Sqlitedb API implementation

.pre-commit-config.yaml

@@ -5,16 +5,6 @@ repos:
   rev: 23.9.1
   hooks:
   - id: black
-- repo: local
-  hooks:
-  - id: tox-code-checks
-    name: Run tox targets -- tests
-    stages: [commit]
-    language: system
-    types: [python]
-    pass_filenames: false
-    verbose: true
-    entry: tox -v
 - repo: https://github.com/pre-commit/mirrors-mypy
   rev: 'v1.10.0'
   hooks:

docs/locking.rst

@@ -5,7 +5,7 @@ To ensure consistent writes, aerovaldb provides a locking mechanism which can be
 
 For :class:`AerovalJsonFileDB` the locking mechanism uses a folder of lock files (`~/.aerovaldb/` by default) to coordinate the lock. It is important that the file system where the lock files are stored supports `fcntl <https://linux.die.net/man/2/fcntl>`.
 
-By default locking is disabled as it has large effect on performance. To enable, set the environment variable `AVDB_USE_LOCKING=1`.
+By default locking is disabled as it may impact performance. To enable, set the environment variable `AVDB_USE_LOCKING=1`.
 
 Overriding the lock-file directory
 ----------------------------------

scripts/build_sqlite_test_database.py

@@ -0,0 +1,34 @@
+import os
+import aerovaldb
+
+# This script is a helper script to create an sqlite database
+# with the same contents as the json test database. It does so
+# by copying each asset from the jsondb into test.sqlite
+
+if os.path.exists("tests/test-db/sqlite/test.sqlite"):
+    os.remove("tests/test-db/sqlite/test.sqlite")
+
+jsondb = aerovaldb.open("json_files:tests/test-db/json")
+sqlitedb = aerovaldb.open("sqlitedb:tests/test-db/sqlite/test.sqlite")
+
+for i, uri in enumerate(list(jsondb.list_all())):
+    print(f"[{i}] - Processing uri {uri}")
+    data = jsondb.get_by_uri(
+        uri, access_type=aerovaldb.AccessType.JSON_STR, default="{}"
+    )
+    sqlitedb.put_by_uri(data, uri)
+
+json_list = list(jsondb.list_all())
+sqlite_list = list(sqlitedb.list_all())
+print("The following URIs exist in jsondb but not sqlitedb")
+for x in json_list:
+    if not (x in sqlite_list):
+        print(x)
+
+print("The following URIs exist in sqlitedb but not jsondb")
+for x in sqlite_list:
+    if not (x in json_list):
+        print(x)
+
+print(f"jsondb number of assets: {len(list(jsondb.list_all()))}")
+print(f"sqlite number of assets: {len(list(sqlitedb.list_all()))}")

setup.cfg

@@ -44,6 +44,7 @@ where=src
 [options.entry_points]
 aerovaldb =
     json_files = aerovaldb.jsondb:AerovalJsonFileDB
+    sqlitedb = aerovaldb.sqlitedb:AerovalSqliteDB
 
 [tox:tox]
 labels =

src/aerovaldb/aerovaldb.py

@@ -5,6 +5,7 @@
 from .types import AccessType
 from .utils import async_and_sync
 from .routes import *
+from .lock import FakeLock, FileLock
 
 
 def get_method(route):
@@ -211,7 +212,11 @@ async def put_glob_stats(
         raise NotImplementedError
 
     def list_glob_stats(
-        self, project: str, experiment: str
+        self,
+        project: str,
+        experiment: str,
+        /,
+        access_type: str | AccessType = AccessType.URI,
     ) -> Generator[str, None, None]:
         """Generator that lists the URI for each glob_stats object.
 
@@ -339,7 +344,11 @@ async def put_timeseries(
         raise NotImplementedError
 
     def list_timeseries(
-        self, project: str, experiment: str
+        self,
+        project: str,
+        experiment: str,
+        /,
+        access_type: str | AccessType = AccessType.URI,
     ) -> Generator[str, None, None]:
         """Returns a list of URIs of all timeseries files for
         a given project and experiment id.
@@ -761,7 +770,13 @@ async def put_map(
         """
         raise NotImplementedError
 
-    def list_map(self, project: str, experiment: str) -> Generator[str, None, None]:
+    def list_map(
+        self,
+        project: str,
+        experiment: str,
+        /,
+        access_type: str | AccessType = AccessType.URI,
+    ) -> Generator[str, None, None]:
         """Lists all map files for a given project / experiment combination.
 
         :param project: The project ID.
@@ -1140,9 +1155,9 @@ async def get_by_uri(
 
         Note:
         -----
-        URI is implementation specific. While AerovalJsonFileDB returns
-        a file path, this behaviour should not be relied upon as other
-        implementations may not.
+        URI is intended to be consistent between implementations. Using get_by_uri()
+        to fetch an identifier which can then be written to another connector using
+        its respective put_by_uri() method.
         """
         raise NotImplementedError
 
@@ -1156,9 +1171,9 @@ async def put_by_uri(self, obj, uri: str):
 
         Note:
         -----
-        URI is implementation specific. While AerovalJsonFileDB returns
-        a file path as the uri, this behaviour should not be relied upon
-        as other implementations will not.
+        URI is intended to be consistent between implementations. Using get_by_uri()
+        to fetch an identifier which can then be written to another connector using
+        its respective put_by_uri() method.
         """
         raise NotImplementedError
 
@@ -1170,3 +1185,43 @@ def lock(self):
         See also: https://aerovaldb.readthedocs.io/en/latest/locking.html
         """
         raise NotImplementedError
+
+    def _normalize_access_type(
+        self, access_type: AccessType | str | None, default: AccessType = AccessType.OBJ
+    ) -> AccessType:
+        """Normalizes the access_type to an instance of AccessType enum.
+
+        :param access_type: AccessType instance or string convertible to AccessType
+        :param default: The type to return if access_type is None. Defaults to AccessType.OBJ
+        :raises ValueError: If str access_type can't be converted to AccessType.
+        :raises ValueError: If access_type is not str or AccessType
+        :return: The normalized AccessType.
+        """
+        if isinstance(access_type, AccessType):
+            return access_type
+
+        if isinstance(access_type, str):
+            try:
+                return AccessType[access_type]
+            except:
+                raise ValueError(
+                    f"String '{access_type}' can not be converted to AccessType."
+                )
+        if access_type is None:
+            return default
+
+        assert False
+
+    def list_all(
+        self, access_type: str | AccessType = AccessType.URI
+    ) -> Generator[str, None, None]:
+        """Iterator to list over the URI of each object
+        stored in the current aerovaldb connection, returning
+        the URI of each.
+
+        :param access_type : What to return (This is implementation specific, but in general
+        each implementation should support URI).
+        :raises : UnsupportedOperation
+            For non-supported acces types.
+        """
+        raise NotImplementedError