server : debug upload file

-sequence file can be reuploaded
-fix missing files
-add size

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

 # coding: utf8
 import gluon.contrib.simplejson
+import os.path
+import defs
+import math
 if request.env.http_origin:
     response.headers['Access-Control-Allow-Origin'] = request.env.http_origin  
     response.headers['Access-Control-Allow-Credentials'] = 'true'
@@ -14,3 +17,26 @@ def index():
 def worker():
     if auth.has_membership("admin"):
         return dict(message=T(''))
+
+## to use after change in the upload folder
+def repair_missing_files():
+    if auth.has_membership("admin"):
+        
+        flist = ""
+        for row in db(db.sequence_file.id>0 and db.sequence_file.data_file != None).select() : 
+            seq_file = defs.DIR_SEQUENCES+row.data_file
+            
+            if not os.path.exists(seq_file) :
+                db.sequence_file[row.id] = dict(data_file = None)
+                flist += " : " + row.filename
+            else :
+                size = os.path.getsize(seq_file)
+                size = math.floor((size/1024)/1024)
+                if size > 1024 :
+                    size = str( round( (size/1024), 3 ) ) + " Go" 
+                else :
+                    size = str( math.floor(size) ) + " Mo" 
+                db.sequence_file[row.id] = dict(size_file = size)
+                
+        res = {"success" : "true", "message" : "path of missing files have been removed from the database"+flist}
+        return gluon.contrib.simplejson.dumps(res, separators=(',',':'))

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

 # coding: utf8
 import gluon.contrib.simplejson
+import defs
+import os
+import math
 if request.env.http_origin:
     response.headers['Access-Control-Allow-Origin'] = request.env.http_origin  
     response.headers['Access-Control-Allow-Credentials'] = 'true'
@@ -81,19 +84,15 @@ def edit_form():
         error += " missing filename"
             
     if error=="" :
-        query = db((db.sequence_file.patient_id==db.sequence_file[request.vars['id']].patient_id)).select()
-        for row in query :
-            if row.filename == request.vars['filename'] :
-                res = {"message": "this sequence file already exists for this patient"}
-                return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
-
         mes = "file " + request.vars['id'] + " : "
         if request.vars['sampling_date'] != None and request.vars['file_info'] != None :
             db.sequence_file[request.vars["id"]] = dict(sampling_date=request.vars['sampling_date'],
                                                         info=request.vars['file_info'],
                                                         pcr=request.vars['pcr'],
                                                         sequencer=request.vars['sequencer'],
-                                                        producer=request.vars['producer'])
+                                                        producer=request.vars['producer'],
+                                                        patient_id=request.vars['patient_id'],
+                                                        filename=request.vars['filename'])
             
         patient_id = db.sequence_file[request.vars["id"]].patient_id
         
@@ -118,6 +117,15 @@ def upload():
             db.sequence_file[request.vars["id"]] = dict(data_file = db.sequence_file.data_file.store(f.file, f.filename))
             mes = f.filename + ": upload finished"
         
+        seq_file = defs.DIR_SEQUENCES+db.sequence_file[request.vars["id"]].data_file
+        size = os.path.getsize(seq_file)
+        size = math.floor((size/1024)/1024)
+        if size > 1024 :
+            size = str( round( (size/1024), 3 ) ) + " Go" 
+        else :
+            size = str( math.floor(size) ) + " Mo" 
+        db.sequence_file[request.vars["id"]] = dict(size_file = size)
+        
         res = {"message": mes}
         return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
   

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

@@ -111,7 +111,7 @@ db.define_table('sequence_file',
                 Field('pcr','text'),
                 Field('sequencer','text'),
                 Field('producer','text'),
-                Field('size_file','integer'),
+                Field('size_file','text'),
                 Field('data_file', 'upload', 
                       uploadfolder=defs.DIR_SEQUENCES,
                       length=1000000000000, autodelete=True))
@@ -274,8 +274,3 @@ def _init_log():
     return MsgUserAdapter(logger, {})
 
 log = _init_log()
-
-
-
-
-

server/web2py/applications/vidjil/views/admin/index.html

@@ -5,3 +5,6 @@ Bientot vous trouverez içi un magnifique panneau d'administration, en attendant
 
 </br>
 <a class="button" onclick="db.call('results_file/index');">liste des fichiers result (data)</a>
+
+</br>
+<a class="button" onclick="db.call('admin/repair_missing_files');">fix missing files problem</a>

server/web2py/applications/vidjil/views/patient/index.html

@@ -21,13 +21,25 @@
 
 
        {{for row in query :}}
-           <tr onclick="db.call('patient/info', {'id' :'{{=row.patient.id}}'} )" >
+        
+        {{confs=""}}
+        {{co = db.fused_file.id.count()}}
+        {{query_conf = db( db.fused_file.patient_id == row.patient.id ).select(db.fused_file.config_id, co, groupby=db.fused_file.config_id).sort(lambda row: co)}}
+        
+        {{for row2 in query_conf:}} 
+            {{confs+=" "+db.config[row2.fused_file.config_id].name}} 
+        {{pass}}
+        
+        {{most_used_conf = -1}}
+        {{if len(query_conf) > 0 :}} 
+            {{most_used_conf = query_conf[0].fused_file.config_id}}
+        {{pass}}
+        
+           <tr onclick="db.call('patient/info', {'id' :'{{=row.patient.id}}' , 'config_id' : {{=most_used_conf}} } )" >
                 <td> {{=row.patient.last_name + " " + row.patient.first_name }} </td>
                 <td> {{=row.patient.birth }} </td>
                 <td> {{=row.patient.info }} </td>
-                <td> {{for row2 in db( db.fused_file.patient_id == row.patient.id ).select(db.fused_file.config_id, distinct=True) :}} 
-                        {{=db.config[row2.config_id].name}} 
-                     {{pass}}</td>
+                <td> {{=confs}}</td>
         <!-- groups/users  -->
                 {{if isAdmin:}} 
                 <td> 

server/web2py/applications/vidjil/views/patient/info.html

@@ -5,7 +5,7 @@
 
 {{patient = db.patient[request.vars["id"]]}}
 
-{{if request.vars["config_id"] and not request.vars["config_id"] == -1 :}}
+{{if request.vars["config_id"] and request.vars["config_id"] != "-1" :}}
     {{config_id = long(request.vars["config_id"])}}
     {{config = True}}
     {{
@@ -98,10 +98,11 @@
     <table class="db_table" id="table">
         <thead>
             <tr><td class="column_200"> file name </td>
-                <td class="column5"> </td>
                 <td class="column2"> sampling date </td>
                 <td> info </td>
                 <td> pcr </td>
+                <td class="column1"> size </td>
+                <td class="column5"> </td>
                 <td class="column5"> </td>
                 <td class="column5"> </td>
 
@@ -124,16 +125,18 @@
                 {{pass}}
 
                  <tr>
-                    <td id="sequence_file_{{=row.sequence_file.id}}"> {{=row.sequence_file.filename[:20]}}
-                      {{if len(row.sequence_file.filename) > 20: }}...{{pass}}
+                    <td {{if row.sequence_file.data_file == None :}} {{=XML("class='inactive' title='file is missing' ")}}  {{pass}} id="sequence_file_{{=row.sequence_file.id}}">
+                         {{=row.sequence_file.filename}}
                     </td>
-                    <td> {{if row.sequence_file.filename == 'plop':}}<a href="{{=URL('patient','download', scheme='https', args=row.sequence_file.data_file)}}" >dl</a>{{pass}}</td>
                     <td> {{=row.sequence_file.sampling_date}} </td>
                     <td> {{=row.sequence_file.info}} </td>
                     <td> {{=row.sequence_file.pcr}} </td>
+                    <td {{if row.sequence_file.data_file == None :}} {{=XML("class='inactive' title='file is missing' ")}} {{pass}} > {{=row.sequence_file.size_file}} </td>
                     {{if (auth.has_permission('admin', 'patient', request.vars["id"]) ):}}
                         <td onclick="db.call('file/edit', {'id' :'{{=row.sequence_file.id}}', 'patient_id' :'{{=request.vars['id']}}'} )" > e </td>
                         <td onclick="db.call('file/confirm', {'id' :'{{=row.sequence_file.id}}', 'patient_id' :'{{=request.vars['id']}}'} )" > X </td>
+                        <td> <a {{if row.sequence_file.data_file == None :}} {{=XML("class='inactive' title='file is missing' ")}} 
+                                {{else:}} href="{{=URL('patient','download', scheme='https', args=row.sequence_file.data_file)}}" {{pass}}  >dl</a></td>
                     {{else:}}<td></td><td></td>{{pass}}
                      
                      
@@ -146,7 +149,7 @@
                    <td class="button" onclick="db.call('results_file/info', { 'results_file_id' : '{{=row.results_file.id}}' } )"> {{=status}} </td>
                    <td onclick="db.call('results_file/confirm', {'results_file_id' :'{{=row.results_file.id}}'})" > X </td>
                    <td>
-                   {{if row.results_file.id == None or ( status != "RUNNING" and status != "QUEUED" and status != "ASSIGNED"):}}
+                   {{if row.sequence_file.data_file != None and ( row.results_file.id == None or ( status != "RUNNING" and status != "QUEUED" and status != "ASSIGNED") ):}}
                        {{if auth.has_permission("run", "results_file") :}}
                            <span class="button" onclick="db.call('default/run_request', { 'sequence_file_id' : '{{=row.sequence_file.id}}', 'config_id' : {{=config_id}} } )"> run >> </span>
                        {{else:}}<span class="button inactive" title="you don't have permission to schedule runs"> run >> </span>{{pass}}