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,
@@ -171,7 +173,7 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
 
         return org_id
 
-    def import_datasets_into_history(self):
+    def import_datasets_into_history(self, config):
         """
         Find datasets in a library, get their ID and import them into the current history if they are not already
         """
@@ -187,14 +189,15 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
         proteins_hda_id = None
 
         gio = GalaxyInstance(url=self.instance_url,
-                             email=self.config[constants.CONF_GALAXY_DEFAULT_ADMIN_EMAIL],
-                             password=self.config[constants.CONF_GALAXY_DEFAULT_ADMIN_PASSWORD]
+                             email=config[constants.CONF_GALAXY_DEFAULT_ADMIN_EMAIL],
+                             password=config[constants.CONF_GALAXY_DEFAULT_ADMIN_PASSWORD]
                              )
         prj_lib = gio.libraries.get_previews(constants.GALAXY_LIBRARY_NAME)
         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"]
@@ -284,7 +287,7 @@ def prepare_history_and_get_wf_param(sp_dict_list, main_dir, config):
             run_workflow_for_current_organism.set_galaxy_instance(config)
             run_workflow_for_current_organism.set_history()
             run_workflow_for_current_organism.install_individual_tools()
-            run_workflow_for_current_organism.import_datasets_into_history()
+            run_workflow_for_current_organism.import_datasets_into_history(config)
 
             analyses_dict_list = run_workflow_for_current_organism.get_analyses()