public Bundle getProjectPatientBundle(AccessToken token) throws FhirServerException {
ProjectPatientMap p =
getProjectPatientMap(
token.getResourceUserId(),
token.getI2b2Token(),
token.getI2b2Url(),
token.getI2b2Domain(),
token.getI2b2Project());
String bundleXml = p.getPatientBundle();
Bundle b = null;
try {
b = JAXBUtil.fromXml(bundleXml, Bundle.class);
} catch (JAXBException e) {
logger.error(e.getMessage(), e);
}
return b;
}
private void fetchPatientList(
String i2b2User, String i2b2Token, String i2b2Url, String i2b2Domain, String projectId)
throws FhirServerException {
status.markProcessing(projectId);
try {
logger.trace("fetching all Patients for project:" + projectId);
String i2b2Xml = null;
Bundle b = new Bundle();
ArrayList<String> list = null;
if (serverConfigs.GetString(ConfigParameter.patientFetchMin) != null
&& serverConfigs.GetString(ConfigParameter.patientFetchMin).equals("true")) {
logger.debug("min call");
i2b2Xml = I2b2Util.getAllPatientsMin(i2b2User, i2b2Token, i2b2Url, i2b2Domain, projectId);
list = I2b2Util.getAllPatientsAsList(i2b2Xml);
for (String id : list) {
Patient p = new Patient();
p = (Patient) FhirUtil.setId(p, id);
BundleEntry be = new BundleEntry();
be.setResource(FhirUtil.getResourceContainer(p));
b.getEntry().add(be);
}
} else {
logger.debug("max call");
i2b2Xml = I2b2Util.getAllPatients(i2b2User, i2b2Token, i2b2Url, i2b2Domain, projectId);
list = I2b2Util.getAllPatientsAsList(i2b2Xml);
b = I2b2Util.getAllPatientsAsFhirBundle(i2b2Xml);
}
String bundleXml = JAXBUtil.toXml(b);
service.put(projectId, list, bundleXml);
} catch (Exception e) {
logger.error(e.getMessage(), e);
throw new FhirServerException("Could not fetch patient list from i2b2 server");
}
status.markComplete(projectId);
}