Connect to KEGG by KEGGAPI

These two days I spend much time on the codes for connecting KEGG by its API. Fortunately the KEGGAPI is updated to adapt to use AXIS 1.4 version, which means that I don't need to do the pretreatment as described at the website.

Here I write some code according to its Javadoc. Having got all the ports opened, it runs pretty well. Thus I know where the previous problem is: The remote machine doesn't allow the script out because only the port 3128 is open.


package org.tingting.bn.mn.networkbuilder.test;

import org.tingting.bn.mn.networkbuilder.domain.KeggConnector;

import keggapi.Definition;
import keggapi.KEGGPortType;

public class TestKeggConnector {

/**
* @param args
*/

public static void main(String[] args){

KeggConnector conn = new KeggConnector();
KEGGPortType serv;

try{
serv = conn.getServ();
Definition result[] = serv.list_pathways("hsa");

for( int i = 0; i <>

Today is my big day

Today is my big day. I'll attend the annual conference of BPRC and give a presentation to sum up my work this year. To say the truth, I am not afraid of the annual report, but of my nominal Big Boss: Fuchu He. He is used to blame his students as far as he doesn't feel happy. The same slides,which got his praise today, is possible be scolded severely tomorrow. Beside, he always don't care the pride of his students. no matter when you are in front of everybody or not, his rebuke comes with no account. Compared to Keith, he is really a harsh supervisor. They are like the two poles of the Earth.
Anyway, I will get myself liberated after the presentation. Don't let his words kill me. God bless me.

Merry Christmas

Merry Christmas! A new year is coming. Work harder and harder!
Today I plan to finish the technical report to Keith.
Here we go.

What would I do today

I attend the regular biweekly report this morning.
I will try my best to write the detailed report for Keith, which will be started after a while.
For the annual conference, I need to prepare two review as requested. So I'd like to do it from now on. One is for the review on network comparison algorithm, the other is the detailed thought record on the pathway alignment and the network comparison algorithm based on the pathway alignment.

Here we go.

What would I do today 2008.12.16

Today I mainly plan to record my thoughts in the draft for the new paper.
Finish the schema and start the experiments.
Plus, I need to prepare for the presentation which would be given on the Tomorrow's conference.
Plus plus, I'd like to form a detailed slides for the discussion with Keith.
Ok, here we go.

(+++: I need to find some time to manage my papers. Keep and print out the useful ones and delete the vice versa. )

It seems that I always change my work plan according to my thoughts arbitrarily.

Let's see what I really did today.
1. I write the schema for the doctoral dissertation, which I am sure will direct my future work helpfully.
2. Record my thoughts(pending)

I Finished the proposal

Finally I finished the proposal. Congratulations!

Would I did today 2008.12.12

proposal. reading

What would I do today

code and reading. and blog.

What I do today 2008.12.9

1. The Chapter of Interfaces and Inner Classes.

2. Record my thoughts on the Doctoral Defense Conference of LiuWei.

What would I do today - 2008.12.08

This morning I attended the pre-defence of Liu wei, one of my group mates. She is the one who started the doctoral study with me together. But now, her study life comes to the end while I'm still struggling in it. Sigh, nothing but pushing myself harder.
Here is my work plan for this afternoon and tonight:
1. Review one paper for CEC'09, which would take me 2~3 hours I guess. (finished)
2. Recompose the proposal for Prof. Wang. It must be finished before his arrival tomorrow. (pending)
3. Finish the First part of Thinking in Java. (finished)

What will I do today 2008.12.1

December 1, the new start for a new month, the last month in this critical year. I've had a clear goal now. What I need to do is doing my best to reach it as soon as possible. Keith, I am sorry I disappoint you again. I swear I'll do it never. Although I cannot help with the situation, I swear I will do my best in every thing if only I start to do it. Let's see.

Today, my plan is to rewrite the report for you, in which all the thoughts we discussed before would be described in length. I try to finish it today. If not, the deadline is 12:00pm tomorrow.

Let's go from now on.
-----------------------
Sigh, I only finished the first three chapter of Thinking in Java. Should I say sorry? No. To whom? No regret, just put more attention and effort in the daily work.

What do I do today 2008.11.23

Nov 23
I should finish the re-coding in Java before the end of this month. Today is Nov 23. it is only 7 days left. Seems that I've given up the attempt for the BIBE'09, which in fact I did nothing for the preparation.

Today I plan (I only have half day for work. )
ONLY one TASK: Continue coding, whatever it is difficult. Try to fix every problem by yourself!

What do I do today 2008.11.20

Nov 20.
1. Morning: did nothing but prepare a skeleton for an report: Different ways for the reconstruction of metabolic networks

2. Afternoon: enrich the report as long as writing code for the experiments.

3. Evening: continue the work of afternoon. Work into deep night, enjoy yourself.

What did I do today 11.19

Nov 19.
1. I took part in the conference in the morning, to present my biweekly report in brief and discuss some problem with my groupmates together.
2. What did I do in the afternoon? I forgot it. It seems that I did nothing in the afternoon.
3. In the evening, I wrote the study plan for Prof.Zhu.

The feeling of working in the deep night is so good. I enjoy it. Keep going on, girl. Believe in yourself.

How to parse a xml without the dtd-validating

Thanks to Samuel now my testXMLReader.java can read XML files without validating the dtd files referred in the second line of each XML files. Here is the code.

testXMLReader.java

package org.tingting.bn.mn.phylotree.test;

import java.io.File;
import java.io.FileNotFoundException;

import javax.xml.bind.JAXBContext;
import javax.xml.bind.Unmarshaller;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
import javax.xml.transform.sax.SAXSource;
import org.tingting.bn.mn.graph.impl.jaxp.Pathway;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import org.xml.sax.SAXNotSupportedException;
import org.xml.sax.XMLReader;

/**
* TestPathwayReader.java is to test PathwayReader
*
* @author Tingting
*
*/

public class TestPathwayReader {

/**
* @param args
*/
public static void main(String[] args) {


String xmlFile = "D:\\Data\\KEGG\\KGML\\aae\\aae00020.xml";

try {
// parse the xml files.
JAXBContext jc = JAXBContext
.newInstance("org.tingting.bn.mn.graph.impl.jaxp");
Unmarshaller u = jc.createUnmarshaller();

Pathway pathway = u.unmarshal(getSAXSource(new File(xmlFile)),
Pathway.class).getValue();

System.out.println(pathway.getName());
} catch (Exception e) {
System.out.println(e);
}

}

// this function helps unmarshal avoid the DTD-validating.
private static SAXSource getSAXSource(File suiteFile)
throws SAXNotSupportedException, SAXException,
ParserConfigurationException, FileNotFoundException {


/*
// These two lines needs the support of xerces
System.setProperty("javax.xml.parsers.SAXParserFactory",
"org.apache.xerces.jaxp.SAXParserFactoryImpl");
*/

SAXParserFactory spf = SAXParserFactory.newInstance();
spf.setNamespaceAware(true);
spf.setValidating(false);

// System.out.println(spf.isValidating());
SAXParser saxParser = spf.newSAXParser();

// System.out.println(saxParser.isValidating());
XMLReader xmlReader = saxParser.getXMLReader();
xmlReader.setFeature("http://xml.org/sax/features/validation", false);
xmlReader
.setFeature(
"http://apache.org/xml/features/nonvalidating/load-external-dtd",
false);
SAXSource source = new SAXSource(xmlReader, new InputSource(suiteFile
.getPath()));

return source;
}

}

What did I do today -- 2008.11.17

First of all, Happy Birthday to my dearest father, the one who gave birth to me 28 years ago.
Secondly, today is Nov 17, the deadline of BIBE 09 is Dec 5, which is only 2 weeks away. I need at least 5 days to compose the manuscript and leave at least 3 days to Keith or Martin for the revision. See, you have no time for the experiments. Seize every second!

Today's work plan:
1. review the paper of CEC09.(unfinished)

I cannot find the information that I want. So, I need to write a letter to the Programmer of CEC09 to make clear two questions. One is when is the deadline of the review. The other is how I can get the full paper and download it. In this case, this work have to be put aside temporarily.
(I finished the letter to the chairman)

2. network reconstruction!! If you cannot retrieve it using Java, then go back to perl and finish it !!

3. Send photos to Prof.Wang. (it didn't finished because the zipped file was still too large to send out. )

What did I do today -- 2008.11.13

Nov.13. It is 21 days away from Dec.5, the deadline of BIBE.
Today I must do:
1. Read the Chapter 9 of On Writing Well and take note. (done)
2. Read the Chapter 1 of Effective Java and take note. (not start)
3. Writing code to retrieve the data from KEGG and construct the network.
(need to retrieve the two paper on KEGG and take note of the network construction process.)

What did I do today - 2008.11.12

Nov 12. The big day is coming soon...
Today I will go to the Forbidden City Theater to listen to a series report: Capital Science Lecture -- Special Session of the Nobel and Turing Laureates.
I'd like to write more about it after I come back from it.
In addition, I need to continue the Java coding for the reconstruction of networks.

What did I do today - 2008.11.11

First of all, Happy the Widower's Day. (It seems that today, 11.11, is only for the bachelor, haha ~ )

What I plan to do today:
1. Finish the reading of the convention of Java coding. (Done)
It is very useful! Here is the linkage: Code Conventions for the Java Programming Language(Sun).

2. Another edition of the convention of Java coding: Code Conventions for the Java Programming Language(Ambysoft). (Done)

3. Go through the book: Effective Java

4. Have a glance on the book: Thinking in Java (the 4th edition)

What did I do today - 2008.11.10

Nov 10. What is I plan to do today.

1. Chapter 7 of On Writing Well. Done.
2. Codes on network construction.(pending)(little progress)
3. Documents on Codes.(not start)