def testPopulationFromCommandLineSequencesAndFastaFile(self):
"""
Using both command line sequences and --databaseFasta must result in
all the command line subjects and those in the file being added to the
returned database.
"""
parser = argparse.ArgumentParser()
specifier = DatabaseSpecifier()
specifier.addArgsToParser(parser)
args = parser.parse_args([
'--databaseFasta', 'file.fasta', '--databaseSequence', 'id1 FFF',
'--databaseSequence', 'id2 RRR'
])
data = '\n'.join(['>id3', 'FFFF', '>id4', 'RRRR'])
mockOpener = mockOpen(read_data=data)
with patch.object(builtins, 'open', mockOpener):
db = specifier.getDatabaseFromArgs(args)
allSubjects = [subject.read for subject in db.getSubjects()]
self.assertEqual(
{
AARead('id1', 'FFF'),
AARead('id2', 'RRR'),
AARead('id3', 'FFFF'),
AARead('id4', 'RRRR'),
}, set(allSubjects))
def testNoArgs(self):
"""
If no arguments are given, getDatabaseFromArgs must return a database.
"""
parser = argparse.ArgumentParser()
specifier = DatabaseSpecifier()
specifier.addArgsToParser(parser)
args = parser.parse_args([])
db = specifier.getDatabaseFromArgs(args)
self.assertIsInstance(db, Database)
def testPassedParamsAreUsed(self):
"""
If specific parameters are given, they must be used.
"""
parser = argparse.ArgumentParser()
specifier = DatabaseSpecifier()
specifier.addArgsToParser(parser)
args = parser.parse_args([])
dbParams = DatabaseParameters()
db = specifier.getDatabaseFromArgs(args, dbParams)
self.assertIs(db.dbParams, dbParams)
def testNoArgsDefaultParameters(self):
"""
The database returned from getDatabaseFromKeywords when it is
passed no keywords must have the default database parameters.
"""
parser = argparse.ArgumentParser()
specifier = DatabaseSpecifier()
specifier.addArgsToParser(parser)
args = parser.parse_args([])
db = specifier.getDatabaseFromArgs(args)
self.assertIs(None, db.dbParams.compare(DatabaseParameters()))
def testPopulationFromCommandLineSequences(self):
"""
Passing --databaseSequence arguments must result in the subjects in the
sequences being added to the returned database.
"""
parser = argparse.ArgumentParser()
specifier = DatabaseSpecifier()
specifier.addArgsToParser(parser)
args = parser.parse_args(
['--databaseSequence', 'id1 FFF', '--databaseSequence', 'id2 RRR'])
db = specifier.getDatabaseFromArgs(args)
allSubjects = [subject.read for subject in db.getSubjects()]
self.assertEqual(
{AARead('id1', 'FFF'), AARead('id2', 'RRR')}, set(allSubjects))
def testPopulationFromFastaFile(self):
"""
Passing a --databaseFasta argument must result in the subjects in the
file being added to the returned database.
"""
parser = argparse.ArgumentParser()
specifier = DatabaseSpecifier()
specifier.addArgsToParser(parser)
args = parser.parse_args(['--databaseFasta', 'file.fasta'])
data = '\n'.join(['>id1', 'FFF', '>id2', 'RRR'])
mockOpener = mockOpen(read_data=data)
with patch.object(builtins, 'open', mockOpener):
db = specifier.getDatabaseFromArgs(args)
allSubjects = [subject.read for subject in db.getSubjects()]
self.assertEqual(
{AARead('id1', 'FFF'), AARead('id2', 'RRR')}, set(allSubjects))
#!/usr/bin/env python
import argparse
from autobahn.asyncio.wamp import ApplicationRunner
from light.autobahn.database import DatabaseComponent
from light.database import DatabaseSpecifier
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description='Start a WAMP-based distributed light-matter database.')
databaseSpecifier = DatabaseSpecifier(allowInMemory=False)
databaseSpecifier.addArgsToParser(parser)
args = parser.parse_args()
# We're always using WAMP for distributed databases.
args.wampServer = True
database = databaseSpecifier.getDatabaseFromArgs(args)
runner = ApplicationRunner(args.wampUrl,
args.realm,
extra=dict(database=database))
runner.run(DatabaseComponent)
import argparse
from time import time
from light.database import DatabaseSpecifier
from light.parameters import DatabaseParameters
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description=('Create a light-matter database from sequences in a '
'FASTA file and/or given on the command line.'))
databaseSpecifier = DatabaseSpecifier(allowInMemory=False)
databaseSpecifier.addArgsToParser(parser)
args = parser.parse_args()
if args.filePrefix is None:
parser.print_help()
raise RuntimeError('You must supply a database save file prefix.')
startTime = time()
dbParams = DatabaseParameters.fromArgs(args)
database = databaseSpecifier.getDatabaseFromArgs(args, dbParams)
print(database.print_(), file=sys.stderr)
print('Database built in %.2f seconds. Saving...' % (time() - startTime),
end=' ',
file=sys.stderr)
# Save.
saveStartTime = time()
database.save()
print('saved in %.2f seconds.' % (time() - saveStartTime), file=sys.stderr)