def save_gene_signature(gene_signature):
"""Saves a gene signature and returns the extraction ID.
"""
with session_scope() as session:
session.add(gene_signature)
session.commit()
return gene_signature.extraction_id
def get_gene_signature(extraction_id):
"""Returns gene signature based on extraction ID.
"""
with session_scope() as session:
return session\
.query(GeneSignature)\
.filter(GeneSignature.extraction_id == extraction_id)\
.first()
def get_tag_by_name(tag_name):
"""Returns tag by name.
"""
with session_scope() as session:
return session\
.query(Tag)\
.filter_by(name=tag_name)\
.first()
def delete_gene_signature(extraction_id):
"""Deletes a gene signature by extraction ID.
"""
with session_scope() as session:
session\
.query(GeneSignature)\
.filter(GeneSignature.extraction_id == extraction_id)\
.delete()
def get_soft_files_by_accession(accession):
"""Returns a list of SOFT files based on a GEO dataset accession ID.
"""
with session_scope() as session:
return session\
.query(SoftFile)\
.filter(SoftFile.dataset_fk == GeoDataset.id)\
.filter(GeoDataset.accession == accession)\
.all()
def get_geo_dataset(accession):
"""Returns a GEO dataset based on accession number.
"""
with session_scope() as session:
instance = session\
.query(GeoDataset)\
.filter_by(accession=accession)\
.first()
return instance
def get_num_gene_signatures():
"""Returns the number of gene signatures in the database.
"""
with session_scope() as session:
return session.query(GeneSignature).count()
def update_object(obj):
"""Update object, i.e. saves any edits.
"""
with session_scope() as session:
session.merge(obj)
def delete_object(obj):
"""Deletes object provided.
"""
with session_scope() as session:
session.delete(obj)