private void getCGEMSData(String url, String fileName, String clientConfig) throws Exception {
CGEMSClient client = new CGEMSClient(url);
CQLQueryResults results = client.query(getCQLQuery(fileName));
CQLQueryResultsIterator iter =
new CQLQueryResultsIterator(results, new FileInputStream(new File(clientConfig)));
if (WRITE_TO_FILE) {
writeToFile("cgems_out.xml", fileName, results);
}
if (DISPLAY_DATA) {
System.out.println("Results for " + fileName);
while (iter.hasNext()) {
gov.nih.nci.caintegrator.domain.study.bean.StudyParticipant de =
(gov.nih.nci.caintegrator.domain.study.bean.StudyParticipant) iter.next();
System.out.println(de.getStudySubjectIdentifier() + " " + de.getInstitutionName());
}
System.out.println("---------------------");
}
}
private void getcaTissueData(String url, String fileName, String clientConfig) throws Exception {
gov.nih.nci.cagrid.catissuecore.client.CaTissueCoreClient client =
new gov.nih.nci.cagrid.catissuecore.client.CaTissueCoreClient(url);
CQLQueryResults results = client.query(getCQLQuery(fileName));
CQLQueryResultsIterator iter =
new CQLQueryResultsIterator(results, new FileInputStream(new File(clientConfig)));
if (WRITE_TO_FILE) {
writeToFile("catissue_out.xml", fileName, results);
}
if (DISPLAY_DATA) {
System.out.println("Results for " + fileName);
while (iter.hasNext()) {
edu.wustl.catissuecore.domainobject.impl.ParticipantImpl de =
(edu.wustl.catissuecore.domainobject.impl.ParticipantImpl) iter.next();
System.out.println(de.getId() + " " + de.getGender());
}
System.out.println("---------------------");
}
}
private void getTumorData(String url, String fileName, String clientConfig) throws Exception {
gov.nih.nci.cagrid.catriptumorregistry.client.CaTRIPTumorRegistryClient client =
new gov.nih.nci.cagrid.catriptumorregistry.client.CaTRIPTumorRegistryClient(url);
CQLQueryResults results = client.query(getCQLQuery(fileName));
CQLQueryResultsIterator iter =
new CQLQueryResultsIterator(results, new FileInputStream(new File(clientConfig)));
if (WRITE_TO_FILE) {
writeToFile("tumor_registry_out.xml", fileName, results);
}
if (DISPLAY_DATA) {
System.out.println("Results for " + fileName);
while (iter.hasNext()) {
edu.duke.cabig.tumorregistry.domain.Patient de =
(edu.duke.cabig.tumorregistry.domain.Patient) iter.next();
System.out.println(de.getId() + " " + de.getSex());
}
System.out.println("---------------------");
}
}
