Run wf

gga_run_workflow_phaeo_jbrowse.py

@@ -68,7 +68,9 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
 
         self.common = self.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 "Found a preexisting organism with the same attributes in the database"
+            self.common = self.common_name + "(" + self.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)
@@ -156,7 +158,9 @@ 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=30
+            )
             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
 
@@ -171,7 +175,7 @@ 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 +191,15 @@ 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 +232,7 @@ 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 +289,7 @@ 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()