server : update sequence file size / total size of patient files

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

@@ -10,9 +10,88 @@ ACCESS_DENIED = "access denied"
 ## return patient file list
 ##
 def info():
+    
+
+    patient = db.patient[request.vars["id"]]
+
+    if request.vars["config_id"] and request.vars["config_id"] != "-1" :
+        config_id = long(request.vars["config_id"])
+        patient_name = patient.first_name + " " + patient.last_name
+        config_name = db.config[request.vars["config_id"]].name
+
+        fused = db(
+            (db.fused_file.patient_id == patient)
+            & (db.fused_file.config_id == config_id)
+        )
+
+        analysis = db(
+            (db.analysis_file.patient_id == patient)
+            & (db.analysis_file.config_id == config_id)
+        )
+        
+        
+        config = True
+        fused_count = fused.count()
+        fused_file = fused.select()
+        fused_filename = patient_name +"_"+ config_name + ".data"
+        analysis_count = analysis.count()
+        analysis_file = analysis.select()
+        analysis_filename = patient_name +"_"+ config_name + ".analysis"
+        
+    else:
+        config_id = -1
+        config = False
+        fused_count = 0
+        fused_file = ""
+        fused_filename = ""
+        analysis_count = 0
+        analysis_file = ""
+        analysis_filename = ""
+
+
+
+    if config :
+
+        query = db(
+                (db.sequence_file.patient_id==db.patient.id)
+                & (db.patient.id==request.vars["id"])
+            ).select(
+                left=db.results_file.on(
+                    (db.results_file.sequence_file_id==db.sequence_file.id)
+                    & (db.results_file.config_id==str(config_id) )
+                ), 
+                orderby = db.sequence_file.id|db.results_file.run_date,
+                groupby = db.sequence_file.id,
+            )
+
+    else:
+
+        query = db(
+                (db.sequence_file.patient_id==db.patient.id)
+                & (db.patient.id==request.vars["id"])
+            ).select(
+                left=db.results_file.on(
+                    (db.results_file.sequence_file_id==db.sequence_file.id)
+                    & (db.results_file.config_id==str(config_id) )
+                )
+            )
+
+
+    
     log.debug('patient (%s)' % request.vars["id"])
     if (auth.has_permission('read', 'patient', request.vars["id"]) ):
-        return dict(message=T('patient'))
+        return dict(query=query,
+                    patient=patient,
+                    config_id=config_id,
+                    fused_count=fused_count,
+                    fused_file=fused_file,
+                    fused_filename=fused_filename,
+                    analysis_count=analysis_count,
+                    analysis_file = analysis_file,
+                    analysis_filename = analysis_filename,
+                    config=config)
+    
+    
     else :
         res = {"message": ACCESS_DENIED}
         log.error(res)
@@ -31,6 +110,7 @@ def index():
     log.debug('patient list')
 
     count = db.sequence_file.id.count()
+    size = db.sequence_file.size_file
     isAdmin = auth.has_membership("admin")
     
     ##retrieve patient list 
@@ -39,6 +119,7 @@ def index():
     ).select(
         db.patient.ALL,
         count,
+        size,
         left=db.sequence_file.on(db.patient.id == db.sequence_file.patient_id),
         groupby=db.patient.id
     )
@@ -66,6 +147,9 @@ def index():
           ).select( orderby=db.auth_permission.group_id, distinct=True )  :
             if db.auth_permission[row3.id].group_id > 2:
                 row.groups += " " + str(db.auth_permission[row3.id].group_id)
+                
+        if row[size] is None :
+            row[size] = 0
     
     ##sort result
     if request.vars["sort"] == "configs" :
@@ -87,6 +171,7 @@ def index():
         
     return dict(query = query,
                 count = count,
+                size = size,
                 isAdmin = isAdmin)
 
 
@@ -124,7 +209,8 @@ def add_form():
                                    last_name=request.vars["last_name"],
                                    birth=request.vars["birth"],
                                    info=request.vars["info"],
-                                   id_label=request.vars["id_label"])
+                                   id_label=request.vars["id_label"],
+                                   creator=auth.user_id)
 
 
             user_group = auth.user_group(auth.user.id)

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

 {{extend 'db_layout.html'}}
+{{import vidjil_utils}}
 
 <h3>Patient list</h3>
 
@@ -37,7 +38,7 @@
                 <td> {{=row.patient.info }} </td>
                 <td> {{=row.confs}}</td>
 {{if isAdmin:}} <td> {{=row.groups}}</td>{{pass}}
-                <td> {{=row[count]}}</td>
+                <td> {{=row[count]}}  {{if row[size] is not None :}} ({{=vidjil_utils.format_size(row[size])}}) {{pass}}</td>
                
                
 {{if isAdmin:}} <td onclick="db.call('patient/permission', {'id' :'{{=row.patient.id}}'} )" > p </td> {{else:}} <td></td> {{pass}}

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

 {{extend 'db_layout.html'}}
-
-{{('message' in globals())}}
-{{if 'message' in globals():}}
-
-{{patient = db.patient[request.vars["id"]]}}
-
-{{if request.vars["config_id"] and request.vars["config_id"] != "-1" :}}
-    {{config_id = long(request.vars["config_id"])}}
-    {{config = True}}
-    {{
-    patient_name = patient.first_name + " " + patient.last_name
-    config_name = db.config[request.vars["config_id"]].name
-
-    fused = db(
-        (db.fused_file.patient_id == patient)
-        & (db.fused_file.config_id == config_id)
-    )
-    fused_count = fused.count()
-    fused_file = fused.select()
-    fused_filename = patient_name +"_"+ config_name + ".data"
-
-
-    analysis = db(
-        (db.analysis_file.patient_id == patient)
-        & (db.analysis_file.config_id == config_id)
-    )
-    analysis_count = analysis.count()
-    analysis_file = analysis.select()
-    analysis_filename = patient_name +"_"+ config_name + ".analysis"
-    }}
-{{else:}}
-    {{config_id = -1}}
-    {{config = False}}
-    {{fused_count = 0}}
-{{pass}}
+{{import vidjil_utils}}
 
 
-{{if config :}}
-{{
-    query = db(
-            (db.sequence_file.patient_id==db.patient.id)
-            & (db.patient.id==request.vars["id"])
-        ).select(
-            left=db.results_file.on(
-                (db.results_file.sequence_file_id==db.sequence_file.id)
-                & (db.results_file.config_id==str(config_id) )
-            ), 
-            orderby = db.sequence_file.id|db.results_file.run_date,
-            groupby = db.sequence_file.id,
-        )
-}}
-{{else:}}
-{{
-    query = db(
-            (db.sequence_file.patient_id==db.patient.id)
-            & (db.patient.id==request.vars["id"])
-        ).select(
-            left=db.results_file.on(
-                (db.results_file.sequence_file_id==db.sequence_file.id)
-                & (db.results_file.config_id==str(config_id) )
-            )
-        )
-}}
-{{pass}}
 
 <div>
 
@@ -131,7 +70,8 @@
                     <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>
+                    <td {{if row.sequence_file.data_file == None :}} {{=XML("class='inactive' title='file is missing' ")}} {{pass}} > 
+                        {{=vidjil_utils.format_size(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>
@@ -207,9 +147,3 @@
 {{pass}}
 
 </div>
-
-{{elif 'content' in globals():}}
-{{=content}}
-{{else:}}
-{{=BEAUTIFY(response._vars)}}
-{{pass}}

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

@@ -25,9 +25,3 @@
     </div>
 
 </div>
-
-{{elif 'content' in globals():}}
-{{=content}}
-{{else:}}
-{{=BEAUTIFY(response._vars)}}
-{{pass}}