lamindb_setup 1.19.0__py3-none-any.whl → 1.19.1__py3-none-any.whl

lamindb_setup/core/__init__.py

@@ -1,34 +1,25 @@
-"""Core setup library.
-
-General
--------
-
-.. autoclass:: SetupSettings
-
-User
-----
-
-.. autoclass:: UserSettings
-
-Instance
---------
-
-.. autoclass:: InstanceSettings
-
-Storage
--------
-
-.. autoclass:: StorageSettings
-
-"""
-
-from . import django, upath
-from ._clone import (
-    upload_sqlite_clone,
-)
-from ._deprecated import deprecated  # documented in lamindb.base
-from ._docs import doc_args  # documented in lamindb.base
-from ._settings import SetupSettings
-from ._settings_instance import InstanceSettings
-from ._settings_storage import StorageSettings
-from ._settings_user import UserSettings
+"""Setup core library.
+
+Settings
+--------
+
+.. autoclass:: SetupSettings
+
+.. autoclass:: UserSettings
+
+.. autoclass:: InstanceSettings
+
+.. autoclass:: StorageSettings
+
+"""
+
+from . import django, upath
+from ._clone import (
+    upload_sqlite_clone,
+)
+from ._deprecated import deprecated  # documented in lamindb.base
+from ._docs import doc_args  # documented in lamindb.base
+from ._settings import SetupSettings
+from ._settings_instance import InstanceSettings
+from ._settings_storage import StorageSettings
+from ._settings_user import UserSettings

lamindb_setup/core/_aws_options.py

@@ -1,276 +1,276 @@
-from __future__ import annotations
-
-import logging
-import os
-import time
-from typing import Any
-
-from lamin_utils import logger
-from upath import UPath
-
-HOSTED_REGIONS = [
-    "eu-central-1",
-    "eu-west-2",
-    "us-east-1",
-    "us-east-2",
-    "us-west-1",
-    "us-west-2",
-]
-lamin_env = os.getenv("LAMIN_ENV")
-if lamin_env is None or lamin_env == "prod":
-    HOSTED_BUCKETS = tuple([f"s3://lamin-{region}" for region in HOSTED_REGIONS])
-else:
-    logger.warning(f"loaded LAMIN_ENV: {lamin_env}")
-    HOSTED_BUCKETS = ("s3://lamin-hosted-test",)  # type: ignore
-
-
-def _keep_trailing_slash(path_str: str) -> str:
-    return path_str if path_str[-1] == "/" else path_str + "/"
-
-
-AWS_CREDENTIALS_EXPIRATION: int = 11 * 60 * 60  # refresh credentials after 11 hours
-
-
-# set anon=True for these buckets if credentials fail for a public bucket to be expanded
-PUBLIC_BUCKETS: tuple[str, ...] = ("cellxgene-data-public", "bionty-assets")
-
-
-# s3-comaptible endpoints managed by lamin
-# None means the standard aws s3 endpoint
-LAMIN_ENDPOINTS: tuple[str | None] = (None,)
-
-
-class NoTracebackFilter(logging.Filter):
-    def filter(self, record):
-        record.exc_info = None  # Remove traceback info from the log record.
-        return True
-
-
-class AWSOptionsManager:
-    # suppress giant traceback logs from aiobotocore when failing to refresh sso etc
-    @staticmethod
-    def _suppress_aiobotocore_traceback_logging():
-        logger = logging.getLogger("aiobotocore.credentials")
-        logger.addFilter(NoTracebackFilter())
-
-    def __init__(self):
-        self._credentials_cache = {}
-        self._parameters_cache = {}  # this is not refreshed
-
-        from aiobotocore.session import AioSession
-        from packaging import version as packaging_version
-
-        # takes 100ms to import, so keep it here to avoid delaying the import of the main module
-        from s3fs import S3FileSystem
-        from s3fs import __version__ as s3fs_version
-
-        if packaging_version.parse(s3fs_version) < packaging_version.parse("2023.12.2"):
-            raise RuntimeError(
-                f"The version of s3fs you have ({s3fs_version}) is impompatible "
-                "with lamindb, please upgrade it: pip install s3fs>=2023.12.2"
-            )
-
-        anon_env = os.getenv("LAMIN_S3_ANON") == "true"
-        # this is cached so will be resued with the connection initialized
-        # these options are set for paths in _path_inject_options
-        # here we set the same options to cache the filesystem
-        fs = S3FileSystem(
-            cache_regions=True,
-            use_listings_cache=True,
-            version_aware=False,
-            config_kwargs={"max_pool_connections": 64},
-            anon=anon_env,
-        )
-
-        self._suppress_aiobotocore_traceback_logging()
-
-        if anon_env:
-            self.anon: bool = True
-            logger.warning(
-                "`anon` mode will be used for all non-managed buckets "
-                "because the environment variable LAMIN_S3_ANON was set to 'true'"
-            )
-        else:
-            try:
-                fs.connect()
-                self.anon = fs.session._credentials is None
-            except Exception as e:
-                logger.warning(
-                    f"There is a problem with your default AWS Credentials: {e}\n"
-                    "`anon` mode will be used for all non-managed buckets"
-                )
-                self.anon = True
-
-        self.anon_public: bool | None = None
-        if not self.anon:
-            try:
-                # use lamindata public bucket for this test
-                fs.call_s3("head_bucket", Bucket="lamindata")
-                self.anon_public = False
-            except Exception:
-                self.anon_public = True
-
-        empty_session = AioSession(profile="lamindb_empty_profile")
-        empty_session.full_config["profiles"]["lamindb_empty_profile"] = {}
-        # this is set downstream to avoid using local configs when we provide credentials
-        # or when we set anon=True
-        self.empty_session = empty_session
-
-    def _find_root(self, path_str: str) -> str | None:
-        roots = self._credentials_cache.keys()
-        if path_str in roots:
-            return path_str
-        roots = sorted(roots, key=len, reverse=True)
-        for root in roots:
-            if path_str.startswith(root):
-                return root
-        return None
-
-    def _is_active(self, root: str) -> bool:
-        return (
-            time.time() - self._credentials_cache[root]["time"]
-        ) < AWS_CREDENTIALS_EXPIRATION
-
-    def _set_cached_credentials(self, root: str, credentials: dict):
-        if root not in self._credentials_cache:
-            self._credentials_cache[root] = {}
-        self._credentials_cache[root]["credentials"] = credentials
-        self._credentials_cache[root]["time"] = time.time()
-
-    def _get_cached_credentials(self, root: str) -> dict:
-        return self._credentials_cache[root]["credentials"]
-
-    def _path_inject_options(
-        self, path: UPath, credentials: dict, extra_parameters: dict | None = None
-    ) -> UPath:
-        connection_options: dict[str, Any] = {}
-        storage_options = path.storage_options
-        if credentials == {}:
-            # otherwise credentials were specified manually for the path
-            if "anon" not in storage_options and (
-                path.fs.key is None or path.fs.secret is None
-            ):
-                anon = self.anon
-                if not anon and self.anon_public and path.drive in PUBLIC_BUCKETS:
-                    anon = True
-                if anon:
-                    connection_options["anon"] = anon
-                    connection_options["session"] = self.empty_session
-        else:
-            connection_options.update(credentials)
-            connection_options["session"] = self.empty_session
-
-        if "cache_regions" in storage_options:
-            connection_options["cache_regions"] = storage_options["cache_regions"]
-        else:
-            connection_options["cache_regions"] = (
-                storage_options.get("endpoint_url", None) is None
-            )
-        # we use cache to avoid some uneeded downloads or credential problems
-        # see in upload_from
-        connection_options["use_listings_cache"] = storage_options.get(
-            "use_listings_cache", True
-        )
-        # normally we want to ignore objects vsrsions in a versioned bucket
-        connection_options["version_aware"] = storage_options.get(
-            "version_aware", False
-        )
-        # this is for better concurrency as the default batch_size is 128
-        # read https://github.com/laminlabs/lamindb-setup/pull/1146
-        if "config_kwargs" not in storage_options:
-            connection_options["config_kwargs"] = {"max_pool_connections": 64}
-        elif "max_pool_connections" not in (
-            config_kwargs := storage_options["config_kwargs"]
-        ):
-            config_kwargs["max_pool_connections"] = 64
-            connection_options["config_kwargs"] = config_kwargs
-
-        if extra_parameters:
-            connection_options.update(extra_parameters)
-
-        return UPath(path, **connection_options)
-
-    def enrich_path(self, path: UPath, access_token: str | None = None) -> UPath:
-        # ignore paths with non-lamin-managed endpoints
-        if (
-            endpoint_url := path.storage_options.get("endpoint_url", None)
-        ) not in LAMIN_ENDPOINTS:
-            if "r2.cloudflarestorage.com" in endpoint_url:
-                # fixed_upload_size should always be True for R2
-                # this option is needed for correct uploads to R2
-                # TODO: maybe set max_pool_connections=64 here also
-                path = UPath(path, fixed_upload_size=True)
-            return path
-        # trailing slash is needed to avoid returning incorrect results with .startswith
-        # for example s3://lamindata-eu should not receive cache for s3://lamindata
-        path_str = _keep_trailing_slash(path.as_posix())
-        root = self._find_root(path_str)
-
-        if root is not None:
-            set_cache = False
-            credentials = self._get_cached_credentials(root)
-            extra_parameters = self._parameters_cache.get(root)
-            if access_token is not None:
-                set_cache = True
-            elif credentials != {}:
-                # update credentials
-                if not self._is_active(root):
-                    set_cache = True
-        else:
-            set_cache = True
-
-        if set_cache:
-            from ._hub_core import access_aws
-            from ._settings import settings
-
-            storage_root_info = access_aws(path_str, access_token=access_token)
-            accessibility = storage_root_info["accessibility"]
-            is_managed = accessibility.get("is_managed", False)
-            if is_managed:
-                credentials = storage_root_info["credentials"]
-                extra_parameters = accessibility["extra_parameters"]
-            else:
-                credentials = {}
-                extra_parameters = None
-
-            if access_token is None:
-                if "storage_root" in accessibility:
-                    root = accessibility["storage_root"]
-                # just to be safe
-                root = None if root == "" else root
-                if root is None:
-                    # heuristic
-                    # do not write the first level for the known hosted buckets
-                    if path_str.startswith(HOSTED_BUCKETS):
-                        root = "/".join(path.path.rstrip("/").split("/")[:2])
-                    else:
-                        # write the bucket for everything else
-                        root = path.drive
-                    root = "s3://" + root
-
-                root = _keep_trailing_slash(root)
-                assert isinstance(root, str)
-                self._set_cached_credentials(root, credentials)
-                self._parameters_cache[root] = extra_parameters
-
-        return self._path_inject_options(path, credentials, extra_parameters)
-
-
-_aws_options_manager: AWSOptionsManager | None = None
-
-
-def get_aws_options_manager() -> AWSOptionsManager:
-    global _aws_options_manager
-
-    if _aws_options_manager is None:
-        _aws_options_manager = AWSOptionsManager()
-
-    return _aws_options_manager
-
-
-def reset_aws_options_cache():
-    global _aws_options_manager
-
-    if _aws_options_manager is not None:
-        _aws_options_manager._credentials_cache = {}
-        _aws_options_manager._parameters_cache = {}
+from __future__ import annotations
+
+import logging
+import os
+import time
+from typing import Any
+
+from lamin_utils import logger
+from upath import UPath
+
+HOSTED_REGIONS = [
+    "eu-central-1",
+    "eu-west-2",
+    "us-east-1",
+    "us-east-2",
+    "us-west-1",
+    "us-west-2",
+]
+lamin_env = os.getenv("LAMIN_ENV")
+if lamin_env is None or lamin_env == "prod":
+    HOSTED_BUCKETS = tuple([f"s3://lamin-{region}" for region in HOSTED_REGIONS])
+else:
+    logger.warning(f"loaded LAMIN_ENV: {lamin_env}")
+    HOSTED_BUCKETS = ("s3://lamin-hosted-test",)  # type: ignore
+
+
+def _keep_trailing_slash(path_str: str) -> str:
+    return path_str if path_str[-1] == "/" else path_str + "/"
+
+
+AWS_CREDENTIALS_EXPIRATION: int = 11 * 60 * 60  # refresh credentials after 11 hours
+
+
+# set anon=True for these buckets if credentials fail for a public bucket to be expanded
+PUBLIC_BUCKETS: tuple[str, ...] = ("cellxgene-data-public", "bionty-assets")
+
+
+# s3-comaptible endpoints managed by lamin
+# None means the standard aws s3 endpoint
+LAMIN_ENDPOINTS: tuple[str | None] = (None,)
+
+
+class NoTracebackFilter(logging.Filter):
+    def filter(self, record):
+        record.exc_info = None  # Remove traceback info from the log record.
+        return True
+
+
+class AWSOptionsManager:
+    # suppress giant traceback logs from aiobotocore when failing to refresh sso etc
+    @staticmethod
+    def _suppress_aiobotocore_traceback_logging():
+        logger = logging.getLogger("aiobotocore.credentials")
+        logger.addFilter(NoTracebackFilter())
+
+    def __init__(self):
+        self._credentials_cache = {}
+        self._parameters_cache = {}  # this is not refreshed
+
+        from aiobotocore.session import AioSession
+        from packaging import version as packaging_version
+
+        # takes 100ms to import, so keep it here to avoid delaying the import of the main module
+        from s3fs import S3FileSystem
+        from s3fs import __version__ as s3fs_version
+
+        if packaging_version.parse(s3fs_version) < packaging_version.parse("2023.12.2"):
+            raise RuntimeError(
+                f"The version of s3fs you have ({s3fs_version}) is impompatible "
+                "with lamindb, please upgrade it: pip install s3fs>=2023.12.2"
+            )
+
+        anon_env = os.getenv("LAMIN_S3_ANON") == "true"
+        # this is cached so will be resued with the connection initialized
+        # these options are set for paths in _path_inject_options
+        # here we set the same options to cache the filesystem
+        fs = S3FileSystem(
+            cache_regions=True,
+            use_listings_cache=True,
+            version_aware=False,
+            config_kwargs={"max_pool_connections": 64},
+            anon=anon_env,
+        )
+
+        self._suppress_aiobotocore_traceback_logging()
+
+        if anon_env:
+            self.anon: bool = True
+            logger.warning(
+                "`anon` mode will be used for all non-managed buckets "
+                "because the environment variable LAMIN_S3_ANON was set to 'true'"
+            )
+        else:
+            try:
+                fs.connect()
+                self.anon = fs.session._credentials is None
+            except Exception as e:
+                logger.warning(
+                    f"There is a problem with your default AWS Credentials: {e}\n"
+                    "`anon` mode will be used for all non-managed buckets"
+                )
+                self.anon = True
+
+        self.anon_public: bool | None = None
+        if not self.anon:
+            try:
+                # use lamindata public bucket for this test
+                fs.call_s3("head_bucket", Bucket="lamindata")
+                self.anon_public = False
+            except Exception:
+                self.anon_public = True
+
+        empty_session = AioSession(profile="lamindb_empty_profile")
+        empty_session.full_config["profiles"]["lamindb_empty_profile"] = {}
+        # this is set downstream to avoid using local configs when we provide credentials
+        # or when we set anon=True
+        self.empty_session = empty_session
+
+    def _find_root(self, path_str: str) -> str | None:
+        roots = self._credentials_cache.keys()
+        if path_str in roots:
+            return path_str
+        roots = sorted(roots, key=len, reverse=True)
+        for root in roots:
+            if path_str.startswith(root):
+                return root
+        return None
+
+    def _is_active(self, root: str) -> bool:
+        return (
+            time.time() - self._credentials_cache[root]["time"]
+        ) < AWS_CREDENTIALS_EXPIRATION
+
+    def _set_cached_credentials(self, root: str, credentials: dict):
+        if root not in self._credentials_cache:
+            self._credentials_cache[root] = {}
+        self._credentials_cache[root]["credentials"] = credentials
+        self._credentials_cache[root]["time"] = time.time()
+
+    def _get_cached_credentials(self, root: str) -> dict:
+        return self._credentials_cache[root]["credentials"]
+
+    def _path_inject_options(
+        self, path: UPath, credentials: dict, extra_parameters: dict | None = None
+    ) -> UPath:
+        connection_options: dict[str, Any] = {}
+        storage_options = path.storage_options
+        if credentials == {}:
+            # otherwise credentials were specified manually for the path
+            if "anon" not in storage_options and (
+                path.fs.key is None or path.fs.secret is None
+            ):
+                anon = self.anon
+                if not anon and self.anon_public and path.drive in PUBLIC_BUCKETS:
+                    anon = True
+                if anon:
+                    connection_options["anon"] = anon
+                    connection_options["session"] = self.empty_session
+        else:
+            connection_options.update(credentials)
+            connection_options["session"] = self.empty_session
+
+        if "cache_regions" in storage_options:
+            connection_options["cache_regions"] = storage_options["cache_regions"]
+        else:
+            connection_options["cache_regions"] = (
+                storage_options.get("endpoint_url", None) is None
+            )
+        # we use cache to avoid some uneeded downloads or credential problems
+        # see in upload_from
+        connection_options["use_listings_cache"] = storage_options.get(
+            "use_listings_cache", True
+        )
+        # normally we want to ignore objects vsrsions in a versioned bucket
+        connection_options["version_aware"] = storage_options.get(
+            "version_aware", False
+        )
+        # this is for better concurrency as the default batch_size is 128
+        # read https://github.com/laminlabs/lamindb-setup/pull/1146
+        if "config_kwargs" not in storage_options:
+            connection_options["config_kwargs"] = {"max_pool_connections": 64}
+        elif "max_pool_connections" not in (
+            config_kwargs := storage_options["config_kwargs"]
+        ):
+            config_kwargs["max_pool_connections"] = 64
+            connection_options["config_kwargs"] = config_kwargs
+
+        if extra_parameters:
+            connection_options.update(extra_parameters)
+
+        return UPath(path, **connection_options)
+
+    def enrich_path(self, path: UPath, access_token: str | None = None) -> UPath:
+        # ignore paths with non-lamin-managed endpoints
+        if (
+            endpoint_url := path.storage_options.get("endpoint_url", None)
+        ) not in LAMIN_ENDPOINTS:
+            if "r2.cloudflarestorage.com" in endpoint_url:
+                # fixed_upload_size should always be True for R2
+                # this option is needed for correct uploads to R2
+                # TODO: maybe set max_pool_connections=64 here also
+                path = UPath(path, fixed_upload_size=True)
+            return path
+        # trailing slash is needed to avoid returning incorrect results with .startswith
+        # for example s3://lamindata-eu should not receive cache for s3://lamindata
+        path_str = _keep_trailing_slash(path.as_posix())
+        root = self._find_root(path_str)
+
+        if root is not None:
+            set_cache = False
+            credentials = self._get_cached_credentials(root)
+            extra_parameters = self._parameters_cache.get(root)
+            if access_token is not None:
+                set_cache = True
+            elif credentials != {}:
+                # update credentials
+                if not self._is_active(root):
+                    set_cache = True
+        else:
+            set_cache = True
+
+        if set_cache:
+            from ._hub_core import access_aws
+            from ._settings import settings
+
+            storage_root_info = access_aws(path_str, access_token=access_token)
+            accessibility = storage_root_info["accessibility"]
+            is_managed = accessibility.get("is_managed", False)
+            if is_managed:
+                credentials = storage_root_info["credentials"]
+                extra_parameters = accessibility["extra_parameters"]
+            else:
+                credentials = {}
+                extra_parameters = None
+
+            if access_token is None:
+                if "storage_root" in accessibility:
+                    root = accessibility["storage_root"]
+                # just to be safe
+                root = None if root == "" else root
+                if root is None:
+                    # heuristic
+                    # do not write the first level for the known hosted buckets
+                    if path_str.startswith(HOSTED_BUCKETS):
+                        root = "/".join(path.path.rstrip("/").split("/")[:2])
+                    else:
+                        # write the bucket for everything else
+                        root = path.drive
+                    root = "s3://" + root
+
+                root = _keep_trailing_slash(root)
+                assert isinstance(root, str)
+                self._set_cached_credentials(root, credentials)
+                self._parameters_cache[root] = extra_parameters
+
+        return self._path_inject_options(path, credentials, extra_parameters)
+
+
+_aws_options_manager: AWSOptionsManager | None = None
+
+
+def get_aws_options_manager() -> AWSOptionsManager:
+    global _aws_options_manager
+
+    if _aws_options_manager is None:
+        _aws_options_manager = AWSOptionsManager()
+
+    return _aws_options_manager
+
+
+def reset_aws_options_cache():
+    global _aws_options_manager
+
+    if _aws_options_manager is not None:
+        _aws_options_manager._credentials_cache = {}
+        _aws_options_manager._parameters_cache = {}