def test_basic_behaviour(self):
'It tests that we can get names using a FileNamingSchema'
fhand = NamedTemporaryFile()
engine = sqlalchemy.create_engine('sqlite:///:memory:')
create_naming_database(engine)
add_project_to_naming_database(engine, name='my_project', code='my',
description='a test project')
naming = DbNamingSchema(engine, project='my_project',
feature_kind='EST')
naming = FileNamingSchema(fhand, naming)
assert naming.get_uniquename(name='hola') == 'myES000001'
assert naming.get_uniquename(name='hola') == 'myES000001'
assert naming.get_uniquename(name='caracol') == 'myES000002'
naming.commit()
fhand.seek(0)
naming = FileNamingSchema(fhand)
naming.kind = 'EST'
assert naming.get_uniquename(name='hola') == 'myES000001'
assert naming.get_uniquename(name='caracol') == 'myES000002'
try:
assert naming.get_uniquename(name='pascual')
self.fail()
#pylint: disable-msg=W0704
except ValueError:
pass
def test_revert_last_name():
'''It test if we can revert the database to its last stste for a kind
and project'''
engine = sqlalchemy.create_engine('sqlite:///:memory:')
create_naming_database(engine)
add_project_to_naming_database(engine, name='my_project', code='my',
description='a test project')
naming = DbNamingSchema(engine, project='my_project',
feature_kind='EST')
naming.get_uniquename()
naming.commit()
naming.get_uniquename()
naming.commit()
names = list(naming.get_names_from_db())
assert names[0]['name'] == 'myES000001'
assert names[-1]['project'] == 'my_project'
assert names[-1]['name'] == 'myES000002'
assert len(names) == 2
naming.revert_last_name()
naming = DbNamingSchema(engine, project='my_project',
feature_kind='EST')
names = list(naming.get_names_from_db())
assert len(names) == 1
assert names[-1]['name'] == 'myES000001'
def xtest_basic_behaviour2():
'It tests that we can get names'
engine = sqlalchemy.create_engine('sqlite:////home/jope/test/naming_db')
create_naming_database(engine)
add_project_to_naming_database(engine, name='Melo', code='ME',
description='Melonomics Ests')
naming = DbNamingSchema(engine, project='Melo', feature_kind='EST')
assert naming.get_uniquename() == 'MEES000001'
assert naming.get_uniquename() == 'MEES000002'
naming.commit(description='Initial')
def test_project_in_database():
'It test the ability to know if the databse is already added'
project = 'test'
engine = sqlalchemy.create_engine('sqlite:///:memory:')
create_naming_database(engine)
assert not project_in_database(engine, project)
add_project_to_naming_database(engine, name=project, code='my',
description='a test project')
assert project_in_database(engine, project)
assert not project_in_database(engine, 'test2')
def test_basic_behaviour():
'It tests that we can get names'
engine = sqlalchemy.create_engine('sqlite:///:memory:')
create_naming_database(engine)
add_project_to_naming_database(engine, name='my_project', code='my',
description='a test project')
naming = DbNamingSchema(engine, project='my_project',
feature_kind='EST')
assert naming.get_uniquename() == 'myES000001'
assert naming.get_uniquename() == 'myES000002'
naming.kind = 'transcribed_cluster'
assert naming.get_uniquename() == 'myTC000001'
naming.commit()
def test_name_persistance():
'The names are stored between db commits'
engine = sqlalchemy.create_engine('sqlite:///:memory:')
create_naming_database(engine)
add_project_to_naming_database(engine, name='my_project', code='my',
description='a test project')
naming = DbNamingSchema(engine, project='my_project',
feature_kind='EST')
assert naming.get_uniquename() == 'myES000001'
naming.commit()
naming = DbNamingSchema(engine, project='my_project',
feature_kind='EST')
assert naming.get_uniquename() == 'myES000002'
def test_rollback():
"If we don't commit we lose the changes"
engine = sqlalchemy.create_engine('sqlite:///:memory:')
create_naming_database(engine)
add_project_to_naming_database(engine, name='my_project', code='my',
description='a test project')
naming = DbNamingSchema(engine, project='my_project',
feature_kind='EST')
assert naming.get_uniquename() == 'myES000001'
naming = DbNamingSchema(engine, project='my_project',
feature_kind='EST')
assert naming.get_uniquename() == 'myES000001'
from franklin.db.naming import _CodeGenerator
def test_fastq():
'It test that we can change the name in the fasta files.'
fhand_in = open(os.path.join(TEST_DATA_DIR, 'solexa.fastq'))
fhand_out = NamedTemporaryFile(suffix='.fasta')
engine = sqlalchemy.create_engine('sqlite:///:memory:')
create_naming_database(engine)
add_project_to_naming_database(engine, name='test_project', code='my',
description='a test project')
naming = DbNamingSchema(engine, 'test_project', feature_kind='EST')
change_names_in_files(fhand_in, fhand_out, naming, 'fastq')
output = open(fhand_out.name).read()
assert "@myES000001" in output
assert "@myES000003" in output
assert open(fhand_out.name).read()[:8] == '@myES000'
def _change_names_in_file(io_options, database, filecache, project,
feature_kind, description):
'It changes the name to a file giving a naming'
# check if the database exits
if database is not None:
engine = sqlalchemy.create_engine( 'sqlite:///%s' % database)
if not os.path.exists(database):
create_naming_database(engine)
# check if the project exists
project_name = project['name']
if not project_in_database(engine, project_name):
if project['code']:
add_project_to_naming_database(engine, name=project_name,
code=project['code'],
description=project['description'])
else:
msg = 'To add a new project to the database the code should be'
msg += ' given'
raise ValueError(msg)
# create a naming schema
naming = DbNamingSchema(engine, project=project_name,
feature_kind=feature_kind)
else:
naming = None
if filecache is not None:
if os.path.exists(filecache):
mode = 'a'
else:
mode = 'w'
fhand = open(filecache, mode)
naming = FileNamingSchema(fhand, naming)
try:
# change name to seqs in file
infhand = io_options['infhand']
outfhand = io_options['outfhand']
format = io_options['format']
change_names_in_files(infhand, outfhand, naming, format)
naming.commit(description=description)
except:
#if we don't commit we lose the changes in the database
raise
def test_get_all_names():
'It test if we can get all names stored in teh database'
engine = sqlalchemy.create_engine('sqlite:///:memory:')
create_naming_database(engine)
add_project_to_naming_database(engine, name='my_project', code='my',
description='a test project')
naming = DbNamingSchema(engine, project='my_project',
feature_kind='EST')
naming.get_uniquename()
naming.commit()
naming.get_uniquename()
naming.commit()
names = list(naming.get_names_from_db())
assert names[0]['project'] == 'my_project'
assert len(names) == 2
naming.project = 'my_project'
name = naming.get_names_from_db().next()
assert name['project'] == 'my_project'
def test_roolback(self):
'If the changes are not commited they are ignored'
fhand = NamedTemporaryFile()
engine = sqlalchemy.create_engine('sqlite:///:memory:')
create_naming_database(engine)
add_project_to_naming_database(engine, name='my_project', code='my',
description='a test project')
naming = DbNamingSchema(engine, project='my_project',
feature_kind='EST')
naming = FileNamingSchema(fhand, naming)
assert naming.get_uniquename(name='hola') == 'myES000001'
naming.commit()
assert naming.get_uniquename(name='caracol') == 'myES000002'
naming = FileNamingSchema(fhand, feature_kind='EST')
try:
assert naming.get_uniquename(name='caracol')
self.fail()
#pylint: disable-msg=W0704
except ValueError:
pass
def test_contig_member():
'It test that we can change the name in the fasta files.'
fhand_in = StringIO(EXAMPLES['contig_member'])
fhand_out = StringIO('')
engine = sqlalchemy.create_engine('sqlite:///:memory:')
filenaming_fhand = NamedTemporaryFile()
filenaming_fhand.write('METC053253:seq1\nMETC053254:seq2\n')
filenaming_fhand.flush()
create_naming_database(engine)
add_project_to_naming_database(engine, name='test_project', code='my',
description='a test project')
naming = FileNamingSchema(filenaming_fhand)
change_names_in_files(fhand_in, fhand_out, naming, 'contig_member')
output = fhand_out.getvalue()
assert "seq1" in output
assert "seq2" in output
def test_fasta():
'It test that we can change the name in the fasta files.'
fhand_in = StringIO(EXAMPLES['fasta'][0])
fhand_out = StringIO('')
engine = sqlalchemy.create_engine('sqlite:///:memory:')
create_naming_database(engine)
add_project_to_naming_database(engine, name='test_project', code='my',
description='a test project')
naming = DbNamingSchema(engine, 'test_project', feature_kind='EST')
change_names_in_files(fhand_in, fhand_out, naming, 'fasta')
assert fhand_out.getvalue() == EXAMPLES['fasta'][1]
# test it with file naming naming schema
#filenaming_fhand = open('/tmp/ppp', 'w')
filenaming_fhand = NamedTemporaryFile()
fhand_in = StringIO(EXAMPLES['fasta'][0])
fhand_out = StringIO('')
engine = sqlalchemy.create_engine('sqlite:///:memory:')
create_naming_database(engine)
add_project_to_naming_database(engine, name='my_project', code='my',
description='a test project')
naming = DbNamingSchema(engine, project='my_project',
feature_kind='EST')
naming = FileNamingSchema(filenaming_fhand, naming)
change_names_in_files(fhand_in, fhand_out, naming, 'fasta')
naming.commit()
assert fhand_out.getvalue() == EXAMPLES['fasta'][1]
fhand_in.seek(0)
filenaming_fhand.seek(0)
fhand_out = StringIO('')
naming = FileNamingSchema(filenaming_fhand, feature_kind='EST')
change_names_in_files(fhand_in, fhand_out, naming, 'fasta')
assert fhand_out.getvalue() == EXAMPLES['fasta'][1]