app.py

import logging
import os
import sqlite3
import time
from logging.config import dictConfig

import dash
import dash_bootstrap_components as dbc
from dash import dcc, html
from flask import Flask

import callbacks.coexpression.callbacks
import callbacks.epigenome.callbacks
import callbacks.homepage.callbacks
import callbacks.homepage.util
import callbacks.lift_over.callbacks
import callbacks.summary.callbacks
import callbacks.template.callbacks
import callbacks.text_mining.callbacks
import callbacks.tf_enrich.callbacks
import pages.navigation.main_nav as main_nav
from callbacks.constants import Constants
from callbacks.file_util import make_dir, path_exists
from config.generate_config import generate_config
from config.parse_config import (
    get_max_logging_gb,
    get_release_version,
    is_debug_mode,
    is_deployed_version,
    is_logging_mode,
    show_if_deployed,
)

# ========================================
# Configuration and Server Initialization
# ========================================

# Create .env file if it does not exist
# IMPORTANT: The created .env file loads the app at the default settings for development
#   Refer to the arguments of the generate_config() call to see these default settings
if not path_exists(".env"):
    generate_config(debug=True, deployed=False, logging=False)

# Configure settings if logging is enabled
if is_logging_mode():
    # Log files are saved inside this folder
    make_dir("logs")

    # Suppress writing GET requests to the log
    log = logging.getLogger("werkzeug")
    log.setLevel(logging.ERROR)

    GB_TO_BYTES = 1e9

    # Use UTC for the log timestamps
    class UTCFormatter(logging.Formatter):
        converter = time.gmtime

    dictConfig(
        {
            "version": 1,
            "formatters": {
                "default": {
                    "()": UTCFormatter,
                    "format": "%(asctime)s%(msecs)03d|%(message)s",
                    "datefmt": "%Y%m%d%H%M%S",
                },
            },
            "handlers": {
                "file": {
                    "class": "logging.handlers.RotatingFileHandler",
                    "backupCount": 1,
                    "maxBytes": get_max_logging_gb() * GB_TO_BYTES,
                    "filename": f"logs/usage.log",
                    "formatter": "default",
                },
            },
            "root": {"level": "DEBUG", "handlers": ["file"]},
        }
    )

# Initialize the Flask server
server = Flask(__name__, static_folder="static")

# ===================
# App Initialization
# ===================


# Returns True if the Bootstrap and Font Awesome folders exist inside the assets folder;
#   False, otherwise
# If the app was installed via Docker, there are two possible scenarios:
#   - If the version for local installation was installed, then this function should return True
#     Rationale: To allow offline usage of the app
#   - If the version for deployment was installed, then this function should return False
#     Rationale: Use CDN for deployed version since internet connection is guaranteed anyway
def detected_locally_hosted_stylesheets():
    bootstrap = False
    fontawesome = False

    for file in os.listdir("assets"):
        if file.startswith("bootstrap-icons"):
            bootstrap = True
        if file.startswith("fontawesome"):
            fontawesome = True

    return bootstrap and fontawesome


# If Bootstrap and Font Awesome stylesheets (and sprites) are locally hosted,
# use the locally hosted stylesheets (and sprites)
if detected_locally_hosted_stylesheets():
    app = dash.Dash(
        __name__,
        use_pages=True,
        server=server,
        title="RicePilaf",
        update_title="Loading...",
        meta_tags=[
            {"name": "viewport", "content": "width=1024"}
        ],  # Same desktop and mobile views
    )

# Otherwise, fetch the Bootstrap and Font Awesome stylesheets from a CDN
else:
    app = dash.Dash(
        __name__,
        use_pages=True,
        external_stylesheets=[
            dbc.themes.BOOTSTRAP,
            dbc.icons.BOOTSTRAP,
            dbc.icons.FONT_AWESOME,
        ],
        server=server,
        title="RicePilaf",
        update_title="Loading...",
        meta_tags=[
            {"name": "viewport", "content": "width=1024"}
        ],  # Same desktop and mobile views
    )

# ============
# Main Layout
# ============

app.layout = lambda: dbc.Container(
    [
        dbc.Row(
            # Display the "demo only" banner if configured to deployed version
            html.Div(
                children=[
                    html.P(
                        [
                            "For heavy workloads, consider running RicePilaf locally. Click ",
                            dcc.Link(
                                [
                                    "here ",
                                    html.I(
                                        id="demo-link",
                                        className="fa-solid fa-up-right-from-square fa-2xs",
                                    ),
                                ],
                                href="https://github.com/bioinfodlsu/rice-pilaf/wiki/1.-Installation",
                                target="_blank",
                                className="top-navbar-item",
                            ),
                            " to install.",
                        ],
                        className="my-auto",
                    )
                ],
                className="banner d-flex justify-content-center py-1 text-white",
                id="demo-banner",
            ),
            style=show_if_deployed(),
        ),
        # Top navbar (i.e., the section containing the RicePilaf logo and link to the User Guide)
        dbc.Row(main_nav.navbar()),
        # Body
        dash.page_container,
        # Footer
        dbc.Row(
            [
                dbc.Col(
                    dcc.Link(
                        html.Img(src="assets/bioinfo_lab_logo.png", height="65px"),
                        href="https://bioinfodlsu.com/",
                        target="_blank",
                    ),
                    className="col-auto text-center my-auto",
                ),
                dbc.Col(
                    [
                        html.Span(f"RicePilaf {get_release_version()}"),
                        html.Span("© 2023", className="ps-3"),
                        html.Span("|", className="px-3"),
                        html.Span(
                            "Bioinformatics Lab, De La Salle University (DLSU), Manila, Philippines"
                        ),
                        html.Br(),
                        html.Span(
                            "Rural Development Administration (RDA), South Korea – International Rice Research Institute (IRRI) – The French National Research Institute for Sustainable Development (IRD)"
                        ),
                        html.Br(),
                        html.Span("Cooperative Project"),
                    ],
                    className="col-sm-11",
                ),
            ],
            className="ps-5 pb-4 pt-4 text-white",
            id="footer",
        ),
        # Session storage
        # Insert your session variables inside the session-container div
        html.Div(
            id="session-container",
            children=[
                # =========
                # Template
                # =========
                dcc.Store(id="template-is-submitted", storage_type="session"),
                dcc.Store(id="template-submitted-addl-genes", storage_type="session"),
                dcc.Store(
                    id="template-submitted-radio-buttons", storage_type="session"
                ),
                dcc.Store(
                    id="template-submitted-checkbox-buttons", storage_type="session"
                ),
                dcc.Store(
                    id="template-submitted-parameter-slider", storage_type="session"
                ),
                # =========
                # Homepage
                # =========
                dcc.Store(id="homepage-is-submitted", storage_type="session"),
                dcc.Store(
                    id="homepage-submitted-genomic-intervals", storage_type="session"
                ),
                dcc.Store(id="current-analysis-page-nav", storage_type="session"),
                dcc.Store(id="homepage-is-resetted", storage_type="session"),
                # ==========
                # Lift-over
                # ==========
                dcc.Store(id="lift-over-is-submitted", storage_type="session"),
                dcc.Store(id="lift-over-active-tab", storage_type="session"),
                dcc.Store(id="lift-over-submitted-other-refs", storage_type="session"),
                dcc.Store(id="lift-over-active-filter", storage_type="session"),
                # ============
                # IGV Browser
                # ============
                dcc.Store(
                    id="epigenome-submitted-genomic-intervals", storage_type="session"
                ),
                dcc.Store(id="epigenome-submitted-tissue", storage_type="session"),
                dcc.Store(id="epigenome-submitted-tracks", storage_type="session"),
                dcc.Store(id="epigenome-is-submitted", storage_type="session"),
                # ==============
                # Coexpression
                # ==============
                dcc.Store(
                    id="coexpression-submitted-parameter-slider", storage_type="session"
                ),
                dcc.Store(id="coexpression-submitted-module", storage_type="session"),
                dcc.Store(id="coexpression-pathway-active-tab", storage_type="session"),
                dcc.Store(
                    id="coexpression-graph-active-layout", storage_type="session"
                ),
                dcc.Store(
                    id="coexpression-submitted-addl-genes", storage_type="session"
                ),
                dcc.Store(id="coexpression-valid-addl-genes", storage_type="session"),
                dcc.Store(id="coexpression-combined-genes", storage_type="session"),
                dcc.Store(id="coexpression-submitted-network", storage_type="session"),
                dcc.Store(
                    id="coexpression-submitted-clustering-algo", storage_type="session"
                ),
                dcc.Store(id="coexpression-is-submitted", storage_type="session"),
                # ==============================
                # Regulatory Feature Enrichment
                # ==============================
                dcc.Store(id="tfbs-is-submitted", storage_type="session"),
                dcc.Store(id="tfbs-submitted-addl-genes", storage_type="session"),
                dcc.Store(id="tfbs-valid-addl-genes", storage_type="session"),
                dcc.Store(id="tfbs-combined-genes", storage_type="session"),
                dcc.Store(
                    id="tfbs-submitted-prediction-technique", storage_type="session"
                ),
                dcc.Store(id="tfbs-submitted-set", storage_type="session"),
                # ============
                # Text Mining
                # ============
                dcc.Store(id="text-mining-submitted-query", storage_type="session"),
                dcc.Store(id="text-mining-is-submitted", storage_type="session"),
                dcc.Store(id="text-mining-filter-query", storage_type="session"),
                dcc.Store(id="text-mining-submitted-filter", storage_type="session"),
                # ========
                # Summary
                # ========
                dcc.Store(id="summary-is-submitted", storage_type="session"),
            ],
        ),
    ],
    fluid=True,
)

callbacks.homepage.callbacks.init_callback(app)
callbacks.lift_over.callbacks.init_callback(app)
callbacks.epigenome.callbacks.init_callback(app)
callbacks.coexpression.callbacks.init_callback(app)
callbacks.tf_enrich.callbacks.init_callback(app)
callbacks.text_mining.callbacks.init_callback(app)
callbacks.summary.callbacks.init_callback(app)

# ====================================
# TEMPLATE for Initializing Callbacks
# ====================================
# callbacks.template.callbacks.init_callback(app)

# ========
# Caching
# ========

# Create folder for caching previously run analyses to avoid repeated computations
make_dir(Constants.TEMP)

# Create database for storing shorthands of cache directory names
try:
    connection = sqlite3.connect(Constants.FILE_STATUS_DB)
    cursor = connection.cursor()

    query = f"CREATE TABLE IF NOT EXISTS {Constants.FILE_STATUS_TABLE} (name TEXT, UNIQUE(name));"

    cursor.execute(query)
    connection.commit()

    cursor.close()
    connection.close()
except sqlite3.Error as error:
    pass

# ===============
# Run the server
# ===============

if __name__ == "__main__":
    if is_deployed_version():
        app.run_server(port="8050", debug=is_debug_mode())
    else:
        app.run_server(host="0.0.0.0", port="8050", debug=is_debug_mode())