Wisconsin Herbarium on Java in Tomcat README This file discusses how to deploy Wisconsin Herbarium Java application. See the Java source code. This code works with the same MySQL database that the production Perl application works with. Note that the Java version has an extremely minimal "view" with bare and basic HTML. The routine to generate the ASN (accepted species name) does (I think) work properly. ############################################################################## installing UW Herbarium onto tomcat ############################################################################## 1. Install ubuntu, and run sudo apt-get update a few times. 2. Install java and tomcat as describe below. 3. Install all of the source code files under tomcat's directory /usr/share/tomcat5.5/webapps 4. Get into webapps/code/BotStuff and compile all code like this: javac -d classes src/edu/wisc/botany/util/Species.java javac -d classes src/edu/wisc/botany/util/Specimen.java javac -d classes src/edu/wisc/botany/util/Taxon.java javac -d classes src/edu/wisc/botany/web/BotServlet.java javac -d classes src/edu/wisc/botany/web/CommonServlet.java javac -d classes src/edu/wisc/botany/web/GenusServlet.java javac -d classes src/edu/wisc/botany/web/SearchSpecimenServlet.java javac -d classes src/edu/wisc/botany/web/DetailServlet.java javac -d classes src/edu/wisc/botany/web/SearchResultsServlet.java javac -d classes src/edu/wisc/botany/web/SpecimenServlet.java javac -d classes src/edu/wisc/botany/web/FamilyServlet.java javac -d classes src/edu/wisc/botany/model/JdbcConnTest.java javac -d classes src/edu/wisc/botany/model/JdbcConn.java javac -d classes src/edu/wisc/botany/model/JdbcTest.java 5. make dir /usr/share/tomcat5.5/webapps/BotStuff/WEB-INF/ 6. Get into webapps/code/BotStuff and copy all the classes like this: tar -cf - ./classes/|(cd ../../BotStuff/WEB-INF/; tar -xf -) 7. Install the DD lines below (in the next entry) into this file: /usr/share/tomcat5.5/webapps/code/BotStuff/WEB-INF/web.xml 8. restart tomcat like this: /etc/init.d/tomcat5.5 restart 9. Visit this location to test operation: http://127.0.0.1:8180/BotStuff/ http://127.0.0.1/BotStuff/ ############################################################################## web.xml data ############################################################################## root@www:/# cat /usr/share/tomcat5.5/webapps/BotStuff/WEB-INF/web.xml <web-app xmlns="http://java.sun.com/xml/ns/j2ee" version="2.4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http:/java.sun.com/dtd/web-app_2_3.dtd"> <servlet> <servlet-name>botservlet</servlet-name> <servlet-class>edu.wisc.botany.web.BotServlet</servlet-class> </servlet> <servlet-mapping> <servlet-name>botservlet</servlet-name> <url-pattern>/botservlet</url-pattern> </servlet-mapping> <servlet> <servlet-name>varlogmessagesservlet</servlet-name> <servlet-class>edu.wisc.botany.web.VarLogMessagesServlet</servlet-class> </servlet> <servlet-mapping> <servlet-name>varlogmessagesservlet</servlet-name> <url-pattern>/varlogmessagesservlet</url-pattern> </servlet-mapping> <servlet> <servlet-name>varlogapache2accessservlet</servlet-name> <servlet-class>edu.wisc.botany.web.VarLogApache2AccessServlet</servlet-class> </servlet> <servlet-mapping> <servlet-name>varlogapache2accessservlet</servlet-name> <url-pattern>/varlogapache2accessservlet</url-pattern> </servlet-mapping> <servlet> <servlet-name>varlogapache2errorservlet</servlet-name> <servlet-class>edu.wisc.botany.web.VarLogApache2ErrorServlet</servlet-class> </servlet> <servlet-mapping> <servlet-name>varlogapache2errorservlet</servlet-name> <url-pattern>/varlogapache2errorservlet</url-pattern> </servlet-mapping> <servlet> <servlet-name>varlogmysqlmysqlservlet</servlet-name> <servlet-class>edu.wisc.botany.web.VarLogMysqlMysqlServlet</servlet-class> </servlet> <servlet-mapping> <servlet-name>varlogmysqlmysqlservlet</servlet-name> <url-pattern>/varlogmysqlmysqlservlet</url-pattern> </servlet-mapping> <servlet> <servlet-name>pdfservlet</servlet-name> <servlet-class>edu.wisc.botany.web.PdfServlet</servlet-class> </servlet> <servlet-mapping> <servlet-name>pdfservlet</servlet-name> <url-pattern>/pdfservlet</url-pattern> </servlet-mapping> <servlet> <servlet-name>commonservlet</servlet-name> <servlet-class>edu.wisc.botany.web.CommonServlet</servlet-class> </servlet> <servlet-mapping> <servlet-name>commonservlet</servlet-name> <url-pattern>/commonservlet</url-pattern> </servlet-mapping> <servlet> <servlet-name>spdetailservlettwo</servlet-name> <servlet-class>edu.wisc.botany.web.SpdetailServletTwo</servlet-class> </servlet> <servlet-mapping> <servlet-name>spdetailservlettwo</servlet-name> <url-pattern>/spdetailservlettwo</url-pattern> </servlet-mapping> <servlet> <servlet-name>searchresultsservlet</servlet-name> <servlet-class>edu.wisc.botany.web.SearchResultsServlet</servlet-class> </servlet> <servlet-mapping> <servlet-name>searchresultsservlet</servlet-name> <url-pattern>/searchresultsservlet</url-pattern> </servlet-mapping> <servlet> <servlet-name>familyservlet</servlet-name> <servlet-class>edu.wisc.botany.web.FamilyServlet</servlet-class> </servlet> <servlet-mapping> <servlet-name>familyservlet</servlet-name> <url-pattern>/familyservlet</url-pattern> </servlet-mapping> <servlet> <servlet-name>genusservlet</servlet-name> <servlet-class>edu.wisc.botany.web.GenusServlet</servlet-class> </servlet> <servlet-mapping> <servlet-name>genusservlet</servlet-name> <url-pattern>/genusservlet</url-pattern> </servlet-mapping> <servlet> <servlet-name>detailservlet</servlet-name> <servlet-class>edu.wisc.botany.web.DetailServlet</servlet-class> </servlet> <servlet-mapping> <servlet-name>detailservlet</servlet-name> <url-pattern>/detailservlet</url-pattern> </servlet-mapping> <servlet> <servlet-name>searchspecimenservlet</servlet-name> <servlet-class>edu.wisc.botany.web.SearchSpecimenServlet</servlet-class> </servlet> <servlet-mapping> <servlet-name>searchspecimenservlet</servlet-name> <url-pattern>/searchspecimenservlet</url-pattern> </servlet-mapping> <servlet> <servlet-name>specimenservlet</servlet-name> <servlet-class>edu.wisc.botany.web.SpecimenServlet</servlet-class> </servlet> <servlet-mapping> <servlet-name>specimenservlet</servlet-name> <url-pattern>/specimenservlet</url-pattern> </servlet-mapping> </web-app> ############################################################################## install java on ubuntu ############################################################################## root@www:~# which java root@www:~# apt-get install sun-java6-bin sun-java6-jre sun-java6-jdk Reading package lists... Done Building dependency tree Reading state information... Done The following extra packages will be installed: java-common odbcinst1debian1 unixodbc Suggested packages: equivs binfmt-support openjdk-6-doc sun-java6-demo sun-java6-source sun-java6-fonts sun-java6-plugin ia32-sun-java6-plugin ttf-baekmuk ttf-unfonts ttf-unfonts-core ttf-kochi-gothic ttf-sazanami-gothic ttf-kochi-mincho ttf-sazanami-mincho ttf-wqy-zenhei libct1 libmyodbc odbc-postgresql Recommended packages: libasound2 libnss-mdns libxtst6 gsfonts-x11 The following NEW packages will be installed: java-common odbcinst1debian1 sun-java6-bin sun-java6-jdk sun-java6-jre unixodbc 0 upgraded, 6 newly installed, 0 to remove and 43 not upgraded. Need to get 54.5MB of archives. After this operation, 161MB of additional disk space will be used. ############################################################################## install tomcat-webapps ############################################################################## root@www:~# apt-get install tomcat5.5-webapps Reading package lists... Done Building dependency tree Reading state information... Done The following extra packages will be installed: ant jsvc libbcel-java libcommons-beanutils-java libcommons-collections-java libcommons-collections3-java libcommons-daemon-java libcommons-dbcp-java libcommons-digester-java libcommons-el-java libcommons-launcher-java libcommons-logging-java libcommons-modeler-java libcommons-pool-java libecj-java libjaxp1.3-java liblog4j1.2-java libmx4j-java libregexp-java libservlet2.3-java libservlet2.4-java libtomcat5.5-java libxerces2-java tomcat5.5 Suggested packages: ant-doc libbcel-java-doc libcommons-beanutils-java-doc libcommons-collections3-java-doc liblogkit-java libavalon-framework-java classpath-doc ecj libgnumail-java jython libservlet2.4-java-gcj libxerces2-java-doc libapache2-mod-jk tomcat5.5-admin Recommended packages: ant-optional ant-gcj libecj-java-gcj libjaxp1.3-java-gcj liblog4j1.2-java-gcj libxerces2-java-gcj The following NEW packages will be installed: ant jsvc libbcel-java libcommons-beanutils-java libcommons-collections-java libcommons-collections3-java libcommons-daemon-java libcommons-dbcp-java libcommons-digester-java libcommons-el-java libcommons-launcher-java libcommons-logging-java libcommons-modeler-java libcommons-pool-java libecj-java libjaxp1.3-java liblog4j1.2-java libmx4j-java libregexp-java libservlet2.3-java libservlet2.4-java libtomcat5.5-java libxerces2-java tomcat5.5 tomcat5.5-webapps ############################################################################## tomcat-webapps installed tomcat5.5 ############################################################################## root@www:~# apt-get install tomcat5.5 Reading package lists... Done Building dependency tree Reading state information... Done tomcat5.5 is already the newest version. tomcat5.5 set to manually installed. 0 upgraded, 0 newly installed, 0 to remove and 43 not upgraded. ############################################################################## checkout where it listens: ############################################################################## root@www:~# netstat -tan Active Internet connections (servers and established) Proto Recv-Q Send-Q Local Address Foreign Address State tcp 0 0 0.0.0.0:993 0.0.0.0:* LISTEN tcp 0 0 0.0.0.0:995 0.0.0.0:* LISTEN tcp 0 0 127.0.0.1:3306 0.0.0.0:* LISTEN tcp 0 0 0.0.0.0:139 0.0.0.0:* LISTEN tcp 0 0 0.0.0.0:110 0.0.0.0:* LISTEN tcp 0 0 0.0.0.0:143 0.0.0.0:* LISTEN tcp 0 0 0.0.0.0:80 0.0.0.0:* LISTEN tcp 0 0 127.0.0.1:53 0.0.0.0:* LISTEN tcp 0 0 127.0.0.1:53 0.0.0.0:* LISTEN tcp 0 0 0.0.0.0:25 0.0.0.0:* LISTEN tcp 0 0 127.0.0.1:953 0.0.0.0:* LISTEN tcp 0 0 0.0.0.0:445 0.0.0.0:* LISTEN tcp6 0 0 :::8009 :::* LISTEN tcp6 0 0 :::8180 :::* LISTEN tcp6 0 0 :::22 :::* LISTEN tcp6 0 0 ::1:953 :::* LISTEN ############################################################################## exercise tomcat start and stop: ############################################################################## root@www:~# /etc/init.d/tomcat5.5 start * Starting Tomcat servlet engine tomcat5.5 ...done. root@www:~# /etc/init.d/tomcat5.5 stop * Stopping Tomcat servlet engine tomcat5.5 ...done. root@www:~# /etc/init.d/tomcat5.5 restart * Starting Tomcat servlet engine tomcat5.5 ...done. root@www:~# cd /usr/share/tomcat5.5 ############################################################################## see the big mess of links in tomcat5.5. from ubuntu ############################################################################## root@www:~# cd /usr/share/tomcat5.5 root@www:/usr/share/tomcat5.5# ls -lh total 12K drwxr-xr-x 2 root root 4.0K 2010-05-01 10:03 bin drwxr-xr-x 6 root root 4.0K 2010-05-01 10:03 common lrwxrwxrwx 1 root root 14 2010-05-01 10:03 conf -> /etc/tomcat5.5 lrwxrwxrwx 1 root root 16 2010-05-01 10:03 doc -> ../doc/tomcat5.5 lrwxrwxrwx 1 root root 23 2010-05-01 10:03 logs -> /var/lib/tomcat5.5/logs drwxr-xr-x 4 root root 4.0K 2010-05-01 10:03 server lrwxrwxrwx 1 root root 25 2010-05-01 10:03 shared -> /var/lib/tomcat5.5/shared lrwxrwxrwx 1 root root 23 2010-05-01 10:03 temp -> /var/lib/tomcat5.5/temp lrwxrwxrwx 1 root root 26 2010-05-01 10:03 webapps -> /var/lib/tomcat5.5/webapps lrwxrwxrwx 1 root root 23 2010-05-01 10:03 work -> /var/lib/tomcat5.5/work root@www:/usr/share/tomcat5.5# ############################################################################## setup tomcat build and develop path...all code and class files under webapps ############################################################################## root@www:/var/lib/tomcat5.5# cd webapps/ root@www:/var/lib/tomcat5.5/webapps# ls root@www:/var/lib/tomcat5.5/webapps# mkdir BotStuff root@www:/var/lib/tomcat5.5/webapps# cd !$ cd BotStuff root@www:/var/lib/tomcat5.5/webapps/BotStuff# mkdir WEB-INF root@www:/var/lib/tomcat5.5/webapps/BotStuff# cd !$ cd WEB-INF root@www:/var/lib/tomcat5.5/webapps/BotStuff/WEB-INF# mkdir classes root@www:/var/lib/tomcat5.5/webapps/BotStuff/WEB-INF# mkdir lib root@www:/var/lib/tomcat5.5/webapps/BotStuff/WEB-INF# mkdir classes/edu/ root@www:/var/lib/tomcat5.5/webapps/BotStuff/WEB-INF# mkdir classes/edu/wisc/ root@www:/var/lib/tomcat5.5/webapps/BotStuff/WEB-INF# mkdir classes/edu/wisc/botany/ root@www:/var/lib/tomcat5.5/webapps/BotStuff/WEB-INF# mkdir classes/edu/wisc/botany/web/ root@www:/var/lib/tomcat5.5/webapps/BotStuff/WEB-INF# mkdir classes/edu/wisc/botany/model/ root@www:/var/lib/tomcat5.5/webapps/BotStuff/WEB-INF# mkdir classes/edu/wisc/botany/util/ root@www:/var/lib/tomcat5.5/webapps/BotStuff/WEB-INF# cd ../ root@www:/var/lib/tomcat5.5/webapps/BotStuff# cd ./ root@www:/var/lib/tomcat5.5/webapps/BotStuff# cd .. root@www:/var/lib/tomcat5.5/webapps# ls BotStuff root@www:/var/lib/tomcat5.5/webapps# mkdir code root@www:/var/lib/tomcat5.5/webapps# cd code/ root@www:/var/lib/tomcat5.5/webapps/code# ls root@www:/var/lib/tomcat5.5/webapps/code# mkdir edu root@www:/var/lib/tomcat5.5/webapps/code# rmdir edu/ root@www:/var/lib/tomcat5.5/webapps/code# mkdir BotStuff root@www:/var/lib/tomcat5.5/webapps/code# cd !$ cd BotStuff root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# mkdir etc root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# mkdir lib root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# mkdir src root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# mkdir classes root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# mkdir web root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# cd src/ root@www:/var/lib/tomcat5.5/webapps/code/BotStuff/src# ls root@www:/var/lib/tomcat5.5/webapps/code/BotStuff/src# mkdir edu root@www:/var/lib/tomcat5.5/webapps/code/BotStuff/src# mkdir edu/wisc root@www:/var/lib/tomcat5.5/webapps/code/BotStuff/src# mkdir edu/wisc/botany root@www:/var/lib/tomcat5.5/webapps/code/BotStuff/src# ############################################################################## setup classpath at login time, notice the last two lines of /root/.bashrc ############################################################################## root@www:/var/lib/tomcat5.5/webapps/code/BotStuff/src# echo $JAVA_HOME root@www:/var/lib/tomcat5.5/webapps/code/BotStuff/src# source /root/.bashrc root@www:/var/lib/tomcat5.5/webapps/code/BotStuff/src# echo $JAVA_HOME /usr/lib/jvm/java-6-sun root@www:/var/lib/tomcat5.5/webapps/code/BotStuff/src# java -version java version "1.6.0_17" Java(TM) SE Runtime Environment (build 1.6.0_17-b04) Java HotSpot(TM) Server VM (build 14.3-b01, mixed mode) root@www:/var/lib/tomcat5.5/webapps/code/BotStuff/src# tail -3 /root/.bashrc #fi export JAVA_HOME=/usr/lib/jvm/java-6-sun export PATH=$PATH:$JAVA_HOME/bin root@www:/var/lib/tomcat5.5/webapps/code/BotStuff/src# ############################################################################## set classpath for ubuntu8.04 on compile command line: ############################################################################## root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# export CLASSPATH=/usr/share/java/*:/usr/share/tomcat5.5/common/lib/*:.:/usr/share/tomcat5.5/webapps/code/BotStuff/classes/ root@www:/usr/share/tomcat5.5/webapps/BotStuff# echo $CLASSPATH /usr/share/java/*:/usr/share/tomcat5.5/common/lib/*:.:/usr/share/tomcat5.5/webapps/code/BotStuff/classes/ ############################################################################## test db connection using JdbcTest.java we just compiled: ############################################################################## root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# cat src/edu/wisc/botany/JdbcTest.java package edu.wisc.botany.model; import java.sql.*; public class JdbcTest { public static void main(String[] args) { try{ Class.forName("com.mysql.jdbc.Driver").newInstance(); Connection conn = DriverManager.getConnection("jdbc:mysql://localhost:3306/herbfifty", "www-data", "apachePASS"); Statement stmt = conn.createStatement(); ResultSet rs; rs = stmt.executeQuery("Select Taxcd, COFC from spdetail LIMIT 3"); while(rs.next()) { System.out.println(rs.getString(1)); System.out.println(rs.getInt(2)); } conn.close(); }catch(Exception e) { System.out.println("oops" + e.getMessage()); } } } root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# ############################################################################## install the jdbc driver for mysql ############################################################################## root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# apt-cache search mysql | grep java libmysql-java - Java database (JDBC) driver for MySQL root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# apt-get install libmysql-java Reading package lists... Done Building dependency tree Reading state information... Done The following NEW packages will be installed: libmysql-java 0 upgraded, 1 newly installed, 0 to remove and 43 not upgraded. Need to get 691kB of archives. After this operation, 766kB of additional disk space will be used. Get:1 http://us.archive.ubuntu.com hardy/main libmysql-java 5.1.5+dfsg-2 [691kB] Fetched 691kB in 2s (339kB/s) Selecting previously deselected package libmysql-java. (Reading database ... 24790 files and directories currently installed.) Unpacking libmysql-java (from .../libmysql-java_5.1.5+dfsg-2_all.deb) ... Setting up libmysql-java (5.1.5+dfsg-2) ... root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# ############################################################################## test servlet container by deploying a test app botservlet ############################################################################## root@www:/usr/share/tomcat5.5/webapps/code/BotStuff# cat src/edu/wisc/botany/web/BotServlet.java package edu.wisc.botany.web; import java.io.IOException; import java.io.PrintWriter; import javax.servlet.ServletException; import javax.servlet.http.HttpServlet; import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; public class BotServlet extends HttpServlet { public void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { PrintWriter out = response.getWriter(); out.println("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 " ); out.println("Transitional//EN\">\n" ); out.println("<html>\n" ); out.println("<head><title>botservlet</title></head>\n" ); out.println("<body>\n" ); out.println("<h1>botservlet works!</h1>\n" ); out.println("</body></html>"); } } root@www:/usr/share/tomcat5.5/webapps/code/BotStuff# ############################################################################## compile test botservlet: ############################################################################## root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# !javac javac -classpath /usr/share/java/*:/usr/share/tomcat5.5/common/lib/*:. -d classes src/edu/wisc/botany/web/BotServlet.java ############################################################################## copy class file just compiled to deployment area of tomcat: ############################################################################## root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# cp classes/edu/wisc/botany/web/BotServlet.class ../../BotStuff/WEB-INF/classes/edu/wisc/botany/web/ ############################################################################## notice carefully the location and contents of the DD web.xml: ############################################################################## root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# javac -classpath /usr/share/java/*:/usr/share/tomcat5.5/common/lib/*:. -d classes src/edu/wisc/botany/web/BotServlet.java root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# root@www:/usr/share/tomcat5.5/webapps/code/BotStuff# cat ../../BotStuff/WEB-INF/web.xml <web-app xmlns="http://java.sun.com/xml/ns/j2ee" version="2.4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http:/java.sun.com/dtd/web-app_2_3.dtd"> <servlet> <servlet-name>botservlet</servlet-name> <servlet-class>edu.wisc.botany.web.BotServlet</servlet-class> </servlet> <servlet-mapping> <servlet-name>botservlet</servlet-name> <url-pattern>/botservlet</url-pattern> </servlet-mapping> </web-app> root@www:/usr/share/tomcat5.5/webapps/code/BotStuff# ############################################################################## restart tomcat, because a deployment descriptor has changed: ############################################################################## root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# /etc/init.d/tomcat5.5 restart * Stopping Tomcat servlet engine tomcat5.5 ...done. * Starting Tomcat servlet engine tomcat5.5 ...done. root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# ############################################################################## after restarting tomcat, to re-read the web.xml, we can get the page: ############################################################################## root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# !wget wget http://127.0.0.1:8180/BotStuff/botservlet --12:32:55-- http://127.0.0.1:8180/BotStuff/botservlet => `botservlet' Connecting to 127.0.0.1:8180... connected. HTTP request sent, awaiting response... 200 OK Length: 171 100%[==========================================================================================>] 171 --.--K/s 12:32:55 (6.61 MB/s) - `botservlet' saved [171/171] ############################################################################## now that we have a working tomcat, lets test our mysql driver ############################################################################## root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# vi src/edu/wisc/botany/model/JdbcTest.java root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# !javac javac -classpath /usr/share/java/*:/usr/share/tomcat5.5/common/lib/*:. -d classes src/edu/wisc/botany/model/JdbcTest.java root@www:/var/lib/tomcat5.5/webapps/code/BotStuff# cd classes root@www:/var/lib/tomcat5.5/webapps/code/BotStuff/classes# java edu/wisc/botany/ BotServlet.class JdbcTest.class model/ web/ root@www:/var/lib/tomcat5.5/webapps/code/BotStuff/classes# java edu/wisc/botany/model/JdbcTest ABAJUP 0 ABIBAL 5 ABIBAL 0 root@www:/var/lib/tomcat5.5/webapps/code/BotStuff/classes# |
tom >
