diff --git a/code/ARAX/ARAXQuery/Overlay/compute_ngd.py b/code/ARAX/ARAXQuery/Overlay/compute_ngd.py index abace417c..cd3dce016 100644 --- a/code/ARAX/ARAXQuery/Overlay/compute_ngd.py +++ b/code/ARAX/ARAXQuery/Overlay/compute_ngd.py @@ -442,37 +442,20 @@ def _get_canonical_curies_map(self, curies): return canonical_curies_map def _setup_ngd_database(self): - # Download the ngd database if there isn't already a local copy or if a newer version is available - #db_path_local = f"{os.path.dirname(os.path.abspath(__file__))}/ngd/{self.ngd_database_name}" - #db_path_remote = f"/data/orangeboard/databases/KG2.3.4/{self.ngd_database_name}" - ngd_filepath = os.path.sep.join([*pathlist[:(RTXindex + 1)], 'code', 'ARAX', 'KnowledgeSources', 'NormalizedGoogleDistance']) + ngd_filepath = os.path.sep.join([*pathlist[:(RTXindex + 1)], + 'code', + 'ARAX', + 'KnowledgeSources', + 'NormalizedGoogleDistance']) db_path_local = f"{ngd_filepath}{os.path.sep}{self.ngd_database_name}" - db_path_remote = RTXConfig.curie_to_pmids_path - # FW: Removed in favor of using the DBmanager but just commenting out in case there is some reason to keep this - # if not os.path.exists(f"{db_path_local}"): - # self.response.debug(f"Downloading fast NGD database because no copy exists... (will take a few minutes)") - # #os.system(f"scp rtxconfig@arax.ncats.io:{db_path_remote} {db_path_local}") - # os.system(f"scp {RTXConfig.curie_to_pmids_username}@{RTXConfig.curie_to_pmids_host}:{RTXConfig.curie_to_pmids_path} {db_path_local}") - # else: - # last_modified_local = int(os.path.getmtime(db_path_local)) - # last_modified_remote_byte_str = subprocess.check_output(f"ssh rtxconfig@arax.ncats.io 'stat -c %Y {db_path_remote}'", shell=True) - # last_modified_remote = int(str(last_modified_remote_byte_str, 'utf-8')) - # if last_modified_local < last_modified_remote: - # self.response.debug(f"Downloading new version of fast NGD database... (will take a few minutes)") - # #os.system(f"scp rtxconfig@arax.ncats.io:{db_path_remote} {db_path_local}") - # os.system(f"scp {RTXConfig.curie_to_pmids_username}@{RTXConfig.curie_to_pmids_host}:{RTXConfig.curie_to_pmids_path} {db_path_local}") - # else: - # self.response.debug(f"Confirmed local NGD database is current") - DBmanager = ARAXDatabaseManager() - if DBmanager.check_versions(): - self.response.debug(f"Downloading databases because mismatch in local versions and remote versions was found... (will take a few minutes)") - self.response = DBmanager.update_databases(response=self.response) # Set up a connection to the database so it's ready for use try: connection = sqlite3.connect(db_path_local) cursor = connection.cursor() except Exception: - self.response.error(f"Encountered an error connecting to ngd sqlite database", error_code="DatabaseSetupIssue") + self.response.error("Encountered an error connecting " + "to ngd sqlite database", + error_code="DatabaseSetupIssue") return None, None else: return connection, cursor @@ -482,4 +465,3 @@ def _close_database(self): self.cursor.close() if self.connection: self.connection.close() -