Run wf

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
@@ -66,9 +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 != "":
-            self.common = 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 "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)
@@ -156,13 +157,14 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
                 tool_inputs={"abbr": self.abbreviation,
                              "genus": self.genus_uppercase,
                              "species": self.chado_species_name,
-                             "common": self.common})
+                             "common": self.common},
+                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,
@@ -194,7 +196,8 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
         if len(prj_lib) == 1:
             library_id = prj_lib[0].id
         else:
-            logging.error("Multiple (or no one) libraries '%s' exist" % constants.GALAXY_LIBRARY_NAME)
+            logging.critical("Multiple (or no one) libraries '%s' exist" % constants.GALAXY_LIBRARY_NAME)
+            sys.exit()
         folder_dict_list = self.instance.libraries.get_folders(library_id=str(library_id))
 
         folders_id_dict = {}
@@ -227,7 +230,7 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
                             elif ldda_name.endswith(self.gff_filename):
                                 gff_ldda_id = ldda_id
 
-        hda_list = self.instance.datasets.get_datasets(self.history_id)
+        hda_list = self.instance.datasets.get_datasets()
         # Finding datasets in history (matching datasets names)
         for hda in hda_list:
             hda_name = hda["name"]
@@ -580,10 +583,12 @@ if __name__ == "__main__":
                     species_strain_sex=species_strain_sex_org2,
                     id="{id}")
                 # Replace values in the workflow dictionary
-                jbrowse_tool_state_org1 = workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1]["tool_state"]
-                jbrowse_tool_state_org1 = jbrowse_tool_state_org1.replace("__MENU_URL_ORG1__", jbrowse_menu_url_org1)
-                jbrowse_tool_state_org2 = workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JRBOWSE_ORG2]["tool_state"]
-                jbrowse_tool_state_org2 = jbrowse_tool_state_org2.replace("__MENU_URL_ORG2__", jbrowse_menu_url_org2)
+                workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1]["tool_state"] = \
+                    workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1]["tool_state"]\
+                    .replace("__MENU_URL_ORG1__", jbrowse_menu_url_org1)
+                workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JRBOWSE_ORG2]["tool_state"] = \
+                    workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JRBOWSE_ORG2]["tool_state"]\
+                    .replace("__MENU_URL_ORG2__", jbrowse_menu_url_org2)
                 # The UNIQUE_ID is specific to a combination genus_species_strain_sex so every combination should have its unique workflow
                 # in galaxy --> define a naming method for these workflows
                 workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JB_TO_CONTAINER]["tool_state"] = \