Render gene via BioGPS

None

//item[@key='_type'][.='plugin']/..
/item/item/item[@key='id']
import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;

import java.util.TreeMap;
import java.awt.Dimension;

if ((selectionValues == void) || (selectionValues == null) || (selectionValues.isEmpty())) {
    throw new RuntimeException("selectionValues must be specified and non-empty");
}

ButtonGroup group = new ButtonGroup();
JPanel messagePanel = new JPanel();
messagePanel.setLayout(new BoxLayout(messagePanel,BoxLayout.Y_AXIS));

messagePanel.add(new JLabel((message == void ? null : message)));

TreeMap map = new TreeMap();
for (int i = 0; i < selectionValues.size(); i++) {
	map.put(selectionValues.get(i), Integer.valueOf(i));
}

JRadioButton[] buttonArray = new JRadioButton[selectionValues.size()];
int i = 0;
for (String s : map.keySet()) {			
	buttonArray[i] = new JRadioButton(s);
	if (i==0) buttonArray[i].setSelected(true);
	group.add(buttonArray[i]);
	messagePanel.add(buttonArray[i]);
	i++;
}

int arraySize = i;

JScrollPane scrollPane = new JScrollPane(messagePanel);
scrollPane.setPreferredSize(new Dimension(200,300));				

JOptionPane.showOptionDialog(null, scrollPane, (title == void ? null : title),
		JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, new Object[]{"OK"}, null);

String answer="";
for (int i = 0; i < arraySize; i++) {
	JRadioButton button = buttonArray[i];
	if (button.isSelected()) {
		answer=map.get(button.getText()).toString();
		break;
	}
}

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);
/item/item/item[@key='name']
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);
Object the_element = the_list.get(Integer.valueOf(the_index));
String url="http://biogps.org/plugin_v1/" + plugin_id +
	   "/renderurl/?geneid=" + gene_id + "&redirect";
import java.awt.Desktop;
import java.net.URI;

if ((url == void) || (url == null)) {
	throw new RuntimeException("Url must be specified");
}

URI uri = null;

uri = new URI(url);

Desktop.getDesktop().browse(uri);

Name	Type	Description
list_biogps_plugins	rest
extract_plugins	xpath	Xpath Expression //item[@key='_type'][.='plugin']/..
extract_id_of_plugin	xpath	Xpath Expression /item/item/item[@key='id']
choose_plugin_by_name	localworker	Script import javax.swing.BoxLayout; import javax.swing.ButtonGroup; import javax.swing.JLabel; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JRadioButton; import java.util.TreeMap; import java.awt.Dimension; if ((selectionValues == void) \|\| (selectionValues == null) \|\| (selectionValues.isEmpty())) { throw new RuntimeException("selectionValues must be specified and non-empty"); } ButtonGroup group = new ButtonGroup(); JPanel messagePanel = new JPanel(); messagePanel.setLayout(new BoxLayout(messagePanel,BoxLayout.Y_AXIS)); messagePanel.add(new JLabel((message == void ? null : message))); TreeMap map = new TreeMap(); for (int i = 0; i < selectionValues.size(); i++) { map.put(selectionValues.get(i), Integer.valueOf(i)); } JRadioButton[] buttonArray = new JRadioButton[selectionValues.size()]; int i = 0; for (String s : map.keySet()) { buttonArray[i] = new JRadioButton(s); if (i==0) buttonArray[i].setSelected(true); group.add(buttonArray[i]); messagePanel.add(buttonArray[i]); i++; } int arraySize = i; JScrollPane scrollPane = new JScrollPane(messagePanel); scrollPane.setPreferredSize(new Dimension(200,300)); JOptionPane.showOptionDialog(null, scrollPane, (title == void ? null : title), JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, new Object[]{"OK"}, null); String answer=""; for (int i = 0; i < arraySize; i++) { JRadioButton button = buttonArray[i]; if (button.isSelected()) { answer=map.get(button.getText()).toString(); break; } }
flatten_name_list	localworker	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);
extract_name_of_plugin	xpath	Xpath Expression /item/item/item[@key='name']
flatten_id_list	localworker	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);
find_corresponding_id	beanshell	Script Object the_element = the_list.get(Integer.valueOf(the_index));
create_render_url	beanshell	Script String url="http://biogps.org/plugin_v1/" + plugin_id + "/renderurl/?geneid=" + gene_id + "&redirect";
Open_web_browser_at_a_URL	localworker	Script import java.awt.Desktop; import java.net.URI; if ((url == void) \|\| (url == null)) { throw new RuntimeException("Url must be specified"); } URI uri = null; uri = new URI(url); Desktop.getDesktop().browse(uri);

Name	Description	Inputs	Outputs
find_corresponding_id		the_list the_index	the_element
create_render_url		plugin_id gene_id	url

Source	Sink
list_biogps_plugins:responseBody	extract_plugins:xml_text
extract_plugins:nodelistAsXML	extract_id_of_plugin:xml_text
flatten_name_list:outputlist	choose_plugin_by_name:selectionValues
extract_name_of_plugin:nodelist	flatten_name_list:inputlist
extract_plugins:nodelistAsXML	extract_name_of_plugin:xml_text
extract_id_of_plugin:nodelist	flatten_id_list:inputlist
choose_plugin_by_name:answer	find_corresponding_id:the_index
flatten_id_list:outputlist	find_corresponding_id:the_list
gene_id	create_render_url:gene_id
find_corresponding_id:the_element	create_render_url:plugin_id
create_render_url:url	Open_web_browser_at_a_URL:url

Render gene via BioGPS

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