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Update to pom to use a different jaxws import.

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1 parent 3f7a16c commit d47d820b114c3cd2a404c39f1a5096ecbbf8263b @eamonnmag eamonnmag committed Mar 8, 2012
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68 pom.xml
@@ -127,24 +127,24 @@
</plugin>
- <!--<plugin>-->
- <!--<groupId>org.codehaus.mojo</groupId>-->
- <!--<artifactId>osxappbundle-maven-plugin</artifactId>-->
- <!--<version>1.0-alpha-1</version>-->
- <!--<configuration>-->
- <!--<mainClass>org.isatools.isacreator.gui.modeselection.ModeSelector</mainClass>-->
- <!--<iconFile>target/classes/images/icon/isacreator_icon.icns</iconFile>-->
- <!--<dictionaryFile>target/classes/packaging/Info.plist</dictionaryFile>-->
- <!--</configuration>-->
- <!--<executions>-->
- <!--<execution>-->
- <!--<phase>package</phase>-->
- <!--<goals>-->
- <!--<goal>bundle</goal>-->
- <!--</goals>-->
- <!--</execution>-->
- <!--</executions>-->
- <!--</plugin>-->
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>osxappbundle-maven-plugin</artifactId>
+ <version>1.0-alpha-1</version>
+ <configuration>
+ <mainClass>org.isatools.isacreator.gui.modeselection.ModeSelector</mainClass>
+ <iconFile>target/classes/images/icon/isacreator_icon.icns</iconFile>
+ <dictionaryFile>target/classes/packaging/Info.plist</dictionaryFile>
+ </configuration>
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <goals>
+ <goal>bundle</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
@@ -182,12 +182,11 @@
</plugin>
<plugin>
- <groupId>org.codehaus.mojo</groupId>
+ <groupId>org.jvnet.jax-ws-commons</groupId>
<artifactId>jaxws-maven-plugin</artifactId>
- <version>1.10</version>
+ <version>2.2</version>
<executions>
<execution>
- <id>CDB</id>
<goals>
<goal>wsimport</goal>
</goals>
@@ -204,16 +203,31 @@
</execution>
</executions>
-
<dependencies>
<dependency>
- <groupId>javax.jws</groupId>
- <artifactId>jsr181-api</artifactId>
- <version>1.0-MR1</version>
-
+ <groupId>com.sun.xml.ws</groupId>
+ <artifactId>jaxws-tools</artifactId>
+ <version>2.1.7</version>
+ <exclusions>
+ <exclusion>
+ <groupId>org.jvnet.staxex</groupId>
+ <artifactId>stax-ex</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+ <dependency>
+ <groupId>org.jvnet.staxex</groupId>
+ <artifactId>stax-ex</artifactId>
+ <version>1.2</version>
+ <exclusions>
+ <exclusion>
+ <groupId>javax.xml.stream</groupId>
+ <artifactId>stax-api</artifactId>
+ </exclusion>
+ </exclusions>
</dependency>
-
</dependencies>
+
</plugin>
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111 src/main/java/org/isatools/isacreator/spreadsheet/SpreadsheetPopupMenus.java
@@ -40,6 +40,7 @@ The ISA Team and the ISA software suite have been funded by the EU Carcinogenomi
import org.isatools.isacreator.configuration.DataTypes;
import org.isatools.isacreator.configuration.FieldObject;
import org.isatools.isacreator.spreadsheet.model.TableReferenceObject;
+import org.isatools.isacreator.visualization.workflowvisualization.*;
import javax.swing.*;
import java.awt.*;
@@ -254,28 +255,7 @@ public void actionPerformed(ActionEvent e) {
final TableReferenceObject tro = spreadsheet.getTableReferenceObject();
- if (spreadsheet.getTableReferenceObject().getMissingFields() != null && tro.getMissingFields().size() != 0) {
- for (final String missingField : tro.getMissingFields().keySet()) {
- if (!spreadsheet.spreadsheetFunctions.checkColumnExists(missingField)) {
- JMenuItem item = new JMenuItem(missingField);
- item.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent ae) {
- popup.setVisible(false);
-
- spreadsheet.spreadsheetFunctions.addFieldToReferenceObject(tro.getMissingFields().get(missingField));
-
- spreadsheet.spreadsheetFunctions.addColumnAfterPosition(missingField, "", -1);
- toRemove[0] = missingField;
-
- }
- });
- addColumn.add(item);
- }
- }
- if (toRemove[0] != null) {
- tro.getMissingFields().remove(toRemove[0]);
- }
- }
+ addMissingFields(popup, addColumn, toRemove, tro);
addColumn.add(new JSeparator());
@@ -286,16 +266,7 @@ public void actionPerformed(ActionEvent ae) {
addColumn.add(addParameter);
}
- if (!columnName.toLowerCase().contains("characteristic") &&
- !columnName.toLowerCase().contains("unit") &&
- !columnName.toLowerCase().contains("factor") &&
- !columnName.toLowerCase().contains("date") &&
- !columnName.toLowerCase().contains("performer") &&
- !columnName.toLowerCase().contains("provider") &&
- !columnName.toLowerCase().contains("comment") &&
- !columnName.toLowerCase().contains("material type")) {
- addColumn.add(addProtocol);
- }
+ addCheckAndAddProtocol(columnName, addColumn, addProtocol);
addColumn.add(new JSeparator());
addColumn.add(addComment);
@@ -391,10 +362,18 @@ public void actionPerformed(ActionEvent event) {
removeHighlight.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent ae) {
if (spreadsheet.highlightActive) {
-
spreadsheet.setRowsToDefaultColor();
}
+ }
+ });
+ JMenuItem viewWorkflowForAssays = new JMenuItem("View workflow for assays");
+ viewWorkflowForAssays.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent actionEvent) {
+// SpreadsheetAnalysis analysis = new TranscriptomicSpreadsheetAnalysis(spreadsheet);
+// analysis.runAnalysis();
+// analysis.getGraph().outputGraph();
+ new WorkflowVisualization().createGUI();
}
});
@@ -430,18 +409,8 @@ public void actionPerformed(ActionEvent actionEvent) {
popup.add(deleteRow);
popup.add(new JSeparator());
- String columnLC = columnName.toLowerCase();
- if (!columnLC.contains("characteristic") &&
- !columnLC.contains("unit") &&
- !columnLC.contains("factor") &&
- !columnLC.contains("date") &&
- !columnLC.contains("performer") &&
- !columnLC.contains("provider") &&
- !columnLC.contains("comment") &&
- !columnLC.contains("material type")
- && spreadsheet.getStudyDataEntryEnvironment() != null) {
- popup.add(addColumn);
- }
+ checkAndAddIfShouldAddColumn(columnName, popup, addColumn);
+
if (spreadsheet.hiddenColumns.size() > 0) {
popup.add(unhideColumns);
}
@@ -470,9 +439,61 @@ public void actionPerformed(ActionEvent actionEvent) {
popup.add(removeHighlight);
}
+// popup.add(new JSeparator());
+// popup.add(viewWorkflowForAssays);
popup.show(jc, x, y);
}
+ private void checkAndAddIfShouldAddColumn(String columnName, JPopupMenu popup, JMenu addColumn) {
+ if (isNotStandardFieldType(columnName)
+ && spreadsheet.getStudyDataEntryEnvironment() != null) {
+ popup.add(addColumn);
+ }
+ }
+
+ private void addCheckAndAddProtocol(String columnName, JMenu addColumn, JMenuItem addProtocol) {
+ if (isNotStandardFieldType(columnName)) {
+ addColumn.add(addProtocol);
+ }
+ }
+
+ private boolean isNotStandardFieldType(String columnName) {
+ columnName = columnName.toLowerCase();
+ return !columnName.contains("characteristic") &&
+ !columnName.contains("unit") &&
+ !columnName.contains("factor") &&
+ !columnName.contains("date") &&
+ !columnName.contains("performer") &&
+ !columnName.contains("provider") &&
+ !columnName.contains("comment") &&
+ !columnName.contains("material type");
+ }
+
+ private void addMissingFields(final JPopupMenu popup, JMenu addColumn, final String[] toRemove, final TableReferenceObject tro) {
+ if (spreadsheet.getTableReferenceObject().getMissingFields() != null && tro.getMissingFields().size() != 0) {
+ for (final String missingField : tro.getMissingFields().keySet()) {
+ if (!spreadsheet.spreadsheetFunctions.checkColumnExists(missingField)) {
+ JMenuItem item = new JMenuItem(missingField);
+ item.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent ae) {
+ popup.setVisible(false);
+
+ spreadsheet.spreadsheetFunctions.addFieldToReferenceObject(tro.getMissingFields().get(missingField));
+
+ spreadsheet.spreadsheetFunctions.addColumnAfterPosition(missingField, "", -1);
+ toRemove[0] = missingField;
+
+ }
+ });
+ addColumn.add(item);
+ }
+ }
+ if (toRemove[0] != null) {
+ tro.getMissingFields().remove(toRemove[0]);
+ }
+ }
+ }
+
/**
* Creates a popup when the user has dragged across cells which allows the user to autofill the columns
* (based on values dragged from), copy the selection, or clear the fields.
View
82 src/main/java/org/isatools/isacreator/visualization/TreeView.java
@@ -76,20 +76,23 @@ The ISA Team and the ISA software suite have been funded by the EU Carcinogenomi
public class TreeView extends Display {
public static String NAME_STRING = "name";
- private static final String tree = "tree";
- private static final String treeNodes = "tree.nodes";
- private static final String treeEdges = "tree.edges";
- private LabelRenderer m_nodeRenderer;
- private EdgeRenderer m_edgeRenderer;
- private int m_orientation;
+ protected static final String tree = "tree";
+ protected static final String treeNodes = "tree.nodes";
+ protected static final String treeEdges = "tree.edges";
+ protected LabelRenderer m_nodeRenderer;
+ protected EdgeRenderer m_edgeRenderer;
+ protected int m_orientation;
public TreeView(Tree t, Dimension size) {
this(t, size, NAME_STRING, Constants.ORIENT_LEFT_RIGHT);
}
public TreeView(Tree t, Dimension size, String label, int orientation) {
super(new Visualization());
+ initialiseTreeView(t, size, label, orientation);
+ }
+ public void initialiseTreeView(Tree t, Dimension size, String label, int orientation) {
this.m_orientation = orientation;
m_vis.add(tree, t);
@@ -136,29 +139,32 @@ public TreeView(Tree t, Dimension size, String label, int orientation) {
// create the tree layout action
NodeLinkTreeLayout treeLayout = new NodeLinkTreeLayout(tree,
m_orientation, 50, 0, 8);
- treeLayout.setLayoutAnchor(new Point2D.Double(25, 75));
+ treeLayout.setLayoutAnchor(new Point2D.Double(size.width / 2, 15));
m_vis.putAction("treeLayout", treeLayout);
CollapsedSubtreeLayout subLayout = new CollapsedSubtreeLayout(tree,
m_orientation);
m_vis.putAction("subLayout", subLayout);
- // create the filtering and layout
- ActionList filter = new ActionList();
+ createAndAddFilter(dca, nodeColor, edgeColor, treeLayout, subLayout);
+ // animated transition
+ createAnimation();
+ // ensure size is reasonable!
+ finaliseVisualizationSteps(size);
+ }
- if (m_orientation == Constants.ORIENT_LEFT_RIGHT) {
- filter.add(new FisheyeTreeFilter(tree, 2));
- }
+ protected void finaliseVisualizationSteps(Dimension size) {
+ size.width = (size.width < 100) ? 200 : size.width;
+ size.height = (size.height < 100) ? 200 : size.height;
- filter.add(new FontAction(treeNodes, FontLib.getFont("Verdana", 14)));
- filter.add(treeLayout);
- filter.add(subLayout);
- filter.add(dca);
- filter.add(nodeColor);
- filter.add(edgeColor);
- m_vis.putAction("filter", filter);
+ setSize(size);
+ setItemSorter(new TreeDepthItemSorter());
+ addControlListeners();
+ setOrientation(m_orientation);
+ m_vis.run("filter");
+ }
- // animated transition
+ protected void createAnimation() {
ActionList animate = new ActionList(1000);
animate.setPacingFunction(new SlowInSlowOutPacer());
animate.add(new QualityControlAnimator());
@@ -168,26 +174,31 @@ public TreeView(Tree t, Dimension size, String label, int orientation) {
animate.add(new RepaintAction());
m_vis.putAction("animate", animate);
m_vis.alwaysRunAfter("filter", "animate");
+ }
+
+ protected void createAndAddFilter(DataColorAction dca, ItemAction nodeColor, ItemAction edgeColor, NodeLinkTreeLayout treeLayout, CollapsedSubtreeLayout subLayout) {
+ // create the filtering and layout
+ ActionList filter = new ActionList();
- // initialize the display
+ if (m_orientation == Constants.ORIENT_LEFT_RIGHT) {
+ filter.add(new FisheyeTreeFilter(tree, 2));
+ }
- // ensure size is reasonable!
- size.width = (size.width < 100) ? 200 : size.width;
- size.height = (size.height < 100) ? 200 : size.height;
+ filter.add(new FontAction(treeNodes, FontLib.getFont("Verdana", 14)));
+ filter.add(treeLayout);
+ filter.add(subLayout);
+ filter.add(dca);
+ filter.add(nodeColor);
+ filter.add(edgeColor);
+ m_vis.putAction("filter", filter);
+ }
- setSize(size);
- setItemSorter(new TreeDepthItemSorter());
+ private void addControlListeners() {
addControlListener(new ZoomToFitControl());
addControlListener(new ZoomControl());
addControlListener(new WheelZoomControl());
addControlListener(new PanControl());
addControlListener(new FocusControl(1, "filter"));
-
- // ------------------------------------------------
-
- // filter graph and perform layout
- setOrientation(m_orientation);
- m_vis.run("filter");
}
public int getOrientation() {
@@ -220,6 +231,7 @@ public void setOrientation(int orientation) {
break;
+
case Constants.ORIENT_TOP_BOTTOM:
m_nodeRenderer.setHorizontalAlignment(Constants.CENTER);
m_edgeRenderer.setHorizontalAlignment1(Constants.CENTER);
@@ -248,7 +260,6 @@ public void setOrientation(int orientation) {
stl.setOrientation(orientation);
}
-
public static class NodeColorAction extends ColorAction {
public NodeColorAction(String group) {
super(group, VisualItem.FILLCOLOR);
@@ -265,6 +276,5 @@ public int getColor(VisualItem item) {
return ColorLib.rgba(255, 255, 255, 0);
}
}
- } // end of inner class TreeMapColorAction
-
-} // end of class TreeMap
+ }
+}

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