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database_reader.py
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40 lines (31 loc) · 1.57 KB
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# Created by Adam Streck, 2013-2015, adam.streck@fu-berlin.de
#
# This file is part of the Toolkit for Reverse Engineering of Molecular Pathways
# via Parameter Identification (TREMPPI)
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>.
def read_components(conn):
return conn.execute('SELECT Name, MaxActivity FROM Components ORDER BY Name').fetchall()
def read_regulations(conn):
return conn.execute('SELECT DISTINCT Source, Threshold, Target FROM Regulations ORDER BY Source, Target, Threshold').fetchall()
def component_regulators_list(conn):
result = {}
cursor = conn.execute('SELECT DISTINCT Target, Source FROM Regulations ORDER BY Target, Source')
for row in cursor:
if str(row[0]) not in result:
result[str(row[0])] = []
result[str(row[0])].append(str(row[1]))
return result
def are_properties_defined(conn):
cursor = conn.execute('SELECT count(*) FROM sqlite_master WHERE type="table" AND name="Properties"')
return int(cursor.fetchone()[0]) > 0