#!/usr/bin/python
import sys,os,re,shutil
# Must import storage before utils
import update_settings as settings
from storage import storage
storage.uri = settings.MONGODB_URI
storage.db_name = settings.MONGODB_DB_NAME
storage.connect()
from time import time
from ftplib import FTP
from defs import CRAWLTYPE_LINE as LINE, CRAWLTYPE_FILE as FILE
from utils import (download, entries_by_pdbid, get_present_entries,
get_missing_entries, read_http, parse_regex, valid_path)
# Each entry has a pdbid and databank_name, this is what makes it unique.
# An entry might also have a file path (present entries) or comment (annotated entries).
# The mtime field tells when the file or comment was added. (number of seconds since january the 1st, 1970, 00:00:00)
# This function is used for file crawling:
def get_pathnames (path):
if path.startswith ("ftp://"):
if not path.endswith ('/'):
path = path + '/'
host = path.split('/')[2]
_dir = path [7 + len(host): ]
#!/usr/bin/python
import sys, os, re, shutil
# Must import storage before utils
import update_settings as settings
from storage import storage
storage.uri = settings.MONGODB_URI
storage.db_name = settings.MONGODB_DB_NAME
storage.connect()
storage.authenticate('whynotadmin', 'waivuy8N')
from time import time
from ftplib import FTP
from defs import CRAWLTYPE_LINE as LINE, CRAWLTYPE_FILE as FILE
from utils import (download, entries_by_pdbid, get_present_entries,
get_missing_entries, read_http, parse_regex, valid_path)
# Each entry has a pdbid and databank_name, this is what makes it unique.
# An entry might also have a file path (present entries) or comment (annotated entries).
# The mtime field tells when the file or comment was added. (number of seconds since january the 1st, 1970, 00:00:00)
# This function is used for file crawling:
def get_pathnames(path):
if path.startswith("ftp://"):
if not path.endswith('/'):
path = path + '/'
def create_app(settings=None):
_log.info("Creating app")
app = Flask(__name__,
static_folder='frontend/static',
template_folder='frontend/templates')
app.config.from_object('whynot_web.default_settings')
if settings:
app.config.update(settings)
else: # pragma: no cover
app.config.from_envvar('WHYNOT_SETTINGS') # pragma: no cover
# Ignore Flask's built-in logging
# app.logger is accessed here so Flask tries to create it
app.logger_name = "nowhere"
app.logger
whynot_logger = logging.getLogger('whynot_web')
# Only log to email during production.
if not app.debug and not app.testing: # pragma: no cover
mail_handler = SMTPHandler(
(app.config["MAIL_SERVER"], app.config["MAIL_SMTP_PORT"]),
app.config["MAIL_FROM"], app.config["MAIL_TO"], "whynot failed")
mail_handler.setLevel(logging.ERROR)
whynot_logger.addHandler(mail_handler)
mail_handler.setFormatter(
logging.Formatter("Message type: %(levelname)s\n" +
"Location: %(pathname)s:%(lineno)d\n" +
"Module: %(module)s\n" +
"Function: %(funcName)s\n" +
"Time: %(asctime)s\n" + "Message:\n" +
"%(message)s"))
# Only log to the console during development and production, but not during
# testing.
if app.testing:
whynot_logger.setLevel(logging.DEBUG)
else:
# This is the formatter used for the Flask app.
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s')
sh.setFormatter(formatter)
whynot_logger.addHandler(sh)
if app.debug:
whynot_logger.setLevel(logging.DEBUG)
else:
whynot_logger.setLevel(logging.INFO)
# Configure storage
from storage import storage
storage.uri = app.config['MONGODB_URI']
storage.db_name = app.config['MONGODB_DB_NAME']
storage.connect()
# Setup the default databanks if there are none
if storage.count('databanks', {}) == 0:
from install import create_databanks
storage.create_index('databanks', 'name')
storage.create_index('entries', 'databank_name')
storage.create_index('entries', 'pdbid')
storage.create_index('entries', 'comment')
databanks = create_databanks()
storage.insert('databanks', databanks)
# Use ProxyFix to correct URL's when redirecting.
from whynot_web.middleware import ReverseProxied
app.wsgi_app = ReverseProxied(app.wsgi_app)
# Register jinja2 filters
from whynot_web.frontend.filters import beautify_docstring
app.jinja_env.filters['beautify_docstring'] = beautify_docstring
# Register blueprints
from whynot_web.frontend.dashboard.views import bp as dashboard_bp
from whynot_web.frontend.rest.rs import bp as rs_bp
app.register_blueprint(dashboard_bp)
app.register_blueprint(rs_bp)
return app
def create_app(settings=None):
_log.info("Creating app")
app = Flask(__name__, static_folder='frontend/static',
template_folder='frontend/templates')
app.config.from_object('whynot_web.default_settings')
if settings:
app.config.update(settings)
else: # pragma: no cover
app.config.from_envvar('WHYNOT_SETTINGS') # pragma: no cover
# Ignore Flask's built-in logging
# app.logger is accessed here so Flask tries to create it
app.logger_name = "nowhere"
app.logger
whynot_logger = logging.getLogger('whynot_web')
# Only log to email during production.
if not app.debug and not app.testing: # pragma: no cover
mail_handler = SMTPHandler((app.config["MAIL_SERVER"],
app.config["MAIL_SMTP_PORT"]),
app.config["MAIL_FROM"],
app.config["MAIL_TO"],
"whynot failed")
mail_handler.setLevel(logging.ERROR)
whynot_logger.addHandler(mail_handler)
mail_handler.setFormatter(
logging.Formatter("Message type: %(levelname)s\n" +
"Location: %(pathname)s:%(lineno)d\n" +
"Module: %(module)s\n" +
"Function: %(funcName)s\n" +
"Time: %(asctime)s\n" +
"Message:\n" +
"%(message)s"))
# Only log to the console during development and production, but not during
# testing.
if app.testing:
whynot_logger.setLevel(logging.DEBUG)
else:
# This is the formatter used for the Flask app.
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s')
sh.setFormatter(formatter)
whynot_logger.addHandler(sh)
if app.debug:
whynot_logger.setLevel(logging.DEBUG)
else:
whynot_logger.setLevel(logging.INFO)
# Configure storage
from storage import storage
storage.uri = app.config['MONGODB_URI']
storage.db_name = app.config['MONGODB_DB_NAME']
storage.connect()
# Setup the default databanks if there are none
if storage.count('databanks', {}) == 0:
from install import create_databanks
storage.create_index('databanks', 'name')
storage.create_index('entries', 'databank_name')
storage.create_index('entries', 'pdbid')
storage.create_index('entries', 'comment')
databanks = create_databanks()
storage.insert('databanks', databanks)
# Use ProxyFix to correct URL's when redirecting.
from whynot_web.middleware import ReverseProxied
app.wsgi_app = ReverseProxied(app.wsgi_app)
# Register jinja2 filters
from whynot_web.frontend.filters import beautify_docstring
app.jinja_env.filters['beautify_docstring'] = beautify_docstring
# Register blueprints
from whynot_web.frontend.dashboard.views import bp as dashboard_bp
from whynot_web.frontend.rest.rs import bp as rs_bp
app.register_blueprint(dashboard_bp)
app.register_blueprint(rs_bp)
return app