From 59992b0069040dd018d55a9caf9eddf0dafd7491 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Sun, 16 May 2021 15:07:15 +0200
Subject: [PATCH] fix run_tool call
---
gga_load_data.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/gga_load_data.py b/gga_load_data.py
index f637fbc..1e2e5c0 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})
--
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