diff options
Diffstat (limited to 'wqflask/wqflask/collect.py')
| -rw-r--r-- | wqflask/wqflask/collect.py | 132 |
1 files changed, 68 insertions, 64 deletions
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index b22e0004..76ef5ca4 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -1,56 +1,47 @@ -from __future__ import print_function, division, absolute_import - - -import os import hashlib import datetime -import time - -import uuid -import hashlib -import base64 - -import urlparse - import simplejson as json -import redis -Redis = redis.StrictRedis() - -from flask import (Flask, g, render_template, url_for, request, make_response, - redirect, flash, jsonify) +from flask import g +from flask import render_template +from flask import url_for +from flask import request +from flask import redirect +from flask import flash from wqflask import app - -from pprint import pformat as pf - -from wqflask.database import db_session - -from wqflask import model - -from utility import Bunch, Struct, hmac +from utility import hmac from utility.formatting import numify +from utility.tools import GN_SERVER_URL +from utility.redis_tools import get_redis_conn -from base import trait +from base.trait import create_trait +from base.trait import retrieve_trait_info +from base.trait import jsonable from base.data_set import create_dataset -import logging from utility.logger import getLogger + logger = getLogger(__name__) +Redis = get_redis_conn() + def process_traits(unprocessed_traits): - if isinstance(unprocessed_traits, basestring): + if isinstance(unprocessed_traits, bytes): + unprocessed_traits = unprocessed_traits.decode('utf-8').split(",") + else: # It's a string unprocessed_traits = unprocessed_traits.split(",") traits = set() for trait in unprocessed_traits: data, _separator, the_hmac = trait.rpartition(':') data = data.strip() if g.user_session.logged_in: - assert the_hmac == hmac.hmac_creation(data), "Data tampering?" + 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: @@ -59,16 +50,18 @@ def report_change(len_before, len_now): else: logger.debug("No new traits were added.") + @app.route("/collections/store_trait_list", methods=('POST',)) def store_traits_list(): - params = request.form + params = request.form - traits = params['traits'] - hash = params['hash'] + traits = params['traits'] + hash = params['hash'] - Redis.set(hash, traits) + Redis.set(hash, traits) + + return hash - return hash @app.route("/collections/add") def collections_add(): @@ -79,19 +72,20 @@ def collections_add(): uc_id = g.user_session.add_collection(collection_name, set()) collections = g.user_session.user_collections - #ZS: One of these might be unnecessary + # ZS: One of these might be unnecessary if 'traits' in request.args: - traits=request.args['traits'] + traits = request.args['traits'] return render_template("collections/add.html", - traits = traits, - collections = collections, - ) + traits=traits, + collections=collections, + ) else: hash = request.args['hash'] return render_template("collections/add.html", - hash = hash, - collections = collections, - ) + hash=hash, + collections=collections, + ) + @app.route("/collections/new") def collections_new(): @@ -126,7 +120,9 @@ def collections_new(): g.user_session.add_traits_to_collection(collection_id, traits) return redirect(url_for('view_collection', uc_id=collection_id)) else: - CauseAnError + # CauseAnError + pass + def create_new(collection_name): params = request.args @@ -143,30 +139,30 @@ def create_new(collection_name): return redirect(url_for('view_collection', uc_id=uc_id)) + @app.route("/collections/list") def list_collections(): params = request.args user_collections = list(g.user_session.user_collections) return render_template("collections/list.html", - params = params, - collections = user_collections, - ) + params=params, + collections=user_collections, + ) + @app.route("/collections/remove", methods=('POST',)) def remove_traits(): params = request.form uc_id = params['uc_id'] - traits_to_remove = params.getlist('traits[]') + traits_to_remove = params['trait_list'] 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) + 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 - return str(len(members_now)) + return redirect(url_for("view_collection", uc_id=uc_id)) @app.route("/collections/delete", methods=('POST',)) @@ -187,7 +183,8 @@ def delete_collection(): else: flash("We've deleted the selected collection.", "alert-info") else: - flash("We've deleted the collection: {}.".format(collection_name), "alert-info") + flash("We've deleted the collection: {}.".format( + collection_name), "alert-info") return redirect(url_for('list_collections')) @@ -197,35 +194,43 @@ def view_collection(): params = request.args uc_id = params['uc_id'] - uc = (collection for collection in g.user_session.user_collections if collection["id"] == uc_id).next() + uc = next( + (collection for collection in g.user_session.user_collections if collection["id"] == uc_id)) traits = uc["members"] trait_obs = [] json_version = [] for atrait in traits: + if ':' not in atrait: + continue name, dataset_name = atrait.split(':') 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) + dataset = create_dataset( + dataset_name, dataset_type="Temp", group_name=group) + trait_ob = create_trait(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_ob = create_trait(name=name, dataset=dataset) + trait_ob = retrieve_trait_info( + trait_ob, dataset, get_qtl_info=True) trait_obs.append(trait_ob) - json_version.append(trait.jsonable(trait_ob)) + json_version.append(jsonable(trait_ob)) - collection_info = dict(trait_obs=trait_obs, - uc = uc) + collection_info = dict( + trait_obs=trait_obs, + uc=uc, + heatmap_data_url=f"{GN_SERVER_URL}heatmaps/clustered") if "json" in params: return json.dumps(json_version) else: return render_template("collections/view.html", - **collection_info - ) + **collection_info + ) + @app.route("/collections/change_name", methods=('POST',)) def change_collection_name(): @@ -237,4 +242,3 @@ def change_collection_name(): g.user_session.change_collection_name(collection_id, new_name) return new_name - |