SampleSetList: refactor some type-specific fields

Pass a helper instance to SampleSetList instead of a set type

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

@@ -222,16 +222,17 @@ def all():
     search, tags = parse_search(request.vars["filter"])
     group_ids = get_involved_groups()
 
+    factory = ModelFactory()
+    helper = factory.get_instance(type=type)
+
     f = time.time()
-    slist = SampleSetList(type, page, step, tags)
+    slist = SampleSetList(helper, page, step, tags)
 
     # failsafe if filtered display all results
     step = len(slist) if step is None else step
     page = 0 if page is None else page
     result = slist.result
 
-    factory = ModelFactory()
-    helper = factory.get_instance(type=type)
     fields = helper.get_fields()
     sort_fields = helper.get_sort_fields()
 

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

@@ -158,6 +158,14 @@ class SampleSet(object):
     def validate(self, data):
         pass
 
+    @abstractmethod
+    def get_dedicated_fields(self):
+        pass
+
+    @abstractmethod
+    def get_dedicated_group(self):
+        pass
+
 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

@@ -32,3 +32,13 @@ class Generic(SampleSet):
         if data["name"].find("|") >= 0:
             error.append("illegal character '|' in name")
         return error
+
+    def get_dedicated_fields(self):
+        table = db[self.type]
+        return [
+            table.name.with_alias('name')
+        ]
+
+    def get_dedicated_group(self):
+        table = db[self.type]
+        return [table.name]

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

@@ -63,6 +63,18 @@ class Patient(SampleSet):
             error.append("illegal character '|' in name")
         return error
 
+    def get_dedicated_fields(self):
+        table = db[self.type]
+        return [
+            table.first_name.with_alias('first_name'),
+            table.last_name.with_alias('last_name'),
+            table.birth.with_alias('birth'),
+        ]
+
+    def get_dedicated_group(self):
+        table = db[self.type]
+        return [table.first_name, table.last_name, table.birth]
+
     def get_name_filter_query(self, query):
         if query is None or query == '':
             return (db[self.type].id > 0)

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

@@ -61,3 +61,14 @@ class Run(SampleSet):
             error.append("illegal character '|' in name")
 
         return error
+
+    def get_dedicated_fields(self):
+        table = db[self.type]
+        return [
+            table.name.with_alias('name'),
+            table.run_date.with_alias('run_date'),
+        ]
+
+    def get_dedicated_group(self):
+        table = db[self.type]
+        return [table.name]

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

@@ -4,9 +4,9 @@ class SampleSetList():
 
     This class is used to load all the required information for such a list.
     '''
-    def __init__(self, type, page=None, step=None, tags=None):
-        self.type = type
-        s_table = db[type]
+    def __init__(self, helper, page=None, step=None, tags=None):
+        self.type = helper.get_type()
+        s_table = db[self.type]
 
         limitby = None
         if page is not None and step is not None:
@@ -16,7 +16,10 @@ class SampleSetList():
                 db.sequence_file.on(db.sample_set_membership.sequence_file_id == db.sequence_file.id),
                 db.fused_file.on(s_table.sample_set_id == db.fused_file.sample_set_id),
                 db.config.on(db.fused_file.config_id == db.config.id),
-                db.auth_permission.on((db.auth_permission.table_name == 'sample_set') & (db.auth_permission.record_id == s_table.sample_set_id) & (db.auth_permission.name == PermissionEnum.access.value)),
+                db.auth_permission.on(
+                    (db.auth_permission.table_name == 'sample_set') &
+                    (db.auth_permission.record_id == s_table.sample_set_id) &
+                    (db.auth_permission.name == PermissionEnum.access.value)),
                 db.auth_group.on(db.auth_permission.group_id == db.auth_group.id),
                 db.auth_membership.on(db.auth_group.id == db.auth_membership.group_id),
                 db.auth_permission.with_alias('anon_permission').on(
@@ -33,17 +36,10 @@ class SampleSetList():
         group_config_names = get_config_names_select()
         group_group_names = get_group_names_select()
 
-        # TODO remove this hack
-        if self.type == 'patient':
-            dedicated_fields = [
-                s_table.first_name.with_alias('first_name'),
-                s_table.last_name.with_alias('last_name'),
-                s_table.birth.with_alias('birth'),
-            ]
-            groupby = [s_table.id, s_table.sample_set_id, s_table.first_name, s_table.last_name, s_table.birth, s_table.info, db.auth_user.last_name]
-        else:
-            dedicated_fields = [s_table.name.with_alias('name')]
-            groupby = [s_table.id, s_table.sample_set_id, s_table.name, s_table.info, db.auth_user.last_name],
+        dedicated_fields = helper.get_dedicated_fields()
+
+        groupby = [s_table.id, s_table.sample_set_id, s_table.info, db.auth_user.last_name]
+        groupby += helper.get_dedicated_group()
 
         query = ((auth.vidjil_accessible_query('read', db.sample_set)) &
             (s_table.sample_set_id == db.sample_set.id) &
@@ -75,7 +71,7 @@ class SampleSetList():
                 *select + dedicated_fields,
                 left=left,
                 limitby = limitby,
-                orderby = ~db[type].id,
+                orderby = ~db[self.type].id,
                 groupby = groupby + [db.tag_ref.record_id|db.tag_ref.table_name],
                 having = count >= len(tags),
                 cacheable=True
@@ -88,7 +84,7 @@ class SampleSetList():
                 left=left,
                 limitby = limitby,
                 groupby = groupby,
-                orderby = ~db[type].id,
+                orderby = ~db[self.type].id,
                 cacheable=True
             )