Workflow v2

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(
@@ -337,8 +337,7 @@ 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)
-            ogs_analysis_id = analysis_output["analysis_id"] 
-            ogs_analysis_id = str(analysis_output_dict["analysis_id"])
+            ogs_analysis_id = str(analysis_output["analysis_id"]) 
                     
         if genome_analysis_id is None:
             add_genome_analysis_job = self.instance.tools.run_tool(
@@ -353,9 +352,9 @@ 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})
+        # 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})
 
 
@@ -988,7 +987,7 @@ if __name__ == "__main__":
             logging.info("Input organism %s: 2 species detected in input dictionary" % k)
 
             # Set workflow path (2 organisms)
-            workflow_path = os.path.join(os.path.abspath(script_dir), "workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v3.ga")
+            workflow_path = os.path.join(os.path.abspath(script_dir), "workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v2.ga")
 
             # Instance object required variables
             instance_url, email, password = None, None, None
@@ -1085,7 +1084,6 @@ if __name__ == "__main__":
             
             # Look for empty parameters values, throw a critical error if a parameter value is invalid
             for param_name, param_value in org2_parameters_dict.items():
-                logging.info("Parameters for organism 1 (%s)" % org2_full_name)
                 if param_value is None or param_value == "":
                     logging.critical("Empty parameter found for organism {0} (parameter: {1}, parameter value: {2})".format(org2_full_name, param_name, param_value))
                     sys.exit()