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[fli-iam#1864] Add NIRS type BIDS #1865

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merged 14 commits into from
Nov 24, 2023
Merged

[fli-iam#1864] Add NIRS type BIDS #1865

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7268050
[fli-iam##1864] Add NIRS type BIDS
youennmerel Sep 19, 2023
4de1b45
[fli-iam#1864] Remove NIRS dataset type
youennmerel Sep 19, 2023
30c2d28
[fli-iam#1864] Correct unit test
youennmerel Sep 20, 2023
ddef761
[fli-iam#1864] Correct review comments
youennmerel Sep 21, 2023
23a270d
[fli-iam#1864] Correct reviews comment
youennmerel Sep 21, 2023
05c4af1
[fli-iam#1864] Add NIRS manufacturer model modality
youennmerel Sep 22, 2023
abd47b1
Merge branch 'develop' into fli-iam##1864
youennmerel Sep 25, 2023
f66e701
[fli-iam#1864] Correct acquisition update rights
youennmerel Sep 25, 2023
5fe0db8
[fli-iam#1864] Set study name in import job
youennmerel Sep 29, 2023
7d89316
Merge branch 'fli-iam:develop' into fli-iam##1864
youennmerel Sep 29, 2023
d1d6dd4
[fli-iam#1864] Correct PR review
youennmerel Oct 24, 2023
47052fb
[fli-iam#1864] remove non alphanumeric characters in BIDS labels
youennmerel Nov 22, 2023
b0b5e5e
[fli-iam#1864] Correct failing TU
youennmerel Nov 23, 2023
435d543
[fli-iam#1864] Correct acq_time parsing
youennmerel Nov 23, 2023
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62 changes: 27 additions & 35 deletions shanoir-ng-datasets/src/main/java/org/shanoir/ng/bids/service/BIDSServiceImpl.java
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Expand Up @@ -19,14 +19,10 @@
import java.util.stream.Collectors;

import org.apache.commons.io.FileUtils;
import org.apache.commons.lang3.StringUtils;
import org.shanoir.ng.dataset.DatasetDescription;
import org.shanoir.ng.dataset.controler.DatasetApiController.CoordinatesSystem;
import org.shanoir.ng.dataset.modality.BidsDataset;
import org.shanoir.ng.dataset.modality.EegDataSetDescription;
import org.shanoir.ng.dataset.modality.EegDataset;
import org.shanoir.ng.dataset.modality.MrDataset;
import org.shanoir.ng.dataset.modality.MrDatasetNature;
import org.shanoir.ng.dataset.modality.PetDataset;
import org.shanoir.ng.dataset.modality.*;
import org.shanoir.ng.dataset.model.Dataset;
import org.shanoir.ng.dataset.model.DatasetExpression;
import org.shanoir.ng.dataset.model.DatasetExpressionFormat;
Expand Down Expand Up @@ -203,7 +199,7 @@ public void deleteBidsFolder(Long studyId, String studyName) {
studyName = this.studyRepo.findById(studyId).get().getName();
}
// Try to delete the BIDS folder recursively if possible
File bidsDir = new File(bidsStorageDir + File.separator + STUDY_PREFIX + studyId + '_' + studyName);
File bidsDir = new File(bidsStorageDir + File.separator + STUDY_PREFIX + studyId + studyName);
if (bidsDir.exists()) {
FileUtils.deleteDirectory(bidsDir);
}
Expand All @@ -214,15 +210,14 @@ public void deleteBidsFolder(Long studyId, String studyName) {

/**
* Returns data from the study formatted as BIDS in a .zip file.
* @param study the study we want to export as BIDS
* @return data from the study formatted as BIDS in a .zip file.
* @throws IOException
*/
@Override
public File exportAsBids(final Long studyId, String studyName) throws IOException {
// Get folder
studyName = studyName.replaceAll("[ _] ", "");
String tmpFilePath = bidsStorageDir + File.separator + STUDY_PREFIX + studyId + '_' + studyName;
studyName = this.formatLabel(studyName);
String tmpFilePath = bidsStorageDir + File.separator + STUDY_PREFIX + studyId + studyName;
File workFolder = new File(tmpFilePath);
if (workFolder.exists()) {
// If the file already exists, just return it
Expand Down Expand Up @@ -267,7 +262,6 @@ private List<Subject> getSubjectsForStudy(final Long studyId) throws JsonParseEx
/**
* Create the study/BASE BIDS folder.
* @param studyName the study name
* @param studyId the study id
* @return the base folder newly created
*/
private File createBaseBidsFolder(File workFolder, String studyName) {
Expand Down Expand Up @@ -317,11 +311,7 @@ private void exportAsBids(final Subject subject, final String studyName, Long st
.append(NEW_LINE);

for (Examination examination : examinationList) {
String sessionLabel = "" + examination.getId();
sessionLabel += (examination.getComment() != null ? "-" + examination.getComment() : "");

sessionLabel = sessionLabel.replaceAll(" ", "");
sessionLabel = sessionLabel.replaceAll("_", "");
String sessionLabel = this.getSessionLabel(examination);

buffer.append(sessionLabel).append(TABULATION)
.append(examination.getExaminationDate()).append(TABULATION)
Expand All @@ -334,7 +324,7 @@ private void exportAsBids(final Subject subject, final String studyName, Long st
File examDir = subjDir;
for (Examination exam : examinationList) {
if (useSessionFolder) {
examDir = createExaminationFolder(exam, subjDir, sessionFile);
examDir = createExaminationFolder(exam, subjDir);
}
exportAsBids(exam, examDir, studyName, subject.getName());
}
Expand All @@ -353,10 +343,9 @@ private void exportAsBids(final Subject subject, final String studyName, Long st
*/
private File createSubjectFolder(String subjectName, final int index, final File baseDir) throws IOException {
// Generate another ID here ?
subjectName = subjectName.replaceAll(" ", "");
subjectName = subjectName.replaceAll("_", "");
subjectName = this.formatLabel(subjectName);

File subjectFolder = new File(baseDir.getAbsolutePath() + File.separator + SUBJECT_PREFIX + index + "-" + subjectName);
File subjectFolder = new File(baseDir.getAbsolutePath() + File.separator + SUBJECT_PREFIX + index + subjectName);
if (!subjectFolder.exists()) {
subjectFolder.mkdirs();
}
Expand All @@ -366,7 +355,6 @@ private File createSubjectFolder(String subjectName, final int index, final File
/**
* Returns data from the examination formatted as BIDS in a .zip file.
* @param examination the examination we want to export as BIDS
* @param subjDir examination BIDS directory where we are working.
* @param studyName the study name
* @param subjectName the subject name
* @return data from the examination formatted as BIDS in a .zip file.
Expand Down Expand Up @@ -403,16 +391,11 @@ private void exportAsBids(final Examination examination, final File examDir, fin
* Create the session/examination BIDS folder
* @param examination the examination for which we want to create the folder
* @param subjectDir the parent folder
* @param sessionFile the session file to complete
* @return the newly created folder
* @throws IOException
*/
private File createExaminationFolder(final Examination examination, final File subjectDir, File sessionFile) throws IOException {
String sessionLabel = "" + examination.getId();
sessionLabel += (examination.getComment() != null ? "-" + examination.getComment() : "");

sessionLabel = sessionLabel.replaceAll(" ", "");
sessionLabel = sessionLabel.replaceAll("_", "");
private File createExaminationFolder(final Examination examination, final File subjectDir) throws IOException {
String sessionLabel = this.getSessionLabel(examination);

// Create exam/session folder
File examFolder = new File(subjectDir.getAbsolutePath() + File.separator + SESSION_PREFIX + sessionLabel);
Expand All @@ -422,6 +405,15 @@ private File createExaminationFolder(final Examination examination, final File s
return examFolder;
}

private String getSessionLabel(Examination examination) {
String label = "" + examination.getId();
if(!StringUtils.isBlank(examination.getComment())){
label += examination.getComment();
}

return formatLabel(label);
}

/**
* Create the list of BIDS files associated to a dataset.
* @param dataset the dataset from which we want the specific BIDS files to be created
Expand All @@ -434,7 +426,7 @@ private File createExaminationFolder(final Examination examination, final File s
private void createDatasetBidsFiles(final Dataset dataset, final File workDir, final String studyName, final String subjectName) throws IOException {
File dataFolder = null;

String subjectNameUpdated = subjectName.replaceAll("[ _] ", "");
String subjectNameUpdated = this.formatLabel(subjectName);
String datasetFilePrefix = workDir.getName().contains(SESSION_PREFIX) ? workDir.getParentFile().getName() + "_" + workDir.getName() : workDir.getName();

dataFolder = createSpecificDataFolder(dataset, workDir, dataFolder, subjectNameUpdated, studyName);
Expand Down Expand Up @@ -556,8 +548,7 @@ private void deleteIfExists(String filePath) {

private File getScansFile(File parentFile, String subjectName) throws IOException {
String fileName = parentFile.getName() + SCANS_FILE_EXTENSION;
subjectName = subjectName.replaceAll(" ", "");
subjectName = subjectName.replaceAll("_", "");
subjectName = this.formatLabel(subjectName);
if (!parentFile.getName().contains(subjectName)) {
fileName = SUBJECT_PREFIX + subjectName + "_" + parentFile.getName() + SCANS_FILE_EXTENSION;
}
Expand Down Expand Up @@ -618,8 +609,6 @@ private void getDatasetFilePathURLs(final Dataset dataset, final List<URL> pathU
* See https://bids-specification.readthedocs.io/en/latest/04-modality-specific-files/03-electroencephalography.html
* for more informations
* @param dataset the dataset we want to export in BIDS
* @param workFolder the examination work folder in which we are working
* @param pathURLs list of file URL
* @param studyName the name of associated study
* @param subjectName the subject name associated
* @param sessionId the session ID / examination ID associated
Expand Down Expand Up @@ -760,8 +749,7 @@ private void participantsSerializer(File parentFolder, List<Subject> subjs) {

for (Subject subject : subjs) {
String subjectName = subject.getName();
subjectName = subjectName.replaceAll(" ", "");
subjectName = subjectName.replaceAll("_", "");
subjectName = this.formatLabel(subjectName);
// Write in the file the values
buffer.append(SUBJECT_PREFIX).append(index++).append("_").append(subjectName).append(CSV_SEPARATOR)
.append(subject.getId()).append(CSV_SEPARATOR)
Expand All @@ -775,4 +763,8 @@ private void participantsSerializer(File parentFolder, List<Subject> subjs) {
}
}

private String formatLabel(String label){
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return label.replaceAll("[^a-zA-Z0-9]+", "");
}

}
5 changes: 4 additions & 1 deletion shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/BidsDataType.java
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Expand Up @@ -36,7 +36,10 @@ public enum BidsDataType {
PET("pet"),

/* Microscopy.*/
MICR("micr");
MICR("micr"),

/* Near-Infrared Spectroscopy */
NIRS("nirs");

private String folderName;

Expand Down
5 changes: 4 additions & 1 deletion shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/model/DatasetModalityType.java
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Expand Up @@ -50,7 +50,10 @@ public enum DatasetModalityType {
MICR_DATASET(9),

// Behavioural Dataset
BEH_DATASET(10);
BEH_DATASET(10),

// Near-Infrared Spectroscopy dataset
NIRS_DATASET(11);

private int id;

Expand Down
58 changes: 46 additions & 12 deletions ...oir-ng-datasets/src/main/java/org/shanoir/ng/dataset/security/DatasetSecurityService.java
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Expand Up @@ -568,36 +568,70 @@ public boolean hasUpdateRightOnDataset(Dataset dataset, String rightStr) throws
}
}

/**
* Check the connected user has the given right for the given dataset acquisition.
* If the study is updated, check the user has the given right in both former and new studies.
*
* @param datasetAcq the dataset acquisition
* @param rightStr the right
* @return true or false
* @throws EntityNotFoundException
*/
public boolean hasUpdateRightOnDatasetAcquisition(DatasetAcquisition datasetAcq, String rightStr) throws EntityNotFoundException {
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if (KeycloakUtil.getTokenRoles().contains("ROLE_ADMIN")) {
return true;
}
if (datasetAcq == null) {
throw new IllegalArgumentException("Dataset acquisition cannot be null here.");
}
if (datasetAcq.getId() == null) {
throw new IllegalArgumentException("Dataset acquisition id cannot be null here.");
}
if (datasetAcq.getExamination() == null || datasetAcq.getExamination().getStudyId() == null) {
return false;
}
DatasetAcquisition dbDatasetAcq = datasetAcquisitionRepository.findById(datasetAcq.getId()).orElse(null);
if (dbDatasetAcq == null) {
throw new EntityNotFoundException("Cannot find dataset acquisition with id " + datasetAcq.getId());
}
if (datasetAcq.getExamination().getStudyId() == dbDatasetAcq.getExamination().getStudyId()) { // study hasn't changed
return this.hasRightOnStudyCenter(datasetAcq.getExamination().getCenterId(), datasetAcq.getExamination().getStudyId(), rightStr);
} else { // study has changed : check user has right on both studies
return this.hasRightOnStudyCenter(datasetAcq.getExamination().getCenterId(), datasetAcq.getExamination().getStudyId(), rightStr) &&
this.hasRightOnStudyCenter(dbDatasetAcq.getExamination().getCenterId(), dbDatasetAcq.getExamination().getStudyId(), rightStr);
}
}

/**
* Check the connected user has the given right for the given dataset acquisition.
* Check the connected user has the given right for the given dataset acquisition DTO.
* If the study is updated, check the user has the given right in both former and new studies.
*
* @param datasetAcq the dataset acquisition
* @param datasetAcqDto the dataset acquisition dto
* @param rightStr the right
* @return true or false
* @throws EntityNotFoundException
*/
public boolean hasUpdateRightOnDatasetAcquisition(DatasetAcquisition datasetAcq, String rightStr) throws EntityNotFoundException {
public boolean hasUpdateRightOnDatasetAcquisitionDTO(DatasetAcquisitionDTO datasetAcqDto, String rightStr) throws EntityNotFoundException {
if (KeycloakUtil.getTokenRoles().contains("ROLE_ADMIN")) {
return true;
}
if (datasetAcq == null) {
if (datasetAcqDto == null) {
throw new IllegalArgumentException("Dataset acquisition cannot be null here.");
}
if (datasetAcq.getId() == null) {
if (datasetAcqDto.getId() == null) {
throw new IllegalArgumentException("Dataset acquisition id cannot be null here.");
}
if (datasetAcq.getExamination() == null || datasetAcq.getExamination().getStudyId() == null) {
if (datasetAcqDto.getExamination() == null || datasetAcqDto.getExamination().getStudyId() == null) {
return false;
}
DatasetAcquisition dbDatasetAcq = datasetAcquisitionRepository.findById(datasetAcq.getId()).orElse(null);
DatasetAcquisition dbDatasetAcq = datasetAcquisitionRepository.findById(datasetAcqDto.getId()).orElse(null);
if (dbDatasetAcq == null) {
throw new EntityNotFoundException("Cannot find dataset acquisition with id " + datasetAcq.getId());
throw new EntityNotFoundException("Cannot find dataset acquisition with id " + datasetAcqDto.getId());
}
if (datasetAcq.getExamination().getStudyId() == dbDatasetAcq.getExamination().getStudyId()) { // study hasn't changed
return this.hasRightOnStudyCenter(datasetAcq.getExamination().getCenterId(), datasetAcq.getExamination().getStudyId(), rightStr);
} else { // study has changed : check user has right on both studies
return this.hasRightOnStudyCenter(datasetAcq.getExamination().getCenterId(), datasetAcq.getExamination().getStudyId(), rightStr) &&
if (datasetAcqDto.getExamination().getStudyId() == dbDatasetAcq.getExamination().getStudyId()) { // study hasn't changed
return this.hasRightOnStudyCenter(datasetAcqDto.getExamination().getCenterId(), datasetAcqDto.getExamination().getStudyId(), rightStr);
} else { // study has changed : check user has right on both studies
return this.hasRightOnStudyCenter(datasetAcqDto.getExamination().getCenterId(), datasetAcqDto.getExamination().getStudyId(), rightStr) &&
this.hasRightOnStudyCenter(dbDatasetAcq.getExamination().getCenterId(), dbDatasetAcq.getExamination().getStudyId(), rightStr);
}
}
Expand Down
16 changes: 1 addition & 15 deletions shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/service/DatasetUtils.java
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Expand Up @@ -5,21 +5,7 @@
import java.util.Iterator;
import java.util.List;

import org.shanoir.ng.dataset.modality.BidsDataset;
import org.shanoir.ng.dataset.modality.CalibrationDataset;
import org.shanoir.ng.dataset.modality.CtDataset;
import org.shanoir.ng.dataset.modality.EegDataset;
import org.shanoir.ng.dataset.modality.GenericDataset;
import org.shanoir.ng.dataset.modality.MegDataset;
import org.shanoir.ng.dataset.modality.MeshDataset;
import org.shanoir.ng.dataset.modality.MrDataset;
import org.shanoir.ng.dataset.modality.ParameterQuantificationDataset;
import org.shanoir.ng.dataset.modality.PetDataset;
import org.shanoir.ng.dataset.modality.RegistrationDataset;
import org.shanoir.ng.dataset.modality.SegmentationDataset;
import org.shanoir.ng.dataset.modality.SpectDataset;
import org.shanoir.ng.dataset.modality.StatisticalDataset;
import org.shanoir.ng.dataset.modality.TemplateDataset;
import org.shanoir.ng.dataset.modality.*;
import org.shanoir.ng.dataset.model.Dataset;
import org.shanoir.ng.dataset.model.DatasetExpression;
import org.shanoir.ng.dataset.model.DatasetExpressionFormat;
Expand Down
2 changes: 1 addition & 1 deletion ...sets/src/main/java/org/shanoir/ng/datasetacquisition/controler/DatasetAcquisitionApi.java
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Expand Up @@ -131,7 +131,7 @@ ResponseEntity<List<DatasetAcquisitionDatasetsDTO>> findDatasetAcquisitionByData
@ApiResponse(responseCode = "500", description = "unexpected error") })
@RequestMapping(value = "/datasetacquisition/{datasetAcquisitionId}", produces = { "application/json" }, consumes = {
"application/json" }, method = RequestMethod.PUT)
@PreAuthorize("hasAnyRole('ADMIN', 'EXPERT') and #datasetAcquisitionId == #datasetAcquisition.getId() and @datasetSecurityService.hasUpdateRightOnDatasetAcquisition(#datasetAcquisition, 'CAN_ADMINISTRATE')")
@PreAuthorize("hasAnyRole('ADMIN', 'EXPERT') and #datasetAcquisitionId == #datasetAcquisition.getId() and @datasetSecurityService.hasRightOnExamination(#datasetAcquisition.examination.id, 'CAN_ADMINISTRATE')")
ResponseEntity<Void> updateDatasetAcquisition(
@Parameter(name = "id of the datasetAcquisition", required = true) @PathVariable("datasetAcquisitionId") Long datasetAcquisitionId,
@Parameter(name = "datasetAcquisition to update", required = true) @Valid @RequestBody DatasetAcquisitionDTO datasetAcquisition, BindingResult result)
Expand Down
10 changes: 8 additions & 2 deletions ...n/java/org/shanoir/ng/datasetacquisition/dto/mapper/DatasetAcquisitionDatasetsMapper.java
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Expand Up @@ -28,7 +28,10 @@
import org.shanoir.ng.dataset.service.DatasetUtils;
import org.shanoir.ng.datasetacquisition.dto.DatasetAcquisitionDatasetsDTO;
import org.shanoir.ng.datasetacquisition.model.DatasetAcquisition;
import org.shanoir.ng.datasetacquisition.model.GenericDatasetAcquisition;
import org.shanoir.ng.datasetacquisition.model.bids.BidsDatasetAcquisition;
import org.shanoir.ng.datasetacquisition.model.ct.CtDatasetAcquisition;
import org.shanoir.ng.datasetacquisition.model.eeg.EegDatasetAcquisition;
import org.shanoir.ng.datasetacquisition.model.mr.MrDatasetAcquisition;
import org.shanoir.ng.datasetacquisition.model.pet.PetDatasetAcquisition;
import org.shanoir.ng.examination.dto.mapper.ExaminationMapper;
Expand All @@ -54,8 +57,11 @@ DatasetAcquisitionDatasetsDTO datasetAcquisitionToDatasetAcquisitionDatasetsDTO(
default DatasetAcquisition createDatasetAcquisition(DatasetAcquisitionDatasetsDTO dto) {
if (dto.getType().equals("Mr")) return new MrDatasetAcquisition();
else if (dto.getType().equals("Pet")) return new PetDatasetAcquisition();
else if (dto.getType().equals("Ct")) return new CtDatasetAcquisition();
else throw new IllegalStateException("Cannot map from a dataset acquisition dto that don't provide a valid type. Given type = " + dto.getType());
else if (dto.getType().equals("Ct")) return new CtDatasetAcquisition();
else if (dto.getType().equals("BIDS")) return new BidsDatasetAcquisition();
else if (dto.getType().equals("Eeg")) return new EegDatasetAcquisition();
else if (dto.getType().equals("Generic")) return new GenericDatasetAcquisition();
else throw new IllegalStateException("Cannot map from a dataset acquisition dto that don't provide a valid type. Given type = " + dto.getType());
}

@ObjectFactory
Expand Down
12 changes: 9 additions & 3 deletions .../src/main/java/org/shanoir/ng/datasetacquisition/dto/mapper/DatasetAcquisitionMapper.java
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Expand Up @@ -23,7 +23,10 @@
import org.mapstruct.ObjectFactory;
import org.shanoir.ng.datasetacquisition.dto.DatasetAcquisitionDTO;
import org.shanoir.ng.datasetacquisition.model.DatasetAcquisition;
import org.shanoir.ng.datasetacquisition.model.GenericDatasetAcquisition;
import org.shanoir.ng.datasetacquisition.model.bids.BidsDatasetAcquisition;
import org.shanoir.ng.datasetacquisition.model.ct.CtDatasetAcquisition;
import org.shanoir.ng.datasetacquisition.model.eeg.EegDatasetAcquisition;
import org.shanoir.ng.datasetacquisition.model.mr.MrDatasetAcquisition;
import org.shanoir.ng.datasetacquisition.model.pet.PetDatasetAcquisition;
import org.shanoir.ng.examination.dto.mapper.ExaminationMapper;
Expand All @@ -49,9 +52,12 @@ DatasetAcquisitionDTO datasetAcquisitionToDatasetAcquisitionDTO(

@ObjectFactory
default DatasetAcquisition createDatasetAcquisition(DatasetAcquisitionDTO dto) {
if (dto.getType().equals("Mr")) return new MrDatasetAcquisition();
else if (dto.getType().equals("Pet")) return new PetDatasetAcquisition();
else if (dto.getType().equals("Ct")) return new CtDatasetAcquisition();
if (dto.getType().equals("Mr")) return new MrDatasetAcquisition();
else if (dto.getType().equals("Pet")) return new PetDatasetAcquisition();
else if (dto.getType().equals("Ct")) return new CtDatasetAcquisition();
else if (dto.getType().equals("BIDS")) return new BidsDatasetAcquisition();
else if (dto.getType().equals("Eeg")) return new EegDatasetAcquisition();
else if (dto.getType().equals("Generic")) return new GenericDatasetAcquisition();
else throw new IllegalStateException("Cannot map from a dataset acquisition dto that don't provide a valid type. Given type = " + dto.getType());
}

Expand Down
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