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