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https://github.com/dataoneorg/hashstore-java

HashStore, a hash-based object store for DataONE data packages
https://github.com/dataoneorg/hashstore-java

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HashStore, a hash-based object store for DataONE data packages

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## HashStore-java: hash-based object storage for DataONE data packages



Version: 1.1.0

- DOI: [doi:10.18739/A2ZG6G87Q](https://doi.org/10.18739/A2ZG6G87Q)



## Contributors



- **Author**: Dou Mok, Jing Tao, Matthew Brooke, Matthew B. Jones

- **License**: [Apache 2](http://opensource.org/licenses/Apache-2.0)

- [Package source code on GitHub](https://github.com/DataONEorg/hashstore-java)

- [**Submit Bugs and feature requests**](https://github.com/DataONEorg/hashstore-java/issues)

- Contact us: support@dataone.org

- [DataONE discussions](https://github.com/DataONEorg/dataone/discussions)



## Citation



Cite this software as:



> Dou Mok, Jing Tao, Matthew Brooke, Matthew B. Jones. 2024.

> HashStore-java: hash-based object storage for DataONE data packages. Arctic Data Center.

> [doi:10.18739/A2QF8JM59](https://doi.org/10.18739/A2QF8JM59)



## Introduction



HashStore-java is a server-side java library that implements an object storage file system for storing

and accessing data and metadata for DataONE services. The package is used in DataONE system

components that need direct, filesystem-based access to data objects, their system metadata, and

extended metadata about the objects. This package is a core component of

the [DataONE federation](https://dataone.org), and supports large-scale object storage for a variety

of repositories, including the [KNB Data Repository](http://knb.ecoinformatics.org),

the [NSF Arctic Data Center](https://arcticdata.io/catalog/),

the [DataONE search service](https://search.dataone.org), and other repositories.



DataONE in general, and HashStore in particular, are open source, community projects.

We [welcome contributions](https://github.com/DataONEorg/hashstore-java/blob/main/CONTRIBUTING.md)

in many forms, including code, graphics, documentation, bug reports, testing, etc. Use

the [DataONE discussions](https://github.com/DataONEorg/dataone/discussions) to discuss these

contributions with us.



## Documentation



Documentation is a work in progress, and can be found on

the [Metacat repository](https://github.com/NCEAS/metacat/blob/feature-1436-storage-and-indexing/docs/user/metacat/source/storage-subsystem.rst#physical-file-layout)

as part of the storage redesign planning. Future updates will include documentation here as the

package matures.



## HashStore Overview



HashStore is an object storage system that provides persistent file-based storage using content

hashes to de-duplicate data. The system stores both objects, references (refs) and metadata in its

respective directories and utilizes an identifier-based API for interacting with the store.

HashStore storage classes (like `FileHashStore`) must implement the HashStore interface to ensure

the expected usage of HashStore.



### Public API Methods



- storeObject

- tagObject

- storeMetadata

- retrieveObject

- retrieveMetadata

- deleteObject

- deleteIfInvalidObject

- deleteMetadata

- getHexDigest



For details, please see the HashStore interface [HashStore.java](https://github.com/DataONEorg/hashstore-java/blob/main/src/main/java/org/dataone/hashstore/HashStore.java)



### How do I create a HashStore?



To create or interact with a HashStore, instantiate a HashStore object with the following set of

properties:



- storePath

- storeDepth

- storeWidth

- storeAlgorithm

- storeMetadataNamespace



```java

String classPackage = "org.dataone.hashstore.filehashstore.FileHashStore";

Path rootDirectory = tempFolder.resolve("metacat");



Properties storeProperties = new Properties();

storeProperties.setProperty("storePath", rootDirectory.toString());

storeProperties.setProperty("storeDepth", "3");

storeProperties.setProperty("storeWidth", "2");

storeProperties.setProperty("storeAlgorithm", "SHA-256");

storeProperties.setProperty(

    "storeMetadataNamespace", "https://ns.dataone.org/service/types/v2.0#SystemMetadata"

);



// Instantiate a HashStore

HashStore hashStore = HashStoreFactory.getHashStore(classPackage, storeProperties);



// Store an object

hashStore.storeObject(stream, pid);

// ...

```



### What does HashStore look like?



```sh

# Example layout in HashStore with a single file stored along with its metadata and reference files.

# This uses a store depth of 3 (number of nested levels/directories - e.g. '/4d/19/81/' within

# 'objects', see below), with a width of 2 (number of characters used in directory name - e.g. "4d",

# "19" etc.) and "SHA-256" as its default store algorithm

## Notes:

## - Objects are stored using their content identifier as the file address

## - The reference file for each pid contains a single cid

## - The reference file for each cid contains multiple pids each on its own line

## - There are two metadata docs under the metadata directory for the pid (sysmeta, annotations)



.../metacat/hashstore

├── hashstore.yaml

└── objects

|   └── 4d

|       └── 19

|           └── 81

|               └── 71eef969d553d4c9537b1811a7b078f9a3804fc978a761bc014c05972c

└── metadata

|   └── 0d

|       └── 55

|           └── 55

|               └── 5ed77052d7e166017f779cbc193357c3a5006ee8b8457230bcf7abcef65e

|                   └── 323e0799524cec4c7e14d31289cefd884b563b5c052f154a066de5ec1e477da7

|                   └── sha256(pid+formatId_annotations)

└── refs

    ├── cids

    |   └── 4d

    |       └── 19

    |           └── 81

    |               └── 71eef969d553d4c9537b1811a7b078f9a3804fc978a761bc014c05972c

    └── pids

        └── 0d

            └── 55

                └── 55

                    └── 5ed77052d7e166017f779cbc193357c3a5006ee8b8457230bcf7abcef65e

```



### Working with objects (store, retrieve, delete)



In HashStore, objects are first saved as temporary files while their content identifiers are

calculated. Once the default hash algorithm list and their hashes are generated, objects are stored

in their permanent location using the store's algorithm's corresponding hash value, the store depth

and the store width. Lastly, objects are 'tagged' with a given identifier (ex. persistent

identifier (pid)). This process produces reference files, which allow objects to be found and

retrieved with a given identifier.

- Note 1: An identifier can only be used once

- Note 2: Each object is stored once and only once using its content identifier (a checksum generated

  from using a hashing algorithm). Clients that attempt to store duplicate objects will receive

  the expected ObjectMetadata - with HashStore handling the de-duplication process under the hood.



By calling the various interface methods for  `storeObject`, the calling app/client can validate,

store and tag an object simultaneously if the relevant data is available. In the absence of an

identifier (ex. persistent identifier (pid)), `storeObject` can be called to solely store an object.

The client is then expected to call `deleteIfInvalidObject` when the relevant metadata is available to

confirm that the object is what is expected. And to finalize the process (to make the object

discoverable), the client calls `tagObject``. In summary, there are two expected paths to store an

object:



```java

// All-in-one process which stores, validates and tags an object

objectMetadata objInfo = storeObject(InputStream, pid, additionalAlgorithm, checksum, checksumAlgorithm, objSize);



// Manual Process

// Store object

objectMetadata objInfo = storeObject(InputStream);

// Validate object, if the parameters do not match, the data object associated with the objInfo

// supplied will be deleted

deleteIfInvalidObject(objInfo, checksum, checksumAlgorithn, objSize);

// Tag object, makes the object discoverable (find, retrieve, delete)

tagObject(pid, cid);

```



**How do I retrieve an object if I have the pid?**



- To retrieve an object, call the Public API method `retrieveObject` which opens a stream to the

  object if it exists.



**How do I delete an object if I have the pid?**



- To delete an object and all its associated reference files, call the Public API

  method `deleteObject()`.

- Note, `deleteObject` and `storeObject` are synchronized processes based on a given `pid`.

  Additionally, `deleteObject` further synchronizes with `tagObject` based on a `cid`. Every

  object is stored once, is unique and shares one cid reference file.



### Working with metadata (store, retrieve, delete)



HashStore's '/metadata' directory holds all metadata for objects stored in HashStore. All metadata

documents related to a 'pid' are stored in a directory determined by calculating the hash of the

pid (based on the store's algorithm). Each specific metadata document is then stored by calculating

the hash of its associated `pid+formatId`. By default, calling `storeMetadata` will use HashStore's

default metadata namespace as the 'formatId' when storing metadata. Should the calling app wish to

store multiple metadata files about an object, the client app is expected to provide a 'formatId'

that represents an object format for the metadata type (ex. `storeMetadata(stream, pid, formatId)`).



**How do I retrieve a metadata file?**



- To find a metadata object, call the Public API method `retrieveMetadata` which returns a stream to

  the metadata file that's been stored with the default metadata namespace if it exists.

- If there are multiple metadata objects, a 'formatId' must be specified when

  calling `retrieveMetadata` (ex. `retrieveMetadata(pid, formatId)`)



**How do I delete a metadata file?**



- Like `retrieveMetadata`, call the Public API method `deleteMetadata(String pid, String formatId)`

  which will delete the metadata object associated with the given pid.

- To delete all metadata objects related to a given 'pid', call `deleteMetadata(String pid)`



### What are HashStore reference files?



HashStore assumes that every object to store has a respective identifier. This identifier is then

used when storing, retrieving and deleting an object. In order to facilitate this process, we create

two types of reference files:



- pid (persistent identifier) reference files

- cid (content identifier) reference files



These reference files are implemented in HashStore underneath the hood with no expectation for

modification from the calling app/client. The one and only exception to this process is when the

calling client/app does not have an identifier, and solely stores an objects raw bytes in

HashStore (calling `storeObject(InputStream)`).



**'pid' Reference Files**



- Pid (persistent identifier) reference files are created when storing an object with an identifier.

- Pid reference files are located in HashStores '/refs/pid' directory

- If an identifier is not available at the time of storing an object, the calling app/client must

  create this association between a pid and the object it represents by calling `tagObject`

  separately.

- Each pid reference file contains a string that represents the content identifier of the object it

  references

- Like how objects are stored once and only once, there is also only one pid reference file for each

  object.



**'cid' Reference Files**



- Cid (content identifier) reference files are created at the same time as pid reference files when

  storing an object with an identifier.

- Cid reference files are located in HashStore's '/refs/cid' directory

- A cid reference file is a list of all the pids that reference a cid, delimited by a new line ("\n")

  character



## Development Build



HashStore is a Java package, and built using the [Maven](https://maven.apache.org/) build tool.



To install `HashStore-java` locally, install Java and Maven on your local machine,

and then install or build the package with `mvn install` or `mvn package`, respectively.



We also maintain a

parallel [Python-based version of HashStore](https://github.com/DataONEorg/hashstore).



## HashStore HashStoreClient Usage



```sh



# Step 1: Get HashStore Jar file

$ mvn clean package -Dmaven.test.skip=true



# Get help

$ java -cp ./target/hashstore-1.1.0-shaded.jar org.dataone.hashstore.HashStoreClient -h



# Step 2: Determine where your hashstore should live (ex. `/var/hashstore`)

## Create a HashStore (long option)

$ java -cp ./target/hashstore-1.1.0-shaded.jar org.dataone.hashstore.HashStoreClient --createhashstore --storepath=/path/to/store --storedepth=3 --storewidth=2 --storealgo=SHA-256 --storenamespace=https://ns.dataone.org/service/types/v2.0#SystemMetadata



## Create a HashStore (short option)

$ java -cp ./target/hashstore-1.1.0-shaded.jar org.dataone.hashstore.HashStoreClient -chs -store /path/to/store -dp 3 -wp 2 -ap SHA-256 -nsp https://ns.dataone.org/service/types/v2.0#SystemMetadata



# Get the checksum of a data object

$ java -cp ./target/hashstore-1.1.0-shaded.jar org.dataone.hashstore.HashStoreClient -store /path/to/store -getchecksum -pid testpid1 -algo SHA-256



# Store a data object

$ java -cp ./target/hashstore-1.1.0-shaded.jar org.dataone.hashstore.HashStoreClient -store /path/to/store -storeobject -path /path/to/data.ext -pid testpid1



# Store a metadata object

$ java -cp ./target/hashstore-1.1.0-shaded.jar org.dataone.hashstore.HashStoreClient -store /path/to/store -storemetadata -path /path/to/metadata.ext -pid testpid1 -format_id https://ns.dataone.org/service/types/v2.0#SystemMetadata



# Retrieve a data object

$ java -cp ./target/hashstore-1.1.0-shaded.jar org.dataone.hashstore.HashStoreClient -store /path/to/store -retrieveobject -pid testpid1



# Retrieve a metadata object

$ java -cp ./target/hashstore-1.1.0-shaded.jar org.dataone.hashstore.HashStoreClient -store /path/to/store -retrievemetadata -pid testpid1 -format_id https://ns.dataone.org/service/types/v2.0#SystemMetadata



# Delete a data object

$ java -cp ./target/hashstore-1.1.0-shaded.jar org.dataone.hashstore.HashStoreClient -store /path/to/store -deleteobject -pid testpid1



# Delete a metadata file

$ java -cp ./target/hashstore-1.1.0-shaded.jar org.dataone.hashstore.HashStoreClient -store /path/to/store -deletemetadata -pid testpid1 -format_id https://ns.dataone.org/service/types/v2.0#SystemMetadata

```



## License



```txt

Copyright [2023] [Regents of the University of California]



Licensed under the Apache License, Version 2.0 (the "License");

you may not use this file except in compliance with the License.

You may obtain a copy of the License at



http://www.apache.org/licenses/LICENSE-2.0



Unless required by applicable law or agreed to in writing, software

distributed under the License is distributed on an "AS IS" BASIS,

WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

See the License for the specific language governing permissions and

limitations under the License.

```



## Acknowledgements



Work on this package was supported by:



- DataONE Network

- Arctic Data Center: NSF-PLR grant #2042102 to M. B. Jones, A. Budden, M. Schildhauer, and J.

  Dozier



Additional support was provided for collaboration by the National Center for Ecological Analysis and

Synthesis, a Center funded by the University of California, Santa Barbara, and the State of

California.



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