Change ens version and add comments

config.yaml

@@ -136,7 +136,7 @@ ensembl:
   conda_create: bash -c "~/anaconda2/bin/conda env create -f {root_dir}/scripts/ensembl/environment.yaml"
   python_script: python {script_path}/create_genes_dictionary.py -o {ensembl_output_dir}/.
     -e -z -n
-  ensembl_release: homo_sapiens_core_98_38
+  ensembl_release: homo_sapiens_core_99_38
   extension_file: _genes.json.gz
   resource: ensembl-filename
   gs_output_dir: annotation-files

modules/GoogleBucketResource.py

@@ -125,6 +125,7 @@ def copy_from(self, original_filename, dest_filename, gs_specific_output_dir = N
         return blob.name
 
 
+    # Extract any date in the format dd-mm-yyyy or yyyy-mm-dd. Return None if date are not available.
     def extract_date_from_file(self, filename):
         date_file = None
         find_date_file = re.search("([0-9]{2}\-[0-9]{2}\-[0-9]{4})", filename)
@@ -137,6 +138,7 @@ def extract_date_from_file(self, filename):
 
         return date_file
 
+    # Return the filename with the recent date. Manage collision of dates only for the recent date.
     def extract_latest_file(self, list_blobs):
         last_recent_file = None
         possible_recent_date_collision = False
@@ -152,7 +154,7 @@ def extract_latest_file(self, list_blobs):
                     last_recent_file = filename
 
         if possible_recent_date_collision:
-            # Raise an error
+            # Raise an error. No filename is unique in the recent date selected.
             logger.error("Error TWO files with the same date: %s %s", last_recent_file,
                          recent_date.strftime('%d-%m-%Y'))
             exit(1)

modules/RetrieveResource.py

@@ -49,6 +49,7 @@ def annotations_downloaded_by_uri(self):
 
                 self.list_files_downloaded[destination_filename] = { 'resource' : entry.resource,
                                                                       'gs_output_dir': self.yaml.annotations_from_buckets.gs_output_dir }
+                logger.info("Files downloaded: %s", destination_filename)
             elif not self.args.skip:
                  raise ValueError("Error during downloading: {}", entry.uri)