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fli-iam#2506 : dataset tag API created (add/remove tags to a dataset …
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64 changes: 64 additions & 0 deletions
64
shanoir-ng-datasets/src/main/java/org/shanoir/ng/tag/controller/StudyTagApi.java
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| /** | ||
| * Shanoir NG - Import, manage and share neuroimaging data | ||
| * Copyright (C) 2009-2019 Inria - https://www.inria.fr/ | ||
| * Contact us on https://project.inria.fr/shanoir/ | ||
| * | ||
| * This program is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU General Public License as published by | ||
| * the Free Software Foundation, either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * You should have received a copy of the GNU General Public License | ||
| * along with this program. If not, see https://www.gnu.org/licenses/gpl-3.0.html | ||
| */ | ||
|
|
||
| package org.shanoir.ng.tag.controller; | ||
|
|
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| import io.swagger.v3.oas.annotations.Operation; | ||
| import io.swagger.v3.oas.annotations.Parameter; | ||
| import io.swagger.v3.oas.annotations.responses.ApiResponse; | ||
| import io.swagger.v3.oas.annotations.responses.ApiResponses; | ||
| import io.swagger.v3.oas.annotations.tags.Tag; | ||
| import org.apache.solr.client.solrj.SolrServerException; | ||
| import org.shanoir.ng.shared.exception.EntityNotFoundException; | ||
| import org.shanoir.ng.shared.exception.RestServiceException; | ||
| import org.springframework.http.ResponseEntity; | ||
| import org.springframework.security.access.prepost.PreAuthorize; | ||
| import org.springframework.validation.BindingResult; | ||
| import org.springframework.web.bind.annotation.*; | ||
|
|
||
| import java.io.IOException; | ||
| import java.util.List; | ||
|
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| @Tag(name = "studytag") | ||
| @RequestMapping("/studytag") | ||
| public interface StudyTagApi { | ||
|
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| @Operation(summary = "addStudyTagsToDataset", description = "Add study tags to a dataset") | ||
| @ApiResponses(value = { @ApiResponse(responseCode = "200", description = "dataset associated to study tags"), | ||
| @ApiResponse(responseCode = "401", description = "unauthorized"), | ||
| @ApiResponse(responseCode = "403", description = "forbidden"), | ||
| @ApiResponse(responseCode = "404", description = "dataset does not exists"), | ||
| @ApiResponse(responseCode = "422", description = "bad parameters"), | ||
| @ApiResponse(responseCode = "500", description = "unexpected error") }) | ||
| @PutMapping(value = "/addStudyTagsToDataset") | ||
| @PreAuthorize("hasRole('ADMIN') or (hasRole('EXPERT') and @datasetSecurityService.hasRightOnDataset(#datasetId, 'CAN_IMPORT'))") | ||
| ResponseEntity<Void> addStudyTagsToDataset( | ||
| @Parameter(description = "id of the dataset", required = true) @RequestParam(value = "datasetId") Long datasetId, | ||
| @Parameter(description = "study tag ids", required = true) @RequestParam(value = "studyTagIds") List<Long> studyTagIds) | ||
| throws RestServiceException, EntityNotFoundException, SolrServerException, IOException; | ||
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| @Operation(summary = "removeStudyTagsFromDataset", description = "Add study tags to a dataset") | ||
| @ApiResponses(value = { @ApiResponse(responseCode = "200", description = "dataset associated to study tags"), | ||
| @ApiResponse(responseCode = "401", description = "unauthorized"), | ||
| @ApiResponse(responseCode = "403", description = "forbidden"), | ||
| @ApiResponse(responseCode = "404", description = "dataset does not exists"), | ||
| @ApiResponse(responseCode = "422", description = "bad parameters"), | ||
| @ApiResponse(responseCode = "500", description = "unexpected error") }) | ||
| @PutMapping(value = "/removeStudyTagsFromDataset") | ||
| @PreAuthorize("hasRole('ADMIN') or (hasRole('EXPERT') and @datasetSecurityService.hasRightOnDataset(#datasetId, 'CAN_IMPORT'))") | ||
| ResponseEntity<Void> removeStudyTagsFromDataset( | ||
| @Parameter(description = "id of the dataset", required = true) @RequestParam(value = "datasetId") Long datasetId, | ||
| @Parameter(description = "study tag ids", required = true) @RequestParam(value = "studyTagIds") List<Long> studyTagIds) | ||
| throws RestServiceException, EntityNotFoundException, SolrServerException, IOException; | ||
| } |
123 changes: 123 additions & 0 deletions
123
shanoir-ng-datasets/src/main/java/org/shanoir/ng/tag/controller/StudyTagApiController.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,123 @@ | ||
| /** | ||
| * Shanoir NG - Import, manage and share neuroimaging data | ||
| * Copyright (C) 2009-2019 Inria - https://www.inria.fr/ | ||
| * Contact us on https://project.inria.fr/shanoir/ | ||
| * | ||
| * This program is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU General Public License as published by | ||
| * the Free Software Foundation, either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * You should have received a copy of the GNU General Public License | ||
| * along with this program. If not, see https://www.gnu.org/licenses/gpl-3.0.html | ||
| */ | ||
|
|
||
| package org.shanoir.ng.tag.controller; | ||
|
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| import com.fasterxml.jackson.databind.ObjectMapper; | ||
| import io.swagger.v3.oas.annotations.Parameter; | ||
| import jakarta.mail.MessagingException; | ||
| import jakarta.servlet.http.HttpServletResponse; | ||
| import jakarta.validation.Valid; | ||
| import org.apache.commons.lang3.StringUtils; | ||
| import org.apache.solr.client.solrj.SolrServerException; | ||
| import org.shanoir.ng.dataset.dto.DatasetDTO; | ||
| import org.shanoir.ng.dataset.dto.DatasetWithDependenciesDTOInterface; | ||
| import org.shanoir.ng.dataset.dto.mapper.DatasetMapper; | ||
| import org.shanoir.ng.dataset.modality.EegDataset; | ||
| import org.shanoir.ng.dataset.modality.EegDatasetMapper; | ||
| import org.shanoir.ng.dataset.modality.MrDataset; | ||
| import org.shanoir.ng.dataset.modality.MrDatasetMapper; | ||
| import org.shanoir.ng.dataset.model.Dataset; | ||
| import org.shanoir.ng.dataset.model.DatasetExpressionFormat; | ||
| import org.shanoir.ng.dataset.repository.DatasetRepository; | ||
| import org.shanoir.ng.dataset.service.CreateStatisticsService; | ||
| import org.shanoir.ng.dataset.service.DatasetDownloaderServiceImpl; | ||
| import org.shanoir.ng.dataset.service.DatasetService; | ||
| import org.shanoir.ng.datasetacquisition.model.DatasetAcquisition; | ||
| import org.shanoir.ng.download.DatasetDownloadError; | ||
| import org.shanoir.ng.download.WADODownloaderService; | ||
| import org.shanoir.ng.examination.model.Examination; | ||
| import org.shanoir.ng.examination.service.ExaminationService; | ||
| import org.shanoir.ng.importer.dto.ProcessedDatasetImportJob; | ||
| import org.shanoir.ng.importer.service.ImporterService; | ||
| import org.shanoir.ng.shared.configuration.RabbitMQConfiguration; | ||
| import org.shanoir.ng.shared.error.FieldErrorMap; | ||
| import org.shanoir.ng.shared.event.ShanoirEvent; | ||
| import org.shanoir.ng.shared.event.ShanoirEventService; | ||
| import org.shanoir.ng.shared.event.ShanoirEventType; | ||
| import org.shanoir.ng.shared.exception.EntityNotFoundException; | ||
| import org.shanoir.ng.shared.exception.ErrorDetails; | ||
| import org.shanoir.ng.shared.exception.ErrorModel; | ||
| import org.shanoir.ng.shared.exception.RestServiceException; | ||
| import org.shanoir.ng.solr.service.SolrService; | ||
| import org.shanoir.ng.tag.model.StudyTag; | ||
| import org.shanoir.ng.tag.service.StudyTagService; | ||
| import org.shanoir.ng.utils.DatasetFileUtils; | ||
| import org.shanoir.ng.utils.KeycloakUtil; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
| import org.springframework.amqp.rabbit.core.RabbitTemplate; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.beans.factory.annotation.Qualifier; | ||
| import org.springframework.beans.factory.annotation.Value; | ||
| import org.springframework.core.io.ByteArrayResource; | ||
| import org.springframework.data.domain.Page; | ||
| import org.springframework.data.domain.Pageable; | ||
| import org.springframework.http.HttpHeaders; | ||
| import org.springframework.http.HttpStatus; | ||
| import org.springframework.http.MediaType; | ||
| import org.springframework.http.ResponseEntity; | ||
| import org.springframework.scheduling.annotation.Scheduled; | ||
| import org.springframework.stereotype.Controller; | ||
| import org.springframework.validation.BindingResult; | ||
| import org.springframework.web.bind.annotation.RequestBody; | ||
| import org.springframework.web.bind.annotation.RequestParam; | ||
|
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||
| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.net.MalformedURLException; | ||
| import java.net.URL; | ||
| import java.nio.file.DirectoryStream; | ||
| import java.nio.file.Files; | ||
| import java.nio.file.Path; | ||
| import java.nio.file.Paths; | ||
| import java.nio.file.attribute.BasicFileAttributes; | ||
| import java.nio.file.attribute.FileTime; | ||
| import java.util.*; | ||
| import java.util.concurrent.TimeUnit; | ||
| import java.util.stream.Collectors; | ||
|
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| @Controller | ||
| public class StudyTagApiController implements StudyTagApi { | ||
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| private static final Logger LOG = LoggerFactory.getLogger(StudyTagApiController.class); | ||
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| @Autowired | ||
| private DatasetService datasetService; | ||
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| @Autowired | ||
| private StudyTagService studyTagService; | ||
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| @Override | ||
| public ResponseEntity<Void> addStudyTagsToDataset(Long datasetId, List<Long> studyTagIds) throws EntityNotFoundException, SolrServerException, IOException { | ||
| Dataset ds = datasetService.findById(datasetId); | ||
| if (Objects.isNull(ds)) {throw new EntityNotFoundException(Dataset.class, datasetId);} | ||
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| studyTagService.addStudyTagsToDataset(ds, studyTagIds); | ||
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| return new ResponseEntity<>(HttpStatus.OK); | ||
| } | ||
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| @Override | ||
| public ResponseEntity<Void> removeStudyTagsFromDataset(Long datasetId, List<Long> studyTagIds) throws EntityNotFoundException, SolrServerException, IOException { | ||
| Dataset ds = datasetService.findById(datasetId); | ||
| if (Objects.isNull(ds)) {throw new EntityNotFoundException(Dataset.class, datasetId);} | ||
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| studyTagService.removeStudyTagsFromDataset(ds, studyTagIds); | ||
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| return new ResponseEntity<>(HttpStatus.OK); | ||
| } | ||
| } |
46 changes: 43 additions & 3 deletions
46
shanoir-ng-datasets/src/main/java/org/shanoir/ng/tag/service/StudyTagService.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,25 +1,65 @@ | ||
| package org.shanoir.ng.tag.service; | ||
|
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| import org.apache.commons.collections4.IterableUtils; | ||
| import org.apache.solr.client.solrj.SolrServerException; | ||
| import org.shanoir.ng.dataset.model.Dataset; | ||
| import org.shanoir.ng.dataset.repository.DatasetRepository; | ||
| import org.shanoir.ng.shared.exception.EntityNotFoundException; | ||
| import org.shanoir.ng.solr.service.SolrService; | ||
| import org.shanoir.ng.tag.model.StudyTag; | ||
| import org.shanoir.ng.tag.repository.StudyTagRepository; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.http.HttpStatus; | ||
| import org.springframework.http.ResponseEntity; | ||
| import org.springframework.stereotype.Service; | ||
| import org.springframework.transaction.annotation.Transactional; | ||
| import org.springframework.validation.BindingResult; | ||
|
|
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| import java.util.List; | ||
| import java.io.IOException; | ||
| import java.util.*; | ||
|
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| @Service | ||
| public class StudyTagService { | ||
|
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| @Autowired | ||
| private StudyTagRepository repository; | ||
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| @Autowired | ||
| private DatasetRepository datasetRepository; | ||
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| @Autowired | ||
| private SolrService solrService; | ||
|
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| public List<StudyTag> findByIds(List<Long> ids){ | ||
| return IterableUtils.toList(repository.findAllById(ids)); | ||
| } | ||
|
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| public boolean existsById(Long id){ | ||
| return repository.existsById(id); | ||
| @Transactional | ||
| public void addStudyTagsToDataset(Dataset dataset, List<Long> studyTagIds) throws SolrServerException, IOException { | ||
| Set<StudyTag> datasetTags = new HashSet<>(dataset.getTags()); | ||
|
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| for (StudyTag tag : findByIds(studyTagIds)) { | ||
| if (tag.getStudy().getId().equals(dataset.getStudyId())) { | ||
| datasetTags.add(tag); | ||
| } | ||
| } | ||
| dataset.setTags(new ArrayList<>(datasetTags)); | ||
| datasetRepository.save(dataset); | ||
| solrService.indexDataset(dataset.getId()); | ||
| } | ||
|
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| @Transactional | ||
| public void removeStudyTagsFromDataset(Dataset dataset, List<Long> studyTagIds) throws SolrServerException, IOException { | ||
| Set<StudyTag> datasetTags = new HashSet<>(dataset.getTags()); | ||
|
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| for (StudyTag tag : findByIds(studyTagIds)) { | ||
| if (tag.getStudy().getId().equals(dataset.getStudyId())) { | ||
| datasetTags.remove(tag); | ||
| } | ||
| } | ||
|
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| dataset.setTags(new ArrayList<>(datasetTags)); | ||
| datasetRepository.save(dataset); | ||
| solrService.indexDataset(dataset.getId()); | ||
| } | ||
| } |
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