Fixing broken use of AnnotationService

dieterich-lab · Jun 11, 2024 · 6f7b7f0 · 6f7b7f0
1 parent a02119d
commit 6f7b7f0
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/server/src/scimodom/services/data.py b/server/src/scimodom/services/data.py
@@ -25,6 +25,7 @@
 from scimodom.services.assembly import AssemblyService, AssemblyVersionError
 from scimodom.services.bedtools import get_bedtools_service
 from scimodom.services.importer import get_importer
+from scimodom.services.modification import get_modification_service
 
 logger = logging.getLogger(__name__)
 
@@ -239,10 +240,10 @@ def create_dataset(self) -> None:
         logger.info("Annotating data now...")
 
         # annotate newly imported data...
-        bedtools_service = get_bedtools_service()
         annotation_service = AnnotationService(
             session=self._session,
-            bedtools_service=bedtools_service,
+            bedtools_service=get_bedtools_service(),
+            modification_service=get_modification_service(),
             taxa_id=self._taxa_id,
         )
         try:

diff --git a/server/src/scimodom/services/project.py b/server/src/scimodom/services/project.py
@@ -25,6 +25,7 @@
 from scimodom.services.annotation import AnnotationService
 from scimodom.services.assembly import AssemblyService
 from scimodom.services.bedtools import get_bedtools_service
+from scimodom.services.modification import get_modification_service
 from scimodom.services.permission import get_permission_service
 import scimodom.utils.specifications as specs
 import scimodom.utils.utils as utils
@@ -163,10 +164,10 @@ def update_assembly_and_annotation(self) -> None:
                     self._session, name=name, taxa_id=taxid
                 )  # commit, unless ...
                 logger.info(f"Calling AnnotationService for {taxid}...")
-                bedtools_service = get_bedtools_service()
                 AnnotationService(
                     session=self._session,
-                    bedtools_service=bedtools_service,
+                    bedtools_service=get_bedtools_service(),
+                    modification_service=get_modification_service(),
                     taxa_id=taxid,
                 ).create_annotation()  # commit, unless ...
         except: