From d486716e074950f9330deafd4aea0dca0dc463cb Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Fri, 22 Nov 2024 11:39:08 -0500 Subject: [PATCH 1/3] chore: set dummy version in pyproject --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 2726595..14ffb36 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "bento_beacon" -version = "0.17.0" +version = "0.0.0" # version is managed outside of Poetry for Beacon description = "GA4GH Beacon v2 microservice for the Bento platform" authors = ["Gordon Krieger "] license = "LGPL-3.0-only" From 9ce4f0ef9edaf466e508608160aa411e282238fe Mon Sep 17 00:00:00 2001 From: Gordon Krieger Date: Tue, 26 Nov 2024 15:29:11 +0000 Subject: [PATCH 2/3] rm unused fn --- bento_beacon/utils/gohan_utils.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/bento_beacon/utils/gohan_utils.py b/bento_beacon/utils/gohan_utils.py index 3e2f185..e853ca5 100644 --- a/bento_beacon/utils/gohan_utils.py +++ b/bento_beacon/utils/gohan_utils.py @@ -52,10 +52,6 @@ def zero_to_one(start, end=None): return int(start) + 1 if end is None else (int(start) + 1, end) -def one_to_zero(start, end): - return (int(start) - 1, end) - - # ------------------------------------------------------- # gohan calls # ------------------------------------------------------- From fb223b609e287f2b23c55148916733b495f49d29 Mon Sep 17 00:00:00 2001 From: Gordon Krieger Date: Tue, 26 Nov 2024 15:36:06 +0000 Subject: [PATCH 3/3] fix: zero_to_one was called incorrectly --- bento_beacon/utils/gohan_utils.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/bento_beacon/utils/gohan_utils.py b/bento_beacon/utils/gohan_utils.py index e853ca5..a2b5c34 100644 --- a/bento_beacon/utils/gohan_utils.py +++ b/bento_beacon/utils/gohan_utils.py @@ -120,8 +120,7 @@ def sequence_query_to_gohan(beacon_args, granularity, ids_only): def range_query_to_gohan(beacon_args, granularity, ids_only): current_app.logger.debug("RANGE QUERY") gohan_args = beacon_to_gohan_generic_mapping(beacon_args) - gohan_args["lowerBound"] = zero_to_one(beacon_args["start"][0]) - gohan_args["upperBound"] = zero_to_one(beacon_args["end"][0]) + gohan_args["lowerBound"], gohan_args["upperBound"] = zero_to_one(beacon_args["start"][0], beacon_args["end"][0]) gohan_args["getSampleIdsOnly"] = ids_only return generic_gohan_query(gohan_args, granularity, ids_only)