fix get_history

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
@@ -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)

speciesData.py

@@ -139,4 +139,5 @@ class SpeciesData:
         self.instance_url = None
         self.instance = None
         self.history_id = None
+        self.history_name = str(self.genus_species)
         self.library_id = None

utilities_bioblend.py

@@ -34,21 +34,24 @@ def get_galaxy_instance(instance_url, email, password):
 
     return instance
 
+
 def get_history(instance, history_name):
     """
     Create or set the working history to the current species one
 
     :return:
     """
-    try:
-        histories = instance.histories.get_histories(name=history_name)
-        history_id = histories[0]["id"]
-        logging.debug("History ID set for {0}: {1}".format(history_name, history_id))
-    except IndexError:
+    histories = instance.histories.get_histories(name=str(history_name))
+    if len(histories) == 0:
         logging.info("Creating history for %s" % history_name)
-        history = instance.histories.create_history(name=history_name)
-        history_id = history["id"]
+        hist_dict = instance.histories.create_history(name=str(history_name))
+        history_id = hist_dict["id"]
         logging.debug("History ID set for {0}: {1}".format(history_name, history_id))
+    if len(histories) == 1:
+        history_id = histories[0]["id"]
+        logging.debug("History ID set for {0}: {1}".format(history_name, history_id))
+    else:
+        logging.critical("Multiple histories exists for {0}".format(history_name))
 
     return history_id