Release v2.1.0

General

• Bump cryptography requirement version to 3.2
• Create tools to handle multiple docker stacks in docker_tools repository (toggl galaxy state, update service)

Input config.yml file

• Fix typo in parameter galaxy_default_admin_user
• Add parameter galaxy_default_admin_key (required to create the admin user galaxy_default_admin_user in Galaxy)
• Check that all required parameters are not empty

Input organisms.yml file

• Add the parameter picture_path in the description section to add this picture in the Tripal homepage
• Add parameter contig_prefix in the data section to list the prefixes used for contig names. Required when they are multiple strains from the same species to map the contig name prefix to the right JBrowse dataset ID in Tripal (see Step "init")
• Add the go summary functionality in Tripal. This functionality can be activated with parameter go set to 1 in the services section
• Remove unused performed_by parameter
• Fix code for empty strain and/or sex

Step "init"

• Add a picture of the species in the Tripal homepage (the picture of the main strain if exists, the picture of another strain if not)
• Fix Tripal site name
• Add env variable JBROWSE_LINKS in the Tripal service, to map the contig name prefix to the right JBrowse dataset ID in Tripal (for Tripal hyperlinks to JBrowse)

Step "get data"

• Change data file names: use prefix strain_sex

Step "run workflow Phaeoexplorer"

• Create a parent module run_workflow_phaeo.py, with classes and methods used by the workflow scripts
• Create file constants_phaeo.py to store constants used in step "run workflow Phaeoexplorer" (workflows and galaxy tools details)
• Script gga_run_workflow_phaeo_jbrowse.py: runs a Galaxy workflow to load the genome, the annotations and the proteins to Chado, Tripal and JBrowse, for one or two strains of the same species
• Work in progress: workflows to load blast and interpro results

gga_load_data.py

@@ -38,33 +38,6 @@ class LoadData(speciesData.SpeciesData):
         self.bam_metadata_cache = {}
         super().__init__(parameters_dictionary)
 
-    def remove_homo_sapiens_from_db(self):
-        """
-        Run the GMOD tool to remove the "Homo sapiens" default organism from the original database
-        Will do nothing if H. sapiens isn't in the database
-
-        """
-
-        logging.debug("Getting 'Homo sapiens' ID in chado database")
-        get_sapiens_id_json_output = utilities_bioblend.run_tool_and_download_single_output_dataset(
-            self.instance,
-            tool_id=constants.GET_ORGANISMS_TOOL, # If this version if not found, Galaxy will use the one that is found
-            history_id=self.history_id,
-            tool_inputs={"genus": "Homo", "species": "sapiens"})
-
-        logging.info("Deleting Homo 'sapiens' in the instance's chado database")
-        try:
-            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
-            utilities_bioblend.run_tool(
-                self.instance,
-                tool_id=constants.DELETE_ORGANISMS_TOOL,
-                history_id=self.history_id,
-                tool_inputs={"organism": sapiens_id})
-        except IndexError:
-            logging.error("Homo sapiens isn't in the instance's chado database (IndexError)")
-            pass
-
     def purge_histories(self):
         """
         Delete all histories in the instance
@@ -256,7 +229,33 @@ class LoadData(speciesData.SpeciesData):
                 logging.info("Did not find metadata in %s " % meta_file)
             return self.get_bam_label(dirname, bam_file)
 
-    
+def remove_homo_sapiens_from_db(instance, history_id):
+    """
+    Run the GMOD tool to remove the "Homo sapiens" default organism from the original database
+    Will do nothing if H. sapiens isn't in the database
+
+    """
+
+    logging.debug("Getting 'Homo sapiens' ID in chado database")
+    get_sapiens_id_json_output = utilities_bioblend.run_tool_and_download_single_output_dataset(
+        instance,
+        tool_id=constants.GET_ORGANISMS_TOOL, # If this version if not found, Galaxy will use the one that is found
+        history_id=history_id,
+        tool_inputs={"genus": "Homo", "species": "sapiens"})
+
+    logging.info("Deleting Homo 'sapiens' in the instance's chado database")
+    try:
+        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
+        utilities_bioblend.run_tool(
+            instance,
+            tool_id=constants.DELETE_ORGANISMS_TOOL,
+            history_id=history_id,
+            tool_inputs={"organism": sapiens_id})
+    except IndexError:
+        logging.error("Homo sapiens isn't in the instance's chado database (IndexError)")
+        pass
+
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Load data into Galaxy library")
 
@@ -268,6 +267,10 @@ if __name__ == "__main__":
                         help="Increase output verbosity",
                         action="store_true")
 
+    parser.add_argument("-vv", "--very_verbose",
+                        help="Increase output verbosity",
+                        action="store_true")
+
     parser.add_argument("--config",
                         type=str,
                         help="Config path, default to 'examples/config.yml'")
@@ -278,11 +281,14 @@ if __name__ == "__main__":
 
     args = parser.parse_args()
 
-    if args.verbose:
+    if args.verbose or args.very_verbose:
         logging.basicConfig(level=logging.DEBUG)
     else:
         logging.basicConfig(level=logging.INFO)
-    logging.getLogger("urllib3").setLevel(logging.INFO)
+
+    if not args.very_verbose:
+        logging.getLogger("urllib3").setLevel(logging.INFO)
+        logging.getLogger("bioblend").setLevel(logging.INFO)
 
     # Parsing the config file if provided, using the default config otherwise
     if args.config:
@@ -338,14 +344,17 @@ if __name__ == "__main__":
             load_data_for_current_species.setup_library()
             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.history_id = utilities_bioblend.get_history(
+            # Get default history
+            history_id = utilities_bioblend.get_history(
                 instance=load_data_for_current_species.instance,
-                history_name=load_data_for_current_species.history_name)
-            
+                history_name="Unnamed history")
+
             # Remove H. sapiens from database if here
             # TODO: set a dedicated history for removing H. sapiens (instead of doing it into a species history)
-            load_data_for_current_species.remove_homo_sapiens_from_db()
+            remove_homo_sapiens_from_db(
+                instance=load_data_for_current_species.instance,
+                history_id=history_id
+            )
 
             # logging.info("Importing datasets into history for %s" % load_data_for_current_species.full_name)
             # load_data_for_current_species.import_datasets_into_history()  # Option "--load-history"