Merge branch 'feature-sc/1469-get-reads-simple' into 'dev'

Get reads (simple UI)

Closes #1469 and #3733

See merge request !439

browser/js/clone.js

@@ -1211,14 +1211,11 @@ Clone.prototype = {
                 if (this.normalized_reads && this.m.normalization_mode == this.m.NORM_EXTERNAL) {
                   html += "<br />[" + this.getReads(this.m.samples.order[j]).toFixed(2) + "]"
                 }
-                if ($('#debug_menu').is(':visible') && (typeof this.m.db_key.config != 'undefined' )) {
-                html += "<br/>"
-                call_reads = "db.call('default/run_request', { "
-                call_reads += "'sequence_file_id': '" + this.m.samples.db_key[this.m.samples.order[j]] + "', "
-                call_reads += "'config_id' : '" + this.m.db_key.config + "', "
-                call_reads += "'grep_reads' : '" + this.id + "' })"
-                console.log(call_reads)
-                html += "<span class='button' onclick=\"" + call_reads + "\"> get reads </span>"
+                if (typeof this.m.db_key.config != 'undefined' ) {
+                    html += "&emsp;"
+                    var sample_set_id = this.m.samples.sequence_file_id[this.m.samples.order[j]];
+                    call_reads = "db.get_read('" + this.id + "', "+ this.index +", " + sample_set_id + ')';
+                    html += '<i onclick="' + call_reads + '; m.closeInfoBox()" class="icon-down" title="Download reads from this clone"></i>';
                 }
                 html += "</td>"
             }

browser/js/database.js

@@ -125,6 +125,31 @@ Database.prototype = {
                          report.reportcontamination()
                      })
     },
+
+    get_read: function(window, clone_id, sequence_file_id) {
+	var self = this;
+        var log = "Reads will be exported in a few minutes. You will be able to download them when they are ready. You can continue using the application.";
+        console.log({"type": "flash", "msg" : log, "priority": 2});
+	self.callProcess('default/run_request',
+			 {'sequence_file_id': sequence_file_id,
+			  'sample_set_id': self.m.sample_set_id,
+			  'config_id': self.m.db_key.config,
+			  'grep_reads': window},
+			 function(a) {
+				// Link to result file and launch download
+                             var path_data = DB_ADDRESS+"/results_file/download?filename=seq/clone.fa-1&results_file_id="+a.result_id
+                             var file_name = "reads__"+clone_id+"__file_id_"+"_"+sequence_file_id+".fa"
+                             var anchor = document.createElement('a');
+                             anchor.setAttribute("download", file_name);
+                             anchor.setAttribute("href",     path_data);
+                             anchor.style = 'display: none';
+                             self.ajax_indicator_stop()
+                             document.body.appendChild(anchor);
+                             anchor.click();
+                             document.body.removeChild(anchor);
+			 });
+    },
+
     
      /**
       * request a side process to the server
@@ -132,7 +157,8 @@ Database.prototype = {
       * */
      callProcess : function (page, args, callback){
          var self=this;
-         
+         this.temporarilyDisableClickedLink();
+	 
          var arg = "";
          if (typeof args != "undefined" && Object.keys(args).length) 
              arg = this.argsToStr(args)
@@ -171,7 +197,6 @@ Database.prototype = {
      * check if a server process is done(recursive)
      * */
      waitProcess: function (processId, interval, callback){
-         console.log("... " +processId)
          var self=this;
          var url = self.db_address + "default/checkProcess?processId="+processId;
          
@@ -185,11 +210,12 @@ Database.prototype = {
              xhrFields: {withCredentials: true},
              success: function (result) {
                  self.connected = true;
+		 console.log(result);
                  result = jQuery.parseJSON(result)
                  if (result.status == "COMPLETED"){
                      callback(result.data);
                  }else if(result.status == "FAILED"){
-                     console.log({"type": "flash", "msg": "process failed", "priority": 1});
+                     console.log({"type": "flash", "msg": "process failed:" + ((typeof result.message !== 'undefined') ? result.message: ''), "priority": 1});
                  }else{
                      setTimeout(function(){ self.waitProcess(processId, interval, callback); }, interval); 
                  }
@@ -214,20 +240,7 @@ Database.prototype = {
      * */
     call: function (page, args) {
         var self = this;
-        try {
-            var event = window.event || arguments.callee.caller.arguments[0] 
-            event.stopPropagation();
-            var target = event.target
-            if (target.getAttribute("disabled")){
-                return;
-            } else {
-                target.setAttribute("disabled", "disabled")
-                self.ajax_indicator_start();
-                setTimeout(function(){target.removeAttribute("disabled")}, 2000)
-            }
-        }
-        catch(err)
-        {}
+	this.temporarilyDisableClickedLink()
         
         var url = self.db_address + page
         if (page.substr(0,4).toLowerCase() == "http") {
@@ -1103,6 +1116,33 @@ Database.prototype = {
         tgt.empty();
         $('body').css('cursor', 'default');
     },
+
+    temporarilyDisableClickedLink: function() {
+	var self = this;
+        try {
+            var event = window.event;
+            if (typeof(event) === 'undefined') {
+                var caller = arguments.callee.caller;
+                while (caller != null && (caller.arguments.length == 0 ||
+                                          ! (caller.arguments[0] instanceof Event)))
+                    caller = caller.caller;
+                if (caller == null)
+                    return;
+                event = caller.arguments[0];
+            }
+            event.stopPropagation();
+            var target = $(event.target)
+            if (target.hasClass("disabledClass")){
+                return;
+            } else {
+                target.addClass("disabledClass")
+                self.ajax_indicator_start();
+                setTimeout(function(){target.removeClass("disabledClass")}, 3000)
+            }
+        }
+        catch(err)
+	{}
+    },
     
     validate_fileform: function (form) { 
         var pp_option = form.pre_process.getElementsByTagName("option");

server/web2py/applications/vidjil/controllers/default.py

@@ -115,6 +115,8 @@ def run_request():
     ##TODO check
     if not "sequence_file_id" in request.vars :
         error += "id sequence file needed, "
+    elif not "sample_set_id" in request.vars:
+        error += "sample set ID needed, "
     if not "config_id" in request.vars:
         error += "id config needed, "
         id_config = None
@@ -170,18 +172,33 @@ def run_extra():
 
 def checkProcess():
     task = db.scheduler_task[request.vars["processId"]]
-    
-    if task.status == "COMPLETED" :
+    results_file = db(db.results_file.scheduler_task_id == task.id).select().first()
+
+    msg = ''
+    sample_set_id = -1
+    if results_file:
+        sample_set_id = get_sample_set_id_from_results_file(results_file.id)
+    if not results_file or not auth.can_view_sample_set(sample_set_id):
+        msg = "You don't have access to this sample"
+    if sample_set_id > -1 and task.status == "COMPLETED" :
         run = db( db.scheduler_run.task_id == task.id ).select()[0]
     
         res = {"success" : "true",
                "status" : task.status,
-               "data" : run.run_result,
+               "data" : {'run_result': run.run_result,
+                         'result_id': results_file.id
+                         },
                "processId" : task.id}
     else :
-        res = {"success" : "true",
-               "status" : task.status,
-               "processId" : task.id}
+        if len(msg) > 0:
+            res = {"success" : "false",
+                   "status" : "FAILED",
+                   "message": msg,
+                   "processId" : task.id}
+        else:
+            res = {"success" : "true",
+                   "status" : task.status,
+                   "processId" : task.id}
         
     log.error(res)
     return gluon.contrib.simplejson.dumps(res, separators=(',',':'))

server/web2py/applications/vidjil/controllers/results_file.py

@@ -11,14 +11,6 @@ if request.env.http_origin:
     response.headers['Access-Control-Allow-Credentials'] = 'true'
     response.headers['Access-Control-Max-Age'] = 86400
 
-def get_sample_set_id(results_file_id):
-    sample_set_id = db((db.sequence_file.id == db.results_file.sequence_file_id)
-                    &(db.results_file.id == results_file_id)
-                    &(db.sample_set_membership.sequence_file_id == db.sequence_file.id)
-                    &(db.sample_set.id == db.sample_set_membership.sample_set_id)
-                ).select(db.sample_set_membership.sample_set_id).first().sample_set_id
-    return sample_set_id
-
 ## return admin_panel
 def index():
     if auth.is_admin():
@@ -90,7 +82,7 @@ def run_all_patients():
 ## display run page result 
 ## need ["results_file_id"]
 def info():
-    sample_set_id = get_sample_set_id(request.vars["results_file_id"])
+    sample_set_id = get_sample_set_id_from_results_file(request.vars["results_file_id"])
     if (auth.can_modify_sample_set(sample_set_id)):
         log.info("access results file info", extra={'user_id': auth.user.id,
                 'record_id': request.vars["results_file_id"],
@@ -101,7 +93,7 @@ def info():
         return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
 
 def output():
-    sample_set_id = get_sample_set_id(request.vars["results_file_id"])
+    sample_set_id = get_sample_set_id_from_results_file(request.vars["results_file_id"])
     if (auth.can_view_sample_set(sample_set_id)):
         results_id = int(request.vars["results_file_id"])
         output_directory = defs.DIR_OUT_VIDJIL_ID % results_id
@@ -123,11 +115,11 @@ def output():
 
 @cache.action()
 def download():
-    sample_set_id = get_sample_set_id(request.vars["results_file_id"])
-    if auth.can_view_sample_set(sample_set_id):
+    sample_set_id = get_sample_set_id_from_results_file(request.vars["results_file_id"])
+    if auth.can_view_sample_set(sample_set_id) and not '..' in request.vars['filename']:
         results_id = int(request.vars["results_file_id"])
         directory = defs.DIR_OUT_VIDJIL_ID % results_id
-        filepath = directory + os.path.basename(request.vars['filename'])
+        filepath = directory + request.vars['filename']
         try:
             log.info("Downloaded results file", extra={'user_id': auth.user.id,
                 'record_id': request.vars["results_file_id"],

server/web2py/applications/vidjil/models/SampleSet.py

@@ -174,3 +174,15 @@ def get_set_group(sid):
               (db.auth_permission.name == PermissionEnum.access.value)
             ).select().first()
     return perm.group_id
+
+def get_sample_set_id_from_results_file(results_file_id):
+    '''
+    Return the sample set ID corresponding to a result file ID
+    '''
+    sample_set_id = db((db.sequence_file.id == db.results_file.sequence_file_id)
+                    &(db.results_file.id == results_file_id)
+                    &(db.sample_set_membership.sequence_file_id == db.sequence_file.id)
+                    &(db.sample_set.id == db.sample_set_membership.sample_set_id)
+                ).select(db.sample_set_membership.sample_set_id).first().sample_set_id
+    return sample_set_id
+

server/web2py/applications/vidjil/models/task.py

@@ -156,6 +156,7 @@ def schedule_run(id_sequence, id_config, grep_reads=None):
     filename= db.sequence_file[id_sequence].filename
 
     res = {"redirect": "reload",
+           "processId": task.id,
            "message": "[%s] c%s: process requested - %s %s" % (data_id, id_config, grep_reads, filename)}
 
     log.info(res)