From 9b65b105536ef459a19ce39767ffdccc2c954933 Mon Sep 17 00:00:00 2001 From: Evan Morris Date: Tue, 28 Jan 2025 13:06:51 -0500 Subject: [PATCH] catching ConnectionError as well for binding-db, fixing genomealliance --- parsers/BINDING/src/loadBINDINGDB.py | 2 ++ parsers/GenomeAlliance/src/loadGenomeAlliance.py | 8 +------- 2 files changed, 3 insertions(+), 7 deletions(-) diff --git a/parsers/BINDING/src/loadBINDINGDB.py b/parsers/BINDING/src/loadBINDINGDB.py index 5be5bf56..90ae9e77 100644 --- a/parsers/BINDING/src/loadBINDINGDB.py +++ b/parsers/BINDING/src/loadBINDINGDB.py @@ -111,6 +111,8 @@ def get_latest_source_version(self) -> str: error_message = f'BINDING-DB timed out attempting to retrieve version...' except ValueError: error_message = f'BINDING-DB get_latest_source_version got a response but could not determine the version..' + except requests.exceptions.ConnectionError as e: + error_message = f'BINDING-DB get_latest_source_version failed: {e}..' self.logger.error(error_message + ' Returning last known valid version: 202501') self.bindingdb_version = '202501' return self.bindingdb_version diff --git a/parsers/GenomeAlliance/src/loadGenomeAlliance.py b/parsers/GenomeAlliance/src/loadGenomeAlliance.py index 01981192..dc5b9459 100644 --- a/parsers/GenomeAlliance/src/loadGenomeAlliance.py +++ b/parsers/GenomeAlliance/src/loadGenomeAlliance.py @@ -38,11 +38,9 @@ def __init__(self, test_mode: bool = False, source_data_dir: str = None): self.latest_version = None self.latest_version = self.get_latest_source_version() - #self.genome_alliance_url = f'https://download.alliancegenome.org/{self.get_latest_source_version()}/ORTHOLOGY-ALLIANCE/COMBINED/' - #self.genome_alliance_ortholog_file = 'ORTHOLOGY-ALLIANCE_COMBINED_25.tsv.gz' self.genome_alliance_url = 'https://fms.alliancegenome.org/download/' - self.self.genome_alliance_ortholog_file = 'ORTHOLOGY-ALLIANCE_COMBINED.tsv.gz' + self.genome_alliance_ortholog_file = 'ORTHOLOGY-ALLIANCE_COMBINED.tsv.gz' self.data_files = [self.genome_alliance_ortholog_file] def get_latest_source_version(self) -> str: @@ -51,11 +49,7 @@ def get_latest_source_version(self) -> str: :return: """ - #if not self.latest_version: - # self.latest_version = '5.3.0' - self.latest_version = requests.get("https://www.alliancegenome.org/api/releaseInfo").json()['releaseVersion'] - return self.latest_version def get_data(self) -> int: