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Commit 59992b00 authored by Loraine Gueguen's avatar Loraine Gueguen
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fix run_tool call

parent ea09cb2e
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2 merge requests!12Release_2.0 next,!9Release 2.0 (merge dev to master)
...@@ -69,7 +69,8 @@ class LoadData(speciesData.SpeciesData): ...@@ -69,7 +69,8 @@ class LoadData(speciesData.SpeciesData):
""" """
logging.debug("Getting 'Homo sapiens' ID in chado database") 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 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, history_id=self.history_id,
tool_inputs={"genus": "Homo", "species": "sapiens"}) tool_inputs={"genus": "Homo", "species": "sapiens"})
...@@ -80,6 +81,7 @@ class LoadData(speciesData.SpeciesData): ...@@ -80,6 +81,7 @@ class LoadData(speciesData.SpeciesData):
get_sapiens_id_final_output = json.loads(get_sapiens_id_json_output)[0] 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 sapiens_id = str(get_sapiens_id_final_output["organism_id"]) # needs to be str to be recognized by the chado tool
utilities.run_tool( utilities.run_tool(
self.instance,
tool_id=constants.DELETE_ORGANISMS_TOOL, tool_id=constants.DELETE_ORGANISMS_TOOL,
history_id=self.history_id, history_id=self.history_id,
tool_inputs={"organism": sapiens_id}) tool_inputs={"organism": sapiens_id})
......
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