fix for chado ids

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})