logger.getLogger(ReportEditor.class);
+
+ @Override
+ public void createPartControl(Composite parent) {
+
+ initMenu();
+ initToolBar();
+
+
+
+ Composite container = new Composite(parent, SWT.NONE);
+ GridLayout layout = new GridLayout(1, false);
+ layout.marginWidth = layout.marginHeight = 0;
+ container.setLayout(layout);
+
+ Control reportViewerControl = reportViewer.createControl(container);
+ reportViewerControl.setLayoutData(new GridData(GridData.FILL_BOTH));
+
+ StatusBar statusBar = new StatusBar();
+ statusBar.setReportViewer(reportViewer);
+ Control statusBarControl = statusBar.createControl(container);
+ statusBarControl.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
+
+ reportViewer.addHyperlinkListener(new DefaultHyperlinkHandler());
+
+
+
+
+
+ /*
+
+// // prepare report and data
+// InputStream is = getServletContext().getResourceAsStream("/WEB-INF/reports/userList.jrxml");
+// JRBeanCollectionDataSource ds = new JRBeanCollectionDataSource(results);
+//
+// // generate pdf file
+// JasperDesign jasperDesign = JRXmlLoader.load(is);
+// JasperReport jasperReport = JasperCompileManager.compileReport(jasperDesign);
+// JasperPrint jasperPrint = JasperFillManager.fillReport(jasperReport, parameters,
+// ds);
+
+
+
+
+ String path;
+ try {
+// path = FileUtil.getFilePath("demo/FirstJasper.jrprint", Activator.PLUGIN_ID);
+ path = FileUtil.getFilePath("demo/PieChartReport.jrprint", Activator.PLUGIN_ID);
+// path = FileUtil.getFilePath("demo/HyperlinkReport.jrprint", Activator.PLUGIN_ID);
+ reportViewer.loadDocument(path, false);
+ } catch (IllegalArgumentException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+
+*/
+
+ getSite().setSelectionProvider(this);
+
+ }
+
+
+
+
+
+
+
+ @Override
+ public void doSave(IProgressMonitor monitor) {
+ }
+
+ @Override
+ public void doSaveAs() {
+ }
+
+ @Override
+ public void init(IEditorSite site, IEditorInput input)
+ throws PartInitException {
+
+ setSite( site );
+ setInput( input );
+
+ }
+
+ @Override
+ public boolean isDirty() {
+ return false;
+ }
+
+ @Override
+ public boolean isSaveAsAllowed() {
+ return false;
+ }
+
+ @Override
+ public void setFocus() {
+ }
+
+
+
+ private void initMenu() {
+
+ MenuManager mm = new MenuManager();
+ mm.add( new GroupMarker(IWorkbenchActionConstants.MB_ADDITIONS));
+ getSite().registerContextMenu("net.bioclipse.jasper.report.context",
+ mm, this);
+
+ MenuManager export = new MenuManager("Export");
+ export.add(new ExportAsPdfAction(reportViewer));
+ export.add(new ExportAsRtfAction(reportViewer));
+ export.add(new ExportAsJasperReportsAction(reportViewer));
+ export.add(new ExportAsHtmlAction(reportViewer));
+ export.add(new ExportAsSingleXlsAction(reportViewer));
+ export.add(new ExportAsMultiXlsAction(reportViewer));
+ export.add(new ExportAsCsvAction(reportViewer));
+ export.add(new ExportAsXmlAction(reportViewer));
+ export.add(new ExportAsXmlWithImagesAction(reportViewer));
+
+ MenuManager file = new MenuManager("File");
+ file.add(new ReloadAction(reportViewer));
+ file.add(new Separator());
+ file.add(export);
+ file.add(new Separator());
+ file.add(new PrintAction(reportViewer));
+ mm.add(file);
+
+ MenuManager view = new MenuManager("View");
+ view.add(new ZoomOutAction(reportViewer));
+ view.add(new ZoomInAction(reportViewer));
+ view.add(new Separator());
+ view.add(new ZoomActualSizeAction(reportViewer));
+ view.add(new ZoomFitPageAction(reportViewer));
+ view.add(new ZoomFitPageWidthAction(reportViewer));
+ mm.add(view);
+
+ MenuManager nav = new MenuManager("Navigate");
+ nav.add(new FirstPageAction(reportViewer));
+ nav.add(new PreviousPageAction(reportViewer));
+ nav.add(new NextPageAction(reportViewer));
+ nav.add(new LastPageAction(reportViewer));
+ mm.add(nav);
+
+ }
+
+
+
+ private void initToolBar() {
+
+ IToolBarManager tbManager = getEditorSite().getActionBars()
+ .getToolBarManager();
+
+ ExportMenuAction exportMenu = new ExportMenuAction(reportViewer);
+ IAction pdfAction = null;
+ exportMenu.getMenuManager().add(
+ pdfAction = new ExportAsPdfAction(reportViewer));
+ exportMenu.getMenuManager().add(
+ new ExportAsRtfAction(reportViewer));
+ exportMenu.getMenuManager().add(
+ new ExportAsJasperReportsAction(reportViewer));
+ exportMenu.getMenuManager().add(new ExportAsHtmlAction(reportViewer));
+ exportMenu.getMenuManager().add(
+ new ExportAsSingleXlsAction(reportViewer));
+ exportMenu.getMenuManager().add(
+ new ExportAsMultiXlsAction(reportViewer));
+ exportMenu.getMenuManager().add(new ExportAsCsvAction(reportViewer));
+ exportMenu.getMenuManager().add(new ExportAsXmlAction(reportViewer));
+ exportMenu.getMenuManager().add(
+ new ExportAsXmlWithImagesAction(reportViewer));
+ exportMenu.setDefaultAction(pdfAction);
+
+ tbManager.add(exportMenu);
+ tbManager.add(new PrintAction(reportViewer));
+ tbManager.add(new ReloadAction(reportViewer));
+ tbManager.add(new Separator());
+ tbManager.add(new FirstPageAction(reportViewer));
+ tbManager.add(new PreviousPageAction(reportViewer));
+ if (SWT.getPlatform().equals("win32")) //$NON-NLS-1$
+ tbManager.add(new PageNumberContributionItem(reportViewer));
+ tbManager.add(new NextPageAction(reportViewer));
+ tbManager.add(new LastPageAction(reportViewer));
+ tbManager.add(new Separator());
+ tbManager.add(new ZoomActualSizeAction(reportViewer));
+ tbManager.add(new ZoomFitPageAction(reportViewer));
+ tbManager.add(new ZoomFitPageWidthAction(reportViewer));
+ tbManager.add(new Separator());
+ tbManager.add(new ZoomOutAction(reportViewer));
+ tbManager.add(new ZoomComboContributionItem(reportViewer));
+ tbManager.add(new ZoomInAction(reportViewer));
+ }
+
+ /**
+ * @see org.eclipse.jface.window.Window#createContents(org.eclipse.swt.widgets.Composite)
+ */
+ protected Control createContents(Composite parent) {
+ Composite container = new Composite(parent, SWT.NONE);
+ GridLayout layout = new GridLayout(1, false);
+ layout.marginWidth = layout.marginHeight = 0;
+ container.setLayout(layout);
+
+ Control reportViewerControl = reportViewer.createControl(container);
+ reportViewerControl.setLayoutData(new GridData(GridData.FILL_BOTH));
+
+ StatusBar statusBar = new StatusBar();
+ statusBar.setReportViewer(reportViewer);
+ Control statusBarControl = statusBar.createControl(container);
+ statusBarControl.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
+
+ reportViewer.addHyperlinkListener(new DefaultHyperlinkHandler());
+
+ return container;
+ }
+
+ /**
+ * Returns the report viewer used for viewing reports.
+ *
+ * @return the report viewer
+ */
+ public IReportViewer getReportViewer() {
+ return reportViewer;
+ }
+
+
+
+
+
+
+
+ @Override
+ public void addSelectionChangedListener(ISelectionChangedListener arg0) {
+ }
+ @Override
+ public ISelection getSelection() {
+ return new StructuredSelection(new Object());
+ }
+ @Override
+ public void removeSelectionChangedListener(ISelectionChangedListener arg0) {
+ }
+ @Override
+ public void setSelection(ISelection arg0) {
+ }
+
+
+ @SuppressWarnings("unchecked")
+ public void openReport(String reportAbsolutePath, Map parameters,
+ Collection beanCollection ) throws BioclipseException {
+
+ logger.debug("Opening jasper report: " + reportAbsolutePath);
+ logger.debug("Number of parameters: " + parameters != null ? parameters.size() : "");
+ logger.debug("Number of beans: " + beanCollection.size());
+
+ FileInputStream fis;
+ try {
+ fis = new FileInputStream(new File(reportAbsolutePath));
+
+ //Create a new JR data source and populate with our collection
+ JRDataSource reportSource =
+ new JRBeanCollectionDataSource(beanCollection );
+ JasperPrint jp = JasperFillManager.fillReport( fis, parameters,
+ reportSource);
+ reportViewer.setDocument(jp);
+ } catch (Exception e) {
+ logger.error(e.getMessage());
+ throw new BioclipseException(e.getMessage(), e);
+ }
+
+ }
+
+}
View
1  plugins/net.bioclipse.logback/src/logback.xml
@@ -25,6 +25,7 @@
<logger name="org.mortbay" level="WARN" />
<logger name="org.eclipse" level="WARN" />
<logger name="org.springframework" level="ERROR" />
+ <logger name="org.hibernate" level="ERROR" />
<logger name="net.bioclipse" level="DEBUG" />
<root>
View
28 plugins/net.bioclipse.logger/.project
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>net.bioclipse.logger</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.pde.ManifestBuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.pde.SchemaBuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.pde.PluginNature</nature>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ </natures>
+</projectDescription>
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