def get_all(self):
"""
get all the genus on the database
:return: json file with all the data
:rtype: string (json format)
"""
result_get = GetRest(function=self.function).performRequest()
return result_get
def get_by_id(self, id_genus: int):
"""
get a genus given it id
:param id_genus: id of the genus
:type id_genus: int
:return: json file with all the data
:rtype: string (json format)
"""
self.function += str(id_genus) + '/'
result_get = GetRest(function=self.function).performRequest()
return result_get
def getBacteriophageByAcc(self, acc_value):
"""
return a bacteriophage according to its acc
:param acc_value: accession number of the bacteriophage that you want to return
:type acc_value: string
:return: json file with all the data
:rtype: string (json format)
"""
self.function += 'accnumber/' + acc_value + '/'
result_get = GetRest(function=self.function).performRequest()
return result_get
def getCouplesByParameters(self, url_parameters: str):
"""
return a couple according the parameters you send
:param url_parameters: string that contains the parameters values (that design the fields)
:type url_parameters: str
:return: json file with all the data
:rtype: string (json format)
"""
self.function += '?' + url_parameters
result_get = GetRest(function=self.function).performRequest()
return result_get
def getById(self, id_cog_interaction_pair: int):
"""
get a cog interaction pair given it id
:param id_cog_interaction_pair: id of the cog interaction pair
:type id_cog_interaction_pair: int
:return: json file with all the data
:rtype: string (json format)
"""
self.function += str(id_cog_interaction_pair) + '/'
result_get = GetRest(function=self.function).performRequest()
return result_get
def getById(self, id_cog_score: int):
"""
get a Cog Score given it id
:param id_cog_score: id of the cog score
:type id_cog_score: int
:return: json file with all the data
:rtype: string (json format)
"""
self.function += str(id_genus) + '/'
result_get = GetRest(function=self.function).performRequest()
return result_get
def getBacteriophageByDesignation(self, designation):
"""
Get a bacteriophage exists according a designation
:param designation: designation name of a bacteriophage
:type designation: string
:return: json file with all the data
:rtype: string (json format)
"""
self.function += 'design/' + designation + '/'
result_get = GetRest(function=self.function).performRequest()
return result_get
def getByOrganismID(self, organism_id):
"""
get all proteins of a given organism
:param organism_id: organism ID
:type organism_id: int
:return: all the proteins of the given organism id
:rtype: ProteinJson
"""
self.function += 'organism_id/' + str(organism_id)
result_get = GetRest(function=self.function).performRequest()
return result_get
def setBacteriumExistsByAcc(self, acc_value):
"""
Verify if a bacterium exists according an accValue
:param acc_value: accession number of the bacterium that you want to check the existence
:type acc_value: string
:return: json file with all the data
:rtype: string (json format)
"""
self.function += 'accnumber/' + acc_value + '/exists/'
result_get = GetRest(function=self.function).performRequest()
return result_get
def getById(self, id_cog_source_info: int):
"""
get a cog source information given it id
:param id_cog_source_info: id of the cog
:type id_cog_source_info: int
:return: json file with all the data
:rtype: string (json format)
"""
self.function += str(id_cog) + '/'
result_get = GetRest(function=self.function).performRequest()
return result_get
def getCoupleByBactPhageIds(self, bact_id: int, phage_id: int):
"""
return a couple according the ids of the bacterium and phage
:param bact_id: If of the bacterium
:param phage_id: If of the bacteriophage
:type bact_id: int
:type phage_id: int
:return: json file with all the data
:rtype: string (json format)
"""
self.function += 'organismsid/' + str(bact_id) + '/' + str(
phage_id) + '/'
result_get = GetRest(function=self.function).performRequest()
return result_get
def getByDesignationFkSpecie(self, designation, fk_specie):
"""
Verify if a strain already exists in the database given a designation and fk_specie
:param designation: designation of the strain
:param fk_specie: fk of the specie
:type designation: string
:type fk_specie: integer
:return: json file with all the data
:rtype: string (json format)
"""
self.function += 'existdesignstrain/' + designation + '/' + str(
fk_specie) + '/'
result_get = GetRest(function=self.function).performRequest()
return result_get
def getIdDDISource(self, id_ddi:int, id_source:int):
"""
get teh id of a ddi source data if already exists in the database
:param id_ddi: ID of the DDI
:param id_source: ID of the Source
:type id_ddi: int
:type id_source: int
:return: json that contain the information about the existence and the id or -1
:rtype: string (json format)
"""
self.function += 'ddi_info_source_existence/' + str(id_ddi) + '/' + str(id_source)
result_get = GetRest(function = self.function).performRequest()
return result_get
def getIdDDIID(self, pfam_a_id: int, pfam_b_id: int):
"""
verify if a ddi already exists given the PFAM a and PFAM B (it verify the reverse)
:param pfam_a_id: ID PFAM domain A
:param pfam_b_id: ID PFAM domain A
:type pfam_a_id: int
:type pfam_b_id: int
:return: json file with the last domain created
:rtype: string (json format)
"""
self.function += 'ddi_existence_id/' + str(pfam_a_id) + '/' + str(
pfam_b_id)
result_get = GetRest(function=self.function).performRequest()
return result_get
def getIdDDI(self, pfam_a: str, pfam_b: str):
"""
verify if a ddi already exists given the PFAM a and PFAM B (it verify the reverse)
:param pfam_a: PFAM domain A
:param pfam_b: PFAM domain A
:type pfam_a: string
:type pfam_b: string
:return: json file with the last domain created
:rtype: string (json format)
"""
pfam_a = pfam_a.upper()
pfam_b = pfam_b.upper()
self.function += 'ddi_existence/' + str(pfam_a) + '/' + str(pfam_b)
result_get = GetRest(function=self.function).performRequest()
return result_get