def setup_app(command, conf, vars):
"""Place any commands to setup abstrackr here"""
load_environment(conf.global_conf, conf.local_conf)
filename = os.path.split(conf.filename)[-1]
if filename == 'test.ini':
# Permanently drop any existing tables
log.info("Dropping existing tables...")
Base.metadata.drop_all(checkfirst=True, bind=Session.bind)
# Create the tables if they don't already exist
log.info("Creating database tables")
Base.metadata.drop_all(checkfirst=True, bind=Session.bind)
Base.metadata.create_all(bind=Session.bind)
log.info("Finished setting up")
g = Group()
g.name = u'admin'
meta.Session.add(g)
p = Permission()
p.name = u'admin'
meta.Session.add(p)
# give myslf a login.
u = User()
u.username = u'byron'
u.fullname = u'byron wallace'
u.experience = 2
u._set_password('pignic')
u.email = u'*****@*****.**'
meta.Session.add(u)
meta.Session.commit()
def setup_app(command, conf, vars):
"""Place any commands to setup abstrackr here"""
# Don't reload the app if it was loaded under the testing environment
if not pylons.test.pylonsapp:
load_environment(conf.global_conf, conf.local_conf)
# Create the tables if they don't already exist
log.info("Creating database tables")
Base.metadata.create_all(bind=Session.bind)
log.info("Finished setting up")
g = Group()
g.name = u'admin'
meta.Session.add(g)
p = Permission()
p.name = u'admin'
meta.Session.add(p)
# give myslf a login.
u = User()
u.username = u'byron'
u.fullname = u'byron wallace'
u.experience = 2
u._set_password('pignic')
u.email = u'*****@*****.**'
meta.Session.add(u)
meta.Session.commit()
def setup_app(command, conf, vars):
"""Place any commands to setup abstrackr here"""
load_environment(conf.global_conf, conf.local_conf)
filename = os.path.split(conf.filename)[-1]
if filename == 'test.ini':
# Permanently drop any existing tables
log.info("Dropping existing tables...")
Base.metadata.drop_all(checkfirst=True, bind=Session.bind)
# Create the tables if they don't already exist
log.info("Creating database tables")
Base.metadata.drop_all(checkfirst=True, bind=Session.bind)
Base.metadata.create_all(bind=Session.bind)
log.info("Finished setting up")
g = Group()
g.name = u'admin'
meta.Session.add(g)
p = Permission()
p.name = u'admin'
meta.Session.add(p)
# give myslf a login.
u = User()
u.username = u'byron'
u.fullname = u'byron wallace'
u.experience = 2
u._set_password('pignic')
u.email = u'*****@*****.**'
meta.Session.add(u)
meta.Session.commit()
def make_app(global_conf, full_stack=True, static_files=True, **app_conf):
"""Create a Pylons WSGI application and return it
``global_conf``
The inherited configuration for this application. Normally from
the [DEFAULT] section of the Paste ini file.
``full_stack``
Whether this application provides a full WSGI stack (by default,
meaning it handles its own exceptions and errors). Disable
full_stack when this application is "managed" by another WSGI
middleware.
``static_files``
Whether this application serves its own static files; disable
when another web server is responsible for serving them.
``app_conf``
The application's local configuration. Normally specified in
the [app:<name>] section of the Paste ini file (where <name>
defaults to main).
"""
# Configure the Pylons environment
config = load_environment(global_conf, app_conf)
# The Pylons WSGI app
app = PylonsApp(config=config)
# Routing/Session/Cache Middleware
app = RoutesMiddleware(app, config['routes.map'], singleton=False)
app = SessionMiddleware(app, config)
# CUSTOM MIDDLEWARE HERE (filtered by error handling middlewares)
# Add the custom repoze.what middleware app here and pass it the config
# variable
app = add_auth(app, config)
if asbool(full_stack):
# Handle Python exceptions
app = ErrorHandler(app, global_conf, **config['pylons.errorware'])
# Display error documents for 401, 403, 404 status codes (and
# 500 when debug is disabled)
if asbool(config['debug']):
app = StatusCodeRedirect(app)
else:
app = StatusCodeRedirect(app, [400, 401, 403, 404, 500])
# Establish the Registry for this application
app = RegistryManager(app)
if asbool(static_files):
# Serve static files
static_app = StaticURLParser(config['pylons.paths']['static_files'])
app = Cascade([static_app, app])
app.config = config
return app
def make_app(global_conf, full_stack=True, static_files=True, **app_conf):
"""Create a Pylons WSGI application and return it
``global_conf``
The inherited configuration for this application. Normally from
the [DEFAULT] section of the Paste ini file.
``full_stack``
Whether this application provides a full WSGI stack (by default,
meaning it handles its own exceptions and errors). Disable
full_stack when this application is "managed" by another WSGI
middleware.
``static_files``
Whether this application serves its own static files; disable
when another web server is responsible for serving them.
``app_conf``
The application's local configuration. Normally specified in
the [app:<name>] section of the Paste ini file (where <name>
defaults to main).
"""
# Configure the Pylons environment
config = load_environment(global_conf, app_conf)
# The Pylons WSGI app
app = PylonsApp(config=config)
# Routing/Session/Cache Middleware
app = RoutesMiddleware(app, config['routes.map'], singleton=False)
app = SessionMiddleware(app, config)
# CUSTOM MIDDLEWARE HERE (filtered by error handling middlewares)
# Add the custom repoze.what middleware app here and pass it the config
# variable
app = add_auth(app, config)
if asbool(full_stack):
# Handle Python exceptions
app = ErrorHandler(app, global_conf, **config['pylons.errorware'])
# Display error documents for 401, 403, 404 status codes (and
# 500 when debug is disabled)
if asbool(config['debug']):
app = StatusCodeRedirect(app)
else:
app = StatusCodeRedirect(app, [400, 401, 403, 404, 500])
# Establish the Registry for this application
app = RegistryManager(app)
if asbool(static_files):
# Serve static files
static_app = StaticURLParser(config['pylons.paths']['static_files'])
app = Cascade([static_app, app])
app.config = config
return app
def setup_app(command, conf, vars):
"""Place any commands to setup abstrackr here"""
load_environment(conf.global_conf, conf.local_conf)
filename = os.path.split(conf.filename)[-1]
if filename == 'test.ini':
# Permanently drop any existing tables
log.info("Dropping existing tables...")
Base.metadata.drop_all(checkfirst=True, bind=Session.bind)
# Create the tables if they don't already exist
log.info("Creating database tables")
Base.metadata.drop_all(checkfirst=True, bind=Session.bind)
Base.metadata.create_all(bind=Session.bind)
log.info("Finished setting up")
g = Group()
g.name = u'admin'
meta.Session.add(g)
p = Permission()
p.name = u'admin'
meta.Session.add(p)
meta.Session.commit()
from sqlalchemy.orm import load_only
from sqlalchemy import func
from sqlalchemy.orm import Load
from sqlalchemy import desc
from random import randrange
from random import sample
from collections import defaultdict
reload(sys)
sys.setdefaultencoding('utf-8')
conf = appconfig('config:development.ini', relative_to='.')
load_environment(conf.global_conf, conf.local_conf)
def _create_reviews(p_id, iter_size, which_iter):
lock_file_path = join(dirname(abspath(__file__)), '_delete_lock.lck')
if not isfile(lock_file_path):
Session.query(
model.Citation).filter(model.Citation.project_id != p_id).delete()
Session.query(
model.Label).filter(model.Label.project_id != p_id).delete()
Session.commit()
open(lock_file_path, 'w+').close()
u_id = 2629
k_init = 400
#import pubmedpy
import time
import csv
from paste.deploy import appconfig
from pylons import config
from abstrackr.config.environment import load_environment
from abstrackr.model.meta import Session
import abstrackr.model as model
from sqlalchemy import and_
conf = appconfig('config:production.ini', relative_to='.')
load_environment(conf.global_conf, conf.local_conf)
### This is fixing Emily's project. The refman ids weren't saved when she imported the project
PROJECT_ID = 219
FILE_PATH = './Abstraktr_Update_Lit_Review_11.12.13.txt'
citations_q = Session.query(model.Citation)
found = 0
not_found = 0
with open(FILE_PATH, 'r') as f:
reader = csv.DictReader(f, delimiter='\t')
for row in reader:
#print(row['id'], row['title'], row['abstract'])
citation = citations_q.filter_by(title=row['title'], project_id=PROJECT_ID).first()
