List all cached resources (#19)

.pre-commit-config.yaml

@@ -17,26 +17,27 @@ repos:
   - id: mixed-line-ending
     args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
 
-- repo: https://github.com/PyCQA/docformatter
-  rev: v1.7.5
-  hooks:
-    - id: docformatter
-      additional_dependencies: [tomli]
-      args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
-      # --config, ./pyproject.toml
+# - repo: https://github.com/PyCQA/docformatter
+#   rev: master
+#   hooks:
+#     - id: docformatter
+#       additional_dependencies: [tomli]
+#       args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
+#       # --config, ./pyproject.toml
 
-- repo: https://github.com/psf/black
-  rev: 24.8.0
-  hooks:
-  - id: black
-    language_version: python3
+# - repo: https://github.com/psf/black
+#   rev: 24.8.0
+#   hooks:
+#   - id: black
+#     language_version: python3
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
   rev: v0.6.8
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]
+    - id: ruff-format
 
 ## If like to embrace black styles even in the docs:
 # - repo: https://github.com/asottile/blacken-docs

src/pybiocfilecache/BiocFileCache.py

@@ -95,11 +95,7 @@ def add(
             raise NoFpathError(f"Resource at '{fpath}' does not exist.")
 
         rid = generate_id()
-        rpath = (
-            f"{self.cache}/{rid}" + (f".{fpath.suffix}" if ext else "")
-            if action != "asis"
-            else str(fpath)
-        )
+        rpath = f"{self.cache}/{rid}" + (f".{fpath.suffix}" if ext else "") if action != "asis" else str(fpath)
 
         # create new record in the database
         res = Resource(
@@ -151,11 +147,7 @@ def query(self, query: str, field: str = "rname") -> List[Resource]:
             List of matching resources from cache.
         """
         with self.sessionLocal() as session:
-            return (
-                session.query(Resource)
-                .filter(Resource[field].ilike("%{}%".format(query)))
-                .all()
-            )
+            return session.query(Resource).filter(Resource[field].ilike("%{}%".format(query))).all()
 
     def _get(self, session: Session, rname: str) -> Optional[Resource]:
         """Get a resource with `rname` from given `Session`.
@@ -170,9 +162,7 @@ def _get(self, session: Session, rname: str) -> Optional[Resource]:
         Returns:
             The `Resource` for the `rname` if available.
         """
-        resource: Optional[Resource] = (
-            session.query(Resource).filter(Resource.rname == rname).first()
-        )
+        resource: Optional[Resource] = session.query(Resource).filter(Resource.rname == rname).first()
 
         if resource is not None:
             # `Resource` may exist but `rpath` could still be being
@@ -182,8 +172,7 @@ def _get(self, session: Session, rname: str) -> Optional[Resource]:
             while not Path(str(resource.rpath)).exists():
                 if time() - start >= timeout:
                     raise RpathTimeoutError(
-                        f"For resource: '{rname}' the rpath does not exist "
-                        f"after {timeout} seconds."
+                        f"For resource: '{rname}' the rpath does not exist " f"after {timeout} seconds."
                     )
                 sleep(0.1)
 
@@ -274,3 +263,12 @@ def update(
                 # but lets just add it to the cache.
                 res = self.add(rname=rname, fpath=fpath, action=action)
             return res
+
+    def list_all(self) -> List[Resource]:
+        """List all resources currently in the cache.
+
+        Returns:
+            List of all Resource objects in the cache.
+        """
+        with self.sessionLocal() as session:
+            return session.query(Resource).all()

src/pybiocfilecache/db/db_config.py

@@ -72,9 +72,7 @@ def create_schema(cache_dir: str) -> Tuple[Engine, sessionmaker]:
     Returns:
         A tuple of sqlalchemy engine and session maker.
     """
-    engine = create_engine(
-        f"sqlite:///{cache_dir}", connect_args={"check_same_thread": False}
-    )
+    engine = create_engine(f"sqlite:///{cache_dir}", connect_args={"check_same_thread": False})
 
     Base.metadata.create_all(bind=engine, checkfirst=True)
     sessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine)

src/pybiocfilecache/utils.py

@@ -60,9 +60,7 @@ def copy_or_move(
     """
 
     if action not in ["copy", "move", "asis"]:
-        raise ValueError(
-            f"Action must be either 'move', 'copy' or 'asis', provided {action}."
-        )
+        raise ValueError(f"Action must be either 'move', 'copy' or 'asis', provided {action}.")
 
     try:
         if action == "copy":
@@ -84,6 +82,4 @@ def setup_logging(loglevel):
       loglevel (int): minimum loglevel for emitting messages
     """
     logformat = "[%(asctime)s] %(levelname)s:%(name)s:%(message)s"
-    logging.basicConfig(
-        level=loglevel, stream=sys.stdout, format=logformat, datefmt="%Y-%m-%d %H:%M:%S"
-    )
+    logging.basicConfig(level=loglevel, stream=sys.stdout, format=logformat, datefmt="%Y-%m-%d %H:%M:%S")

tests/test_cache.py

@@ -41,6 +41,9 @@ def test_add_get_operations():
     frec3 = open(rec3.rpath, "r").read().strip()
     assert frec3 == "test2"
 
+    rtrip = bfc.list_all()
+    assert len(rtrip) == 3
+
     bfc.purge()