LT-66 Import DICOM Studies
- Add a toolbar in the top of worklist - Add Import button in the worklist toolbar - Upload all files in the selected folder to import from client to server - Import uploaded files via DIMSE - Delete uploaded files from server when import is completed - Handle import status in client - Show/Update progress dialog in client while uploading and importing files - Show Import button only if import is supported for the default service type (DICOMWeb is currently not supported)
This commit is contained in:
Evren Ozkan
parent
064743a8f7
commit
a2124c03e9
@ -115,6 +115,7 @@
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ViewerStudies: true,
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LesionManager: true,
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Timepoints: true,
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Measurements: true
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Measurements: true,
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StudyImportStatus: true
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}
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}
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@ -201,10 +201,10 @@ DIMSE.retrieveInstances = function(studyInstanceUID, seriesInstanceUID, params,
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return future.wait();
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};
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DIMSE.storeInstances = function(fileList) {
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DIMSE.storeInstances = function(fileList, callback) {
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var handle = conn.storeInstances(fileList);
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handle.on('file', function(err, file) {
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console.log(err, file);
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callback(err, file);
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});
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};
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1
Packages/viewerbase/both/collections.js
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1
Packages/viewerbase/both/collections.js
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@ -0,0 +1 @@
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StudyImportStatus = new Meteor.Collection('studyImportStatus');
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@ -2,3 +2,5 @@ ViewerStudies = new Meteor.Collection(null);
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ViewerStudies._debugName = 'ViewerStudies';
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ClientId = Random.id();
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Meteor.subscribe('studyImportStatus');
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107
Packages/viewerbase/lib/importStudies.js
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107
Packages/viewerbase/lib/importStudies.js
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@ -0,0 +1,107 @@
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/**
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* Imports selected studies from local into worklist
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* @param filesToImport Files located in the client machine to import
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*/
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importStudies = function(filesToImport, importCallback) {
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if (filesToImport.length < 1) {
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return;
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}
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var fileUploadStatus = { numberOfFilesUploaded: 0, numberOfFilesFailed: 0 };
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var numberOfFilesToUpload = filesToImport.length;
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var studiesToImport = [];
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progressDialog.show("Uploading Files...", numberOfFilesToUpload);
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// Upload files to the server
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filesToImport.forEach(function(fileToUpload) {
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var xhr = new XMLHttpRequest();
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xhr.open('POST', "/uploadFilesToImport", true);
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xhr.setRequestHeader("filename", fileToUpload.name);
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xhr.onload = function() {
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// Failed to upload a file
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if (xhr.readyState === 4 && xhr.status !== 200) {
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updateFileUploadStatus(fileUploadStatus, false);
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return;
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}
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studiesToImport.push(xhr.responseText);
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updateFileUploadStatus(fileUploadStatus, true);
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var numberOfFilesProcessedToUpload = fileUploadStatus.numberOfFilesUploaded + fileUploadStatus.numberOfFilesFailed;
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progressDialog.update(numberOfFilesProcessedToUpload);
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if (numberOfFilesToUpload === numberOfFilesProcessedToUpload) {
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// The upload is completed, so import files
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importStudiesInternal(studiesToImport, importCallback);
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if (fileUploadStatus.numberOfFilesFailed > 0) {
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//TODO: Some files failed to upload, so let user know
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console.log("Failed to upload " + studyImportStatus.numberOfStudiesFailed + " of " + numberOfStudiesToImport + " files");
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}
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}
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};
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// Failed to upload a file
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xhr.onerror = function() {
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updateFileUploadStatus(fileUploadStatus, false);
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};
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xhr.send(fileToUpload);
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});
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};
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function updateFileUploadStatus(fileUploadStatus, isSuccess) {
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if (!isSuccess) {
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fileUploadStatus.numberOfFilesFailed++;
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} else {
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fileUploadStatus.numberOfFilesUploaded++;
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}
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}
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function importStudiesInternal(studiesToImport, importCallback) {
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var numberOfStudiesToImport = studiesToImport.length;
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progressDialog.show("Importing Studies...", numberOfStudiesToImport);
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// Create/Insert a new study import status item
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Meteor.call("createStudyImportStatus", function(err, studyImportStatusId) {
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if (err) {
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console.log(err);
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return;
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}
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// Handle when it is updated
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StudyImportStatus.find(studyImportStatusId).observe({
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changed: function(studyImportStatus) {
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if (!studyImportStatus) {
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return;
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}
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var numberOfStudiesProcessedToImport = studyImportStatus.numberOfStudiesImported + studyImportStatus.numberOfStudiesFailed;
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progressDialog.update(numberOfStudiesProcessedToImport);
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if (numberOfStudiesProcessedToImport == numberOfStudiesToImport) {
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// The entire import operation is completed, so remove the study import status item
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Meteor.call("removeStudyImportStatus", studyImportStatus._id);
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if (studyImportStatus.numberOfStudiesFailed > 0) {
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//TODO: Some files failed to import, so let user know
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console.log("Failed to import " + studyImportStatus.numberOfStudiesFailed + " of " + numberOfStudiesToImport + " files");
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}
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// Let the caller know that import operation is completed
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if (importCallback) {
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importCallback();
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}
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}
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}
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});
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// Import studies with study import status id to get callbacks
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Meteor.call("importStudies", studiesToImport, studyImportStatusId);
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});
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}
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@ -147,6 +147,7 @@ Package.onUse(function(api) {
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api.addFiles('lib/setFocusToActiveViewport.js', 'client');
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api.addFiles('lib/updateAllViewports.js', 'client');
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api.addFiles('lib/exportStudies.js', 'client');
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api.addFiles('lib/importStudies.js', 'client');
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api.addFiles('lib/encodeQueryData.js', 'server');
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//api.export('accountsConfig', 'client');
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@ -166,6 +167,7 @@ Package.onUse(function(api) {
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api.export('setFocusToActiveViewport', 'client');
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api.export('updateAllViewports', 'client');
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api.export('exportStudies', 'client');
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api.export('importStudies', 'client');
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api.export('getActiveViewportElement', 'client');
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api.export('encodeQueryData', 'server');
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@ -198,6 +200,7 @@ Package.onUse(function(api) {
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api.addFiles('server/lib/namespace.js', 'server');
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api.addFiles('server/methods/getStudyMetadata.js', 'server');
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api.addFiles('server/methods/worklistSearch.js', 'server');
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api.addFiles('server/methods/importStudies.js', 'server');
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// DICOMWeb instance, study, and metadata retrieval
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api.addFiles('server/services/qido/instances.js', 'server');
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@ -215,5 +218,12 @@ Package.onUse(function(api) {
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api.addFiles('server/services/remote/retrieveMetadata.js', 'server');
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api.export('Services', 'server');
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api.export('importStudies', 'server');
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api.export('importSupported', 'server');
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// Collections
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api.addFiles('both/collections.js', [ 'client', 'server' ]);
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api.addFiles('server/collections.js', 'server');
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api.export('StudyImportStatus', [ 'client', 'server' ]);
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});
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3
Packages/viewerbase/server/collections.js
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3
Packages/viewerbase/server/collections.js
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@ -0,0 +1,3 @@
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Meteor.publish('studyImportStatus', function() {
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return StudyImportStatus.find();
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});
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125
Packages/viewerbase/server/methods/importStudies.js
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125
Packages/viewerbase/server/methods/importStudies.js
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@ -0,0 +1,125 @@
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var fs = Npm.require('fs');
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var fiber = Npm.require('fibers');
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WebApp.connectHandlers.use('/uploadFilesToImport', function(req, res) {
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if (!req.headers.filename) {
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// Response: BAD REQUEST (400)
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res.statusCode = 400;
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res.end();
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}
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// Store files in temp location (they will be deleted when their import operations are completed)
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var dicomDir = '/tmp/dicomDir';
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createFolderIfNotExist(dicomDir);
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var fullFileName = dicomDir + '/' + req.headers.filename;
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var file = fs.createWriteStream(fullFileName);
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file.on('error',function(error){
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console.log(error);
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// Response: INTERNAL SERVER ERROR (500)
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res.statusCode = 400;
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res.end();
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});
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file.on('finish',function(){
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// Response: SUCCESS (200)
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res.writeHead(200, {'Content-Type': 'text/plain'});
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res.end(fullFileName);
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});
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// Pipe the request to the file
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req.pipe(file);
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});
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Meteor.methods({
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/**
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* Returns true if import is supported for default service type
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* @returns {boolean}
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*/
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importSupported: function() {
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if (Meteor.settings.dimse && Meteor.settings.defaultServiceType === 'dimse') {
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return true;
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}
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//TODO: Support importing studies into dicomWeb
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return false;
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},
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/**
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* Imports studies from local into worklist
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* @param studiesToImport Studies to import
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* @param studyImportStatusId Study import status collection id to track import status
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*/
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importStudies: function(studiesToImport, studyImportStatusId) {
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if (Meteor.settings.dicomWeb && Meteor.settings.defaultServiceType === 'dicomWeb') {
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//TODO: Support importing studies into dicomWeb
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console.log('Importing studies into dicomWeb is currently not supported.');
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} else if (Meteor.settings.dimse && Meteor.settings.defaultServiceType === 'dimse') {
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importStudiesDIMSE(studiesToImport, studyImportStatusId);
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} else {
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throw 'No properly configured server was available over DICOMWeb or DIMSE.';
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}
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},
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/**
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* Create a new study import status item and insert it into the collection to track import status
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* @returns {studyImportStatusId: string}
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*/
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createStudyImportStatus: function() {
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var studyImportStatus = { numberOfStudiesImported: 0, numberOfStudiesFailed: 0 };
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return StudyImportStatus.insert(studyImportStatus);
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},
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/**
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* Remove the study import status item from the collection
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* @param id Collection id of the study import status in the collection
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*/
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removeStudyImportStatus: function(id) {
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StudyImportStatus.remove(id);
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}
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});
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function importStudiesDIMSE(studiesToImport, studyImportStatusId) {
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// Perform C-Store to import studies and handle the callbacks to update import status
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DIMSE.storeInstances(studiesToImport, function(err, file) {
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// Use fiber to be able to modify meteor collection in callback
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fiber(function() {
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// Update the import status
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if (err) {
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StudyImportStatus.update({_id: studyImportStatusId}, {$inc: {'numberOfStudiesFailed': 1}});
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console.log("Failed to import study via DIMSE: ", file, err);
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} else {
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StudyImportStatus.update({_id: studyImportStatusId}, {$inc: {'numberOfStudiesImported': 1}});
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console.log("Study successfully imported via DIMSE: ", file);
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}
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// The import operation of this file is completed, so delete it if still exists
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if (fileExists(file)) {
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fs.unlink(file);
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}
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}).run();
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});
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}
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function createFolderIfNotExist(folder) {
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var folderParts = folder.split('/');
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var folderPart = folderParts[0];
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for (var i = 1; i < folderParts.length; i++) {
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folderPart += '/' + folderParts[i];
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if (!folderExists(folderPart)) {
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fs.mkdirSync(folderPart);
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}
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}
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}
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function fileExists(folder) {
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try {
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return fs.statSync(folder).isFile();
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} catch (err) {
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return false;
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}
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}
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function folderExists(folder) {
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try {
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return fs.statSync(folder).isDirectory();
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} catch (err) {
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return false;
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}
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}
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@ -1,4 +1,5 @@
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<template name="worklistResult">
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{{>worklistToolbar}}
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<table id="tblStudyList" class="worklistResult table table-striped noselect">
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<thead>
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<tr>
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@ -0,0 +1,12 @@
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<template name="worklistToolbar">
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<div id='worklistToolbar'>
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<div class="btn-group">
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{{#if importSupported }}
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<span class="btn btn-default btn-file">
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<i class="fa fa-upload"></i>
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<input id="btnImport" title="Import" type="file" webkitdirectory directory multiple>
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</span>
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{{/if }}
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</div>
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</div>
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</template>
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@ -0,0 +1,28 @@
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Template.worklistToolbar.events({
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'change #btnImport': function(e) {
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// Get selected files located in the client machine
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var selectedFiles = $.map(e.currentTarget.files, function(value) {
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return value;
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});
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importStudies(selectedFiles);
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}
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});
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Template.worklistToolbar.helpers({
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importSupported: function() {
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var importSupported = Session.get('importSupported');
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if (importSupported) {
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return true;
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}
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return false;
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}
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});
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Meteor.call("importSupported", function(err, result) {
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if (!err && result) {
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Session.set('importSupported', true);
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} else {
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Session.set('importSupported', false);
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}
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});
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@ -0,0 +1,27 @@
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#worklistToolbar
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background-color: black
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text-align: right
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width: 100%
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height: auto
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.btn-file
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position: relative
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overflow: hidden
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width: 30px
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height: 30px
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padding: 5px
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line-height: 20px
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input[type=file]
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position: absolute
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top: 0
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right: 0
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min-width: 100%
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min-height: 100%
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font-size: 100 px
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text-align: right
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opacity: 0
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outline: none
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background: white
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cursor: inherit
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display: block
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@ -47,6 +47,10 @@ Package.onUse(function (api) {
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api.addFiles('client/components/studyContextMenu/studyContextMenu.js', 'client');
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api.addFiles('client/components/studyContextMenu/studyContextMenu.styl', 'client');
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api.addFiles('client/components/worklistToolbar/worklistToolbar.html', 'client');
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api.addFiles('client/components/worklistToolbar/worklistToolbar.js', 'client');
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api.addFiles('client/components/worklistToolbar/worklistToolbar.styl', 'client');
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// Library functions
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api.addFiles('lib/getStudyMetadata.js', 'client');
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api.addFiles('lib/getStudiesMetadata.js', 'client');
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