fixed geniml updates

bbconf/config_parser/bedbaseconfig.py

@@ -10,7 +10,7 @@
 import yacman
 import zarr
 from botocore.exceptions import BotoCoreError, EndpointConnectionError
-from geniml.region2vec import Region2VecExModel
+from geniml.region2vec.main import Region2VecExModel
 from geniml.search import BED2BEDSearchInterface, QdrantBackend, Text2BEDSearchInterface
 from geniml.search.query2vec import BED2Vec, Text2Vec
 from pephubclient import PEPHubClient

bbconf/modules/bedfiles.py

@@ -6,7 +6,7 @@
 import numpy as np
 from geniml.bbclient import BBClient
 from geniml.io import RegionSet
-from genimtools.tokenizers import RegionSet as GRegionSet
+from gtars.tokenizers import RegionSet as GRegionSet
 from pephubclient.exceptions import ResponseError
 from qdrant_client.models import Distance, PointIdsList, VectorParams
 from sqlalchemy import and_, delete, func, select
@@ -754,15 +754,33 @@ def upload_file_qdrant(
         :param payload: additional metadata to store alongside vectors
         :return: None
         """
+
+        _LOGGER.debug(f"Adding bed file to qdrant. bed_id: {bed_id}")
+        bed_embedding = self._embed_file(bed_file)
+
+        self._qdrant_engine.load(
+            ids=[bed_id],
+            vectors=bed_embedding,
+            payloads=[{**payload}],
+        )
+        return None
+
+    def _embed_file(self, bed_file: Union[str, RegionSet]) -> np.ndarray:
+        """
+        Create embeding for bed file
+
+        :param bed_id: bed file id
+        :param bed_file: path to the bed file, or RegionSet object
+
+        :return np array of embeddings
+        """
         if self._qdrant_engine is None:
             raise QdrantInstanceNotInitializedError
-
         if not self._config.r2v:
             raise BedBaseConfError(
                 "Could not add add region to qdrant. Invalid type, or path. "
             )
 
-        _LOGGER.debug(f"Adding bed file to qdrant. bed_id: {bed_id}")
         if isinstance(bed_file, str):
             bed_region_set = GRegionSet(bed_file)
         elif isinstance(bed_file, RegionSet) or isinstance(bed_file, GRegionSet):
@@ -771,19 +789,9 @@ def upload_file_qdrant(
             raise BedBaseConfError(
                 "Could not add add region to qdrant. Invalid type, or path. "
             )
-        # Not really working
-        # bed_embedding = np.mean([self._config.r2v.encode(r) for r in bed_region_set], axis=0)
-
         bed_embedding = np.mean(self._config.r2v.encode(bed_region_set), axis=0)
-
-        # Upload bed file vector to the database
         vec_dim = bed_embedding.shape[0]
-        self._qdrant_engine.load(
-            ids=[bed_id],
-            vectors=bed_embedding.reshape(1, vec_dim),
-            payloads=[{**payload}],
-        )
-        return None
+        return bed_embedding.reshape(1, vec_dim)
 
     def text_to_bed_search(
         self, query: str, limit: int = 10, offset: int = 0
@@ -814,7 +822,7 @@ def text_to_bed_search(
             if result_meta:
                 results_list.append(QdrantSearchResult(**result, metadata=result_meta))
         return BedListSearchResult(
-            count=self.bb_agent.get_stats.bedfiles_number,
+            count=self.bb_agent.get_stats().bedfiles_number,
             limit=limit,
             offset=offset,
             results=results_list,
@@ -842,7 +850,7 @@ def bed_to_bed_search(
             if result_meta:
                 results_list.append(QdrantSearchResult(**result, metadata=result_meta))
         return BedListSearchResult(
-            count=self.bb_agent.get_stats.bedfiles_number,
+            count=self.bb_agent.get_stats().bedfiles_number,
             limit=limit,
             offset=offset,
             results=results_list,

manual_testing.py

@@ -4,10 +4,10 @@
 import zarr
 from dotenv import load_dotenv
 from geniml.io import RegionSet
-from genimtools.tokenizers import TreeTokenizer
-from genimtools.utils import read_tokens_from_gtok
+from gtars.tokenizers import TreeTokenizer
+from gtars.utils import read_tokens_from_gtok
 
-# from genimtools.tokenizers import RegionSet
+# from gtars.tokenizers import RegionSet
 
 
 load_dotenv()

requirements/requirements-all.txt

@@ -1,6 +1,6 @@
 yacman >= 0.9.1
 sqlalchemy >= 2.0.0
-geniml >= 0.4.1
+geniml >= 0.4.2
 psycopg >= 3.1.15
 colorlogs
 pydantic >= 2.6.4
@@ -11,6 +11,4 @@ sqlalchemy_schemadisplay
 zarr
 pyyaml >= 6.0.1 # for s3fs because of the errors
 s3fs >= 2024.3.1
-# quick fix for gesnim
-scipy <= 1.11.0
 pandas

tests/test_common.py

@@ -9,7 +9,7 @@
 @pytest.mark.skipif(SERVICE_UNAVAILABLE, reason="Database is not available")
 def test_get_stats(bbagent_obj):
     with ContextManagerDBTesting(config=bbagent_obj.config, add_data=True, bedset=True):
-        return_result = bbagent_obj.get_stats
+        return_result = bbagent_obj.get_stats()
 
         assert return_result
         assert return_result.bedfiles_number == 1