Release 2.0

gga_load_data.py:

• Factorize goto_species_dir(), create_galaxy_instance(), run_tool(), get_species_dir()
• Move constants at the beginning
• Revert upload_from_local() to upload_from_galaxy_fs() (to enable symlink, instead of copy)
• Add missing get_bam_label()

README:

• update contributors

gga_load_data.py

@@ -67,25 +67,22 @@ class LoadData(speciesData.SpeciesData):
         """
 
         logging.debug("Getting 'Homo sapiens' ID in chado database")
-        get_sapiens_id_job = self.instance.tools.run_tool(
+        get_sapiens_id_job_output_dataset_id = utilities.run_tool_and_get_single_output_dataset_id(self.instance,
             tool_id=GET_ORGANISMS_TOOL,
             history_id=self.history_id,
             tool_inputs={"genus": "Homo", "species": "sapiens"})
-        get_sapiens_id_job_output_dataset_id = get_sapiens_id_job["outputs"][0]["id"]
         get_sapiens_id_json_output = self.instance.datasets.download_dataset(dataset_id=get_sapiens_id_job_output_dataset_id)
+
+        logging.debug("Deleting Homo 'sapiens' in the instance's chado database")
         try:
-            logging.debug("Deleting Homo 'sapiens' in the instance's chado database")
             get_sapiens_id_final_output = json.loads(get_sapiens_id_json_output)[0]
-            sapiens_id = str(
-                get_sapiens_id_final_output["organism_id"])  # needs to be str to be recognized by the chado tool
-            self.instance.tools.run_tool(
+            sapiens_id = str(get_sapiens_id_final_output["organism_id"])  # needs to be str to be recognized by the chado tool
+            utilities.run_tool(
                 tool_id=DELETE_ORGANISMS_TOOL,
                 history_id=self.history_id,
-                tool_inputs={"organism": str(sapiens_id)})
-        except bioblend.ConnectionError:
-            logging.debug("Homo sapiens isn't in the instance's chado database (bioblend.ConnectionError)")
+                tool_inputs={"organism": sapiens_id})
         except IndexError:
-            logging.debug("Homo sapiens isn't in the instance's chado database (IndexError)")
+            logging.error("Homo sapiens isn't in the instance's chado database (IndexError)")
             pass
 
     def purge_histories(self):
@@ -98,7 +95,6 @@ class LoadData(speciesData.SpeciesData):
         """
 
         histories = self.instance.histories.get_histories()
-        self.instance.histories.get_histories(deleted=False)
         for h in histories:
             self.instance.histories.delete_history(history_id=h["id"])