Merge pull request #223 from ISA-tools/development

Merging Development in to master.
ISA-tools · Aug 7, 2013 · afc2c4a · afc2c4a
2 parents a399032 + d6d8b13
commit afc2c4a
Show file tree

Hide file tree

Showing 124 changed files with 1,272 additions and 3,243 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,73 @@
+# Files created/used by ISAcreator #
+####################################
+profiles.sup
+
+
+# MVN compiled output directories #
+###################################
+target/
+overlays/
+
+# Files created by Eclipse #
+############################
+.settings/
+.project
+.classpath
+
+# Files created by IntelliJ IDEA #
+##################################
+*.iml
+*.ipr
+*.iws
+.idea/
+
+# Files created by NetBeans #
+#############################
+nbproject/private/
+build/
+nbbuild/
+dist/
+nbdist/
+nbactions.xml
+nb-configuration.xml
+META-INF/
+
+
+# Compiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.sqlite
+
+# OS generated files #
+######################
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+Icon?
+ehthumbs.db
+Thumbs.db
diff --git a/ProgramData/AEArrayDesigns.txt → ProgramData/files/AEArrayDesigns.txt b/ProgramData/AEArrayDesigns.txt → ProgramData/files/AEArrayDesigns.txt
diff --git a/README.md b/README.md
@@ -16,14 +16,21 @@
 
 <a href="http://www.jetbrains.com/idea/" style="width:88px; height:31px;"><span style="margin: 0;padding: 0;position: absolute;top: -1px;left: 4px;font-size: 10px;cursor:pointer;"></span><img src="http://www.jetbrains.com/img/logos/recommend_idea1.gif" alt="The best Java IDE" border="0"/></a>
 
+### Running ISAcreator
+
+To run ISAcreator locally:
+1. Clone the code to your machine. You may clone from the primary repository at ISA-tools/ISAcreator, or from your own fork.
+2. Compile the code (`mvn assembly:assembly -Dmaven.test.skip=true -Pbuild`) - the build profile automatically sets some system variables like version etc. from information held within the pom.
+3. Run the code (`java -cp target/ISAcreator-1.7.1-jar-with-dependencies.jar org.isatools.isacreator.launch.ISAcreatorApplication`)
+
 ### Contributing
 
-You should read this article about Git Flow: <http://scottchacon.com/2011/08/31/github-flow.html>. It's a really useful tutorial on how to use Git for collaborative development.
+You should read this article about Github Flow: <http://scottchacon.com/2011/08/31/github-flow.html>. Although we don't strictly use Github flow, it's a really useful tutorial on how to use Git for collaborative development.
 
 1. Fork it.
 2. Clone your forked repository to your machine
-3. Create a branch (`git checkout -b myisacreator`)
-4. Make your changes
+3. Create a branch off of the development branch (`git checkout -b myisacreator`)
+4. Make and test your changes
 5. Run the tests (`mvn clean test`)
 6. Commit your changes (`git commit -am "Added something useful"`)
 7. Push to the branch (`git push origin myisacreator`)

diff --git a/package.sh b/package.sh
@@ -4,7 +4,6 @@
 #
 
 #MVNOPTS="--offline"
-
 get_tag_data () {
  local tag=$1
  local xml_file=$2
@@ -34,16 +33,16 @@ rm -rf src/main/resources/Configurations
 mkdir Configurations
 mkdir src/main/resources/Configurations
 cd Configurations
-wget https://github.com/downloads/ISA-tools/Configuration-Files/isaconfig-default_v2011-02-18.zip --no-check-certificate
-cp isaconfig-default_v2011-02-18.zip ../src/main/resources/Configurations/
-unzip isaconfig-default_v2011-02-18.zip
-rm isaconfig-default_v2011-02-18.zip
+wget https://bitbucket.org/eamonnmag/isatools-downloads/downloads/isaconfig-default_v2013-02-13.zip --no-check-certificate
+cp isaconfig-default_v2013-02-13.zip ../src/main/resources/Configurations/
+unzip isaconfig-default_v2013-02-13.zip
+rm isaconfig-default_v2013-02-13.zip
 cd ../
 
 ## keeping configurations in resources so that they are included in the jar
 cd src/main/resources/Configurations
-unzip isaconfig-default_v2011-02-18.zip
-rm isaconfig-default_v2011-02-18.zip
+unzip isaconfig-default_v2013-02-13.zip
+rm isaconfig-default_v2013-02-13.zip
 cd ../../../..
 
 mvn $MVNOPTS -Dmaven.test.skip=true clean assembly:assembly

diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
  <groupId>org.isatools</groupId>
  <artifactId>ISAcreator</artifactId>
  <packaging>bundle</packaging>
- <version>1.7.0</version>
+ <version>1.7.2</version>
  <name>ISAcreator</name>
  <url>http://www.isa-tools.org</url>
 
@@ -80,9 +80,7 @@
  <executable>apt</executable>
  <fork>true</fork>
  <debug>true</debug>
- <compilerArguments>
- <s>${project.build.directory}</s>
- </compilerArguments>
+
  <meminitial>128m</meminitial>
  <maxmem>512m</maxmem>
  </configuration>
@@ -192,7 +190,9 @@
  </execution>
 
  </executions>
+
  <dependencies>
+
  <dependency>
  <groupId>com.sun.xml.ws</groupId>
  <artifactId>jaxws-tools</artifactId>
@@ -204,6 +204,7 @@
  </exclusion>
  </exclusions>
  </dependency>
+
  <dependency>
  <groupId>org.jvnet.staxex</groupId>
  <artifactId>stax-ex</artifactId>
@@ -215,6 +216,7 @@
  </exclusion>
  </exclusions>
  </dependency>
+
  </dependencies>
 
  </plugin>
@@ -230,6 +232,7 @@
  <goal>shade</goal>
  </goals>
  <configuration>
+ <createDependencyReducedPom>false</createDependencyReducedPom>
  <transformers>
  <transformer
  implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
@@ -290,9 +293,9 @@
  </dependency>
 
  <dependency>
- <groupId>org.prefuse</groupId>
+ <groupId>prefuse</groupId>
  <artifactId>prefuse</artifactId>
- <version>20071021</version>
+ <version>1.0.1</version>
  </dependency>
 
  <dependency>
@@ -404,35 +407,14 @@
  <dependency>
  <groupId>org.apache.felix</groupId>
  <artifactId>org.apache.felix.main</artifactId>
- <version>1.8.0</version>
- </dependency>
-
- <dependency>
- <groupId>org.isatools</groupId>
- <artifactId>automacron</artifactId>
- <version>0.1.1</version>
- <exclusions>
- <exclusion>
- <artifactId>commons-httpclient</artifactId>
- <groupId>commons-httpclient</groupId>
- </exclusion>
- <exclusion>
- <artifactId>org.isatools</artifactId>
- <groupId>ISAcreator</groupId>
- </exclusion>
- </exclusions>
+ <version>4.2.1</version>
  </dependency>
 
- <dependency>
- <groupId>org.neo4j</groupId>
- <artifactId>neo4j</artifactId>
- <version>1.8.M07</version>
- </dependency>
 
  <dependency>
  <groupId>org.isatools</groupId>
  <artifactId>import_layer</artifactId>
- <version>1.5</version>
+ <version>1.6</version>
  <exclusions>
  <exclusion>
  <groupId>uk.ac.ebi</groupId>
@@ -448,8 +430,6 @@
 
 
  <!-- Dependencies for GS code -->
-
-
  <dependency>
  <groupId>genomespace</groupId>
  <artifactId>cdk</artifactId>
@@ -572,6 +552,15 @@
  </properties>
 
  </profile>
+
+ <profile>
+ <id>build</id>
+ <properties>
+ <isacreator.version>${pom.version}</isacreator.version>
+ <isacreator.alwaysShowInvestigation>false</isacreator.alwaysShowInvestigation>
+ </properties>
+
+ </profile>
  </profiles>
 
 

diff --git a/src/main/java/org/isatools/isacreator/api/ImportConfiguration.java b/src/main/java/org/isatools/isacreator/api/ImportConfiguration.java
@@ -1,15 +1,11 @@
 package org.isatools.isacreator.api;
 
-import org.isatools.isacreator.configuration.MappingObject;
 import org.isatools.isacreator.configuration.io.ConfigXMLParser;
-import org.isatools.isacreator.gui.ISAcreator;
 import org.isatools.isacreator.managers.ApplicationManager;
 import org.isatools.isacreator.managers.ConfigurationManager;
 import org.isatools.isacreator.settings.ISAcreatorProperties;
-import org.isatools.isacreator.spreadsheet.model.TableReferenceObject;
 
 import java.io.File;
-import java.util.List;
 
 /**
  * Created by the ISATeam.

diff --git a/src/main/java/org/isatools/isacreator/assayselection/platform/PlatformParser.java b/src/main/java/org/isatools/isacreator/assayselection/platform/PlatformParser.java
@@ -50,7 +50,7 @@ The ISA Team and the ISA software suite have been funded by the EU Carcinogenomi
 
 public class PlatformParser {
 
- private static final String PLATFORM_FILE = "/required/platforms.xml";
+ private static final String PLATFORM_FILE = "/defaults/assayinfo/platforms.xml";
 
 
  public Map<FileType, List<Platform>> loadPlatformFile() {

diff --git a/src/main/java/org/isatools/isacreator/autofilteringlist/FilterableListCellRenderer.java b/src/main/java/org/isatools/isacreator/autofilteringlist/FilterableListCellRenderer.java
@@ -62,13 +62,6 @@ public class FilterableListCellRenderer extends JComponent
  DefaultListCellRenderer listCellRenderer;
  JLabel image;
 
- static {
- ResourceInjector.addModule("org.jdesktop.fuse.swing.SwingModule");
- ResourceInjector.get("autofilteringlist-package.style").load(
- FilterableListCellRenderer.class.getResource("/dependency-injections/autofilteringlist-package.properties"));
- }
-
-
  /**
  * CustomListCellRenderer Constructor
  */

diff --git a/src/main/java/org/isatools/isacreator/calendar/CalendarGUI.java b/src/main/java/org/isatools/isacreator/calendar/CalendarGUI.java
@@ -60,12 +60,6 @@ public class CalendarGUI extends JFrame implements ActionListener {
  static final int WIDTH = 200;
  static final int HEIGHT = 230;
 
- static {
- ResourceInjector.addModule("org.jdesktop.fuse.swing.SwingModule");
- ResourceInjector.get("calendar-package.style").load(
- CalendarGUI.class.getResource("/dependency-injections/calendar-package.properties"));
- }
-
  @InjectedResource
  private ImageIcon closeIcon, closeIconOver, okIcon, okIconOver;
 

diff --git a/src/main/java/org/isatools/isacreator/common/ClearFieldUtility.java b/src/main/java/org/isatools/isacreator/common/ClearFieldUtility.java
@@ -50,7 +50,6 @@ public class ClearFieldUtility extends JLabel {
  @InjectedResource
  private ImageIcon clearIcon, clearIconOver;
 
-
  public ClearFieldUtility(final JTextField toClear) {
 
  ResourceInjector.get("common-package.style").inject(this);

diff --git a/src/main/java/org/isatools/isacreator/common/CustomTextField.java b/src/main/java/org/isatools/isacreator/common/CustomTextField.java
@@ -37,7 +37,6 @@ The ISA Team and the ISA software suite have been funded by the EU Carcinogenomi
 
 package org.isatools.isacreator.common;
 
-import org.isatools.isacreator.archiveoutput.ArchiveOutputWindow;
 import org.jdesktop.fuse.InjectedResource;
 import org.jdesktop.fuse.ResourceInjector;
 
@@ -56,14 +55,6 @@ The ISA Team and the ISA software suite have been funded by the EU Carcinogenomi
 
 public class CustomTextField extends JPanel {
 
- static {
- ResourceInjector.addModule("org.jdesktop.fuse.swing.SwingModule");
-
- ResourceInjector.get("common-package.style").load(
- ArchiveOutputWindow.class.getResource("/dependency-injections/common-package.properties"));
- }
-
-
  private String fieldName;
 
  private JTextField textField;