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()