org.sigpath.task.xml
Class TExportBase

java.lang.Object
  org.sigpath.task.DBTask
      org.sigpath.task.xml.TExportBase

All Implemented Interfaces:

Task

Direct Known Subclasses:

TExportChangeLog, TExportComplex, TExportComponents, TExportConcentrationMeasurement, TExportEnzymaticReaction, TExportKinetic, TExportKineticCustom, TExportLiteratureReference, TExportLiteratureReferences, TExportModel, TExportModels, TExportModifiedChemical, TExportNamedChemical, TExportNamedChemicalInteraction, TExportOrganism, TExportPathway, TExportPendingList, TExportPendingReviews, TExportProtein, TExportReaction, TExportReferences, TExportSmallMolecule, TExportStandaloneModel, TExportUserComment

public abstract class TExportBase
extends DBTask

Base Class for Exporting SigPath Entities to XML.

Author:

Ethan Cerami, Fabien Campagne

Field Summary

protected DataSource	dataSource
protected HashMap	idMap map spid -> castor object.
protected List	idRefActions list of idref actions.
protected SigpathSubmission	root
protected boolean	standaloneOutput

Fields inherited from class org.sigpath.task.DBTask

dbManager, embeddedTask, entityManager, errors, ftsm, progressListener, sigpathFactory, unitManager, userManager, xdebug

Constructor Summary

	TExportBase(DataSource dataSource, SigpathSubmission root, HashMap spidsToTempIDs) Creates an exporter that gets data to export from a DataSource.
	TExportBase(DataSource dataSource, SigpathSubmission root, HashMap spidsToTempIDs, List idRefActions) Creates an exporter that gets data to export from a DataSource.
protected	TExportBase(SigpathSubmission root, HashMap spidsToTempIDs)
protected	TExportBase(SigpathSubmission root, HashMap spidsToTempIDs, List idRefActions)

Method Summary

protected Change_log	addChangeLog(SigPathEntity spe) Adds Change Log Information to XML Document.
protected Reviews	addReviews(SigPathEntity spe) Adds Review Information to XML Document.
protected void	addStandalone(Model spModel) adds a standalone model to the submission (assumes the submission is standalone)
protected String	clearEmptyField(String description)
Molecule[]	componentsToMolecules(SigPathEntity entity) Converts the components of a complex into XLM molecules.
protected String	constructReactionSummary(Interaction interaction)
protected InteractionRef	createInteractionReference(Interaction interaction) Return an XML interaction-ref element.
Molecule	createMolecule(Chemical sp_chem, HashMap spidsToTempIDs, SigpathSubmission root) Creates a Castor molecule object given a SigPath chemical.
static ExternalReference	findUniqueAcDb(ExternalReferences refs, EntityManager em) Find a pair of accession code/database that uniquely identifies this molecule in the current database.
protected String	getACDB(Chemical chemical) Returns a valid ACDB for a Chemical object.
String	getCreatedBy(PendingList jdoInstance)
CustomKinetic	getCustomKinetic(Kinetic kinetic) Gets the kinetic custom when the parameter is of class (KineticCustom).
DataSource	getDataSource()
protected EnzymaticParameters	getEnzymaticReactionParameters(EnzymaticReaction spEnzymaticReaction)
protected Enzyme	getEnzyme(EnzymaticReaction jdoInstance)
ExcludedReactions	getExcludedReactions(Model spModel)
protected Formula	getFormula(KineticCustom kinetic)
protected HashMap	getIdMap() Gets HashMap.
protected KineticBindings	getKineticBindings(KineticInteraction kInt)
protected KineticRef	getKineticRef(KineticInteraction reaction)
ModelCompartments	getModelCompartments(Model spModel)
NamedChemicalRef[]	getNamedChemicalRef(NamedChemicalInteraction jdoInstance)
protected ParametersBindingsDeclaration	getParametersBindingsDeclaration(KineticCustom kinetic)
protected PreviousVersion	getPreviousVersion(Model spModel) Get Prevoius Version from Model.
Left	getReactionLeftSide(Collection left)
Modifiers	getReactionMidleSide(Collection modifiers)
protected Parameters	getReactionParameters(Reaction reaction)
Right	getReactionRightSide(Collection right)
protected SpeciesBindingsDeclaration	getSpeciesBindingsDeclaration(KineticCustom kinetic)
protected TargetUnit	getTargetUnit(Model spModel)
boolean	isStandaloneOutput() Deprecated. Use TExportStandaloneModel instead
protected void	postProcessConcentrationMeasurement(ConcentrationMeasurement spCM, Concentration_measurement cm)
protected void	postProcessEnzymaticReaction(EnzymaticReaction enzymaticReaction, EnzymaticReaction castorInstance)
protected void	postProcessModel(Model spModel, Model model)
void	postProcessPendingList(PendingList jdoInstance, Pending_list castorInstance)
protected void	postProcessReaction(Reaction jdoInstance, Reaction castorInstance)
protected void	processChemicals(Collection molecs, StringBuffer text) get short names for chemicals and builds a reaction's description while doing this
protected void	setDataSource(DataSource source)
protected void	setProcessingUnit(String spid)
static boolean	setSpid(Chemical sp_chem, Molecule mol) Sets a spid attribute on the molecule only if the chemical does not refers to background information, and if no idref is provided for the molecule.
void	setStandaloneOutput(boolean standaloneOutput) Deprecated. Use TExportStandaloneModel instead

Methods inherited from class org.sigpath.task.DBTask

_execute, close, delete, execute, getDbManager, getErrors, isEmbeddedTask, isTaskThrewException, reindex, resolve, setDbManager, setEmbeddedTask, setEmbeddedTask, setObtainTransactionsFrom, setProgressListener, setTaskThrewException

Methods inherited from class java.lang.Object

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

Field Detail

idMap

protected HashMap idMap

map spid -> castor object.

root

protected SigpathSubmission root

standaloneOutput

protected boolean standaloneOutput

dataSource

protected DataSource dataSource

idRefActions

protected List idRefActions

list of idref actions.

Constructor Detail

TExportBase

protected TExportBase(SigpathSubmission root,
                      HashMap spidsToTempIDs)

TExportBase

public TExportBase(DataSource dataSource,
                   SigpathSubmission root,
                   HashMap spidsToTempIDs)

Creates an exporter that gets data to export from a DataSource.

Parameters:

root - Castor SigpathSubmission object

spidsToTempIDs - map of spids to temporary ids

TExportBase

protected TExportBase(SigpathSubmission root,
                      HashMap spidsToTempIDs,
                      List idRefActions)

TExportBase

public TExportBase(DataSource dataSource,
                   SigpathSubmission root,
                   HashMap spidsToTempIDs,
                   List idRefActions)

Creates an exporter that gets data to export from a DataSource.

Parameters:

root - Castor SigpathSubmission object

spidsToTempIDs - map of spids to temporary ids

Method Detail

getDataSource

public DataSource getDataSource()

setDataSource

protected void setDataSource(DataSource source)

getIdMap

protected HashMap getIdMap()

Gets HashMap.

Returns:

Hashmap of SPIDs to TempIDs

isStandaloneOutput

public boolean isStandaloneOutput()

Deprecated. Use TExportStandaloneModel instead

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)

Deprecated. Use TExportStandaloneModel instead

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 nzymatic 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 - true to generate standalone output. false (default) otherwise.

addChangeLog

protected Change_log addChangeLog(SigPathEntity spe)

Adds Change Log Information to XML Document.

addReviews

protected Reviews addReviews(SigPathEntity spe)

Adds Review Information to XML Document.

addStandalone

protected void addStandalone(Model spModel)

adds a standalone model to the submission (assumes the submission is standalone)

Parameters:

spModel -

clearEmptyField

protected String clearEmptyField(String description)

componentsToMolecules

public Molecule[] componentsToMolecules(SigPathEntity entity)
                                 throws SigPathDatabaseException

Converts the components of a complex into XLM molecules.

Parameters:

entity -

Returns:

Throws:

SigPathDatabaseException

createMolecule

public Molecule createMolecule(Chemical sp_chem,
                               HashMap spidsToTempIDs,
                               SigpathSubmission root)

Creates a Castor molecule object given a SigPath chemical. If the chemical has already been added to the submission then the molecule is created with an idRef to that castor chemical. If the chemical has not already been added and it is a complex or a modified chemical, then the Castor complex or modified chemical is created and the molecule has an idRef to that castor component. If the chemical has not already been added, and it is not a complex or a modified chemical then the molecule is created with the accession code/database pair and organism. SigPath tries to optimize which accession code/database pair to use, so that the pair identifies a single chemical in the current database. The current strategy is to look for accession codes from SwissProt, find the first one which uniquely identifies a chemical in the current database and return it. If no accession code for SwissProt is available, then the first accession code found is used.

Parameters:

sp_chem - Sigpath Chemical

spidsToTempIDs - HashMap that maps spids to idRefs

root - SigpathSubmission root

Returns:

org.sigpath.bioimport.reaction2.Molecule Castor molecule

findUniqueAcDb

public static ExternalReference findUniqueAcDb(ExternalReferences refs,
                                               EntityManager em)
                                        throws SigPathDatabaseException

Find a pair of accession code/database that uniquely identifies this molecule in the current database. If there are swiss-prot accession codes, use the one which finds only one molecule in the current source database otherwise, just take the first accession code.

Throws:

SigPathDatabaseException

setSpid

public static boolean setSpid(Chemical sp_chem,
                              Molecule mol)

Sets a spid attribute on the molecule only if the chemical does not refers to background information, and if no idref is provided for the molecule.

Parameters:

sp_chem - Chemical (source)

mol - molecule (destination).

Returns:

True if the spid attribute was set, false otherwise.

getCustomKinetic

public CustomKinetic getCustomKinetic(Kinetic kinetic)

Gets the kinetic custom when the parameter is of class (KineticCustom). The method uses the TExportKineticCustom export class

Parameters:

kinetic -

Returns:

CustomKinetic

getEnzymaticReactionParameters

protected EnzymaticParameters getEnzymaticReactionParameters(EnzymaticReaction spEnzymaticReaction)

getEnzyme

protected Enzyme getEnzyme(EnzymaticReaction jdoInstance)
                    throws SigPathDatabaseException

Throws:

SigPathDatabaseException

getFormula

protected Formula getFormula(KineticCustom kinetic)
                      throws SigPathDatabaseException

Throws:

SigPathDatabaseException

getKineticBindings

protected KineticBindings getKineticBindings(KineticInteraction kInt)
                                      throws SigPathDatabaseException

Throws:

SigPathDatabaseException

getKineticRef

protected KineticRef getKineticRef(KineticInteraction reaction)
                            throws SigPathDatabaseException

Parameters:

reaction -

Returns:

Throws:

SigPathDatabaseException

getNamedChemicalRef

public NamedChemicalRef[] getNamedChemicalRef(NamedChemicalInteraction jdoInstance)
                                       throws SigPathDatabaseException

Throws:

SigPathDatabaseException

getParametersBindingsDeclaration

protected ParametersBindingsDeclaration getParametersBindingsDeclaration(KineticCustom kinetic)
                                                                  throws SigPathDatabaseException

Throws:

SigPathDatabaseException

getReactionLeftSide

public Left getReactionLeftSide(Collection left)
                         throws SigPathDatabaseException

Throws:

SigPathDatabaseException

getReactionMidleSide

public Modifiers getReactionMidleSide(Collection modifiers)
                               throws SigPathDatabaseException

Throws:

SigPathDatabaseException

getReactionParameters

protected Parameters getReactionParameters(Reaction reaction)

getReactionRightSide

public Right getReactionRightSide(Collection right)
                           throws SigPathDatabaseException

Throws:

SigPathDatabaseException

getSpeciesBindingsDeclaration

protected SpeciesBindingsDeclaration getSpeciesBindingsDeclaration(KineticCustom kinetic)
                                                            throws SigPathDatabaseException

Throws:

SigPathDatabaseException

postProcessConcentrationMeasurement

protected void postProcessConcentrationMeasurement(ConcentrationMeasurement spCM,
                                                   Concentration_measurement cm)

getACDB

protected String getACDB(Chemical chemical)

Returns a valid ACDB for a Chemical object. Preference is given to the SWISSPROT database

Parameters:

chemical - The chemical to get the ACDB for

Returns:

A valid ACDB or null if none could be found

postProcessEnzymaticReaction

protected void postProcessEnzymaticReaction(EnzymaticReaction enzymaticReaction,
                                            EnzymaticReaction castorInstance)
                                     throws SigPathDatabaseException

Throws:

SigPathDatabaseException

postProcessReaction

protected void postProcessReaction(Reaction jdoInstance,
                                   Reaction castorInstance)
                            throws SigPathDatabaseException

Throws:

SigPathDatabaseException

setProcessingUnit

protected void setProcessingUnit(String spid)

createInteractionReference

protected InteractionRef createInteractionReference(Interaction interaction)

Return an XML interaction-ref element.

Parameters:

interaction - The interaction the reference will point to.

Returns:

InteractionRef

constructReactionSummary

protected String constructReactionSummary(Interaction interaction)
                                   throws SigPathDatabaseException

Throws:

SigPathDatabaseException

processChemicals

protected void processChemicals(Collection molecs,
                                StringBuffer text)
                         throws SigPathDatabaseException

get short names for chemicals and builds a reaction's description while doing this

Parameters:

molecs -

text -

Throws:

SigPathDatabaseException

getPreviousVersion

protected PreviousVersion getPreviousVersion(Model spModel)

Get Prevoius Version from Model.

Parameters:

spModel: - datamodel Model class

Returns:

org.sigpath.bioimport.reaction2.PreviousVersion

getTargetUnit

protected TargetUnit getTargetUnit(Model spModel)

getModelCompartments

public ModelCompartments getModelCompartments(Model spModel)

getExcludedReactions

public ExcludedReactions getExcludedReactions(Model spModel)

postProcessModel

protected void postProcessModel(Model spModel,
                                Model model)

getCreatedBy

public String getCreatedBy(PendingList jdoInstance)

postProcessPendingList

public void postProcessPendingList(PendingList jdoInstance,
                                   Pending_list castorInstance)