From 2eed92307f60b33249c665e82e8ce8dad753dd8d Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Tue, 4 May 2021 16:47:55 +0200
Subject: [PATCH] fix for chado ids
---
run_workflow_phaeoexplorer.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py
index 30ad7e5..3d800e7 100755
--- a/run_workflow_phaeoexplorer.py
+++ b/run_workflow_phaeoexplorer.py
@@ -287,7 +287,7 @@ class RunWorkflow(speciesData.SpeciesData):
org_job_out_id = add_org_job["outputs"][0]["id"]
org_json_output = self.instance.datasets.download_dataset(dataset_id=org_job_out_id)
org_output = json.loads(org_json_output)
- org_id = str(organism_output_dict["organism_id"]) # id needs to be a str to be recognized by chado tools
+ org_id = str(org_output["organism_id"]) # id needs to be a str to be recognized by chado tools
else:
add_org_job = self.instance.tools.run_tool(
tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_add_organism/organism_add_organism/%s" % tool_version,
@@ -299,7 +299,7 @@ class RunWorkflow(speciesData.SpeciesData):
org_job_out_id = add_org_job["outputs"][0]["id"]
org_json_output = self.instance.datasets.download_dataset(dataset_id=org_job_out_id)
org_output = json.loads(org_json_output)
- org_id = str(organism_output_dict["organism_id"]) # id needs to be a str to be recognized by chado tools
+ org_id = str(org_output["organism_id"]) # id needs to be a str to be recognized by chado tools
get_analyses = self.instance.tools.run_tool(
@@ -338,7 +338,7 @@ class RunWorkflow(speciesData.SpeciesData):
analysis_json_output = self.instance.datasets.download_dataset(dataset_id=analysis_job_out_id)
analysis_output = json.loads(analysis_json_output)
ogs_analysis_id = analysis_output["analysis_id"]
- ogs_analysis_id = str(analysis_output_dict["analysis_id"])
+ ogs_analysis_id = str(ogs_analysis_id["analysis_id"])
if genome_analysis_id is None:
add_genome_analysis_job = self.instance.tools.run_tool(
@@ -353,7 +353,7 @@ class RunWorkflow(speciesData.SpeciesData):
analysis_job_out_id = analysis_outputs[0]["id"]
analysis_json_output = self.instance.datasets.download_dataset(dataset_id=analysis_job_out_id)
analysis_output = json.loads(analysis_json_output)
- genome_analysis_id = str(analysis_output_dict["analysis_id"])
+ genome_analysis_id = str(analysis_output["analysis_id"])
print({"org_id": org_id, "genome_analysis_id": genome_analysis_id, "ogs_analysis_id": ogs_analysis_id})
return({"org_id": org_id, "genome_analysis_id": genome_analysis_id, "ogs_analysis_id": ogs_analysis_id})
--
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