From aabba1a3c434fbf7d1436eaea10807f83defc907 Mon Sep 17 00:00:00 2001
From: Etienne Boileau <boileau@uni-heidelberg.de>
Date: Sun, 4 Aug 2024 19:56:43 +0200
Subject: [PATCH] WIP delete selection

---
 server/src/scimodom/app.py                 |  9 ++++++---
 server/src/scimodom/cli/dataset.py         | 12 +++++++++---
 server/src/scimodom/cli/project.py         |  3 +++
 server/src/scimodom/services/file.py       |  9 +++++++++
 server/tests/unit/services/test_dataset.py |  4 ++++
 5 files changed, 31 insertions(+), 6 deletions(-)

diff --git a/server/src/scimodom/app.py b/server/src/scimodom/app.py
index 316caa73..b96fa41b 100644
--- a/server/src/scimodom/app.py
+++ b/server/src/scimodom/app.py
@@ -435,13 +435,16 @@ def batch(input_directory, request_uuids, annotation):
         multiple=True,
         required=False,
         type=click.INT,
-        help="Selection ID(s) to delete. Repeat parameter to pass multiple selection IDs. Use at your own risk!",
+        help="Selection ID(s) to delete. Repeat parameter to pass multiple selection IDs.",
     )
     @click.argument("smid", type=click.STRING)
     def delete(smid, selection):
         """Delete a project and all associated
-        data from the database. Deleting
-        selections at your own risk.
+        data from the database. If given, delete
+        selections (and gene cache) associated
+        with the project data. Selections
+        may be associated with other datasets,
+        delete at your own risk!
 
         SMID is the Sci-ModoM project ID.
         """
diff --git a/server/src/scimodom/cli/dataset.py b/server/src/scimodom/cli/dataset.py
index 2724657c..21b91c30 100644
--- a/server/src/scimodom/cli/dataset.py
+++ b/server/src/scimodom/cli/dataset.py
@@ -20,6 +20,7 @@
 from scimodom.services.annotation import AnnotationSource
 from scimodom.services.assembly import AssemblyNotFoundError, get_assembly_service
 from scimodom.services.dataset import get_dataset_service
+from scimodom.services.file import get_file_service
 from scimodom.services.project import get_project_service
 from scimodom.utils.project_dto import (
     ProjectMetaDataDto,
@@ -295,9 +296,14 @@ def add_selection(
 
 def delete_selection(selection: Selection) -> None:
     session = get_session()
-    session.delete(selection)
-    session.commit()
-    # TODO delete gene cache
+    file_service = get_file_service()
+    try:
+        session.delete(selection)
+        file_service.delete_gene_cache(selection.id)
+        session.commit()
+    except Exception:
+        session.rollback()
+        raise
 
 
 def get_selection_from_dataset(dataset: Dataset) -> Iterator[Selection]:
diff --git a/server/src/scimodom/cli/project.py b/server/src/scimodom/cli/project.py
index 212a919b..35f64b4e 100644
--- a/server/src/scimodom/cli/project.py
+++ b/server/src/scimodom/cli/project.py
@@ -210,6 +210,9 @@ def delete_project(smid: str, selection_ids: list[int]) -> None:
     BAM files associated with a dataset belonging
     to this project are deleted from the file system.
 
+    If given, selection IDs are deleted and
+    gene cache files are removed.
+
     :param smid: Project ID (SMID)
     :type smid: str
     :param selection_ids: List of selection IDs to delete,
diff --git a/server/src/scimodom/services/file.py b/server/src/scimodom/services/file.py
index 6c1f990c..6cb81415 100644
--- a/server/src/scimodom/services/file.py
+++ b/server/src/scimodom/services/file.py
@@ -196,6 +196,15 @@ def update_gene_cache(self, selection_id: int, genes: Iterable[str]) -> None:
                 print(g, file=fh)
             flock(fh.fileno(), LOCK_UN)
 
+    def delete_gene_cache(self, selection_id: int) -> None:
+        """Remove a gene cache file for a given selection.
+
+        :param selection_id: Selection ID
+        :type selection_id: int
+        """
+        path = Path(self._get_gene_cache_dir(), str(selection_id))
+        path.unlink()
+
     def _get_gene_cache_dir(self) -> Path:
         return Path(self._data_path, self.CACHE_DEST)
 
diff --git a/server/tests/unit/services/test_dataset.py b/server/tests/unit/services/test_dataset.py
index ff5cd636..88a08350 100644
--- a/server/tests/unit/services/test_dataset.py
+++ b/server/tests/unit/services/test_dataset.py
@@ -28,6 +28,10 @@ class MockFileService:
     def __init__(self, session):
         self._session = session
         self.deleted_bam_files: list[str] = []
+        self.deleted_gene_cache: list[int] = []
+
+    def delete_gene_cache(self, selection_id: int) -> None:
+        self.deleted_gene_cache.append(selection_id)
 
     def remove_bam_file(self, bam_file):
         self.deleted_bam_files.append(bam_file.original_file_name)