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Merge pull request #70 from pinellolab/personal-card-website
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Restore personal card display on website
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@ManuelTgn
ManuelTgn authored Nov 18, 2024
2 parents be703f8 + 8ff6dae commit 0aae818
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81 changes: 50 additions & 31 deletions app.py
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Original file line number Diff line number Diff line change
@@ -1,68 +1,88 @@
"""Define the Flask-based server app basics """
"""Main module for the CRISPRme web application.
This module sets up the Flask and Dash applications, configures the server, and initializes the web application. It also defines stylesheets, caching, and various application settings.
Attributes:
WEBADDRESS (str): The web address for accessing the application.
IPADDRESS (str): The IP address and port for local access to the web application.
URL (str): The server URL.
external_stylesheets (list): List of external stylesheets for the web application.
server (Flask): The Flask server instance.
app (Dash): The Dash application instance.
app_directory (str): The directory of the current application.
current_working_directory (str): The current working directory.
operators (list): List of filtering operators used for querying tables.
ONLINE (bool): Flag indicating if the application is online or offline.
DISPLAY_OFFLINE (str): CSS display property for offline mode.
DISPLAY_ONLINE (str): CSS display property for online mode.
pool_executor (ProcessPoolExecutor): Executor for running multiple jobs
concurrently.
CACHE_CONFIG (dict): Configuration settings for caching.
cache (Cache): Cache instance for the application.
"""

from flask_caching import Cache

import dash_bootstrap_components as dbc

import concurrent.futures
import concurrent.futures
import flask
import dash
import sys
import os


WEBADDRESS = "http://crisprme.di.univr.it"
IPADDRESS = "127.0.0.1:8080"


def __start_message() -> None:
""" (PRIVATE)
Write server start message to stderr.
def _start_message() -> None:
"""Prints a startup message to the standard error stream.
...
This function outputs a message indicating that the server has started and
provides the URL to access the web application.
Parameters
----------
None
Args:
None
Returns
-------
None
Returns:
None
"""

sys.stderr.write("SERVER STARTED\n")
sys.stderr.write(f"GO TO {IPADDRESS} TO USE THE WEB APP\n\n")
sys.stderr.write(f"GO TO http://{IPADDRESS} TO USE THE WEB APP\n\n")


URL = "" # server URL
external_stylesheets = [
"https://codepen.io/chriddyp/pen/bWLwgP.css", dbc.themes.BOOTSTRAP
"https://codepen.io/chriddyp/pen/bWLwgP.css",
dbc.themes.BOOTSTRAP,
] # CSS stylesheet used to style the website
server = flask.Flask(__name__) # define flask app.server
app = dash.Dash(
__name__,
external_stylesheets=external_stylesheets,
suppress_callback_exceptions=True,
server=server
__name__,
external_stylesheets=external_stylesheets,
suppress_callback_exceptions=True,
server=server, # type: ignore
) # initialize server app
app_directory = os.path.dirname(os.path.realpath(__file__)) # current location
__start_message() # print server start message
current_working_directory = os.getcwd() + '/' # This for files TODO: remove
app.title = "CRISPRme" # assign flask app name
_start_message() # print server start message
current_working_directory = os.getcwd() + "/" # This for files TODO: remove
app.title = "CRISPRme" # type: ignore - assign flask app name
# necessary if update element in a callback generated in another callback
# app.config['suppress_callback_exceptions'] = True
app.css.config.serve_locally = True
app.scripts.config.serve_locally = True
# define filtering operators used when querying tables
operators = [
["ge ", ">="],
["le ", "<="],
["lt ", "<"],
["gt ", ">"],
["ge ", ">="],
["le ", "<="],
["lt ", "<"],
["gt ", ">"],
["ne ", "!="],
["eq ", "="],
["contains "]
]
ONLINE = False # NOTE change to True for online version, False for offline
["contains "],
]
ONLINE = True # NOTE change to True for online version, False for offline
DISPLAY_OFFLINE = ""
DISPLAY_ONLINE = ""
if ONLINE:
Expand All @@ -75,8 +95,7 @@ def __start_message() -> None:
CACHE_CONFIG = {
# try 'filesystem' if you don't want to setup redis
"CACHE_TYPE": "filesystem",
"CACHE_DIR": ("Cache") # os.environ.get('REDIS_URL', 'localhost:6379')
"CACHE_DIR": ("Cache"), # os.environ.get('REDIS_URL', 'localhost:6379')
}
cache = Cache() # initialize cache
cache.init_app(app.server, config=CACHE_CONFIG) # start web-app

187 changes: 97 additions & 90 deletions index.py
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Original file line number Diff line number Diff line change
@@ -1,19 +1,39 @@
#!/usr/bin/env python
"""The script creates the index page, constituting the back bone of CRISPRme web
interface. The web interface can also be created locally, to provide an easy-to-use
GUI to submit not released or private data and perform the off-targets search.
"""Main module for the CRISPRme web application.
This module initializes the web application, sets up the server, and defines the
layout and callbacks for page navigation. It handles the routing of different pages
based on the URL and manages the server's running mode.
Attributes:
MODEFILE (str): The filename for storing the running mode.
HOST (str): The host address for the server.
PORTWEB (int): The port number for the website.
PORTLOCAL (int): The port number for the local server.
server (Flask): The Flask server instance.
navbar (html.Div): The navigation bar component of the web application.
app.layout (html.Div): The layout structure of the Dash application.
"""


from pages import (
main_page,
navbar_creation,
results_page,
load_page,
history_page,
help_page,
contacts_page
main_page,
navbar_creation,
results_page,
load_page,
history_page,
help_page,
contacts_page,
)
from app import (
URL,
IPADDRESS,
WEBADDRESS,
ONLINE,
app,
current_working_directory,
cache,
)
from app import app, URL, current_working_directory, cache
from utils import check_directories

from dash.dependencies import Input, Output, State
Expand All @@ -38,9 +58,9 @@
app.layout = html.Div(
[
navbar,
dcc.Location(id='url', refresh=False),
html.Div(id='page-content'),
html.P(id='signal', style={'visibility': 'hidden'})
dcc.Location(id="url", refresh=False),
html.Div(id="page-content"),
html.P(id="signal", style={"visibility": "hidden"}),
]
)

Expand All @@ -49,27 +69,27 @@
@app.callback(
[Output("page-content", "children"), Output("job-link", "children")],
[Input("url", "href"), Input("url", "pathname"), Input("url", "search")],
[State("url", "hash")]
[State("url", "hash")],
)
def change_page(href: str, path: str, search: str, hash_guide: str) -> Tuple:
"""The function switches between the selected pages.
...
Parameters
----------
href : str
URL
path : str
Current path
search : str
Current search
hash_guide : str
Guide hash
Returns
-------
Tuple
"""Handles page changes based on the current URL and its components.
This callback function updates the content of the web application based on
the provided URL parameters. It determines which page to display and returns
the corresponding content and link based on the path and search parameters.
Args:
href (str): The full URL of the current page.
path (str): The path component of the URL.
search (str): The query string of the URL.
hash_guide (str): The hash component of the URL.
Returns:
Tuple: A tuple containing the children for the page content and the job
link.
Raises:
TypeError: If any of the input parameters are not of type str.
"""

if not isinstance(href, str):
Expand All @@ -81,99 +101,86 @@ def change_page(href: str, path: str, search: str, hash_guide: str) -> Tuple:
if not isinstance(hash_guide, str):
raise TypeError(f"Expected {str.__name__}, got {type(hash_guide).__name__}")
if path == "/load": # show loading page
return (
load_page.load_page(),
os.path.join("".join(href.split("/")[:-1]), "/load", search)
)
# define url to display on load page to check on job status
# if online show the webaddress, show the ip address otherwise
job_loading_url = WEBADDRESS if ONLINE else IPADDRESS
return (load_page.load_page(), f"{job_loading_url}/load{search}")
if path == "/result": # display results page
job_id = search.split("=")[-1]
job_id = search.split("=")[-1] # recover job id from url
if not hash_guide or hash_guide is None:
return results_page.result_page(job_id), os.path.join(URL, "load", search)
elif "new" in hash_guide: # TODO: change name to guide page
elif "new" in hash_guide: # targets table tab
return (
results_page.guidePagev3(job_id, hash_guide.split("#")[1]),
os.path.join(URL, "load", search)
os.path.join(URL, "load", search),
)
elif "-Sample-" in hash_guide:
elif "-Sample-" in hash_guide: # sample tab
return (
results_page.sample_page(job_id, hash_guide.split("#")[1]),
os.path.join(URL, "load", search)
os.path.join(URL, "load", search),
)
elif "-Pos-" in hash_guide:
elif "-Pos-" in hash_guide: # genomic region tab
return (
results_page.cluster_page(job_id, hash_guide.split("#")[1]),
os.path.join(URL, "load", search)
os.path.join(URL, "load", search),
)
return results_page.result_page(job_id), os.path.join(URL, "load", search)

if path == "/user-guide": # display manual page
return help_page.helpPage(), os.path.join(URL, "load", search)
if path == "/contacts": # display contacts page
return contacts_page.contact_page(), os.path.join(URL, "load", search)
if path == "/history": # display results history page
return history_page.history_page(), os.path.join(URL, "load", search)
if path == "/index": # display main page
return main_page.index_page(), "/index"
return main_page.index_page(), "/index"
return main_page.index_page(), "/index" # display main page


def index():
"""The function creates the index page, managing the whole CRISPRme web
interface. The webpage displays four main pages (accessible by the user):
- Home page
- Manual page
- Contacts page
- History page (accessible only locally)
"""Starts the CRISPRme web application server.
The webpage can be created locally, using the appropriate command line
arguments.
This function checks the directory structure for consistency, determines the
running mode (local or website), and starts the Dash application server
accordingly. It also handles the creation of a mode file to track the current
running mode and clears the cache before starting the server.
...
Args:
None
Parameters
----------
None
Returns:
None
Returns
-------
None
Raises:
OSError: If there is an issue writing the mode file.
"""

# check CRISPRme directory tree consistency
check_directories(current_working_directory)
# check if debug mode is active
# TODO: replace using argparse in crisprme.py
debug = False
if "--debug" in sys.argv[1:]:
debug = True
# check if local server or website
website = False
if "--website" in sys.argv[1:]:
website = True
# keep track of running mode
try:
handle = open(os.path.join(current_working_directory, MODEFILE), mode="w")
if website: # 'server' mode
handle.write("server")
else: # 'local' mode
handle.write("local")
except OSError:
raise OSError(f"An error occurred while writing {MODEFILE}")
finally:
handle.close()
if website:
debug = "--debug" in sys.argv[1:] # check if debug mode is active
website = "--website" in sys.argv[1:] # check if local server or website
try: # keep track of the running mode (debugging purposes)
modefname = os.path.join(current_working_directory, MODEFILE)
with open(modefname, mode="w") as outfile:
mode = "server" if website else "local"
outfile.write(mode)
except IOError as e:
raise OSError("Cannot write mode file") from e
if website: # online web-interface running
app.run_server(
host=HOST, port=PORTWEB, debug=debug, dev_tools_ui=debug, dev_tools_props_check=debug
host=HOST,
port=PORTWEB, # type: ignore
debug=debug,
dev_tools_ui=debug,
dev_tools_props_check=debug,
)
cache.clear() # clear cache once server is closed
else: # local web-interface running
app.run_server(
host=HOST, port=PORTLOCAL, debug=debug, dev_tools_ui=debug, dev_tools_props_check=debug
)
app.run_server(
host=HOST, port=PORTWEB, debug=debug, dev_tools_ui=debug, dev_tools_props_check=debug
host=HOST,
port=PORTLOCAL, # type: ignore
debug=debug,
dev_tools_ui=debug,
dev_tools_props_check=debug,
)
cache.clear() # clear cache once server is closed
cache.clear() # clear cache once server is closed


if __name__ == "__main__":
Expand Down
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