Author: pwang
Date: 2008-09-11 12:08:23 -0700 (Thu, 11 Sep 2008)
New Revision: 14886
Modified:
csplugins/trunk/ucsd/pwang/SessionForWebPlugin/src/SessionForWebPlugin/HTMLSessionExporter.java
Log:
Correct sub-directory for CellCircuit web site
Modified:
csplugins/trunk/ucsd/pwang/SessionForWebPlugin/src/SessionForWebPlugin/HTMLSessionExporter.java
===================================================================
---
csplugins/trunk/ucsd/pwang/SessionForWebPlugin/src/SessionForWebPlugin/HTMLSessionExporter.java
2008-09-11 19:06:47 UTC (rev 14885)
+++
csplugins/trunk/ucsd/pwang/SessionForWebPlugin/src/SessionForWebPlugin/HTMLSessionExporter.java
2008-09-11 19:08:23 UTC (rev 14886)
@@ -4,7 +4,6 @@
import java.util.List;
import java.util.Map;
import java.util.HashMap;
-import java.util.Iterator;
import java.util.Set;
import java.util.TreeSet;
import java.io.File;
@@ -14,7 +13,6 @@
import java.awt.image.BufferedImage;
import javax.swing.tree.TreeModel;
import javax.imageio.ImageIO;
-
import cytoscape.Cytoscape;
import cytoscape.CyNetwork;
import cytoscape.view.CyNetworkView;
@@ -24,6 +22,7 @@
import cytoscape.task.Task;
import cytoscape.task.TaskMonitor;
import cytoscape.task.util.TaskManager;
+import cytoscape.data.CyAttributes;
import cytoscape.data.writers.InteractionWriter;
import cytoscape.data.writers.CytoscapeSessionWriter;
@@ -69,7 +68,7 @@
{
List<String> networkIDs = networkIDs();
//crap(networkIDs);
- if (settings.destination ==
settings.DESTINATION_ZIP_ARCHIVE_4CELLCIRCUITS) {
+ if (settings.destination ==
SessionExporterSettings.DESTINATION_ZIP_ARCHIVE_4CELLCIRCUITS) {
generateNetworkFiles(networkIDs);
}
else {
@@ -305,6 +304,26 @@
tempStream.close();
} // end writeSession()
+ private String getSpeciesSubDirectory(String
speciesStr){
+ // Turn the string "Saccharomyces
cerevisia,Homo sapiens" into "Saccharomyces_cerevisia_Homo_sapiens"
+ if (speciesStr == null ||
speciesStr.trim().equals("")) {
+ return "unknown_species";
+ }
+ String retValue = "";
+ String[] items = speciesStr.split(",");
+ for (int i=0; i< items.length; i++){
+ String oneSpecies = items[i];
+ String[] components =
oneSpecies.split(" ");
+ for (int j=0; j<components.length; j++
) {
+ if (!retValue.equals("")) {
+ retValue += "_";
+ }
+ retValue += components[j];
+ }
+ }
+ return retValue;
+ }
+
private void generateNetworkFiles(List<String>
networkIDs) throws Exception
{
Map viewMap = Cytoscape.getNetworkViewMap();
@@ -321,9 +340,15 @@
// export the sif file
setStatus("Exporting SIF for: " +
networkTitle);
setPercentCompleted(10 + 80 *
currentNetwork / networkCount);
- if (settings.destination ==
settings.DESTINATION_ZIP_ARCHIVE_4CELLCIRCUITS) {
+ if (settings.destination ==
SessionExporterSettings.DESTINATION_ZIP_ARCHIVE_4CELLCIRCUITS) {
ZipBundle2 zipBundle2 =
(ZipBundle2) bundle;
- zipBundle2.openEntry("sif",
Bundle.sifFile(networkTitle));
+
+ CyAttributes cyAttrs =
Cytoscape.getNetworkAttributes();
+ String species =
cyAttrs.getStringAttribute(networkID, "species");
+ String speciesSubDir =
getSpeciesSubDirectory(species);
+
+
zipBundle2.openEntry("sif/"+speciesSubDir, Bundle.sifFile(networkTitle));
+
CyNetwork network =
Cytoscape.getNetwork(networkID);
InteractionWriter.writeInteractions(network, zipBundle2.entryWriter(), null);
}
@@ -344,7 +369,7 @@
BufferedImage image =
GraphViewToImage.convert(view, settings);
if (image != null)
{
- if (settings.destination ==
settings.DESTINATION_ZIP_ARCHIVE_4CELLCIRCUITS) {
+ if (settings.destination ==
SessionExporterSettings.DESTINATION_ZIP_ARCHIVE_4CELLCIRCUITS) {
ZipBundle2 zipBundle2 =
(ZipBundle2) bundle;
zipBundle2.openEntry("img", Bundle.imageFile(networkTitle,
settings.imageFormat));
ImageIO.write(image,
settings.imageFormat, bundle.entryOutputStream());
@@ -362,7 +387,7 @@
// generate thumbnail
setStatus("Generating thumbnail for: "
+ networkTitle);
setPercentCompleted(10 + 80 *
currentNetwork / networkCount + 40 / networkCount);
- if (settings.destination ==
settings.DESTINATION_ZIP_ARCHIVE_4CELLCIRCUITS) {
+ if (settings.destination ==
SessionExporterSettings.DESTINATION_ZIP_ARCHIVE_4CELLCIRCUITS) {
ZipBundle2 zipBundle2 =
(ZipBundle2) bundle;
zipBundle2.openEntry("thm_img",
ZipBundle2.thumbnailFile(networkTitle, settings.imageFormat));
BufferedImage thumbnail =
Thumbnails.createThumbnail(image, settings);
@@ -378,7 +403,7 @@
if (needToHalt)
return;
- if (settings.destination ==
settings.DESTINATION_ZIP_ARCHIVE_4CELLCIRCUITS) {
+ if (settings.destination ==
SessionExporterSettings.DESTINATION_ZIP_ARCHIVE_4CELLCIRCUITS) {
continue;
}
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