org.sigpath.bioimport
Class XMLExport

java.lang.Object
  org.sigpath.bioimport.XMLExport

public class XMLExport
extends Object

Performs XML Export of Sigpath Data.

Constructor Summary

XMLExport(PrintStream out, String schemaURL, boolean standaloneOutput, boolean interactive)
Creates a new xml exmport using the specified schema url and print stream.

XMLExport(XDebug xdebug)
Creates a new xml exmport using the default schema url.

XMLExport(XDebug xdebug, String schema)
Creates a new xml exmport using the specified schema url.

Method Summary

static Vector	collectModifiedChemicals()
static void	displayCommandLineUsage() Displays the Command Line Usage.
String	displaySubmission(SigpathSubmission submission) Outputs XML.
String	exportAll() Exports everything.
String	exportAll(List list) Exports everything in the list.
String	exportBySpid(String spid) Exports the SigPathEntity that that spid refers to.
SigpathSubmission	exportComplex(SigpathSubmission submission, HashMap spidsToTempIDs, String spid) If spid is null exports all complexes.
SigpathSubmission	exportComponents(SigpathSubmission submission, HashMap spidsToTempIDs, String spid) If spid is null exports all complexes and modified chemicals.
SigpathSubmission	exportConcentrations(SigpathSubmission submission, HashMap spidsToTempIDs, String spid)
void	exportDataSource(SPDBManager dbm, SigpathSubmission submission, HashMap spidsToCastorInstances, DataSource dataSource) Export SigPath instances to XML
SigpathSubmission	exportModels(SigpathSubmission submission, HashMap spidsToTempIDs, String spid)
SigpathSubmission	exportModifiedChemical(SigpathSubmission submission, HashMap spidsToTempIDs, String spid) If spid is null exports all modified chemicals.
SigpathSubmission	exportNamedChemicalInteractions(SigpathSubmission submission, HashMap spidsToTempIDs, String spid) If spid is null exports all named chemical interactions.
SigpathSubmission	exportNamedChemicals(SigpathSubmission submission, HashMap spidsToTempIDs, String spid) If spid is null exports all named chemicals.
SigpathSubmission	exportPathways(SigpathSubmission submission, HashMap spidsToTempIDs, DataSource dataSource) Export Pathways - If spid is null exports all Pathways.
SigpathSubmission	exportPendingReviews(SigpathSubmission submission, HashMap spidsToTempIDs, DataSource dataSource) Export PendingList - If spid is null exports all Pathways.
SigpathSubmission	exportProteins(SigpathSubmission submission, HashMap spidsToTempIDs, String spid) If spid is null exports all proteins.
SigpathSubmission	exportSmallMolecules(SigpathSubmission submission, HashMap spidsToTempIDs, String spid) Export small molecules to XML Submission.
List	getIdrefActions()
int	getNumOfTempIDs()
XDebug	getXDebug() Get the XDebug object associated with this export.
boolean	isStandaloneOutput() Should this model be exported standalone?
static void	main(String[] args)
void	setProgressListener(ProgressListener progressListener) Set a progress listener for this export.
void	setStandaloneOutput(boolean standaloneOutput) Decide if the output should be standalone.
void	writeSubmission(SigpathSubmission submission, Writer writer) Writes the submission to the given writer object.
void	writeSubmissionWithoutValidation(SigpathSubmission submission, Writer writer) Deprecated.

Methods inherited from class java.lang.Object

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

Constructor Detail

XMLExport

public XMLExport(XDebug xdebug)

Creates a new xml exmport using the default schema url.

Parameters:

xdebug - debug object

XMLExport

public XMLExport(XDebug xdebug,
                 String schema)

Creates a new xml exmport using the specified schema url.

Parameters:

xdebug - debug object

schema - url of the schema to use

XMLExport

public XMLExport(PrintStream out,
                 String schemaURL,
                 boolean standaloneOutput,
                 boolean interactive)
          throws IOException,
                 SigPathDatabaseException,
                 MarshalException,
                 ValidationException

Creates a new xml exmport using the specified schema url and print stream.

Parameters:

out - PrintStream to write xml to

schemaURL - URL of the schema to use when generating the xml

standaloneOutput - true if the output should include all the data it needs to be a complete submission

interactive - true if the export should prompt the user for input.

Throws:

IOException

SigPathDatabaseException

MarshalException

ValidationException

Method Detail

getXDebug

public XDebug getXDebug()

Get the XDebug object associated with this export.

Returns:

the XDebug object

setProgressListener

public void setProgressListener(ProgressListener progressListener)

Set a progress listener for this export.

Parameters:

progressListener -

displayCommandLineUsage

public static void displayCommandLineUsage()

Displays the Command Line Usage.

writeSubmission

public void writeSubmission(SigpathSubmission submission,
                            Writer writer)
                     throws IOException,
                            ValidationException,
                            MarshalException

Writes the submission to the given writer object.

Parameters:

submission - Submission to write

writer - The writer

Throws:

IOException

ValidationException

MarshalException

writeSubmissionWithoutValidation

public void writeSubmissionWithoutValidation(SigpathSubmission submission,
                                             Writer writer)
                                      throws IOException,
                                             ValidationException,
                                             MarshalException

Deprecated.

Writes the submission to the given writer object.

Parameters:

submission - Submission to write

writer - The writer

Throws:

IOException

ValidationException

MarshalException

displaySubmission

public String displaySubmission(SigpathSubmission submission)
                         throws MarshalException,
                                ValidationException,
                                IOException

Outputs XML.

Throws:

MarshalException

ValidationException

IOException

exportSmallMolecules

public SigpathSubmission exportSmallMolecules(SigpathSubmission submission,
                                              HashMap spidsToTempIDs,
                                              String spid)
                                       throws SigPathDatabaseException

Export small molecules to XML Submission. If spid arguemnt is null, will export all small molecules.

Parameters:

submission - The castor xml submission where the molecules will be written

spidsToTempIDs - The spid to xml-id map. Relation between spid and xml id is written in this map during the call

spid - SigPath identifier of one molecule, or null, to export all molecules.

Throws:

SigPathDatabaseException

exportProteins

public SigpathSubmission exportProteins(SigpathSubmission submission,
                                        HashMap spidsToTempIDs,
                                        String spid)
                                 throws SigPathDatabaseException

If spid is null exports all proteins.

Throws:

SigPathDatabaseException

exportComponents

public SigpathSubmission exportComponents(SigpathSubmission submission,
                                          HashMap spidsToTempIDs,
                                          String spid)
                                   throws SigPathDatabaseException

If spid is null exports all complexes and modified chemicals.

Throws:

SigPathDatabaseException

exportComplex

public SigpathSubmission exportComplex(SigpathSubmission submission,
                                       HashMap spidsToTempIDs,
                                       String spid)
                                throws SigPathDatabaseException

If spid is null exports all complexes.

Throws:

SigPathDatabaseException

exportModifiedChemical

public SigpathSubmission exportModifiedChemical(SigpathSubmission submission,
                                                HashMap spidsToTempIDs,
                                                String spid)
                                         throws SigPathDatabaseException

If spid is null exports all modified chemicals.

Throws:

SigPathDatabaseException

exportNamedChemicals

public SigpathSubmission exportNamedChemicals(SigpathSubmission submission,
                                              HashMap spidsToTempIDs,
                                              String spid)
                                       throws SigPathDatabaseException

If spid is null exports all named chemicals.

Throws:

SigPathDatabaseException

exportConcentrations

public SigpathSubmission exportConcentrations(SigpathSubmission submission,
                                              HashMap spidsToTempIDs,
                                              String spid)
                                       throws SigPathDatabaseException

Throws:

SigPathDatabaseException

exportModels

public SigpathSubmission exportModels(SigpathSubmission submission,
                                      HashMap spidsToTempIDs,
                                      String spid)
                               throws SigPathDatabaseException

Throws:

SigPathDatabaseException

exportPathways

public SigpathSubmission exportPathways(SigpathSubmission submission,
                                        HashMap spidsToTempIDs,
                                        DataSource dataSource)
                                 throws SigPathDatabaseException

Export Pathways - If spid is null exports all Pathways.

Throws:

SigPathDatabaseException

exportPendingReviews

public SigpathSubmission exportPendingReviews(SigpathSubmission submission,
                                              HashMap spidsToTempIDs,
                                              DataSource dataSource)
                                       throws SigPathDatabaseException

Export PendingList - If spid is null exports all Pathways.

Throws:

SigPathDatabaseException

exportNamedChemicalInteractions

public SigpathSubmission exportNamedChemicalInteractions(SigpathSubmission submission,
                                                         HashMap spidsToTempIDs,
                                                         String spid)
                                                  throws SigPathDatabaseException

If spid is null exports all named chemical interactions.

Throws:

SigPathDatabaseException

exportBySpid

public String exportBySpid(String spid)
                    throws SigPathDatabaseException,
                           IOException,
                           ValidationException,
                           MarshalException

Exports the SigPathEntity that that spid refers to.

Parameters:

spid - of the entity to export.

Returns:

Xml representation of the entity.

Throws:

SigPathDatabaseException

IOException

ValidationException

MarshalException

exportAll

public String exportAll(List list)
                 throws SigPathDatabaseException,
                        ValidationException,
                        MarshalException,
                        IOException

Exports everything in the list.

Parameters:

list - List of spids

Throws:

SigPathDatabaseException

ValidationException

MarshalException

IOException

getNumOfTempIDs

public int getNumOfTempIDs()

getIdrefActions

public List getIdrefActions()

exportDataSource

public void exportDataSource(SPDBManager dbm,
                             SigpathSubmission submission,
                             HashMap spidsToCastorInstances,
                             DataSource dataSource)
                      throws SigPathDatabaseException

Export SigPath instances to XML

Parameters:

submission - The submission where to store exported instances

spidsToCastorInstances - Id to castor instance map.

dataSource - Source of SigPathEntity instances.

Throws:

SigPathDatabaseException

exportAll

public String exportAll()
                 throws SigPathDatabaseException,
                        ValidationException,
                        MarshalException,
                        IOException

Exports everything.

Throws:

SigPathDatabaseException

ValidationException

MarshalException

IOException

collectModifiedChemicals

public static Vector collectModifiedChemicals()
                                       throws SigPathDatabaseException

Throws:

SigPathDatabaseException

isStandaloneOutput

public boolean isStandaloneOutput()

Should this model be exported standalone?

Returns:

true if the model should be exported so that it can be reimported in a fresh database.

setStandaloneOutput

public void setStandaloneOutput(boolean standaloneOutput)

Decide if the output should be standalone. Standalone outputs will contain all the information needed to reconstruct a model in a fresh database. In practice, when standalone output is set to true, the XML output will include molecules even if they are background information. The model will also include reactions and enzymatic reactions that it references. Standalone outputs are useful to generate standalone XML submissions for models. This comes handy when building regression tests for model export.

Parameters:

standaloneOutput - frue to generate standalone output. false (default) otherwise.

main

public static void main(String[] args)
                 throws IOException,
                        ValidationException,
                        MarshalException,
                        SigPathDatabaseException

Throws:

IOException

ValidationException

MarshalException

SigPathDatabaseException