Quality control fixes and enhancements

docker-compose/database/db-changes/datasets/0036_dicom_condition_change.sql

@@ -0,0 +1,3 @@
+update study_card_condition set cardinality = 1 where cardinality is NULL;
+alter table study_card_condition modify scope varchar(47);
+update study_card_condition set scope = 'StudyCardDICOMConditionOnDatasets' where scope like 'StudyCardDICOMCondition';

docker-compose/database/db-changes/datasets/0038_quality_control_or_conditions.sql

@@ -0,0 +1,4 @@
+ALTER TABLE `study_card_rule`
+ADD COLUMN `or_conditions` bit(1) NOT NULL DEFAULT 0;
+ALTER TABLE `quality_examination_rule`
+ADD COLUMN `or_conditions` bit(1) NOT NULL DEFAULT 0;

docker-compose/database/db-changes/users/0004_task_new_column.sql

@@ -0,0 +1 @@
+alter table events add column report longtext;

shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/model/Dataset.java

@@ -130,6 +130,10 @@ public abstract class Dataset extends AbstractEntity {
 	@OneToOne(cascade = CascadeType.ALL)
 	private DatasetMetadata updatedMetadata;
 
+	@JsonIgnore
+	@Transient
+	public String SOPInstanceUID;
+
 	/**
 	 * @return the creationDate
 	 */
@@ -392,4 +396,11 @@ public void setDownloadable(boolean downloadable) {
 		this.downloadable = downloadable;
 	}
 
+	public String getSOPInstanceUID() {
+		return SOPInstanceUID;
+	}
+
+	public void setSOPInstanceUID(String sOPInstanceUID) {
+		SOPInstanceUID = sOPInstanceUID;
+	}
 }

shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/security/DatasetSecurityService.java

@@ -174,11 +174,13 @@ public boolean hasRightOnSubjectName(String subjectName, String rightStr) {
     public boolean hasRightOnSubjectStudies(List<SubjectStudy> subjectstudies, String rightStr) {
         if (KeycloakUtil.getTokenRoles().contains(ROLE_ADMIN)) {
             return true;
-        }
-        for (SubjectStudy subjectStudy : subjectstudies) {
-            boolean hasRight = commService.hasRightOnStudy(subjectStudy.getStudy().getId(), rightStr);
-            if (!hasRight) {
-                return false;
+        } 
+        if (subjectstudies != null) {
+            for (SubjectStudy subjectStudy : subjectstudies) {
+                boolean hasRight = commService.hasRightOnStudy(subjectStudy.getStudy().getId(), rightStr);
+                if (!hasRight) {
+                    return false;
+                }
             }
         }
         return true;

shanoir-ng-datasets/src/main/java/org/shanoir/ng/datasetacquisition/controler/DatasetAcquisitionApiController.java

@@ -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;
@@ -34,7 +33,11 @@
 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;
@@ -55,9 +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 {
@@ -116,7 +122,7 @@ public int createNewEegDatasetAcquisition(Message importJobAsString) throws IOEx
 	@Transactional
 	@WithMockKeycloakUser(authorities = { "ROLE_ADMIN" })
 	public void createNewDatasetAcquisition(Message importJobStr) throws JsonParseException, JsonMappingException, IOException, AmqpRejectAndDontRequeueException {
-	    ImportJob importJob = objectMapper.readValue(importJobStr.getBody(), ImportJob.class);
+		ImportJob importJob = objectMapper.readValue(importJobStr.getBody(), ImportJob.class);
 		try {
 			createAllDatasetAcquisitions(importJob, importJob.getUserId());
 		} catch (Exception e) {

shanoir-ng-datasets/src/main/java/org/shanoir/ng/datasetacquisition/dto/mapper/DatasetAcquisitionDatasetsMapper.java

@@ -19,7 +19,6 @@
 import org.mapstruct.DecoratedWith;
 import org.mapstruct.Mapper;
 import org.mapstruct.MapperConfig;
-import org.mapstruct.Mapping;
 import org.mapstruct.MappingInheritanceStrategy;
 import org.mapstruct.ObjectFactory;
 import org.shanoir.ng.dataset.dto.DatasetDTO;

shanoir-ng-datasets/src/main/java/org/shanoir/ng/dicom/DicomProcessing.java

@@ -20,7 +20,13 @@
 import org.dcm4che3.data.Attributes;
 import org.dcm4che3.data.Tag;
 import org.dcm4che3.io.DicomInputStream;
+import org.shanoir.ng.download.AcquisitionAttributes;
+import org.shanoir.ng.download.ExaminationAttributes;
+import org.shanoir.ng.importer.dto.Dataset;
 import org.shanoir.ng.importer.dto.DatasetFile;
+import org.shanoir.ng.importer.dto.Serie;
+import org.shanoir.ng.importer.dto.Study;
+import org.shanoir.ng.shared.exception.ShanoirException;
 import org.springframework.stereotype.Service;
 
 @Service
@@ -41,4 +47,40 @@ public Attributes getDicomObjectAttributes(DatasetFile image, Boolean isEnhanced
 		}
 	}
 
+    public ExaminationAttributes<String> getDicomExaminationAttributes(Study study, Boolean isEnhanced) throws ShanoirException {
+		ExaminationAttributes<String> attributes = new ExaminationAttributes<String>();
+		if (study != null) {
+			for (Serie serie : study.getSeries()) {
+				attributes.addAcquisitionAttributes(serie.getSeriesInstanceUID(), getDicomAcquisitionAttributes(serie, isEnhanced));
+			}
+		}
+		return attributes;
+    }
+
+	public ExaminationAttributes<String> getDicomExaminationAttributes(Study study) throws ShanoirException {
+		ExaminationAttributes<String> attributes = new ExaminationAttributes<String>();
+		if (study != null) {
+			for (Serie serie : study.getSeries()) {
+				attributes.addAcquisitionAttributes(serie.getSeriesInstanceUID(), getDicomAcquisitionAttributes(serie));
+			}
+		}
+		return attributes;
+    }
+
+	public AcquisitionAttributes<String> getDicomAcquisitionAttributes(Serie serie, Boolean isEnhanced) throws ShanoirException {
+		AcquisitionAttributes<String> attributes = new AcquisitionAttributes<String>();
+		for (Dataset dataset : serie.getDatasets()) {
+			try {
+				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);
+			}
+		}
+		return attributes;
+	}
+
+	public AcquisitionAttributes<String> getDicomAcquisitionAttributes(Serie serie) throws ShanoirException {
+		return getDicomAcquisitionAttributes(serie, serie.getIsEnhanced());
+	}
+
 }

shanoir-ng-datasets/src/main/java/org/shanoir/ng/download/AcquisitionAttributes.java

@@ -0,0 +1,119 @@
+/**
+ * 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.download;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
+import java.util.Set;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ConcurrentMap;
+
+import org.dcm4che3.data.Attributes;
+
+/**
+ * The parametrized type is the type for the uid keys
+ */
+public class AcquisitionAttributes<T> {
+
+	private ConcurrentMap<T, Optional<Attributes>> datasetMap = new ConcurrentHashMap<>();
+
+	public Attributes getDatasetAttributes(T id) {
+		return datasetMap.get(id).orElse(null);
+	}
+
+	public List<Attributes> getAllDatasetAttributes() {
+		List<Attributes> list = new ArrayList<>();
+		for (Optional<Attributes> attributes : datasetMap.values()) {
+			if (attributes.isPresent()) {
+				list.add(attributes.get());
+			}
+		}
+		return list;
+	}
+
+	public void addDatasetAttributes(T id, Attributes attributes) {
+		if (id == null) throw new IllegalArgumentException("id cant be null here");
+		this.datasetMap.put(id, Optional.ofNullable(attributes));
+	}
+
+	@Override
+    public String toString() {
+        StringBuilder sb = new StringBuilder();
+        for (T dsId : datasetMap.keySet()) {
+            sb.append("dataset ").append(dsId).append("\n");
+			if (datasetMap.get(dsId).isPresent()) {
+				for(String line : datasetMap.get(dsId).get().toString(1000, 1000).split("\n")) {
+					sb.append("\t").append(line).append("\n");
+				}
+			} else {
+				sb.append("\tnull\n");
+			}
+        }
+        return sb.toString();
+    }
+
+	public Set<T> getDatasetIds() {
+        return datasetMap.keySet();
+    }
+
+	public void merge(AcquisitionAttributes<T> dicomAcquisitionAttributes) {
+		for (T datasetId : dicomAcquisitionAttributes.getDatasetIds()) {
+			addDatasetAttributes(datasetId, dicomAcquisitionAttributes.getDatasetAttributes(datasetId));
+		}
+	}
+
+    public Attributes getFirstDatasetAttributes() {
+        if (datasetMap != null && datasetMap.size() > 0) {
+			return datasetMap.entrySet().iterator().next().getValue().orElse(null);
+		} else {
+			return null;
+		}
+    }
+
+	@Override
+	public boolean equals(Object obj) {
+		if (obj == null || !(obj instanceof AcquisitionAttributes<?>)) {
+			return false;
+		} 
+		try {
+			@SuppressWarnings("unchecked")
+			AcquisitionAttributes<T> other = (AcquisitionAttributes<T>) obj;
+			for(T id : datasetMap.keySet()) {
+				Attributes attributes = datasetMap.get(id).orElse(null);
+				Attributes otherAttributes = other.getDatasetAttributes(id);
+				if (otherAttributes == null || !otherAttributes.equals(attributes)) {
+					return false;
+				}
+			}
+			return true;
+		} catch (ClassCastException e) {
+			return false;
+		}
+
+	}
+
+	public Class<?> getParametrizedType() {
+		if (this.datasetMap != null && !this.datasetMap.keySet().isEmpty()) {
+			return this.datasetMap.keySet().iterator().next().getClass();
+		} else {
+			return null;
+		}
+	}
+
+    public boolean has(T acqId) {
+        return datasetMap.containsKey(acqId);
+    }
+}

shanoir-ng-datasets/src/main/java/org/shanoir/ng/download/DicomJsonUtils.java

@@ -53,6 +53,7 @@ public class DicomJsonUtils {
     public static final String STUDY_INSTANCE_UID = "0020000D";
     public static final String SERIE_INSTANCE_UID = "0020000E";
     public static final String OBJECT_INSTANCE_UID = "00080018";
+
     public static final String VALUE = "Value";
 
     public static final String STUDIES = "studies";