Merge branch 'develop' into fli-iam#2084

docker-compose/database/4_add_studyStatistics_procedure.sql

@@ -10,25 +10,28 @@
 -- 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
 
+
 USE studies;
 
 DROP PROCEDURE IF EXISTS getStudyStatistics;
 
 delimiter //
 CREATE PROCEDURE getStudyStatistics(IN studyId INT)
 BEGIN
-SELECT
+SELECT DISTINCT
     e.study_id AS study_id,
     c.id AS center_id,
     c.name AS center_name,
     sc.subject_name_prefix AS center_prefix,
     s.id AS subject_id,
     s.name AS common_name,
     e.id AS examination_id,
+    e.comment AS examination_comment,
     e.examination_date AS examination_date,
     da.id AS dataset_acquisition_id,
     da.creation_date AS import_date,
     d.id AS dataset_id,
+    dm.name AS dataset_name,
     (CASE dm.dataset_modality_type WHEN 1 THEN 'Mr' 
                                    WHEN 2 THEN 'Meg' 
                                    WHEN 3 THEN 'Ct' 
@@ -53,12 +56,14 @@ INNER JOIN
 INNER JOIN
     datasets.dataset_metadata dm ON d.updated_metadata_id = dm.id
 INNER JOIN
-    datasets.subject_study ss ON d.subject_id = ss.subject_id
+    studies.subject_study ss ON d.subject_id = ss.subject_id
 INNER JOIN 
     studies.subject s ON ss.subject_id = s.id
 INNER JOIN
     studies.study_center sc ON c.id = sc.center_id
-WHERE e.study_id = studyId;
+WHERE e.study_id = studyId 
+AND ss.study_id = studyId 
+AND sc.study_id = studyId;
 END //
 
-delimiter ;
+delimiter ;

docker-compose/database/db-changes/datasets/0048_add_uniquekey_dataset.sql

@@ -0,0 +1,2 @@
+ALTER TABLE dataset ADD CONSTRAINT UK_qrxunikj09qwx7ci6fpopyyuh UNIQUE key (origin_metadata_id);
+ALTER TABLE dataset ADD CONSTRAINT UK_q5hjffag30a00rysle2hyhyov UNIQUE key (updated_metadata_id);

docker-compose/database/db-changes/studies/0018_add_studyStatistics_procedure.sql

@@ -18,7 +18,7 @@ DROP PROCEDURE IF EXISTS getStudyStatistics;
 delimiter //
 CREATE PROCEDURE getStudyStatistics(IN studyId INT)
 BEGIN
-SELECT
+SELECT DISTINCT
     e.study_id AS study_id,
     c.id AS center_id,
     c.name AS center_name,
@@ -54,12 +54,14 @@ INNER JOIN
 INNER JOIN
     datasets.dataset_metadata dm ON d.updated_metadata_id = dm.id
 INNER JOIN
-    datasets.subject_study ss ON d.subject_id = ss.subject_id
+    studies.subject_study ss ON d.subject_id = ss.subject_id
 INNER JOIN 
     studies.subject s ON ss.subject_id = s.id
 INNER JOIN
     studies.study_center sc ON c.id = sc.center_id
-WHERE e.study_id = studyId;
+WHERE e.study_id = studyId 
+AND ss.study_id = studyId 
+AND sc.study_id = studyId;
 END //
 
 delimiter ;

docker-compose/database/db-changes/studies/0019_studyStatistics_procedure_new_columns.sql

@@ -0,0 +1,69 @@
+-- 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
+
+
+USE studies;
+
+DROP PROCEDURE IF EXISTS getStudyStatistics;
+
+delimiter //
+CREATE PROCEDURE getStudyStatistics(IN studyId INT)
+BEGIN
+SELECT DISTINCT
+    e.study_id AS study_id,
+    c.id AS center_id,
+    c.name AS center_name,
+    sc.subject_name_prefix AS center_prefix,
+    s.id AS subject_id,
+    s.name AS common_name,
+    e.id AS examination_id,
+    e.comment AS examination_comment,
+    e.examination_date AS examination_date,
+    da.id AS dataset_acquisition_id,
+    da.creation_date AS import_date,
+    d.id AS dataset_id,
+    dm.name AS dataset_name,
+    (CASE dm.dataset_modality_type WHEN 1 THEN 'Mr' 
+                                   WHEN 2 THEN 'Meg' 
+                                   WHEN 3 THEN 'Ct' 
+                                   WHEN 4 THEN 'Spect' 
+                                   WHEN 5 THEN 'Pet' 
+                                   WHEN 6 THEN 'Egg' 
+                                   WHEN 7 THEN 'Generic' 
+                                   WHEN 8 THEN 'Ieeg' 
+                                   WHEN 9 THEN 'Micr' 
+                                   WHEN 10 THEN 'Beh'
+                                   WHEN 11 THEN 'Nirs'
+                                   WHEN 12 THEN 'Xa' END) AS modality,
+    (CASE ss.quality_tag WHEN 1 THEN 'Valid' WHEN 2 THEN 'Warning' WHEN 3 THEN 'Error' END) AS quality
+FROM
+    datasets.examination e
+INNER JOIN 
+    datasets.center c ON e.center_id = c.id
+INNER JOIN
+    datasets.dataset_acquisition da ON e.id = da.examination_id
+INNER JOIN
+    datasets.dataset d ON da.id = d.dataset_acquisition_id
+INNER JOIN
+    datasets.dataset_metadata dm ON d.updated_metadata_id = dm.id
+INNER JOIN
+    studies.subject_study ss ON d.subject_id = ss.subject_id
+INNER JOIN 
+    studies.subject s ON ss.subject_id = s.id
+INNER JOIN
+    studies.study_center sc ON c.id = sc.center_id
+WHERE e.study_id = studyId 
+AND ss.study_id = studyId 
+AND sc.study_id = studyId;
+END //
+
+delimiter ;

shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/MrDataset.java

@@ -2,12 +2,12 @@
  * 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
  */
@@ -27,7 +27,7 @@
 
 /**
  * MR dataset.
- * 
+ *
  * @author msimon
  *
  */
@@ -71,7 +71,7 @@ public class MrDataset extends Dataset {
 	/** Metadata updated by study card. */
 	@OneToOne(cascade = CascadeType.ALL)
 	private MrDatasetMetadata updatedMrMetadata;
-	
+
 	/** Store temporarily the first image acquisition time until all images are processed*/
 	@Transient
 	private LocalDateTime  firstImageAcquisitionTime;
@@ -82,14 +82,9 @@ public class MrDataset extends Dataset {
 
 	public MrDataset() {}
 
-	public MrDataset(Dataset d, MrProtocol mrpro) {
+	public MrDataset(Dataset d) {
 		super(d);
 		MrDataset mrDataset = (MrDataset) d;
-		MrProtocol mrp = new MrProtocol(mrpro, this);
-		this.diffusionGradients = new ArrayList<>(mrDataset.getDiffusionGradients().size());
-		for (DiffusionGradient dg : mrDataset.getDiffusionGradients()) {
-			this.diffusionGradients.add(new DiffusionGradient(dg, this, mrp));
-		}
 
 		this.echoTime = new ArrayList<>(mrDataset.getEchoTime().size());
 		for (EchoTime et : mrDataset.getEchoTime()) {
@@ -111,7 +106,7 @@ public MrDataset(Dataset d, MrProtocol mrpro) {
 		} else {
 			this.mrQualityProcedureType = null;
 		}
-		this.originMrMetadata = mrDataset.getOriginMrMetadata();
+		this.originMrMetadata = new MrDatasetMetadata(mrDataset.getOriginMrMetadata());
 
 		this.repetitionTime = new ArrayList<>(mrDataset.getRepetitionTime().size());
 		for (RepetitionTime rt : mrDataset.getRepetitionTime()) {

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

@@ -165,7 +165,6 @@ public Dataset(Dataset d) {
 		}
 
 		this.importedStudyId = d.getImportedStudyId();
-		this.studyId = d.getStudyId();
 		this.subjectId = d.getSubjectId();
 		this.downloadable = d.downloadable;
 		this.updatedMetadata = new DatasetMetadata(d.getUpdatedMetadata());

shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/service/DatasetCopyServiceImpl.java

@@ -56,7 +56,7 @@ public Object[] moveDataset(Dataset ds, Long studyId, Map<Long, Examination> exa
             Dataset newDs = null;
             if (ds.getDatasetAcquisition() != null &&  ds.getDatasetAcquisition().getId() != null) {
                 if ("Mr".equals(dsType)) {
-                    newDs = new MrDataset(ds, ((MrDatasetAcquisition) ds.getDatasetAcquisition()).getMrProtocol());
+                    newDs = new MrDataset(ds);
                 } else {
                     newDs = DatasetUtils.copyDatasetFromDataset(ds);
                 }

shanoir-ng-datasets/src/main/java/org/shanoir/ng/datasetacquisition/model/mr/MrProtocol.java

@@ -226,7 +226,7 @@ public MrProtocol(MrProtocol mrPro, MrDataset mrDs) {
 		this.numberOfAverages = mrPro.getNumberOfAverages();
 		this.numberOfPhaseEncodingSteps = mrPro.getNumberOfPhaseEncodingSteps();
 		this.numberOfTemporalPositions = mrPro.getNumberOfTemporalPositions();
-		this.originMetadata = mrPro.getOriginMetadata();
+		this.originMetadata = new MrProtocolMetadata(mrPro.getOriginMetadata());
 		if (mrPro.getPatientPosition() != null) {
 			this.patientPosition = mrPro.getPatientPosition().getId();
 		} else {
@@ -241,7 +241,11 @@ public MrProtocol(MrProtocol mrPro, MrDataset mrDs) {
 		this.sliceThickness = mrPro.getSliceThickness();
 		this.temporalResolution = mrPro.getTemporalResolution();
 		this.magneticFieldStrength = mrPro.getMagneticFieldStrength();
-		this.updatedMetadata = mrPro.getUpdatedMetadata();
+		if (mrPro.getUpdatedMetadata() != null) {
+			this.updatedMetadata = new MrProtocolSCMetadata(mrPro.getUpdatedMetadata());
+		} else {
+			this.updatedMetadata = null;
+		}
 	}
 
 	/**