PR corrections done with DB migration

antarest/study/repository.py

@@ -1,9 +1,11 @@
 import datetime
 import enum
 import typing as t
+from typing import List, Tuple, Union
 
 from pydantic import BaseModel, NonNegativeInt
 from sqlalchemy import func, not_, or_  # type: ignore
+from sqlalchemy import select, func
 from sqlalchemy.orm import Session, joinedload, with_polymorphic  # type: ignore
 
 from antarest.core.interfaces.cache import ICache
@@ -273,9 +275,17 @@ def get_all_raw(self, exists: t.Optional[bool] = None) -> t.Sequence[RawStudy]:
         return studies
 
     def delete(self, id: str) -> None:
+    def delete(self, ids: Union[str, List[str]]) -> None:
+        logger.debug(f"Deleting study {id}")
+        if isinstance(ids, str):
+            # if id is str, convert it to list with one element
+            ids = [ids]
         session = self.session
-        u: Study = session.query(Study).get(id)
-        session.delete(u)
+        for study_id in ids:
+            study: Study = session.query(Study).get(study_id)
+            if study:
+                session.delete(study)
+                self._remove_study_from_cache_listing(study_id)
         session.commit()
 
     def update_tags(self, study: Study, new_tags: t.Sequence[str]) -> None:
@@ -292,3 +302,20 @@ def update_tags(self, study: Study, new_tags: t.Sequence[str]) -> None:
         study.tags = [Tag(label=tag) for tag in new_labels] + existing_tags
         self.session.merge(study)
         self.session.commit()
+
+    def list_duplicates(self) -> List[Tuple[str, str]]:
+        """
+            Get list of duplicates as tuples (id, path).
+        """
+        session = self.session
+        subquery = (
+            session.query(Study.path)
+            .group_by(Study.path)
+            .having(func.count()>1)
+            .subquery()
+        )
+        query = (
+            session.query(Study.id, Study.path)
+            .filter(Study.path.in_(subquery))
+        )
+        return query.all()

antarest/study/service.py

@@ -1,4 +1,6 @@
 import base64
+import collections
+import typing as t
 import contextlib
 import io
 import json
@@ -696,20 +698,19 @@ def get_input_matrix_startdate(
         return get_start_date(file_study, output_id, level)
 
     def remove_duplicates(self) -> None:
-        study_paths: t.Dict[str, t.List[str]] = {}
-        for study in self.repository.get_all():
-            if isinstance(study, RawStudy) and not study.archived:
-                path = str(study.path)
-                if path not in study_paths:
-                    study_paths[path] = []
-                study_paths[path].append(study.id)
-
-        for studies_with_same_path in study_paths.values():
-            if len(studies_with_same_path) > 1:
-                logger.info(f"Found studies {studies_with_same_path} with same path, de duplicating")
-                for study_name in studies_with_same_path[1:]:
-                    logger.info(f"Removing study {study_name}")
-                    self.repository.delete(study_name)
+        duplicates: List[Tuple[str, str]] = self.repository.list_duplicates()
+        ids: List[str] = []
+        # ids with same path
+        duplicates_by_path: t.Dict[str, t.List[str]] = collections.defaultdict(list)
+        for study_id, path in duplicates:
+            duplicates_by_path[path].append(study_id)
+        for path, study_ids in duplicates_by_path.items():
+            ids.extend(study_ids[1:])
+            # delete list ids
+        self.repository.delete(ids)
+        #db.session.query(RawStudy).filter(RawStudy.id.in_(ids)).delete(synchronize_session=False)
+        db.session.commit()
+
 
     def sync_studies_on_disk(self, folders: t.List[StudyFolder], directory: t.Optional[Path] = None) -> None:
         """

tests/storage/test_service.py

@@ -350,19 +350,28 @@ def test_partial_sync_studies_from_disk() -> None:
     )
 
 
-@pytest.mark.unit_test
-def test_remove_duplicate() -> None:
-    ma = RawStudy(id="a", path="a")
-    mb = RawStudy(id="b", path="a")
+@with_db_context
+def test_remove_duplicate(db_session: Session) -> None:
+    with db_session:
+        db_session.add(RawStudy(id="a", path="/path/to/a"))
+        db_session.add(RawStudy(id="b", path="/path/to/a"))
+        db_session.add(RawStudy(id="c", path="/path/to/c"))
+        db_session.commit()
+        study_count = db_session.query(RawStudy).filter(RawStudy.path == "/path/to/a").count()
+        assert study_count == 2 # there are 2 studies with same path before removing duplicates
 
-    repository = Mock()
-    repository.get_all.return_value = [ma, mb]
+    repository = StudyMetadataRepository(Mock(), db_session)
     config = Config(storage=StorageConfig(workspaces={DEFAULT_WORKSPACE_NAME: WorkspaceConfig()}))
     service = build_study_service(Mock(), repository, config)
-
     service.remove_duplicates()
-    repository.delete.assert_called_once_with(mb.id)
-
+    # example with 1 duplicate with same path
+    with db_session:
+        study_count = db_session.query(RawStudy).filter(RawStudy.path == "/path/to/a").count()
+    assert study_count == 1
+    # example with no duplicates with same path
+    with db_session:
+        study_count = db_session.query(RawStudy).filter(RawStudy.path == "/path/to/c").count()
+    assert study_count == 1
 
 # noinspection PyArgumentList
 @pytest.mark.unit_test