move init_db_helper to vidjil_utils

it belongs in a module rather than a controller since it does not serve
any pages.

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

@@ -9,7 +9,6 @@
 ## - call exposes all registered services (none by default)
 #########################################################################
 
-from gluon.main import save_password
 import defs
 import vidjil_utils
 import StringIO
@@ -73,7 +72,7 @@ def init_db_form():
         if "force" in request.vars and request.vars["force"].lower() == 'true':
             force = True
         if error == "":
-            init_db_helper(force=force, admin_email=request.vars['email'], admin_password=request.vars['password'])
+            vidjil_utils.init_db_helper(db, auth, force=force, admin_email=request.vars['email'], admin_password=request.vars['password'])
         else :
             res = {"success" : "false",
                    "message" : error}
@@ -83,107 +82,6 @@ def init_db_form():
     res = {"redirect" : "default/user/login"}
     return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
 
-def init_db_helper(force=False, admin_email="plop@plop.com", admin_password="1234"):
-    if (force) or (db(db.auth_user.id > 0).count() == 0) : 
-        if force:
-            vidjil_utils.reset_db(db)
-
-        id_first_user=""
-
-        ## création du premier user
-        id_first_user=db.auth_user.insert(
-            password = db.auth_user.password.validate(admin_password)[0],
-            email = admin_email,
-            first_name = 'System',
-            last_name = 'Administrator'
-        )
-
-        # set web2py administration interface password to the same as vidjil admin password
-        save_password(admin_password, 443)
-
-        ## création des groupes de base
-        id_admin_group=db.auth_group.insert(role='admin')
-        id_sa_group=db.auth_group.insert(role='user_1')
-        id_public_group=db.auth_group.insert(role="public")
-
-        db.auth_membership.insert(user_id=id_first_user, group_id=id_admin_group)
-        db.auth_membership.insert(user_id=id_first_user, group_id=id_sa_group)
-        db.auth_membership.insert(user_id=id_first_user, group_id=id_public_group)
-
-        ## base Vidjil configs
-
-        db.config.insert(
-            name = 'default + extract reads',
-            program = 'vidjil',
-            command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g -e 1 -2 -d -w 50 -U ',
-            fuse_command = '-t 100',
-            info = 'Same as the default "multi+inc+xxx" (multi-locus, with some incomplete/unusual/unexpected recombinations), and extract analyzed reads in the "out" temporary directory.'
-        )
-        db.config.insert(
-            name = 'multi+inc+xxx',
-            program = 'vidjil',
-            command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g -e 1 -2 -d -w 50 ',
-            fuse_command = '-t 100',
-            info = 'multi-locus, with some incomplete/unusual/unexpected recombinations'
-        )
-        db.config.insert(
-            name = 'multi+inc',
-            program = 'vidjil',
-            command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g -e 1 -w 50 ',
-            fuse_command = '-t 100',
-            info = 'multi-locus, with some incomplete/unusual recombinations'
-        )
-        db.config.insert(
-            name = 'multi',
-            program = 'vidjil',
-            command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g:IGH,IGK,IGL,TRA,TRB,TRG,TRD -i -e 1 -d -w 50 ',
-            fuse_command = '-t 100',
-            info = 'multi-locus, only complete recombinations'
-        )
-        db.config.insert(
-            name = 'TRG',
-            program = 'vidjil',
-            command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g:TRG ',
-            fuse_command = '-t 100',
-            info = 'TRG, VgJg'
-        )
-        db.config.insert(
-            name = 'IGH',
-            program = 'vidjil',
-            command = '-c clones -w 60 -d -3 -z 100 -r 1 -g germline/homo-sapiens.g:IGH ',
-            fuse_command = '-t 100',
-            info = 'IGH, Vh(Dh)Jh'
-        )
-
-        ## permission
-        ## system admin have admin/read/create rights on all patients, groups and configs
-        auth.add_permission(id_admin_group, PermissionEnum.access.value, db.sample_set, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.access.value, db.patient, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.access.value, db.run, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.access.value, db.generic, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.access.value, db.config, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.access.value, db.pre_process, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.access.value, db.auth_group, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.sample_set, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.patient, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.generic, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.run, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.admin_group.value, db.auth_group, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.admin_config.value, db.config, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.admin_pre_process.value, db.pre_process, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.read.value, db.sample_set, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.read.value, db.patient, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.read.value, db.run, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.read.value, db.generic, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.read_group.value, db.auth_group, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.read_config.value, db.config, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.read_pre_process.value, db.pre_process, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.create.value, db.sample_set, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.create_group.value, db.auth_group, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.create_config.value, db.config, 0)
-        auth.add_permission(id_admin_group, PermissionEnum.create_pre_process.value, db.pre_process, 0)
-        auth.add_permission(id_admin_group, 'impersonate', db.auth_user, 0)
-
 def init_from_csv():
     if db(db.auth_user.id > 0).count() == 0:
         res = {"success" : "true", "message" : "Importing " + defs.DB_BACKUP_FILE}

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

 #coding: utf-8
 from gluon.tools import Auth
 from gluon.dal import Row, Set, Query
-from enum import Enum
-
-class PermissionEnum(Enum):
-    admin = 'admin'
-    read = 'read'
-    access = 'access'
-    upload = 'upload'
-    create = 'create'
-    run = 'run'
-    save = 'save'
-    admin_config = 'admin'
-    read_config = 'read'
-    create_config = 'create_config'
-    admin_group = 'admin'
-    read_group = 'read'
-    create_group = 'create'
-    admin_pre_process = 'admin'
-    read_pre_process = 'read'
-    create_pre_process = 'create'
-    anon = 'anon'
+
+from permission_enum import PermissionEnum
 
 class VidjilAuth(Auth):
     admin = None

server/web2py/applications/vidjil/modules/vidjil_utils.py

+# -*- coding: utf-8 -*-
 import math
 import re
 import defs
@@ -584,3 +585,106 @@ def reset_db(db):
         # lets not forget to renable foreign keys
         if mysql:
             db.executesql('SET FOREIGN_KEY_CHECKS = 1;')
+
+def init_db_helper(db, auth, force=False, admin_email="plop@plop.com", admin_password="1234"):
+    from gluon.main import save_password
+    from permission_enum import PermissionEnum
+    if (force) or (db(db.auth_user.id > 0).count() == 0) : 
+        if force:
+            reset_db(db)
+
+        id_first_user=""
+
+        ## création du premier user
+        id_first_user=db.auth_user.insert(
+            password = db.auth_user.password.validate(admin_password)[0],
+            email = admin_email,
+            first_name = 'System',
+            last_name = 'Administrator'
+        )
+
+        # set web2py administration interface password to the same as vidjil admin password
+        save_password(admin_password, 443)
+
+        ## création des groupes de base
+        id_admin_group=db.auth_group.insert(role='admin')
+        id_sa_group=db.auth_group.insert(role='user_1')
+        id_public_group=db.auth_group.insert(role="public")
+
+        db.auth_membership.insert(user_id=id_first_user, group_id=id_admin_group)
+        db.auth_membership.insert(user_id=id_first_user, group_id=id_sa_group)
+        db.auth_membership.insert(user_id=id_first_user, group_id=id_public_group)
+
+        ## base Vidjil configs
+
+        db.config.insert(
+            name = 'default + extract reads',
+            program = 'vidjil',
+            command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g -e 1 -2 -d -w 50 -U ',
+            fuse_command = '-t 100',
+            info = 'Same as the default "multi+inc+xxx" (multi-locus, with some incomplete/unusual/unexpected recombinations), and extract analyzed reads in the "out" temporary directory.'
+        )
+        db.config.insert(
+            name = 'multi+inc+xxx',
+            program = 'vidjil',
+            command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g -e 1 -2 -d -w 50 ',
+            fuse_command = '-t 100',
+            info = 'multi-locus, with some incomplete/unusual/unexpected recombinations'
+        )
+        db.config.insert(
+            name = 'multi+inc',
+            program = 'vidjil',
+            command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g -e 1 -w 50 ',
+            fuse_command = '-t 100',
+            info = 'multi-locus, with some incomplete/unusual recombinations'
+        )
+        db.config.insert(
+            name = 'multi',
+            program = 'vidjil',
+            command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g:IGH,IGK,IGL,TRA,TRB,TRG,TRD -i -e 1 -d -w 50 ',
+            fuse_command = '-t 100',
+            info = 'multi-locus, only complete recombinations'
+        )
+        db.config.insert(
+            name = 'TRG',
+            program = 'vidjil',
+            command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g:TRG ',
+            fuse_command = '-t 100',
+            info = 'TRG, VgJg'
+        )
+        db.config.insert(
+            name = 'IGH',
+            program = 'vidjil',
+            command = '-c clones -w 60 -d -3 -z 100 -r 1 -g germline/homo-sapiens.g:IGH ',
+            fuse_command = '-t 100',
+            info = 'IGH, Vh(Dh)Jh'
+        )
+
+        ## permission
+        ## system admin have admin/read/create rights on all patients, groups and configs
+        auth.add_permission(id_admin_group, PermissionEnum.access.value, db.sample_set, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.access.value, db.patient, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.access.value, db.run, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.access.value, db.generic, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.access.value, db.config, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.access.value, db.pre_process, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.access.value, db.auth_group, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.sample_set, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.patient, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.generic, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.run, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.admin_group.value, db.auth_group, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.admin_config.value, db.config, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.admin_pre_process.value, db.pre_process, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.read.value, db.sample_set, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.read.value, db.patient, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.read.value, db.run, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.read.value, db.generic, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.read_group.value, db.auth_group, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.read_config.value, db.config, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.read_pre_process.value, db.pre_process, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.create.value, db.sample_set, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.create_group.value, db.auth_group, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.create_config.value, db.config, 0)
+        auth.add_permission(id_admin_group, PermissionEnum.create_pre_process.value, db.pre_process, 0)
+        auth.add_permission(id_admin_group, 'impersonate', db.auth_user, 0)