Reverse Engineered 2 newtables and TomCat 5.5 does not start

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This topic has 1 reply, 2 voices, and was last updated 16 years, 7 months ago by Loyal Water.

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June 11, 2008 at 2:50 pm #285817 Reply

datapower
Member

We added 2 new tables in the Oracle database and now I rev. engineered them and got the followings:
==========================
package com.imc.nida.sbir.common.hibernate;

import java.util.HashSet;
import java.util.Set;

/**
* AnlysAnnGeneRef generated by MyEclipse Persistence Tools
*/

public class AnlysAnnGeneRef implements java.io.Serializable {

// Fields

private long aagnrId;

private String aagnrGeneSymbol;

private String aagnrGeneTitle;

private Set anlysAnnProbesetGeneRefs = new HashSet(0);

// Constructors

/** default constructor */
public AnlysAnnGeneRef() {
}

/** full constructor */
public AnlysAnnGeneRef(String aagnrGeneSymbol, String aagnrGeneTitle,
Set anlysAnnProbesetGeneRefs) {
this.aagnrGeneSymbol = aagnrGeneSymbol;
this.aagnrGeneTitle = aagnrGeneTitle;
this.anlysAnnProbesetGeneRefs = anlysAnnProbesetGeneRefs;
}

// Property accessors

public long getAagnrId() {
return this.aagnrId;
}

public void setAagnrId(long aagnrId) {
this.aagnrId = aagnrId;
}

public String getAagnrGeneSymbol() {
return this.aagnrGeneSymbol;
}

public void setAagnrGeneSymbol(String aagnrGeneSymbol) {
this.aagnrGeneSymbol = aagnrGeneSymbol;
}

public String getAagnrGeneTitle() {
return this.aagnrGeneTitle;
}

public void setAagnrGeneTitle(String aagnrGeneTitle) {
this.aagnrGeneTitle = aagnrGeneTitle;
}

public Set getAnlysAnnProbesetGeneRefs() {
return this.anlysAnnProbesetGeneRefs;
}

public void setAnlysAnnProbesetGeneRefs(Set anlysAnnProbesetGeneRefs) {
this.anlysAnnProbesetGeneRefs = anlysAnnProbesetGeneRefs;
}

}
=============================
package com.imc.nida.sbir.common.hibernate;

/**
* AnlysAnnProbesetGeneRef generated by MyEclipse Persistence Tools
*/

public class AnlysAnnProbesetGeneRef implements java.io.Serializable {

// Fields

private long aapgrId;

private AnlysAnnGeneRef anlysAnnGeneRef;

private AnlysProbeset anlysProbeset;

// Constructors

/** default constructor */
public AnlysAnnProbesetGeneRef() {
}

/** full constructor */
public AnlysAnnProbesetGeneRef(AnlysAnnGeneRef anlysAnnGeneRef,
AnlysProbeset anlysProbeset) {
this.anlysAnnGeneRef = anlysAnnGeneRef;
this.anlysProbeset = anlysProbeset;
}

// Property accessors

public long getAapgrId() {
return this.aapgrId;
}

public void setAapgrId(long aapgrId) {
this.aapgrId = aapgrId;
}

public AnlysAnnGeneRef getAnlysAnnGeneRef() {
return this.anlysAnnGeneRef;
}

public void setAnlysAnnGeneRef(AnlysAnnGeneRef anlysAnnGeneRef) {
this.anlysAnnGeneRef = anlysAnnGeneRef;
}

public AnlysProbeset getAnlysProbeset() {
return this.anlysProbeset;
}

public void setAnlysProbeset(AnlysProbeset anlysProbeset) {
this.anlysProbeset = anlysProbeset;
}

}
=====================================
<?xml version=”1.0″ encoding=”utf-8″?>
<!DOCTYPE hibernate-mapping PUBLIC “-//Hibernate/Hibernate Mapping DTD 3.0//EN”
“http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd”>
<!–
Mapping file autogenerated by MyEclipse Persistence Tools
–>
<hibernate-mapping>
<class name=”com.imc.nida.sbir.common.hibernate.AnlysAnnGeneRef” table=”ANLYS_ANN_GENE_REF” schema=”SBIR”>
<id name=”aagnrId” type=”java.lang.Long”>
<column name=”AAGNR_ID” precision=”22″ scale=”0″ />
<generator class=”assigned” />
</id>
<property name=”aagnrGeneSymbol” type=”java.lang.String”>
<column name=”AAGNR_GENE_SYMBOL” length=”4000″ />
</property>
<property name=”aagnrGeneTitle” type=”java.lang.String”>
<column name=”AAGNR_GENE_TITLE” length=”4000″ />
</property>
<set name=”anlysAnnProbesetGeneRefs” inverse=”true”>
<key>
<column name=”AAGNR_ID” precision=”22″ scale=”0″ />
</key>
<one-to-many class=”com.imc.nida.sbir.common.hibernate.AnlysAnnProbesetGeneRef” />
</set>
</class>
</hibernate-mapping>
=================================================
<?xml version=”1.0″ encoding=”utf-8″?>
<!DOCTYPE hibernate-mapping PUBLIC “-//Hibernate/Hibernate Mapping DTD 3.0//EN”
“http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd”>
<!–
Mapping file autogenerated by MyEclipse Persistence Tools
–>
<hibernate-mapping>
<class name=”com.imc.nida.sbir.common.hibernate.AnlysAnnProbesetGeneRef” table=”ANLYS_ANN_PROBESET_GENE_REF” schema=”SBIR”>
<id name=”aapgrId” type=”java.lang.Long”>
<column name=”AAPGR_ID” precision=”22″ scale=”0″ />
<generator class=”assigned” />
</id>
<many-to-one name=”anlysAnnGeneRef” class=”com.imc.nida.sbir.common.hibernate.AnlysAnnGeneRef” fetch=”select”>
<column name=”AAGNR_ID” precision=”22″ scale=”0″ />
</many-to-one>
<many-to-one name=”anlysProbeset” class=”com.imc.nida.sbir.common.hibernate.AnlysProbeset” fetch=”select”>
<column name=”ANPB_ID” precision=”22″ scale=”0″ />
</many-to-one>
</class>
</hibernate-mapping>
=====================================
The DDL of the 2 oracle tables are as follows:
CREATE TABLE ANLYS_ANN_GENE_REF
(
AAGNR_ID NUMBER,
AAGNR_GENE_SYMBOL VARCHAR2(4000 BYTE),
AAGNR_GENE_TITLE VARCHAR2(4000 BYTE)
)
TABLESPACE SBIR_DATA
PCTUSED 0
PCTFREE 10
INITRANS 1
MAXTRANS 255
STORAGE (
INITIAL 64K
MINEXTENTS 1
MAXEXTENTS 2147483645
PCTINCREASE 0
BUFFER_POOL DEFAULT
)
NOLOGGING
NOCOMPRESS
NOCACHE
NOPARALLEL
MONITORING;

CREATE UNIQUE INDEX PK_AAGNR_ID ON ANLYS_ANN_GENE_REF
(AAGNR_ID)
NOLOGGING
TABLESPACE SBIR_DATA
PCTFREE 10
INITRANS 2
MAXTRANS 255
STORAGE (
INITIAL 64K
MINEXTENTS 1
MAXEXTENTS 2147483645
PCTINCREASE 0
BUFFER_POOL DEFAULT
)
NOPARALLEL;

ALTER TABLE ANLYS_ANN_GENE_REF ADD (
CONSTRAINT PK_AAGNR_ID
PRIMARY KEY
(AAGNR_ID)
USING INDEX
TABLESPACE SBIR_DATA
PCTFREE 10
INITRANS 2
MAXTRANS 255
STORAGE (
INITIAL 64K
MINEXTENTS 1
MAXEXTENTS 2147483645
PCTINCREASE 0
));

GRANT SELECT ON ANLYS_ANN_GENE_REF TO DW_SBIR;

GRANT SELECT ON ANLYS_ANN_GENE_REF TO ETL_COMMON_SBIR;

GRANT SELECT ON ANLYS_ANN_GENE_REF TO SBIR_ANALYSIS;
=================================================
CREATE TABLE ANLYS_ANN_PROBESET_GENE_REF
(
AAPGR_ID NUMBER,
ANPB_ID NUMBER,
AAGNR_ID NUMBER
)
TABLESPACE SBIR_DATA
PCTUSED 0
PCTFREE 10
INITRANS 1
MAXTRANS 255
STORAGE (
INITIAL 64K
MINEXTENTS 1
MAXEXTENTS 2147483645
PCTINCREASE 0
BUFFER_POOL DEFAULT
)
NOLOGGING
NOCOMPRESS
NOCACHE
NOPARALLEL
MONITORING;

CREATE UNIQUE INDEX PK_AAPGR_ID ON ANLYS_ANN_PROBESET_GENE_REF
(AAPGR_ID)
NOLOGGING
TABLESPACE SBIR_DATA
PCTFREE 10
INITRANS 2
MAXTRANS 255
STORAGE (
INITIAL 64K
MINEXTENTS 1
MAXEXTENTS 2147483645
PCTINCREASE 0
BUFFER_POOL DEFAULT
)
NOPARALLEL;

ALTER TABLE ANLYS_ANN_PROBESET_GENE_REF ADD (
CONSTRAINT PK_AAPGR_ID
PRIMARY KEY
(AAPGR_ID)
USING INDEX
TABLESPACE SBIR_DATA
PCTFREE 10
INITRANS 2
MAXTRANS 255
STORAGE (
INITIAL 64K
MINEXTENTS 1
MAXEXTENTS 2147483645
PCTINCREASE 0
));

ALTER TABLE ANLYS_ANN_PROBESET_GENE_REF ADD (
CONSTRAINT FK_AAPGR_REFS_ANLYS_PROBESET
FOREIGN KEY (ANPB_ID)
REFERENCES ANLYS_PROBESET (ANPB_ID));

ALTER TABLE ANLYS_ANN_PROBESET_GENE_REF ADD (
CONSTRAINT FK_AAPGR_REFS_A_A_GENE_REF
FOREIGN KEY (AAGNR_ID)
REFERENCES ANLYS_ANN_GENE_REF (AAGNR_ID));

GRANT SELECT ON ANLYS_ANN_PROBESET_GENE_REF TO DW_SBIR;

GRANT SELECT ON ANLYS_ANN_PROBESET_GENE_REF TO ETL_COMMON_SBIR;

GRANT SELECT ON ANLYS_ANN_PROBESET_GENE_REF TO SBIR_ANALYSIS;
======================================

TomCat 5.5 error when trying to start is :

Jun 11, 2008 3:16:41 PM org.apache.catalina.core.StandardContext start
SEVERE: Error listenerStart
Jun 11, 2008 3:16:41 PM org.apache.catalina.core.StandardContext start
SEVERE: Context [/sbir] startup failed due to previous errors
======================================
My Web.xml is :

<?xml version=”1.0″ encoding=”ISO-8859-1″?>

<!DOCTYPE web-app PUBLIC “-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN” “http://java.sun.com/j2ee/dtds/web-app_2_3.dtd”>

<!– $Id: web.xml,v 1.9 2007/08/23 20:42:21 anoosh Exp $ –>

<web-app>

<context-param>
<param-name>log4jConfigLocation</param-name>
<param-value>/WEB-INF/classes/log4j.properties</param-value>
</context-param>

<context-param>
<param-name>contextConfigLocation</param-name>
<param-value>/WEB-INF/conf/loadQCRepContext.xml</param-value>
</context-param>

<listener>
<listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
</listener>

<listener>
<listener-class>
com.imc.nida.sbir.web.server.ServerStopListener
</listener-class>
</listener>

<!– servlet filters for authentication and Hibernate session management –>

<!–filter-mapping>
<filter-name>HibernateSessionFilter</filter-name>
<url-pattern>*.htm</url-pattern>
</filter-mapping–>

<!– Servlets –>

<servlet>
<servlet-name>action</servlet-name>
<servlet-class>org.apache.struts.action.ActionServlet</servlet-class>
<init-param>
<param-name>application</param-name>
<param-value>ApplicationMessages</param-value>
</init-param>
<init-param>
<param-name>config</param-name>
<param-value>/WEB-INF/struts-config.xml</param-value>
</init-param>
<init-param>
<param-name>debug</param-name>
<param-value>2</param-value>
</init-param>
<init-param>
<param-name>detail</param-name>
<param-value>2</param-value>
</init-param>
<init-param>
<param-name>validate</param-name>
<param-value>true</param-value>
</init-param>
<load-on-startup>2</load-on-startup>
</servlet>
<!–
<servlet>
<servlet-name>PreLoadServlet</servlet-name>
<servlet-class>com.imc.nida.sbir.web.servlet.PreLoadServlet</servlet-class>
<load-on-startup>1</load-on-startup>
</servlet>
–>
<!–
<servlet>
<servlet-name>OpenRServeServlet</servlet-name>
<servlet-class>com.imc.nida.sbir.web.servlet.OpenRServeServlet</servlet-class>
<load-on-startup>1</load-on-startup>
</servlet>
–>
<servlet>
<servlet-name>ImageDisplayServlet</servlet-name>
<servlet-class>com.imc.nida.sbir.web.servlet.ImageDisplayServlet</servlet-class>
</servlet>
<servlet>
<servlet-name>ShowImageServlet</servlet-name>
<servlet-class>com.imc.nida.sbir.web.servlet.ShowImageServlet</servlet-class>
</servlet>

<!– Servlet Mappings –>

<!– if you change this url pattern, you must also change it in Constants.java –>
<!–
<servlet-mapping>
<servlet-name>OpenRServeServlet</servlet-name>
<url-pattern>/OpenRServeServlet</url-pattern>
</servlet-mapping>

–>
<servlet-mapping>
<servlet-name>ImageDisplayServlet</servlet-name>
<url-pattern>/ImageDisplayServlet</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>ShowImageServlet</servlet-name>
<url-pattern>/ShowImageServlet</url-pattern>
</servlet-mapping>

<servlet-mapping>
<servlet-name>action</servlet-name>
<url-pattern>*.htm</url-pattern>
</servlet-mapping>

<!– The Usual Welcome File List –>
<welcome-file-list>
<welcome-file>index.jsp</welcome-file>
</welcome-file-list>
<!–
<error-page>
<error-code>404</error-code>
<location>/login.htm</location>
</error-page>
–>

<!– Tag Library Descriptors –>

<taglib>
<taglib-uri>/tags/struts-bean</taglib-uri>
<taglib-location>/WEB-INF/struts-bean.tld</taglib-location>
</taglib>
<taglib>
<taglib-uri>/tags/struts-html</taglib-uri>
<taglib-location>/WEB-INF/struts-html.tld</taglib-location>
</taglib>
<taglib>
<taglib-uri>/tags/struts-logic</taglib-uri>
<taglib-location>/WEB-INF/struts-logic.tld</taglib-location>
</taglib>
<taglib>
<taglib-uri>/tags/struts-nested</taglib-uri>
<taglib-location>/WEB-INF/struts-nested.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>/tags/datetime</taglib-uri>
<taglib-location>/WEB-INF/taglibs-datetime.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>/tags/tiles</taglib-uri>
<taglib-location>/WEB-INF/struts-tiles.tld</taglib-location>
</taglib>
<taglib>
<taglib-uri>/tags/jstl/core</taglib-uri>
<taglib-location>/WEB-INF/c.tld</taglib-location>
</taglib>
<taglib>
<taglib-uri>http://displaytag.sourceforge.net/</taglib-uri>
<taglib-location>/WEB-INF/displaytag-11.tld</taglib-location>
</taglib>

<!– web.xml element order

<!ELEMENT web-app (icon?, display-name?, description?, distributable?,
context-param*, servlet*, servlet-mapping*, session-config?,
mime-mapping*, welcome-file-list?, error-page*, taglib*,
resource-ref*, security-constraint*, login-config?, security-role*,
env-entry*, ejb-ref*)>

–>
</web-app>
=====================================
The hibernate session factory section in loadQCRepContext.xml is:

<bean id=”sessionFactory” class=”org.springframework.orm.hibernate3.LocalSessionFactoryBean”>
<property name=”dataSource”>
<ref local=”dataSource”/>
</property>
<property name=”mappingResources”>
<list>
<value>../conf/qcRep_sql.hbm.xml</value>

<value>../conf/db/AnlysAnnAffy.hbm.xml</value>
<value>../conf/db/AnlysAnnChrLoc.hbm.xml</value>
<value>../conf/db/AnlysAnnEc.hbm.xml</value>
<value>../conf/db/AnlysAnnEnsembl.hbm.xml</value>
<value>../conf/db/AnlysAnnEntrezgene.hbm.xml</value>
<value>../conf/db/AnlysAnnGenesymb.hbm.xml</value>
<!– <value>../conf/db/AnlysAnnGeneRef.hbm.xml</value> –>
<value>../conf/db/AnlysAnnGenetitle.hbm.xml</value>
<value>../conf/db/AnlysAnnGo.hbm.xml</value>
<value>../conf/db/AnlysAnnOmim.hbm.xml</value>
<value>../conf/db/AnlysAnnParties.hbm.xml</value>
<!– <value>../conf/db/AnlysAnnProbesetGeneRef.hbm.xml</value> –>
<value>../conf/db/AnlysAnnPbRefIntPars.hbm.xml</value>
<value>../conf/db/AnlysAnnPw.hbm.xml</value>
<value>../conf/db/AnlysAnnRefGo.hbm.xml</value>
<value>../conf/db/AnlysAnnSp.hbm.xml</value>
<value>../conf/db/AnlysAnnUnigeneid.hbm.xml</value>
<value>../conf/db/AnlysCelfile.hbm.xml</value>
<value>../conf/db/AnlysCelfileFactorDetail.hbm.xml</value>
<value>../conf/db/AnlysDesignDetail.hbm.xml</value>
<value>../conf/db/AnlysFactor.hbm.xml</value>
<value>../conf/db/AnlysFactorValues.hbm.xml</value>
<value>../conf/db/AnlysGeneexpAnalysis.hbm.xml</value>
<value>../conf/db/AnlysGeneexpSliceFactor.hbm.xml</value>
<value>../conf/db/AnlysGenotypeAnalysi.hbm.xml</value>
<value>../conf/db/AnlysGroupComparison.hbm.xml</value>
<value>../conf/db/AnlysGroupComparisonBckup.hbm.xml</value>
<value>../conf/db/AnlysGroupcompExternalFile.hbm.xml</value>
<value>../conf/db/AnlysGrpfdradjExternalFile.hbm.xml</value>
<value>../conf/db/AnlysGrpfweradjExternalFile.hbm.xml</value>
<value>../conf/db/AnlysMainProcess.hbm.xml</value>
<value>../conf/db/AnlysNormalization.hbm.xml</value>
<value>../conf/db/AnlysParameter.hbm.xml</value>
<value>../conf/db/AnlysProbeset.hbm.xml</value>
<value>../conf/db/AnlysProbesetExternalFile.hbm.xml</value>
<value>../conf/db/AnlysProcessCelfile.hbm.xml</value>
<value>../conf/db/AnlysProcessDetail.hbm.xml</value>
<value>../conf/db/AnlysProcessImages.hbm.xml</value>
<value>../conf/db/AnlysProcessSliceFactor.hbm.xml</value>
<value>../conf/db/AnlysImageType.hbm.xml</value>
<value>../conf/db/AnlysPwComparison.hbm.xml</value>
<value>../conf/db/AnlysRawdata.hbm.xml</value>
<value>../conf/db/AnlysStep.hbm.xml</value>
<value>../conf/db/AnlysStepdetail.hbm.xml</value>
<value>../conf/db/AnlysWfStepdetail.hbm.xml</value>
<value>../conf/db/AnlysWfStepParameter.hbm.xml</value>
<value>../conf/db/AnlysWorkflow.hbm.xml</value>
<value>../conf/db/LabChip.hbm.xml</value>
<value>../conf/db/LabHybridization.hbm.xml</value>
<value>../conf/db/LabProtocol.hbm.xml</value>
<value>../conf/db/LabProtocolParameter.hbm.xml</value>
<value>../conf/db/LabProtocolParameterVal.hbm.xml</value>
<value>../conf/db/LabQcInfo.hbm.xml</value>
<value>../conf/db/LabQcParameter.hbm.xml</value>
<value>../conf/db/LabSample.hbm.xml</value>
<value>../conf/db/LabSampleAssn.hbm.xml</value>
<value>../conf/db/LabSamplePrep.hbm.xml</value>
<value>../conf/db/SubjectDetail.hbm.xml</value>
<value>../conf/db/TestExternal.hbm.xml</value>
<value>../conf/db/VwApdCelfileDetails.hbm.xml</value>

</list>
</property>
<property name=”hibernateProperties”>
<props>
<prop key=”hibernate.dialect”>org.hibernate.dialect.Oracle9Dialect</prop>
<prop key=”hibernate.show_sql”>false</prop>
<prop key=”hibernate.use_outer_join”>true</prop>
<prop key=”hibernate.max_fetch_depth”>1</prop>
</props>
</property>

</bean>

====================================
I have to comment out the hbm.xml value lines for the 2 new tables in the sessionFactory bean above for TomCat to start other wise i get the SEVERE: error listenerStart message.
Any help would be greatly appreciated. Thanks in advance.

June 12, 2008 at 9:28 am #285834 Reply

Loyal Water
Member

Can you paste the entire error message here for me.

Also, please go to MyEclipse > Installation Summary > Installation Details and paste the information here for me.
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