tsdat.io.storage
¶
Classes¶
DatastreamStorage is the base class for providing |
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DisposableLocalTempFile is a context manager wrapper class for a temp file on |
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Provides a context manager wrapper class for a list of |
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Provides is a context manager wrapper class for a list of |
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Each DatastreamStorage should contain a corresponding |
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class
tsdat.io.storage.
DatastreamStorage
(parameters: Union[Dict, None] = None)[source]¶ Bases:
abc.ABC
DatastreamStorage is the base class for providing access to processed data files in a persistent archive. DatastreamStorage provides shortcut methods to find files based upon date, datastream name, file type, etc. This is the class that should be used to save and retrieve processed data files. Use the DatastreamStorage.from_config() method to construct the appropriate subclass instance based upon a storage config file.
Class Methods
Deletes datastream data in the datastream store in between the
Checks if any data exists in the datastream store for the provided
Fetches files from the datastream store using the datastream_name,
Finds all files of the given type from the datastream store with the
Load a yaml config file which provides the storage constructor
Saves a local file to the datastream store.
Given a path to a local file, save that file to the storage.
Each subclass should define the tmp property, which provides
Method Descriptions
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abstract
delete
(self, datastream_name: str, start_time: str, end_time: str, filetype: str = None) → None[source]¶ Deletes datastream data in the datastream store in between the specified time range.
- Parameters
datastream_name (str) – The datastream_name as defined by ME Data Standards.
start_time (str) – The start time or date to start searching for data (inclusive). Should be like “20210106” to search for data beginning on or after January 6th, 2021.
end_time (str) – The end time or date to stop searching for data (exclusive). Should be like “20210108” to search for data ending before January 8th, 2021.
filetype (str, optional) – A file type from the DatastreamStorage.file_filters keys. If no type is specified, all files will be deleted. Defaults to None.
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abstract
exists
(self, datastream_name: str, start_time: str, end_time: str, filetype: str = None) → bool[source]¶ Checks if any data exists in the datastream store for the provided datastream and time range.
- Parameters
datastream_name (str) – The datastream_name as defined by ME Data Standards.
start_time (str) – The start time or date to start searching for data (inclusive). Should be like “20210106” to search for data beginning on or after January 6th, 2021.
end_time (str) – The end time or date to stop searching for data (exclusive). Should be like “20210108” to search for data ending before January 8th, 2021.
filetype (str, optional) – A file type from the DatastreamStorage.file_filters keys. If none specified, all files will be checked. Defaults to None.
- Returns
True if data exists, False otherwise.
- Return type
bool
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abstract
fetch
(self, datastream_name: str, start_time: str, end_time: str, local_path: str = None, filetype: int = None)[source]¶ Fetches files from the datastream store using the datastream_name, start_time, and end_time to specify the file(s) to retrieve. If the local path is not specified, it is up to the subclass to determine where to put the retrieved file(s).
- Parameters
datastream_name (str) – The datastream_name as defined by ME Data Standards.
start_time (str) – The start time or date to start searching for data (inclusive). Should be like “20210106” to search for data beginning on or after January 6th, 2021.
end_time (str) – The end time or date to stop searching for data (exclusive). Should be like “20210108” to search for data ending before January 8th, 2021.
local_path (str, optional) – The path to the directory where the data should be stored. Defaults to None.
filetype (int, optional) – A file type from the DatastreamStorage.file_filters keys If no type is specified, all files will be returned. Defaults to None.
- Returns
A list of paths where the retrieved files were stored in local storage. This is a context manager class, so it this method should be called via the ‘with’ statement and all files referenced by the list will be cleaned up when it goes out of scope.
- Return type
DisposableLocalTempFileList:
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abstract
find
(self, datastream_name: str, start_time: str, end_time: str, filetype: str = None) → List[str][source]¶ Finds all files of the given type from the datastream store with the given datastream_name and timestamps from start_time (inclusive) up to end_time (exclusive). Returns a list of paths to files that match the criteria.
- Parameters
datastream_name (str) – The datastream_name as defined by ME Data Standards.
start_time (str) – The start time or date to start searching for data (inclusive). Should be like “20210106.000000” to search for data beginning on or after January 6th, 2021.
end_time (str) – The end time or date to stop searching for data (exclusive). Should be like “20210108.000000” to search for data ending before January 8th, 2021.
filetype (str, optional) – A file type from the DatastreamStorage.file_filters keys If no type is specified, all files will be returned. Defaults to None.
- Returns
A list of paths in datastream storage in ascending order
- Return type
List[str]
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static
from_config
(storage_config_file: str)[source]¶ Load a yaml config file which provides the storage constructor parameters.
- Parameters
storage_config_file (str) – The path to the config file to load
- Returns
A subclass instance created from the config file.
- Return type
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save
(self, dataset_or_path: Union[str, xarray.Dataset], new_filename: str = None) → List[Any][source]¶ Saves a local file to the datastream store.
- Parameters
dataset_or_path (Union[str, xr.Dataset]) – The dataset or local path to the file to save. The file should be named according to ME Data Standards naming conventions so that this method can automatically parse the datastream, date, and time from the file name.
new_filename (str, optional) – If provided, the new filename to save as. This parameter should ONLY be provided if using a local path for dataset_or_path. Must also follow ME Data Standards naming conventions. Defaults to None.
- Returns
A list of paths where the saved files were stored in storage. Path type is dependent upon the specific storage subclass.
- Return type
List[Any]
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abstract
save_local_path
(self, local_path: str, new_filename: str = None) → Any[source]¶ Given a path to a local file, save that file to the storage.
- Parameters
local_path (str) – Local path to the file to save. The file should be named according to ME Data Standards naming conventions so that this method can automatically parse the datastream, date, and time from the file name.
new_filename (str, optional) – If provided, the new filename to save as. This parameter should ONLY be provided if using a local path for dataset_or_path. Must also follow ME Data Standards naming conventions. Defaults to None.
- Returns
The path where this file was stored in storage. Path type is dependent upon the specific storage subclass.
- Return type
Any
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property
tmp
(self)[source]¶ Each subclass should define the tmp property, which provides access to a TemporaryStorage object that is used to efficiently handle reading/writing temporary files used during the processing pipeline, or to perform fileystem actions on files other than processed datastream files that reside in the same filesystem as the DatastreamStorage. Is is not intended to be used outside of the pipeline.
- Raises
NotImplementedError – [description]
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abstract
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class
tsdat.io.storage.
DisposableLocalTempFile
(filepath: str, disposable=True)[source]¶ DisposableLocalTempFile is a context manager wrapper class for a temp file on the LOCAL FILESYSTEM. It will ensure that the file is deleted when it goes out of scope.
- Parameters
filepath (str) – Path to a local temp file that could be deleted when it goes out of scope.
disposable (bool, optional) – True if this file should be automatically deleted when it goes out of scope. Defaults to True.
Class Methods
Method Descriptions
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class
tsdat.io.storage.
DisposableLocalTempFileList
(filepath_list: List[str], delete_on_exception=False, disposable=True)[source]¶ Bases:
list
Provides a context manager wrapper class for a list of temp files on the LOCAL FILESYSTEM. It ensures that if specified, the files will be auto-deleted when the list goes out of scope.
- Parameters
filepath_list (List[str]) – A list of local temp files
delete_on_exception (bool, optional) – Should the local temp files be deleted if an error was thrown when processing. Defaults to False.
disposable (bool, optional) – Should the local temp files be auto-deleted when they go out of scope. Defaults to True.
Initialize self. See help(type(self)) for accurate signature.
Class Methods
Method Descriptions
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class
tsdat.io.storage.
DisposableStorageTempFileList
(filepath_list: List[str], storage, disposable_files: Union[List, None] = None)[source]¶ Bases:
list
Provides is a context manager wrapper class for a list of temp files on the STORAGE FILESYSTEM. It will ensure that the specified files are deleted when the list goes out of scope.
- Parameters
filepath_list (List[str]) – A list of files in temporary storage area
storage (TemporaryStorage) – The temporary storage service used to clean up temporary files.
disposable_files (list, optional) – Which of the files from the filepath_list should be auto-deleted when the list goes out of scope. Defaults to []
Initialize self. See help(type(self)) for accurate signature.
Class Methods
Method Descriptions
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class
tsdat.io.storage.
TemporaryStorage
(storage: DatastreamStorage)[source]¶ Bases:
abc.ABC
Each DatastreamStorage should contain a corresponding TemporaryStorage class which provides access to a TemporaryStorage object that is used to efficiently handle reading/writing temporary files used during the processing pipeline, or to perform fileystem actions on files other than processed datastream files that reside in the same filesystem as the DatastreamStorage.
TemporaryStorage methods return a context manager so that the created temporary files can be automatically removed when they go out of scope.
TemporaryStorage is a helper class intended to be used in the internals of pipeline implementations only. It is not meant as an external API for interacting with files in DatastreamStorage.
TODO: rename to a more intuitive name…
- Parameters
storage (DatastreamStorage) – A reference to the corresponding DatastreamStorage
Class Methods
Clean any extraneous files from the temp working dirs. Temp files
Create a new, temporary directory under the local tmp area managed by
Remove a file from storage temp area if the file exists. If the file
If provided a path to an archive file, this function will extract the
Fetch a file from temp storage to a local temp folder. If
Look in DatastreamStorage for the first processed file before the given date.
Construct a filepath for a temporary file that will be located in the
Return true if this file should be excluded from the zip file check.
Default method to get a local temporary folder for use when retrieving
Method Descriptions
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clean
(self)[source]¶ Clean any extraneous files from the temp working dirs. Temp files could be in two places:
the local temp folder - used when fetching files from the store
the storage temp folder - used when extracting zip files in some stores (e.g., AWS)
This method removes the local temp folder. Child classes can extend this method to clean up their respective storage temp folders.
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create_temp_dir
(self) → str[source]¶ Create a new, temporary directory under the local tmp area managed by TemporaryStorage.
- Returns
Path to the local dir.
- Return type
str
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abstract
delete
(self, file_path: str)[source]¶ Remove a file from storage temp area if the file exists. If the file does not exist, this method will NOT raise an exception.
- Parameters
file_path (str) – The path of a file located in the same filesystem as the storage.
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abstract
extract_files
(self, file_path: Union[str, List[str]]) → DisposableStorageTempFileList[source]¶ If provided a path to an archive file, this function will extract the archive into a temp directory IN THE SAME FILESYSTEM AS THE STORAGE. This means, for example that if storage was in an s3 bucket ,then the files would be extracted to a temp dir in that s3 bucket. This is to prevent local disk limitations when running via Lambda.
If the file is not an archive, then the same file will be returned.
This method supports zip, tar, and tar.g file formats.
- Parameters
file_path (Union[str, List[str]]) – The path of a file or a list of files that should be processed together, located in the same filesystem as the storage.
- Returns
A list of paths to the files that were extracted. Files will be located in the temp area of the storage filesystem.
- Return type
-
abstract
fetch
(self, file_path: str, local_dir=None, disposable=True) → Union[DisposableLocalTempFile, str][source]¶ Fetch a file from temp storage to a local temp folder. If disposable is True, then a DisposableLocalTempFile will be returned so that it can be used with a context manager.
- Parameters
file_path (str) – The path of a file located in the same filesystem as the storage.
local_dir ([type], optional) – The destination folder for the file. If not specified, it will be created int the storage-approved local temp folder. defaults to None.
disposable (bool, optional) – True if this file should be auto-deleted when it goes out of scope. Defaults to True.
- Returns
If disposable, return a DisposableLocalTempFile, otherwise return the path to the local file.
- Return type
Union[DisposableLocalTempFile, str]
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abstract
fetch_previous_file
(self, datastream_name: str, start_time: str) → DisposableLocalTempFile[source]¶ Look in DatastreamStorage for the first processed file before the given date.
- Parameters
datastream_name (str) – The datastream_name as defined by ME Data Standards.
start_time (str) – The start time or date to start searching for data (inclusive). Should be like “20210106” to search for data beginning on or after January 6th, 2021.
- Returns
If a previous file was found, return the local path to the fetched file. Otherwise return None. (Return value wrapped in DisposableLocalTempFile so it can be auto-deleted if needed.)
- Return type
-
get_temp_filepath
(self, filename: str = None, disposable: bool = True) → DisposableLocalTempFile[source]¶ Construct a filepath for a temporary file that will be located in the storage-approved local temp folder and will be deleted when it goes out of scope.
- Parameters
filename (str, optional) – The filename to use for the temp file. If no filename is provided, one will be created. Defaults to None
disposable (bool, optional) – If true, then wrap in DisposableLocalTempfile so that the file will be removed when it goes out of scope. Defaults to True.
- Returns
Path to the local file. The file will be automatically deleted when it goes out of scope.
- Return type
-
ignore_zip_check
(self, filepath: str) → bool[source]¶ Return true if this file should be excluded from the zip file check. We need this for Office documents, since they are actually zip files under the hood, so we don’t want to try to unzip them.
- Parameters
filepath (str) – the file we are potentially extracting
- Returns
whether we should check if it is a zip or not
- Return type
bool