Classification of GEO assays using RapidAnalytics

Value

Xpath Expression

/eSummaryResult/DocSum/Item[@Name='Samples']/Item[@Name='Sample']/Item[@Name='Accession']

Xpath Expression

/default:MINiML/default:Sample/default:Data-Table/default:Internal-Data

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Script

import java.util.TreeMap;
import java.util.HashSet;

TreeMap dataTable = new TreeMap();
HashMap idToLabel = new HashMap();

private void addToTable(String singleData, String id, String label) {
	idToLabel.put(id,label);
	String[] lines = singleData.split("\n");
	System.out.println("LINES: " + lines.length);
	for (String line : lines) {
		if (line != null) {
			if (line.length() > 0 ) {
				String[] bits = line.split("\t");
				if (bits.length == 2) {
					addSingleData(id, bits[0], bits[1]);
				}
			}
		}
	}
	
	
}

private void addSingleData(String id, String probeID, String value) {
	TreeMap dataColumn = dataTable.get(id);
	if (dataColumn == null) {
		dataColumn = new TreeMap();
		dataColumn.put(probeID,value);
		dataTable.put(id, dataColumn);
	} else {
		dataColumn.put(probeID,value);
	}
}

private String convertToCSV() {
	StringBuilder sb = new StringBuilder();
	sb.append("assayID");
	sb.append(",");
	sb.append("experimentType");

	String exampleAssay = dataTable.keySet().iterator().next();
	Set probeIDs = dataTable.get(exampleAssay).keySet();

	for (String probeID : probeIDs) {
		sb.append(",");
		sb.append(probeID);
	}
	sb.append("\n");

	for (String assayID : dataTable.keySet()) {
		sb.append(assayID);
		sb.append(",");
		sb.append(idToLabel.get(assayID));
		TreeMap probeData = dataTable.get(assayID);
		for(String probeID : probeData.keySet()) {
			String value = probeData.get(probeID);
			sb.append(",");
			sb.append(value);
		}
		sb.append("\n");
	}
	

	return sb.toString();
}


for (int i = 0; i < listOfIDs.size(); i++) {
	String singleData = listOfData.get(i);
	String label = listOfLabels.get(i);
	String id = listOfIDs.get(i);
	if (singleData != null) {
		if (singleData.length() > 0 ) {
			addToTable(singleData, id, label);
		}
	}
}

dataTableCSV = convertToCSV();

Xpath Expression

/eSummaryResult/DocSum/Item[@Name='Samples']/Item[@Name='Sample']/Item[@Name='Title']

Script

String uri = "";

if (Desktop.isDesktopSupported()) {
	d = Desktop.getDesktop();
	uri = "http://rpc295.cs.man.ac.uk:8081/RAWS/plot" + repositoryEntry + "?renderer=Table+%2F+Plot+View";
	URI u = new URI(uri);
	d.browse(u);
}