fix time_sleep and chado_species_name. Change common_name for org

gga_run_workflow_phaeo_jbrowse.py

@@ -7,7 +7,6 @@ import os
 import logging
 import sys
 import json
-import time
 from bioblend.galaxy.objects import GalaxyInstance
 
 import utilities
@@ -66,11 +65,11 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
 
         self.abbreviation = self.genus_uppercase[0] + ". " + self.chado_species_name
 
-        self.common = self.name
+        self.common = self.genus_uppercase + " " + self.chado_species_name
         if not self.common_name is None and self.common_name != "":
             # common_name only is not sufficient as may not be unique between the different strains of the species and
-            # galaxy will throw error "Found a preexisting organism with the same attributes in the database"
-            self.common = self.common_name + "(" + self.name + ")"
+            # galaxy will throw error "OrgWorkflowParam"
+            self.common = self.common + " (" + self.common_name + ")"
 
         self.genome_analysis_name = "genome v{0} of {1}".format(self.genome_version, self.full_name)
         self.genome_analysis_programversion = "genome v{0}".format(self.genome_version)
@@ -159,14 +158,13 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
                              "genus": self.genus_uppercase,
                              "species": self.chado_species_name,
                              "common": self.common},
-                time_sleep=30
+                time_sleep=10
             )
             organism_dict = json.loads(add_organism_tool_dataset)
             org_id = str(organism_dict["organism_id"])  # id needs to be a str to be recognized by chado tools
 
         # Synchronize newly added organism in Tripal
         logging.info("Synchronizing organism %s in Tripal" % self.full_name)
-        time.sleep(60)
         utilities_bioblend.run_tool(
             instance=self.instance,
             tool_id=constants_phaeo.ORGANISM_SYNC_TOOL_ID,

runWorkflowPhaeo.py

@@ -3,7 +3,6 @@
 
 import logging
 import json
-import time
 
 import utilities_bioblend
 import speciesData
@@ -15,7 +14,7 @@ class OrgWorkflowParam:
     def __init__(self, genus_uppercase, chado_species_name, full_name, species_folder_name,
                  org_id, history_id, instance):
         self.genus_uppercase = genus_uppercase
-        self.chado_species_name = chado_species_name,
+        self.chado_species_name = chado_species_name
         self.full_name = full_name
         self.species_folder_name = species_folder_name
         self.org_id = org_id
@@ -79,7 +78,7 @@ class RunWorkflow(speciesData.SpeciesData):
                          "programversion": programversion,
                          "sourcename": sourcename,
                          "date_executed": constants_phaeo.ADD_ANALYSIS_TOOL_PARAM_DATE},
-            time_sleep = 30
+            time_sleep = 10
         )
         analysis_dict = json.loads(add_analysis_tool_dataset)
         analysis_id = str(analysis_dict["analysis_id"])
@@ -88,7 +87,6 @@ class RunWorkflow(speciesData.SpeciesData):
 
     def sync_analysis(self, analysis_id):
 
-        time.sleep(60)
         utilities_bioblend.run_tool(
             instance=self.instance,
             tool_id=constants_phaeo.ANALYSIS_SYNC_TOOL_ID,