def test_commit_intermediate_results(self):
src = ecmdb.Ecmdb(cache_dirname=self.cache_dirname,
download_backups=False,
load_content=False,
verbose=True,
max_entries=5,
commit_intermediate_results=True)
src.load_content()
def test_download_all(self):
src = ecmdb.Ecmdb(download_backups=False,
load_content=True,
clear_content=True,
clear_requests_cache=False,
verbose=True)
src.upload_backups()
session = src.session
self.assertGreater(session.query(ecmdb.Compound).count(), 3500)
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
src = ecmdb.Ecmdb(cache_dirname=cls.cache_dirname,
download_backups=False,
load_content=False,
verbose=True,
max_entries=12)
src.load_content()
src.session.close()
src.engine.dispose()
def build_ecmdb(self):
"""
Collects ECMDB.sqlite file and integrates its data into the common ORM
"""
ecmDB = ecmdb.Ecmdb(
cache_dirname=self.cache_dirname, verbose=self.verbose)
ecm_ses = ecmDB.session
ecmdb_compound = ecm_ses.query(ecmdb.Compound).all()
max_entries = self.max_entries
if self.load_entire_small_dbs:
max_entries = float('inf')
entries = 0
for metabolite in ecmdb_compound:
if entries < max_entries:
concentration = metabolite.concentrations
ref = metabolite.cross_references
compart = metabolite.compartments
syn = metabolite.synonyms
metadata = self.get_or_create_object(
models.Metadata, name=metabolite.name)
tax = self.session.query(
models.Taxon).filter_by(ncbi_id=562).first()
metadata.taxon.append(tax) if tax else metadata.taxon.append(
self.get_or_create_object(models.Taxon, ncbi_id=562))
metadata.resource = [self.get_or_create_object(
models.Resource, namespace=docs.namespace, _id=docs.id) for docs in ref]
metadata.cell_compartment = [self.get_or_create_object(
models.CellCompartment, name=areas.name) for areas in compart]
metadata.synonym = [self.get_or_create_object(
models.Synonym, name=syns.name) for syns in syn]
self.property.structure = self.get_or_create_object(models.Structure, type='Structure', name=metabolite.name,
_value_inchi=metabolite.structure,
_structure_formula_connectivity=metabolite._structure_formula_connectivity, _metadata=metadata)
self.entity.metabolite = self.get_or_create_object(models.Metabolite, type='Metabolite', name=metabolite.name,
metabolite_name=metabolite.name, description=metabolite.description, comment=metabolite.comment, structure=self.property.structure,
_metadata=metadata)
index = 0 if concentration else -1
if index == -1:
continue
for rows in concentration:
new_metadata = self.get_or_create_object(
models.Metadata, name=metabolite.name + ' Concentration ' + str(index))
new_metadata.taxon = metadata.taxon
new_metadata.cell_compartment = metadata.cell_compartment
new_metadata.synonym = metadata.synonym
new_metadata.cell_line.append(
self.get_or_create_object(models.CellLine, name=rows.strain))
new_metadata.conditions.append(self.get_or_create_object(models.Conditions, growth_status=rows.growth_status,
media=rows.media, temperature=rows.temperature, growth_system=rows.growth_system))
new_metadata.resource = [self.get_or_create_object(
models.Resource, namespace=docs.namespace, _id=docs.id) for docs in rows.references]
self.property.concentration = self.get_or_create_object(models.Concentration, type='Concentration', name=metabolite.name + ' Concentration ' + str(index),
value=rows.value, error=rows.error, units='uM', _metadata=new_metadata, metabolite=self.entity.metabolite)
index += 1
entries += 1
self.vprint('Comitting')
self.session.commit()
def setUp(self):
self.src = ecmdb.Ecmdb(cache_dirname=self.cache_dirname,
download_backups=False,
load_content=False,
verbose=True,
max_entries=12)
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
cls.src = ecmdb.Ecmdb(cache_dirname=cls.cache_dirname,
download_backups=True,
load_content=False,
verbose=True)
def test_download_from_backup(self):
src = ecmdb.Ecmdb(cache_dirname=self.cache_dirname)
session = src.session
self.assertGreater(session.query(ecmdb.Compound).count(), 3500)