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Team:Freiburg software/Code/SynBioWaveRobotServlet.java
From 2009.igem.org
SynBioWaveRobotServlet
/*
* Copyright: synbiowave
*
* License: GPL
*
* Authors: Jörg Wassolesk & Paul Staab
*
* Version: 0.1
*
* DESCRIPTION:
* This is the main class of the main SynBioWave-Robot.
*/
package org.synbiowave;
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.net.URL;
import java.net.URLConnection;
import java.util.ArrayList;
import java.util.Date;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.TreeSet;
import org.biojavax.bio.db.HashRichSequenceDB;
import org.biojavax.bio.db.RichSequenceDB;
import org.synbiowave.biobrick.BioBrickManager;
import org.synbiowave.biojava.Util;
import org.synbiowave.database.DatastoreManager;
import org.synbiowave.database.Sequence;
import org.synbiowave.menu.MenuItem;
import org.synbiowave.sequence.SequenceView;
import org.synbiowave.servlet.AbstractSbwRobotServlet;
import com.google.wave.api.Annotation;
import com.google.wave.api.Blip;
import com.google.wave.api.Element;
import com.google.wave.api.ElementType;
import com.google.wave.api.Event;
import com.google.wave.api.EventType;
import com.google.wave.api.Gadget;
import com.google.wave.api.GadgetView;
import com.google.wave.api.Image;
import com.google.wave.api.Range;
import com.google.wave.api.RobotMessageBundle;
import com.google.wave.api.TextView;
import com.google.wave.api.Wavelet;
//@SuppressWarnings("serial")
public class SynBioWaveRobotServlet extends AbstractSbwRobotServlet
{
private static final long serialVersionUID = 9128671957338019728L;
private TreeSet<String> biobrickIDs=null;
private String bValue="";
//------------------------------------------------------------------------
//General Part
//------------------------------------------------------------------------
@Override
public String myName() {
return "synbiowave@appspot.com";
}
@Override
public void createMenu(MenuItem menu) {
MenuItem fileMenu = new MenuItem("menu","File",this.generateKey());
menu.appendSubItem(fileMenu);
MenuItem fileimportMenu = new MenuItem("menu","Import",this.generateKey());
fileMenu.appendSubItem(fileimportMenu);
MenuItem uploadformbutton = new MenuItem("button", "File", this.generateKey());
fileimportMenu.appendSubItem(uploadformbutton);
MenuItem uploadForm = new MenuItem("form","Upload",this.generateKey());
uploadformbutton.appendSubItem(uploadForm);
MenuItem upload = new MenuItem("upload","upload",this.generateKey());
upload.setOption("target", "https://" + this.myName().replace("@", ".") + "/_wave/robot/jsonrpc");
upload.setOption("enctype", "multipart/form-data");
uploadForm.appendSubItem(upload);
MenuItem importBioBrick = new MenuItem("button", "BioBrick part", this.generateKey());
fileimportMenu.appendSubItem(importBioBrick);
MenuItem importDatastore = new MenuItem("button", "Datastore sequence", this.generateKey());
fileimportMenu.appendSubItem(importDatastore);
MenuItem fileexportMenu = new MenuItem("menu","Export",this.generateKey());
fileMenu.appendSubItem(fileexportMenu);
MenuItem downloadFilebutton = new MenuItem("button","File",this.generateKey());
fileexportMenu.appendSubItem(downloadFilebutton);
MenuItem downloadForm = new MenuItem("form","Download","noreload");
downloadFilebutton.appendSubItem(downloadForm);
MenuItem download = new MenuItem("download","Blub","Download");
downloadForm.appendSubItem(download);
download.setOption("target", "https://" + this.myName().replace("@", ".") + "/_wave/robot/jsonrpc");
downloadForm.createSubItem("radio", "fasta", this.generateKey()).setOption("group", "format");
downloadForm.createSubItem("radio", "gb", this.generateKey()).setOption("group", "format");
MenuItem sequenceMenu = new MenuItem("menu","Sequence",this.generateKey());
menu.appendSubItem(sequenceMenu);
sequenceMenu.createSubItem("button","Circular View", this.generateKey());
MenuItem helpMenu = new MenuItem("menu","Help",this.generateKey());
menu.appendSubItem(helpMenu);
helpMenu.createSubItem("checkbox", "debug", this.generateKey());
}
//------------------------------------------------------------------------
//Menu-Part
//------------------------------------------------------------------------
private final String gadgetURL = "http://synbiowave.svn.sourceforge.net/viewvc/synbiowave/trunk/menuGadget/menuGadget.xml";
private String uiMenuJson = "{}";
private void appendMenuGadgetIfNeccessary(Blip blip)
{
GadgetView gv = blip.getDocument().getGadgetView();
boolean hasmenu = false;
for ( Gadget gadget : gv.getGadgets() )
{
if ( gadget.getField("url").contentEquals(this.gadgetURL) )
{
hasmenu = true;
}
}
if ( ! hasmenu )
{
Gadget menuGadged = new Gadget(this.gadgetURL);
menuGadged.setField("ui.structure", this.uiMenuJson );
blip.getDocument().insert(0, "SynBioWave \n");
blip.getDocument().insertElement(12, menuGadged);
}
}
private void generateMenuData(Wavelet wavelet) throws Exception
{
MenuItem menu = new MenuItem("ui","ui", this.generateKey());
Map<String,String> data = wavelet.getDataDocuments();
for ( String key : data.keySet() )
{
if ( key.contains("ui.menu.") )
{
menu.importMenu( new MenuItem( data.get(key) ) );
}
}
this.uiMenuJson = menu.writeJson();
wavelet.setDataDocument("ui.completemenu", this.uiMenuJson);
}
private void updateMenusIfNeccessary(Wavelet wavelet) throws Exception
{
if (wavelet.getDataDocument("menu.update").contains("1"))
{
this.generateMenuData(wavelet);
for ( Blip blip : new RecChildBlipListBuilder(wavelet.getRootBlip()).getRecChildList() )
{
//blip.getDocument().append("trying to update this blip\n");
GadgetView gv = blip.getDocument().getGadgetView();
for ( Gadget gadget : gv.getGadgets() )
{
if ( gadget.getField("url").contentEquals(this.gadgetURL) )
{
Gadget menuGadget = new Gadget(this.gadgetURL);
menuGadget.setField("ui.structure", this.uiMenuJson );
gv.replace(gadget, menuGadget);
}
}
wavelet.setDataDocument("menu.update", "0");
}
}
}
//------------------------------------------------------------------------
//Basic functions
//------------------------------------------------------------------------
private void appendCircView(Event event) throws Exception {
Sequence sequence=DatastoreManager.getByID(new Sequence(),super.currentSequence);
URL url=new URL("http://samserver.homedns.org:8080/Rebase/RebaseServlet");
URLConnection conn=url.openConnection();
conn.setDoOutput(true);
org.biojava.bio.seq.Sequence s= Util.convertToRichSequence(sequence);
RichSequenceDB rsdb=new HashRichSequenceDB();
rsdb.addSequence(s);
Util.write(conn.getOutputStream(),rsdb.getRichSequenceIterator(),"genbank");
BufferedReader br=new BufferedReader(new InputStreamReader(conn.getInputStream()));
String name=br.readLine();
event.getWavelet().appendBlip().getDocument().appendElement(new Image("http://samserver.homedns.org/"+name,500,500,name));
br.close();}
private void importBioBrick(Event event) throws Exception
{
biobrickIDs=BioBrickManager.readBioBrickIDs();
Element bbInput=new Element(ElementType.INPUT);
bbInput.setProperty("name","bbInput");
bbInput.setProperty("defaultValue","");
Element bbButton=new Element(ElementType.BUTTON);
bbButton.setProperty("name","bbButton");
bbButton.setProperty("value","Import");
TextView rtv=event.getWavelet().getRootBlip().getDocument();
rtv.insert(rtv.getText().indexOf("Active Sequence:"),"\nPlease insert parts name:\n");
rtv.insertElement(rtv.getText().indexOf("Active Sequence:"),bbInput);
rtv.insertElement(rtv.getText().indexOf("Active Sequence:"),bbButton);
rtv.insert(rtv.getText().indexOf("Active Sequence:"),"\n");
int maxElements=4;
Iterator<String> tailSetIterator=biobrickIDs.iterator();
while(tailSetIterator.hasNext()&&maxElements>0){rtv.insert(rtv.getText().indexOf("Active Sequence:"),tailSetIterator.next()+"\n");maxElements--;}
rtv.insert(rtv.getText().indexOf("Active Sequence:"),"...\n");
}
private void importDatastore(Event event) throws Exception
{
Element dbInput=new Element(ElementType.INPUT);
dbInput.setProperty("name","dbInput");
dbInput.setProperty("defaultValue","");
Element dbButton=new Element(ElementType.BUTTON);
dbButton.setProperty("name","dbButton");
dbButton.setProperty("value","Import");
TextView rtv=event.getWavelet().getRootBlip().getDocument();
rtv.insert(rtv.getText().indexOf("Active Sequence:"),"Please insert sequence name:\n");
rtv.insertElement(rtv.getText().indexOf("Active Sequence:"),dbInput);
rtv.insertElement(rtv.getText().indexOf("Active Sequence:"),dbButton);
rtv.insert(rtv.getText().indexOf("Active Sequence:"),"\n");
int maxElements=4;
Iterator<Sequence> tailSetIterator=DatastoreManager.getAll(new Sequence()).iterator();
while(tailSetIterator.hasNext()&&maxElements>0){rtv.insert(rtv.getText().indexOf("Active Sequence:"),tailSetIterator.next().getName()+"\n");maxElements--;}
rtv.insert(rtv.getText().indexOf("Active Sequence:"),"...\n");
}
//------------------------------------------------------------------------
//Events
//------------------------------------------------------------------------
@Override
public void processSbwEvents(RobotMessageBundle bundle) {
for(Event event:bundle.getEvents()){
try{
Blip blip=event.getBlip();
TextView tv=blip.getDocument();
if(event.getType()==EventType.WAVELET_SELF_ADDED){
try{
this.generateMenuData(event.getWavelet());
event.getWavelet().setDataDocument("menu.update","0");
this.appendMenuGadgetIfNeccessary(event.getBlip());
event.getWavelet().getRootBlip().getDocument().append("Active Sequence: none ");}
catch(Exception e){event.getBlip().getDocument().append("Error generating menu:"+e.toString());}}
else if(event.getType()==EventType.FORM_BUTTON_CLICKED){
if(event.getButtonName().contains("bbButton")){
String value = getInputValue(tv);
tv.delete(new Range(tv.getText().indexOf("\nPlease insert parts name:\n"),tv.getText().indexOf("Active Sequence:")));
String id=biobrickIDs.ceiling(value);
if(id!=null){
try{
String s=BioBrickManager.readBioBrickSequence(id);
List<Map<String,String>> features=BioBrickManager.readBioBrickFeatures(id);
Sequence sequence=new Sequence("biobrick",event.getTimestamp(),event.getWavelet().getWaveId(),event.getWavelet().getWaveletId(),event.getBlip().getBlipId(),s,SequenceView.isSequence(s));
sequence.setName(id);
for(Map<String,String> feature:features){
if(feature.get("END").equals("0")){sequence.addAnnotation(new Annotation(feature.get("TYPE_CATEGORY"),feature.get("TYPE"),new Range(Integer.parseInt(feature.get("START")),s.length())));}
else{sequence.addAnnotation(new Annotation(feature.get("TYPE_CATEGORY"),feature.get("TYPE"),new Range(Integer.parseInt(feature.get("START")),Integer.parseInt(feature.get("END")))));}}
super.currentSequence=DatastoreManager.store(sequence).getId();
String gadgetView=SequenceView.getHTMLView(sequence.getSequence(),sequence.getType());
Gadget seqView=new Gadget("http://samnode.de/SequenceView.xml");
seqView.setField("names","(br /)(br /)(br /)"+sequence.getName()+"(br /)(br /)");
seqView.setField("sequences",gadgetView);
event.getWavelet().appendBlip().getDocument().getGadgetView().append(seqView);}
catch(Exception exc){tv.replace("Error receiving biobrick data:"+exc.toString());}}
else{tv.append("BioBrick part not found, please choose other part ...");}}
else if(event.getButtonName().contains("dbButton")){
String value = getInputValue(tv);
tv.delete(new Range(tv.getText().indexOf("\nPlease insert parts name:\n"),tv.getText().indexOf("Active Sequence:")));
try{
Sequence sequence=DatastoreManager.getGreaterThanKeyValue(new Sequence(),"name",value).get(0);
super.currentSequence=sequence.getId();
if(!sequence.getWaveletID().get(0).equals(event.getWavelet().getWaveletId())){
String gadgetView=SequenceView.getHTMLView(sequence.getSequence(),sequence.getType());
Gadget seqView=new Gadget("http://samnode.de/SequenceView.xml");
seqView.setField("names","(br /)(br /)(br /)"+sequence.getName()+"(br /)(br /)");
seqView.setField("sequences",gadgetView);
event.getWavelet().appendBlip().getDocument().getGadgetView().append(seqView);}}
catch(Exception exc){tv.replace("Error receiving sequence:"+exc.toString());}}}
else if(event.getType()==EventType.BLIP_SUBMITTED){
if(event.getBlip().getDocument().getText().contains("#save")){
event.getBlip().getDocument().getGadgetView().append(new Gadget("http://samnode.de/downgadget.xml"));}
else if(event.getBlip().getDocument().getText().contains("#cgView")){
try{ appendCircView(event); }
catch(Exception e1){event.getBlip().getDocument().append("Error displaying circular view:"+e1.toString());}}
else if(event.getBlip().getDocument().getText().contains("#biobrick")){
try{ this.importBioBrick(event); }
catch(Exception exc){event.getBlip().getDocument().append(exc.toString());}}
else if(event.getBlip().getDocument().getText().contains("#msa")){
ArrayList<String> sequences=new ArrayList<String>();
sequences.add("tcgcgcgatcgcgatcgcatagcatacgcatcatcatctcatcatgcgacgcattatacgacgatagactacgacgactacgcgacgacatagcgcagcgagcatagcagcagcatagcagcagcagctacgactacgactacgactcatctcagc");
sequences.add("jdhfksjfhskjfhkfjshfuheuhfksuehfksjhsjzegfjhseifhkjcshegzfesfkjgfjhbesjhrvfjehfksuegfshvfbshegvhfgvsejhfsjhvsehfbjhesvfhsebfhsbfhsejhekfjbvehsvbjhesfvbjshevsehvhsvehvsejhsejhbsejfhbsjhefvbesjfbjeshvsehbfjsehfbsejfhbsejhvsehevbj");
sequences.add("ugcugcugacugauguacguagcgagcagucguagcugaucguagucgaugcgacgaugcuagcuagcuagcuagcuagcuagcgagcuagcuagcugaugcuagcuag");
sequences.add("tacgagctacgactagcatcagcgagcggacatcgacgatcgactacgatcagctac");
String gadgetView=SequenceView.getHTMLView(sequences);
Gadget seqView=new Gadget("http://samnode.de/SequenceView.xml");
seqView.setField("names","(br /)(br /)seq1(br /)seq2(br /)seq3(br /)seq4(br /)(br /)");
seqView.setField("sequences",gadgetView);
event.getWavelet().appendBlip().getDocument().getGadgetView().append(seqView);}
else if(event.getBlip().getDocument().getText().contains("#datastore")){
try{ this.importDatastore(event); }
catch(Exception exc){event.getBlip().getDocument().append(exc.toString());}}}
else if(event.getType()==EventType.DOCUMENT_CHANGED){
try{this.updateMenusIfNeccessary(event.getWavelet());}
catch(Exception e){event.getBlip().getDocument().append("Error updating menu:"+e.toString());}
if(!tv.getAnnotations("style/backgroundColor").isEmpty()){
Range range=tv.getAnnotations("style/backgroundColor").get(0).getRange();
tv.deleteAnnotations("style/backgroundColor");
String sequence=tv.getText().substring(range.getStart(),range.getEnd());
try{
Sequence nSequence=new Sequence(event.getModifiedBy(),event.getTimestamp(),event.getWavelet().getWaveId(),event.getWavelet().getWaveId(),event.getBlip().getBlipId(),sequence,SequenceView.isSequence(sequence));
nSequence.setName(event.getModifiedBy()+"("+new Date(event.getTimestamp()).toString()+")");
super.currentSequence=DatastoreManager.store(nSequence).getId();}
catch(Exception e){event.getBlip().getDocument().append("Error storing sequence:"+e.toString());}
super.replaceWithSimpleView(event,range,tv.getText().substring(range.getStart(),range.getEnd()));}
String type=null;
String value=null;
int start=0;
List<Element> elements=tv.getElements();
Map<String,String> properties=null;
for(Element element:elements){
properties=element.getProperties();
if(properties.containsKey("name")){
if(properties.get("name").equals("bbInput")||properties.get("name").equals("dbInput")){
type=properties.get("name");
value=properties.get("value").trim();}
else if(properties.get("name").equals("bbButton")||properties.get("name").equals("dbButton")){
start=tv.getPosition(element)+2;}}}
if(!value.equals(this.bValue)){
this.bValue=value;
if(type!=null){
String preview="";
int maxElements=4;
if(type.equals("bbInput")){
Iterator<String> tailSetIterator=biobrickIDs.tailSet(value).iterator();
while(tailSetIterator.hasNext()&&maxElements>0){preview+=tailSetIterator.next()+"\n";maxElements--;}}
if(type.equals("dbInput")){
Iterator<Sequence> tailSetIterator=DatastoreManager.getGreaterThanKeyValue(new Sequence(),"name",value).iterator();
while(tailSetIterator.hasNext()&&maxElements>0){preview+=tailSetIterator.next()+"\n";maxElements--;}}
preview+="...\n";
tv.replace(new Range(start,tv.getText().indexOf("Active Sequence:")),preview);}}}}
catch(Exception e){}}}//event.getBlip().getDocument().append("Error prossesing events:"+e.toString());}}}
private String getInputValue(TextView tv) {
String value=null;
List<Element> elements=tv.getElements();
Map<String,String> properties=null;
for(Element element:elements){
properties=element.getProperties();
if(properties.containsKey("name")){
if(properties.get("name").contains("Input")){
value=properties.get("value").trim();}}}
return value;
}
@Override
public void processSbwMenuEvents(String buttonLabel,LinkedHashMap<String,String> formValues,Event event){
if(buttonLabel.contains("upload")){
try{
while(super.currentSequence==null||DatastoreManager.getByID(new Sequence(),super.currentSequence)==null){}
Sequence sequence=DatastoreManager.getByID(new Sequence(),super.currentSequence);
String gadgetView=SequenceView.getHTMLView(sequence.getSequence(),sequence.getType());
Gadget seqView=new Gadget("http://samnode.de/SequenceView.xml");
seqView.setField("names","(br /)(br /)(br /)"+sequence.getName()+"(br /)(br /)");
seqView.setField("sequences",gadgetView);
event.getWavelet().appendBlip().getDocument().getGadgetView().append(seqView);}
catch(Exception exc){event.getWavelet().appendBlip().getDocument().append("Error on upload:"+exc.toString());}}
else if (buttonLabel.contains("Circular View"))
{
try
{
this.appendCircView(event);
}
catch(Exception exc)
{
event.getBlip().getDocument().append("Error displaying circular view:"+exc.toString());
}
}
else if (buttonLabel.contains("BioBrick"))
{
try
{
this.importBioBrick(event);
}
catch(Exception exc)
{
event.getBlip().getDocument().append("BioBrick-Error: " + exc.toString());
}
}
else if (buttonLabel.contains("Datastore"))
{
try
{
this.importDatastore(event);
}
catch(Exception exc)
{
event.getBlip().getDocument().append("Datastore-Error: " + exc.toString());
}
}
}
}
