ENH: Add function to retrieve all the scan sessions. And use appropriate patient-id when importing a dicom/raw file

Author: juanprietob

index.js

@@ -224,6 +224,39 @@ xnat.getSubjectExperiments = function(projectid, subjectid){
 })
 }
 
+xnat.getSubjectSession = function(projectid, subjectid, sessionid){
+return new Promise(function(resolve, reject){
+
+var params = {
+format: "json"
+}
+
+var url;
+if(sessionid){
+url = "/data/archive/projects/" + projectid + "/subjects/" + subjectid + "/experiments/" + sessionid + "?" + qs.stringify(params);
+}else{
+url = "/data/archive/projects/" + projectid + "/subjects/" + subjectid + "/experiments?" + qs.stringify(params);
+}
+
+var options = {
+url: xnat.getXnatUrl() + url,
+jar: xnat.jar
+}
+
+request(options, function(err, res, body){
+if(err){
+reject(err);
+}else{
+if(res.statusCode === 200){
+resolve(JSON.parse(body));
+}else{
+reject(body);
+}
+}
+});
+})
+}
+
 xnat.createSubject = function(projectid, subjectid) {
 return new Promise(function(resolve, reject){
 var options = {
@@ -245,7 +278,7 @@ xnat.createSubject = function(projectid, subjectid) {
 });
 }
 
-xnat.uploadImage = function(projectid, subjectid, sessionid, filename){
+xnat.uploadImage = function(projectid, subjectid, experimentid, filename){
 return new Promise(function(resolve, reject){
 
 var params = {
@@ -254,7 +287,7 @@ xnat.uploadImage = function(projectid, subjectid, sessionid, filename){
 dest: "/archive/projects/" + projectid,
 "import-handler" : "gradual-DICOM",
 SUBJECT_ID: subjectid,
-EXPT_LABEL: sessionid
+EXPT_LABEL: experimentid
 }
 
 var options = {
@@ -278,6 +311,99 @@ xnat.uploadImage = function(projectid, subjectid, sessionid, filename){
 })
 }
 
+xnat.uploadConvertedImage = function(projectid, subjectid, experimentid, scanid, filename){
+return new Promise(function(resolve, reject){
+
+var params = {
+inbody: true
+}
+
+var options = {
+url: xnat.getXnatUrl() + "/data/archive/projects/" + projectid + "/subjects/" + subjectid + "/experiments/" + experimentid + "/scans/" + scanid + "/files/" + path.basename(filename) + "?" + qs.stringify(params),
+method: "PUT",
+jar: xnat.jar,
+body: fs.readFileSync(filename)
+}
+
+request(options, function(err, res, body){
+if(err){
+reject(err);
+}else{
+if(res.statusCode === 200){
+console.log("File imported");
+resolve(body);
+}else{
+reject(body);
+}
+}
+});
+})
+}
+
+xnat.getScanFiles = function(projectid, subjectid, experimentid, scanid){
+return new Promise(function(resolve, reject){
+
+var params = {
+format: "json"
+}
+
+var options = {
+url: xnat.getXnatUrl() + "/data/archive/projects/" + projectid + "/subjects/" + subjectid + "/experiments/" + experimentid + "/scans/" + scanid + "/files?" + qs.stringify(params),
+method: "GET",
+jar: xnat.jar
+}
+
+request(options, function(err, res, body){
+if(err){
+reject(err);
+}else{
+try{
+if(res.statusCode === 200){
+var images = JSON.parse(body);
+resolve(images.ResultSet.Result);
+}else{
+reject(body);
+}
+}catch(e){
+console.error("xnat.getScanFiles", e);
+reject(e);
+}
+
+}
+});
+});
+}
+
+xnat.deleteFile = function(uri){
+return new Promise(function(resolve, reject){
+
+var options = {
+url: xnat.getXnatUrl() + uri,
+method: "DELETE",
+jar: xnat.jar
+}
+
+request(options, function(err, res, body){
+if(err){
+reject(err);
+}else{
+try{
+if(res.statusCode === 200){
+console.log("File deleted")
+resolve(body);
+}else{
+reject(body);
+}
+}catch(e){
+console.error("xnat.getScanFiles", e);
+reject(e);
+}
+
+}
+});
+});
+}
+
 xnat.triggerPipelines = function(projectid, subjectid, experimentid){
 return new Promise(function(resolve, reject){
 
@@ -450,6 +576,10 @@ xnat.upload = function(){
 require(path.join(__dirname, 'upload'))(xnat);
 }
 
+xnat.importConverted = function(){
+require(path.join(__dirname, 'importConverted'))(xnat);
+}
+
 const getConfigFile = function () {
  return new Promise(function(resolve, reject){
  try {

upload.js

@@ -105,13 +105,15 @@ module.exports = function(xnat){
 pid = patientid;
 }else{
 pid = dcmData.dataset["00100020"].value;
+pid = pid.replace(/[ .:|&;$%@"<>()+,]/g, "_");
 }
 
 var sessid;
 if(sessionid){
 sessid = sessionid;
 }else{
-sessid = dcmData.dataset["00080020"].value;
+//Create a unique session id. With the old one it might conflict with existing sessions. 
+sessid = pid + "-" + dcmData.dataset["00080020"].value;
 }
 return xnat.uploadImage(projectid, pid, sessid, file);
 })