def test_mass_analyzers(self):
"""Add mass analyzer info to files"""
with tempfile.TemporaryDirectory() as temp_path:
test_db_path = "sqlite:///" + temp_path + "/phosphopedia.db"
# Add fake raw files to database
nfiles = 10
for ind in range(nfiles):
open(temp_path + f"/file_{ind}.raw", "w").close()
print()
dataset_manager = managers.DatasetManager(test_db_path)
dataset_manager.add_datasets([temp_path])
sample_manager = managers.SampleManager(test_db_path)
analyzer_file_id = sample_manager.lookup_id("LOC000001", "file_1")
with self.assertRaises(NoResultFound):
sample_manager.get_parameters(analyzer_file_id)
sample_manager.add_mass_analyzers(analyzer_file_id, "FTMS", "ITMS")
params = sample_manager.get_parameters(analyzer_file_id)
self.assertEqual(params.ms1Analyzer, "FTMS")
self.assertEqual(params.ms2Analyzer, "ITMS")
sample_manager.add_mass_analyzers(analyzer_file_id, "FTMS", "FTMS")
params = sample_manager.get_parameters(analyzer_file_id)
self.assertEqual(params.ms1Analyzer, "FTMS")
self.assertEqual(params.ms2Analyzer, "FTMS")
def test_local_update(self):
"""Load in raw files saved in a local drive"""
with tempfile.TemporaryDirectory() as temp_path:
test_db_path = "sqlite:///" + temp_path + "/phosphopedia.db"
# Add fake raw files to database
nfiles = 100
for ind in range(nfiles):
open(temp_path + f"/file_{ind}.raw", "w").close()
print()
manager = managers.DatasetManager(test_db_path)
manager.add_datasets([temp_path])
# Make sure all files added
sample_query = manager.database\
.session\
.query(schema.Sample)\
.order_by(schema.Sample.sampleName)
sample_entries = manager.database.safe_run(sample_query.all)
self.assertEqual(len(sample_entries), nfiles)
# Add more fake raw files
nfiles = 150
for ind in range(nfiles):
open(temp_path + f"/file_{ind}.raw", "w").close()
print()
manager.add_datasets([temp_path])
# Make sure dataset only added once and new files added
dataset_query = manager.database\
.session\
.query(schema.Dataset)\
.filter(schema.Dataset.title == temp_path.split("/")[-1])
dataset_entries = manager.database.safe_run(dataset_query.all)
self.assertEqual(len(dataset_entries), 1)
sample_query = manager.database\
.session\
.query(schema.Sample)\
.order_by(schema.Sample.sampleName)
sample_entries = manager.database.safe_run(sample_query.all)
self.assertEqual(len(sample_entries), nfiles)
def test_error(self):
"""Add error code to files"""
with tempfile.TemporaryDirectory() as temp_path:
test_db_path = "sqlite:///" + temp_path + "/phosphopedia.db"
# Add fake raw files to database
nfiles = 10
for ind in range(nfiles):
open(temp_path + f"/file_{ind}.raw", "w").close()
print()
dataset_manager = managers.DatasetManager(test_db_path)
dataset_manager.add_datasets([temp_path])
sample_manager = managers.SampleManager(test_db_path)
error_file_id = sample_manager.lookup_id("LOC000001", "file_0")
sample_manager.add_error(error_file_id, "testError")
manifest = sample_manager.get_sample_manifest()
self.assertEqual(manifest.shape[0], nfiles - 1)
def test_remote_update(self):
"""Test remote connection to ProteomeXchange"""
prev_wd = os.getcwd()
with tempfile.TemporaryDirectory() as temp_path:
os.chdir(temp_path)
test_db_path = "sqlite:///" + temp_path + "/phosphopedia.db"
print()
accession = "PXD001492"
manager = managers.DatasetManager(test_db_path)
manager.add_datasets([accession])
# Make sure all files added
project = ppx.find_project(accession, local=temp_path)
nfiles = len(project.remote_files("*.raw"))
sample_query = manager.database\
.session\
.query(schema.Sample)\
.order_by(schema.Sample.sampleName)
sample_entries = manager.database.safe_run(sample_query.all)
self.assertEqual(len(sample_entries), nfiles)
os.chdir(prev_wd)