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THE AUSTRALIAN NATIONAL UNIVERSITY FACULTY OF ENGINEERING AND INFORMATION TECHNOLOGY DEPARTMENT OF COMPUTER SCIENCE Development of Web Scope (Using the Hibernate Package for Meta-Data) Le MA (u4086599) Semester 2, 2006 This is the final report for the COMP6703 eScience Project (Semester 2, 2006), supervisors are Dr. Henry Gardner and Dr. Raju Karia. TABLE OF CONTENTS ACKNOWLEDGMENTS ABSTRACT 1. INTRODUCTION................................................................................................. 4 1.1. OVERVIEW……………......................................................................................4 1.2. INTRODUCTION TO HIBERNATE..................................................................7 1.3. INTRODUCTION TO MDSPLUS........................................................................8 1.4. INTRODUCTION TO WEBSCOPE......................................................................10 1.5. INTRODUCTION TO Java Servlets and JSP......................................................11 1.6. INTRODUCTION TO Apache TomCat……......................................................12 1.7. INTRODUCTION TO Previous Project……......................................................12 2. REQUIREMENT ANALYSIS............................................................................15 2.1. SOFTWARE REQUIREMENTS...........................................................................15 2.2. OPERATING SYSTEM……….............................................................................15 2.3. LANGUAGES……………...................................................................................15 2.4. CLIENT REQUIREMENTS.................................................................................16 3. SCHEDULING……………………………….....................................................17 3.1. PLANNED TIME TABLE ………………………………...........................................17 3.1. Actual TIME TABLE ………………………………................................................18 4. MODELING………..............................................................................................20 4.1. DATA BASE DESIGN …….……………………………............................................20 4.2 Key Methods and relevant Algorithms …...…….............................................22 4.3 State machine for the “metadata” classes.………….……………………................23 5. IMPLEMENTATION...........................................................................................26 5.1 Writing prototypes of each parts of the system based on the requirements ………….……………………................26 5.2 Core techniques …….……………………………...................................................26 6. CONCLUSION, DISSCUSSION AND FUTURE WORK…….......................29 6.1 Design Discussion….……………………………....................................................29 6.2 Key API commands.…………………………….....................................................30 6.3 Architectural Consideration …………………......................................................31 6.4 Testing ………………..……………………….....................................................32 7. CONCLUSION AND FUTURE WOR ............................................................35 7.1. CONCLUSTION.............................................................................................35 7.2. FUTURE WORK ............................................................................................35 8. REFERENCE .......................................................................................................35 8.1. BOOKS................................................................................................................35 8.2. Internet References ........................................................................................... 36 APPENDIX A GANTT CHART...............................................................................37 APPENDIX B USER GUIDE……………................................................................38 2 Acknowledgments During the whole process of my project – Development of Web Scope, my supervisors Dr. Henry Gardner and Dr. Ruju Karia have given me endless help from collecting system requirements, making efficient schedule; and later during the implementation stage, my supervisors gave me the most important technical support and advice. I have received unselfish help from the former project student Ajith Mannanakunnel Jose, he came at his spare time and gave me fully introduction of the former project system, and quite useful technical help. Also, I have to thanks Hugh Fisher who installed the computer which I am working on and the required software for the project. Abstract This report describes the project “Development of Web Scope” of eScience department of the Australian National University. This project is an extension to the work done by the former eScience students Shi Hu in semester1 2005 and Ajith Mannanakunnel Jose in semester2 2005. The main functional goal of the whole project is retrieving the nuclear fusion datasets from the MDSPlus based server and contribute metadata which contains the information of the relevant data retrieved from the sever dynamically back through a web browser. The highlight feature of this project is to use Java Servlets, JSP and Java Hibernate package within the TomCat to generate, save and retrieve metadata dynamically. 3 1 Introduction 1.1 Overview 1.1.1 Background The general idea of doing this whole project is to set up a web based system which can allow user around the globe to retrieve the data from the MDSPlus database through the internet and contribute some metadata based on the retrieved datasets back to the sever side database in order to share the knowledge. The previous project which had been done by students Shi Hu and Ajith Mannanakunnel Jose had already developed the Web Scope which can connect to the MDSPlus server and retrieve datasets from the MDSPlus sever, also cache the retrieved datasets at the client side by using the Java object relational mapping solution “Hibernate”. At present the researchers cannot contribute to the datasets which they have their own opinions or some kinds of suggestions, they can not send metadata back to the server database. Furthermore, different researchers may require creating different forms of metadata based on the original datasets. The project is an attempt to resolve the existing issues with dynamically contributing the metadata back to the MDSPlus server. The highlight of this project is the use of Java object relational mapping solution “Hibernate” together with JAVA Servlets and JSP to solve the dynamically operating metadata issues with current data retrieval system. 1.1.2 Purpose 1.1.2.1 User Side The purpose of doing this project is to enable users to generate, save and retrieve metadata dynamically by using the Web Scope application. 1.1.2.2 Technical Aspect The purpose of doing this project is to enable the attempt of writing, compiling and loading Java class dynamically, and implement Java’s dynamic ability in reality. 1.1.2.3 Reasons The reason for adding these functions to the existing project is : • To allow client to create the format of the metadata which they are going to contribute to the database by themselves, it provides wide freedom to the client. 4 • To change the traditional way of writing and compiling Java classes. • To attempt to load Java classes at runtime by calling the Java class loader. 1.1.3 Target results and project clients 1.1.3.1 Target results The “Development of Web Scope” project has three target results besides several benefits that may flow through. They are: • Allowed client to create metadata table dynamically • Allowed client to save metadata dynamically • Allowed client to retrieve the saved metadata dynamically The above mentioned target outcomes can help the project clients in the following way. Clients can create metadata which are based on the data retrieved from the MDSPlus dynamically by using the dynamic metadata table, the metadata can be shared by the others who review the same node in the MDSPlus, the clients can share useful knowledge from each other by creating or reviewing metadata based on the data from MDSPlus. All clients can contribute metadata as they want and do not need to follow strict format. This would improve the quality of the metadata which was saved to the sever database. 1.1.3.2 Deliverables The project deliverables are mentioned in the table below: Deliverable Due Date Initial Presentation 5th August 2006 Software Demonstration November 2006 Final Presentation November 2006 Source Code Submission November 2006 5 1.1.3.3 Customers The project customers who are ensuring the success of achieving target outcomes are nuclear fusion researchers or scientists from different parts of the globe. 1.1.4 Stakeholders The stakeholders of this project are described below. Stakeholder Name Contact Details Supervisor Mr. Raju Karia rjkaria@smartchat.net.au Supervisor Dr. Henry Gardner Henry.Gardner@anu.edu.au Developer Mr. Le Ma xiaomagetony@yahoo.com.au 6 1.2 Introduction to Hibernate Hibernate is a powerful, high performance object/relational persistence and query service. 1.2.1 Dual – Layer Cache Architecture Hibernate applies Dual-layer Cache Architecture, which means there are two level of cache in Hibernate, the JVM cache and the Session cache. Through these two levels of cache the data caching process become more efficient and faster. This feature was implemented completely by the former student – Ajith. 1.2.2 Transparent Persistence Hibernate can create tables dynamically based on the XML mapping file which contains the information of the class relative to the table and the class file which sets up the content of the table. Also, it allows saving data to the database and retrieves data from the databse. 1.2.3 Query options Hibernate offers plenty of query options, developers can write plain SQL, object- oriented HQL(Hibernate Query Language), programmatic Criteria and example queries. It is quite flexible for developers, and powerful for querying. 1.2.4 Cooperate with Java Servlets Hibernate cooperates with Java Servlets within the Apache TomCat to set up the communication between the client and web server. There would be many Hibernate sessions during one servlets session, the Hibernate session can fulfill user’s one or more action during the specific user service. For example, when user required to set up one table in order to save data into database, the servlets session will collect the user’s information and the relevant web information, and the Hibernate session will set up the table based on the XML mapping file and the class file by being called within the servlet session. 7 1.3 Introduction to MDSPlus 1.3.1 A set of tools MDSPlus is a set of tools for data acquisition and storage. A typical data acquisition cycle might involve: • Initialize o copy model file to shot file o find all the action descriptions and order them into a dispatch table o dispatch all initialization actions • Pulse o fire high-speed timing system which runs experiment and data acquisition hardware • Store o dispatch all store actions o dispatch all analysis actions 1.3.2 A methodology MDSPlus is a methodology for management of complex scientific data. 1.3.3 Data type MDSPlus supports a rich set of primitive and composite data type, The simple data types include signed and unsigned integers (1, 2, 4, 8, and 16 Bytes), single and double precision real numbers, single and double precision complex numbers, and character data. Arrays of these data types with up to 7 dimensions can be represented. The most important composite types include: SIGNALS, which contain data plus associated independent axes (eg. temperature vs space and time); and DEVICES, which are used to associate setup parameters, actions (task descriptions), and data for data acquisition or automated analysis. MDSplus devices provide a well structured mechanism for implementing data driven applications. 1.3.4 Client/Server model A user with appropriate permissions, can access data from an MDSplus server anywhere on the internet. Access is "service" rather than file oriented. Data on remote servers is read directly from within applications, no file transfers are used. 1.3.5 Development The MDSPlus is developed jointly by the Massachusetts Institute of Technology, the Center for Nuclear Resarch (Padua, Italy), and the Los Alamos National Lab, MDSplus is the most widely used system for data management in the magnetic fusion energy program. It is currently installed at over 30 sites spread over 4 continents. 8 1.4 Introduction to Web Scope The “Web Scope” is a new system proposed by my client Raju Karia and supervisor Dr.Henry Gardner. It was first used by the former project student Ajith. The following diagram describes the “Web Scope”. As described in the figure above, the Web Scope is running on a web server – the TomCat, and it maintains the HSQLDB, the Hibernate database. 1.5 Introduction to Java Servlets and JSP Servlets are Java classes run by a Web server which has an interpreter that supports the Java Servlet specification. Java Servlets can used for these purpose: • Collecting user input from a form on a Web page • Receiving information from arguments specified as part of a URL • Running programs on the computer that runs the Web server • Storing and retrieving cookies, files that store a user’s preferences and other information on his computer • Sending data back to a user in the form of an HTML document, GIF graphic, or another format Java Servlets have several advantages in the following aspects: 9 • Proving a standard way to extend web servers to support dynamic content generation • Offering full support for sessions, a way to keep track of a particular user over time as a Web site’s pages are being viewed • Having the same portability as the Java language • Running efficiently in memory Java Servlets work in the following way: When a client makes a request involving a servlet, the server loads and executes the appropriate Java classes. Those classes generate content, and the server sends the content back to the client. The most specific difference to others such as CGI script, is – persistence. Instead of shutting down at the end of each request, the servlet can remain loaded, ready to handle subsequent requests. The lifecycle is : All of these approaches which come from the Java Servlets can be enhanced by JavaServer Pages (JSP). JSP is a way to create Web pages that mix static HTML with the output of servlets and Java expressions. Using JSP, Java code can be placed on Web pages among HTML markup and edited like any other page. 1.6 Introduction to Apache TomCat Apache TomCat is a web container developed at the Apache Software Foundation (ASF). Tomcat implements the servlet and the JavaServer Pages (JSP) specifications from Sun Microsystems, providing an environment for Java code to run in cooperation with a web server. 10 In this project, Apache Tomcat is used as the web container. 1.7 Previous Project 1.7.1 Current Way of Retrieving Data from MDSPlus The researchers use software like “EScope” or “JScope” to connect to the MDSPlus server and retrieve the required data. The major steps involved in this data retrieval process are as follows: • Researchers connect to the MDSPlus server, and requests data sets using client side application called “EScope”. • Based on the “EScope” client’s request the MDSPlus retrieves datasets from its own data storage mechanism. • MDSPlus server sends the retrieved datasets to the “EScope” client. • “EScope” Client displays the datasets as graphs. 1.7.2 Shi Hu’s Project The first attempt of the project was done by student Shi Hu in semester 1, 2005. The whole structure is as below: 11 This system works in the following way: • Data from the MDSPlus server is initially downloaded from the MDSPlus server using an application called “Importer” and stored in the local HSQL database. • An application called “DBserver” is used to serve the requests from the clients (EScope). Based on the client requests the datasets from the HSQL database is returned to the clients. • Using client application called “EScope viewer” a connection is established with the “DB Server“, and retrieves the required dataset from the local database (HSQLDB) associated with it. EScope client plots graphs based on the retrieved datasets. 1.7.3 Ajith’s Project The second attempt of the project was done by previous student Ajith Mannanakunnel Jose, the whole structure is as below: 12 This system works in the following way: • The original data is stored in MDSPlus Server and the retrieved data is stored in HSQLDB for later requirement. • Web Scope is used to serve the requests from the clients. Based on the client requests, it will search from the local database – HSQLDB; if the required data does not exist in the HSQLDB, it will send the requests to the MDSPlus Server and retrieve data back to HSQLDB. • Web Browser is used to show the applications of the system and allow client to input requests and review datasets also with the applets. 13 2 Requirement Analyses 2.1 Software Requirements The main software and other tools used for the development of “Web Scope” are given below. • Jakarta Tom Cat 5.05 • Hibernate3.1 • JDK1.5 • HSQLDB • FireFox (or any Java Applet enabled Web Browser) • Emacs Editor 2.2 Operating System Os Name Version Linux Debian 2.3 Languages 14 2.4 Client Requirements The following table shows the major requirements specified by the client. No. Name Description Priority R1 Using Hibernate The “Web Scope” application should use the benefits of “Hibernate” to efficiently cache the datasets retrieved from MDSPlus. HIGH R2 Using Web Browser Allow users to connect to MDSPlus server and retrieve the required datasets using a web browser. HIGH R3 Dynamically creating metadata table Allow users to create metadata table dynamically based on the specific requirement. HIGH R4 Saving metadata Allow users to save metadata into the HSQLDB. HIGH R5 Viewing metadata Allow users to view all the user contributed metadata. HIGH R6 Platform independence The “Web Scope” application should work from all the major platform. HIGH 15 3 Scheduling 3.1 Planned Time Table The whole project was divided to five different phases and specific time slots were allotted for each of the phases. The following table shows the time table scheduled initially for the project. Phase Date Expected Duration(days) Tasks Notes 1 17 th Jul- 6th Aug 21 9 Understanding requirements 9 Prepare for first presentation z Choose and meet supervisor z Understand requirements z Decide tools and install software on the computer z Study old reports z Make slides for first presentation 2 7th Aug – 27th Aug 21 Modeling z Analyze existing project done by Ajith z Modeling and design architecture for the new project z Learn various software 3 28 th Aug – 8th Oct 48 Implementation z Do coding, Testing and Debugging 4 9 th Oct – 22nd Oct 14 Documentation and final report creation z Complete all documents z Write the final report 5 23rd Oct – 29th Oct 7 Preparation for final presentation z Edit slides for final persentation 16 3.2 Actual Time Table The following table shows the actual time table for the project. Phase Date Expected Duration(days) Tasks Notes 1 17 th Jul- 6th Aug 21 9 Understanding requirements 9 Prepare for first presentation z Choose and meet supervisor z Understand requirements z Decide tools and install software on the computer z Study old reports z Make slides for first presentation 2 7th Aug – 2nd Aug 28 Modeling z Analyze existing project done by Ajith z Modeling and design architecture for the new project z Learn various software 3 3rd Aug – 15th Oct 48 Implementation z Do coding, Testing and Debugging 4 16th Oct – 29th Oct 14 Documentation and final report creation z Complete all documents z Write the final report 5 30 th Oct – 5th Oct 7 Preparation for final presentation z Edit slides for final presentation The major issues faced during the project are described below: • The whole project was divided into two major parts – echo2 and dynamic metadata, and my task is changed from the whole project to the second part – dynamic metadata. 17 • It took one week to set up the project machine (the computer with Linux) and two weeks to get the key of the student project room. So, one week was added to the modeling part, due to the function check and understand. • The project is an extension of previous students’ project, so, it took not much time on the modeling part, but it took long time to understand the function of each part of the system. • Hibernate, Java Servlets and JSP are quite new to me, so it also took time to learn those new techniques during the whole project. • The major issue during the implementation part is that how to find out and use these methods or classes of Hibernate and Java. For example, the Java compiler at runtime, the “Javac.compile()” which is included in the “Method” class of Java package. Also, the usage of the method. 18 4 Modeling 4.1 Database Design The main database structure is inherited from the former project (please refer to appendix A for more information of the database), and the new table which was added to the database are shown below: Table Name Explanation DYNAMICTABLE Store all detail of the table which user dynamically created base on the retrieved datasets. METADATA Store all metadata information contributed by the user based on the retrieved datasets “Hibernate” is used to handle all interactions with the database. The process is as below: 1. create Java persistent classes represent the database tables. 2. map Java classes into the Hibernate mapping file (please refer to the appendix B form more information). 3. Hibernate dynamically creates the tables based on the mapping file, and performs relevant actions, such as save data into database or retrieve data from database. These two new tables are different from the originals because both of them are created dynamically when the application is running. The whole process of creating these tables is as below: 1. user inputs relevant information to the application. 2. Java persistent classes are created and compiled dynamically after the input action. 3. Java persistent classes information is added to the Hibernate mapping file dynamically. 4. Java persistent classes are loaded by the JVM dynamically 19 5. Hibernate dynamically creates the tables. All the tables in the database have an id field as primary key and the values are dynamically generated by the Hibernate package. Because the “DYNAMICTABLE” and “METADATA” table are generated dynamically during the runtime of the application, so they are not exist until user acts the corresponded operations. But once they are created, there are several reference variables are set up into the table, the relationship among these tables are as below: Has a 1 NODE Id: long Experiment: String Shot:int Sever: String Port: int nodePath: String havaGraph: Boolean METADATA Id : long Node : long User : long Dynamic field Due to the “METADATA” table is created dynamically, and the variables which will be involved into the table are unknown, so we just put the “Dynamic field” into the table to refer to these variables. Also, this is the exact way we try to satisfy every user, and to let users to contribute the metadata in the way they want. 0 .. * Linked to 0 .. * Linked to Has a 1 USERS Id: long Institution:String Address: String Email: String Password: String Education: String 20 4.2 Key Methods and relevant Algorithms Java ClassLoader Class loaders are a powerful mechanism for dynamically loading software components on the Java platform. Class loaders existed in the first version of the Java Development Kit (JDK 1.0). The original purpose was to enable applet class loading in the HotJava browser. Since that time, the use of class loaders has been extended to handle wider range of software components. The purpose of using class loaders is to support dynamically loading of software components on the Java platform. The unit of software distribution is a class. Classes are distributed using a machine-independent, standard, binary representation known as the class file format (such as metadata.class of this project). Class files are produced by Java compilers, and can be loaded into any Java virtual machine. The Java virtual machine executes the byte code stored in class file. In this project, most of class files were produced by the Java compilers before the web scope was running. It means that Java files were created by programming code, and then were compiled manually by using the command line (such as Javac ..). After that, the class files were produced and then were put into the location of Aapach TomCat. When the web scope application is running, the class files can be loaded automatically. However, those class files which were produced dynamically during the application can not be loaded by the Java virtual machine automatically. So, we need call the class loader to load those classes to be used by the application. The method of loading classes is ClassLoader.loadClass(), it is the entry point to the ClassLoader. Its signature is as follows: Class loadClass(String name, Boolean resolve); The “name” parameter specifies the name of the class that the Java virtual machine needs. 21 The “resolve” parameter tells the method whether or not the class needs to be resolved. It is a flag to tell the class loader that classes referenced by this class name should be resolved (that is, any referenced classes should be loaded as well)or not. 4.3 State machine for the “metadata” classes The “metadata” classes were produced dynamically during the web scope running time, they were created by users, and they would contain the information of the metadata which users want to contribute to the database based on the current datasets they were retrieving. The state machine of these classes are as follow: Note: because the class name is defined by different users, so we can not give the exact name of the class, we use “newMetaData” to refer to the class. 22 1. Creating Java file fielName= = Tablename; loop for (i=0; i"+makeJavaScript(colNumber)+""+title+"

"+title+"

"+mainMessage+"

"+makeHtml Table(colNumber)+"

"+footerMessage+"

"; All of these code was keep in one line, it is like writing the HTML document to generate a web site. The reason for me to do this is that the original project was applying these code to generate the relevant application, and this project as I mentioned was include two sub project, another student ZhongShan Tan was using ECHO2 to rewrite the original one. So it could be a further work for later student to combine these two project together and to avoid this problem. 6.2 Key API commands 1. Java compiler The Javac compiler is stored in the tool.jar library found in the lib/ directory of the JDK. An application can access the Javac compiler programmatically. It is quite similar as the command line of Javac compiler. The com.sun.tools.Javac.Main is the main entry point. The following code shows the process of using Javac. 29 private static com.sun.tools.Javac.Main Javac = new com.sun.tools.Javac.Main(); String filePath="/usr/share/www/tomcat/webapps/WebScope/WEB- INF/classes/databaseAccessDomain/"; String [] arg=new String[]{filePath+tableName+".Java"}; int state=Javac.compile(arg); 2. Java classLoader I have told lots about the Java classloader previously, here I just give an example of how to use it in action. try { URL url = file.toURL(); URL[] urls = new URL[]{url}; ClassLoader cl=new URLClassLoader(urls); Class c=cl.loadClass(tableName+".class"); Object t=c.newInstance(); }catch (InstantiationException e) 3. Servlet Java servlet is used to control the communication between the user and the server through the web applications. The following code shows the process of one kind of communication which send the sever’s name and port number to the server to make the connection. public void doGet(HttpServletRequest req,HttpServletResponse res)throws IOException,ServletException{ try{ req1=req; webServerName=req.getServerName(); webServerPort=req.getServerPort(); urlSuffix="/WebScope/SaveNewTable"; status=req.getParameter("status"); … 4. Hibernate schema Hibernate can create database tables based on the xml mapping file and the relevant classes. One major thing is to create a schema before any data 30 transformation. I was really struggle with it. Here is a whole progress of saving data to table using Hibernate. try{ Transaction transaction=hsession.beginTransaction(); metaInfo=new MetaDataInfo(); conf= new Configuration(); schema= new SchemaExport(conf); schema.create(true,true); logRef=(LogInfo)session.getAttribute("storedLogInfoObject"); metaInfo.setSessionStart(new Date()); metaInfo.setMetaDataName(metaName); metaInfo.setMetaDataValue(metaValue); metaInfo.setMetaExplanation(metaExplanation); metaInfo.setMetaKeyword(metaKeyword); metaInfo.setLog(logRef); metaInfo.setUser(user); metaInfo.setNode(node); hsession.save(metaInfo); hsession.flush(); transaction.commit(); }catch(Exception e) 6.3 Architectural Consideration The proxy object is an object that implements exactly the same interface as the real object and can be used anywhere the real object is expected. In my project, I use the proxy pattern for the dynamic classes which are created during the runtime based on client’s input. The structure of the proxy pattern is as below: 31 Different tables will be created based on client’s different inputs, but only one proxy class is used as the interface to the realtables. The proxy is used to make modifications to a dynamic class transparent to its caller. The process of using proxy to up-to-date class to its caller is as below: 6.4 Testing Here the Proxy is a class functioning as a dynamic class’s access interface. The link between the proxy and the dynamic class should updated when the dynamic class reloads or new dynamic class is created. 6.4 Testing Functional testing is used in this project, all details are as below: 1. Dynamic Java file creation. In this project, when user inputs the required table name which is the dynamic Java file name, and the column number and names which are the methods involved in the Java file also the element of the dynamic table. When user clicks the “submit” button in the “Dynamic Table Creation” form, the dynamic Java file should be created and save under the folder Client <> DynamicTable +request() Proxy +request() RealTable +request() 4. return 3. return 1. invoke 2.forward invocation Client Proxy DynamicCla ss 32 “~/webapps/WebScope/WEB-INF/classes/databaseAccessDomain/” and the file should be a legal Java file which can be compiled later. 2. Dynamic XML file creation and compilation. Together with the dynamic Java file generation, a dynamic XML file named “Dynamic.hbm.xml” should be created at the same time as the Java file, under the folder “~/www/tomcat/webapps/WebScope/WEB-INF/classes/”, it should be a legal XML file which can used by Hibernate to mapping the classes with the database tables. 33 3. Dynamic Java file compilation When user creates a new Java file, the system should allow user to compile the Java file in order to input data and save them to the database. When user click the button “Submit Meta Data” in the form of “”, the Java file which created previously should be compiled and the Class file should be created and saved at the same location as the Java file. 34 7. Conclusion and Future work 7.1 Conclusion 1. Learned how the Hibernate and Servlet & JSP cooperate with each other within the Apache TomCat. 2. Learned the dynamic ability of Java. It involves the runtime code compilation and the runtime class loading. 3. Using software design patter in reality programming. The proxy design pattern is applied to the dynamic classes. 4. One of the hard part of completing the project is to understand and the reconfiguration of the previous project. 5. Understand the Servlets session and Hibernate session is another hard issue during the development of the whole project. 7.2 Future work 1. Implementation of a metadata index based search engine which can help searching the datasets with specific features from the database. Such as allow client to search the metadata according to particular date. 2. Implementation of different privileges log on for the current system. For example, the system administrator can view the details of all the users and set up the relevant access power. 3. Combine the current system with ZhongShan Tan’s project.(the other student of the project, who works on the echo2) 8. Reference 8.1 Books 1. “Hibernate in Action” by Christian Bauer and Gavin King .Published by Manning Publications. co 2. “Core Java 2, Volume 1” by Cay S, Gary Cornell. Published by Sun Microsystems 3. "The Core Web Programming”. Published by Sun Microsystems. This book was the Bible for me during the whole development process 35 4. "The Complete Java Reference" by Schmidt, published by McGraw Hill 5. "Java Examples in a Nutshell" by Flanagan, published by O'REILLY 6. "Using the Hibernate Package for Caching the MDSPlus Data", the final report for the COMP6703 eScience Project (Semester1, 2005) course, by Shi Hu. 7. "Development of Web Scope", the final report for the COMP6703 eScience Project (Semester2, 2005) course, by Ajith Mannanakunnel Jose. 8. The Study brick, provided as a part of the course "Networked and Scientific Data Presentation",COMP6442 8.2 Internet References 1. http://www.mdsplus.org/ Gives details about the MDSPlus server. 2. http://www.Hibernate.org/ Gives all the required information about the Hibernate software package. 3. http://www. jakarta.apache.org/tomcat/ Gives information about setting up/running the Jakarta tomcat server 4. http://Java.sun.com/applets/ gives the details about Java applets 5. http://Java.sun.com/docs/books/tutorial/applet/practical/gui.html Gives the details about Java applets 6. http://Java.sun.com/j2se/1.5.0/docs/api/Java/applet/Applet.html Gives the details about Java applets 36 7. http://kr.fujitsu.com/products/solutions/ebiz_platform/was/technical/tutorial/web/kiso/ kiso01.html Gives details about synchronizing the data transfer from servlets to applets 8. http://jdj.sys-con.com/read/36044.htm Gives information about the Java object serialization 9. http://www.htmlhelp.com/ Gives a lot of information regarding the various html syntax –suggested for expert users 10. http://www.w3.org/ The website gives clear idea about the various web designing standards. 11. http://www.w3schools.com/js/tryit.asp?filename=tryjs_function2 Describes how to pass variables to a Java script function 12. http://www.w3schools.com/js/js_functions.asp Gives valuable information about the JavaScript functions 13. http://www.htmlcodetutorial.com/ Provides valuable information regarding various HTML and XHTML syntaxes 14. http://www.groan-zone.net/jscript.html A good source of information regarding the Java scripts 15. http://mindprod.com/jgloss/volatile.html Provides information about various Java keywords 16. "Remote server communication and application delivery" by Alan Newman, Revision 1.0, December 2004.(a journal , http://www.symbian.com) 17. http://prl.anu.edu.au/H-1NF Information regarding the H1-NF plasma experiment at ANU 37 APPENDIX A GANTT CHART 38 APPENDIX B Note: the following user guide is modified slightly from the previous student Ajith’s report. Installation Guide A) Prerequisites: The “Web Scope” application requires the JDK and Tom Cat running on the target machine prior to its installation. The various steps involved in the installation of Tomcat and JRE are explained below as on the web site of Tomcat [3]: I) Requires JRE 5.0 or later versions • Download the Java 2 Standard Edition Runtime Environment (JRE), release version 5.0 or later, from http://Java.sun.com/j2se. • Install the JRE according to the instructions included with the release. • Set an environment variable named JAVA_HOME to the pathname of the directory into which the JRE is installed, e.g. c:\j2sdk5.0 (Windows) or /usr/local/Java/j2sdk5.0 (Unix). II) Requires the TomCat5.05 or Later • Download the Tomcat version 5.05 or later from http://jakarta.apache.org/site/downloads/. • Unzip the tomcat to the required location (e.g.: unzip jakarta-tomcat-5.zip), so that the distribution resides in its own directory (conventionally named "jakarta-tomcat-5"). For the purposes of the remainder of this document, the symbolic name "$CATALINA_HOME" is used to refer to the full pathname 39 of the release directory. To run the Tomcat: Tomcat can be started by executing the following commands: $CATALINA_HOME\bin\startup.bat (Windows) $CATALINA_HOME/bin/startup.sh (Unix) After startup, the default web applications included with Tomcat will be available by visiting: http://localhost:8080/ To Shut Down the Tomcat: Tomcat can be shut down by executing the following command: $CATALINA_HOME\bin\shutdown (Windows) $CATALINA_HOME/bin/shutdown.sh (Unix) B) Installation of Web Scope: The following table shows the organization of the various files in the “WebScope” distribution folder: File Name Path “Web Scope” source code WebScope/Src “Web Scope” setup WebScope/Setup Applet classes WebScope/graphApplet/classes Applet source code WebScope/graphApplet/src The various steps involved in the installation of “Web Scope” are explained below: 1. Placing “Web Scope” on Tomcat 40 • Copy the file “WebScope.war “ which is supplied along with the WebScope distribution package (WebScope/Setup/WebScope.war or WebScope\Setup\WebScope.war ) to the “webapps” folder of the Tomcat root directory ($CATALINA_HOME/webapps/ or $CATALINA_HOME\webapps\) Command: cp WebScope.war $CATALINA_HOME/webapps/ (Unix) copy WebScop.war $CATALINA_HOME\webapps\ (Windows) 2. Running the database (HSQLDB) • Prior to running the database, move to the location where the database is to be placed. Go to the folder: $CATALINA_HOME /webapps/WebScope/WEB-INF/classes/ (Unix) $CATALINA_HOME\webapps\WebScope\WEB-INF\classes\ (Windows) Run the database: Command: Java –Xmx1024m -cp $CATALINA_HOME/webapps/WebScope/WEB- INF/lib/hsqldb.jar org.hsqldb.Server -database.0 hdb -dbname.0 hdb (Unix) Java –Xmx1024m -cp $CATALINA_HOME\webapps\WebScope\WEB- INF\lib\hsqldb.jar org.hsqldb.Server -database.0 hdb -dbname.0 hdb (Windows) 3. Placing the Applet classes into the Tomcat • Copy the “.class” files of the “graphApplet/classes/” folder 41 (WebScope/graphApplet/classes ) to the folder “WebScope” ($CATALINA_HOME/webapps/WebScope/) Go to the following folder in the provided “WebScope” setup file: ~/WebScope/graphApplet/classes/ (Unix) C:\WebScope\graphApplet\classes\ (Windows) Commands: i) cp *.class $CATALINA_HOME/webapps/WebScope/ cp databaseAccessDomain $CATALINA_HOME/webapps/WebScope/ (Unix) ii) copy *.class $CATALINA_HOME\webapps\ WebScope\ copy databaseAccessDomain $CATALINA_HOME\webapps\ WebScope\ (Windows) User’s Guide This is the user’s guide associated with the final report of ‘Development of Web Scope’. It gives a brief idea to the users about the usage of ‘Web Scope’ application. This guide is divided into two sections • Using Web Scope • Setting up the Web Scope from the supplied distribution package (WebScope.zip) I) Using Web Scope 1. How to get into Web Scope? 42 Web Scope runs within the Tomcat web server. So the users need to connect to the Web Scope through a web browser. The following steps have to be done to get into the Web Scope. a) Open a web browser (it should have the right plug-in to run the Applets ) b) Use the URL http://localhost:8080/WebScope/login in the address bar (Instead of the “localhost” you can give the name of the machine on which the Tomcat is running. e.g. http://esci15:8080/WebScope/login ) Now you must be seeing the “Login Page”, like the one shown below: The users need to provide their user id and password in the fields provided to start using the “Web Scope” application. If you are a new user to the Web Scope application, need to go through a registration process to get the user id and Password. The new user registration process can be started by clicking the link “Click here to register”. 2. What to do during the registration with Web Scope? This process is included in “Web Scope” to collect the details of the users. It is a very simple process as the user just needs to fill the fields with their details. It is mandatory to fill all the fields provided, otherwise users won’t be able to complete the registration process. 43 The following picture shows the New User Registration page. 3. How to view all the available Nodes in a specific location? How to download a Node? Viewing all Nodes in a specific location Users need to specify the server name, the port number, experiment name and the shot number to view the list of nodes in that location. Following figure shows the “Connect to MDSPlus server” page. 44 User just need to specify the necessary details in the fields provided and click the connect button to view all the available nodes in a specific location. Otherwise they can use the default field values. Once the user presses the connect button, the user will be taken to a page which shows all the retrieved nodes in a List Box. The following figure shows a web page with all the retrieved nodes from a specific location. 45 Downloading a specific Node User need to select the required node from the List box shown in the figure above and click the ‘Download’ button to download the specific node data. The downloaded node data can be plotted as graphs or as data tables. The following figure shows a web page plotting the downloaded node data as a graph. 46 The following figure shows a web page showing the downloaded node data as a table. 4. How to contribute Meta Data to Web Scope? 47 4.1 static way User can contribute a metadata to the ‘Web Scope’, based on the node that the user downloaded. Users can define a name, value, explanation and keyword to the metadata that they are contributing. After filling all the fields they just need to click the ‘Submit Metadata’ button. The following figure shows the section for contributing metadata to the Web Scope. 4.2 Dynamic way User can contribute the Metadata dynamically back to the database. Step1. Fulfilling the table form with table name and the column number of the table. 48 Step2. Input the columns names and the Data type it will contain. Step3.Input the metadata value respect to the columns. 49 Step4. System messge. II) Setting up the Web Scope Unzip the distribution package Unzip the distribution package (‘WebScope.zip’) to the home directory. After unzipping the package you will see the following folders inside the ‘WebScope’ folder: You will be seeing three folders at present: + src ( Contains the source code of Web Scope ) - databaseAccessDomain - mdsServerAccessDomain - webScopeDomain + setup ( Contains a 'WebScope.war' file, which is to be moved to the Tomcat and a 'WEB-INF' folder, from which the .war file is made ) - WebScope.war - 'WEB-INF' + graphApplet ( Contains the source code and class files of the applet required to plot the graphs ) -classes -src 50 What is Next? 1) I Want to Run Web Scope application and see how it works? 2) I want to compile the various source files of Web Scope? Note: for the rest of this document $CATALINA_HOME refers to the full path name of Tomcat directory To Run the Web Scope Application: Step1: Start the Tomcat web server Command: $CATALINA_HOME/bin/startup.sh (Unix) $CATALINA_HOME/bin/startup.bat (Windows) (For detailed explanation about the installation of Tomcat see Appendix C of the report "Development of Web Scope") Step2: Copy or move the WebScope.war file to Tomcat Go to the setup folder inside the distribution package of WebScope: (WebScope/setup/) Command: cp WebScope.war $CATALINA_HOME/webapps/ (Unix) copy WebScope.war $CATALINA_HOME\webapps\ (Windows) Step3: Start the database Go to the classes folder in the Tomcat: ($CATALINA_HOME/webapps/WebScope/WEB-INF/classes) Command: java –Xmx1024m -cp $CATALINA_HOME/webapps/WebScope/WEB- INF/lib/hsqldb.jar org.hsqldb.Server -database.0 hdb -dbname.0 hdb (Unix) Step4: Copy or move the applet class files to the Tomcat Go to the ‘graphApplet/classes’ folder inside the distribution package of WebScope:(WebScope/graphApplet/classes) Command: cp *.class $CATALINA_HOME/webapps/WebScope/ cp databaseAccessDomain $CATALINA_HOME/webapps/WebScope/ (Unix) copy *.class $CATALINA_HOME\webapps\WebScope\ copy databaseAccessDomain $CATALINA_HOME\webapps\WebScope\ 51 (Windows) Step5: Now the Web Scope is ready and running Open your web browser (preferably the FireFox or any other with the plug- in for showing applets) Type the following command to the URL bar of the web browser: "http://localhost:8080/WebScope/login" Or You can specify the name of machine on which the Tomcat is running (if you are trying to access the web scope from a different machine) e.g.: "http://esci15:8080/WebScope/login" To Compile The various Source Files, supplied along with the Web Scope Distribution Package: Step1: Compiling the source files of folder ‘WebScope/src’ Go to the "src" folder (WebScope/src/) Choose the file which you want to compile (no need to compile the files of databaseAccessDomain) Command: Example for compiling classes in the ‘mdsServerAccessDomain’ javac -d ~/WebScope/setup/WEB-INF/classes/ -classpath $CATALINA_HOME/common/lib/servlet-api.jar:~/WebScope/setup/WEB- INF/lib/hibernate3.jar/:. mdsServerAccessDomain/MDSServerConnect.java Example for compiling classes in the ‘webScopeDomain’ javac -d ~/WebScope/setup/WEB-INF/classes/ -classpath $CATALINA_HOME/common/lib/servlet-api.jar:~/WebScope/setup/WEB- INF/lib/hibernate3.jar/:. webScopDomain/SaveMetaDataInfo.java Note: you might have to provide the full path '/home/users/u4083453/' for the home directory, instead of '~/' so that the command might look like the one below: javac -d /home/users/u4083453/WebScope/setup/WEB-INF/classes/ - classpath /home/users/u4083453/apache-tomcat-5.5.12/common/lib/servlet- api.jar:/home/users/u4083453/WebScope/setup/WEB-INF/lib/hibernate3.jar/:. mdsServerAccessDomain/DBDataRetriver.java Step2: Making the WebScope.war file Go to the "setup" folder (WebScope/setup/) Command: 52 jar cvMf WebScope.war WEB-INF/ Step3: Compiling the source files of graph applet (WebScope/graphApplet/src) Go to the "src" folder (WebScope/graphApplet/src/) Command: javac -d WebScope/graphApplet/classes/ RetreiveMainFrame.java 53