diff options
Diffstat (limited to 'wqflask/wqflask/collect.py')
| -rw-r--r-- | wqflask/wqflask/collect.py | 393 |
1 files changed, 117 insertions, 276 deletions
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index ba555094..fa6e03b4 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -8,7 +8,6 @@ import time import uuid import hashlib -import hmac import base64 import urlparse @@ -28,214 +27,70 @@ from pprint import pformat as pf from wqflask.database import db_session from wqflask import model -from wqflask import user_manager -from utility import Bunch, Struct +from utility import Bunch, Struct, hmac from utility.formatting import numify from base import trait from base.data_set import create_dataset -def get_collection(): - if g.user_session.logged_in: - return UserCollection() - else: - return AnonCollection() - #else: - # CauseError - -class AnonCollection(object): - """User is not logged in""" - def __init__(self, collection_name): - anon_user = user_manager.AnonUser() - self.key = anon_user.key - self.name = collection_name - self.id = None - self.created_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') - self.changed_timestamp = self.created_timestamp #ZS: will be updated when changes are made - - #ZS: Find id and set it if the collection doesn't already exist - if Redis.get(self.key) == "None" or Redis.get(self.key) == None: - Redis.set(self.key, None) #ZS: For some reason I get the error "Operation against a key holding the wrong kind of value" if I don't do this - else: - collections_list = json.loads(Redis.get(self.key)) - collection_position = 0 #ZS: Position of collection in collection_list, if it exists - collection_exists = False - for i, collection in enumerate(collections_list): - if collection['name'] == self.name: - collection_position = i - collection_exists = True - self.id = collection['id'] - break - - if self.id == None: - self.id = str(uuid.uuid4()) - - def get_members(self): - traits = [] - collections_list = json.loads(Redis.get(self.key)) - for collection in collections_list: - if collection['id'] == self.id: - traits = collection['members'] - return traits - - @property - def num_members(self): - num_members = 0 - collections_list = json.loads(Redis.get(self.key)) - for collection in collections_list: - if collection['id'] == self.id: - num_members = collection['num_members'] - return num_members - - def add_traits(self, params): - #assert collection_name == "Default", "Unexpected collection name for anonymous user" - self.traits = list(process_traits(params['traits'])) - #len_before = len(Redis.smembers(self.key)) - existing_collections = Redis.get(self.key) - print("existing_collections:", existing_collections) - if existing_collections != None and existing_collections != "None": - collections_list = json.loads(existing_collections) - collection_position = 0 #ZS: Position of collection in collection_list, if it exists - collection_exists = False - for i, collection in enumerate(collections_list): - if collection['id'] == self.id: - collection_position = i - collection_exists = True - break - if collection_exists: - collections_list[collection_position]['members'].extend(self.traits) - collections_list[collection_position]['num_members'] = len(collections_list[collection_position]['members']) - collections_list[collection_position]['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') - else: - collection_dict = {"id" : self.id, - "name" : self.name, - "created_timestamp" : self.created_timestamp, - "changed_timestamp" : self.changed_timestamp, - "num_members" : len(self.traits), - "members" : self.traits} - collections_list.append(collection_dict) - else: - collections_list = [] - collection_dict = {"id" : self.id, - "name" : self.name, - "created_timestamp" : self.created_timestamp, - "changed_timestamp" : self.changed_timestamp, - "num_members" : len(self.traits), - "members" : self.traits} - collections_list.append(collection_dict) - - Redis.set(self.key, json.dumps(collections_list)) - #Redis.sadd(self.key, *list(traits)) - #Redis.expire(self.key, 60 * 60 * 24 * 5) - #len_now = len(Redis.smembers(self.key)) - #report_change(len_before, len_now) - - def remove_traits(self, params): - traits_to_remove = [(":").join(trait.split(":")[:2]) for trait in params.getlist('traits[]')] - existing_collections = Redis.get(self.key) - collection_position = 0 - collections_list = json.loads(existing_collections) - for i, collection in enumerate(collections_list): - if collection['id'] == self.id: - collection_position = i - collection_exists = True - break - collections_list[collection_position]['members'] = [trait for trait in collections_list[collection_position]['members'] if trait not in traits_to_remove] - collections_list[collection_position]['num_members'] = len(collections_list[collection_position]['members']) - collections_list[collection_position]['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') - len_now = collections_list[collection_position]['num_members'] - #print("before in redis:", json.loads(Redis.get(self.key))) - Redis.set(self.key, json.dumps(collections_list)) - #print("currently in redis:", json.loads(Redis.get(self.key))) - - # We need to return something so we'll return this...maybe in the future - # we can use it to check the results - return str(len_now) - - -class UserCollection(object): - """User is logged in""" - - def add_traits(self, params, collection_name): - print("---> params are:", params.keys()) - print(" type(params):", type(params)) - if collection_name=="Default": - uc = g.user_session.user_ob.get_collection_by_name("Default") - # Doesn't exist so we'll create it - if not uc: - return create_new("Default") - else: - uc = model.UserCollection.query.get(params['existing_collection'].split(":")[0]) - members = list(uc.members_as_set()) #set(json.loads(uc.members)) - len_before = len(members) - - traits = process_traits(params['traits']) - - members_now = members - for trait in traits: - if trait in members: - continue - else: - members_now.append(trait) - - #members_now = list(members | traits) - len_now = len(members_now) - uc.members = json.dumps(members_now) - - uc.changed_timestamp = datetime.datetime.utcnow() - - db_session.commit() - - print("added to existing, now set is:" + str(uc.members)) - report_change(len_before, len_now) - - # Probably have to change that - return redirect(url_for('view_collection', uc_id=uc.id)) +import logging +from utility.logger import getLogger +logger = getLogger(__name__) def process_traits(unprocessed_traits): - #print("unprocessed_traits are:", unprocessed_traits) if isinstance(unprocessed_traits, basestring): unprocessed_traits = unprocessed_traits.split(",") traits = set() for trait in unprocessed_traits: - #print("trait is:", trait) - data, _separator, hmac = trait.rpartition(':') + data, _separator, the_hmac = trait.rpartition(':') data = data.strip() - assert hmac==user_manager.actual_hmac_creation(data), "Data tampering?" - traits.add (str(data)) + if g.user_session.logged_in: + assert the_hmac == hmac.hmac_creation(data), "Data tampering?" + traits.add(str(data)) + return traits def report_change(len_before, len_now): new_length = len_now - len_before if new_length: - print("We've added {} to your collection.".format( - numify(new_length, 'new trait', 'new traits'))) flash("We've added {} to your collection.".format( numify(new_length, 'new trait', 'new traits'))) else: - print("No new traits were added.") + logger.debug("No new traits were added.") + +@app.route("/collections/store_trait_list", methods=('POST',)) +def store_traits_list(): + params = request.form + traits = params['traits'] + hash = params['hash'] + + Redis.set(hash, traits) + + return hash @app.route("/collections/add") def collections_add(): - traits=request.args['traits'] - if g.user_session.logged_in: - user_collections = g.user_session.user_ob.user_collections - print("user_collections are:", user_collections) + collections = g.user_session.user_collections + if len(collections) < 1: + collection_name = "Your Default Collection" + uc_id = g.user_session.add_collection(collection_name, set()) + collections = g.user_session.user_collections + + #ZS: One of these might be unnecessary + if 'traits' in request.args: + traits=request.args['traits'] return render_template("collections/add.html", - traits = traits, - collections = user_collections, - ) + traits = traits, + collections = collections, + ) else: - anon_collections = user_manager.AnonUser().get_collections() - collection_names = [] - for collection in anon_collections: - collection_names.append({'id':collection['id'], 'name':collection['name']}) + hash = request.args['hash'] return render_template("collections/add.html", - traits = traits, - collections = collection_names, + hash = hash, + collections = collections, ) @app.route("/collections/new") @@ -244,85 +99,70 @@ def collections_new(): if "sign_in" in params: return redirect(url_for('login')) - if "create_new" in params: - print("in create_new") collection_name = params['new_collection'] + if collection_name.strip() == "": + collection_name = datetime.datetime.utcnow().strftime('Collection_%b_%d_%H:%M') return create_new(collection_name) elif "add_to_existing" in params: - print("in add to existing") - collection_name = params['existing_collection'].split(":")[1] - if g.user_session.logged_in: - return UserCollection().add_traits(params, collection_name) + if 'existing_collection' not in params: + collections = g.user_session.user_collections + for collection in collections: + if collection["name"] == "Default Collection": + collection_id = collection["id"] + collection_name = collection["name"] + default_collection_exists = True + if not default_collection_exists: + return create_new("Your Default Collection") else: - ac = AnonCollection(collection_name) - ac.add_traits(params) - return redirect(url_for('view_collection', collection_id=ac.id)) + collection_id = params['existing_collection'].split(":")[0] + collection_name = params['existing_collection'].split(":")[1] + + if "hash" in params: + unprocessed_traits = Redis.get(params['hash']) + else: + unprocessed_traits = params['traits'] + traits = list(process_traits(unprocessed_traits)) + g.user_session.add_traits_to_collection(collection_id, traits) + return redirect(url_for('view_collection', uc_id=collection_id)) else: CauseAnError def create_new(collection_name): params = request.args - unprocessed_traits = params['traits'] + if "hash" in params: + unprocessed_traits = Redis.get(params['hash']) + Redis.delete(params['hash']) + else: + unprocessed_traits = params['traits'] + traits = process_traits(unprocessed_traits) - if g.user_session.logged_in: - uc = model.UserCollection() - uc.name = collection_name - print("user_session:", g.user_session.__dict__) - uc.user = g.user_session.user_id - uc.members = json.dumps(list(traits)) - db_session.add(uc) - db_session.commit() - return redirect(url_for('view_collection', uc_id=uc.id)) - else: - current_collections = user_manager.AnonUser().get_collections() - ac = AnonCollection(collection_name) - ac.changed_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') - ac.add_traits(params) - return redirect(url_for('view_collection', collection_id=ac.id)) + uc_id = g.user_session.add_collection(collection_name, traits) + + return redirect(url_for('view_collection', uc_id=uc_id)) @app.route("/collections/list") def list_collections(): params = request.args - print("PARAMS:", params) - if g.user_session.logged_in: - user_collections = list(g.user_session.user_ob.user_collections) - print("user_collections are:", user_collections) - return render_template("collections/list.html", - params = params, - collections = user_collections, - ) - else: - anon_collections = user_manager.AnonUser().get_collections() - print("anon_collections are:", anon_collections) - return render_template("collections/list.html", - params = params, - collections = anon_collections) + user_collections = list(g.user_session.user_collections) + return render_template("collections/list.html", + params = params, + collections = user_collections, + ) @app.route("/collections/remove", methods=('POST',)) def remove_traits(): params = request.form - print("params are:", params) - - if "uc_id" in params: - uc_id = params['uc_id'] - uc = model.UserCollection.query.get(uc_id) - traits_to_remove = params.getlist('traits[]') - traits_to_remove = process_traits(traits_to_remove) - print("\n\n after processing, traits_to_remove:", traits_to_remove) - all_traits = uc.members_as_set() - members_now = all_traits - traits_to_remove - print(" members_now:", members_now) - uc.members = json.dumps(list(members_now)) - uc.changed_timestamp = datetime.datetime.utcnow() - db_session.commit() - else: - collection_name = params['collection_name'] - members_now = AnonCollection(collection_name).remove_traits(params) + uc_id = params['uc_id'] + traits_to_remove = params.getlist('traits[]') + traits_to_remove = process_traits(traits_to_remove) + logger.debug("\n\n after processing, traits_to_remove:", traits_to_remove) + + members_now = g.user_session.remove_traits_from_collection(uc_id, traits_to_remove) # We need to return something so we'll return this...maybe in the future # we can use it to check the results @@ -332,20 +172,22 @@ def remove_traits(): @app.route("/collections/delete", methods=('POST',)) def delete_collection(): params = request.form - print("params:", params) - if g.user_session.logged_in: - uc_id = params['uc_id'] - uc = model.UserCollection.query.get(uc_id) - # Todo: For now having the id is good enough since it's so unique - # But might want to check ownership in the future - collection_name = uc.name - db_session.delete(uc) - db_session.commit() + uc_id = "" + + uc_id = params['uc_id'] + if len(uc_id.split(":")) > 1: + for this_uc_id in uc_id.split(":"): + collection_name = g.user_session.delete_collection(this_uc_id) else: - collection_name = params['collection_name'] - user_manager.AnonUser().delete_collection(collection_name) + collection_name = g.user_session.delete_collection(uc_id) - flash("We've deleted the collection: {}.".format(collection_name), "alert-info") + if uc_id != "": + if len(uc_id.split(":")) > 1: + flash("We've deleted the selected collections.", "alert-info") + else: + flash("We've deleted the collection: {}.".format(uc_id), "alert-info") + else: + flash("We've deleted the collection: {}.".format(collection_name), "alert-info") return redirect(url_for('list_collections')) @@ -353,47 +195,46 @@ def delete_collection(): @app.route("/collections/view") def view_collection(): params = request.args - print("PARAMS in view collection:", params) - if "uc_id" in params: - uc_id = params['uc_id'] - uc = model.UserCollection.query.get(uc_id) - traits = json.loads(uc.members) - else: - user_collections = json.loads(Redis.get(user_manager.AnonUser().key)) - this_collection = {} - for collection in user_collections: - if collection['id'] == params['collection_id']: - this_collection = collection - break - #this_collection = user_collections[params['collection_id']] - traits = this_collection['members'] - - print("in view_collection traits are:", traits) + uc_id = params['uc_id'] + uc = (collection for collection in g.user_session.user_collections if collection["id"] == uc_id).next() + traits = uc["members"] trait_obs = [] json_version = [] for atrait in traits: name, dataset_name = atrait.split(':') - dataset = create_dataset(dataset_name) - - trait_ob = trait.GeneralTrait(name=name, dataset=dataset) - trait_ob = trait.retrieve_trait_info(trait_ob, dataset, get_qtl_info=True) + if dataset_name == "Temp": + group = name.split("_")[2] + dataset = create_dataset(dataset_name, dataset_type = "Temp", group_name = group) + trait_ob = trait.GeneralTrait(name=name, dataset=dataset) + else: + dataset = create_dataset(dataset_name) + trait_ob = trait.GeneralTrait(name=name, dataset=dataset) + trait_ob = trait.retrieve_trait_info(trait_ob, dataset, get_qtl_info=True) trait_obs.append(trait_ob) - json_version.append(trait.jsonable(trait_ob, dataset_name)) + json_version.append(trait.jsonable(trait_ob)) + + collection_info = dict(trait_obs=trait_obs, + uc = uc) - if "uc_id" in params: - collection_info = dict(trait_obs=trait_obs, - uc = uc) - else: - collection_info = dict(trait_obs=trait_obs, - collection_name=this_collection['name']) if "json" in params: - print("json_version:", json_version) return json.dumps(json_version) else: return render_template("collections/view.html", **collection_info ) + +@app.route("/collections/change_name", methods=('POST',)) +def change_collection_name(): + params = request.form + + collection_id = params['collection_id'] + new_name = params['new_name'] + + g.user_session.change_collection_name(collection_id, new_name) + + return new_name + |