Java tutorial
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(By way * of non-limiting example, you will not contribute any code obtained by you under the GNU General Public License or other * so-called "reciprocal" license.) *******************************************************************************/ package edu.stanford.epad.epadws.xnat; import java.io.File; import java.io.FileInputStream; import java.io.IOException; import java.util.Collection; import java.util.HashSet; import java.util.Properties; import java.util.Set; import javax.servlet.http.HttpServletResponse; import org.apache.commons.httpclient.HttpClient; import org.apache.commons.httpclient.methods.PostMethod; import org.apache.commons.httpclient.methods.PutMethod; import org.apache.commons.io.IOUtils; import edu.stanford.epad.common.dicom.DicomReader; import edu.stanford.epad.common.util.EPADLogger; import edu.stanford.epad.epadws.aim.AIMUtil; import edu.stanford.epad.epadws.processing.events.EventTracker; /** * Methods for creating XNAT entities, such as projects, subjects, and experiments. * * * @author martin */ public class XNATCreationOperations { private static final EPADLogger log = EPADLogger.getInstance(); private static final String XNAT_UPLOAD_PROPERTIES_FILE_NAME = "xnat_upload.properties"; private static final EventTracker eventTracker = EventTracker.getInstance(); public static int createXNATProject(String xnatProjectLabel, String projectName, String description, String jsessionID) { String xnatProjectURL = XNATUtil.buildXNATProjectCreationURL(xnatProjectLabel, projectName, description); HttpClient client = new HttpClient(); PostMethod method = new PostMethod(xnatProjectURL); int xnatStatusCode; method.setRequestHeader("Cookie", "JSESSIONID=" + jsessionID); try { log.info("Invoking XNAT with URL " + xnatProjectURL); xnatStatusCode = client.executeMethod(method); if (XNATUtil.unexpectedXNATCreationStatusCode(xnatStatusCode)) log.warning("Failure calling XNAT to create project; status code = " + xnatStatusCode); else eventTracker.recordProjectEvent(jsessionID, projectName); } catch (IOException e) { log.warning("IO exception calling XNAT to create project", e); xnatStatusCode = HttpServletResponse.SC_INTERNAL_SERVER_ERROR; } finally { method.releaseConnection(); } if (xnatStatusCode == HttpServletResponse.SC_CONFLICT) xnatStatusCode = HttpServletResponse.SC_OK; return xnatStatusCode; } public static int createXNATSubject(String xnatProjectLabel, String patientID, String patientName, String jsessionID) { String xnatSubjectLabel = XNATUtil.subjectID2XNATSubjectLabel(patientID); String xnatSubjectURL = XNATUtil.buildXNATSubjectCreationURL(xnatProjectLabel, xnatSubjectLabel, patientName); HttpClient client = new HttpClient(); PostMethod method = new PostMethod(xnatSubjectURL); int xnatStatusCode; method.setRequestHeader("Cookie", "JSESSIONID=" + jsessionID); try { log.info("Creating patient " + patientName + " in project " + xnatProjectLabel + " in XNAT"); xnatStatusCode = client.executeMethod(method); if (XNATUtil.unexpectedXNATCreationStatusCode(xnatStatusCode)) log.warning( "Failure calling XNAT with URL " + xnatSubjectURL + "; status code = " + xnatStatusCode); else eventTracker.recordPatientEvent(jsessionID, xnatProjectLabel, xnatSubjectLabel); } catch (IOException e) { log.warning("Error calling XNAT with URL " + xnatSubjectURL, e); xnatStatusCode = HttpServletResponse.SC_INTERNAL_SERVER_ERROR; } finally { method.releaseConnection(); } if (xnatStatusCode == HttpServletResponse.SC_CONFLICT) xnatStatusCode = HttpServletResponse.SC_OK; return xnatStatusCode; } public static int createXNATDICOMStudyExperiment(String xnatProjectLabel, String xnatSubjectLabel, String studyUID, String jsessionID) { String xnatStudyURL = XNATUtil.buildXNATDICOMStudyCreationURL(xnatProjectLabel, xnatSubjectLabel, studyUID); HttpClient client = new HttpClient(); PutMethod putMethod = new PutMethod(xnatStudyURL); int xnatStatusCode; putMethod.setRequestHeader("Cookie", "JSESSIONID=" + jsessionID); try { log.info("Creating study " + studyUID + " for patient " + xnatSubjectLabel + " in project " + xnatProjectLabel + " in XNAT"); xnatStatusCode = client.executeMethod(putMethod); if (XNATUtil.unexpectedXNATCreationStatusCode(xnatStatusCode)) log.warning("Failure calling XNAT with URL " + xnatStudyURL + "; status code = " + xnatStatusCode); else eventTracker.recordStudyEvent(jsessionID, xnatProjectLabel, xnatSubjectLabel, studyUID); } catch (IOException e) { log.warning("Error calling XNAT with URL " + xnatStudyURL, e); xnatStatusCode = HttpServletResponse.SC_INTERNAL_SERVER_ERROR; } finally { putMethod.releaseConnection(); } if (xnatStatusCode == HttpServletResponse.SC_CONFLICT) xnatStatusCode = HttpServletResponse.SC_OK; return xnatStatusCode; } /** * Take a directory containing a list of DICOM files and create XNAT representations of the each DICOM image in the * directory. * <p> * This method expects a properties file called xnat_upload.properties in the upload directory. This file should * contain a property called XNATProjectName, which identifies the project ID for the new patients and their studies, * and XNATSessionID, which contains the session key of the user initiating the upload. * <p> * If the header of a DICOM image is missing the patient name, patient ID, or study instance UID field then it is * skipped. * * @param dicomUploadDirectory */ public static void createXNATEntitiesFromDICOMFilesInUploadDirectory(File dicomUploadDirectory) { String propertiesFilePath = dicomUploadDirectory.getAbsolutePath() + File.separator + XNAT_UPLOAD_PROPERTIES_FILE_NAME; File xnatUploadPropertiesFile = new File(propertiesFilePath); try { Thread.sleep(2000); // Give it a couple of seconds for the property file to appear } catch (InterruptedException e1) { } if (!xnatUploadPropertiesFile.exists()) log.warning("Could not find XNAT upload properties file " + propertiesFilePath); else { Properties xnatUploadProperties = new Properties(); FileInputStream propertiesFileStream = null; try { log.info("Found XNAT upload properties file " + propertiesFilePath); propertiesFileStream = new FileInputStream(xnatUploadPropertiesFile); xnatUploadProperties.load(propertiesFileStream); String xnatProjectLabel = xnatUploadProperties.getProperty("XNATProjectName"); String xnatSessionID = xnatUploadProperties.getProperty("XNATSessionID"); String xnatUserName = xnatUploadProperties.getProperty("XNATUserName"); int numberOfDICOMFiles = 0; if (xnatProjectLabel != null && xnatSessionID != null) { for (File dicomFile : listDICOMFiles(dicomUploadDirectory)) { String dicomPatientName = DicomReader.getPatientName(dicomFile); String dicomPatientID = DicomReader.getPatientID(dicomFile); String studyUID = DicomReader.getStudyIUID(dicomFile); String modality = DicomReader.getModality(dicomFile); if (dicomPatientID != null && dicomPatientName != null && studyUID != null) { dicomPatientName = dicomPatientName.toUpperCase(); // DCM4CHEE stores the patient name as upper case String xnatSubjectLabel = XNATUtil.subjectID2XNATSubjectLabel(dicomPatientID); createXNATSubject(xnatProjectLabel, xnatSubjectLabel, dicomPatientName, xnatSessionID); createXNATDICOMStudyExperiment(xnatProjectLabel, xnatSubjectLabel, studyUID, xnatSessionID); if ("SEG".equals(modality)) { try { AIMUtil.generateAIMFileForDSO(dicomFile, xnatUserName, xnatProjectLabel); } catch (Exception x) { log.warning("Error generating DSO Annotation:", x); } } } else log.warning("Missing patient name, ID or studyUID in DICOM file " + dicomFile.getAbsolutePath()); numberOfDICOMFiles++; } if (numberOfDICOMFiles != 0) log.info("Found " + numberOfDICOMFiles + " DICOM file(s) in upload directory"); else log.warning("No DICOM files found in upload directory!"); } else { log.warning( "Missing XNAT project name and/or session ID in properties file" + propertiesFilePath); } } catch (IOException e) { log.warning("Error processing upload in directory " + propertiesFilePath, e); } finally { IOUtils.closeQuietly(propertiesFileStream); } } } private static Collection<File> listDICOMFiles(File dir) { Set<File> files = new HashSet<File>(); if (dir.listFiles() != null) { for (File entry : dir.listFiles()) { if (isDicomFile(entry)) files.add(entry); else files.addAll(listDICOMFiles(entry)); } } return files; } private static boolean isDicomFile(File file) { return file.isFile() && (file.getName().toLowerCase().endsWith(".dcm") || file.getName().toLowerCase().endsWith(".dso")); // return file.isFile() && DicomFileUtil.hasMagicWordInHeader(file); } }