uk.ac.ebi.intenz.tools.export

Class ExporterApp

java.lang.Object

uk.ac.ebi.intenz.tools.export.ExporterApp

public class ExporterApp
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static org.apache.log4j.Logger	LOGGER

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	ExporterApp(String dbConfig)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	exportBiopax(Collection<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> enzymeList, String biopaxFile)
protected void	exportKegg(Collection<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> enzymes, String keggFile)
protected void	exportSitemap(Collection<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> enzymeList, Map<String,Object> descriptions, String sitemapFile)
protected void	exportXML(Collection<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> enzymeList, Map<String,Object> descriptions, String toDir) Exports data in XML format.
protected void	finalize()
static Map<String,Object>	getDescriptions(Connection con) Builds a map of EC numbers (as String) to EnzymeClass, EnzymeSubClass or EnzymeSubSubClass objects from which to retrieve names and descriptions.
protected List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry>	getEnzymeList(String ecString) Gets the list of enzymes to be exported.
static void	main(String[] args) Exports IntEnz data in the following formats: XML (both flavours ASCII and XCHARS), using the XmlExporter class. Site map XML file (sitemap.xml) to be used in Google sitemaps to make every IntEnz entry available to Google indexing.

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

LOGGER

public static final org.apache.log4j.Logger LOGGER

Constructor Detail

ExporterApp

protected ExporterApp(String dbConfig)
               throws SQLException,
                      IOException,
                      uk.ac.ebi.intenz.domain.exceptions.DomainException

Throws:

SQLException

IOException

uk.ac.ebi.intenz.domain.exceptions.DomainException

Method Detail

main

public static void main(String[] args)
                 throws ClassNotFoundException,
                        SQLException,
                        uk.ac.ebi.rhea.mapper.MapperException,
                        IOException,
                        uk.ac.ebi.intenz.domain.exceptions.DomainException

Exports IntEnz data in the following formats:

• XML (both flavours ASCII and XCHARS), using the XmlExporter class.
• Site map XML file (sitemap.xml) to be used in Google sitemaps to make every IntEnz entry available to Google indexing. Other search engines accept this standard too.
• BioPAX, using the biopax module.
• KEGG enzyme.

Parameters:

args -

• -intenzDb <config>: database configuration file for IntEnz.
• [-intenzXml <output dir>]: export as IntEnzXML .
• [-biopax <file name>]: export as one BioPAX OWL file.
• [-sitemap <file name>]: export as a Sitemap XML file.
• [-keggEnzyme <file name>]: export as a KEGG enzyme file.
• [-ec <EC number>]: export only the passed EC number. if not set, all of the public entries are exported.

Throws:

uk.ac.ebi.intenz.domain.exceptions.DomainException

IOException

SQLException

uk.ac.ebi.rhea.mapper.MapperException

ClassNotFoundException

finalize

protected void finalize()
                 throws Throwable

Overrides:

finalize in class Object

Throws:

Throwable

getEnzymeList

protected List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> getEnzymeList(String ecString)
                                                                  throws SQLException,
                                                                         uk.ac.ebi.rhea.mapper.MapperException,
                                                                         uk.ac.ebi.intenz.domain.exceptions.DomainException

Gets the list of enzymes to be exported.

Parameters:

ecString - An EC number. If null, every exportable enzyme is included.

Throws:

SQLException

uk.ac.ebi.intenz.domain.exceptions.DomainException

uk.ac.ebi.rhea.mapper.MapperException

getDescriptions

public static Map<String,Object> getDescriptions(Connection con)
                                          throws SQLException,
                                                 uk.ac.ebi.intenz.domain.exceptions.DomainException

Builds a map of EC numbers (as String) to EnzymeClass, EnzymeSubClass or EnzymeSubSubClass objects from which to retrieve names and descriptions.

Parameters:

con - a database connection.

Returns:

a map of EC numbers (as String) to EnzymeClass, EnzymeSubClass or EnzymeSubSubClass objects.

Throws:

SQLException

uk.ac.ebi.intenz.domain.exceptions.DomainException

exportXML

protected void exportXML(Collection<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> enzymeList,
             Map<String,Object> descriptions,
             String toDir)
                  throws Exception

Exports data in XML format.

Parameters:

enzymeList -

descriptions -

toDir - destination directory for XML files.

Throws:

Exception

exportSitemap

protected void exportSitemap(Collection<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> enzymeList,
                 Map<String,Object> descriptions,
                 String sitemapFile)
                      throws IOException,
                             javax.xml.bind.JAXBException,
                             SAXException

Throws:

IOException

javax.xml.bind.JAXBException

SAXException

exportBiopax

protected void exportBiopax(Collection<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> enzymeList,
                String biopaxFile)
                     throws IOException,
                            IllegalAccessException,
                            InvocationTargetException

Throws:

IOException

IllegalAccessException

InvocationTargetException

exportKegg

protected void exportKegg(Collection<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> enzymes,
              String keggFile)
                   throws Exception

Throws:

Exception