Coverage for application/utils.py : 51%

from datetime import datetime 

import json 

import logging 

from pathlib import Path 

import shutil 

import sys 

import tempfile 

from xml.etree import ElementTree 

import cophi 

import flask 

import numpy as np 

import pandas as pd 

from werkzeug.utils import secure_filename 

from application import database 

TEMPDIR = tempfile.gettempdir() 

DATABASE = Path(TEMPDIR, "topicsexplorer.db") 

LOGFILE = Path(TEMPDIR, "topicsexplorer.log") 

DATA_EXPORT = Path(TEMPDIR, "topicsexplorer-data") 

def init_app(name): 

"""Initialize Flask application. 

""" 

logging.debug("Initializing flask app...") 

if getattr(sys, "frozen", False): 

logging.debug("Application is frozen.") 

root = Path(sys._MEIPASS) 

else: 

logging.debug("Application is not frozen.") 

root = Path("application") 

app = flask.Flask(name, 

template_folder=str(Path(root, "templates")), 

static_folder=str(Path(root, "static"))) 

return app 

def init_logging(level): 

"""Initialize logging. 

""" 

logging.basicConfig(level=level, 

format="%(message)s", 

filename=str(LOGFILE), 

filemode="w") 

# Disable logging for Flask and Werkzeug: 

logging.getLogger("flask").setLevel(logging.ERROR) 

logging.getLogger("werkzeug").setLevel(logging.ERROR) 

def init_db(app): 

"""Initialize SQLite database. 

""" 

logging.debug("Initializing database...") 

db = database.get_db() 

with app.open_resource("schema.sql") as schemafile: 

schema = schemafile.read().decode("utf-8") 

db.executescript(schema) 

db.commit() 

database.close_db() 

def format_logging(message): 

"""Format log messages. 

""" 

if "n_documents" in message: 

n = message.split("n_documents: ")[1] 

return "Number of documents: {}".format(n) 

elif "vocab_size" in message: 

n = message.split("vocab_size: ")[1] 

return "Number of types: {}".format(n) 

elif "n_words" in message: 

n = message.split("n_words: ")[1] 

return "Number of tokens: {}".format(n) 

elif "n_topics" in message: 

n = message.split("n_topics: ")[1] 

return "Number of topics: {}".format(n) 

elif "n_iter" in message: 

return "Initializing topic model..." 

elif "log likelihood" in message: 

iteration, _ = message.split("> log likelihood: ") 

return "Iteration {}".format(iteration[1:]) 

else: 

return message 

def load_textfile(textfile): 

"""Load text file, return title and content. 

""" 

filename = Path(secure_filename(textfile.filename)) 

title = filename.stem 

suffix = filename.suffix 

content = textfile.read().decode("utf-8") 

if suffix in {".xml", ".html"}: 

content = remove_markup(content) 

return title, content 

def remove_markup(text): 

"""Parse XML and drop tags. 

""" 

logging.info("Removing markup...") 

tree = ElementTree.fromstring(text) 

plaintext = ElementTree.tostring(tree, 

encoding="utf8", 

method="text") 

return plaintext.decode("utf-8") 

def get_documents(textfiles): 

"""Get Document objects. 

""" 

logging.info("Fetching documents...") 

for textfile in textfiles: 

title, content = textfile 

yield cophi.model.Document(content, title) 

def get_stopwords(data, corpus): 

"""Get stopwords from file or corpus. 

""" 

logging.info("Fetching stopwords...") 

if "stopwords" in data: 

_, stopwords = load_textfile(data["stopwords"]) 

stopwords = cophi.model.Document(stopwords).tokens 

else: 

stopwords = corpus.mfw(data["mfw"]) 

return stopwords 

def get_data(corpus, topics, iterations, stopwords, mfw): 

"""Get data from HTML forms. 

""" 

logging.info("Fetching user data...") 

data = {"corpus": flask.request.files.getlist("corpus"), 

"topics": int(flask.request.form["topics"]), 

"iterations": int(flask.request.form["iterations"])} 

if flask.request.files.get("stopwords", None): 

data["stopwords"] = flask.request.files["stopwords"] 

else: 

data["mfw"] = int(flask.request.form["mfw"]) 

return data 

def get_topics(model, vocabulary, maximum=100): 

"""Get topics from topic model. 

""" 

for distribution in model.topic_word_: 

words = list(np.array(vocabulary)[np.argsort(distribution)][:-maximum-1:-1]) 

yield "{}, ...".format(", ".join(words[:3])), words 

def get_document_topic(model, titles, descriptors): 

"""Get document-topic distribution from topic model. 

""" 

document_topic = pd.DataFrame(model.doc_topic_) 

document_topic.index = titles 

document_topic.columns = descriptors 

return document_topic 

def get_cosine(matrix, descriptors): 

"""Calculate cosine similarity between columns. 

""" 

d = matrix.T @ matrix 

norm = (matrix * matrix).sum(0, keepdims=True) ** .5 

similarities = d / norm / norm.T 

return pd.DataFrame(similarities, index=descriptors, columns=descriptors) 

def scale(vector, minimum=50, maximum=100): 

"""Min-max scaler for a vector. 

""" 

return np.interp(vector, (vector.min(), vector.max()), (minimum, maximum)) 

def export_data(): 

logging.info("Creating data archive...") 

if DATA_EXPORT.exists(): 

unlink_content(DATA_EXPORT) 

else: 

DATA_EXPORT.mkdir() 

model, stopwords = database.select("data_export") 

document_topic, topics, document_similarities, topic_similarities = model 

logging.info("Preparing document-topic distributions...") 

document_topic = pd.read_json(document_topic, orient="index") 

document_topic.columns = [col.replace(",", "").replace(" ...", "") for col in document_topic.columns] 

logging.info("Preparing topics...") 

topics = pd.read_json(topics, orient="index") 

topics.index = ["Topic {}".format(n) for n in range(topics.shape[0])] 

topics.columns = ["Word {}".format(n) for n in range(topics.shape[1])] 

logging.info("Preparing topic similarity matrix...") 

topic_similarities = pd.read_json(topic_similarities) 

topic_similarities.columns = [col.replace(",", "").replace(" ...", "") for col in topic_similarities.columns] 

topic_similarities.index = [ix.replace(",", "").replace(" ...", "") for ix in topic_similarities.index] 

logging.info("Preparing document similarity matrix...") 

document_similarities = pd.read_json(document_similarities) 

data_export = {"document-topic-distribution": document_topic, 

"topics": topics, 

"topic-similarities": topic_similarities, 

"document-similarities": document_similarities, 

"stopwords": json.loads(stopwords)} 

for name, data in data_export.items(): 

if name in {"stopwords"}: 

with Path(DATA_EXPORT, "{}.txt".format(name)).open("w", encoding="utf-8") as file: 

for word in data: 

file.write("{}\n".format(word)) 

else: 

path = Path(DATA_EXPORT, "{}.csv".format(name)) 

data.to_csv(path, sep=";", encoding="utf-8") 

shutil.make_archive(DATA_EXPORT, "zip", DATA_EXPORT) 

def unlink_content(directory, pattern="*"): 

"""Deletes the content of a directory. 

""" 

logging.info("Cleaning up in data directory...") 

for p in directory.rglob(pattern): 

if p.is_file(): 

p.unlink() 

def series2array(s): 

for i, v in zip(s.index, s): 

yield [i, v]