def connect_and_delete_old_lists():
config = parse_config(CONFIG_FILENAME)
db = create_db_connection(config.dbconfig)
cur = db.cursor()
delete_old_items(cur)
cur.close()
db.commit()
db.close()
create_sql_for_predictions(config, sql_builder, DataType.PREFERENCE, update_progress)
update_progress("STAGE: Executing preferences SQL files.")
run_sql_pipeline(config, sql_builder.sql_pipeline)
def run_sql_pipeline(config, sql_pipeline):
"""
Run all the sql commands in sql_pipeline against the database.
:param config: pred.Config: global configuration containing what data to download/convert/load.
:param sql_pipeline: loaddatabase.SQLPipeline: list of sql commands to be run
"""
runner = SqlRunner(config, update_progress)
sql_pipeline.run(runner.execute)
runner.close()
if __name__ == '__main__':
funcs = {
'all': run_all_command,
'download': download_files_command,
'download_models': download_models_command,
'run_sql': run_sql_command,
'run_sql_models' : run_sql_models_command,
'run_sql_predictions': run_sql_predictions,
'run_sql_preferences': run_sql_preferences,
}
parser = argparse.ArgumentParser(description='Loads prediction database based on imadsconf.yaml')
parser.add_argument('command', choices=funcs.keys())
args = parser.parse_args()
funcs[args.command](parse_config(CONFIG_FILENAME))
update_progress("STAGE: Executing preferences SQL files.")
run_sql_pipeline(config, sql_builder.sql_pipeline)
def run_sql_pipeline(config, sql_pipeline):
"""
Run all the sql commands in sql_pipeline against the database.
:param config: pred.Config: global configuration containing what data to download/convert/load.
:param sql_pipeline: loaddatabase.SQLPipeline: list of sql commands to be run
"""
runner = SqlRunner(config, update_progress)
sql_pipeline.run(runner.execute)
runner.close()
if __name__ == '__main__':
funcs = {
'all': run_all_command,
'download': download_files_command,
'download_models': download_models_command,
'run_sql': run_sql_command,
'run_sql_models': run_sql_models_command,
'run_sql_predictions': run_sql_predictions,
'run_sql_preferences': run_sql_preferences,
}
parser = argparse.ArgumentParser(
description='Loads prediction database based on imadsconf.yaml')
parser.add_argument('command', choices=funcs.keys())
args = parser.parse_args()
funcs[args.command](parse_config(CONFIG_FILENAME))
import psycopg2.extras
from flask import Flask, request, render_template, jsonify, g, make_response, Response
from pred.config import parse_config, CONFIG_FILENAME
from pred.webserver.dbdatasource import DataSources
from pred.webserver.predictionsearch import get_predictions_with_guess, get_all_values
from pred.webserver.customlist import save_custom_file
from pred.webserver.dnasequence import lookup_dna_sequence
from pred.webserver.sequencelist import SequenceList
from pred.webserver.customjob import CustomJob, JobStatus
from pred.webserver.customresult import CustomResultData
from pred.webserver.errors import ClientException, ServerException, ErrorType
logging.basicConfig(stream=sys.stderr)
app = Flask(__name__)
g_config = parse_config(CONFIG_FILENAME)
g_dbconfig = g_config.dbconfig
def log_info(message):
print(message)
def get_db():
db = getattr(g, '_database', None)
if db is None:
log_info("Creating database connection.")
db = g._database = create_db_connection(g_dbconfig)
return db
import psycopg2
import psycopg2.extras
from flask import Flask, request, render_template, jsonify, g, make_response, Response
from pred.config import parse_config, CONFIG_FILENAME
from pred.webserver.dbdatasource import DataSources
from pred.webserver.predictionsearch import get_predictions_with_guess, get_all_values
from pred.webserver.customlist import save_custom_file
from pred.webserver.dnasequence import lookup_dna_sequence
from pred.webserver.sequencelist import SequenceList
from pred.webserver.customjob import CustomJob, JobStatus
from pred.webserver.customresult import CustomResultData
from pred.webserver.errors import ClientException, ServerException, ErrorType
app = Flask(__name__)
g_config = parse_config(CONFIG_FILENAME)
g_dbconfig = g_config.dbconfig
def log_info(message):
print(message)
def get_db():
db = getattr(g, '_database', None)
if db is None:
log_info("Creating database connection.")
db = g._database = create_db_connection(g_dbconfig)
return db
