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app.py
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app.py
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import os
import sys
import csv
import jinja2
import sass
import re
from jsmin import jsmin
from flask import Flask
from flask import render_template, jsonify, request, make_response, send_from_directory
from flask_sqlalchemy import SQLAlchemy
from datetime import datetime
os.makedirs("templates", exist_ok=True)
sys.path.insert(1, "static/")
app = Flask(__name__)
app.config.from_object(os.environ['APP_SETTINGS'])
app.config['SQLALCHEMY_TRACK_MODIFICATIONS'] = False
uri = os.getenv("DATABASE_URL")
# or other relevant config var
if uri.startswith("postgres://"):
uri = uri.replace("postgres://", "postgresql://", 1)
app.config['SQLALCHEMY_DATABASE_URI'] = uri
db = SQLAlchemy(app)
from function_search_taxonomy import find_latin_name, find_tax_id
from models import *
def generate_js(file_name):
species_cat = dict()
species_wiki = dict()
species_ncbi = dict()
months = dict()
appartenance = dict()
name_to_index = dict()
for enum_id, sp in enumerate(db.session.query(Specie).all()):
species_cat[sp.name] = sp.category
species_wiki[sp.name] = sp.wiki
species_ncbi[sp.name] = sp.NCBI
months[sp.name] = []
name_to_index[sp.name] = enum_id
appartenance[name_to_index[sp.name]] = reverse_cat[sp.category]
associations_plant = set()
for assoc in db.session.query(Interaction).all():
associations_plant.add(
(name_to_index[assoc.source], name_to_index[assoc.target], reverse_interactions[assoc.interaction]))
index_to_name = reverse_dict(name_to_index)
print(os.getcwd())
javascript = open(file_name, "w")
javascript.write("var graph = {\n")
# nodes for javascript file
javascript.write('\t"nodes":[\n')
javascript.write(
",\n".join(['\t\t{{"name":"{0}","group":{1},"value":{2},"wiki":"{3}","ncbi":"{4}"}}'.format(name,
appartenance[index],
index,
species_wiki[name],
species_ncbi[name])
for index, name in index_to_name.items()]))
javascript.write('\n\t],\n')
# Forward list
javascript.write('\t"forward":[\n')
javascript.write(",\n".join(['\t\t[' + ','.join(
['{{"target":{0},"value":"{1}","group":{2}}}'.format(target, interactions[inter], appartenance[target])
for source, target, inter
in associations_plant if source == index]) + ']' for index, _ in index_to_name.items()]))
javascript.write('\n\t],\n')
# Backward list
javascript.write('\t"backward":[\n')
javascript.write(",\n".join(['\t\t[' + ','.join(
['{{"source":{0},"value":"{1}","group":{2}}}'.format(source, interactions[inter], appartenance[source])
for source, target, inter
in associations_plant if target == index]) + ']' for index, _ in index_to_name.items()]))
javascript.write('\n\t]\n};')
javascript.write('\nvar names_liste = ["' + '","'.join(sorted(set(species_cat))) + '"];')
javascript.write("\nvar groups = {\n")
javascript.write(
",\n".join(['\t{0}:"{1}"'.format(cat_index, cat_name) for cat_index, cat_name in categories.items()]))
javascript.write('\n};')
javascript.write("\nvar color = {\n")
javascript.write(
",\n".join(['\t{0}:"{1}"'.format(color_index, color_name) for color_index, color_name in color.items()]))
javascript.write('\n};')
javascript.write('\nvar cat_animals = [' + ','.join(sorted([str(reverse_cat[c]) for c in cat_animals])) + '];')
javascript.write('\nvar cat_pests = [' + ','.join(sorted([str(reverse_cat[c]) for c in cat_pests])) + '];')
javascript.write(
'\nvar cat_helpers = [' + ','.join(sorted([str(reverse_cat[c]) for c in (cat_animals - cat_pests)])) + '];')
javascript.write('\nvar cat_plants = [' + ','.join(sorted([str(reverse_cat[c]) for c in cat_plants])) + '];')
javascript.write('\nvar interactions = ["' + '","'.join(sorted(set(interactions.values()))) + '"];')
backward = ', '.join(
['"{0}":"{1}"'.format(value, interaction_backward[value].lower()) for value in
sorted(set(interactions.values()))])
forward = ', '.join(
['"{0}":"{1}"'.format(value, interaction_forward[value].lower()) for value in
sorted(set(interactions.values()))])
javascript.write('\nvar filter_name_dico = {"backward":{' + backward + '}, "forward":{' + forward + '}};')
javascript.close()
examples = []
for index, name in index_to_name.items():
name_associations = [l for l in associations_plant if l[0] == index]
name_interactions = set([l[2] for l in name_associations])
if len(name_interactions) == len(description_interactions):
for interaction in sorted(name_interactions, key=lambda x: abs(x)):
source, target, inter = [l for l in name_associations if (l[2] == interaction)][0]
assert inter == interaction
example = dict()
example["name_source"] = index_to_name[source]
example["color_source"] = color[appartenance[source]]
example["name_target"] = index_to_name[target]
example["color_target"] = color[appartenance[target]]
example["link"] = interactions[inter]
example["description"] = "{0} {1} {2}".format(example["name_source"],
interaction_forward[interactions[inter]].lower(),
example["name_target"].lower())
examples.append(example)
break
categories_list = []
for cat in [sorted(cat_plants), sorted(cat_animals)]:
categories_list += [(k, color[reverse_cat[k]]) for k in cat]
return months, index_to_name, appartenance, examples, categories_list, sorted(
[reverse_cat[cat] for cat in cat_plants]), sorted([reverse_cat[cat] for cat in cat_animals]), {
"backward": interaction_backward, "forward": interaction_forward}
def render_index():
months, plants, appartenance, examples, categories, cat_plants, cat_animals, dict_interactions = generate_js(
"static/js/data.js")
minified = ""
if not app.config['DEBUG']:
minified = "min."
for js_path in ["static/js/MonPotager.js", "static/js/data.js"]:
with open(js_path, 'r') as js_file:
jsminified = jsmin(js_file.read())
jsminified_file = open(js_path.replace('.js', ".min.js"), "w")
jsminified_file.write(jsminified)
jsminified_file.close()
print(OKBLUE + "Minifying " + js_path + ENDC)
css = open("static/css/MonPotager." + minified + "css", "w")
css.write(
sass.compile(filename='static/MonPotager.css.scss',
output_style=('nested' if app.config['DEBUG'] else "compressed")))
css.close()
env = jinja2.Environment(loader=jinja2.FileSystemLoader('./'))
template = env.get_template('static/MonPotager.html')
first_letter = sorted(set([name[0].upper() for key, name in plants.items() if (appartenance[key] in cat_plants)]))
sorted_appartenance = sorted(appartenance.items(), key=lambda pl: plants[pl[0]].lower())
template.stream(timestamp=datetime.now().timestamp(),
months=months,
plants=plants,
examples=examples,
minified=minified,
cat_plants=cat_plants,
cat_animals=cat_animals,
categories=categories,
first_letter=first_letter,
interactions=dict_interactions,
appartenance=sorted_appartenance).dump('templates/index.html')
print(OKGREEN + "Application generated.\nOpen the file {0}/templates/index.html to open the application.".format(
os.getcwd()) + ENDC)
@app.route("/species/new-entry", methods=["GET", "POST"])
def create_entry():
req = request.get_json()
try:
name = req['namaesp']
wikipedia = find_latin_name(name)
taxonomic_dico = find_tax_id(wikipedia)
sp = Specie(
name=taxonomic_dico[name][0].strip(),
common_name=taxonomic_dico[name][0].strip(),
category=req['catesp'],
wiki=taxonomic_dico[name][1],
taxonomy=taxonomic_dico[name][2],
latin_name=taxonomic_dico[name][3],
TaxID=taxonomic_dico[name][4],
NCBI="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=" + taxonomic_dico[name][4]
)
sp.is_valid()
db.session.add(sp)
db.session.commit()
render_index()
return make_response(jsonify("L'espèce a été ajoutée avec succès à la base de données.\n" + str(sp)), 200)
except ValidationError as e:
db.session.rollback()
return make_response(jsonify("Erreur de validation : " + str(e)), 400)
except Exception as e:
db.session.rollback()
return make_response(jsonify("Erreur du serveur : " + str(e)), 500)
@app.route('/association/new-entry', methods=["POST", "GET"])
def create_association():
req = request.get_json()
inter = Interaction(
source=req["espSource"],
target=req["espCible"],
interaction=interactions[description_interactions[req["espInteraction"]]],
references=req["espReference"]
)
try:
inter.is_valid()
db.session.add(inter)
db.session.commit()
render_index()
return make_response(jsonify("L'interaction a été ajoutée avec succès à la base de données.\n" + str(inter)),
200)
except ValidationError as e:
db.session.rollback()
return make_response(jsonify("Erreur de validation : " + str(e)), 400)
except Exception as e:
db.session.rollback()
return make_response(jsonify("Erreur du serveur : " + str(e)), 500)
@app.route("/")
def monpotager():
if not os.path.isfile('templates/index.html'):
render_index()
return render_template('index.html')
@app.route("/render")
def re_render():
render_index()
return render_template('index.html')
@app.route('/favicon.ico')
def favicon():
return send_from_directory(os.path.join(app.root_path, 'static'),
'favicon.ico', mimetype='image/vnd.microsoft.icon')
def reset_db():
db.drop_all()
db.create_all()
db.session.query(Interaction).delete()
db.session.commit()
db.session.query(Specie).delete()
db.session.commit()
with open('static/database/especes_v2.csv', 'r', newline='', encoding='utf-8') as csvfile:
speciesreader = csv.reader(csvfile, delimiter=',', quotechar='"')
next(speciesreader)
for line in speciesreader:
sp = Specie(
name=line[7],
common_name=line[0],
category=line[1],
wiki=line[2],
taxonomy=line[3],
latin_name=line[4],
TaxID=line[5],
NCBI=line[6],
)
try:
sp.is_valid()
db.session.add(sp)
db.session.commit()
except Exception as e:
print(e)
with open('static/database/associations.csv', 'r', newline='', encoding='utf-8') as csvfile:
associationsreader = csv.reader(csvfile, delimiter=',', quotechar='"')
next(associationsreader)
for source, assoc, target, references, _, _ in associationsreader:
inter = Interaction(source=source, target=target, interaction=interactions[description_interactions[assoc]],
references=references)
try:
inter.is_valid()
db.session.add(inter)
db.session.commit()
except Exception as e:
print(e)
render_index()
@app.route(os.environ['SEED_PATH'])
def seed_db():
reset_db()
return render_template('index.html')
# run the application
if __name__ == "__main__":
app.run(threaded=True)