updated based on the issues when running

update_sc_name/update_scientific_name.py

@@ -1,31 +1,52 @@
+import logging
 import os.path
 import shutil
 from argparse import ArgumentParser
 
 from ebi_eva_common_pyutils import command_utils
+from ebi_eva_common_pyutils.logger import logging_config
 from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle
-from ebi_eva_common_pyutils.pg_utils import execute_query
-from ebi_eva_common_pyutils.taxonomy.taxonomy import get_scientific_name_from_eva, normalise_taxon_scientific_name
+from ebi_eva_common_pyutils.pg_utils import execute_query, get_all_results_for_query
+from ebi_eva_common_pyutils.taxonomy.taxonomy import normalise_taxon_scientific_name, get_scientific_name_from_ensembl
 
+logger = logging_config.get_logger(__name__, logging.DEBUG)
 
-def update_path_reference_sequence(taxonomy, old_sc_name, ref_seq_dir, new_sc_name):
+
+def get_scientific_name_from_eva(taxonomy_id, private_config_xml_file, profile):
+    with get_metadata_connection_handle(profile, private_config_xml_file) as pg_conn:
+        query = f"select scientific_name from evapro.taxonomy where taxonomy_id={taxonomy_id}"
+        result = get_all_results_for_query(pg_conn, query)
+        return result[0][0]
+
+
+def update_path_reference_sequence(taxonomy, old_sc_name, new_sc_name, ref_seq_dir, ref_seq_dir_name, retain_old_dir):
     nmz_old_sc_name = normalise_taxon_scientific_name(old_sc_name)
-    old_species_ref_dir = os.path.join(ref_seq_dir, nmz_old_sc_name)
+    old_species_ref_dir = os.path.join(ref_seq_dir, ref_seq_dir_name) \
+        if ref_seq_dir_name else os.path.join(ref_seq_dir, nmz_old_sc_name)
     nmz_new_sc_name = normalise_taxon_scientific_name(new_sc_name)
     new_species_ref_dir = os.path.join(ref_seq_dir, nmz_new_sc_name)
 
+    logger.warning(f"normalize old scientific name : {nmz_old_sc_name}, old species ref dir: {old_species_ref_dir}, "
+                   f"normalize new scientific name: {nmz_new_sc_name}, new species ref dir: {new_species_ref_dir}")
+
+    if old_species_ref_dir == new_species_ref_dir:
+        logger.warning(f"new species ref dir is same as old species ref dir. No need to update path reference")
+        return
+
     if not os.path.exists(old_species_ref_dir):
-        raise Exception(f'For taxonomy {taxonomy}, could not find any directory with name '
-                        f'"{nmz_old_sc_name}" in reference sequence directory {ref_seq_dir}')
+        raise Exception(f'For taxonomy {taxonomy}, could not find any directory with name "{old_species_ref_dir}"')
     else:
         if os.path.exists(new_species_ref_dir):
+            logger.warning(f"new species reference directory exists. syncing files between old and new dirs")
             sync_command = f"rsync -a --ignore-existing {old_species_ref_dir}/ {new_species_ref_dir}/"
             command_utils.run_command_with_output("merge old_species_dir and new_species_dir", sync_command)
-            shutil.rmtree(old_species_ref_dir)
-            os.symlink(new_species_ref_dir, old_species_ref_dir)
+            if not retain_old_dir:
+                shutil.rmtree(old_species_ref_dir)
+                os.symlink(new_species_ref_dir, old_species_ref_dir)
         else:
-            os.rename(old_species_ref_dir, new_species_ref_dir)
-            os.symlink(new_species_ref_dir, old_species_ref_dir)
+            if not retain_old_dir:
+                os.rename(old_species_ref_dir, new_species_ref_dir)
+                os.symlink(new_species_ref_dir, old_species_ref_dir)
 
 
 def update_scientific_name_in_eva_db(private_config_xml_file, profile, taxonomy_id, new_sc_name):
@@ -36,13 +57,16 @@ def update_scientific_name_in_eva_db(private_config_xml_file, profile, taxonomy_
         execute_query(pg_conn, query)
 
 
-def qc_updates(private_config_xml_file, profile, taxonomy, old_sc_name, new_sc_name, ref_seq_dir):
+def qc_updates(private_config_xml_file, profile, taxonomy, old_sc_name, new_sc_name, ref_seq_dir, ref_seq_dir_name,
+               retain_old_dir):
     # check if reference sequence dir is created with new name
-    old_species_ref_dir = os.path.join(ref_seq_dir, normalise_taxon_scientific_name(old_sc_name))
+    old_species_ref_dir = os.path.join(ref_seq_dir, ref_seq_dir_name) \
+        if ref_seq_dir_name else os.path.join(ref_seq_dir, normalise_taxon_scientific_name(old_sc_name))
     new_species_ref_dir = os.path.join(ref_seq_dir, normalise_taxon_scientific_name(new_sc_name))
     assert os.path.exists(new_species_ref_dir)
     assert os.path.exists(old_species_ref_dir)
-    assert os.path.islink(old_species_ref_dir)
+    if not retain_old_dir and old_species_ref_dir != new_species_ref_dir:
+        assert os.path.islink(old_species_ref_dir)
 
     # check if scientific name is updated in evapro db
     sc_name_from_db = get_scientific_name_from_eva(taxonomy, private_config_xml_file, profile)
@@ -58,20 +82,28 @@ def main():
                            default="production_processing", required=False)
     argparser.add_argument("--taxonomy", type=int, help="taxonomy id e.g. 9606", required=True)
     argparser.add_argument("--scientific-name", help=f"""new scientific name for taxonomy
-                                                     (put in "" for names having space in between)""", required=True)
+                                                     (put in "" for names having space in between)""", required=False)
     argparser.add_argument("--ref-seq-dir", help="path to reference seq directory", required=True)
+    argparser.add_argument("--ref-seq-dir-name", help="name of the reference directory if it could not be "
+                                                      "derived by normalizing scientific name in table", required=False)
+    argparser.add_argument("--retain-old-dir", action='store_true', default=False,
+                           help="Don't convert old reference dir to a link if its a valid dir for some other taxonomy")
     args = argparser.parse_args()
 
     # update directory name in reference sequence directory
     old_sc_name = get_scientific_name_from_eva(args.taxonomy, args.private_config_xml_file, args.profile)
-    update_path_reference_sequence(args.taxonomy, old_sc_name, args.ref_seq_dir, args.scientific_name)
+    new_sc_name = args.scientific_name or get_scientific_name_from_ensembl(args.taxonomy)
+    logger.warning(f"old scientific name: {old_sc_name}, new scientific name: {new_sc_name}")
+
+    update_path_reference_sequence(args.taxonomy, old_sc_name, new_sc_name, args.ref_seq_dir, args.ref_seq_dir_name,
+                                   args.retain_old_dir)
 
     # update scientific name in evapro db
-    update_scientific_name_in_eva_db(args.private_config_xml_file, args.profile, args.taxonomy, args.scientific_name)
+    update_scientific_name_in_eva_db(args.private_config_xml_file, args.profile, args.taxonomy, new_sc_name)
 
     # check if everything is successfully updated
-    qc_updates(args.private_config_xml_file, args.profile, args.taxonomy, old_sc_name, args.scientific_name,
-               args.ref_seq_dir)
+    qc_updates(args.private_config_xml_file, args.profile, args.taxonomy, old_sc_name, new_sc_name, args.ref_seq_dir,
+               args.ref_seq_dir_name, args.retain_old_dir)
 
 
 if __name__ == "__main__":