Run wf

gga_load_data.py

@@ -2,7 +2,6 @@
 # -*- coding: utf-8 -*-
 import re
 
-import bioblend
 import argparse
 import os
 import logging
@@ -39,27 +38,6 @@ class LoadData(speciesData.SpeciesData):
         self.bam_metadata_cache = {}
         super().__init__(parameters_dictionary)
 
-    def get_history(self):
-        """
-        Create or set the working history to the current species one
-
-        :return:
-        """
-        try:
-            histories = self.instance.histories.get_histories(name=str(self.genus_species))
-            if len(histories) == 1:
-                self.history_id = histories[0]["id"]
-                logging.debug("History ID set for {0} {1}: {2}".format(self.genus, self.species, self.history_id))
-            else:
-                logging.critical("Multiple histories exists for {0}: {1}".format(self.genus, self.species))
-        except IndexError:
-            logging.info("Creating history for {0} {1}".format(self.genus, self.species))
-            hist_dict = self.instance.histories.create_history(name=str(self.genus_species))
-            self.history_id = hist_dict["id"]
-            logging.debug("History ID set for {0} {1}: {2}".format(self.genus, self.species, self.history_id))
-
-        return self.history_id
-
     def remove_homo_sapiens_from_db(self):
         """
         Run the GMOD tool to remove the "Homo sapiens" default organism from the original database
@@ -130,7 +108,7 @@ class LoadData(speciesData.SpeciesData):
             existing = gio.libraries.get_previews(name=constants.GALAXY_LIBRARY_NAME)
             for lib in existing:
                 if not lib.deleted:
-                    logging.info('Pre-existing {0} library {1}} found, removing it'.format(constants.GALAXY_LIBRARY_NAME, lib.id))
+                    logging.info('Pre-existing {0} library {1} found, removing it'.format(constants.GALAXY_LIBRARY_NAME, lib.id))
                     gio.libraries.delete(lib.id)
 
             logging.info("Creating new %s library" % constants.GALAXY_LIBRARY_NAME)
@@ -304,6 +282,7 @@ if __name__ == "__main__":
         logging.basicConfig(level=logging.DEBUG)
     else:
         logging.basicConfig(level=logging.INFO)
+    logging.getLogger("urllib3").setLevel(logging.INFO)
 
     # Parsing the config file if provided, using the default config otherwise
     if args.config:
@@ -360,7 +339,9 @@ if __name__ == "__main__":
             logging.debug("Successfully set up library in galaxy for {0} {1}".format(load_data_for_current_species.genus, load_data_for_current_species.species))
 
             # Set or get the history for the current organism
-            load_data_for_current_species.get_history()
+            load_data_for_current_species.history_id = utilities_bioblend.get_history(
+                instance=load_data_for_current_species.instance,
+                history_name=load_data_for_current_species.history_name)
             
             # Remove H. sapiens from database if here
             # TODO: set a dedicated history for removing H. sapiens (instead of doing it into a species history)