Adds the refactored forms in seperate file. They were removed from th…

…e route file, they had to much logic. #85 Adds new functions to select the file headers, from default or from a line in file

components/forms/upload_data.js

@@ -0,0 +1,137 @@
+var fs=require('fs')
+var path=require('path')
+var formidable=require('formidable')
+var detect=require('detect-file-type')
+var formidable = require('formidable')
+var processTargetsFile=require('./../miRNADB/targets/psRNAtargetFile')
+
+function uploadFile(req,uploadDir){
+  return new Promise((res,rej)=>{
+
+    // create an incoming form object
+    var form = new formidable.IncomingForm();
+
+    // specify that we want to allow the user to upload multiple files in a single request
+    form.multiples = false;
+    //Calculate file hash
+    form.hash = 'md5';
+    // store all uploads in the /uploads directory
+    form.uploadDir = path.join(uploadDir,"/de_matrices");
+
+    // every time a file has been uploaded successfully,
+    // rename it to it's original name
+    form.on('file', function(field, file) {
+      detect.fromFile(file.path,function(err,result){
+        if (err) rej(err)
+        if (result===null){
+          fs.rename(file.path, path.join(form.uploadDir, file.name), (err)=>{
+            if(err) rej(err)
+            file={hash:form.openedFiles[0].hash, name:form.openedFiles[0].name}
+            res(file);
+          });
+        }else{
+          fs.unlink(file.path, (err)=>{
+            err ? rej(err) : res({hash:'',name:"UnsupportedFile"}) 
+          })
+        } 
+      })
+    });
+
+    // log any errors that occur
+    form.on('error', function(err) {
+      rej(err);
+    });
+
+    // once all the files have been uploaded, send a response to the client
+    form.on('end', function() {
+      //Not necessary for single file
+    });
+
+    // parse the incoming request containing the form data
+    form.parse(req);
+
+  })
+}
+
+
+function uploadTargets(req,uploadDir,){
+  return new Promise((res,rej)=>{
+      // create an incoming form object
+    var form = new formidable.IncomingForm();
+
+    // specify that we want to allow the user to upload multiple files in a single request
+    form.multiples = false;
+    //Calculate file hash
+    form.hash = 'md5';
+    // store all uploads in the /uploads directory
+    form.uploadDir = uploadDir;
+
+    // every time a file has been uploaded successfully,
+    // rename it to it's original name
+    form.on('file', function(field, file) {
+      detect.fromFile(file.path,function(err,result){
+        if (err) rej(err);
+        if (result===null){
+          let destinationDir=path.join(uploadDir,`/${req.params.studyid}/targets`)
+          let destinationFile=path.join(destinationDir, file.name)
+          fs.exists(destinationDir, (exists)=>{
+            if(exists){
+             rename(file.path, destinationFile) 
+            }else{
+              fs.mkdir(destinationDir, { recursive: true }, (err)=>{
+                if (err){ 
+                  rej(err);
+                }else{
+                  rename(file.path, destinationFile)  
+                }
+              })  
+            }
+            function rename(inFile,outFile){
+              fs.rename(inFile,outFile, (err)=>{
+                if(err){
+                  rej(err);
+                }else{
+                  file={hash:form.openedFiles[0].hash, name:form.openedFiles[0].name}
+                  processTargetsFile.getPreview(outFile,0).then(result=>{
+                    result instanceof Error ? rej(result) : res({filePreview:result,file});             
+                  })
+                }
+              });
+            }
+          })          
+        }else{
+          fs.unlink(file.path, (err)=>{
+            err ? rej(err) : res({hash:'',name:"UnsupportedFile"})
+          })
+        } 
+      })
+    });
+
+    // log any errors that occur
+    form.on('error', function(err) {
+      console.log('An error has occured: \n' + err);
+      rej(err);
+    });
+
+    // once all the files have been uploaded, send a response to the client
+    form.on('end', function() {
+      //Not necessary for single file
+    });
+
+    // parse the incoming request containing the form data
+    form.parse(req);
+
+  })
+}
+
+
+
+module.exports={uploadFile,uploadTargets}
+
+
+
+
+
+
+
+

components/miRNADB/targets/psRNAtargetFile.js

@@ -1,31 +1,79 @@
 //Process data to insert into database
 var db = require('./../sqldb/index');
 const fs = require('fs')
-const minsize=2
-module.exports=function(targetsFile){
+const MINSIZE=2
+const PREVIEW_LINES=10
+
+module.exports={getPreview}
+
+
+
+
+function getPreview(targetsFile){
 	fs.readFile(targetsFile,'utf8', (err, data) => {
   		if (err) throw err;
   		//console.log(data);
   		let lines=data.split("\n")
   		lines.forEach((line)=>{
   		    line=line.split("\t")
-  		    if(line.length>minsize) insertLine(line)
+  		    if(line.length>MINSIZE) insertLine(line)
   		})
 	}) 
 }
 
+
+
+
+function getPreview(targetsFile,iteration){
+  return new Promise((res,rej)=>{
+    var rs = fs.createReadStream(targetsFile, {encoding: 'utf8'});
+    var acc = '';
+    var pos = 0;
+    let savedLines=0
+    var index = 0;
+
+    rs.on('data', function (chunk) {
+      matches = chunk.match(/\n/g);
+      acc += chunk;
+      lines=matches.length
+
+      if(lines>=PREVIEW_LINES){
+        rs.close()
+        if(matches.length>1){
+          var lastLines=PREVIEW_LINES-savedLines
+          let i=0;
+          while (i<lastLines){
+            index=chunk.indexOf("\n",index)+1
+            i+=1
+          }
+        }else{
+          index=chunk.indexOf('\n')
+        }
+      }else{
+        pos+=chunk.length;
+        savedLines+=lines
+      }
+    }).on('close', function () {
+      res(acc.slice(0, pos + index).split('\n'));
+    }).on('error', function (err) {
+        rej(err);
+    })
+  })
+}
+
+
 function insertLine(line){
 
 	return db.sequelize.transaction(function (t) {
 	  // chain all your queries here. make sure you return them.
 	  //miRNA_Acc.	Target_Acc.	Expectation	UPE	miRNA_start	miRNA_end	Target_start	Target_end	miRNA_aligned_fragment	Target_aligned_fragment	Inhibition	Target_Desc.
 	  return db.Feature.create({
 	  	genome_id:3,
-        name: line[1],
-        source: "psRNAtarget",
-        type: "targetPrediction",
-        start:line[4],
-        end:line[5],
+      name: line[1],
+      source: "psRNAtarget",
+      type: "targetPrediction",
+      start:line[4],
+      end:line[5],
 	  }, {transaction: t}).then(function (feature) {
         let featureId=feature.dataValues.id
         let miRNA_sequence=line[0].split("-")[0]
@@ -35,12 +83,7 @@ function insertLine(line){
         	sequence=sequence
         	throw "lklk"
         })
-//		return user.setShooter({
-//		  firstName: 'John',
-//		  lastName: 'Boothe'
-//		}, {transaction: t});
 	  });
-
 	}).then(function (result) {
 		result
 	  // Transaction has been committed