VIVO-801 Move RDB migrator from VIVO to Vitro
Older instances of Vitro might want to use it.
This commit is contained in:
j2blake
parent
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commit
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15 changed files with 0 additions and 506 deletions
1
.gitignore
vendored
1
.gitignore
vendored
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@ -9,4 +9,3 @@
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/ontology/public/catalog-v0001.xml
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/ontology/public/catalog-v0001.xml
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rdf/auth/firsttime/test-user-model.owl
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rdf/auth/firsttime/test-user-model.owl
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utilities/rdbmigration/.work
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10
build.xml
10
build.xml
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@ -134,14 +134,4 @@
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</sync>
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</sync>
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</target>
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</target>
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<!-- =================================
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target: migrateConfigurationModels
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================================= -->
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<target name="migrateConfigurationModels" description="description">
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<dirname property="nihvivobase.dir" file="${ant.file.nihvivo}" />
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<property name="rdbmigration.dir" location="${nihvivobase.dir}/utilities/rdbmigration" />
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<ant dir="${rdbmigration.dir}" target="all"></ant>
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</target>
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</project>
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</project>
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@ -1,134 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<!-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
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<!-- ======================================================================
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A tool to migrate RDB data into TDB.
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====================================================================== -->
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<project name="RDB-migration" default="describe">
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<property name="working.dir" location=".work" />
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<property name="src.dir" location="src" />
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<property name="lib.dir" location="lib" />
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<!-- =================================
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target: describe
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================================= -->
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<target name="describe"
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description="--> Describe the targets (this is the default).">
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<echo>
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all - Compiles and runs the RDB migration tool.
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</echo>
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</target>
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<!-- =================================
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target: all
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================================= -->
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<target name="all"
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depends="clean, run"
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description="Build from scratch and run the migration.">
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</target>
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<!-- - - - - - - - - - - - - - - - - -
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target: clean
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- - - - - - - - - - - - - - - - - -->
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<target name="clean">
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<delete dir="${working.dir}" />
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</target>
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<!-- - - - - - - - - - - - - - - - - -
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target: setup
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- - - - - - - - - - - - - - - - - -->
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<target name="setup" depends="getBuildProperties, getRuntimeProperties">
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<mkdir dir="${working.dir}" />
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</target>
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<!-- - - - - - - - - - - - - - - - - -
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target: getBuildProperties
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- - - - - - - - - - - - - - - - - -->
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<target name="getBuildProperties">
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<property name="vivo.distribution.dir" location="../.." />
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<property name="build.properties.file"
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location="${vivo.distribution.dir}/build.properties" />
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<fail message="You must create a "${build.properties.file}" file.">
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<condition>
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<not>
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<available file="${build.properties.file}" />
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</not>
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</condition>
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</fail>
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<property file="${build.properties.file}" />
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<fail unless="vitro.core.dir"
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message="${build.properties.file} must contain a value for vitro.core.dir" />
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<fail unless="vitro.home"
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message="${build.properties.file} must contain a value for vitro.home" />
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</target>
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<!-- - - - - - - - - - - - - - - - - -
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target: getRuntimeProperties
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- - - - - - - - - - - - - - - - - -->
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<target name="getRuntimeProperties">
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<property name="runtime.properties.file"
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location="${vitro.home}/runtime.properties" />
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<fail message="You must create a "${runtime.properties.file}" file.">
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<condition>
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<not>
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<available file="${runtime.properties.file}" />
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</not>
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</condition>
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</fail>
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<property file="${runtime.properties.file}" />
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<fail unless="VitroConnection.DataSource.url"
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message="${runtime.properties.file} must contain a value for VitroConnection.DataSource.url" />
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<fail unless="VitroConnection.DataSource.username"
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message="${runtime.properties.file} must contain a value for VitroConnection.DataSource.username" />
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<fail unless="VitroConnection.DataSource.password"
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message="${runtime.properties.file} must contain a value for VitroConnection.DataSource.password" />
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</target>
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<!-- - - - - - - - - - - - - - - - - -
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target: compile
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- - - - - - - - - - - - - - - - - -->
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<target name="compile" depends="setup">
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<path id="main.compile.classpath">
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<fileset dir="${lib.dir}" includes="*.jar" />
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</path>
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<javac srcdir="${src.dir}"
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destdir="${working.dir}"
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debug="true"
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deprecation="true"
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encoding="UTF8"
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includeantruntime="false"
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optimize="true"
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source="1.7">
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<classpath refid="main.compile.classpath" />
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</javac>
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</target>
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<!-- - - - - - - - - - - - - - - - - -
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target: run
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- - - - - - - - - - - - - - - - - -->
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<target name="run" depends="compile">
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<path id="migrate.run.classpath">
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<pathelement location="${working.dir}" />
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<path refid="main.compile.classpath" />
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</path>
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<java classname="edu.cornell.mannlib.vivo.utilities.rdbmigration.RdbMigrator"
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fork="yes"
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failonerror="true">
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<arg value="${vitro.home}" />
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<arg value="${VitroConnection.DataSource.url}" />
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<arg value="${VitroConnection.DataSource.username}" />
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<arg value="${VitroConnection.DataSource.password}" />
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<jvmarg value="-Xms512m"/>
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<jvmarg value="-Xmx2048m"/>
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<classpath refid="migrate.run.classpath" />
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</java>
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</target>
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</project>
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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package edu.cornell.mannlib.vivo.utilities.rdbmigration;
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import java.io.BufferedReader;
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import java.io.File;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.sql.Connection;
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import java.sql.DatabaseMetaData;
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import java.sql.Date;
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import java.sql.DriverManager;
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import java.sql.PreparedStatement;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.sql.Statement;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Properties;
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import org.apache.commons.lang.StringUtils;
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import com.hp.hpl.jena.db.DBConnection;
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import com.hp.hpl.jena.db.GraphRDB;
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import com.hp.hpl.jena.graph.Node;
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import com.hp.hpl.jena.query.Dataset;
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import com.hp.hpl.jena.sparql.core.DatasetGraph;
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import com.hp.hpl.jena.tdb.TDBFactory;
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/**
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* A free-standing application that walks the user through the process of
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* copying VIVO configuration data from RDB to TDB.
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*/
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public class RdbMigrator {
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private static final String TABLE_RDB = "jena_graph";
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private static final String TABLE_MIGRATED = "vivo_rdb_migrated";
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private static final List<String> EXPECTED_MODELS = Arrays
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.asList(new String[] {
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"http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadata",
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"http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadata-displayModel",
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"http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadataTBOX",
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"http://vitro.mannlib.cornell.edu/default/vitro-kb-userAccounts" });
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private final String vivoHomeDir;
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private final String jdbcUrl;
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private final String username;
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private final String password;
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private File targetDir;
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private boolean alreadyMigrated;
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private List<String> modelsToCopy;
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/**
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* Confirm all of the parameters. Ask the user for approval. Do the
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* migration.
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*
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* @throws UserDeclinedException
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* If the user decides not to continue.
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*/
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public RdbMigrator(String vivoHomeDir, String jdbcUrl, String username,
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String password) throws UserDeclinedException, IOException,
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SQLException {
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this.vivoHomeDir = vivoHomeDir;
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this.jdbcUrl = jdbcUrl;
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this.username = username;
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this.password = password;
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testDbConnection();
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checkThatRdbExists();
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confirmTargetDirectory();
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if (doesTdbExist()) {
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askContinueOverTdb();
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}
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if (isAlreadyMigrated()) {
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askMigrateAgain();
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}
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getListOfRdbModels();
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if (isUnexpectedModels()) {
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askMigrateAllModels();
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}
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askApprovalForMigrationPlan();
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migrate();
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}
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private void testDbConnection() {
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try (Connection conn = getSqlConnection()) {
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// Just open and close it.
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} catch (SQLException e) {
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quit("Can't log in to database: '" + jdbcUrl + "', '" + username
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+ "', '" + password + "'\n" + e.getMessage());
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}
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}
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private void checkThatRdbExists() throws SQLException {
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try (Connection conn = getSqlConnection()) {
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DatabaseMetaData md = conn.getMetaData();
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try (ResultSet rs = md.getTables(null, null, TABLE_RDB, null);) {
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if (!rs.next()) {
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quit("The database at '" + jdbcUrl
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+ "' contains no RDB tables.");
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}
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}
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}
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}
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private void confirmTargetDirectory() {
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File vivoHome = new File(vivoHomeDir);
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if (!vivoHome.isDirectory()) {
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quit("'" + vivoHome + "' is not a directory.");
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}
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if (!vivoHome.canWrite()) {
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quit("Can't write to '" + vivoHome + "'.");
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}
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targetDir = new File(vivoHome, "tdbmodels");
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}
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private boolean doesTdbExist() {
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if (!targetDir.exists()) {
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return false;
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}
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if (!targetDir.isDirectory()) {
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quit("'" + targetDir + "' is not a directory.");
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}
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if (!targetDir.canWrite()) {
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quit("Can't write to '" + targetDir + "'.");
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}
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String[] filenames = targetDir.list();
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if (filenames == null || filenames.length == 0) {
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return false;
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}
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return true;
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}
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private void askContinueOverTdb() throws UserDeclinedException, IOException {
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ask("A directory of TDB files exists at '" + targetDir + "'.\n"
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+ " Migration will replace the existing triples.\n"
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+ "Continue? (y/n)");
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}
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private boolean isAlreadyMigrated() throws SQLException {
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try (Connection conn = getSqlConnection()) {
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DatabaseMetaData md = conn.getMetaData();
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try (ResultSet rs = md.getTables(null, null, TABLE_MIGRATED, null);) {
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if (rs.next()) {
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alreadyMigrated = true;
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announceMigrationDate(conn);
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return true;
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} else {
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return false;
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}
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}
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}
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}
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private void announceMigrationDate(Connection conn) {
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String migrationDate = "UNKNOWN DATE";
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String query = String.format("SELECT date FROM %s LIMIT 1",
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TABLE_MIGRATED);
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try (Statement stmt = conn.createStatement();
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java.sql.ResultSet rs = stmt.executeQuery(query)) {
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if (rs.next()) {
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migrationDate = rs.getString("DATE");
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}
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} catch (SQLException e) {
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// go with default answer.
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}
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System.out.println("It looks like this RDB data has already been "
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+ "migrated to TDB, on " + migrationDate
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+ "\n (found a table named '" + TABLE_MIGRATED + "')");
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}
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private void askMigrateAgain() throws UserDeclinedException, IOException {
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ask("Migrate again? (y/n)");
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}
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private void getListOfRdbModels() throws SQLException {
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try (Connection conn = getSqlConnection();
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ClosingDBConnection rdb = new ClosingDBConnection(conn)) {
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modelsToCopy = rdb.getAllModelNames().toList();
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}
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}
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private boolean isUnexpectedModels() {
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List<String> unexpectedModels = new ArrayList<>(modelsToCopy);
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unexpectedModels.removeAll(EXPECTED_MODELS);
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if (unexpectedModels.isEmpty()) {
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return false;
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}
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System.out
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.println("VIVO requires only these models from RDB:\n "
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+ StringUtils.join(EXPECTED_MODELS, "\n ")
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+ "\nYour RDB triple-store contains these additional models:\n "
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+ StringUtils.join(unexpectedModels, "\n "));
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return true;
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}
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private void askMigrateAllModels() throws IOException, UserDeclinedException {
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System.out.println("Migrate all models, or only the required models?\n"
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+ " Enter 'all' or 'only', or anything else to quit.");
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BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
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String s = br.readLine();
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if (s != null) {
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if (s.trim().toLowerCase().equals("all")) {
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return;
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} else if (s.trim().toLowerCase().equals("only")) {
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modelsToCopy = EXPECTED_MODELS;
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return;
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}
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}
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throw new UserDeclinedException("Enter 'all' or 'only'.");
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}
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|
||||||
private void askApprovalForMigrationPlan() throws SQLException,
|
|
||||||
UserDeclinedException, IOException {
|
|
||||||
int modelCount = 0;
|
|
||||||
int tripleCount = 0;
|
|
||||||
try (Connection conn = getSqlConnection();
|
|
||||||
ClosingDBConnection rdb = new ClosingDBConnection(conn)) {
|
|
||||||
for (String modelName : modelsToCopy) {
|
|
||||||
modelCount++;
|
|
||||||
try (ClosingGraphRDB graph = new ClosingGraphRDB(rdb, modelName)) {
|
|
||||||
tripleCount += graph.size();
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
String warning = alreadyMigrated ? " Existing triples will be over-written.\n"
|
|
||||||
: "";
|
|
||||||
String question = String.format("Migrating %d triples in %d models "
|
|
||||||
+ "to TDB files in '%s'\n%sContinue? (y/n)", tripleCount,
|
|
||||||
modelCount, targetDir, warning);
|
|
||||||
ask(question);
|
|
||||||
}
|
|
||||||
|
|
||||||
private void quit(String message) {
|
|
||||||
throw new IllegalArgumentException(
|
|
||||||
"--------------------------------------------------------------\n"
|
|
||||||
+ message
|
|
||||||
+ "\n--------------------------------------------------------------");
|
|
||||||
}
|
|
||||||
|
|
||||||
private void ask(String string) throws UserDeclinedException, IOException {
|
|
||||||
System.out.println(string);
|
|
||||||
BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
|
|
||||||
String s = br.readLine();
|
|
||||||
if ((s == null) || (!s.trim().toLowerCase().equals("y"))) {
|
|
||||||
throw new UserDeclinedException("OK.");
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
private static class UserDeclinedException extends Exception {
|
|
||||||
public UserDeclinedException(String message) {
|
|
||||||
super(message);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
public void migrate() throws SQLException {
|
|
||||||
copyData();
|
|
||||||
writeMigrationRecord();
|
|
||||||
}
|
|
||||||
|
|
||||||
private void copyData() throws SQLException {
|
|
||||||
try (Connection conn = getSqlConnection();
|
|
||||||
ClosingDBConnection rdb = new ClosingDBConnection(conn)) {
|
|
||||||
Dataset tdbDataset = TDBFactory.createDataset(targetDir
|
|
||||||
.getAbsolutePath());
|
|
||||||
copyGraphs(rdb, tdbDataset);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
@SuppressWarnings("deprecation")
|
|
||||||
private void copyGraphs(ClosingDBConnection rdb, Dataset tdbDataset) {
|
|
||||||
DatasetGraph tdbDsGraph = tdbDataset.asDatasetGraph();
|
|
||||||
for (String modelName : modelsToCopy) {
|
|
||||||
try (ClosingGraphRDB graph = new ClosingGraphRDB(rdb, modelName)) {
|
|
||||||
tdbDsGraph.addGraph(Node.createURI(modelName), graph);
|
|
||||||
System.out
|
|
||||||
.println(String.format(" copied %4d triples from %s",
|
|
||||||
graph.size(), modelName));
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
private void writeMigrationRecord() throws SQLException {
|
|
||||||
String createTable = String.format("CREATE TABLE %s (date DATE)",
|
|
||||||
TABLE_MIGRATED);
|
|
||||||
String deleteOldDates = String.format("DELETE FROM %s", TABLE_MIGRATED);
|
|
||||||
String insertDate = String.format("INSERT INTO %s (date) VALUES (?)",
|
|
||||||
TABLE_MIGRATED);
|
|
||||||
try (Connection conn = getSqlConnection();
|
|
||||||
Statement stmt = conn.createStatement();
|
|
||||||
PreparedStatement pstmt = conn.prepareStatement(insertDate)) {
|
|
||||||
if (alreadyMigrated) {
|
|
||||||
stmt.executeUpdate(deleteOldDates);
|
|
||||||
} else {
|
|
||||||
stmt.executeUpdate(createTable);
|
|
||||||
}
|
|
||||||
pstmt.setDate(1, new Date(System.currentTimeMillis()));
|
|
||||||
pstmt.executeUpdate();
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
private Connection getSqlConnection() throws SQLException {
|
|
||||||
Properties connectionProps;
|
|
||||||
connectionProps = new Properties();
|
|
||||||
connectionProps.put("user", username);
|
|
||||||
connectionProps.put("password", password);
|
|
||||||
return DriverManager.getConnection(jdbcUrl, connectionProps);
|
|
||||||
}
|
|
||||||
|
|
||||||
private static class ClosingDBConnection extends DBConnection implements
|
|
||||||
AutoCloseable {
|
|
||||||
ClosingDBConnection(Connection sqlConnection) {
|
|
||||||
super(sqlConnection, "MySQL");
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
private static class ClosingGraphRDB extends GraphRDB implements
|
|
||||||
AutoCloseable {
|
|
||||||
ClosingGraphRDB(DBConnection rdb, String modelName) {
|
|
||||||
super(rdb, modelName, null,
|
|
||||||
GraphRDB.OPTIMIZE_ALL_REIFICATIONS_AND_HIDE_NOTHING, false);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// ----------------------------------------------------------------------
|
|
||||||
// Main routine
|
|
||||||
// ----------------------------------------------------------------------
|
|
||||||
|
|
||||||
@SuppressWarnings("unused")
|
|
||||||
public static void main(String[] args) {
|
|
||||||
if (args.length != 4) {
|
|
||||||
System.out.println("Usage: RdbMigrator vivoHomeDir, jdbcUrl, "
|
|
||||||
+ "username, password");
|
|
||||||
}
|
|
||||||
|
|
||||||
try {
|
|
||||||
new RdbMigrator(args[0], args[1], args[2], args[3]);
|
|
||||||
} catch (IllegalArgumentException | UserDeclinedException e) {
|
|
||||||
System.out.println(e.getMessage());
|
|
||||||
} catch (Exception e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
Loading…
Add table
Reference in a new issue