snakemake-interface-storage-plugins 4.3.3
This package provides a stable interface for interactions between Snakemake and its storage plugins.
Requires Python: >=3.11

# snakemake-interface-storage-plugins

This package provides a stable interface for interactions between Snakemake and its storage plugins.

Plugins should implement the following skeleton to comply with this interface.
It is recommended to use [Snakedeploy to set up the skeleton](https://snakedeploy.readthedocs.io/en/stable/snakemake_developers/scaffold_snakemake_plugins.html) (and automated testing) within a python package.

```python
from dataclasses import dataclass, field
from typing import Any, Iterable, Optional, List
from snakemake_interface_storage_plugins.settings import StorageProviderSettingsBase
from snakemake_interface_storage_plugins.storage_provider import (
    StorageProviderBase,
    StorageQueryValidationResult,
    ExampleQuery,
    Operation,
)
from snakemake_interface_storage_plugins.storage_object import (
    StorageObjectRead,
    StorageObjectWrite,
    StorageObjectGlob,
    StorageObjectTouch,
    retry_decorator,
)
from snakemake_interface_storage_plugins.io import IOCacheStorageInterface


# Optional:
# Define settings for your storage plugin (e.g. host url, credentials).
# They will occur in the Snakemake CLI as --storage-<storage-plugin-name>-<param-name>
# Make sure that all defined fields are 'Optional' and specify a default value
# of None or anything else that makes sense in your case.
# Note that we allow storage plugin settings to be tagged by the user. That means,
# that each of them can be specified multiple times (an implicit nargs=+), and
# the user can add a tag in front of each value (e.g. tagname1:value1 tagname2:value2).
# This way, a storage plugin can be used multiple times within a workflow with different
# settings.
@dataclass
class StorageProviderSettings(StorageProviderSettingsBase):
    myparam: Optional[int] = field(
        default=None,
        metadata={
            "help": "Some help text",
            # Optionally request that setting is also available for specification
            # via an environment variable. The variable will be named automatically as
            # SNAKEMAKE_<storage-plugin-name>_<param-name>, all upper case.
            # This mechanism should only be used for passwords, usernames, and other
            # credentials.
            # For other items, we rather recommend to let people use a profile
            # for setting defaults
            # (https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles).
            "env_var": False,
            # Optionally specify a function that parses the value given by the user.
            # This is useful to create complex types from the user input.
            "parse_func": ...,
            # If a parse_func is specified, you also have to specify an unparse_func
            # that converts the parsed value back to a string.
            "unparse_func": ...,
            # Optionally specify that setting is required when the executor is in use.
            "required": True,
            # Optionally specify multiple args with "nargs": True
        },
    )


# Required:
# Implementation of your storage provider
# This class can be empty as the one below.
# You can however use it to store global information or maintain e.g. a connection
# pool.
# Inside of the provider, you can use self.logger (a normal Python logger of type 
# logging.Logger) to log any additional informations or
# warnings.
class StorageProvider(StorageProviderBase):
    # For compatibility with future changes, you should not overwrite the __init__
    # method. Instead, use __post_init__ to set additional attributes and initialize
    # futher stuff.

    def __post_init__(self):
        # This is optional and can be removed if not needed.
        # Alternatively, you can e.g. prepare a connection to your storage backend here.
        # and set additional attributes.
        pass

    @classmethod
    def example_queries(cls) -> List[ExampleQuery]:
        """Return valid example queries (at least one) with description."""
        ...

    def rate_limiter_key(self, query: str, operation: Operation) -> Any:
        """Return a key for identifying a rate limiter given a query and an operation.

        This is used to identify a rate limiter for the query.
        E.g. for a storage provider like http that would be the host name.
        For s3 it might be just the endpoint URL.
        """
        ...

    def default_max_requests_per_second(self) -> float:
        """Return the default maximum number of requests per second for this storage
        provider."""
        ...

    def use_rate_limiter(self) -> bool:
        """Return False if no rate limiting is needed for this provider."""
        ...

    @classmethod
    def is_valid_query(cls, query: str) -> StorageQueryValidationResult:
        """Return whether the given query is valid for this storage provider."""
        # Ensure that also queries containing wildcards (e.g. {sample}) are accepted
        # and considered valid. The wildcards will be resolved before the storage
        # object is actually used.
        ...

    # If required, overwrite the method postprocess_query from StorageProviderBase
    # in order to e.g. normalize the query or add information from the settings to it.
    # Otherwise, remove this method as it will be inherited from the base class.
    def postprocess_query(self, query: str) -> str:
        return query

    # This can be used to change how the rendered query is displayed in the logs to
    # prevent accidentally printing sensitive information e.g. tokens in a URL.
    def safe_print(self, query: str) -> str:
        """Process the query to remove potentially sensitive information when printing.
        """
        return query


# Required:
# Implementation of storage object. If certain methods cannot be supported by your
# storage (e.g. because it is read-only see
# snakemake-storage-http for comparison), remove the corresponding base classes
# from the list of inherited items.
# Inside of the object, you can use self.provider to access the provider (e.g. for )
# self.provider.logger, see above, or self.provider.settings).
class StorageObject(
    StorageObjectRead,
    StorageObjectWrite,
    StorageObjectGlob,
    StorageObjectTouch
):
    # For compatibility with future changes, you should not overwrite the __init__
    # method. Instead, use __post_init__ to set additional attributes and initialize
    # futher stuff.

    def __post_init__(self):
        # This is optional and can be removed if not needed.
        # Alternatively, you can e.g. prepare a connection to your storage backend here.
        # and set additional attributes.
        pass

    async def inventory(self, cache: IOCacheStorageInterface):
        """From this file, try to find as much existence and modification date
        information as possible. Only retrieve that information that comes for free
        given the current object.
        """
        # This is optional and can be left as is

        # If this is implemented in a storage object, results have to be stored in
        # the given IOCache object, using self.cache_key() as key.
        # Optionally, this can take a custom local suffix, needed e.g. when you want 
        # to cache more items than the current query: self.cache_key(local_suffix=...)
        pass

    def get_inventory_parent(self) -> Optional[str]:
        """Return the parent directory of this object."""
        # this is optional and can be left as is
        return None

    def local_suffix(self) -> str:
        """Return a unique suffix for the local path, determined from self.query."""
        ...

    def cleanup(self):
        """Perform local cleanup of any remainders of the storage object."""
        # self.local_path() should not be removed, as this is taken care of by
        # Snakemake.
        ...

    # Fallible methods should implement some retry logic.
    # The easiest way to do this (but not the only one) is to use the retry_decorator
    # provided by snakemake-interface-storage-plugins.
    @retry_decorator
    def exists(self) -> bool:
        # return True if the object exists
        ...

    @retry_decorator
    def mtime(self) -> float:
        # return the modification time
        ...

    @retry_decorator
    def size(self) -> int:
        # return the size in bytes
        ...

    @retry_decorator
    def local_footprint(self) -> int:
        # Local footprint is the size of the object on the local disk.
        # For directories, this should return the recursive sum of the
        # directory file sizes.
        # If the storage provider supports ondemand eligibility (see retrieve_object()
        # below), this should return 0 if the object is not downloaded but e.g.
        # mounted upon retrieval.
        # If this method is not overwritten here, it defaults to self.size().
        ...

    @retry_decorator
    def retrieve_object(self):
        # Ensure that the object is accessible locally under self.local_path()
        # Optionally, this can make use of the attribute self.is_ondemand_eligible,
        # which indicates that the object could be retrieved on demand,
        # e.g. by only symlinking or mounting it from whatever network storage this
        # plugin provides. For example, objects with self.is_ondemand_eligible == True
        # could mount the object via fuse instead of downloading it.
        # The job can then transparently access only the parts that matter to it
        # without having to wait for the full download.
        # On demand eligibility is calculated via Snakemake's access pattern annotation.
        # If no access pattern is annotated by the workflow developers,
        # self.is_ondemand_eligible is by default set to False.
        ...

    # The following two methods are only required if the class inherits from
    # StorageObjectReadWrite.

    @retry_decorator
    def store_object(self):
        # Ensure that the object is stored at the location specified by
        # self.local_path().
        ...

    @retry_decorator
    def remove(self):
        # Remove the object from the storage.
        ...

    # The following method is only required if the class inherits from
    # StorageObjectGlob.

    @retry_decorator
    def list_candidate_matches(self) -> Iterable[str]:
        """Return a list of candidate matches in the storage for the query."""
        # This is used by glob_wildcards() to find matches for wildcards in the query.
        # The method has to return concretized queries without any remaining wildcards.
        # Use snakemake_executor_plugins.io.get_constant_prefix(self.query) to get the
        # prefix of the query before the first wildcard.
        ...

    # The following method is only required if the class inherits from
    # StorageObjectTouch
    @retry_decorator
    def touch(self):
        """Touch the object, updating its modification date."""
        ...
```