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Quality control fixes and enhancements #1851

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merged 74 commits into from
Dec 12, 2023
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36cd104
test qc with progress bar
julien-louis Sep 7, 2023
bd3d8a5
forgot front
julien-louis Sep 7, 2023
27020db
perf fix
julien-louis Sep 7, 2023
dd29847
test parallelisation
julien-louis Sep 8, 2023
9f49de5
dicom conditions with cardinality
julien-louis Sep 20, 2023
59ac38f
bugfix
julien-louis Sep 20, 2023
a062a71
fix spel error
julien-louis Sep 20, 2023
d0bc1ba
add cardinality to rule string description
julien-louis Sep 20, 2023
04efac1
new operations
julien-louis Sep 21, 2023
2e7e132
add debug logs
julien-louis Sep 21, 2023
2e3b67e
tmp
julien-louis Sep 25, 2023
5c533be
add quality tags in subject node in tree
julien-louis Sep 25, 2023
94b2b1a
merge develop
julien-louis Oct 16, 2023
d0c580e
merge stash
julien-louis Oct 16, 2023
564aef5
add sql
julien-louis Oct 16, 2023
cb9ac83
merge develop
julien-louis Oct 18, 2023
de47be2
tmp save
julien-louis Oct 19, 2023
7a5fbdb
rename sql
julien-louis Nov 3, 2023
7db3786
perf optimizations
julien-louis Nov 10, 2023
f13765f
better messages && better unknown values management
julien-louis Nov 13, 2023
719ba39
fix quality tag at import
julien-louis Nov 13, 2023
5c47dd1
cleanup useless
julien-louis Nov 14, 2023
0981ef5
quality test sample v1
julien-louis Nov 14, 2023
840bd17
merge develop
julien-louis Nov 14, 2023
d798811
quality test sample
julien-louis Nov 15, 2023
1e88699
OR between conditions + update bug fix
julien-louis Nov 16, 2023
873cd02
better study card error msg
julien-louis Nov 16, 2023
8fe4556
fix scripts
julien-louis Nov 16, 2023
ca2713b
forgot that
julien-louis Nov 17, 2023
a1a30ad
fix test thanks jc
julien-louis Nov 17, 2023
5f0bb47
restore .projects from develop
julien-louis Nov 21, 2023
ec80ee2
fix bug
julien-louis Nov 22, 2023
4c2192d
remove eager
julien-louis Nov 22, 2023
281a10f
faild -> failed
julien-louis Nov 22, 2023
a96c986
removed unused DatasetAttributes
julien-louis Nov 22, 2023
3f0733a
new name for dataset -> dataset name (for qc)
julien-louis Nov 22, 2023
1d3d1c1
change misused PacsException to ShanoirException
julien-louis Nov 22, 2023
3f2098f
use UIDs instead of hashs
julien-louis Nov 24, 2023
2649368
use UIDs instead of hashs
julien-louis Nov 24, 2023
25d8892
fix swagger param description
julien-louis Nov 24, 2023
691ec1f
merge develop
julien-louis Nov 24, 2023
27ebc99
rename scripts
julien-louis Nov 24, 2023
b7a4a8d
cache for pacs metadata fetching + display report at import
julien-louis Nov 27, 2023
67642cf
change sql scripts numbers
julien-louis Nov 27, 2023
df0f9ca
remove calling from context in entity
julien-louis Nov 27, 2023
0d26a09
fix multiple datasets bug
julien-louis Nov 27, 2023
aab91f8
clean code
julien-louis Nov 28, 2023
f5a4fa9
clean up
julien-louis Nov 28, 2023
576a534
test
julien-louis Nov 28, 2023
f9d8e44
fix irritating bug
julien-louis Nov 28, 2023
55e13cd
fix progress bar on samples + add logs to debug silent bug
julien-louis Nov 29, 2023
c02725d
add tmp logs
julien-louis Nov 29, 2023
7d965e2
add tmp logs
julien-louis Nov 29, 2023
e7aa5b4
fix bug + remove logs
julien-louis Nov 29, 2023
6e48edc
fix bug
julien-louis Nov 29, 2023
15eb3c8
fix bug
julien-louis Nov 29, 2023
18aa043
fix date bug in tasks
julien-louis Nov 29, 2023
5e34c64
remove live reporting
julien-louis Nov 29, 2023
41a6ba5
fix config : es2018 -> es 2022
julien-louis Nov 30, 2023
a9d9b29
no report in tasks list, load on click instead
julien-louis Nov 30, 2023
3cc1809
fix unwanted jdbc inheritance
julien-louis Nov 30, 2023
f86d2a3
updating all subject studies at once to gain perf
julien-louis Dec 1, 2023
451cafa
quick fix for report transfert at quality check at import
julien-louis Dec 8, 2023
6d94bce
null pointer fix
julien-louis Dec 8, 2023
9465a9a
add temp logs for debug
julien-louis Dec 8, 2023
0159876
display time in tasks table
julien-louis Dec 8, 2023
551a1f2
display time in tasks table
julien-louis Dec 8, 2023
142f28f
remove test logs
julien-louis Dec 8, 2023
5aa5cae
fix missing report at import
julien-louis Dec 11, 2023
7b0d1be
fix messages
julien-louis Dec 11, 2023
37376d6
remove test
julien-louis Dec 11, 2023
f6b3e32
remove test
julien-louis Dec 11, 2023
04ea663
remove log
julien-louis Dec 11, 2023
0f694af
quality check only on imported data, not all exam
julien-louis Dec 11, 2023
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remove test logs
julien-louis committed Dec 8, 2023
commit 142f28f77fca1a881394590f588a794767a4345d
Original file line number Diff line number Diff line change
@@ -14,11 +14,10 @@

package org.shanoir.ng.datasetacquisition.controler;

import com.fasterxml.jackson.core.JsonParseException;
import com.fasterxml.jackson.databind.JsonMappingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import io.swagger.v3.oas.annotations.Parameter;
import jakarta.validation.Valid;
import java.io.IOException;
import java.util.Comparator;
import java.util.List;

import org.apache.solr.client.solrj.SolrServerException;
import org.shanoir.ng.datasetacquisition.dto.DatasetAcquisitionDTO;
import org.shanoir.ng.datasetacquisition.dto.DatasetAcquisitionDatasetsDTO;
@@ -28,14 +27,17 @@
import org.shanoir.ng.datasetacquisition.dto.mapper.ExaminationDatasetAcquisitionMapper;
import org.shanoir.ng.datasetacquisition.model.DatasetAcquisition;
import org.shanoir.ng.datasetacquisition.service.DatasetAcquisitionService;
import org.shanoir.ng.importer.dto.Dataset;
import org.shanoir.ng.importer.dto.EegImportJob;
import org.shanoir.ng.importer.dto.ImportJob;
import org.shanoir.ng.importer.service.EegImporterService;
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.exception.*;
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.shared.exception.ShanoirException;
import org.shanoir.ng.utils.KeycloakUtil;
import org.shanoir.ng.utils.SecurityContextUtil;
import org.shanoir.ng.utils.usermock.WithMockKeycloakUser;
@@ -56,9 +58,12 @@
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestBody;

import java.io.IOException;
import java.util.Comparator;
import java.util.List;
import com.fasterxml.jackson.core.JsonParseException;
import com.fasterxml.jackson.databind.JsonMappingException;
import com.fasterxml.jackson.databind.ObjectMapper;

import io.swagger.v3.oas.annotations.Parameter;
import jakarta.validation.Valid;

@Controller
public class DatasetAcquisitionApiController implements DatasetAcquisitionApi {
@@ -117,7 +122,6 @@ public int createNewEegDatasetAcquisition(Message importJobAsString) throws IOEx
@Transactional
@WithMockKeycloakUser(authorities = { "ROLE_ADMIN" })
public void createNewDatasetAcquisition(Message importJobStr) throws JsonParseException, JsonMappingException, IOException, AmqpRejectAndDontRequeueException {
LoggerFactory.getLogger(this.getClass()).error("############################################# import job\n" + importJobStr);
ImportJob importJob = objectMapper.readValue(importJobStr.getBody(), ImportJob.class);
try {
createAllDatasetAcquisitions(importJob, importJob.getUserId());
Original file line number Diff line number Diff line change
@@ -27,7 +27,6 @@
import org.shanoir.ng.importer.dto.Serie;
import org.shanoir.ng.importer.dto.Study;
import org.shanoir.ng.shared.exception.ShanoirException;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Service;

@Service
@@ -72,7 +71,6 @@ public AcquisitionAttributes<String> getDicomAcquisitionAttributes(Serie serie,
AcquisitionAttributes<String> attributes = new AcquisitionAttributes<String>();
for (Dataset dataset : serie.getDatasets()) {
try {
LoggerFactory.getLogger(this.getClass()).error("############################################# 1" + dataset.getFirstImageSOPInstanceUID());
attributes.addDatasetAttributes(dataset.getFirstImageSOPInstanceUID(), getDicomObjectAttributes(serie.getFirstDatasetFileForCurrentSerie(), isEnhanced));
} catch (IOException e) {
throw new ShanoirException("Could not read dicom metadata from file for serie " + serie.getSopClassUID(), e);
Original file line number Diff line number Diff line change
@@ -713,7 +713,6 @@ private void constructDicom(final File serieIDFolderFile, final Serie serie, fin
} else {
Dataset dataset = new Dataset();
dataset.setFirstImageSOPInstanceUID(image.getSOPInstanceUID());
LOG.error("############################################" + dataset.getFirstImageSOPInstanceUID());
ExpressionFormat expressionFormat = new ExpressionFormat();
expressionFormat.setType("dcm");
dataset.getExpressionFormats().add(expressionFormat);