diff --git a/.gitignore b/.gitignore
index 3c81f317e2..dbd12221d2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -26,9 +26,7 @@ docker-compose/boutiques/boutiques
shanoir-ng-preclinical/null*
shanoir-uploader/src/main/resources/key
shanoir-uploader/src/main/resources/profile.OFSEP/key
-shanoir-uploader/src/main/resources/profile.OFSEP-qualif/key
-shanoir-uploader/src/main/resources/profile.OFSEP-NG-qualif/key
-shanoir-uploader/src/main/resources/profile.OFSEP-NG/key
+shanoir-uploader/src/main/resources/profile.OFSEP-Qualif/key
shanoir-uploader/src/main/resources/pseudonymus
shanoir-uploader/src/test/resources/acr_phantom_t1/
shanoir-ng-tests/tests/geckodriver.log
diff --git a/shanoir-ng-anonymization/src/main/resources/anonymization.xlsx b/shanoir-ng-anonymization/src/main/resources/anonymization.xlsx
index 9b3181e3c8..0431e6aa03 100644
Binary files a/shanoir-ng-anonymization/src/main/resources/anonymization.xlsx and b/shanoir-ng-anonymization/src/main/resources/anonymization.xlsx differ
diff --git a/shanoir-ng-back/pom.xml b/shanoir-ng-back/pom.xml
index 2c05c1ed24..cb2bba7be8 100644
--- a/shanoir-ng-back/pom.xml
+++ b/shanoir-ng-back/pom.xml
@@ -49,7 +49,7 @@ along with this program. If not, see https://www.gnu.org/licenses/gpl-3.0.html
<java.version>17</java.version>
<mapstruct.version>1.5.3.Final</mapstruct.version>
<keycloak.version>22.0.1</keycloak.version>
- <dcm4che.version>5.30.0</dcm4che.version>
+ <dcm4che.version>5.31.0</dcm4che.version>
</properties>
<dependencyManagement>
diff --git a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/datasetacquisition/model/mr/ContrastAgentUsed.java b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/datasetacquisition/model/mr/ContrastAgentUsed.java
index 99f00d5abb..9b84efff50 100644
--- a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/datasetacquisition/model/mr/ContrastAgentUsed.java
+++ b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/datasetacquisition/model/mr/ContrastAgentUsed.java
@@ -41,7 +41,10 @@ public enum ContrastAgentUsed {
GADOVIST(7),
// Clariscan
- CLARISCAN(8);
+ CLARISCAN(8),
+
+ // Dotarem
+ DOTAREM(9);
private int id;
diff --git a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/importer/dto/Serie.java b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/importer/dto/Serie.java
index 86b6159ae4..8447d4c985 100644
--- a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/importer/dto/Serie.java
+++ b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/importer/dto/Serie.java
@@ -245,10 +245,11 @@ public void setSequenceName(String sequenceName) {
public DatasetFile getFirstDatasetFileForCurrentSerie() {
if (getDatasets() == null
- || getDatasets().get(0) == null
- || getDatasets().get(0).getExpressionFormats() == null
- || getDatasets().get(0).getExpressionFormats().get(0) == null
- || getDatasets().get(0).getExpressionFormats().get(0).getDatasetFiles() == null) {
+ || getDatasets().get(0) == null
+ || getDatasets().get(0).getExpressionFormats() == null
+ || getDatasets().get(0).getExpressionFormats().get(0) == null
+ || getDatasets().get(0).getExpressionFormats().get(0).getDatasetFiles() == null
+ || getDatasets().get(0).getExpressionFormats().get(0).getDatasetFiles().get(0) == null) {
return null;
}
return getDatasets().get(0).getExpressionFormats().get(0).getDatasetFiles().get(0);
diff --git a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/importer/service/ImporterService.java b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/importer/service/ImporterService.java
index 93db909824..2f38a45451 100644
--- a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/importer/service/ImporterService.java
+++ b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/importer/service/ImporterService.java
@@ -221,7 +221,7 @@ private Set<DatasetAcquisition> generateAcquisitions(Examination examination, Im
try {
dicomAttributes = dicomProcessing.getDicomObjectAttributes(serie.getFirstDatasetFileForCurrentSerie(), serie.getIsEnhanced());
} catch (IOException e) {
- throw new ShanoirException("Unable to retrieve dicom attributes in file " + serie.getFirstDatasetFileForCurrentSerie().getPath(), e);
+ throw new ShanoirException("Unable to retrieve dicom attributes in serie: " + serie.getSeriesDescription(), e);
}
// Generate acquisition object with all sub objects : datasets, protocols, expressions, ...
diff --git a/shanoir-ng-front/src/app/import/query-pacs/query-pacs.component.html b/shanoir-ng-front/src/app/import/query-pacs/query-pacs.component.html
index b0bc8e6ec0..0470f0d26e 100644
--- a/shanoir-ng-front/src/app/import/query-pacs/query-pacs.component.html
+++ b/shanoir-ng-front/src/app/import/query-pacs/query-pacs.component.html
@@ -14,7 +14,7 @@
<form [formGroup]="form" novalidate>
- <div class="header command-zone">1. Query Neurinfo PACS</div>
+ <div class="header command-zone">1. Query PACS</div>
<fieldset class="step">
<ol>
<legend>
@@ -69,4 +69,4 @@
</ol>
</fieldset>
<button class="next" [disabled]="!form.valid" (click)="queryPACS()">Query</button>
-</form>
\ No newline at end of file
+</form>
diff --git a/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterApiController.java b/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterApiController.java
index 01585a3d2f..2747cbfd2f 100644
--- a/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterApiController.java
+++ b/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterApiController.java
@@ -29,7 +29,6 @@
import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
-import java.util.Iterator;
import java.util.List;
import java.util.Properties;
import java.util.regex.Matcher;
@@ -75,8 +74,6 @@
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.core.io.ByteArrayResource;
-import org.springframework.http.HttpEntity;
-import org.springframework.http.HttpMethod;
import org.springframework.http.HttpStatus;
import org.springframework.http.HttpStatusCode;
import org.springframework.http.MediaType;
@@ -87,7 +84,6 @@
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RequestPart;
-import org.springframework.web.client.RestTemplate;
import org.springframework.web.multipart.MultipartFile;
import com.fasterxml.jackson.databind.ObjectMapper;
@@ -145,9 +141,6 @@ public class ImporterApiController implements ImporterApi {
@Value("${shanoir.import.directory}")
private String importDir;
- @Autowired
- private RestTemplate restTemplate;
-
@Autowired
private DicomDirGeneratorService dicomDirGeneratorService;
@@ -268,7 +261,6 @@ public ResponseEntity<Void> startImportJob(
final File importJobDir = new File(userImportDir, tempDirId);
if (importJobDir.exists()) {
importJob.setWorkFolder(importJobDir.getAbsolutePath());
- cleanSeries(importJob);
LOG.info("Starting import job for user {} (userId: {}) with import job folder: {}", KeycloakUtil.getTokenUserName(), userId, importJob.getWorkFolder());
importerManagerService.manageImportJob(importJob);
return new ResponseEntity<>(HttpStatus.OK);
@@ -279,24 +271,6 @@ public ResponseEntity<Void> startImportJob(
}
}
- private void cleanSeries(final ImportJob importJob) {
- for (Iterator<Patient> patientIt = importJob.getPatients().iterator(); patientIt.hasNext();) {
- Patient patient = patientIt.next();
- List<Study> studies = patient.getStudies();
- for (Iterator<Study> studyIt = studies.iterator(); studyIt.hasNext();) {
- Study study = studyIt.next();
- List<Serie> series = study.getSeries();
- for (Iterator<Serie> serieIt = series.iterator(); serieIt.hasNext();) {
- Serie serie = serieIt.next();
- if (serie.isIgnored() || serie.isErroneous() || !serie.getSelected()) {
- LOG.info("Serie {} cleaned from import (ignored, erroneous, not selected).", serie.getSeriesDescription());
- serieIt.remove();
- }
- }
- }
- }
- }
-
@Override
public ResponseEntity<ImportJob> queryPACS(
@Parameter(name = "DicomQuery", required = true) @Valid @RequestBody final DicomQuery dicomQuery)
@@ -309,7 +283,6 @@ public ResponseEntity<ImportJob> queryPACS(
importJob.setWorkFolder("");
importJob.setFromPacs(true);
importJob.setUserId(KeycloakUtil.getTokenUserId());
-
} catch (ShanoirException e) {
throw new RestServiceException(
new ErrorModel(HttpStatus.UNPROCESSABLE_ENTITY.value(), e.getMessage(), null));
@@ -332,12 +305,11 @@ public ResponseEntity<ImportJob> importDicomZipFile(
MockMultipartFile multiPartFile;
try {
multiPartFile = new MockMultipartFile(tempFile.getName(), tempFile.getName(), APPLICATION_ZIP, new FileInputStream(tempFile.getAbsolutePath()));
-
// Import dicomfile
return uploadDicomZipFile(multiPartFile);
} catch (IOException e) {
LOG.error("ERROR while loading zip fiole, please contact an administrator");
- e.printStackTrace();
+ LOG.error(e.getMessage(), e);
return new ResponseEntity<>(HttpStatus.NOT_ACCEPTABLE);
} finally {
// Delete temp file which is useless now
@@ -374,12 +346,9 @@ public ResponseEntity<EegImportJob> uploadEEGZipFile(
if (!userImportDir.exists()) {
userImportDir.mkdirs(); // create if not yet existing
}
-
// Unzip the file and get the elements
File tempFile = ImportUtils.saveTempFile(userImportDir, eegFile);
-
File importJobDir = ImportUtils.saveTempFileCreateFolderAndUnzip(tempFile, eegFile, false);
-
EegImportJob importJob = new EegImportJob();
importJob.setUserId(userId);
importJob.setArchive(eegFile.getOriginalFilename());
diff --git a/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterManagerService.java b/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterManagerService.java
index 9d5a0c3310..60f8dc02cc 100644
--- a/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterManagerService.java
+++ b/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterManagerService.java
@@ -142,35 +142,18 @@ public void manageImportJob(final ImportJob importJob) {
} else {
throw new ShanoirException("Unsupported type of import.");
}
+ // we do the clean series here: at this point we are sure for all imports, that the ImagesCreatorAndDicomFileAnalyzer
+ // has been run and correctly classified everything. So no need to check afterwards for erroneous series.
+ cleanSeries(importJob);
event.setProgress(0.25F);
eventService.publishEvent(event);
for (Iterator<Patient> patientsIt = patients.iterator(); patientsIt.hasNext();) {
Patient patient = patientsIt.next();
- // perform anonymization only in case of profile explicitly set
- if (importJob.getAnonymisationProfileToUse() == null || !importJob.getAnonymisationProfileToUse().isEmpty()) {
- String anonymizationProfile = (String) this.rabbitTemplate.convertSendAndReceive(RabbitMQConfiguration.STUDY_ANONYMISATION_PROFILE_QUEUE, importJob.getStudyId());
- importJob.setAnonymisationProfileToUse(anonymizationProfile);
- }
- ArrayList<File> dicomFiles = getDicomFilesForPatient(importJob, patient, importJobDir.getAbsolutePath());
- final Subject subject = patient.getSubject();
-
- if (subject == null) {
- LOG.error("Error: subject == null in importJob.");
- throw new ShanoirException("Error: subject == null in importJob.");
- }
-
- final String subjectName = subject.getName();
-
- event.setMessage("Pseudonymizing DICOM files for subject [" + subjectName + "]...");
- eventService.publishEvent(event);
-
- try {
- ANONYMIZER.anonymizeForShanoir(dicomFiles, importJob.getAnonymisationProfileToUse(), subjectName, subjectName);
- } catch (Exception e) {
- LOG.error(e.getMessage(), e);
- throw new ShanoirException("Error during pseudonymization.");
+ // DICOM files coming from ShUp are already pseudonymized
+ if (!importJob.isFromShanoirUploader()) {
+ pseudonymize(importJob, event, importJobDir, patient);
}
Long converterId = importJob.getConverterId();
datasetsCreatorAndNIfTIConverter.createDatasetsAndRunConversion(patient, importJobDir, converterId, importJob);
@@ -188,6 +171,54 @@ public void manageImportJob(final ImportJob importJob) {
}
}
+ /**
+ * cleanSeries is important here for import-from-zip file: when the ImagesCreatorAndDicomFileAnalyzer
+ * has declared some series as e.g. erroneous, we have to remove them from the import. For import-from
+ * pacs or from-sh-up it is different, as the ImagesCreatorAndDicomFileAnalyzer is called afterwards.
+ * Same here for multi-exam-imports: it calls uploadDicomZipFile method, where series could be classed
+ * as erroneous and when startImportJob is called, we want them to be removed from the import.
+ *
+ * @param importJob
+ */
+ private void cleanSeries(final ImportJob importJob) {
+ for (Iterator<Patient> patientIt = importJob.getPatients().iterator(); patientIt.hasNext();) {
+ Patient patient = patientIt.next();
+ List<Study> studies = patient.getStudies();
+ for (Iterator<Study> studyIt = studies.iterator(); studyIt.hasNext();) {
+ Study study = studyIt.next();
+ List<Serie> series = study.getSeries();
+ for (Iterator<Serie> serieIt = series.iterator(); serieIt.hasNext();) {
+ Serie serie = serieIt.next();
+ if (serie.isIgnored() || serie.isErroneous() || !serie.getSelected()) {
+ LOG.info("Serie {} cleaned from import (ignored, erroneous, not selected).", serie.getSeriesDescription());
+ serieIt.remove();
+ }
+ }
+ }
+ }
+ }
+
+ private void pseudonymize(final ImportJob importJob, ShanoirEvent event, final File importJobDir, Patient patient)
+ throws FileNotFoundException, ShanoirException {
+ if (importJob.getAnonymisationProfileToUse() == null || !importJob.getAnonymisationProfileToUse().isEmpty()) {
+ ArrayList<File> dicomFiles = getDicomFilesForPatient(importJob, patient, importJobDir.getAbsolutePath());
+ final Subject subject = patient.getSubject();
+ if (subject == null) {
+ LOG.error("Error: subject == null in importJob.");
+ throw new ShanoirException("Error: subject == null in importJob.");
+ }
+ final String subjectName = subject.getName();
+ event.setMessage("Pseudonymizing DICOM files for subject [" + subjectName + "]...");
+ eventService.publishEvent(event);
+ try {
+ ANONYMIZER.anonymizeForShanoir(dicomFiles, importJob.getAnonymisationProfileToUse(), subjectName, subjectName);
+ } catch (Exception e) {
+ LOG.error(e.getMessage(), e);
+ throw new ShanoirException("Error during pseudonymization.");
+ }
+ }
+ }
+
private void sendFailureMail(ImportJob importJob, String errorMessage) {
EmailDatasetImportFailed generatedMail = new EmailDatasetImportFailed();
generatedMail.setExaminationId(importJob.getExaminationId().toString());
@@ -195,9 +226,7 @@ private void sendFailureMail(ImportJob importJob, String errorMessage) {
generatedMail.setSubjectName(importJob.getSubjectName());
generatedMail.setStudyName(importJob.getStudyName());
generatedMail.setUserId(importJob.getUserId());
-
generatedMail.setErrorMessage(errorMessage != null ? errorMessage : "An unexpected error occured, please contact Shanoir support.");
-
sendMail(importJob, generatedMail);
}
@@ -208,7 +237,6 @@ private void sendFailureMail(ImportJob importJob, String errorMessage) {
*/
private void sendMail(ImportJob job, EmailBase email) {
List<Long> recipients = new ArrayList<>();
-
// Get all recpients
List<StudyUser> users = (List<StudyUser>) studyUserRightRepo.findByStudyId(job.getStudyId());
for (StudyUser user : users) {
@@ -221,7 +249,6 @@ private void sendMail(ImportJob job, EmailBase email) {
return;
}
email.setRecipients(recipients);
-
try {
rabbitTemplate.convertAndSend(RabbitMQConfiguration.IMPORT_DATASET_FAILED_MAIL_QUEUE, objectMapper.writeValueAsString(email));
} catch (AmqpException | JsonProcessingException e) {
@@ -310,8 +337,8 @@ private void downloadAndMoveDicomFilesToImportJobDir(final File importJobDir, Li
/**
* Using Java HashSet here to avoid duplicate files for Pseudonymization.
- * For performance reasons already init with 5000 buckets, assuming,
- * that we will normally never have more than 5000 files to process.
+ * For performance reasons already init with 10000 buckets, assuming,
+ * that we will normally never have more than 10000 files to process.
* Maybe to be evaluated later with more bigger imports.
*
* @param importJob
@@ -321,7 +348,7 @@ private void downloadAndMoveDicomFilesToImportJobDir(final File importJobDir, Li
* @throws FileNotFoundException
*/
private ArrayList<File> getDicomFilesForPatient(final ImportJob importJob, final Patient patient, final String workFolderPath) throws FileNotFoundException {
- Set<File> pathsSet = new HashSet<>(5000);
+ Set<File> pathsSet = new HashSet<>(10000);
List<Study> studies = patient.getStudies();
for (Iterator<Study> studiesIt = studies.iterator(); studiesIt.hasNext();) {
Study study = studiesIt.next();
diff --git a/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/DatasetsCreatorAndNIfTIConverterService.java b/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/DatasetsCreatorAndNIfTIConverterService.java
index 2c8940a472..ad436371a6 100644
--- a/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/DatasetsCreatorAndNIfTIConverterService.java
+++ b/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/DatasetsCreatorAndNIfTIConverterService.java
@@ -36,13 +36,10 @@
import java.util.Set;
import java.util.stream.Collectors;
-import jakarta.transaction.Transactional;
-
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.filefilter.DirectoryFileFilter;
import org.apache.commons.io.filefilter.RegexFileFilter;
-import org.apache.poi.ss.formula.eval.NotImplementedException;
import org.shanoir.ng.importer.model.Dataset;
import org.shanoir.ng.importer.model.DatasetFile;
import org.shanoir.ng.importer.model.DiffusionGradient;
@@ -69,6 +66,8 @@
import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.stereotype.Service;
+import jakarta.transaction.Transactional;
+
/**
* The NIfTIConverter does the actual conversion of dcm to nii files.
* To use the converter the dcm files have to be put in separate folders.
@@ -149,36 +148,35 @@ public void createDatasetsAndRunConversion(Patient patient, File workFolder, Lon
Study study = studiesIt.next();
List<Serie> series = study.getSelectedSeries();
float progress = 0;
-
int nbSeries = series.size();
int cpt = 1;
-
for (Iterator<Serie> seriesIt = series.iterator(); seriesIt.hasNext();) {
Serie serie = seriesIt.next();
-
- progress = progress + (0.5f / series.size());
- importJob.getShanoirEvent().setProgress(progress);
- importJob.getShanoirEvent().setMessage("Converting to NIfTI for serie [" + (serie.getProtocolName() == null ? serie.getSeriesInstanceUID() : serie.getProtocolName()) + "] (" + cpt + "/" + nbSeries + ")...");
- shanoirEventService.publishEvent(importJob.getShanoirEvent());
-
- File serieIDFolderFile = createSerieIDFolderAndMoveFiles(workFolder, seriesFolderFile, serie);
- boolean serieIdentifiedForNotSeparating;
- try {
- serieIdentifiedForNotSeparating = checkSerieForPropertiesString(serie, seriesProperties);
- // if the serie is not one of the series, that should not be separated, please separate the series,
- // otherwise just do not separate the series and keep all images for one nii conversion
- serie.setDatasets(new ArrayList<Dataset>());
- constructDicom(serieIDFolderFile, serie, serieIdentifiedForNotSeparating);
- // we exclude MR Spectroscopy (MRS) from NIfTI conversion, see MRS on GitHub Wiki
- if (serie.getIsSpectroscopy() != null && !serie.getIsSpectroscopy()) {
- constructNifti(serieIDFolderFile, serie, converterId);
+ // do not convert an erroneous serie
+ if (!serie.isErroneous() && !serie.isIgnored()) {
+ progress = progress + (0.5f / series.size());
+ importJob.getShanoirEvent().setProgress(progress);
+ importJob.getShanoirEvent().setMessage("Converting to NIfTI for serie [" + (serie.getProtocolName() == null ? serie.getSeriesInstanceUID() : serie.getProtocolName()) + "] (" + cpt + "/" + nbSeries + ")...");
+ shanoirEventService.publishEvent(importJob.getShanoirEvent());
+ File serieIDFolderFile = createSerieIDFolderAndMoveFiles(workFolder, seriesFolderFile, serie);
+ boolean serieIdentifiedForNotSeparating;
+ try {
+ serieIdentifiedForNotSeparating = checkSerieForPropertiesString(serie, seriesProperties);
+ // if the serie is not one of the series, that should not be separated, please separate the series,
+ // otherwise just do not separate the series and keep all images for one nii conversion
+ serie.setDatasets(new ArrayList<Dataset>());
+ constructDicom(serieIDFolderFile, serie, serieIdentifiedForNotSeparating);
+ // we exclude MR Spectroscopy (MRS) from NIfTI conversion, see MRS on GitHub Wiki
+ if (serie.getIsSpectroscopy() != null && !serie.getIsSpectroscopy()) {
+ constructNifti(serieIDFolderFile, serie, converterId);
+ }
+ } catch (NoSuchFieldException | SecurityException e) {
+ LOG.error(e.getMessage());
}
- } catch (NoSuchFieldException | SecurityException e) {
- LOG.error(e.getMessage());
+ // as images/non-images are migrated to datasets, clear the list now
+ serie.getImages().clear();
+ serie.getNonImages().clear();
}
- // as images/non-images are migrated to datasets, clear the list now
- serie.getImages().clear();
- serie.getNonImages().clear();
cpt++;
}
}
diff --git a/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dicom/ImagesCreatorAndDicomFileAnalyzerService.java b/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dicom/ImagesCreatorAndDicomFileAnalyzerService.java
index 14cda143d7..0549c1be25 100644
--- a/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dicom/ImagesCreatorAndDicomFileAnalyzerService.java
+++ b/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dicom/ImagesCreatorAndDicomFileAnalyzerService.java
@@ -157,7 +157,7 @@ private void filterAndCreateImages(String folderFileAbsolutePath, Serie serie, b
for (Iterator<Instance> instancesIt = instances.iterator(); instancesIt.hasNext();) {
Instance instance = instancesIt.next();
File instanceFile = getFileFromInstance(instance, serie, folderFileAbsolutePath, isImportFromPACS);
- processOneDicomFileForAllInstances(instanceFile, images, folderFileAbsolutePath);
+ processDicomFilePerInstanceAndCreateImage(instanceFile, images, folderFileAbsolutePath);
}
serie.setNonImages(nonImages);
serie.setNonImagesNumber(nonImages.size());
@@ -221,14 +221,13 @@ public File getFileFromInstance(Instance instance, Serie serie, String folderFil
* @param nonImages
* @param images
*/
- private void processOneDicomFileForAllInstances(File dicomFile, List<Image> images, String folderFileAbsolutePath) throws Exception {
+ private void processDicomFilePerInstanceAndCreateImage(File dicomFile, List<Image> images, String folderFileAbsolutePath) throws Exception {
try (DicomInputStream dIS = new DicomInputStream(dicomFile)) { // keep try to finally close input stream
Attributes attributes = dIS.readDataset();
// Some DICOM files with a particular SOPClassUID are ignored: such as Raw Data Storage etc.
if (DicomSerieAndInstanceAnalyzer.checkInstanceIsIgnored(attributes)) {
// do nothing here as instances list will be emptied after split between images and non-images
} else {
- // divide here between non-images and images, non-images at first
Image image = new Image();
/**
* Attention: the path of each image is always relative: either to the temporary folder created
@@ -242,7 +241,7 @@ private void processOneDicomFileForAllInstances(File dicomFile, List<Image> imag
} catch (IOException iOE) {
throw iOE;
} catch (Exception e) {
- LOG.error("Error while processing DICOM file: " + dicomFile.getAbsolutePath());
+ LOG.error("Error while processing DICOM file, one for entire serie: " + dicomFile.getAbsolutePath());
throw e;
}
}
diff --git a/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dicom/query/QueryPACSService.java b/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dicom/query/QueryPACSService.java
index e04a4a8ea5..d81580eff1 100644
--- a/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dicom/query/QueryPACSService.java
+++ b/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dicom/query/QueryPACSService.java
@@ -26,19 +26,22 @@
import org.apache.commons.lang3.StringUtils;
import org.dcm4che3.data.Attributes;
+import org.dcm4che3.data.ElementDictionary;
import org.dcm4che3.data.Tag;
import org.dcm4che3.data.UID;
+import org.dcm4che3.data.VR;
import org.dcm4che3.net.ApplicationEntity;
import org.dcm4che3.net.Association;
import org.dcm4che3.net.Connection;
import org.dcm4che3.net.Device;
-import org.dcm4che3.net.DimseRSP;
+import org.dcm4che3.net.DimseRSPHandler;
import org.dcm4che3.net.IncompatibleConnectionException;
+import org.dcm4che3.net.Priority;
import org.dcm4che3.net.QueryOption;
+import org.dcm4che3.net.Status;
import org.dcm4che3.net.pdu.AAssociateRQ;
import org.dcm4che3.net.pdu.PresentationContext;
import org.dcm4che3.net.service.QueryRetrieveLevel;
-import org.dcm4che3.tool.findscu.FindSCU.InformationModel;
import org.shanoir.ng.importer.dicom.DicomSerieAndInstanceAnalyzer;
import org.shanoir.ng.importer.dicom.InstanceNumberSorter;
import org.shanoir.ng.importer.dicom.SeriesNumberSorter;
@@ -52,7 +55,6 @@
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.stereotype.Service;
-import org.weasis.dicom.op.CFind;
import org.weasis.dicom.op.CMove;
import org.weasis.dicom.param.AdvancedParams;
import org.weasis.dicom.param.DicomNode;
@@ -93,26 +95,74 @@ public class QueryPACSService {
private DicomNode called;
+ private Association association;
+
@Value("${shanoir.import.pacs.store.aet.called.name}")
private String calledNameSCP;
public QueryPACSService() {} // for ShUp usage
+ /**
+ * Used within microservice MS Import on the server, via PostConstruct.
+ */
@PostConstruct
private void initDicomNodes() {
// Initialize connection configuration parameters here: to be used for all queries
- this.calling = new DicomNode(callingName, callingHost, callingPort); // ShUp
- this.called = new DicomNode(calledName, calledHost, calledPort); // PACS
+ this.calling = new DicomNode(callingName, callingHost, callingPort);
+ this.called = new DicomNode(calledName, calledHost, calledPort);
+ LOG.info("Query: DicomNodes initialized via CDI: calling ({}, {}, {}) and called ({}, {}, {})",
+ callingName, callingHost, callingPort, calledName, calledHost, calledPort);
}
+ /**
+ * Do configuration of QueryPACSService from outside. Used by ShanoirUploader.
+ *
+ * @param calling
+ * @param called
+ * @param calledNameSCP
+ */
public void setDicomNodes(DicomNode calling, DicomNode called, String calledNameSCP) {
this.calling = calling;
this.called = called;
this.calledNameSCP = calledNameSCP;
this.maxPatientsFromPACS = 10;
+ LOG.info("Query: DicomNodes initialized via method call (ShUp): calling ({}, {}, {}) and called ({}, {}, {})",
+ calling.getAet(), calling.getHostname(), calling.getPort(), called.getAet(), called.getHostname(), called.getPort());
+ }
+
+ private void connectAssociation(DicomNode calling, DicomNode called) {
+ ExecutorService executor = Executors.newSingleThreadExecutor();
+ ScheduledExecutorService scheduledExecutor = Executors.newSingleThreadScheduledExecutor();
+ try {
+ // calling: create a device, a connection and an application entity
+ Device device = new Device(this.getClass().getName());
+ device.setExecutor(executor);
+ device.setScheduledExecutor(scheduledExecutor);
+ ApplicationEntity callingAE = new ApplicationEntity(calling.getAet());
+ Connection callingConn = new Connection();
+ device.addConnection(callingConn);
+ device.addApplicationEntity(callingAE);
+ callingAE.addConnection(callingConn);
+ // called: create a connection and an AAssociateRQ
+ Connection calledConn = new Connection(null, called.getHostname(), called.getPort());
+ AAssociateRQ aarq = new AAssociateRQ();
+ aarq.setCallingAET(calling.getAet());
+ aarq.setCalledAET(called.getAet());
+ aarq.addPresentationContext(new PresentationContext(1,
+ UID.Verification, UID.ImplicitVRLittleEndian));
+ aarq.addPresentationContext(new PresentationContext(2,
+ UID.PatientRootQueryRetrieveInformationModelFind, UID.ImplicitVRLittleEndian));
+ aarq.addPresentationContext(new PresentationContext(3,
+ UID.StudyRootQueryRetrieveInformationModelFind, UID.ImplicitVRLittleEndian));
+ this.association = callingAE.connect(calledConn, aarq);
+ LOG.info("connectAssociation finished between calling {} and called {}", calling.getAet(), called.getAet());
+ } catch (IOException | InterruptedException | IncompatibleConnectionException | GeneralSecurityException e) {
+ LOG.error(e.getMessage(), e);
+ }
}
public ImportJob queryCFIND(DicomQuery dicomQuery) throws ShanoirImportException {
+ connectAssociation(calling, called);
ImportJob importJob = new ImportJob();
/**
* In case of any patient specific search field is filled, work on patient level. Highest priority.
@@ -122,7 +172,7 @@ public ImportJob queryCFIND(DicomQuery dicomQuery) throws ShanoirImportException
|| StringUtils.isNotBlank(dicomQuery.getPatientBirthDate())) {
// For Patient Name and Patient ID, wild card search is not allowed
if (!dicomQuery.getPatientName().contains("*") && !dicomQuery.getPatientID().contains("*")) {
- queryPatientLevel(dicomQuery, calling, called, importJob);
+ queryPatientLevel(dicomQuery, importJob);
}
// @Todo: implement wild card search
// Do Fuzzy search on base of patient name here
@@ -136,13 +186,26 @@ public ImportJob queryCFIND(DicomQuery dicomQuery) throws ShanoirImportException
*/
} else if (StringUtils.isNotBlank(dicomQuery.getStudyDescription())
|| StringUtils.isNotBlank(dicomQuery.getStudyDate())) {
- queryStudyLevel(dicomQuery, calling, called, importJob);
+ queryStudyLevel(dicomQuery, importJob);
} else {
throw new ShanoirImportException("DicomQuery: missing parameters.");
}
+ releaseAssociation();
return importJob;
}
+ private void releaseAssociation() {
+ try {
+ this.association.release();
+ } catch (IOException e) {
+ LOG.error(e.getMessage(), e);
+ }
+ ExecutorService executorService = (ExecutorService) this.association.getDevice().getExecutor();
+ executorService.shutdown();
+ this.association.getDevice().getScheduledExecutor().shutdown();
+ LOG.info("releaseAssociation finished between calling {} and called {}", calling.getAet(), called.getAet());
+ }
+
public void queryCMOVE(Serie serie) {
queryCMOVE(serie.getSeriesInstanceUID());
}
@@ -163,61 +226,32 @@ public void handleProgression(DicomProgress progress) {
}
public boolean queryECHO(String calledAET, String hostName, int port, String callingAET) {
+ connectAssociation(calling, called);
LOG.info("DICOM ECHO: Starting with configuration {}, {}, {} <- {}", calledAET, hostName, port, callingAET);
- ExecutorService executor = Executors.newSingleThreadExecutor();
- ScheduledExecutorService scheduledExecutor = Executors.newSingleThreadScheduledExecutor();
try {
- // set up calling configuration
- Device device = new Device("c-echo-scu");
- ApplicationEntity callingAE = new ApplicationEntity(callingAET);
- Connection callingConn = new Connection();
- device.addApplicationEntity(callingAE);
- device.addConnection(callingConn);
- device.setExecutor(executor);
- device.setScheduledExecutor(scheduledExecutor);
- callingAE.addConnection(callingConn);
-
- Connection calledConn = new Connection(null, hostName, port);
- AAssociateRQ aarq = new AAssociateRQ();
- aarq.setCallingAET(callingAET);
- aarq.setCalledAET(calledAET);
- aarq.addPresentationContext(new PresentationContext(1,
- UID.Verification, UID.ImplicitVRLittleEndian));
- Association as = callingAE.connect(calledConn, aarq);
- as.cecho();
- as.release();
+ this.association.cecho();
} catch (IOException e) {
LOG.error(e.getMessage(), e);
return false;
} catch (InterruptedException e) {
LOG.error(e.getMessage(), e);
return false;
- } catch (IncompatibleConnectionException e) {
- LOG.error(e.getMessage(), e);
- return false;
- } catch (GeneralSecurityException e) {
- LOG.error(e.getMessage(), e);
- return false;
- } finally {
- executor.shutdown();
- scheduledExecutor.shutdown();
- }
+ }
+ releaseAssociation();
return true;
}
/**
* This method queries on patient root level.
* @param dicomQuery
- * @param calling
- * @param called
* @param importJob
*/
- private void queryPatientLevel(DicomQuery dicomQuery, DicomNode calling, DicomNode called, ImportJob importJob) {
+ private void queryPatientLevel(DicomQuery dicomQuery, ImportJob importJob) {
DicomParam patientName = initDicomParam(Tag.PatientName, dicomQuery.getPatientName());
DicomParam patientID = initDicomParam(Tag.PatientID, dicomQuery.getPatientID());
DicomParam patientBirthDate = initDicomParam(Tag.PatientBirthDate, dicomQuery.getPatientBirthDate());
DicomParam[] params = { patientName, patientID, patientBirthDate, new DicomParam(Tag.PatientBirthName), new DicomParam(Tag.PatientSex) };
- List<Attributes> attributesPatients = queryCFIND(params, QueryRetrieveLevel.PATIENT, calling, called);
+ List<Attributes> attributesPatients = queryCFind(params, QueryRetrieveLevel.PATIENT);
if (attributesPatients != null) {
// Limit the max number of patients returned
int patientsNbre = attributesPatients.size();
@@ -230,7 +264,7 @@ private void queryPatientLevel(DicomQuery dicomQuery, DicomNode calling, DicomNo
boolean patientExists = patients.stream().anyMatch(p -> p.getPatientID().equals(patient.getPatientID()));
if (!patientExists) {
patients.add(patient);
- queryStudies(calling, called, dicomQuery, patient);
+ queryStudies(dicomQuery, patient);
}
}
importJob.setPatients(patients);
@@ -244,13 +278,13 @@ private void queryPatientLevel(DicomQuery dicomQuery, DicomNode calling, DicomNo
* @param called
* @param importJob
*/
- private void queryStudyLevel(DicomQuery dicomQuery, DicomNode calling, DicomNode called, ImportJob importJob) {
+ private void queryStudyLevel(DicomQuery dicomQuery, ImportJob importJob) {
DicomParam studyDescription = initDicomParam(Tag.StudyDescription, dicomQuery.getStudyDescription());
DicomParam studyDate = initDicomParam(Tag.StudyDate, dicomQuery.getStudyDate());
DicomParam[] params = { studyDescription, studyDate, new DicomParam(Tag.PatientName),
new DicomParam(Tag.PatientID), new DicomParam(Tag.PatientBirthDate), new DicomParam(Tag.PatientBirthName),
new DicomParam(Tag.PatientSex), new DicomParam(Tag.StudyInstanceUID) };
- List<Attributes> attributesStudies = queryCFIND(params, QueryRetrieveLevel.STUDY, calling, called);
+ List<Attributes> attributesStudies = queryCFind(params, QueryRetrieveLevel.STUDY);
if (attributesStudies != null) {
List<Patient> patients = new ArrayList<>();
for (int i = 0; i < attributesStudies.size(); i++) {
@@ -260,7 +294,7 @@ private void queryStudyLevel(DicomQuery dicomQuery, DicomNode calling, DicomNode
// handle studies
Study study = new Study(attributesStudies.get(i));
patient.getStudies().add(study);
- querySeries(calling, called, study);
+ querySeries(study);
}
// Limit the max number of patients returned
if (maxPatientsFromPACS < patients.size()) {
@@ -310,7 +344,7 @@ private DicomParam initDicomParam(int tag, String value) {
* @param dicomQuery
* @param patient
*/
- private void queryStudies(DicomNode calling, DicomNode called, DicomQuery dicomQuery, Patient patient) {
+ private void queryStudies(DicomQuery dicomQuery, Patient patient) {
DicomParam[] params = {
new DicomParam(Tag.PatientID, patient.getPatientID()),
new DicomParam(Tag.PatientName, patient.getPatientName()),
@@ -318,13 +352,13 @@ private void queryStudies(DicomNode calling, DicomNode called, DicomQuery dicomQ
new DicomParam(Tag.StudyDate, dicomQuery.getStudyDate()),
new DicomParam(Tag.StudyDescription, dicomQuery.getStudyDescription())
};
- List<Attributes> attributesStudies = queryCFIND(params, QueryRetrieveLevel.STUDY, calling, called);
+ List<Attributes> attributesStudies = queryCFind(params, QueryRetrieveLevel.STUDY);
if (attributesStudies != null) {
List<Study> studies = new ArrayList<>();
for (int i = 0; i < attributesStudies.size(); i++) {
Study study = new Study(attributesStudies.get(i));
studies.add(study);
- querySeries(calling, called, study);
+ querySeries(study);
}
studies.sort((p1, p2) -> p1.getStudyDate().compareTo(p2.getStudyDate()));
patient.setStudies(studies);
@@ -337,7 +371,7 @@ private void queryStudies(DicomNode calling, DicomNode called, DicomQuery dicomQ
* @param called
* @param study
*/
- private void querySeries(DicomNode calling, DicomNode called, Study study) {
+ private void querySeries(Study study) {
DicomParam[] params = {
new DicomParam(Tag.StudyInstanceUID, study.getStudyInstanceUID()),
new DicomParam(Tag.SeriesInstanceUID),
@@ -351,14 +385,14 @@ private void querySeries(DicomNode calling, DicomNode called, Study study) {
new DicomParam(Tag.ManufacturerModelName),
new DicomParam(Tag.DeviceSerialNumber)
};
- List<Attributes> attributesList = queryCFIND(params, QueryRetrieveLevel.SERIES, calling, called);
+ List<Attributes> attributesList = queryCFind(params, QueryRetrieveLevel.SERIES);
if (attributesList != null) {
List<Serie> series = new ArrayList<Serie>();
for (int i = 0; i < attributesList.size(); i++) {
Attributes attributes = attributesList.get(i);
Serie serie = new Serie(attributes);
if (!DicomSerieAndInstanceAnalyzer.checkSerieIsIgnored(attributes)) {
- queryInstances(calling, called, serie, study);
+ queryInstances(serie, study);
if (!serie.getInstances().isEmpty()) {
DicomSerieAndInstanceAnalyzer.checkSerieIsEnhanced(serie, attributes);
DicomSerieAndInstanceAnalyzer.checkSerieIsSpectroscopy(serie);
@@ -386,14 +420,14 @@ private void querySeries(DicomNode calling, DicomNode called, Study study) {
* @param called
* @param serie
*/
- private void queryInstances(DicomNode calling, DicomNode called, Serie serie, Study study) {
+ private void queryInstances(Serie serie, Study study) {
DicomParam[] params = {
new DicomParam(Tag.StudyInstanceUID, study.getStudyInstanceUID()),
new DicomParam(Tag.SeriesInstanceUID, serie.getSeriesInstanceUID()),
new DicomParam(Tag.SOPInstanceUID),
new DicomParam(Tag.InstanceNumber)
};
- List<Attributes> attributes = queryCFIND(params, QueryRetrieveLevel.IMAGE, calling, called);
+ List<Attributes> attributes = queryCFind(params, QueryRetrieveLevel.IMAGE);
if (attributes != null) {
List<Instance> instances = new ArrayList<>();
for (int i = 0; i < attributes.size(); i++) {
@@ -409,38 +443,75 @@ private void queryInstances(DicomNode calling, DicomNode called, Serie serie, St
/**
* This method does a C-FIND query and returns the results.
- * @param params
+ *
+ * The state of each c-find query is a local attribute of the method.
+ * So, when e.g. on the server 3 users call in parallel queryCFind,
+ * each one has its own DimseRSPHandler and its own state, so this
+ * might work, in case the association is not caching aspects.
+ *
+ * @param keys
* @param level
- * @param calling
- * @param called
* @return
*/
- private List<Attributes> queryCFIND(DicomParam[] params, QueryRetrieveLevel level, final DicomNode calling, final DicomNode called) {
- AdvancedParams options = new AdvancedParams();
+ private List<Attributes> queryCFind(DicomParam[] keys, QueryRetrieveLevel level) {
+ String cuid = null;
if (level.equals(QueryRetrieveLevel.PATIENT)) {
- options.setInformationModel(InformationModel.PatientRoot);
+ cuid = UID.PatientRootQueryRetrieveInformationModelFind;
} else if (level.equals(QueryRetrieveLevel.STUDY)) {
- options.setInformationModel(InformationModel.StudyRoot);
+ cuid = UID.StudyRootQueryRetrieveInformationModelFind;
} else if (level.equals(QueryRetrieveLevel.SERIES)) {
- options.setInformationModel(InformationModel.StudyRoot);
+ cuid = UID.StudyRootQueryRetrieveInformationModelFind;
} else if (level.equals(QueryRetrieveLevel.IMAGE)) {
- options.setInformationModel(InformationModel.StudyRoot);
+ cuid = UID.StudyRootQueryRetrieveInformationModelFind;
}
- logQuery(params, options);
- DicomState state = CFind.process(options, calling, called, 0, level, params);
- return state.getDicomRSP();
- }
-
- /**
- * This method logs the params and options of the PACS query.
- * @param params
- * @param options
- */
- private void logQuery(DicomParam[] params, AdvancedParams options) {
- LOG.info("Calling PACS, C-FIND with level: {} and params:", options.getInformationModel());
- for (int i = 0; i < params.length; i++) {
- LOG.info("Tag: {}, Value: {}", params[i].getTagName(), Arrays.toString(params[i].getValues()));
+ DicomState state = new DicomState(new DicomProgress());
+ DimseRSPHandler rspHandler = new DimseRSPHandler(this.association.nextMessageID()) {
+ @Override
+ public void onDimseRSP(Association as, Attributes cmd, Attributes data) {
+ super.onDimseRSP(as, cmd, data);
+ int status = cmd.getInt(Tag.Status, -1);
+ if (Status.isPending(status)) {
+ state.addDicomRSP(data);
+ } else {
+ state.setStatus(status);
+ }
+ }
+ };
+ try {
+ Attributes attributes = new Attributes();
+ attributes.setString(Tag.QueryRetrieveLevel, VR.CS, level.name());
+ for (DicomParam p : keys) {
+ addAttributes(attributes, p);
+ }
+ LOG.info("Calling PACS, C-FIND with level: {}", level);
+ for (int i = 0; i < keys.length; i++) {
+ LOG.info("Tag: {}, Value: {}", keys[i].getTagName(), Arrays.toString(keys[i].getValues()));
+ }
+ association.cfind(cuid, Priority.NORMAL, attributes, null, rspHandler);
+ if (association.isReadyForDataTransfer()) {
+ association.waitForOutstandingRSP();
+ }
+ } catch (IOException | InterruptedException e) {
+ LOG.error("Error in c-find query: ", e);
}
+ return state.getDicomRSP();
}
+
+ private void addAttributes(Attributes attrs, DicomParam param) {
+ int tag = param.getTag();
+ String[] ss = param.getValues();
+ VR vr = ElementDictionary.vrOf(tag, attrs.getPrivateCreator(tag));
+ if (ss == null || ss.length == 0) {
+ // Returning key
+ if (vr == VR.SQ) {
+ attrs.newSequence(tag, 1).add(new Attributes(0));
+ } else {
+ attrs.setNull(tag, vr);
+ }
+ } else {
+ // Matching key
+ attrs.setString(tag, vr, ss);
+ }
+ }
}
diff --git a/shanoir-ng-studies/src/main/java/org/shanoir/ng/study/controler/StudyApi.java b/shanoir-ng-studies/src/main/java/org/shanoir/ng/study/controler/StudyApi.java
index 1108d70eac..7f603fa96b 100644
--- a/shanoir-ng-studies/src/main/java/org/shanoir/ng/study/controler/StudyApi.java
+++ b/shanoir-ng-studies/src/main/java/org/shanoir/ng/study/controler/StudyApi.java
@@ -30,7 +30,6 @@
import org.shanoir.ng.study.dua.DataUserAgreement;
import org.shanoir.ng.study.model.Study;
import org.shanoir.ng.study.model.StudyUser;
-import org.springframework.core.io.Resource;
import org.springframework.http.ResponseEntity;
import org.springframework.security.access.prepost.PostAuthorize;
import org.springframework.security.access.prepost.PreAuthorize;
diff --git a/shanoir-ng-studies/src/main/java/org/shanoir/ng/study/controler/StudyApiController.java b/shanoir-ng-studies/src/main/java/org/shanoir/ng/study/controler/StudyApiController.java
index d93bd905d9..3ae3c7f341 100644
--- a/shanoir-ng-studies/src/main/java/org/shanoir/ng/study/controler/StudyApiController.java
+++ b/shanoir-ng-studies/src/main/java/org/shanoir/ng/study/controler/StudyApiController.java
@@ -21,16 +21,12 @@
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
-import java.text.SimpleDateFormat;
-import java.time.LocalDate;
-import java.time.format.DateTimeFormatter;
import java.util.ArrayList;
-import java.util.Date;
+import java.util.Arrays;
import java.util.List;
import java.util.Map;
import org.apache.commons.io.FileUtils;
-import org.joda.time.format.DateTimeFormat;
import org.shanoir.ng.shared.core.model.IdName;
import org.shanoir.ng.shared.error.FieldErrorMap;
import org.shanoir.ng.shared.event.ShanoirEvent;
@@ -210,6 +206,7 @@ public ResponseEntity<StudyDTO> saveNewStudy(@RequestBody final Study study, fin
Study createdStudy;
try {
+ addCurrentUserAsStudyUserIfEmptyStudyUsers(study);
createdStudy = studyService.create(study);
eventService.publishEvent(new ShanoirEvent(ShanoirEventType.CREATE_STUDY_EVENT,
createdStudy.getId().toString(), KeycloakUtil.getTokenUserId(), "", ShanoirEvent.SUCCESS));
@@ -220,6 +217,19 @@ public ResponseEntity<StudyDTO> saveNewStudy(@RequestBody final Study study, fin
return new ResponseEntity<>(studyMapper.studyToStudyDTO(createdStudy), HttpStatus.OK);
}
+ private void addCurrentUserAsStudyUserIfEmptyStudyUsers(final Study study) {
+ if (study.getStudyUserList() == null) {
+ List<StudyUser> studyUserList = new ArrayList<StudyUser>();
+ StudyUser studyUser = new StudyUser();
+ studyUser.setStudy(study);
+ studyUser.setUserId(KeycloakUtil.getTokenUserId());
+ studyUser.setUserName(KeycloakUtil.getTokenUserName());
+ studyUser.setStudyUserRights(Arrays.asList(StudyUserRight.CAN_SEE_ALL, StudyUserRight.CAN_DOWNLOAD, StudyUserRight.CAN_IMPORT, StudyUserRight.CAN_ADMINISTRATE));
+ studyUserList.add(studyUser);
+ study.setStudyUserList(studyUserList);
+ }
+ }
+
@Override
public ResponseEntity<StudyStorageVolumeDTO> getDetailedStorageVolume(@PathVariable("studyId") final Long studyId) throws RestServiceException {
StudyStorageVolumeDTO dto = studyService.getDetailedStorageVolume(studyId);
diff --git a/shanoir-ng-studies/src/main/java/org/shanoir/ng/study/service/StudyServiceImpl.java b/shanoir-ng-studies/src/main/java/org/shanoir/ng/study/service/StudyServiceImpl.java
index 66bc237cb3..d959b3be04 100644
--- a/shanoir-ng-studies/src/main/java/org/shanoir/ng/study/service/StudyServiceImpl.java
+++ b/shanoir-ng-studies/src/main/java/org/shanoir/ng/study/service/StudyServiceImpl.java
@@ -118,7 +118,6 @@ public class StudyServiceImpl implements StudyService {
@Autowired
private SubjectStudyRepository subjectStudyRepository;
-
@Override
public void deleteById(final Long id) throws EntityNotFoundException {
final Study study = studyRepository.findById(id).orElse(null);
@@ -154,8 +153,10 @@ public Study create(final Study study) throws MicroServiceCommunicationException
}
}
- for (SubjectStudy subjectStudy : study.getSubjectStudyList()) {
- subjectStudy.setStudy(study);
+ if (study.getSubjectStudyList() != null) {
+ for (SubjectStudy subjectStudy : study.getSubjectStudyList()) {
+ subjectStudy.setStudy(study);
+ }
}
if (study.getTags() != null) {
@@ -185,15 +186,16 @@ public Study create(final Study study) throws MicroServiceCommunicationException
}
}
- List<SubjectStudy> subjectStudyListSave = new ArrayList<SubjectStudy>(study.getSubjectStudyList());
+ List<SubjectStudy> subjectStudyListSave = null;
+ if (study.getSubjectStudyList() != null) {
+ subjectStudyListSave = new ArrayList<SubjectStudy>(study.getSubjectStudyList());
+ }
Map<Long, List<SubjectStudyTag>> subjectStudyTagSave = new HashMap<>();
study.setSubjectStudyList(null);
Study studyDb = studyRepository.save(study);
- //studyDb.setSubjectStudyList(new ArrayList<SubjectStudy>());
if (subjectStudyListSave != null) {
updateTags(subjectStudyListSave, studyDb.getTags());
- //ListDependencyUpdate.updateWith(studyDb.getSubjectStudyList(), subjectStudyListSave);
studyDb.setSubjectStudyList(new ArrayList<>());
for (SubjectStudy subjectStudy : subjectStudyListSave) {
SubjectStudy newSubjectStudy = new SubjectStudy();
@@ -203,7 +205,6 @@ public Study create(final Study study) throws MicroServiceCommunicationException
newSubjectStudy.setSubjectType(subjectStudy.getSubjectType());
newSubjectStudy.setStudy(studyDb);
subjectStudyTagSave.put(subjectStudy.getSubject().getId(), subjectStudy.getSubjectStudyTags());
- //newSubjectStudy.setSubjectStudyTags(subjectStudy.getSubjectStudyTags());
studyDb.getSubjectStudyList().add(newSubjectStudy);
}
studyDb = studyRepository.save(studyDb);
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/ShUpConfig.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/ShUpConfig.java
index e3860623da..e5d1379fbd 100644
--- a/shanoir-uploader/src/main/java/org/shanoir/uploader/ShUpConfig.java
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/ShUpConfig.java
@@ -70,6 +70,8 @@ public class ShUpConfig {
public static final String RANDOM_SEED = "random.seed";
+ public static final String PROFILE = "profile";
+
/**
* Static variables
*/
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/action/DownloadOrCopyRunnable.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/action/DownloadOrCopyRunnable.java
index a10c38d08f..a632c4a784 100644
--- a/shanoir-uploader/src/main/java/org/shanoir/uploader/action/DownloadOrCopyRunnable.java
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/action/DownloadOrCopyRunnable.java
@@ -66,12 +66,12 @@ public void run() {
/**
* 2. Fill MRI information into serie from first DICOM file of each serie
- * This has already been done for CD/DVD import, but not yet here for PACS
+ * This has already been done for CD/DVD import, but not yet here for PACS.
*/
if (this.isFromPACS) {
for (Iterator iterator = selectedSeries.iterator(); iterator.hasNext();) {
SerieTreeNode serieTreeNode = (SerieTreeNode) iterator.next();
- dicomFileAnalyzer.getAdditionalMetaDataFromFirstInstanceOfSerie(filePathDicomDir, serieTreeNode.getSerie(), null, isFromPACS);
+ dicomFileAnalyzer.getAdditionalMetaDataFromFirstInstanceOfSerie(uploadFolder.getAbsolutePath(), serieTreeNode.getSerie(), null, isFromPACS);
}
}
} catch (FileNotFoundException e) {
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/action/FindDicomActionListener.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/action/FindDicomActionListener.java
index 918ff875a5..037699401c 100644
--- a/shanoir-uploader/src/main/java/org/shanoir/uploader/action/FindDicomActionListener.java
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/action/FindDicomActionListener.java
@@ -246,7 +246,7 @@ private void fillMediaWithPatients(Media media, final List<Patient> patients) {
for (Iterator iterator = patients.iterator(); iterator.hasNext();) {
Patient patient = (Patient) iterator.next();
final PatientTreeNode patientTreeNode = media.initChildTreeNode(patient);
- logger.info("Patient info read from DICOMDIR: " + patient.toString());
+ logger.info("Patient info read: " + patient.toString());
// add patients
media.addTreeNode(patient.getPatientID(), patientTreeNode);
List<Study> studies = patient.getStudies();
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/action/ImportFinishRunnable.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/action/ImportFinishRunnable.java
index 307310fe49..f3ceaab523 100644
--- a/shanoir-uploader/src/main/java/org/shanoir/uploader/action/ImportFinishRunnable.java
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/action/ImportFinishRunnable.java
@@ -60,13 +60,12 @@ public void run() {
boolean anonymizationSuccess = false;
try {
String anonymizationProfile = ShUpConfig.profileProperties.getProperty(ANONYMIZATION_PROFILE);
- anonymizationSuccess = anonymizer.anonymize(uploadFolder, anonymizationProfile, subjectName);
+ anonymizationSuccess = anonymizer.pseudonymize(uploadFolder, anonymizationProfile, subjectName);
} catch (IOException e) {
logger.error(uploadFolder.getName() + ": " + e.getMessage(), e);
}
if (anonymizationSuccess) {
- logger.info(uploadFolder.getName() + ": DICOM files successfully anonymized.");
/**
* Write import-job.json to disk
*/
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/action/init/InitialStartupState.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/action/init/InitialStartupState.java
index 772e3644e3..c0cab11ef6 100644
--- a/shanoir-uploader/src/main/java/org/shanoir/uploader/action/init/InitialStartupState.java
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/action/init/InitialStartupState.java
@@ -49,7 +49,9 @@ public class InitialStartupState implements State {
private static final String SU_V6_0_3 = ".su_v6.0.3";
private static final String SU_V6_0_4 = ".su_v6.0.4";
-
+
+ private static final String SU_V7_0_1 = ".su_v7.0.1";
+
public void load(StartupStateContext context) throws Exception {
initShanoirUploaderFolder();
initLogging();
@@ -60,8 +62,8 @@ public void load(StartupStateContext context) throws Exception {
logger.info(System.getProperty("java.vendor.url"));
logger.info(System.getProperty("java.version"));
InetAddress inetAddress = InetAddress.getLocalHost();
- logger.info("IP Address:- " + inetAddress.getHostAddress());
- logger.info("Host Name:- " + inetAddress.getHostName());
+ logger.info("IP Address: " + inetAddress.getHostAddress());
+ logger.info("Host Name: " + inetAddress.getHostName());
// Disable http request to check for quartz upload
System.setProperty("org.quartz.scheduler.skipUpdateCheck", "true");
System.setProperty("jdk.http.auth.tunneling.disabledSchemes", "");
@@ -70,6 +72,7 @@ public void load(StartupStateContext context) throws Exception {
initLanguage();
copyPseudonymus();
initProfiles();
+ initProfile();
initStartupDialog(context);
context.setState(new ProxyConfigurationState());
context.nextState();
@@ -78,7 +81,8 @@ public void load(StartupStateContext context) throws Exception {
private void doMigration() throws IOException {
// as properties, that exist already are not replaced/changed, start with the last version before,
// as considered as more important
- // overwrite with properties from ShanoirUploader v6.0.4 or v6.0.3, if existing
+ // overwrite with properties from ShanoirUploader v7.0.1, v6.0.4 or v6.0.3, if existing
+ migrateFromVersion(SU_V7_0_1);
migrateFromVersion(SU_V6_0_4);
migrateFromVersion(SU_V6_0_3);
// migrate properties from ShanoirUploader v5.2
@@ -91,11 +95,11 @@ private void migrateFromVersion(String version) throws IOException {
final File shanoirUploaderFolderForVersion = new File(shanoirUploaderFolderPathForVersion);
boolean shanoirUploaderFolderExistsForVersion = shanoirUploaderFolderForVersion.exists();
if (shanoirUploaderFolderExistsForVersion) {
- logger.info("Start migrating properties from version " + version + " (.su == v5.2) of ShUp.");
+ logger.info("Start migrating properties from version " + version + " of ShUp.");
copyPropertiesFile(shanoirUploaderFolderForVersion, ShUpConfig.shanoirUploaderFolder, ShUpConfig.LANGUAGE_PROPERTIES);
copyPropertiesFile(shanoirUploaderFolderForVersion, ShUpConfig.shanoirUploaderFolder, ShUpConfig.PROXY_PROPERTIES);
copyPropertiesFile(shanoirUploaderFolderForVersion, ShUpConfig.shanoirUploaderFolder, ShUpConfig.DICOM_SERVER_PROPERTIES);
- logger.info("Finished migrating properties from version " + version + " (.su == v5.2) of ShUp: language, proxy, dicom_server.");
+ logger.info("Finished migrating properties from version " + version + " of ShUp: language, proxy, dicom_server.");
}
}
@@ -297,4 +301,10 @@ private void initLanguage() {
}
}
+ private void initProfile() throws FileNotFoundException, IOException {
+ String profile = ShUpConfig.basicProperties.getProperty(ShUpConfig.PROFILE);
+ if (profile != null && !profile.isEmpty()) {
+ ShUpConfig.profileSelected = profile;
+ }
+ }
}
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/action/init/ProxyConfigurationState.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/action/init/ProxyConfigurationState.java
index 6a9266d888..1bd5a2e6bc 100644
--- a/shanoir-uploader/src/main/java/org/shanoir/uploader/action/init/ProxyConfigurationState.java
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/action/init/ProxyConfigurationState.java
@@ -37,7 +37,7 @@ public void load(StartupStateContext context) {
switch (httpResponseCode){
case 200 :
context.getShUpStartupDialog().updateStartupText("\n" + ShUpConfig.resourceBundle.getString("shanoir.uploader.startup.test.proxy.success"));
- context.setState(new SelectProfileManualConfigurationState());
+ context.setState(new SelectProfileConfigurationState());
context.nextState();
break;
default:
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/action/init/SelectProfileConfigurationState.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/action/init/SelectProfileConfigurationState.java
new file mode 100644
index 0000000000..4bc75a3a7c
--- /dev/null
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/action/init/SelectProfileConfigurationState.java
@@ -0,0 +1,25 @@
+package org.shanoir.uploader.action.init;
+
+
+import org.apache.log4j.Logger;
+import org.shanoir.uploader.ShUpConfig;
+
+public class SelectProfileConfigurationState implements State {
+
+ private static Logger logger = Logger.getLogger(SelectProfileConfigurationState.class);
+
+ public void load(StartupStateContext context) {
+ if(ShUpConfig.profileSelected == null) {
+ context.setState(new SelectProfileManualConfigurationState());
+ context.nextState();
+ } else {
+ logger.info("Profile found in basic.properties. Used as default: " + ShUpConfig.profileSelected);
+ SelectProfilePanelActionListener actionListener = new SelectProfilePanelActionListener(null, null);
+ actionListener.configureSelectedProfile(ShUpConfig.profileSelected);
+ context.getShUpStartupDialog().updateStartupText("\nProfile: " + ShUpConfig.profileSelected);
+ context.setState(new AuthenticationConfigurationState());
+ context.nextState();
+ }
+ }
+
+}
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/action/init/SelectProfilePanelActionListener.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/action/init/SelectProfilePanelActionListener.java
index 12deea5f8f..6d410c95c4 100644
--- a/shanoir-uploader/src/main/java/org/shanoir/uploader/action/init/SelectProfilePanelActionListener.java
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/action/init/SelectProfilePanelActionListener.java
@@ -30,14 +30,16 @@ public SelectProfilePanelActionListener(SelectProfileConfigurationPanel selectPr
public void actionPerformed(ActionEvent e) {
String selectedProfile = (String) selectProfilePanel.selectProfileCB.getSelectedItem();
ShUpConfig.profileSelected = selectedProfile;
+ configureSelectedProfile(selectedProfile);
+ sSC.nextState();
+ }
+
+ public void configureSelectedProfile(String selectedProfile) {
String filePath = File.separator + ShUpConfig.PROFILE_DIR + selectedProfile;
ShUpConfig.profileDirectory = new File(ShUpConfig.shanoirUploaderFolder, filePath);
logger.info("Profile directory set to: " + ShUpConfig.profileDirectory.getAbsolutePath());
File profilePropertiesFile = new File(ShUpConfig.profileDirectory, ShUpConfig.PROFILE_PROPERTIES);
loadPropertiesFromFile(profilePropertiesFile, ShUpConfig.profileProperties);
-
- ShUpConfig.encryption.decryptIfEncryptedString(profilePropertiesFile,
- ShUpConfig.profileProperties, "shanoir.server.user.password");
logger.info("Profile " + selectedProfile + " successfully initialized.");
File keycloakJson = new File(ShUpConfig.profileDirectory, ShUpConfig.KEYCLOAK_JSON);
@@ -47,7 +49,7 @@ public void actionPerformed(ActionEvent e) {
} else {
logger.error("Error: missing keycloak.json! Connection with sh-ng will not work.");
return;
- }
+ }
// check if pseudonymus has been copied in case of true
if (Boolean.parseBoolean(ShUpConfig.profileProperties.getProperty(ShUpConfig.MODE_PSEUDONYMUS))) {
@@ -72,7 +74,6 @@ public void actionPerformed(ActionEvent e) {
return;
}
}
- sSC.nextState();
}
private void loadPropertiesFromFile(final File propertiesFile, final Properties properties) {
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/DicomServerClient.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/DicomServerClient.java
index a38f4bb1a7..c4a9556b1f 100644
--- a/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/DicomServerClient.java
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/DicomServerClient.java
@@ -42,6 +42,7 @@ public class DicomServerClient implements IDicomServerClient {
private File workFolder;
public DicomServerClient(final Properties dicomServerProperties, final File workFolder) {
+ logger.info("New DicomServerClient created with properties: " + dicomServerProperties.toString());
config.initWithPropertiesFile(dicomServerProperties);
this.workFolder = workFolder;
// Initialize connection configuration parameters here: to be used for all queries
@@ -126,17 +127,25 @@ public boolean accept(File dir, String name) {
}
}
};
- File[] newFileNames = uploadFolder.listFiles(oldFileNamesAndDICOMFilter);
- logger.debug("newFileNames: " + newFileNames.length);
- for (int i = 0; i < newFileNames.length; i++) {
- fileNamesForSerie.add(newFileNames[i].getName());
+ File serieFolder = new File (uploadFolder.getAbsolutePath() + File.separator + seriesInstanceUID);
+ if (serieFolder.exists()) {
+ File[] newFileNames = serieFolder.listFiles(oldFileNamesAndDICOMFilter);
+ logger.debug("newFileNames: " + newFileNames.length);
+ for (int i = 0; i < newFileNames.length; i++) {
+ fileNamesForSerie.add(newFileNames[i].getName());
+ }
+ serieTreeNode.setFileNames(fileNamesForSerie);
+ retrievedDicomFiles.addAll(fileNamesForSerie);
+ oldFileNames.addAll(fileNamesForSerie);
+ logger.info(uploadFolder.getName() + ":\n\n Download of " + fileNamesForSerie.size()
+ + " DICOM files for serie " + seriesInstanceUID + ": " + serieTreeNode.getDisplayString()
+ + " was successful.\n\n");
+ } else {
+ logger.error(uploadFolder.getName() + ":\n\n Download of " + fileNamesForSerie.size()
+ + " DICOM files for serie " + seriesInstanceUID + ": " + serieTreeNode.getDisplayString()
+ + " has failed.\n\n");
+ return null;
}
- serieTreeNode.setFileNames(fileNamesForSerie);
- retrievedDicomFiles.addAll(fileNamesForSerie);
- oldFileNames.addAll(fileNamesForSerie);
- logger.info(uploadFolder.getName() + ":\n\n Download of " + fileNamesForSerie.size()
- + " DICOM files for serie " + seriesInstanceUID + ": " + serieTreeNode.getDisplayString()
- + " was successful.\n\n");
} else {
logger.error(uploadFolder.getName() + ":\n\n Download of " + fileNamesForSerie.size()
+ " DICOM files for serie " + seriesInstanceUID + ": " + serieTreeNode.getDisplayString()
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/anonymize/Anonymizer.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/anonymize/Anonymizer.java
index 838c5326eb..59c7e4ab8c 100644
--- a/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/anonymize/Anonymizer.java
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/anonymize/Anonymizer.java
@@ -7,35 +7,39 @@
import org.apache.log4j.Logger;
import org.shanoir.anonymization.anonymization.AnonymizationService;
import org.shanoir.anonymization.anonymization.AnonymizationServiceImpl;
+import org.shanoir.uploader.dicom.retrieve.DcmRcvManager;
public class Anonymizer {
private static Logger logger = Logger.getLogger(Anonymizer.class);
- public boolean anonymize(final File uploadFolder,
+ public boolean pseudonymize(final File uploadFolder,
final String profile, final String subjectName)
throws IOException {
- ArrayList<File> dicomFiles = getListOfDicomFiles(uploadFolder);
+ ArrayList<File> dicomFiles = new ArrayList<File>();
+ getListOfDicomFiles(uploadFolder, dicomFiles);
try {
AnonymizationService anonymizationService = new AnonymizationServiceImpl();
anonymizationService.anonymizeForShanoir(dicomFiles, profile, subjectName, subjectName);
+ logger.info("--> " + dicomFiles.size() + " DICOM files successfully pseudonymized.");
} catch (Exception e) {
- logger.error("anonymization service: ", e);
+ logger.error("pseudonymization service: ", e);
return false;
}
return true;
}
- private ArrayList<File> getListOfDicomFiles(final File uploadFolder)
- throws IOException {
- ArrayList<File> dicomFileList = new ArrayList<File>();
- File[] listOfFiles = uploadFolder.listFiles();
+ private void getListOfDicomFiles(final File folder, ArrayList<File> dicomFiles) throws IOException {
+ File[] listOfFiles = folder.listFiles();
for (File file : listOfFiles) {
- if (file.isFile() && !file.getName().endsWith(".xml")) {
- dicomFileList.add(file);
+ if (file.isFile() && file.getName().endsWith(DcmRcvManager.DICOM_FILE_SUFFIX)) {
+ dicomFiles.add(file);
+ } else {
+ if (file.isDirectory()) {
+ getListOfDicomFiles(file, dicomFiles);
+ }
}
}
- return dicomFileList;
}
}
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/query/SerieTreeNode.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/query/SerieTreeNode.java
index 56022c4621..6d421585a4 100644
--- a/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/query/SerieTreeNode.java
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/query/SerieTreeNode.java
@@ -44,6 +44,8 @@ public class SerieTreeNode implements DicomTreeNode {
private List<String> fileNames;
+ private MRI mriInformation;
+
// constructor for JAXB
public SerieTreeNode() {
this.serie = new Serie();
@@ -274,21 +276,27 @@ public DicomTreeNode initChildTreeNode(Object arg0) {
@XmlElement
public MRI getMriInformation() {
- MRI mriInformation = new MRI();
- InstitutionDicom institutionDicom = this.serie.getInstitution();
- if(institutionDicom != null) {
- mriInformation.setInstitutionName(institutionDicom.getInstitutionName());
- mriInformation.setInstitutionAddress(institutionDicom.getInstitutionAddress());
- }
- EquipmentDicom equipmentDicom = this.serie.getEquipment();
- if(equipmentDicom != null) {
- mriInformation.setManufacturer(equipmentDicom.getManufacturer());
- mriInformation.setManufacturersModelName(equipmentDicom.getManufacturerModelName());
- mriInformation.setDeviceSerialNumber(equipmentDicom.getDeviceSerialNumber());
- mriInformation.setStationName(equipmentDicom.getStationName());
- mriInformation.setMagneticFieldStrength(equipmentDicom.getMagneticFieldStrength());
+ if (this.mriInformation == null) {
+ this.mriInformation = new MRI();
+ InstitutionDicom institutionDicom = this.serie.getInstitution();
+ if(institutionDicom != null) {
+ this.mriInformation.setInstitutionName(institutionDicom.getInstitutionName());
+ this.mriInformation.setInstitutionAddress(institutionDicom.getInstitutionAddress());
+ }
+ EquipmentDicom equipmentDicom = this.serie.getEquipment();
+ if(equipmentDicom != null) {
+ this.mriInformation.setManufacturer(equipmentDicom.getManufacturer());
+ this.mriInformation.setManufacturersModelName(equipmentDicom.getManufacturerModelName());
+ this.mriInformation.setDeviceSerialNumber(equipmentDicom.getDeviceSerialNumber());
+ this.mriInformation.setStationName(equipmentDicom.getStationName());
+ this.mriInformation.setMagneticFieldStrength(equipmentDicom.getMagneticFieldStrength());
+ }
}
- return mriInformation;
+ return this.mriInformation;
+ }
+
+ public void setMriInformation(MRI mriInformation) {
+ this.mriInformation = mriInformation;
}
@Override
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/retrieve/DcmRcvManager.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/retrieve/DcmRcvManager.java
index 4c442fc7c9..872ec89abc 100644
--- a/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/retrieve/DcmRcvManager.java
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/retrieve/DcmRcvManager.java
@@ -12,8 +12,6 @@
/**
* The DcmRcvHelper handles the download of DICOM files.
- * It's a local service / server which is started, when
- * the ShanoirUploader is started.
*
* @author mkain
*
@@ -26,7 +24,7 @@ public class DcmRcvManager {
* In the brackets '{ggggeeee}' the dicom attribute value is used to be replaced.
* We store in a folder with the SeriesInstanceUID and the file name of the SOPInstanceUID.
*/
- private static final String STORAGE_PATTERN = "{00080018}";
+ private static final String STORAGE_PATTERN = "{0020000E}" + File.separator + "{00080018}";
public static final String DICOM_FILE_SUFFIX = ".dcm";
@@ -53,6 +51,11 @@ public void configure(final ConfigBean configBean) {
this.lParams = new ListenerParams(params, true, STORAGE_PATTERN + DICOM_FILE_SUFFIX, null, null);
}
+ /**
+ * Called from a synchronized method only, so should not be a problem for multiple usages.
+ *
+ * @param folderPath
+ */
public void startSCPServer(final String folderPath) {
try {
if(this.listener != null)
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/gui/MainWindow.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/gui/MainWindow.java
index 7f4ac0c97c..2b8f3901d4 100644
--- a/shanoir-uploader/src/main/java/org/shanoir/uploader/gui/MainWindow.java
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/gui/MainWindow.java
@@ -549,6 +549,7 @@ public void actionPerformed(ActionEvent e) {
gbc_queryButton.gridy = 6;
queryPanel.add(queryButton, gbc_queryButton);
queryButton.setEnabled(false);
+ frame.getRootPane().setDefaultButton(queryButton);
queryButton.addActionListener(fAL);
JSeparator separator = new JSeparator();
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/model/rest/Study.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/model/rest/Study.java
index 4ccc002abd..f877b8d3c4 100644
--- a/shanoir-uploader/src/main/java/org/shanoir/uploader/model/rest/Study.java
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/model/rest/Study.java
@@ -13,10 +13,11 @@ public class Study implements Comparable<Study> {
private String name;
+ private String studyStatus;
+
private List<StudyCard> studyCards;
- @JsonProperty("studyCenterList")
- private List<Center> centers;
+ private List<StudyCenter> studyCenterList;
private Boolean compatible;
@@ -36,6 +37,14 @@ public void setName(String name) {
this.name = name;
}
+ public String getStudyStatus() {
+ return studyStatus;
+ }
+
+ public void setStudyStatus(String studyStatus) {
+ this.studyStatus = studyStatus;
+ }
+
public List<StudyCard> getStudyCards() {
return studyCards;
}
@@ -44,13 +53,12 @@ public void setStudyCards(List<StudyCard> studyCards) {
this.studyCards = studyCards;
}
- public List<Center> getCenters() {
- return centers;
+ public List<StudyCenter> getStudyCenterList() {
+ return studyCenterList;
}
- public void setCenters(List<Center> centers) {
- this.centers = centers;
- Collections.sort(this.centers);
+ public void setStudyCenterList(List<StudyCenter> studyCenterList) {
+ this.studyCenterList = studyCenterList;
}
public Boolean getCompatible() {
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/model/rest/StudyCenter.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/model/rest/StudyCenter.java
new file mode 100644
index 0000000000..ab2f6348b7
--- /dev/null
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/model/rest/StudyCenter.java
@@ -0,0 +1,25 @@
+package org.shanoir.uploader.model.rest;
+
+public class StudyCenter {
+
+ private Center center;
+
+ private Study study;
+
+ public Center getCenter() {
+ return center;
+ }
+
+ public void setCenter(Center center) {
+ this.center = center;
+ }
+
+ public Study getStudy() {
+ return study;
+ }
+
+ public void setStudy(Study study) {
+ this.study = study;
+ }
+
+}
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/service/rest/ShanoirUploaderServiceClient.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/service/rest/ShanoirUploaderServiceClient.java
index 152f524794..c4f8ef2987 100644
--- a/shanoir-uploader/src/main/java/org/shanoir/uploader/service/rest/ShanoirUploaderServiceClient.java
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/service/rest/ShanoirUploaderServiceClient.java
@@ -51,8 +51,12 @@ public class ShanoirUploaderServiceClient {
private static Logger logger = Logger.getLogger(ShanoirUploaderServiceClient.class);
private static final String SHANOIR_SERVER_URL = "shanoir.server.url";
+
+ private static final String SERVICE_STUDIES_CREATE = "service.studies.create";
private static final String SERVICE_STUDIES_NAMES_CENTERS = "service.studies.names.centers";
+
+ private static final String SERVICE_STUDYCARDS_CREATE = "service.studycards.create";
private static final String SERVICE_STUDYCARDS_FIND_BY_STUDY_IDS = "service.studycards.find.by.study.ids";
@@ -86,8 +90,12 @@ public class ShanoirUploaderServiceClient {
private String serverURL;
+ private String serviceURLStudiesCreate;
+
private String serviceURLStudiesNamesAndCenters;
+ private String serviceURLStudyCardsCreate;
+
private String serviceURLStudyCardsByStudyIds;
private String serviceURLStudyCardsApplyOnStudy;
@@ -96,14 +104,14 @@ public class ShanoirUploaderServiceClient {
private String serviceURLAcquisitionEquipments;
+ private String serviceURLSubjectsCreate;
+
private String serviceURLSubjectsFindByIdentifier;
private String serviceURLDatasets;
private String serviceURLDatasetsDicomWebStudies;
- private String serviceURLSubjectsCreate;
-
private String serviceURLExaminationsCreate;
private String serviceURLImporterCreateTempDir;
@@ -133,8 +141,12 @@ public ShanoirUploaderServiceClient() {
this.serverURL = ShUpConfig.profileProperties.getProperty(SHANOIR_SERVER_URL);
+ this.serviceURLStudiesCreate = this.serverURL
+ + ShUpConfig.endpointProperties.getProperty(SERVICE_STUDIES_CREATE);
this.serviceURLStudiesNamesAndCenters = this.serverURL
+ ShUpConfig.endpointProperties.getProperty(SERVICE_STUDIES_NAMES_CENTERS);
+ this.serviceURLStudyCardsCreate = this.serverURL
+ + ShUpConfig.endpointProperties.getProperty(SERVICE_STUDYCARDS_CREATE);
this.serviceURLStudyCardsByStudyIds = this.serverURL
+ ShUpConfig.endpointProperties.getProperty(SERVICE_STUDYCARDS_FIND_BY_STUDY_IDS);
this.serviceURLStudyCardsApplyOnStudy = this.serverURL
@@ -521,6 +533,48 @@ public CloseableHttpResponse downloadDatasetsByStudyId(Long studyId, String form
return null;
}
+ public Study createStudy(final Study study) {
+ try {
+ String json = Util.objectWriter.writeValueAsString(study);
+ try (CloseableHttpResponse response = httpService.post(this.serviceURLStudiesCreate, json, false)) {
+ int code = response.getCode();
+ if (code == HttpStatus.SC_OK) {
+ Study studyCreated = Util.getMappedObject(response, Study.class);
+ return studyCreated;
+ } else {
+ logger.error("Error in createStudy: with study " + study.getName()
+ + " (status code: " + code + ", message: " + apiResponseMessages.getOrDefault(code, "unknown status code") + ")");
+ }
+ }
+ } catch (JsonProcessingException e) {
+ logger.error(e.getMessage(), e);
+ } catch (IOException ioE) {
+ logger.error(ioE.getMessage(), ioE);
+ }
+ return null;
+ }
+
+ public Center createStudyCard(final StudyCard studyCard) {
+ try {
+ String json = Util.objectWriter.writeValueAsString(studyCard);
+ try (CloseableHttpResponse response = httpService.post(this.serviceURLStudyCardsCreate, json, false)) {
+ int code = response.getCode();
+ if (code == HttpStatus.SC_OK) {
+ Center centerCreated = Util.getMappedObject(response, Center.class);
+ return centerCreated;
+ } else {
+ logger.error("Error in createStudy: with study " + studyCard.getName()
+ + " (status code: " + code + ", message: " + apiResponseMessages.getOrDefault(code, "unknown status code") + ")");
+ }
+ }
+ } catch (JsonProcessingException e) {
+ logger.error(e.getMessage(), e);
+ } catch (IOException ioE) {
+ logger.error(ioE.getMessage(), ioE);
+ }
+ return null;
+ }
+
public Center createCenter(final Center center) {
try {
String json = Util.objectWriter.writeValueAsString(center);
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/upload/UploadServiceJob.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/upload/UploadServiceJob.java
index 73a37167c4..86d00bf28e 100644
--- a/shanoir-uploader/src/main/java/org/shanoir/uploader/upload/UploadServiceJob.java
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/upload/UploadServiceJob.java
@@ -94,7 +94,7 @@ private void processFolderForServer(final File folder, final UploadJobManager up
final File uploadJobFile, CurrentNominativeDataController currentNominativeDataController) {
NominativeDataUploadJobManager nominativeDataUploadJobManager = null;
final List<File> filesToTransfer = new ArrayList<File>();
- final Collection<File> files = Util.listFiles(folder, null, false);
+ final Collection<File> files = Util.listFiles(folder, null, true);
for (Iterator<File> filesIt = files.iterator(); filesIt.hasNext();) {
final File file = (File) filesIt.next();
// do not transfer nominativeDataUploadJob as only for display in ShUp
diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/utils/ImportUtils.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/utils/ImportUtils.java
index 95fe8be125..d5bc44d4d0 100644
--- a/shanoir-uploader/src/main/java/org/shanoir/uploader/utils/ImportUtils.java
+++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/utils/ImportUtils.java
@@ -21,6 +21,7 @@
import org.shanoir.uploader.action.DicomDataTransferObject;
import org.shanoir.uploader.dicom.IDicomServerClient;
import org.shanoir.uploader.dicom.query.SerieTreeNode;
+import org.shanoir.uploader.dicom.retrieve.DcmRcvManager;
import org.shanoir.uploader.model.rest.IdName;
import org.shanoir.uploader.model.rest.Study;
import org.shanoir.uploader.model.rest.StudyCard;
@@ -290,7 +291,7 @@ public static List<String> copyFilesToUploadFolder(ImagesCreatorAndDicomFileAnal
List<String> newFileNamesOfSerie = new ArrayList<String>();
for (Instance instance : serie.getInstances()) {
File sourceFile = dicomFileAnalyzer.getFileFromInstance(instance, serie, filePathDicomDir, false);
- String dicomFileName = sourceFile.getAbsolutePath().replace(File.separator, "_");
+ String dicomFileName = sourceFile.getAbsolutePath().replace(File.separator, "_") + DcmRcvManager.DICOM_FILE_SUFFIX;
File destFile = new File(uploadFolder.getAbsolutePath() + File.separator + dicomFileName);
FileUtil.copyFile(sourceFile, destFile);
newFileNamesOfSerie.add(dicomFileName);
diff --git a/shanoir-uploader/src/main/resources/endpoint.properties b/shanoir-uploader/src/main/resources/endpoint.properties
index ef1959ded2..ebcd3a1643 100644
--- a/shanoir-uploader/src/main/resources/endpoint.properties
+++ b/shanoir-uploader/src/main/resources/endpoint.properties
@@ -1,5 +1,6 @@
-service.studies=/shanoir-ng/studies/studies/
+service.studies.create=/shanoir-ng/studies/studies
service.studies.names.centers=/shanoir-ng/studies/studies/namesAndCenters
+service.studycards.create=/shanoir-ng/datasets/studycards
service.studycards.find.by.study.ids=/shanoir-ng/datasets/studycards/search
service.studycards.apply.on.study=/shanoir-ng/datasets/studycards/apply_on_study/
service.centers.create=/shanoir-ng/studies/centers
diff --git a/shanoir-uploader/src/main/resources/profile.Neurinfo-Qualif/profile.properties b/shanoir-uploader/src/main/resources/profile.Neurinfo-Qualif/profile.properties
index 5d3c73d84a..f22c46a13a 100644
--- a/shanoir-uploader/src/main/resources/profile.Neurinfo-Qualif/profile.properties
+++ b/shanoir-uploader/src/main/resources/profile.Neurinfo-Qualif/profile.properties
@@ -14,16 +14,7 @@ mode.subject.study.identifier=true
anonymization.profile=Profile Neurinfo
-##########################################################
-# Server properties for accessing to Shanoir-old server
-##########################################################
-shanoir.server.user.name=
-shanoir.server.user.password=
-shanoir.server.uploader.service.url=
-shanoir.server.uploader.service.qname.local.part=
-shanoir.server.uploader.service.qname.namespace.uri=
-
##########################################################
# Server properties for accessing to Shanoir-NG server
##########################################################
-shanoir.server.url=https\://shanoir-qualif.irisa.fr
+shanoir.server.url=https\://shanoir-qualif.irisa.fr
\ No newline at end of file
diff --git a/shanoir-uploader/src/main/resources/profile.Neurinfo/profile.properties b/shanoir-uploader/src/main/resources/profile.Neurinfo/profile.properties
index bd3aae3d7c..e39fd64dc6 100644
--- a/shanoir-uploader/src/main/resources/profile.Neurinfo/profile.properties
+++ b/shanoir-uploader/src/main/resources/profile.Neurinfo/profile.properties
@@ -14,16 +14,7 @@ mode.subject.study.identifier=true
anonymization.profile=Profile Neurinfo
-##########################################################
-# Server properties for accessing to Shanoir-old server
-##########################################################
-shanoir.server.user.name=
-shanoir.server.user.password=
-shanoir.server.uploader.service.url=
-shanoir.server.uploader.service.qname.local.part=
-shanoir.server.uploader.service.qname.namespace.uri=
-
##########################################################
# Server properties for accessing to Shanoir-NG server
##########################################################
-shanoir.server.url=https\://shanoir.irisa.fr
+shanoir.server.url=https\://shanoir.irisa.fr
\ No newline at end of file
diff --git a/shanoir-uploader/src/main/resources/profile.OFSEP-Qualif/profile.properties b/shanoir-uploader/src/main/resources/profile.OFSEP-Qualif/profile.properties
index a4f3217193..995774c032 100644
--- a/shanoir-uploader/src/main/resources/profile.OFSEP-Qualif/profile.properties
+++ b/shanoir-uploader/src/main/resources/profile.OFSEP-Qualif/profile.properties
@@ -14,16 +14,7 @@ mode.subject.study.identifier=false
anonymization.profile=Profile OFSEP
-##########################################################
-# Server properties for accessing to Shanoir-old server
-##########################################################
-shanoir.server.user.name=
-shanoir.server.user.password=
-shanoir.server.uploader.service.url=
-shanoir.server.uploader.service.qname.local.part=
-shanoir.server.uploader.service.qname.namespace.uri=
-
##########################################################
# Server properties for accessing to Shanoir-NG server
##########################################################
-shanoir.server.url=https\://shanoir-ofsep-qualif.irisa.fr
+shanoir.server.url=https\://shanoir-ofsep-qualif.irisa.fr
\ No newline at end of file
diff --git a/shanoir-uploader/src/main/resources/profile.OFSEP/profile.properties b/shanoir-uploader/src/main/resources/profile.OFSEP/profile.properties
index 352f6355f3..e2d4366fff 100644
--- a/shanoir-uploader/src/main/resources/profile.OFSEP/profile.properties
+++ b/shanoir-uploader/src/main/resources/profile.OFSEP/profile.properties
@@ -14,16 +14,7 @@ mode.subject.study.identifier=false
anonymization.profile=Profile OFSEP
-##########################################################
-# Server properties for accessing to Shanoir-old server
-##########################################################
-shanoir.server.user.name=
-shanoir.server.user.password=
-shanoir.server.uploader.service.url=
-shanoir.server.uploader.service.qname.local.part=
-shanoir.server.uploader.service.qname.namespace.uri=
-
##########################################################
# Server properties for accessing to Shanoir-NG server
##########################################################
-shanoir.server.url=https\://shanoir-ofsep.irisa.fr
+shanoir.server.url=https\://shanoir-ofsep.irisa.fr
\ No newline at end of file
diff --git a/shanoir-uploader/src/main/resources/profile.dev/profile.properties b/shanoir-uploader/src/main/resources/profile.dev/profile.properties
index dcfcf1bd7a..5a94ca403f 100644
--- a/shanoir-uploader/src/main/resources/profile.dev/profile.properties
+++ b/shanoir-uploader/src/main/resources/profile.dev/profile.properties
@@ -14,16 +14,7 @@ mode.subject.study.identifier=true
anonymization.profile=Profile Neurinfo
-##########################################################
-# Server properties for accessing to Shanoir-old server
-##########################################################
-shanoir.server.user.name=
-shanoir.server.user.password=
-shanoir.server.uploader.service.url=
-shanoir.server.uploader.service.qname.local.part=
-shanoir.server.uploader.service.qname.namespace.uri=
-
##########################################################
# Server properties for accessing to Shanoir-NG server
##########################################################
-shanoir.server.url=https\://shanoir-ng-nginx
+shanoir.server.url=https\://shanoir-ng-nginx
\ No newline at end of file
diff --git a/shanoir-uploader/src/test/java/org/shanoir/uploader/test/importer/ZipFileImportTest.java b/shanoir-uploader/src/test/java/org/shanoir/uploader/test/importer/ZipFileImportTest.java
index 846922acbc..57e5f38251 100644
--- a/shanoir-uploader/src/test/java/org/shanoir/uploader/test/importer/ZipFileImportTest.java
+++ b/shanoir-uploader/src/test/java/org/shanoir/uploader/test/importer/ZipFileImportTest.java
@@ -13,11 +13,13 @@
import org.shanoir.ng.importer.model.Patient;
import org.shanoir.ng.importer.model.Serie;
import org.shanoir.ng.importer.model.Study;
+import org.shanoir.uploader.model.rest.Center;
import org.shanoir.uploader.model.rest.Examination;
import org.shanoir.uploader.model.rest.HemisphericDominance;
import org.shanoir.uploader.model.rest.IdName;
import org.shanoir.uploader.model.rest.ImagedObjectCategory;
import org.shanoir.uploader.model.rest.Sex;
+import org.shanoir.uploader.model.rest.StudyCenter;
import org.shanoir.uploader.model.rest.Subject;
import org.shanoir.uploader.model.rest.SubjectStudy;
import org.shanoir.uploader.model.rest.SubjectType;
@@ -30,13 +32,13 @@ public class ZipFileImportTest extends AbstractTest {
private static Logger logger = Logger.getLogger(ZipFileImportTest.class);
+ private static final String ACR_PHANTOM_T1_ZIP = "acr_phantom_t1.zip";
+
@Test
public void importDicomZipTest() throws Exception {
- org.shanoir.uploader.model.rest.Study study = new org.shanoir.uploader.model.rest.Study();
- study.setId(Long.valueOf(3));
- study.setName("DemoStudy");
+ org.shanoir.uploader.model.rest.Study study = createStudyAndStudyCard();
for (int i = 0; i < 1; i++) {
- ImportJob importJob = step1UploadDicom("acr_phantom_t1.zip");
+ ImportJob importJob = step1UploadDicom(ACR_PHANTOM_T1_ZIP);
if (!importJob.getPatients().isEmpty()) {
selectAllSeriesForImport(importJob);
Subject subject = step2CreateSubject(importJob, study);
@@ -45,6 +47,22 @@ public void importDicomZipTest() throws Exception {
}
}
}
+
+ private org.shanoir.uploader.model.rest.Study createStudyAndStudyCard() {
+ org.shanoir.uploader.model.rest.Study study = new org.shanoir.uploader.model.rest.Study();
+ final String randomStudyName = "Study-Name-" + UUID.randomUUID().toString();
+ study.setName(randomStudyName);
+ study.setStudyStatus("IN_PROGRESS");
+ List<StudyCenter> studyCenterList = new ArrayList<StudyCenter>();
+ final StudyCenter studyCenter = new StudyCenter();
+ final Center center = new Center();
+ center.setId(Long.valueOf(1));
+ studyCenter.setCenter(center);
+ studyCenterList.add(studyCenter);
+ study.setStudyCenterList(studyCenterList);
+ shUpClient.createStudy(study);
+ return study;
+ }
private void createSubjectStudy(org.shanoir.uploader.model.rest.Study study, Subject subject) {
SubjectStudy subjectStudy = new SubjectStudy();