--- a/.hgignore	Fri Dec 12 16:45:47 2014 +0100
+++ b/.hgignore	Tue Dec 16 11:14:55 2014 +0100
@@ -2,5 +2,5 @@
 dev/.vagrant/
 files/
 *.pyc
-src\catedit\config.py
-src/catedit/log/
\ No newline at end of file
+src/catedit/config.py
+src/catedit/log/

--- a/src/catedit/__init__.py	Fri Dec 12 16:45:47 2014 +0100
+++ b/src/catedit/__init__.py	Tue Dec 16 11:14:55 2014 +0100
@@ -0,0 +1,35 @@
+from flask import Flask, session
+from flask.ext.github import GitHub
+from flask.ext.cache import Cache
+from settings import *
+from config import *
+from logging import *
+
+# set up app and database
+app = Flask(__name__)
+app.config.from_object(appSettings)
+cache = Cache(app, config={"CACHE_TYPE": "simple"})
+app.config.from_object(appConfig)
+
+github = GitHub(app)
+
+# set up logging
+if app.config["LOGGING"]:
+    file_handler = FileHandler(filename=app.config["LOG_FILE_PATH"])
+    file_handler.setFormatter(Formatter('''
+    Message type:       %(levelname)s
+    Location:           %(pathname)s:%(lineno)d
+    Module:             %(module)s
+    Function:           %(funcName)s
+    Time:               %(asctime)s
+
+    Message:
+
+    %(message)s
+    '''))
+    app.logger.addHandler(file_handler)
+    app.logger.setLevel(app.config["LOGGING_LEVEL"])
+
+# session management
+
+app.secret_key = "extremely_secure_and_very_secret_key"

--- a/src/catedit/api.py	Fri Dec 12 16:45:47 2014 +0100
+++ b/src/catedit/api.py	Tue Dec 16 11:14:55 2014 +0100
@@ -1,6 +1,6 @@
 from flask.ext.restful import Resource, fields, Api, reqparse
 from flask import request
-from app import app, cache
+from catedit import app, cache
 from models import Category, CategoryManager
 from rdflib import Graph, RDF
 from utils import *
@@ -8,7 +8,9 @@
 from config import *
 import os
 
+
 api = Api(app)
+logger = app.logger
 
 cat_parser = reqparse.RequestParser()
 cat_parser.add_argument('label', type=str)
@@ -41,29 +43,30 @@
         cat_manager_instance = CategoryManager()
 
         new_property_list = []
-        # print args["property_predicate"]
-        # print args["property_object"]
+
+        logger.debug(args["property_predicate"])
+        logger.debug(args["property_object"])
         for property_predicate, property_object in zip(
                 args["property_predicate"],
                 args["property_object"]):
             if property_object:
                 property_object_to_append = property_object
                 # if URIRef category, we must prefix id with namespace
-                if app.config["PROPERTY_LIST"] \
-                             [property_predicate] \
-                             ["object_type"] == "uriref-category" :
-                    property_object_to_append = app.config["ONTOLOGY_NAMESPACE"] \
-                                                + property_object
-                    # print property_object_to_append
+                if (app.config["PROPERTY_LIST"]
+                              [property_predicate]
+                              ["object_type"]) == "uriref-category":
+                    property_object_to_append = \
+                        app.config["ONTOLOGY_NAMESPACE"] + property_object
+                    logger.debug(property_object_to_append)
                 new_property_list.append((property_predicate,
                                           property_object_to_append))
-        # print new_property_list
+        logger.debug(new_property_list)
         c = cat_manager_instance.load_cat(cat_id)
         c.edit_category(new_description=args["description"],
                         new_label=args["label"],
                         new_other_properties=new_property_list)
         cat_manager_instance.save_cat(c, message=args["commit_message"])
-        # print "put id: "+c.cat_id
+        logger.debug("put id: "+c.cat_id)
         cache.clear()
         return c.cat_graph.serialize(format='turtle'), 200
         # Maybe not send the whole cat back, see if it's worth it
@@ -72,28 +75,28 @@
     def post(self):
         args = cat_parser.parse_args()
         property_list = []
-        # print args["property_predicate"]
-        # print args["property_object"]
+        logger.debug(args["property_predicate"])
+        logger.debug(args["property_object"])
         for property_predicate, property_object in zip(
                 request.form.getlist('property_predicate'),
                 request.form.getlist('property_object')):
             if property_object:
-                if app.config["PROPERTY_LIST"] \
-                             [property_predicate] \
-                             ["object_type"] == "uriref-category":
+                if (app.config["PROPERTY_LIST"]
+                              [property_predicate]
+                              ["object_type"]) == "uriref-category":
                     property_list.append((property_predicate,
                                           app.config["ONTOLOGY_NAMESPACE"]
-                                          +property_object))
+                                          + property_object))
                 else:
                     property_list.append((property_predicate,
                                           property_object))
-        # print property_list
+        logger.debug(property_list)
         c = Category(label=args["label"],
                      description=args["description"],
                      other_properties=property_list)
         cat_manager_instance = CategoryManager()
         cat_manager_instance.save_cat(c, message=args["commit_message"])
-        # print "post id: "+c.cat_id
+        logger.debug("post id: "+c.cat_id)
         cache.clear()
         return c.cat_graph.serialize(format='turtle'), 201
 
@@ -105,7 +108,7 @@
         else:
             message = request.form["delete_message"]
         cat_manager_instance.delete_cat(cat_id, message=message)
-        # print "delete id: "+cat_id
+        logger.debug("delete id: "+cat_id)
         cache.clear()
         return 204
 

--- a/src/catedit/app.py	Fri Dec 12 16:45:47 2014 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-from flask import Flask, session
-from flask.ext.github import GitHub
-from flask.ext.cache import Cache
-from settings import *
-from config import *
-from logging import *
-
-# set up app and database
-app = Flask(__name__)
-app.config.from_object(appSettings)
-cache = Cache(app, config={"CACHE_TYPE": "simple"})
-app.config.from_object(appConfig)
-
-github = GitHub(app)
-
-# set up logging
-if app.config["LOGGING"]:
-    file_handler = FileHandler(filename=app.config["LOG_FILE_PATH"])
-    file_handler.setFormatter(Formatter('''
-    Message type:       %(levelname)s
-    Location:           %(pathname)s:%(lineno)d
-    Module:             %(module)s
-    Function:           %(funcName)s
-    Time:               %(asctime)s
-
-    Message:
-
-    %(message)s
-    '''))
-    app.logger.addHandler(file_handler)
-    app.logger.setLevel(app.config["LOGGING_LEVEL"])
-
-# session management
-
-app.secret_key = "extremely_secure_and_very_secret_key"

--- a/src/catedit/main.py	Fri Dec 12 16:45:47 2014 +0100
+++ b/src/catedit/main.py	Tue Dec 16 11:14:55 2014 +0100
@@ -1,4 +1,4 @@
-from app import app
+from catedit import app
 
 from api import api
 from models import *

--- a/src/catedit/models.py	Fri Dec 12 16:45:47 2014 +0100
+++ b/src/catedit/models.py	Tue Dec 16 11:14:55 2014 +0100
@@ -2,10 +2,12 @@
 from flask.ext.restful import fields
 from rdflib import Graph, RDF, RDFS, BNode, Literal, URIRef
 from uuid import uuid4
-from StringIO import StringIO
-from app import *
+from io import StringIO
 from slugify import slugify
 import persistence
+from catedit import app
+
+logger = app.logger
 
 """
 Namespace: ld.iri-research.org/ontology/categorisation/#
@@ -24,9 +26,10 @@
                  other_properties=None, graph=None):
         if not(graph):
             # cat_id = uuid4().hex - Alternate method of generating ids
-            cat_id = "category_id_"+slugify(label)
+            cat_id = "category_id_"+slugify(bytes(label))
             self.cat_graph = Graph()
-            self.this_category = URIRef(app.config["ONTOLOGY_NAMESPACE"]+cat_id)
+            self.this_category = URIRef(app.config["ONTOLOGY_NAMESPACE"] +
+                                        cat_id)
             self.cat_graph.add((self.this_category, RDF.ID, Literal(cat_id)))
 
             if label:
@@ -64,7 +67,8 @@
 
     @property
     def description(self):
-        return_value = self.cat_graph.value(self.this_category, RDF.Description)
+        return_value = \
+            self.cat_graph.value(self.this_category, RDF.Description)
         if return_value is None:
             return None
         else:
@@ -119,22 +123,22 @@
         (can be [] so it deletes everything)
         """
         if new_other_properties is not False or \
-           (new_other_properties is None and \
-           self.properties is not None):
-            # print "before suppressing properties: "
-            # print self.properties
-            # print "will replace with: "
-            # print new_other_properties
+            (new_other_properties is None and
+             self.properties is not None):
+            logger.debug("before suppressing properties: ")
+            logger.debug(self.properties)
+            logger.debug("will replace with: ")
+            logger.debug(new_other_properties)
             for key in app.config["PROPERTY_LIST"]:
                 self.cat_graph.remove((self.this_category,
                                        app.config["PROPERTY_LIST"]
                                                  [key]
                                                  ["rdflib_class"],
                                        None))
-            # print "now properties are: "
-            # print self.properties
-            # print "making new properties: "
-            # print new_other_properties
+            logger.debug("now properties are: ")
+            logger.debug(self.properties)
+            logger.debug("making new properties: ")
+            logger.debug(new_other_properties)
             for (predicate, obj) in new_other_properties:
                 self.cat_graph.add((self.this_category,
                                     app.config["PROPERTY_LIST"]
@@ -174,24 +178,35 @@
             if cat.cat_id != app.config["ONTOLOGY_NAMESPACE"]+deleted_cat_id:
                 new_property_list_for_cat = []
                 for (predicate, obj) in cat.properties:
-                    if not ((app.config["PROPERTY_LIST"]
-                                       [predicate]
-                                       ["object_type"] == "uriref-category") and
-                            (obj == app.config["ONTOLOGY_NAMESPACE"]+deleted_cat_id)):
+                    if not (
+                        (app.config["PROPERTY_LIST"]
+                                   [predicate]
+                                   ["object_type"] == "uriref-category") and
+                        (obj == (app.config["ONTOLOGY_NAMESPACE"] +
+                                 deleted_cat_id))
+                    ):
                         new_property_list_for_cat.append((predicate, obj))
-                cat.edit_category(new_other_properties=new_property_list_for_cat)
-                self.save_cat(cat, message=message+", cleaning up other properties")
+                cat.edit_category(
+                    new_other_properties=new_property_list_for_cat
+                )
+                self.save_cat(
+                    cat,
+                    message=message+", cleaning up other properties"
+                )
         p = getattr(persistence, app.config["PERSISTENCE_METHOD"])()
         p.delete(name=deleted_cat_id, message=message)
 
     def list_cat(self):
         p = getattr(persistence, app.config["PERSISTENCE_METHOD"])()
         cat_serial_list = p.list()
-        # print cat_serial_list
+        logger.debug(cat_serial_list)
         cat_list = []
         for cat_serial in cat_serial_list:
             loaded_cat_graph = Graph()
-            loaded_cat_graph.parse(source=StringIO(cat_serial), format='turtle')
+            loaded_cat_graph.parse(
+                source=StringIO(cat_serial),
+                format='turtle'
+            )
             c = Category(graph=loaded_cat_graph)
             cat_list.append(c)
         return cat_list

--- a/src/catedit/persistence.py	Fri Dec 12 16:45:47 2014 +0100
+++ b/src/catedit/persistence.py	Tue Dec 16 11:14:55 2014 +0100
@@ -1,6 +1,5 @@
-from flask.ext.github import GitHubError
 from abc import ABCMeta, abstractmethod
-from app import app, github, session
+from catedit import app
 from base64 import b64encode, b64decode
 import os
 import json
@@ -39,13 +38,13 @@
 class PersistenceToFile(Persistence):
     def save(self, **kwargs):
         path_to_save = app.config["FILE_SAVE_DIRECTORY"]+kwargs["name"]
-        file = open(path_to_save, 'w+')
+        file = open(path_to_save, 'wb')
         file.write(kwargs["content"])
         file.close()
 
     def load(self, **kwargs):
         path_to_load = app.config["FILE_SAVE_DIRECTORY"]+kwargs["name"]
-        file = open(path_to_load, 'r')
+        file = open(path_to_load, 'rb')
         file_content = file.read()
         file.close()
         return file_content
@@ -58,17 +57,19 @@
     def list(self, **kwargs):
         file_content_list = []
         for file_name in os.listdir(app.config["FILE_SAVE_DIRECTORY"]):
+            if not file_name or file_name[0] == ".":
+                continue
             file = open(app.config["FILE_SAVE_DIRECTORY"]+file_name)
             file_content = file.read()
-            file.close
+            file.close()
             file_content_list.append(file_content)
-        # print file_content_list
+        # logger.debug(file_content_list)
         return file_content_list
 
 
 class PersistenceToGithub(Persistence):
     def save(self, **kwargs):
-        # print kwargs["content"]
+        # logger.debug(kwargs["content"])
         request_data = {"content": b64encode(kwargs["content"]),
                         "message": kwargs["message"]}
         try:
@@ -81,7 +82,7 @@
             request_data["sha"] = filedict["sha"]
         except GitHubError:
             pass
-        # print json.dumps(request_data)
+        # logger.debug(json.dumps(request_data))
         try:
             github.request('PUT',
                            "repos/"
@@ -139,7 +140,7 @@
                                        + "/contents/"
                                        + app.config["CATEGORIES_PATH"])
             filenames_list = [file["name"] for file in files_in_repo]
-            # print filenames_list
+            # logger.debug(filenames_list)
         except GitHubError:
             pass
         file_content_list = []
@@ -154,5 +155,5 @@
                 file_content_list.append(b64decode(filedict["content"]))
             except GitHubError:
                 pass
-        # print file_content_list
+        # logger.debug(file_content_list)
         return file_content_list

--- a/src/catedit/settings.py	Fri Dec 12 16:45:47 2014 +0100
+++ b/src/catedit/settings.py	Tue Dec 16 11:14:55 2014 +0100
@@ -1,4 +1,4 @@
-from rdflib import *
+from rdflib import URIRef, RDF, RDFS, Literal
 from rdflib.namespace import SKOS
 
 
@@ -21,10 +21,10 @@
     CATEGORY_NAMESPACE = "http://ld.iri-research.org/categorisation/category/"
 
     # Saving file for local persistence
-    FILE_SAVE_DIRECTORY = "../../files/"
+    FILE_SAVE_DIRECTORY = "../../run/files/"
 
     # Logging config
-    LOG_FILE_PATH = "log/log.txt"
+    LOG_FILE_PATH = "../../run/log/log.txt"
     LOGGING = False
 
     # Github repository config
@@ -80,4 +80,4 @@
 
     # Category persistence parameters
 
-    PERSISTENCE_METHOD = "PersistenceToGithub"
+    PERSISTENCE_METHOD = "PersistenceToFile"

--- a/src/catedit/utils.py	Fri Dec 12 16:45:47 2014 +0100
+++ b/src/catedit/utils.py	Tue Dec 16 11:14:55 2014 +0100
@@ -3,15 +3,19 @@
 from rdflib.compare import *
 
 '''
-    This function will compare two categories from their Graph object serializations
+    This function will compare two categories from their Graph object
+    serializations.
     Exact return values are to be defined, some ideas
     * check if the 2 categories are the same? (same ID, isomorphic)
-    * check if the 2 categories are the same but different version? (same ID, not isomorphic)
-    * check if unique, non empty parameters changed and list them (label and description)
+    * check if the 2 categories are the same but different version?
+      (same ID, not isomorphic)
+    * check if unique, non empty parameters changed and list them
+      (label and description)
     * returns 2 lists of properties: only_in_first, only_in_second
     * more?
 '''
 
+
 def compare_two_cat(cat_serial_1, cat_serial_2):
     cat1 = Category(cat_serial_1)
     cat2 = Category(cat_serial_2)

--- a/src/catedit/views.py	Fri Dec 12 16:45:47 2014 +0100
+++ b/src/catedit/views.py	Tue Dec 16 11:14:55 2014 +0100
@@ -1,4 +1,4 @@
-from app import app, github
+from catedit import app, github
 from models import Category, CategoryManager
 from flask import render_template, request, redirect, url_for, session
 from flask.ext.github import GitHubError
@@ -7,13 +7,23 @@
 from wtforms import StringField, TextAreaField
 from wtforms.validators import DataRequired
 from rdflib import Graph
-from StringIO import StringIO
+from io import StringIO
 
+logger = app.logger
 
 class NewCategoryMinimalForm(Form):
-    label = StringField("Nom de la categorie (obligatoire)", validators=[DataRequired()])
-    description = TextAreaField("Description de la categorie (obligatoire)", validators=[DataRequired()])
-    commit_message = StringField("Message de soumission (Obligatoire)", validators=[DataRequired()])
+    label = StringField(
+        "Nom de la categorie (obligatoire)",
+        validators=[DataRequired()]
+        )
+    description = TextAreaField(
+        "Description de la categorie (obligatoire)",
+        validators=[DataRequired()]
+        )
+    commit_message = StringField(
+        "Message de soumission (Obligatoire)",
+        validators=[DataRequired()]
+        )
 
 
 @app.route('/', methods=['GET'])
@@ -24,9 +34,9 @@
     # list categories
     if delete_cat_id is None:
         serialized_cat_list = cat_api_instance.get()
-        # print serialized_cat_list
+        logger.debug(serialized_cat_list)
         cat_list = []
-        # print cat_list
+        logger.debug(cat_list)
         for serialized_cat in serialized_cat_list:
             cat_rdf_graph = Graph()
             cat_rdf_graph.parse(source=StringIO(serialized_cat),
@@ -37,7 +47,7 @@
                              "cat_description": c.description,
                              "cat_id": c.cat_id,
                              "cat_properties": c.properties})
-            # print c.properties
+            logger.debug(c.properties)
         return render_template('catrecap.html',
                                cat_list=cat_list)
     else:
@@ -81,7 +91,7 @@
                 TextAreaField("Description de la categorie",
                               validators=[DataRequired()],
                               default=c.description))
-        # print "CatForm fields preset to "+c.label+" and "+c.description
+        logger.debug("CatForm fields preset to "+c.label+" and "+c.description)
 
         cat_form = NewCategoryMinimalForm(request.form)
 
@@ -147,25 +157,25 @@
     try:
         repoList = []
         repoList = github.get("user/repos")
-        # for repo in repoList:
-        #     print repo["name"]
+        for repo in repoList:
+            logger.debug(repo["name"])
         session["user_can_edit"] = True
-        if not any (repo["name"] == app.config["REPOSITORY_NAME"]
-                    for repo in repoList):
+        if not any(repo["name"] == app.config["REPOSITORY_NAME"]
+                   for repo in repoList):
             session["user_can_edit"] = False
-        # print session["user_can_edit"]
+        logger.debug(session["user_can_edit"])
     except GitHubError:
-        # print "error getting repos!"
+        logger.debug("error getting repos!")
         pass
 
-    # print session["user_login"]
+    logger.debug(session["user_login"])
     return redirect(url_for('cat_recap'))
 
 
 @github.access_token_getter
 def token_getter():
     if session.get("user_logged", None):
-        print "I made an authentified request"
+        logger.debug("I made an authentified request")
         return session["user_code"]