From 7cf2461c9ac6eee1bb8c38f1713283f6327f0e61 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi <sasha99250@gmail.com>
Date: Thu, 8 Jan 2026 16:10:09 -0500
Subject: [PATCH 1/3] Added method for getting available reference genomes

---
 bbconf/bbagent.py          | 21 +++++++++++++++++++++
 bbconf/modules/bedfiles.py | 31 ++++++++++++++++---------------
 2 files changed, 37 insertions(+), 15 deletions(-)

diff --git a/bbconf/bbagent.py b/bbconf/bbagent.py
index ca8de8c8..2a6169d5 100644
--- a/bbconf/bbagent.py
+++ b/bbconf/bbagent.py
@@ -6,6 +6,7 @@
 
 import numpy as np
 from sqlalchemy.orm import Session
+from sqlalchemy.engine import ScalarResult
 from sqlalchemy.sql import and_, distinct, func, or_, select
 
 from bbconf.config_parser.bedbaseconfig import BedBaseConfig
@@ -21,6 +22,7 @@
     UsageBedSetMeta,
     UsageFiles,
     UsageSearch,
+    ReferenceGenome,
 )
 from bbconf.models.base_models import (
     AllFilesInfo,
@@ -778,3 +780,22 @@ def _get_geo_stats(self, sa_session: Session) -> GEOStatistics:
                 median=round(statistics.median(file_sizes), 2),
             ),
         )
+
+    def get_reference_genomes(self) -> Dict[str, str]:
+        """
+        Get mapping of genome aliases to reference genome names.
+
+        :return: dict mapping genome_alias -> reference_genome_name
+        """
+
+        genomes = {}
+
+        with Session(self.config.db_engine.engine) as session:
+            results: ScalarResult[ReferenceGenome] = session.scalars(
+                select(ReferenceGenome)
+            )
+
+            for genome in results:
+                genomes[genome.digest] = genome.alias
+
+        return genomes
diff --git a/bbconf/modules/bedfiles.py b/bbconf/modules/bedfiles.py
index 1792725a..80d2a447 100644
--- a/bbconf/modules/bedfiles.py
+++ b/bbconf/modules/bedfiles.py
@@ -556,21 +556,22 @@ def add(
             if not overwrite:
                 bed_metadata = StandardMeta(**metadata)
 
-                ## OLD:
-                # self._update_sources(
-                #     identifier=identifier,
-                #     global_sample_id=metadata_standard.global_sample_id,
-                #     global_experiment_id=metadata_standard.global_experiment_id,
-                # )
-
-                with Session(self._sa_engine) as session:
-                    statement = select(Bed).where(Bed.id == identifier)
-                    bed_object = session.scalar(statement)
-                    self._update_metadata(
-                        sa_session=session,
-                        bed_object=bed_object,
-                        bed_metadata=bed_metadata,
-                    )
+                ## UPDATE ONLY sources:
+                self._update_sources(
+                    identifier=identifier,
+                    global_sample_id=bed_metadata.global_sample_id,
+                    global_experiment_id=bed_metadata.global_experiment_id,
+                )
+
+                ## IF we want to update all metadata on add if exists: (DO not remove this code)
+                # with Session(self._sa_engine) as session:
+                #     statement = select(Bed).where(Bed.id == identifier)
+                #     bed_object = session.scalar(statement)
+                #     self._update_metadata(
+                #         sa_session=session,
+                #         bed_object=bed_object,
+                #         bed_metadata=bed_metadata,
+                #     )
                 if not nofail:
                     raise BedFIleExistsError(
                         f"Bed file with id: {identifier} already exists in the database."

From d54f9bc6fb53f614d96e7426751abcda5b8b8041 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi <sasha99250@gmail.com>
Date: Tue, 20 Jan 2026 23:59:27 -0500
Subject: [PATCH 2/3] added docs and bumped version

---
 bbconf/_version.py | 2 +-
 docs/changelog.md  | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/bbconf/_version.py b/bbconf/_version.py
index f075dd36..745162e7 100644
--- a/bbconf/_version.py
+++ b/bbconf/_version.py
@@ -1 +1 @@
-__version__ = "0.14.1"
+__version__ = "0.14.2"
diff --git a/docs/changelog.md b/docs/changelog.md
index 74b80c0c..f021748f 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -3,6 +3,10 @@
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
 
+### [0.14.2] - 2026-01-21
+### Added:
+- Added method that fetches available reference genomes 
+
 ### [0.14.0] - 2025-12-18
 ### Fixed:
 - Insertion of tokenized files

From 7ab038b66da3ab138b63cc4ef045492397dbc660 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi <sasha99250@gmail.com>
Date: Wed, 21 Jan 2026 00:01:11 -0500
Subject: [PATCH 3/3] updated requirements versions

---
 requirements/requirements-all.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
index 9c3e7060..6c97f84d 100644
--- a/requirements/requirements-all.txt
+++ b/requirements/requirements-all.txt
@@ -1,7 +1,7 @@
 yacman >= 0.9.1
 sqlalchemy >= 2.0.0
-gtars >= 0.5.2
-geniml[ml] >= 0.8.3
+gtars >= 0.5.3
+geniml[ml] >= 0.8.4
 psycopg >= 3.1.15
 coloredlogs
 pydantic >= 2.9.0