From f3cef51b86686bc640ca501893ace3c303a24974 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Tue, 11 May 2021 18:07:44 +0200
Subject: [PATCH] Factorize run_tool()
---
gga_load_data.py | 18 +++++++-----------
utilities.py | 22 ++++++++++++++++++++++
2 files changed, 29 insertions(+), 11 deletions(-)
diff --git a/gga_load_data.py b/gga_load_data.py
index 4c18272..9590fd5 100755
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -67,25 +67,22 @@ class LoadData(speciesData.SpeciesData):
"""
logging.debug("Getting 'Homo sapiens' ID in chado database")
- get_sapiens_id_job = self.instance.tools.run_tool(
+ get_sapiens_id_job_output_dataset_id = utilities.run_tool_and_get_single_output_dataset_id(self.instance,
tool_id=GET_ORGANISMS_TOOL,
history_id=self.history_id,
tool_inputs={"genus": "Homo", "species": "sapiens"})
- get_sapiens_id_job_output_dataset_id = get_sapiens_id_job["outputs"][0]["id"]
get_sapiens_id_json_output = self.instance.datasets.download_dataset(dataset_id=get_sapiens_id_job_output_dataset_id)
+
+ logging.debug("Deleting Homo 'sapiens' in the instance's chado database")
try:
- logging.debug("Deleting Homo 'sapiens' in the instance's chado database")
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
- self.instance.tools.run_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(
tool_id=DELETE_ORGANISMS_TOOL,
history_id=self.history_id,
- tool_inputs={"organism": str(sapiens_id)})
- except bioblend.ConnectionError:
- logging.debug("Homo sapiens isn't in the instance's chado database (bioblend.ConnectionError)")
+ tool_inputs={"organism": sapiens_id})
except IndexError:
- logging.debug("Homo sapiens isn't in the instance's chado database (IndexError)")
+ logging.error("Homo sapiens isn't in the instance's chado database (IndexError)")
pass
def purge_histories(self):
@@ -98,7 +95,6 @@ class LoadData(speciesData.SpeciesData):
"""
histories = self.instance.histories.get_histories()
- self.instance.histories.get_histories(deleted=False)
for h in histories:
self.instance.histories.delete_history(history_id=h["id"])
diff --git a/utilities.py b/utilities.py
index 93c3e72..e633843 100755
--- a/utilities.py
+++ b/utilities.py
@@ -6,6 +6,7 @@ import logging
import sys
import os
import subprocess
+import bioblend
def parse_config(config_file):
@@ -172,3 +173,24 @@ def get_unique_species_dict_list(sp_dict_list):
unique_species_list_of_dict.append(v)
return unique_species_list_of_dict
+
+def run_tool(instance, tool_id, history_id, tool_inputs):
+
+ output_dict = None
+ try:
+ logging.debug("Running tool {0} with tool inputs: {1}".format(tool_id, tool_inputs))
+ output_dict = instance.tools.run_tool(
+ tool_id=tool_id,
+ history_id=history_id,
+ tool_inputs=tool_inputs)
+ except bioblend.ConnectionError:
+ logging.error("Unexpected HTTP response (bioblend.ConnectionError) when running tool {0} with tool inputs: {1}".format(tool_id, tool_inputs))
+
+ return output_dict
+
+def run_tool_and_get_single_output_dataset_id(instance, tool_id, history_id, tool_inputs):
+
+ output_dict = run_tool(instance, tool_id, history_id, tool_inputs)
+ single_output_dataset_id = output_dict["outputs"][0]["id"]
+
+ return single_output_dataset_id
\ No newline at end of file
--
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