Bugfix/ckg internal server error

ckg/analytics_core/utils.py

@@ -5,7 +5,7 @@
 import io
 import base64
 import bs4 as bs
-import dash_html_components as html
+from dash import html
 import requests
 import networkx as nx
 from networkx.readwrite import json_graph

ckg/analytics_core/viz/viz.py

@@ -3,8 +3,8 @@
 import pandas as pd
 import ast
 from collections import defaultdict
-import dash_core_components as dcc
-import dash_html_components as html
+from dash import dcc
+from dash import html
 import matplotlib
 import matplotlib.pyplot as plt
 import plotly
@@ -13,7 +13,7 @@
 import plotly.figure_factory as FF
 import plotly.express as px
 import math
-import dash_table
+from dash import dash_table
 import plotly.subplots as tools
 import plotly.io as pio
 from scipy.spatial.distance import pdist, squareform

ckg/ckg_utils.py

@@ -153,4 +153,5 @@ class DictDFEncoder(json.JSONEncoder):
     def default(self, obj):
         if hasattr(obj, 'to_json'):
             return obj.to_json(orient='records')
-        return json.JSONEncoder.default(self, obj)
+        return json.JSONEncoder.default(self, obj)
+

ckg/report_manager/app.py

@@ -1,21 +1,42 @@
 import os
+import subprocess
+from datetime import datetime
+from uuid import uuid4
+
+import dash
 import flask
 import redis
-import dash
+from dash import html, dcc, Output, Input
+
+import ckg.report_manager.user as user
 from ckg import ckg_utils
+from ckg.graphdb_builder import builder_utils
+from ckg.report_manager import utils
+from ckg.report_manager.worker import run_minimal_update_task, \
+    run_full_update_task
+
+ckg_config = ckg_utils.read_ckg_config()
+log_config = ckg_config['report_manager_log']
+logger = builder_utils.setup_logging(log_config, key="app")
+config = builder_utils.setup_config('builder')
+separator = config["separator"]
 
-server = flask.Flask('app')
+flask_server = flask.Flask('app')
 cwd = os.path.dirname(os.path.abspath(__file__))
 assets_path = os.path.join(cwd, 'assets')
-app = dash.Dash('app', server=server, assets_folder=assets_path, meta_tags=[{"name": "viewport", "content": "width=device-width, initial-scale=1"}])
-
+os.chdir(cwd)
+pages_path = "./pages"
+app = dash.Dash("app", server=flask_server, assets_folder=assets_path,
+                external_stylesheets=[assets_path + "custom.css"],
+                meta_tags=[{"name": "viewport", "content": "width=device-width, initial-scale=1"}],
+                use_pages=True,
+                pages_folder=pages_path)
 
 r = redis.StrictRedis.from_url('redis://localhost:6379')
 
 with open(os.path.join(assets_path, "app_template.html"), 'r', encoding='utf8') as f:
     template = f.read()
 
-
 app.index_string = template
 app.scripts.config.serve_locally = False
 app.config.suppress_callback_exceptions = True
@@ -25,3 +46,174 @@
 for js in external_js:
     app.scripts.append_script({"external_url": js})
 
+app.layout = html.Div(children=[
+    html.Div(id="user-status-header"),
+    html.Hr(),
+
+    dcc.Loading(children=[html.Div([dcc.Location(id='url', refresh=False),
+                                    html.Div(id='page-content',
+                                             style={'padding-top': 10},
+                                             className='container-fluid'),
+                                    dash.page_container])],
+                style={'text-align': 'center',
+                       'top': '50%',
+                       'left': '50%',
+                       'height': '250px'},
+                type='cube', color='#2b8cbe'),
+])
+
+
+@dash.callback(
+    Output("user-status-header", "children"),
+    Input("url", "pathname"),
+)
+def update_authentication_status(_):
+    session_cookie = flask.request.cookies.get('custom-auth-session')
+    logged_in = session_cookie is not None
+    if logged_in:
+        return dcc.Link([html.Form([html.Button('Logout', type='submit')], action='/apps/logout', method='post',
+                                   style={'position': 'absolute', 'right': '0px'}, id='logout')],
+                        href="/apps/logoutPage")
+    return dcc.Link(html.Form([html.Button('Login', type='submit')],
+                              style={'position': 'absolute', 'right': '0px'}, id='login'), href="/apps/loginPage")
+
+
+@flask_server.route('/apps/login', methods=['POST', 'GET'])
+def route_login():
+    data = flask.request.form
+    username = data.get('username')
+    password = data.get('password')
+    if not username or not password:
+        flask.abort(401)
+    elif not user.User(username).verify_password(password):
+        return flask.redirect('/login_error')
+    else:
+        rep = flask.redirect('/')
+        rep.set_cookie('custom-auth-session',
+                       username + '_' + datetime.now().strftime('%Y%m-%d%H-%M%S-') + str(uuid4()))
+        return rep
+
+
+@flask_server.route('/apps/logout', methods=['POST'])
+def route_logout():
+    # Redirect back to the index and remove the session cookie.
+    rep = flask.redirect('/')
+    rep.set_cookie('custom-auth-session', '', expires=0)
+    return rep
+
+
+@flask_server.route('/create_user', methods=['POST', 'GET'])
+def route_create_user():
+    data = flask.request.form
+    name = data.get('name')
+    surname = data.get('surname')
+    affiliation = data.get('affiliation')
+    acronym = data.get('acronym')
+    email = data.get('email')
+    alt_email = data.get('alt_email')
+    phone = data.get('phone')
+    uname = name[0] + surname
+    username = uname
+
+    registered = 'error_exists'
+    iter = 1
+    while registered == 'error_exists':
+        u = user.User(username=username.lower(), name=name, surname=surname, affiliation=affiliation, acronym=acronym,
+                      phone=phone, email=email, alternative_email=alt_email)
+        registered = u.register()
+        if registered is None:
+            rep = flask.redirect('/apps/admin?error_new_user={}'.format('Failed Database'))
+        elif registered == 'error_exists':
+            username = uname + str(iter)
+            iter += 1
+        elif registered == 'error_email':
+            rep = flask.redirect('/apps/admin?error_new_user={}'.format('Email already registered'))
+        elif registered == 'error_database':
+            rep = flask.redirect('/apps/admin?error_new_user={}'.format('User could not be saved in the database'))
+        else:
+            rep = flask.redirect('/apps/admin?new_user={}'.format(username))
+
+    return rep
+
+
+@flask_server.route('/update_minimal', methods=['POST', 'GET'])
+def route_minimal_update():
+    session_cookie = flask.request.cookies.get('custom-auth-session')
+    username = session_cookie.split('_')[0]
+    internal_id = datetime.now().strftime('%Y%m-%d%H-%M%S-')
+    result = run_minimal_update_task.apply_async(args=[username], task_id='run_minimal_' + session_cookie + internal_id,
+                                                 queue='update')
+
+    rep = flask.redirect('/apps/admin/running=minimal')
+
+    return rep
+
+
+@flask_server.route('/update_full', methods=['POST', 'GET'])
+def route_full_update():
+    session_cookie = flask.request.cookies.get('custom-auth-session')
+    data = flask.request.form
+    download = data.get('dwn-radio') == 'true'
+    username = session_cookie.split('_')[0]
+    internal_id = datetime.now().strftime('%Y%m-%d%H-%M%S-')
+    result = run_full_update_task.apply_async(args=[username, download],
+                                              task_id='run_full_' + session_cookie + internal_id, queue='update')
+
+    rep = flask.redirect('/apps/admin/running=full')
+
+    return rep
+
+
+@flask_server.route('/downloads/<value>')
+def route_report_url(value):
+    uri = os.path.join(ckg_config['downloads_directory'], value + '.zip')
+    return flask.send_file(uri, download_name=value + '.zip', as_attachment=True, max_age=-1)
+
+
+@flask_server.route('/example_files')
+def route_example_files_url():
+    uri = os.path.join(ckg_config['data_directory'], 'example_files.zip')
+    return flask.send_file(uri, download_name='example_files.zip', as_attachment=True, max_age=-1)
+
+
+@flask_server.route('/apps/templates<value>')
+def serve_static(value):
+    cwd = os.path.dirname(os.path.abspath(__file__))
+    directory = os.path.join(cwd, 'apps/templates/')
+    filename = os.path.join(directory, value)
+    url = filename + '.zip'
+    if not os.path.isfile(url):
+        utils.compress_directory(filename, os.path.join(directory, 'files'), compression_format='zip')
+
+    return flask.send_file(url, download_name=f"{value}.zip", as_attachment=True, max_age=-1)
+
+
+@flask_server.route('/tmp/<value>')
+def route_upload_url(value):
+    page_id, project_id = value.split('_')
+    directory = ckg_config['tmp_directory']
+    filename = os.path.join(directory, 'Uploaded_files_' + project_id)
+    url = filename + '.zip'
+
+    return flask.send_file(url, download_name=filename.split('/')[-1] + '.zip', as_attachment=True,
+                           max_age=-1)
+
+
+def main():
+    logger.info("Starting CKG App")
+    celery_working_dir = os.path.dirname(os.path.abspath(__file__))
+    os.chdir(celery_working_dir)
+    queues = [('creation', 1, 'INFO'), ('compute', 3, 'INFO'), ('update', 1, 'INFO')]
+    print(type(ckg_config))
+    print(ckg_config["log_directory"] + "/celery.log")
+    for queue, processes, log_level in queues:
+        celery_cmdline = 'celery -A ckg.report_manager.worker worker --loglevel={} --logfile={} --concurrency={} -E -Q {}'.format(
+            log_level, ckg_config["log_directory"] + "/celery.log", processes, queue).split(" ")
+        logger.info("Ready to call {} ".format(celery_cmdline))
+        subprocess.Popen(celery_cmdline)
+        logger.info("Done calling {} ".format(celery_cmdline))
+    app.run_server(debug=False, host='0.0.0.0')
+
+
+if __name__ == '__main__':
+    main()