diff --git a/gga_load_data.py b/gga_load_data.py index f637fbcb655ec1da14ed72c42a45cc3bca89a4c0..1e2e5c00d453c69aae031283e758bf35f83630a3 100755 --- a/gga_load_data.py +++ b/gga_load_data.py @@ -69,7 +69,8 @@ class LoadData(speciesData.SpeciesData): """ logging.debug("Getting 'Homo sapiens' ID in chado database") - get_sapiens_id_job_output_dataset_id = utilities.run_tool_and_get_single_output_dataset_id(self.instance, + get_sapiens_id_job_output_dataset_id = utilities.run_tool_and_get_single_output_dataset_id( + self.instance, tool_id=constants.GET_ORGANISMS_TOOL, # If this version if not found, Galaxy will use the one that is found history_id=self.history_id, tool_inputs={"genus": "Homo", "species": "sapiens"}) @@ -80,6 +81,7 @@ class LoadData(speciesData.SpeciesData): get_sapiens_id_final_output = json.loads(get_sapiens_id_json_output)[0] sapiens_id = str(get_sapiens_id_final_output["organism_id"]) # needs to be str to be recognized by the chado tool utilities.run_tool( + self.instance, tool_id=constants.DELETE_ORGANISMS_TOOL, history_id=self.history_id, tool_inputs={"organism": sapiens_id})