def main():
create_app(debug=settings.DEBUG)
import nsweb.models #registers models
print("Initializing DatabaseBuilder...")
# Create a new builder from a pickled Dataset instance and populate the DB
# pass reset_dataset=False after first run to avoid rebuilding dataset
dataset = settings.PICKLE_DATABASE
db.app = app # Set context on DB
builder = database_builder.DatabaseBuilder(
db,
dataset=dataset,
studies=os.path.join(settings.ASSET_DIR, 'database.txt'),
features=os.path.join(settings.ASSET_DIR, 'features.txt'),
reset_db=True,
reset_dataset=False)
# reset_db=False, reset_dataset=False)
print("Adding analyses...")
if settings.PROTOTYPE:
analyses = [
'emotion', 'language', 'memory', 'pain', 'visual', 'attention',
'sensory'
]
elif settings.ANALYSIS_FILTER_FILE is not None:
filt = pd.read_csv(settings.ANALYSIS_FILTER_FILE,
sep='\t',
index_col=0)
analyses = filt[filt['keep'] == 1].index.tolist()
print("Keeping %d analysis terms." % len(analyses))
else:
analyses = None
builder.add_term_analyses(analyses=analyses, add_images=True, reset=True)
print("Adding studies...")
if settings.PROTOTYPE:
builder.add_studies(analyses=analyses, limit=500)
else:
builder.add_studies(analyses=analyses)
print("Adding feature-based meta-analysis images...")
builder.generate_analysis_images(analyses=analyses,
add_to_db=False,
overwrite=True)
print("Adding topic sets...")
builder.add_topics(generate_images=False,
add_images=True,
reset=True,
top_n=40)
# print "Adding cognitive atlas information for available terms..."
# builder.add_cognitive_atlas_nodes()
print("Adding genes...")
builder.add_genes()
print("Memory-mapping key image sets...")
builder.memory_map_images(include=['terms', 'topics', 'genes'], reset=True)
def main():
create_app(debug=settings.DEBUG)
import nsweb.models #registers models
print("Initializing DatabaseBuilder...")
# Create a new builder from a pickled Dataset instance and populate the DB
# pass reset_dataset=False after first run to avoid rebuilding dataset
dataset = settings.PICKLE_DATABASE
db.app = app # Set context on DB
builder = database_builder.DatabaseBuilder(
db, dataset=dataset,
studies=os.path.join(settings.ASSET_DIR, 'database.txt'),
features=os.path.join(settings.ASSET_DIR, 'features.txt'),
reset_db=True, reset_dataset=True, download_data=True)
# reset_db=False, reset_dataset=False)
print("Adding analyses...")
if settings.PROTOTYPE:
analyses = ['emotion', 'language', 'memory', 'pain', 'visual',
'attention', 'sensory']
elif settings.ANALYSIS_FILTER_FILE is not None:
filt = pd.read_csv(settings.ANALYSIS_FILTER_FILE, sep='\t',
index_col=0)
analyses = filt[filt['keep'] == 1].index.tolist()
print("Keeping %d analysis terms." % len(analyses))
else:
analyses = None
builder.add_term_analyses(analyses=analyses, add_images=True, reset=True)
print("Adding studies...")
if settings.PROTOTYPE:
builder.add_studies(analyses=analyses, limit=500)
else:
builder.add_studies(analyses=analyses)
print("Adding feature-based meta-analysis images...")
builder.generate_analysis_images(
analyses=analyses, add_to_db=False, overwrite=True)
print("Adding topic sets...")
builder.add_topics(generate_images=True, add_images=True, reset=True, top_n=40)
# print "Adding cognitive atlas information for available terms..."
# builder.add_cognitive_atlas_nodes()
print("Adding genes...")
builder.add_genes()
print("Memory-mapping key image sets...")
builder.memory_map_images(include=['terms', 'topics', 'genes'], reset=True)
def main():
create_app(debug=settings.DEBUG)
import nsweb.models #registers models
print "Initializing DatabaseBuilder..."
# Create a new builder from a pickled Dataset instance and populate the DB
# pass reset_dataset=False after first run to avoid rebuilding dataset
dataset = settings.PICKLE_DATABASE
db.app = app # Set context on DB
builder = database_builder.DatabaseBuilder(
db, dataset=dataset,
studies=os.path.join(settings.ASSET_DIR, 'database.txt'),
features=os.path.join(settings.ASSET_DIR, 'features.txt'),
reset_db=True, reset_dataset=True)
# reset_db=False, reset_dataset=False)
print "Adding analyses..."
if settings.PROTOTYPE:
analyses = ['emotion', 'language', 'memory', 'pain', 'visual',
'attention', 'sensory']
else:
analyses = None
builder.add_term_analyses(analyses=analyses, add_images=True, reset=True)
print "Adding studies..."
if settings.PROTOTYPE:
builder.add_studies(analyses=analyses, limit=500)
else:
builder.add_studies(analyses=analyses)
print "Adding feature-based meta-analysis images..."
builder.generate_analysis_images(
analyses=analyses, add_to_db=False, overwrite=True)
# print "Adding topic sets..."
# builder.add_topics(generate_images=True, add_images=True, top_n=40)
# print "Adding cognitive atlas information for available terms..."
# builder.add_cognitive_atlas_nodes()
print "Memory-mapping key image sets..."
builder.memory_map_images(include=['terms'], reset=True)
from nsweb.core import app, db, create_app
from flask.ext.script import Manager
from flask import url_for
from flask.ext.migrate import Migrate, MigrateCommand
from nsweb.models import *
create_app()
migrate = Migrate(app, db)
manager = Manager(app)
manager.add_command('db', MigrateCommand)
# Found @ http://stackoverflow.com/questions/13317536/get-a-list-of-all-routes-defined-in-the-app
@manager.command
def list_routes():
import urllib
output = []
for rule in app.url_map.iter_rules():
methods = ','.join(rule.methods)
line = urllib.unquote("{:50s} {:20s} {}".format(rule.endpoint, methods, rule))
output.append(line)
for line in sorted(output):
print(line)
@manager.command
def reset_locations():
from nsweb.models.locations import Location
for l in Location.query.all():
db.session.delete(l)
# db.session.query(Location).delete()
def db(scope='session'):
create_app(debug=True, test=True)
database.app = app # Set DB context
database.drop_all()
database.create_all()
return database
from nsweb.core import create_app, app
# set up the flask app
create_app()
def main():
app.run(debug=app.debug, port=5001, host='0.0.0.0')
if __name__ == "__main__":
main()
