/*
* (non-Javadoc)
*
* @see ca.unb.cs.pcsf.db.DBAccessService#getParticipantById(java.lang.String)
*/
public Participant getParticipantById(String participantId) {
logger.debug(LOGPRE + "getParticipantById() start" + LOGPRE);
Participant participant = new Participant();
String selectRequest = "select * from `" + DOMAIN_PARTICIPANT + "`";
List<Item> items = this.getDataFromDomain(selectRequest);
Item findItem = new Item();
if (!items.isEmpty()) {
for (Item item : items) {
if (item.getName().equals(participantId)) {
findItem = item;
break;
}
}
}
if (findItem != null) {
participant.setId(findItem.getName());
for (Attribute attribute : findItem.getAttributes()) {
if (attribute.getName().equals(PARTICIPANT_ATTRIBUTE_NAME))
participant.setName(attribute.getValue());
if (attribute.getName().equals(PARTICIPANT_ATTRIBUTE_EMAIL))
participant.setEmail(attribute.getValue());
if (attribute.getName().equals(PARTICIPANT_ATTRIBUTE_COLLABORATION_ID))
participant.setCollaborationId(attribute.getValue());
if (attribute.getName().equals(PARTICIPANT_ATTRIBUTE_IS_REG))
participant.setIsReg(attribute.getValue());
}
}
logger.debug(LOGPRE + "getParticipantById() end" + LOGPRE);
return participant;
}
public static void copyParticipantInfo(Participant src, Participant dest) {
dest.setId(src.getId());
dest.setBirthDate(src.getBirthDate());
dest.setAge(src.getAge(null));
dest.setEducation(src.getEducation());
dest.setGroup(src.getGroup());
dest.setLanguage(src.getLanguage());
dest.setName(src.getName());
dest.setRole(src.getRole());
dest.setSES(src.getSES());
dest.setSex(src.getSex());
}
/**
* Get a participant record from the data base by name and collaboration id.
*
* @param participantName
* @param collaborationId
* @return a participant
*/
private Participant getParticipantByNameAndCollaborationId(
String participantName, String collaborationId) {
logger.debug(LOGPRE + "getParticipantByNameAndCollaborationId() start" + LOGPRE);
Participant participant = new Participant();
String selectRequest =
"select * from `"
+ DOMAIN_PARTICIPANT
+ "` where "
+ PARTICIPANT_ATTRIBUTE_NAME
+ " = '"
+ participantName
+ "' AND "
+ PARTICIPANT_ATTRIBUTE_COLLABORATION_ID
+ "='"
+ collaborationId
+ "'";
List<Item> items = this.getDataFromDomain(selectRequest);
if (items != null) {
Item item = items.get(0);
participant.setId(item.getName());
for (Attribute attribute : item.getAttributes()) {
if (attribute.getName().equals(PARTICIPANT_ATTRIBUTE_NAME))
participant.setName(attribute.getValue());
if (attribute.getName().equals(PARTICIPANT_ATTRIBUTE_EMAIL))
participant.setEmail(attribute.getValue());
if (attribute.getName().equals(PARTICIPANT_ATTRIBUTE_COLLABORATION_ID))
participant.setCollaborationId(attribute.getValue());
if (attribute.getName().equals(PARTICIPANT_ATTRIBUTE_IS_REG))
participant.setIsReg(attribute.getValue());
}
}
logger.debug(LOGPRE + "getParticipantByNameAndCollaborationId() end" + LOGPRE);
return participant;
}
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;
}