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;

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)));

JRadioButton[] buttonArray = new JRadioButton[selectionValues.size()];
for (int i = 0; i < buttonArray.length; i++) {			
	buttonArray[i] = new JRadioButton(selectionValues.get(i));
	if (i==0) buttonArray[i].setSelected(true);
	group.add(buttonArray[i]);
	messagePanel.add(buttonArray[i]);
}				

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

String answer="";
for (int i = 0; i < buttonArray.length; i++) {
	JRadioButton button = buttonArray[i];
	if (button.isSelected()) {
		answer="" + i;
	}
}

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;

Desktop.getDesktop().browse(new URI(the_url));

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; 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))); JRadioButton[] buttonArray = new JRadioButton[selectionValues.size()]; for (int i = 0; i < buttonArray.length; i++) { buttonArray[i] = new JRadioButton(selectionValues.get(i)); if (i==0) buttonArray[i].setSelected(true); group.add(buttonArray[i]); messagePanel.add(buttonArray[i]); } JOptionPane.showOptionDialog(null, messagePanel, (title == void ? null : title), JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, new Object[]{"OK"}, null); String answer=""; for (int i = 0; i < buttonArray.length; i++) { JRadioButton button = buttonArray[i]; if (button.isSelected()) { answer="" + i; } }
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_render_url	beanshell	Script import java.awt.Desktop; import java.net.URI; Desktop.getDesktop().browse(new URI(the_url));

Name	Inputs	Outputs
find_corresponding_id	the_list the_index	the_element
create_render_url	plugin_id gene_id	url
open_render_url	the_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_render_url:the_url

Render gene via BioGPS

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Xpath Expression

Xpath Expression

Script

Script

Xpath Expression

Script

Script

Script

Script

Reviews (0)

Comments (0)

Other workflows that use similar services (0)