/**
* Set the DAO Factory that holds required DAOs for resolving ids.
*
* @param factory the DAO factory
*/
public void setDAOFactory(DAOFactory factory) {
this.factory = factory;
// set DAO in sub DAOs
featureConverter.setDAOFactory(factory);
hostOrganismConverter.setDAOFactory(factory);
interactorConverter.setDAOFactory(factory);
confidenceConverter.setDAOFactory(factory);
parameterConverter.setDAOFactory(factory);
participantIdentificationMethodConverter.setDAOFactory(factory);
experimentalRoleConverter.setDAOFactory(factory);
experimentalPreparationConverter.setDAOFactory(factory);
experimentalInteractorConverter.setDAOFactory(factory);
}
public psidev.psi.mi.xml254.jaxb.Participant toJaxb(
psidev.psi.mi.xml.model.Participant mParticipant) throws ConverterException {
if (mParticipant == null) {
throw new IllegalArgumentException("You must give a non null model Participant.");
}
checkDependencies();
psidev.psi.mi.xml254.jaxb.Participant jParticipant =
new psidev.psi.mi.xml254.jaxb.Participant();
// Initialise the JAXB object reading the model
// 1. set attributes
jParticipant.setId(mParticipant.getId());
// 2. set sub elements
// interactor / interaction
if (mParticipant.hasInteractor() || mParticipant.hasInteractorRef()) {
// compact form: export ref
if (PsimiXmlForm.FORM_COMPACT
== ConverterContext.getInstance().getConverterConfig().getXmlForm()) {
if (mParticipant.hasInteractorRef())
jParticipant.setInteractorRef(mParticipant.getInteractorRef().getRef());
else jParticipant.setInteractorRef(mParticipant.getInteractor().getId());
}
// not compact form : export the full interactor
else {
jParticipant.setInteractor(interactorConverter.toJaxb(mParticipant.getInteractor()));
}
} else if (mParticipant.hasInteraction()) {
jParticipant.setInteractionRef(mParticipant.getInteraction().getId());
} else {
throw new ConverterException(
"Neither an interactor or an interaction was present in participant "
+ mParticipant.getId());
}
// BiologigicalRoles
if (mParticipant.hasBiologicalRole()) {
jParticipant.setBiologicalRole(cvTypeConverter.toJaxb(mParticipant.getBiologicalRole()));
}
// Names
if (mParticipant.hasNames()) {
jParticipant.setNames(namesConverter.toJaxb(mParticipant.getNames()));
}
// Xrefs
if (mParticipant.hasXref()) {
jParticipant.setXref(xrefConverter.toJaxb(mParticipant.getXref()));
}
// ConfidenceList
if (mParticipant.hasConfidences()) {
if (jParticipant.getConfidenceList() == null) {
jParticipant.setConfidenceList(new ConfidenceList());
}
for (psidev.psi.mi.xml.model.Confidence mConfidence : mParticipant.getConfidenceList()) {
jParticipant
.getConfidenceList()
.getConfidences()
.add(confidenceConverter.toJaxb(mConfidence));
}
}
// ExperimentalInteractor
if (mParticipant.hasExperimentalInteractors()) {
if (jParticipant.getExperimentalInteractorList() == null) {
jParticipant.setExperimentalInteractorList(
new psidev.psi.mi.xml254.jaxb.ExperimentalInteractorList());
}
for (ExperimentalInteractor mExperimentalInteractor :
mParticipant.getExperimentalInteractors()) {
jParticipant
.getExperimentalInteractorList()
.getExperimentalInteractors()
.add(experimentalInteractorConverter.toJaxb(mExperimentalInteractor));
}
}
// ExperimentalPreparations
if (mParticipant.hasExperimentalPreparations()) {
if (jParticipant.getExperimentalPreparationList() == null) {
jParticipant.setExperimentalPreparationList(
new psidev.psi.mi.xml254.jaxb.ExperimentalPreparationList());
}
for (ExperimentalPreparation mExperimentalPreparation :
mParticipant.getExperimentalPreparations()) {
jParticipant
.getExperimentalPreparationList()
.getExperimentalPreparations()
.add(experimentalPreparationConverter.toJaxb(mExperimentalPreparation));
}
}
// ExperimentalRoles
if (mParticipant.hasExperimentalRoles()) {
if (jParticipant.getExperimentalRoleList() == null) {
jParticipant.setExperimentalRoleList(new psidev.psi.mi.xml254.jaxb.ExperimentalRoleList());
}
for (ExperimentalRole mExperimentalRole : mParticipant.getExperimentalRoles()) {
jParticipant
.getExperimentalRoleList()
.getExperimentalRoles()
.add(experimentalRoleConverter.toJaxb(mExperimentalRole));
}
}
// Features
if (mParticipant.hasFeatures()) {
if (jParticipant.getFeatureList() == null) {
jParticipant.setFeatureList(new psidev.psi.mi.xml254.jaxb.FeatureList());
}
for (Feature mFeature : mParticipant.getFeatures()) {
jParticipant.getFeatureList().getFeatures().add(featureConverter.toJaxb(mFeature));
}
}
// HostOrganisms
if (!mParticipant.getHostOrganisms().isEmpty()) {
if (jParticipant.getHostOrganismList() == null) {
jParticipant.setHostOrganismList(new HostOrganismList());
}
for (HostOrganism mHostOrganism : mParticipant.getHostOrganisms()) {
jParticipant
.getHostOrganismList()
.getHostOrganisms()
.add(hostOrganismConverter.toJaxb(mHostOrganism));
}
}
// Parameters
if (mParticipant.hasParameters()) {
if (jParticipant.getParameterList() == null) {
jParticipant.setParameterList(new ParameterList());
}
for (Parameter mParameter : mParticipant.getParameters()) {
jParticipant.getParameterList().getParameters().add(parameterConverter.toJaxb(mParameter));
}
}
// ParticipantIdentificationMethod
if (mParticipant.hasParticipantIdentificationMethods()) {
if (jParticipant.getParticipantIdentificationMethodList() == null) {
jParticipant.setParticipantIdentificationMethodList(
new psidev.psi.mi.xml254.jaxb.ParticipantIdentificationMethodList());
}
for (ParticipantIdentificationMethod mParticipantIdentificationMethod :
mParticipant.getParticipantIdentificationMethods()) {
jParticipant
.getParticipantIdentificationMethodList()
.getParticipantIdentificationMethods()
.add(participantIdentificationMethodConverter.toJaxb(mParticipantIdentificationMethod));
}
}
// Attributes
if (mParticipant.hasAttributes()) {
if (jParticipant.getAttributeList() == null) {
jParticipant.setAttributeList(new AttributeList());
}
for (Attribute mAttribute : mParticipant.getAttributes()) {
jParticipant.getAttributeList().getAttributes().add(attributeConverter.toJaxb(mAttribute));
}
}
return jParticipant;
}
public Participant fromJaxb(psidev.psi.mi.xml254.jaxb.Participant jParticipant)
throws ConverterException {
if (jParticipant == null) {
throw new IllegalArgumentException("You must give a non null JAXB Participant.");
}
checkDependencies();
Participant mParticipant = new Participant();
// Initialise the model reading the Jaxb object
// 1. set attributes
mParticipant.setId(jParticipant.getId());
// 2. set encapsulated objects
// interactor/interaction
Interactor mInteractor = null;
Interaction mInteraction = null;
boolean foundInteractor = false;
if (jParticipant.getInteractorRef() != null) {
foundInteractor = true;
mInteractor = factory.getInteractorDAO().retreive(jParticipant.getInteractorRef());
if (mInteractor == null) {
mParticipant.setInteractorRef(new InteractorRef(jParticipant.getInteractorRef()));
} else {
mParticipant.setInteractor(mInteractor);
}
} else if (jParticipant.getInteractor() != null) {
foundInteractor = true;
mInteractor = interactorConverter.fromJaxb(jParticipant.getInteractor());
mParticipant.setInteractor(mInteractor);
} else if (jParticipant.getInteractionRef() != null) {
foundInteractor = true;
mInteraction = factory.getInteractionDAO().retreive(jParticipant.getInteractionRef());
if (mInteraction == null) {
mParticipant.setInteractionRef(new InteractionRef(jParticipant.getInteractionRef()));
} else {
mParticipant.setInteraction(mInteraction);
}
}
if (!foundInteractor) {
throw new ConverterException(
"Could not find either an interactor or an interaction for participant (id="
+ jParticipant.getId()
+ ").");
}
// BiologigicalRoles
if (jParticipant.getBiologicalRole() != null) {
mParticipant.setBiologicalRole(
cvTypeConverter.fromJaxb(jParticipant.getBiologicalRole(), BiologicalRole.class));
}
// Names
if (jParticipant.getNames() != null) {
mParticipant.setNames(namesConverter.fromJaxb(jParticipant.getNames()));
}
// Xrefs
if (jParticipant.getXref() != null) {
mParticipant.setXref(xrefConverter.fromJaxb(jParticipant.getXref()));
}
// ConfidenceList
if (jParticipant.getConfidenceList() != null) {
for (psidev.psi.mi.xml254.jaxb.Confidence jConfidence :
jParticipant.getConfidenceList().getConfidences()) {
mParticipant.getConfidenceList().add(confidenceConverter.fromJaxb(jConfidence));
}
}
// ExperimentalInteractor
if (jParticipant.getExperimentalInteractorList() != null) {
for (psidev.psi.mi.xml254.jaxb.ExperimentalInteractor jExperimentalInteractor :
jParticipant.getExperimentalInteractorList().getExperimentalInteractors()) {
mParticipant
.getExperimentalInteractors()
.add(experimentalInteractorConverter.fromJaxb(jExperimentalInteractor));
}
}
// ExperimentalPreparations
if (jParticipant.getExperimentalPreparationList() != null) {
for (psidev.psi.mi.xml254.jaxb.ExperimentalPreparation jExperimentalPreparation :
jParticipant.getExperimentalPreparationList().getExperimentalPreparations()) {
mParticipant
.getExperimentalPreparations()
.add(experimentalPreparationConverter.fromJaxb(jExperimentalPreparation));
}
}
// ExperimentalRoles
if (jParticipant.getExperimentalRoleList() != null) {
for (psidev.psi.mi.xml254.jaxb.ExperimentalRole jExperimentalRole :
jParticipant.getExperimentalRoleList().getExperimentalRoles()) {
mParticipant
.getExperimentalRoles()
.add(experimentalRoleConverter.fromJaxb(jExperimentalRole));
}
}
// Features
if (jParticipant.getFeatureList() != null) {
for (psidev.psi.mi.xml254.jaxb.Feature jFeature :
jParticipant.getFeatureList().getFeatures()) {
mParticipant.getFeatures().add(featureConverter.fromJaxb(jFeature));
}
}
// HostOrganisms
if (jParticipant.getHostOrganismList() != null) {
for (psidev.psi.mi.xml254.jaxb.HostOrganism jOrganism :
jParticipant.getHostOrganismList().getHostOrganisms()) {
mParticipant.getHostOrganisms().add(hostOrganismConverter.fromJaxb(jOrganism));
}
}
// Parameters
// We handle interaction's and participant's parameters as they may be different JAXB Type.
// psidev.psi.mi.xml254.jaxb.Parameter
// psidev.psi.mi.xml254.jaxb.InteractionElementType.ParameterList.Parameter
// TODO once the schema is fixed, revert to a single converter.
if (jParticipant.getParameterList() != null) {
for (psidev.psi.mi.xml254.jaxb.Parameter jParameter :
jParticipant.getParameterList().getParameters()) {
mParticipant.getParameters().add(parameterConverter.fromJaxb(jParameter));
}
}
// ParticipantIdentificationMethod
if (jParticipant.getParticipantIdentificationMethodList() != null) {
for (psidev.psi.mi.xml254.jaxb.ParticipantIdentificationMethod
jParticipantIdentificationMethod :
jParticipant
.getParticipantIdentificationMethodList()
.getParticipantIdentificationMethods()) {
mParticipant
.getParticipantIdentificationMethods()
.add(
participantIdentificationMethodConverter.fromJaxb(
jParticipantIdentificationMethod));
}
}
// attributes
if (jParticipant.getAttributeList() != null) {
for (psidev.psi.mi.xml254.jaxb.Attribute attribute :
jParticipant.getAttributeList().getAttributes()) {
mParticipant.getAttributes().add(attributeConverter.fromJaxb(attribute));
}
}
// store the participant via DAO
PsiDAO<Participant> participantDAO = factory.getParticipantDAO();
participantDAO.store(mParticipant);
return mParticipant;
}