Pixilib · salimkanoun · May 19, 2020 · May 4, 2020 · May 6, 2020 · May 16, 2020
diff --git a/News b/News
@@ -16,30 +16,31 @@ GaelO
   BugFix : dicomdir breaks dicom parsing
 
 -- GaelO 1.1.0 29/04/20 --
-Features : 
-  - Visit group to manage multiple modalities (in which each modality will have it's visit type)
-  - User's data edition panel
-  - Docker : 
-    - SMTP service for (mail() function)
-    - Cron services to automatize recurrent tasks
-  - Patient Visit Manager can be redifined through inheritance for custom visit creation workflow and status determination
-  - FTP/SFTP class to retrieve data from remote server (ex : automatic import of included patient list)
-  - Json Import for centers
-  - Possibility to declare patient code prefix per study at study creation (to avoid wrong patient import)
-  - Possibility to associate file upload with specific form
-
-Enhancements : 
-  - Tree filter in right click to filter visits according to some status (depending on current role)
-  - Anon profile, optional visit, local form needed, Qc needed, Review needed are now defined per visit type
-  - Monitors now recieve QC decision emails
-  - Supervisors are notified in case of a not done visit creation
-  - Email notification when visit review is awaiting adjudication or concluded
-  - Export button on DataTables now export only visible (filtered) data
-  - Replaced Jquery datepicker by Bootrastrp datepicker
-  - Simplified download interface for DICOM (supervisor)
-  - faster visit status determination in upload manager (supervisor)
-  - Add OHIF viewer for supervisors and investigators
-  - Reduced ZIP compression level of Dicom before upload to decrease CPU comsuption in the client
-  - Small memory usage reduction when zipping dicom
+
+  Features : 
+    - Visit group to manage multiple modalities (in which each modality will have it's visit type)
+    - User's data edition panel
+    - Docker : 
+      - SMTP service for (mail() function)
+      - Cron services to automatize recurrent tasks
+    - Patient Visit Manager can be redifined through inheritance for custom visit creation workflow and status determination
+    - FTP/SFTP class to retrieve data from remote server (ex : automatic import of included patient list)
+    - Json Import for centers
+    - Possibility to declare patient code prefix per study at study creation (to avoid wrong patient import)
+    - Possibility to associate file upload with specific form
+
+  Enhancements : 
+    - Tree filter in right click to filter visits according to some status (depending on current role)
+    - Anon profile, optional visit, local form needed, Qc needed, Review needed are now defined per visit type
+    - Monitors now recieve QC decision emails
+    - Supervisors are notified in case of a not done visit creation
+    - Email notification when visit review is awaiting adjudication or concluded
+    - Export button on DataTables now export only visible (filtered) data
+    - Replaced Jquery datepicker by Bootrastrp datepicker
+    - Simplified download interface for DICOM (supervisor)
+    - faster visit status determination in upload manager (supervisor)
+    - Add OHIF viewer for supervisors and investigators
+    - Reduced ZIP compression level of Dicom before upload to decrease CPU comsuption in the client
+    - Small memory usage reduction when zipping dicom
 
 
diff --git a/src/assets/javascripts/dicomupload/DicomFile.js b/src/assets/javascripts/dicomupload/DicomFile.js
@@ -129,93 +129,84 @@ class DicomFile {
 		}
 	}
 
-	/**
-	 * Get value of a dicom attribute
-	 */
-	get(id, dataSet = this.dataSet) {
-		id = id.toLowerCase();
-
-		// Recursively look for the dicom attribute
-		for (let elmtName in dataSet.elements) {
-			let elmt = dataSet.elements[elmtName];
-
-			// Check if this is a SQ element
-			if (elmt.items !== undefined) {
-				for (let it of elmt.items) {
-					// Get value of the dicom attribute in the dataset of the SQ
-					let got = this.get(id, it.dataSet);
-					if (got !== undefined) {
-						return got;
-					}
-				}
-			}
-
-			if (elmtName == `x${id}` && elmt.length > 0) {
-				// Return the value of the dicom attribute
-				return this.string(elmt);
-			}
+	getRadiopharmaceuticalTag(tagAddress){
+		try{
+			let elmt = this.dataSet.elements['x00540016']
+			let radioPharmElements = elmt.items[0].dataSet.elements
+			return this.string(radioPharmElements['x'+tagAddress])
+		}catch ( error ) { 
+			console.log(error)
+			return undefined 
+		}
+	}
 
+	getDicomTag(tagAddress){
+		let elmt = this.dataSet.elements['x'+tagAddress]
+		if ( elmt.length > 0) {
+			// Return the value of the dicom attribute
+			return this.string(elmt);
 		}
-		return undefined;
+		else return undefined
 	}
+
 	getAccessionNumber() {
-		return this.get("00080050");
+		return this.getDicomTag("00080050");
 	}
 	getAcquisitionDate() {
-		return this.get("00080020");
+		return this.getDicomTag("00080020");
 	}
 	getInstanceNumber() {
-		return this.get("00200013");
+		return this.getDicomTag("00200013");
 	}
 	getModality() {
-		return this.get("00080060");
+		return this.getDicomTag("00080060");
 	}
 	getPatientBirthDate() {
-		return this.get("00100030");
+		return this.getDicomTag("00100030");
 	}
 	getPatientID() {
-		return this.get("00100020");
+		return this.getDicomTag("00100020");
 	}
 	getPatientName() {
-		return this.get("00100010");
+		return this.getDicomTag("00100010");
 	}
 	getPatientSex() {
-		return this.get("00100040");
+		return this.getDicomTag("00100040");
 	}
 	getSeriesInstanceUID() {
-		return this.get("0020000E");
+		return this.getDicomTag("0020000e");
 	}
 	getSeriesDate() {
-		return this.get("00080021");
+		return this.getDicomTag("00080021");
 	}
 	getSeriesDescription() {
-		return this.get("0008103E");
+		return this.getDicomTag("0008103e");
 	}
 	getSOPInstanceUID() {
-		return this.get("00080018");
+		return this.getDicomTag("00080018");
 	}
 	getSOPClassUID() {
-		return this.get("00080016");
+		return this.getDicomTag("00080016");
 	}
-	//SK A TESTER : On ne pourrait utiliser que le 0002,0222
+	//SK A TESTER : On ne pourrait utiliser que le 0002,0002
 	//Ce tag est un duplicat de 00080016 cf https://stackoverflow.com/questions/32689446/is-it-true-that-dicom-media-storage-sop-instance-uid-sop-instance-uid-why
 	getMediaStorageSOP(){
-		return this.get("00020002")
+		return this.getDicomTag("00020002")
 	}
 	getSeriesNumber() {
-		return this.get("00200011");
+		return this.getDicomTag('00200011')
 	}
 	getStudyInstanceUID() {
-		return this.get("0020000D");
+		return this.getDicomTag('0020000d')
 	}
 	getStudyDate() {
-		return this.get("00080020");
+		return this.getDicomTag("00080020");
 	}
 	getStudyID() {
-		return this.get("00200010");
+		return this.getDicomTag("00200010");
 	}
 	getStudyDescription() {
-		return this.get("00081030");
+		return this.getDicomTag("00081030");
 	}
 
 	/**

diff --git a/src/assets/javascripts/dicomupload/DicomUploadModel.js b/src/assets/javascripts/dicomupload/DicomUploadModel.js
@@ -58,8 +58,6 @@ class DicomUploadModel {
 		// ~
 	}
 
-	// ~
-
 	getStudy(studyInstanceUID) {
 		for (let st of this.studies) {
 			if (st.studyInstanceUID == studyInstanceUID) {
@@ -93,8 +91,6 @@ class DicomUploadModel {
 		return null;
 	}
 
-	// ~
-
 	isKnownStudy(dicomFile) {
 		return this.getStudy(dicomFile.getStudyInstanceUID()) !== null;
 	}
@@ -141,8 +137,6 @@ class DicomUploadModel {
 		}
 	}
 
-	// ~
-
 	hasQueuedStudies() {
 		for (let st of this.queuedStudies) {
 			if (st.hasQueuedSeries()) {
@@ -184,8 +178,6 @@ class DicomUploadModel {
 		}
 	}
 
-	// ~
-
 	/**
 	* Register the study, serie, instance of a dicom file if not known yet
 	* @throws 'Secondary Capture Image Storage are not allowed.'
@@ -258,8 +250,6 @@ class DicomUploadModel {
 		}
 	}
 
-	// ~
-
 	checkStudies() {
 		for (let st of this.studies) {
 
@@ -299,8 +289,6 @@ class DicomUploadModel {
 		}
 	}
 
-	// ~
-
 	checkSeries(st) {
 		function isset(e) {
 			return !(e == 'null' || e === undefined || e == '');
@@ -314,29 +302,25 @@ class DicomUploadModel {
 			if (!isset(dicomFile.getModality())) {
 				sr.setWarning('missingTag00080060', 'Missing tag: Modality', true);
 			} else {
-				if (!isset(dicomFile.getStudyDate())) {
-					sr.setWarning('missingTag00080020', 'Missing tag: StudyDate', true);
+				if (!isset(dicomFile.getDicomTag('00080021')) && !isset(dicomFile.getDicomTag('00080022')) ) {
+					sr.setWarning('missingTag00080022', 'Missing tag: SeriesDate', true);
 				}
 				if (sr.modality == 'PT') {
-					if (!isset(dicomFile.get('00101030'))) {
+					if ( !isset(dicomFile.getDicomTag('00101030')) ) {
 						sr.setWarning('missingTag00101030', 'Missing tag: Patient Weight', true);
 					}
-					if (!isset(dicomFile.get('00080030'))) {
-						sr.setWarning('missingTag00101030', 'Missing tag: Modality', true);
+					if ( !isset(dicomFile.getDicomTag('00080031'))  && !isset(dicomFile.getDicomTag('00080032')) ) {
+						sr.setWarning('missingTag00101031', 'Missing tag: Series Time', true);
 					}
-					if (!isset(dicomFile.get('00181074'))) {
+					if ( !isset(dicomFile.getRadiopharmaceuticalTag('00181074')) ) {
 						sr.setWarning('missingTag00181074', 'Missing tag: Radionuclide Total Dose', true);
 					}
-					if (!isset(dicomFile.get('00181072'))) {
+					if (!isset(dicomFile.getRadiopharmaceuticalTag('00181072')) && !isset(dicomFile.getRadiopharmaceuticalTag('00181078')) ) {
 						sr.setWarning('missingTag00181072', 'Missing tag: Radiopharmaceutical Start Time', true);
 					}
-					if (!isset(dicomFile.get('00181075'))) {
+					if ( !isset(dicomFile.getRadiopharmaceuticalTag('00181075')) ) {
 						sr.setWarning('missingTag00181075', 'Missing tag: Radionuclide Half Life', true);
 					}
-					/*
-					if (!isset(dicomFile.get('00181077'))) {
-						sr.setWarning('missingTag00181077', 'Missing tag: RadiopharmaceuticalSpecificActivity', true);
-					}*/
 				}
 			}
 
@@ -358,8 +342,6 @@ class DicomUploadModel {
 		}
 	}
 
-	// ~
-
 	findExpectedVisit(st) {
 		let thisP = st.getPatientName();
 

diff --git a/src/includes/jsLibrairies.php b/src/includes/jsLibrairies.php
@@ -129,7 +129,7 @@
 
 <script src="https://cdnjs.cloudflare.com/ajax/libs/PapaParse/5.1.0/papaparse.min.js"></script>
 
-<?php $uploaderVersion="3.2"?>
+<?php $uploaderVersion="3.4"?>
 <!-- JavaScript  CustomJS/CSS -->
 <script type="text/javascript" src="assets/javascripts/dicomupload/_browserSupport.js?version=<?= $uploaderVersion?>" defer></script>
 <script type="text/javascript" src="assets/javascripts/dicomupload/CheckPatientPanel.js?version=<?= $uploaderVersion?>" defer></script>

diff --git a/src/includes/jsLibrairies_main.php b/src/includes/jsLibrairies_main.php
@@ -124,7 +124,7 @@
 
 <script src="https://cdnjs.cloudflare.com/ajax/libs/PapaParse/5.1.0/papaparse.min.js"></script>
 
-<?php $uploaderVersion="3.2"?>
+<?php $uploaderVersion="3.4"?>
 <!-- JavaScript  CustomJS/CSS -->
 <script type="text/javascript" src="assets/javascripts/dicomupload/_browserSupport.js?version=<?= $uploaderVersion?>" ></script>
 <script type="text/javascript" src="assets/javascripts/dicomupload/CheckPatientPanel.js?version=<?= $uploaderVersion?>" ></script>

diff --git a/src/models/Form_Processor_File.php b/src/models/Form_Processor_File.php
@@ -48,6 +48,13 @@ protected function getMaxSizeMb() : int{
 		return 5;
 	}
 
+	private function createEmptySpecificForm(){
+		$insertion = $this->linkpdo->prepare('INSERT INTO '.$this->specificTable.' (id_review) VALUES (:id_review)');
+		$insertion->execute(array(
+			'id_review' => $this->reviewObject->id_review )
+		);
+	}
+
 	/**
 	 * Store or overwirte a file, each file is defined by a Key (visit specific)
 	 */
@@ -56,6 +63,7 @@ public function storeAssociatedFile(string $fileKey, string $mime, int $fileSize
 		//If first form upload create a draft form to insert file uploaded data
 		if (empty($this->reviewObject)) {
 			$this->createReview();
+			$this->createEmptySpecificForm();
 		}else {
 			//If review exist but validated throw exception
 			if ($this->reviewObject->validated) {