Merge pull request #1930 from michaelkain/auto-test-import

ShUp: new version v8.0.0 (after refactor) final fixes

shanoir-ng-datasets/src/main/java/org/shanoir/ng/importer/dto/Serie.java

@@ -18,6 +18,7 @@
 import java.util.List;
 
 import org.shanoir.ng.shared.dateTime.LocalDateAnnotations;
+import org.shanoir.ng.shared.dicom.EquipmentDicom;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
 

shanoir-ng-datasets/src/main/java/org/shanoir/ng/importer/service/BidsImporterService.java

@@ -183,7 +183,7 @@ private void importDataset(ImportJob importJob, BidsDataType bidsDataType, Datas
 
 		Map<String, BidsDataset> datasetsByName = new HashMap<>();
 
-		Map<String, Integer> equipments = objectMapper.readValue((String) this.rabbitTemplate.convertSendAndReceive(RabbitMQConfiguration.ACQUISITION_EQUIPEMENT_CODE_QUEUE, "all"), Map.class);
+		Map<String, Integer> equipments = objectMapper.readValue((String) this.rabbitTemplate.convertSendAndReceive(RabbitMQConfiguration.ACQUISITION_EQUIPMENT_CODE_QUEUE, "all"), Map.class);
 		Long equipmentId = 0L;
 
 		for (File importedFile : filesToImport) {

shanoir-ng-datasets/src/main/java/org/shanoir/ng/studycard/model/condition/StudyCardCondition.java

@@ -14,26 +14,34 @@
 
 package org.shanoir.ng.studycard.model.condition;
 
-import com.fasterxml.jackson.annotation.JsonSubTypes;
-import com.fasterxml.jackson.annotation.JsonTypeInfo;
-import com.fasterxml.jackson.annotation.JsonTypeInfo.As;
-import com.fasterxml.jackson.annotation.JsonTypeInfo.Id;
-import jakarta.persistence.*;
-import jakarta.validation.constraints.NotNull;
+import java.util.List;
+
 import org.hibernate.annotations.Check;
 import org.hibernate.annotations.GenericGenerator;
 import org.shanoir.ng.shared.core.model.AbstractEntity;
 import org.shanoir.ng.studycard.model.Operation;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.util.List;
+import com.fasterxml.jackson.annotation.JsonSubTypes;
+import com.fasterxml.jackson.annotation.JsonTypeInfo;
+import com.fasterxml.jackson.annotation.JsonTypeInfo.As;
+import com.fasterxml.jackson.annotation.JsonTypeInfo.Id;
+
+import jakarta.persistence.Column;
+import jakarta.persistence.DiscriminatorColumn;
+import jakarta.persistence.DiscriminatorType;
+import jakarta.persistence.ElementCollection;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Inheritance;
+import jakarta.persistence.InheritanceType;
+import jakarta.validation.constraints.NotNull;
 
 @Entity
 @Check(constraints = "(dicomTag IS NOT NULL AND shanoirField IS NULL) OR (dicomTag IS NULL AND shanoirField IS NOT NULL)") 
 @GenericGenerator(name = "IdOrGenerate", strategy = "org.shanoir.ng.shared.model.UseIdOrGenerate")
 @Inheritance(strategy = InheritanceType.SINGLE_TABLE)
-@DiscriminatorColumn(name="scope", discriminatorType = DiscriminatorType.STRING)
+@DiscriminatorColumn(name="scope", discriminatorType = DiscriminatorType.STRING, length = 47)
 @JsonTypeInfo(use = Id.NAME, include = As.PROPERTY, property = "scope")
 @JsonSubTypes({
     @JsonSubTypes.Type(value = StudyCardDICOMConditionOnDatasets.class, name = "StudyCardDICOMConditionOnDatasets"),

shanoir-ng-datasets/src/main/java/org/shanoir/ng/studycard/service/RabbitMqStudyCardService.java

@@ -40,7 +40,7 @@ public class RabbitMqStudyCardService {
 	private StudyCardRepository studyCardService;
 
 	@Autowired
-	ObjectMapper mapper;
+	private ObjectMapper mapper;
 
 	@RabbitListener(queues = RabbitMQConfiguration.FIND_STUDY_CARD_QUEUE)
 	@RabbitHandler
@@ -59,10 +59,9 @@ public String findStudyCard(String message) {
 	public Long getBestStudyCard(String message) {
 		try {
 			Properties properties = mapper.readValue(message, Properties.class);
-			String equipmentId = String.valueOf(properties.getProperty("EQUIPMENT_ID_PROPERTY"));
+			Long equipmentId = Long.valueOf(properties.getProperty("EQUIPMENT_ID_PROPERTY"));
 			Long studyId = Long.valueOf(properties.getProperty("STUDY_ID_PROPERTY"));
 			Long studyCardId = Long.valueOf(properties.getProperty("STUDYCARD_ID_PROPERTY"));
-
 			List<StudyCard> studyCards = this.studyCardService.findByStudyId(studyId);
 			for (StudyCard sc : studyCards) {
 				if (sc.getAcquisitionEquipmentId().equals(equipmentId)) {
@@ -74,4 +73,5 @@ public Long getBestStudyCard(String message) {
 			throw new AmqpRejectAndDontRequeueException(e);
 		}
 	}
+
 }

shanoir-ng-datasets/src/main/resources/logback-spring.xml

@@ -52,9 +52,9 @@ along with this program. If not, see https://www.gnu.org/licenses/gpl-3.0.html
         <appender-ref ref="DIMSE_FILE_LOG" />
     </logger>
 
-
     <root level="INFO">
         <appender-ref ref="FILE" />
         <appender-ref ref="CONSOLE" />
     </root>
+
 </configuration>

shanoir-ng-datasets/src/main/resources/scripts/import.sql

@@ -44,34 +44,4 @@ VALUES
 INSERT INTO study_cards
 	(id, acquisition_equipment_id, disabled, last_edit_timestamp, name, nifti_converter_id, study_id)
 VALUES 
-	(1,1,false,0,'StudyCard1',1,1),
-	(2,null,false,0,'QualityCard_UCAN',null,1);
-
-INSERT INTO study_card_rule
-	(id, study_card_id, scope,or_conditions)
-VALUES
-	(1,2,'DatasetAcquisition',false),
-	(2,2,'Dataset',false);
-
-INSERT INTO study_card_condition
-	(id, dicom_tag, operation, scope, cardinality)
-VALUES 
-	(1,2,4,'StudyCardDICOMCondition', 1),
-	(2,2,4,'StudyCardDICOMCondition', 1);
-
-INSERT INTO study_card_condition_join
-	(study_card_rule_id, condition_id) 
-VALUES
-	(1,1),
-	(2,2);
-
-INSERT INTO study_card_condition_values
-	(study_card_condition_id, value)
-VALUES
-	(1,'tof'),
-	(1,'flight'),
-	(2,'gado'),
-	(2,'gd'),
-	(2,'gadolinium'),
-	(2,'contrast'),
-	(2,'enhanced');
+	(1,1,false,0,'StudyCard1',1,1);

shanoir-ng-exchange/src/main/java/org/shanoir/ng/exchange/imports/subject/IdentifierCalculator.java

@@ -64,7 +64,7 @@ public String calculateIdentifierWithHashs(final String firstNameHash, final Str
 	 * @throws NoSuchAlgorithmException
 	 * @throws UnsupportedEncodingException
 	 */
-	public String calculateIdentifier(final String firstName, final String lastName, final Date birthDate) throws NoSuchAlgorithmException, UnsupportedEncodingException {
+	public String calculateIdentifier(final String firstName, final String lastName, final String birthDate) throws NoSuchAlgorithmException, UnsupportedEncodingException {
 		final String subjectIdentifierSeed = firstName + lastName + birthDate;
 		String hex = calculateSHA(subjectIdentifierSeed);
 		return hex;

shanoir-ng-exchange/src/test/java/org/shanoir/ng/exchange/imports/subject/IdentifierCalculatorTest.java

@@ -2,9 +2,6 @@
 
 import java.io.UnsupportedEncodingException;
 import java.security.NoSuchAlgorithmException;
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.Date;
 
 import org.junit.Assert;
 import org.junit.Before;
@@ -26,25 +23,10 @@ public class IdentifierCalculatorTest {
 	private static final String FIRST_NAME = "firstName";
 
 	private static final String LAST_NAME = "lastName";
-
-	private static final SimpleDateFormat sdf = new SimpleDateFormat("dd/MM/yyyy");
-
-	private Date birthDate;
 
-	@SuppressWarnings("deprecation")
 	@Before
 	public void setup() {
 		identifierCalculator = new IdentifierCalculator();
-		try {
-			birthDate = sdf.parse("01/01/2020");
-			/**
-			 * This behaviour is strange and is there to produce the same result
-			 * as when using the Web GUI of sh-old, where 01:00:00 is set programmatically
-			 * in the backend, even if not entered by the user, maybe because of time zone problems.
-			 */
-			birthDate.setHours(1);
-		} catch (ParseException e) {
-		}
 	}
 
 	@Test
@@ -57,9 +39,9 @@ public void testCalculateIdentifierWithHashs() throws UnsupportedEncodingExcepti
 
 	@Test
 	public void testCalculateIdentifier() throws UnsupportedEncodingException, NoSuchAlgorithmException {
-		String subjectIdentifier = identifierCalculator.calculateIdentifier(FIRST_NAME, LAST_NAME, birthDate);
+		String subjectIdentifier = identifierCalculator.calculateIdentifier(FIRST_NAME, LAST_NAME, "01/01/2020");
 		// Values have been acquired during tests with master sh-old
-		// Assert.assertEquals("AC-844A74B6-74", subjectIdentifier);
+		Assert.assertEquals("AB-859C-100131", subjectIdentifier);
 	}
 
 }

shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterApi.java

@@ -14,10 +14,8 @@
 
 package org.shanoir.ng.importer;
 
-import java.io.FileNotFoundException;
 import java.io.IOException;
 
-import org.shanoir.ng.exchange.model.Exchange;
 import org.shanoir.ng.importer.dicom.query.DicomQuery;
 import org.shanoir.ng.importer.model.EegImportJob;
 import org.shanoir.ng.importer.model.ImportJob;

shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterApiController.java

@@ -283,7 +283,7 @@ public ResponseEntity<ImportJob> queryPACS(
 			importJob.setWorkFolder("");
 			importJob.setFromPacs(true);
 			importJob.setUserId(KeycloakUtil.getTokenUserId());
-		} catch (ShanoirException e) {
+		} catch (Exception e) {
 			throw new RestServiceException(
 					new ErrorModel(HttpStatus.UNPROCESSABLE_ENTITY.value(), e.getMessage(), null));
 		}

shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterManagerService.java

@@ -315,9 +315,10 @@ private void downloadAndMoveDicomFilesToImportJobDir(final File importJobDir, Li
 					event.setMessage("Downloading DICOM files from PACS for serie [" + (serie.getProtocolName() == null ? serie.getSeriesInstanceUID() : serie.getProtocolName()) + "] (" + cpt + "/" + nbSeries + ")");
 					eventService.publishEvent(event);
 
-					queryPACSService.queryCMOVE(serie);
-					String serieID = serie.getSeriesInstanceUID();
-					File serieIDFolderDir = new File(importJobDir + File.separator + serieID);
+					String studyInstanceUID = study.getStudyInstanceUID();
+					String seriesInstanceUID = serie.getSeriesInstanceUID();
+					queryPACSService.queryCMOVE(studyInstanceUID, seriesInstanceUID);
+					File serieIDFolderDir = new File(importJobDir + File.separator + seriesInstanceUID);
 
 					if(!serieIDFolderDir.exists()) {
 						serieIDFolderDir.mkdirs();
@@ -327,9 +328,9 @@ private void downloadAndMoveDicomFilesToImportJobDir(final File importJobDir, Li
 					for (Iterator<Instance> iterator = serie.getInstances().iterator(); iterator.hasNext();) {
 						Instance instance = iterator.next();
 						String sopInstanceUID = instance.getSopInstanceUID();
-						File oldFile = new File(dicomStoreSCPServer.getStorageDirPath() + File.separator + serieID + File.separator + sopInstanceUID + DicomStoreSCPServer.DICOM_FILE_SUFFIX);
+						File oldFile = new File(dicomStoreSCPServer.getStorageDirPath() + File.separator + seriesInstanceUID + File.separator + sopInstanceUID + DicomStoreSCPServer.DICOM_FILE_SUFFIX);
 						if (oldFile.exists()) {
-							File newFile = new File(importJobDir.getAbsolutePath() + File.separator + serieID + File.separator + oldFile.getName());
+							File newFile = new File(importJobDir.getAbsolutePath() + File.separator + seriesInstanceUID + File.separator + oldFile.getName());
 							oldFile.renameTo(newFile);
 							LOG.debug("Moving file: {} to ", oldFile.getAbsolutePath(), newFile.getAbsolutePath());
 						} else {

shanoir-ng-import/src/main/java/org/shanoir/ng/importer/bids/BidsImporterApi.java

@@ -26,11 +26,11 @@
 import org.springframework.web.bind.annotation.RequestPart;
 import org.springframework.web.multipart.MultipartFile;
 
-import io.swagger.v3.oas.annotations.tags.Tag;
 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;
 
 /**
  * 

shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/NIfTIConverter.java

@@ -14,9 +14,6 @@
 
 package org.shanoir.ng.importer.dcm2nii;
 
-import jakarta.persistence.Column;
-import jakarta.persistence.Entity;
-
 import org.hibernate.annotations.GenericGenerator;
 import org.hibernate.validator.constraints.NotBlank;
 import org.shanoir.ng.shared.hateoas.HalEntity;
@@ -25,6 +22,9 @@
 
 import com.fasterxml.jackson.annotation.JsonPropertyOrder;
 
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+
 /**
  * The class NIfTIConverter.
  * 

shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/NIfTIConverterApi.java

@@ -24,11 +24,12 @@
 import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
-import io.swagger.v3.oas.annotations.tags.Tag;
+
 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;
 
 /**
  * @author yyao

shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dicom/DicomSerieAndInstanceAnalyzer.java

@@ -8,8 +8,6 @@
 import org.shanoir.ng.utils.ImportUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.stereotype.Component;
 
 /**
  * This class is a helper class, that will in the future be used to detect

shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dicom/ImagesCreatorAndDicomFileAnalyzerService.java

@@ -29,7 +29,6 @@
 import org.dcm4che3.data.UID;
 import org.dcm4che3.emf.MultiframeExtractor;
 import org.dcm4che3.io.DicomInputStream;
-import org.shanoir.ng.importer.model.EquipmentDicom;
 import org.shanoir.ng.importer.model.Image;
 import org.shanoir.ng.importer.model.Instance;
 import org.shanoir.ng.importer.model.InstitutionDicom;
@@ -38,6 +37,7 @@
 import org.shanoir.ng.importer.model.Study;
 import org.shanoir.ng.shared.dateTime.DateTimeUtils;
 import org.shanoir.ng.shared.dicom.EchoTime;
+import org.shanoir.ng.shared.dicom.EquipmentDicom;
 import org.shanoir.ng.shared.event.ShanoirEvent;
 import org.shanoir.ng.shared.event.ShanoirEventService;
 import org.slf4j.Logger;
@@ -213,7 +213,7 @@ public File getFileFromInstance(Instance instance, Serie serie, String folderFil
 			return instanceFile;
 		} else {
 			throw new FileNotFoundException(
-					"instanceFilePath in DicomDir: missing file: " + instanceFilePath);
+					"instanceFilePath: missing file: " + instanceFilePath);
 		}
 	}