def get(self, ref_taxonid, comp_taxonid, chromosome):
# check that the reference species are available in the application
ref_species_exists = check_species_exists(ref_taxonid)
if ref_species_exists is False:
message = f'The species with ID: <{ref_taxonid}> is not represented in the database ' \
f'and thus there is no associated genes data.'
raise InvalidRequestArgumentValueException(400, message)
# check that the comparison species are available in the application
comp_species_exists = check_species_exists(comp_taxonid)
if comp_species_exists is False:
message = f'The species with ID: <{comp_taxonid}> is not represented in the database ' \
f'and thus there is no associated genes data.'
raise InvalidRequestArgumentValueException(400, message)
# check that the reference chromosome is valid (for that species)
chromosome_exists = check_chromosome_exists(ref_taxonid, chromosome)
if chromosome_exists is False:
message = f'The species with ID: <{ref_taxonid}> does not have chromosome: <{chromosome}>'
raise InvalidRequestArgumentValueException(400, message)
res = get_homologs_by_species_ids_and_reference_chromosome(
ref_taxonid, comp_taxonid, chromosome)
return res, 200
def get(self, species_id, trait_id, chromosome):
"""
Returns SNP variants data for the specified species, trait and chromosome.
"""
# check whether the specified species is available in the application
species_exists = check_species_exists(species_id)
if species_exists is False:
message = f'The species with ID: <{species_id}> is not represented in the database and thus there is ' \
f'no associated SNP variants data.'
raise InvalidRequestArgumentValueException(400, message)
# check whether there is data available for that trait
trait_exists = check_trait_exists(species_id, trait_id)
if trait_exists is False:
message = f'The species with ID: <{species_id}> is represented in the database, ' \
f'but there is no SNP variants data available for trait with ID: <{trait_id}>. ' \
f'Please check the documentation to make sure the correct trait ID is provided.'
raise InvalidRequestArgumentValueException(400, message)
# check that the specified chromosome is valid (for that species)
chromosome_exists = check_chromosome_exists(species_id, chromosome)
if chromosome_exists is False:
message = f'The species with ID: <{species_id}> is represented in the database, ' \
f'but has no associated data for chromosome: <{chromosome}>.'
raise InvalidRequestArgumentValueException(400, message)
res = get_snps_by_species_trait_and_chromosome(species_id, trait_id,
chromosome)
return res, 200
def get(self, species_id):
"""
Returns cytogenetic bands data for the specified species.
"""
species_exists = check_species_exists(species_id)
if species_exists is False:
message = f'The species with ID: <{species_id}> is not represented in the database and thus there is ' \
f'no associated bands data.'
raise InvalidRequestArgumentValueException(400, message)
res = get_bands_by_species(species_id)
return res, 200
def _get_genes_data_by_species_and_chromosome(species_id, chromosome):
"""
Calls a service to get features based on specific species and chromosome, checks the result and handles a response.
:param species_id: NCBI species ID, such as 9606 (H. sapiens), 10090 (M. musculus), etc.
:param chromosome: species chromosome ID
:return: a list of Gene objects (or an empty) and a status code
"""
res = get_genes_by_species_chromosome(species_id, chromosome)
if not res:
species_exists = check_species_exists(species_id)
if species_exists:
message = f'The species with ID: <{species_id}> is represented in the database, ' \
f'but has no associated data for chromosome: <{chromosome}>.'
else:
message = f'The species with ID: <{species_id}> is not represented in the database and thus there is ' \
f'no associated genes data.'
abort(400, message=message)
return res, 200
def get(self, species_id, chromosome):
"""
Returns cytogenetic bands data for the specified species and chromosome.
"""
# check that the species are available in the application
species_exists = check_species_exists(species_id)
if species_exists is False:
message = f'The species with ID: <{species_id}> is not represented in the database and thus there is ' \
f'no associated cytogenetic bands data.'
raise InvalidRequestArgumentValueException(400, message)
# check that the specified chromosome is valid (for that species)
chromosome_exists = check_chromosome_exists(species_id, chromosome)
if chromosome_exists is False:
message = f'The species with ID: <{species_id}> is represented in the database, ' \
f'but has no associated data for chromosome: <{chromosome}>.'
raise InvalidRequestArgumentValueException(400, message)
res = get_bands_by_species_and_chromosome(species_id, chromosome)
return res, 200