def create_organism(self):
"""
Insert an organism in the database. If its a:
- Phage, insert without verify if it exists in the database
- Bacterium, insert after verifying if any other bacterium with the same GI OR accession number exists in the database
The id of the organis is updated
:return: id of the organism
:rtype: int
"""
value_organisme = None
sqlObj = _Organisms_sql_new()
if self.fk_type == 2:
value_organisme = sqlObj.insert_organisme_phage(
self.gi, self.acc_num, self.qty_proteins, self.assembled,
self.qty_contig, self.fk_source, self.fk_strain, self.fk_type,
self.fk_whole_genome, self.fk_source_data)
else:
value_organisme = sqlObj.insert_organism_if_not_exist(
self.gi, self.acc_num, self.qty_proteins, self.assembled,
self.qty_contig, self.fk_source, self.fk_strain, self.fk_type,
self.fk_whole_genome, self.fk_source_data)
self.id_organism = value_organisme
return value_organisme
def get_organism_id_by_strain_like(strain_design_end):
dict_orga = {}
sqlObj = _Organisms_sql_new()
orga_result = sqlObj.get_organism_id_design_By_end_strain(
strain_design_end)
for elements in orga_result:
dict_orga[elements[0]] = [elements[1], elements[2]]
return dict_orga
def get_id_organism_by_acc(acc):
"""
get id organism based on its acc. it is work only if the acc is different that NA
:return: id of the organism
:rtype: int
"""
id_organism = -1
sqlObj = _Organisms_sql_new()
if (acc.lower() != 'na'):
id_organism = sqlObj.get_id_organism_by_acc(acc)
return id_organism
def remove_organism_by_id(id_organism):
"""
remove an organism given its id
:param id_organism: id of the organism
:type id_organism: int - required
:return: whole dna id removed
:rtype: int
"""
sqlObj = _Organisms_sql_new()
id_couple = sqlObj.remove_organism_by_id(id_organism)
return id_couple
def get_ids_all_organisms():
"""
get a list of all organisms ids in the database
:return: list of ids
:rtype: list(int)
"""
list_ids = []
sqlObj = _Organisms_sql_new()
results = sqlObj.get_ids_all_organisms()
if len(results) > 0:
for element in results:
list_ids.append(element[0])
return list_ids
def get_id_fk_whole_dna_by_id(self, id_organism):
"""
get the organism ID given the whole genome ID
:param id_organism: Whole genome id
:type id_organism: id_organism - required
:return: id of the organism
:rtype: int
"""
sqlObj = _Organisms_sql_new()
fk_whole_dna = sqlObj.get_fk_whoe_dna_from_id(id_organism)
return fk_whole_dna
def get_id_organism_by_designation(designation):
"""
get id organism based on its designation
:param designation: designation of the organism
:type designation: designation - required
:return: id of the organism
:rtype: int
"""
sqlObj = _Organisms_sql_new()
id_organism = -1
id_organism = sqlObj.get_id_organism_by_strain_designation(designation)
return id_organism
def get_all_Organisms():
"""
Return all organisms in the database
:return: array of Organism
:rtype: array(Organism)
"""
listOfOrganisms = []
sqlObj = _Organisms_sql_new()
results = sqlObj.select_all_organisms_all_attributes()
for element in results:
listOfOrganisms.append(
Organism(element[0], element[1], element[2], element[3],
element[4], element[5], element[6], element[7],
element[8], element[9]))
return listOfOrganisms
def create_bacterium_with_verification(self):
"""
Insert a Bacterium (organism) in the database only if any other phage exists with the same designation
The id of the organis is updated
:return: id of the organism
:rtype: int
"""
sqlObj = _Organisms_sql_new()
id_organism = sqlObj.insert_organism_no_validation(
self.gi, self.acc_num, self.qty_proteins, self.assembled,
self.qty_contig, self.fk_source, self.fk_strain, self.fk_type,
self.fk_whole_genome, self.fk_source_data)
self.id_organism = id_organism
return id_organism
def get_organism_by_id(id_organism):
"""
Get an organism by its id
:return: Organism object
:rtype: Organism
"""
sqlObj = _Organisms_sql_new()
orga_result = sqlObj.get_organism_by_id(id_organism)
if orga_result != -1:
orga_obj = Organism(orga_result[0], orga_result[1], orga_result[2],
orga_result[3], orga_result[4], orga_result[5],
orga_result[6], orga_result[7], orga_result[8],
orga_result[9], orga_result[10])
return orga_obj
else:
print('No organism with this id')
return -1
def get_organism_id_by_acc_or_designation(acc, designation):
"""
get the organism ID given the acc and the designation. First the acc is checked and if it is 'NA' it check the designation in strain table. It check that the organisme need to be a phage. The organism need to be a phage. If there is any one it is return -1
:param designation: designation of the Phage
:type designation: id_organism - required
:return: id of the organism
:rtype: int
"""
id_organism = -1
sqlObj = _Organisms_sql_new()
if (acc.lower() != 'na'):
id_organism = sqlObj.get_id_organism_by_acc(acc)
elif (id_organism == -1):
id_organism = sqlObj.get_id_organism_by_strain_designation(
designation)
return id_organism
def get_id_organism_by_taxonomy(self, genus, specie, strain):
"""
get the organism id based on the taxonomy designations.
:param genus: designation of the genus
:param specie: designation of the specie
:param strain: designation of the strain
:type genus: string - required
:type specie: string - required
:type strain: string - required
:return: id of the organism
:rtype: int
"""
sqlObj = _Organisms_sql_new()
id_organism = sqlObj.get_organism_list_id_by_taxonomy_sql(
genus, specie, strain)
return id_organism
def get_ids_all_organisms_by_params(type_organism=1, source_data=1):
"""
get a list of all organisms by type and source of data
:param type_organism: type of organism (Bacterium, Phage,...)
:param source_data: source of data (NCBI, PhageDB, RAST,...)
:type type_organism: designation - required
:type source_data: designation - required
:return: list of ids
:rtype: list(int)
"""
list_ids = []
sqlObj = _Organisms_sql_new()
results = sqlObj.get_ids_all_organisms_by_type_and_source_data(
type_organism, source_data)
if len(results) > 0:
for element in results:
list_ids.append(element[0])
return list_ids
def get_organism_by_fk_strain(fk_id_strain):
"""
get all organism give the fk of the strain
:param fk_id_strain: id of the specie
:type fk_id_strain: int - required
:return: list of organisms
:rtype: int
"""
listOfOrganisms = []
sqlObj = _Organisms_sql_new()
results = sqlObj.select_all_organisms_all_attributes_by_strain(
fk_id_strain)
for element in results:
listOfOrganisms.append(
Organism(element[0], element[1], element[2], element[3],
element[4], element[5], element[6], element[7],
element[8], element[9], element[10]))
return listOfOrganisms
def get_all_organisms_by_type(fk_type):
"""
get all organisms by type.
NOTE: 1 - Bacteirum
2- Phage
:param fk_type: id of the type
:type fk_type: int - required
:return: list of organisms
:rtype: int
"""
listOfOrganisms = []
sqlObj = _Organisms_sql_new()
results = sqlObj.select_all_organisms_all_attributes_by_type(fk_type)
for element in results:
listOfOrganisms.append(
Organism(element[0], element[1], element[2], element[3],
element[4], element[5], element[6], element[7],
element[8], element[9]))
return listOfOrganisms