refactor id strings and id extraction

For adding files to sample_sets. Alters the existing id strings by
removing dates.
I wanted to clean things up a little and alter the way id_strings are
created/decoded before making them a little more flexible in order to
produce more aesthetically pleasing id_strings.

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

@@ -15,19 +15,14 @@ if request.env.http_origin:
     response.headers['Access-Control-Allow-Credentials'] = 'true'
     response.headers['Access-Control-Max-Age'] = 86400
 
-def extract_id(target, error):
+def extract_set_type(target):
     mapping = {
         'p': 'patient',
         'r': 'run',
         's': 'generic'
     }
-    try:
-        t_split = target.strip().split(' ')
-        tid = int(' '.join(t_split[1:]).split('(')[-1][:-1])
-        ttype = mapping[t_split[0].split(':')[1]]
-        return ttype, tid
-    except:
-        raise ValueError('invalid input %s' % target)
+    return mapping[target.split(':')[1][0]]
+
 
 def manage_filename(filename):
     filepath = ""
@@ -170,6 +165,9 @@ def submit():
             datetime.datetime.strptime(""+request.vars['sampling_date'], '%Y-%m-%d')
         except ValueError:
             error += "date (wrong format), "
+
+    mf = ModelFactory()
+    helpers = {}
             
     set_ids = request.vars['set_ids'].split(',')
     set_ids = [x.strip() for x in set_ids]
@@ -178,9 +176,11 @@ def submit():
     for sid in set_ids:
         if sid != '':
             try:
-                set_type, set_id = extract_id(sid, error)
+                set_type = extract_set_type(sid)
                 if set_type not in id_dict:
+                    helpers[set_type] = mf.get_instance(set_type)
                     id_dict[set_type] = []
+                set_id = helpers[set_type].parse_id_string(sid)
                 id_dict[set_type].append(set_id)
                 if not auth.can_modify(set_type, set_id) :
                     error += " missing permission for %s %d" % (set_type, set_id)

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

@@ -12,6 +12,7 @@ if request.env.http_origin:
     
 def anon_names(data):
     for row in data:
+        # TODO use helper ?
         row.name = vidjil_utils.anon_ids(row.id)
     return data
 

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

@@ -128,6 +128,13 @@ class SampleSet(object):
     def get_id_string(self, data):
         pass
 
+    def parse_id_string(self, string):
+        try:
+            value = string[string.find("(")+1:string.find(")")]
+            return int(value)
+        except:
+            raise ValueError('invalid input %s' % string)
+
 def get_sample_name(sample_set_id):
     '''
     Return the name associated with a sample set (eg. a run or a

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

@@ -26,4 +26,4 @@ class Generic(SampleSet):
 
     def get_id_string(self, data):
         name = data.name if data.name is not None else "Unnamed Sample Set"
-        return ":s %s  (%d)" % (name, data.id)
+        return ":s %s (%d)" % (name, data.id)

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

@@ -45,6 +45,5 @@ class Patient(SampleSet):
 
     def get_id_string(self, data):
         name = self.get_name(data)
-        birth = "[%s]" % str(data.birth)
-        id = "(%d)" % data.id
-        return ":p %s  %s  %s" % (birth, name, id)
+        ident = "(%d)" % data.id
+        return ":p %s %s" % (name, ident)

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

@@ -41,6 +41,5 @@ class Run(SampleSet):
 
     def get_id_string(self, data):
         name = data.name
-        run_date = "[%s]" % str(data.run_date)
-        id = "(%d)" % data.id
-        return ":r %s  %s  %s" % (run_date, name, id)
+        ident = "(%d)" % data.id
+        return ":r %s %s" % (name, ident)