dservercore 0.20.2

Web API to register/lookup/search for dtool dataset metadata

• GitHub: https://github.com/jic-dtool/dservercore

• PyPI: https://pypi.python.org/pypi/dservercore

• Free software: MIT License

Features

• Use a dataset UUID to lookup one more URIs where the dataset is stored

• Search for datasets of interest using free text search

• Built in support to manage users

• Built in support to manage base URIs

• Build in support to manage a user permissions on base URIs

• Built in support for authentication using JSON web tokens

Introduction

dtool is a command line tool for packaging data and metadata into a dataset. A dtool dataset manages data and metadata without the need for a central database.

However, if one has to manage more than a hundred datasets it can be helpful to have the datasets’ metadata stored in a central server to enable one to quickly find datasets of interest.

dserver provides a web API for registering datasets’ metadata and provides functionality to lookup, list and search for datasets.

When managing many groups data it can be useful to ensure that users can only access metadata associated with datasets stored in base URI’s that they have been given access to. dserver therefore provides means to manage users, base URIs and users’ permissions on those base URIs.

dserver is consumed by the dtool-lookup-client, and the dtool-lookup-webapp. Third party applications making use of the dserver have also been created, notably the livMatS/dtool-lookup-gui.

dservercore provides the core Flask app central to dserver’s modular, pluggable framework.

Installation

Install dservercore:

$ pip install dservercore

For a minimal setup, dserver requires search and retrieve plugins. Pick search and retrieve plugins of your choice and install those. Here, the dserver-search-plugin-mongo and dserver-retrieve-plugin-mongo serve as default for demonstration:

$ pip install dserver-search-plugin-mongo
$ pip install dserver-retrieve-plugin-mongo

Setup and configuration

Configure the Flask app

dserver is a Flask app. Flask needs to know where to look for the app. One therefore needs to define the FLASK_APP environment variable:

$ export FLASK_APP=dservercore

Configure search and retrieve plugins

dserver is agnostic of how descriptive data is stored and searched. The implementation is delegated to search and retrieve plugins. Refer to their documentation for details on their configuration.

In the sample case of dserver-search-plugin-mongo and dserver-retrieve-plugin-mongo, the same Mongo database can be used for both search and information retrieval.

Create a directory where the MongoDB data will be stored:

$ mkdir data

Start Mongo DB, for example using docker:

$ docker run -d -p 27017:27017 -v `pwd`/data:/data/db mongo

Configure the search plugin with:

export SEARCH_MONGO_URI="mongodb://localhost:27017/"
export SEARCH_MONGO_DB="dserver"
export SEARCH_MONGO_COLLECTION="datasets"

and the retrieve plugin with:

export RETRIEVE_MONGO_URI="mongodb://localhost:27017/"
export RETRIEVE_MONGO_DB="dserver"
export RETRIEVE_MONGO_COLLECTION="datasets"

This must happen before issuing any flask commands as below.

Configure the SQL database

dserver stores administrative metadata in a SQL database. By default it uses a SQLite database. However, this can be configured by setting the SQLALCHEMY_DATABASE_URI, i.e using something along the lines of:

export SQLALCHEMY_DATABASE_URI=mysql://username:password@server/db

Importantly, you will need an according Python connector for whatever SQL database you decide to use, e.g. psycopg2 for PostgreSQL or mysqlclient for MySQL.

For more information see flask-SQLAlchemy.

Versioning of the relational database is handled using flask-Migrate

Populate the SQL database with tables using the commands below:

$ flask db init
$ flask db migrate
$ flask db upgrade

Configure a public and private key pair

dserver implements authentication using JSON Web Tokens. Private and public key can for example be generated with:

openssl genrsa -out /path/to/private/jwt_key 2048
openssl rsa -in /path/to/private/jwt_key -pubout -outform PEM -out /path/to/public/jwt_key.pub

It is possible to delegate the generation of JSON Web Tokens to a different service as long as one has access to the public key:

export JWT_PUBLIC_KEY_FILE=~/.ssh/id_rsa.pub

If one has access to the private key as well one can use the flask user token command line utility to generate a token for the user. To enable this one has to set the JWT_PRIVATE_KEY_FILE environment variable:

export JWT_PRIVATE_KEY_FILE=~/.ssh/id_rsa

Mac users be warned that the Mac’s implementation ssh-keygen may result in files that do not adhere to the RFC standard. As such you may get a warning along the lines of:

ValueError: Could not deserialize key data.

In this case you need to find a version of ssh-keygen that generates files that adhere to the RFC standard, the easiest is probably to generate them in Linux.

Making use of JSON Web Tokens from a different server

When making use of JSON Web Tokens from a different server it may be easier to use configure the server using the pubic key directly rather than the public key file:

export JWT_PUBLIC_KEY="ssh-rsa XXXXXX user@localhost"

Inspecting the flask app configuration

Inspect the Flask app configuration with:

$ flask config show
{
  "DEBUG": false,
  "TESTING": false,
  "PROPAGATE_EXCEPTIONS": null,
  "SECRET_KEY": "***",
  ...
}

The output is JSON-formatted with lower-case keys and will include plugin configuration parameters as well.

Inspect the installed dserver components with:

$ flask config versions
{
  "dservercore": "0.17.2",
  "dserver_retrieve_plugin_mongo": "0.1.0",
  "dserver_search_plugin_mongo": "0.1.0"
}

Starting the flask app

The Flask web app can be started using the command below:

$ flask run

Populating dserver using the CLI

Indexing a base URI

Datasets can be stored on filesystem and in object storage such as AWS S3. In an AWS S3 bucket datasets are stored in a flat structure and the bucket itself is the base URI. To index all the datasets in the S3 bucket, the base URI, one first needs to register it in dserver:

flask base_uri add s3://dtool-demo

One can then index it using the command:

$ flask base_uri index s3://dtool-demo
Registered: s3://dtool-demo/8ecd8e05-558a-48e2-b563-0c9ea273e71e
Registered: s3://dtool-demo/907e1b52-d649-476a-b0bc-643ef769a7d9
Registered: s3://dtool-demo/af6727bf-29c7-43dd-b42f-a5d7ede28337
Registered: s3://dtool-demo/ba92a5fa-d3b4-4f10-bcb9-947f62e652db
Registered: s3://dtool-demo/c58038a4-3a54-425e-9087-144d0733387f
Registered: s3://dtool-demo/faa44606-cb86-4877-b9ea-643a3777e021

It is possible to list all the base URIs registered in dserver:

$ flask base_uri list
[
  {
    "base_uri": "s3://dtool-demo",
    "users_with_search_permissions": [],
    "users_with_register_permissions": []
  }
]

In the output above it is worth noting that there are two types of permissions associated with a base URI. “Search” permissions allow a user to search for datasets in a base URI. “Register” permissions allow a user to register a dataset in dserver if it is stored in the specific base URI.

Adding a user and managing permissions

The command below adds the user olssont to dserver:

$ flask user add olssont

The command below gives the user olssont search permissions on the s3://dtool-demo base URI:

$ flask user search_permission olssont s3://dtool-demo

The command below gives the user olssont register permissions on the s3://dtool-demo base URI:

$ flask user register_permission olssont s3://dtool-demo

Creating an admin user

The command below adds the user overlord, with admin privileges, to the dtool lookup server:

$ flask user add --is_admin overlord

Generating a JSON Web Token for a registered user

The command below can be used to generate a token for a user to authenticate with when using the web API:

$ flask user token olssont
eyJhbGciOiJSUzI1NiIsInR5... (truncated)

Listing the registered users

The command below lists the users registered in dserver:

$ flask user list
[
  {
    "username": "olssont",
    "is_admin": false,
    "register_permissions_on_base_uris": [
      "s3://dtool-demo"
    ],
    "search_permissions_on_base_uris": [
      "s3://dtool-demo"
    ]
  },
  {
    "username": "overlord",
    "is_admin": true,
    "register_permissions_on_base_uris": [],
    "search_permissions_on_base_uris": []
  }
]

Deleting a user

The command below can be used to delete a user:

$ flask user delete overlord

Adding and removing admin privileges from an existing user

The command below can be used to give an existing user admin privileges:

$ flask user update --is_admin olssont

The command below can be used to remove admin privileges from an existing user:

$ flask user update olssont

dserver API

dserver makes use of the authorized header to pass through the JSON web token for authorization. Below we create environment variables for the token and the header used in the curl commands:

$ TOKEN=$(flask user token olssont)
$ HEADER="Authorization: Bearer $TOKEN"

Standard user usage

Looking up URIs based on a dataset’s UUID

A dataset can be uniquely identified by it’s UUID (Universally Unique Identifier). Below we create an environment variable with the UUID of a dataset in the s3://dtool-demo bucket:

$ UUID=8ecd8e05-558a-48e2-b563-0c9ea273e71e

It is possible to list all the location a dataset is located in using the command below:

$ curl -H $HEADER http://localhost:5000/uuids/$UUID

Response content:

[
  {
    "base_uri": "s3://dtool-demo",
    "name": "Escherichia-coli-ref-genome",
    "uri": "s3://dtool-demo/8ecd8e05-558a-48e2-b563-0c9ea273e71e",
    "uuid": "8ecd8e05-558a-48e2-b563-0c9ea273e71e"
  }
]

Note that it is possible for a dataset to be registered in more than one base URI. As such looking up a dataset by UUID can result in multiple hits.

Summary information about datasets

An overall summary of datasets accessible to a user can be accessed using the request below:

$ curl -H "$HEADER" http://localhost:5000/users/olssont/summary

The response will contain JSON content along the lines of:

{
    "number_of_datasets": 3,
    "creator_usernames": ["queen"],
    "base_uris": ["s3://mr-men", "s3://snow-white"],
    "datasets_per_creator": {"queen": 3},
    "datasets_per_base_uri": {"s3://mr-men": 1, "s3://snow-white": 2},
    "tags": ["fruit", "veg"],
    "datasets_per_tag": {"fruit": 2, "veg": 1}
}

Listing all datasets

All the dataset’s that a user has permissions to search for can be listed using the request below:

$ curl -H "$HEADER" http://localhost:5000/uris

Some of the output of the command above is displayed below:

[
  {
    "base_uri": "s3://dtool-demo",
    "created_at": 1604860720.736269,
    "creator_username": "olssont",
    "frozen_at": 1604864525.691079,
    "name": "Escherichia-coli-ref-genome",
    "uri": "s3://dtool-demo/8ecd8e05-558a-48e2-b563-0c9ea273e71e",
    "uuid": "8ecd8e05-558a-48e2-b563-0c9ea273e71e"
  },
  ... (truncated)
  {
    "base_uri": "s3://dtool-demo",
    "created_at": 1604860720.736269,
    "creator_username": "olssont",
    "frozen_at": 1604864525.691079,
    "name": "Escherichia-coli-reads-ERR022075",
    "uri": "s3://dtool-demo/faa44606-cb86-4877-b9ea-643a3777e021",
    "uuid": "faa44606-cb86-4877-b9ea-643a3777e021"
  }
]

Searching for specific datasets

The command below does a full text search for the word “microscopy” in the descriptive metadata:

$ curl -H "$HEADER" -H "Content-Type: application/json"  \
    -X POST -d '{"free_text": "microscopy"}'  \
    http://localhost:5000/uris

Below is the result of this search:

[
  {
    "base_uri": "s3://dtool-demo",
    "created_at": "1530803916.74",
    "creator_username": "olssont",
    "frozen_at": "1536749825.85",
    "name": "hypocotyl3",
    "uri": "s3://dtool-demo/ba92a5fa-d3b4-4f10-bcb9-947f62e652db",
    "uuid": "ba92a5fa-d3b4-4f10-bcb9-947f62e652db"
  }
]

Below is a JSON string specifying a more complex query that will search for datasets with “apples” in the “s3://snow-white” bucket created by either “grumpy” or “dopey”, and has both of the tags “fruit” and “veg”:

{
    "base_uris": ["s3://snow-white"],
    "creator_usernames": ["grumpy", "dopey"],
    "free_text": "apples",
    "tags": ["fruit", "veg"]
}

Note

The search engine make use of “OR” logic for the items in base_uris and creator_usernames lists, but uses “AND” logic for filtering the search based on the items in the tags list.

Accessing a dataset’s readme, annotations and manifest

The command below retrieves the readme for the dataset with the URI s3://dtool-demo/ba92a5fa-d3b4-4f10-bcb9-947f62e652db:

$ curl -H "$HEADER" -H "Content-Type: application/json"  \
    http://localhost:5000/readmes/s3/dtool-demo/ba92a5fa-d3b4-4f10-bcb9-947f62e652db

The command below retrieves the annotations for the dataset with the URI s3://dtool-demo/ba92a5fa-d3b4-4f10-bcb9-947f62e652db:

$ curl -H "$HEADER" -H "Content-Type: application/json"  \
    http://localhost:5000/annotations/s3/dtool-demo/ba92a5fa-d3b4-4f10-bcb9-947f62e652db

The command below retrieves the tags for the dataset with the URI s3://dtool-demo/ba92a5fa-d3b4-4f10-bcb9-947f62e652db:

$ curl -H "$HEADER" -H "Content-Type: application/json"  \
    http://localhost:5000/tags/s3/dtool-demo/ba92a5fa-d3b4-4f10-bcb9-947f62e652db

The command below retrieves the manifest for the dataset with the URI s3://dtool-demo/ba92a5fa-d3b4-4f10-bcb9-947f62e652db:

$ curl -H "$HEADER" -H "Content-Type: application/json"  \
    http://localhost:5000/manifests/s3/dtool-demo/ba92a5fa-d3b4-4f10-bcb9-947f62e652db

Getting information about one’s own permissions

A user can find out about his/her own permissions using the command below:

$ curl -H "$HEADER" http://localhost:5000/users/olssont

Response content:

{
  "is_admin": false,
  "register_permissions_on_base_uris": [
    "s3://dtool-demo"
  ],
  "search_permissions_on_base_uris": [
    "s3://dtool-demo"
  ],
  "username": "olssont"
}

Data champion user usage

A data champion is different from a regular user in that he/she has “register” permissions on a base URI. This means that a data champion can register metadata about a data to dserver.

Registering a dataset

Below is an example of how to register a dataset:

$ DATASET_INFO='
{
  "uuid": "3fa85f64-5717-4562-b3fc-2c963f66afa6",
  "base_uri": "s3://dtool-demo",
  "uri": "s3://dtool-demo/8ecd8e05-558a-48e2-b563-0c9ea273e71e",
  "name": "Escherichia-coli-ref-genome",
  "type": "dataset",
  "readme": "{\"accession_id\":\"U00096.3\",\"description\":\"U00096.3genomewithBowtie2indices\",\"index_build_cmd\":\"bowtie2-buildU00096.3.fastareference\",\"index_builder\":\"bowtie2-buildversion2.3.3\",\"link\":\"https://www.ebi.ac.uk/ena/data/view/U00096.3\",\"organism\":\"Escherichiacolistr.K-12substr.MG1655\"},",
  "manifest": {
    "dtoolcore_version": "3.18.2",
    "hash_function": "md5sum_hexdigest",
    "items": {
      "26f0d76fb3c3e34f0c7c8b7c3461b7495761835c": {
        "hash": "06d80eb0c50b49a509b49f2424e8c805",
        "relpath": "dog.txt",
        "size_in_bytes": 3,
        "utc_timestamp": 1716979579.898408
      },
      "d25102a700e072b528db79a0f22b3a5ffe5e8f5d": {
        "hash": "68238cd792d215bdfdddc7bbb6d10db4",
        "relpath": "parrot.txt",
        "size_in_bytes": 6,
        "utc_timestamp": 1716979579.902415
      }
    }
  },
  "creator_username": "olssont",
  "frozen_at": "1537916653.7",
  "created_at": "1537802877.62",
  "annotations": {},
  "tags": [],
  "number_of_items": 2,
  "size_in_bytes": 9
}'
$ curl -H "$HEADER" -H "Content-Type: application/json"  \
    -X PUT -d "$DATASET_INFO"  \
    http://localhost:5000/uris/s3/dtool-demo/ba92a5fa-d3b4-4f10-bcb9-947f62e652db

The required keys are defined in the variable dservercore.utils.DATASET_INFO_REQUIRED_KEYS.

Admin user usage

The administrative user can register new users, base URIs and manage who has permissions to search for and register datasets. Below we update the header to use the token from the overlord admin user:

$ TOKEN=$(flask user token overlord)
$ HEADER="Authorization: Bearer $TOKEN"

Listing registered users

To list all the registered users an admin user can use the below:

$ curl -H "$HEADER" http://localhost:5000/users

Response content:

[
  {
    "is_admin": false,
    "username": "olssont"
  },
  {
    "is_admin": true,
    "username": "overlord"
  }
]

Registering users

An admin user can register other users:

$ curl -H "$HEADER" -H "Content-Type: application/json"  \
    -X PUT -d '{"username": "joe", "is_admin": true}'  \
    http://localhost:5000/users/joe

Registering a base URI

An admin user can register a new base URI s3://another-bucket:

$ curl -H "$HEADER" -H "Content-Type: application/json"  \
    -X PUT -d '{
      "base_uri": "s3://another-bucket",
      "users_with_search_permissions": ["joe"],
      "users_with_register_permissions": ["olssont"]
    }' http://localhost:5000/base-uris/s3/another-bucket

Listing registered base URIs

An admin user can list all registered base URIs:

$ curl -H "$HEADER" http://localhost:5000/base-uris

Response content:

[
  {
    "base_uri": "s3://dtool-demo",
  },
  {
    "base_uri": "s3://another-bucket",
  }
]

Updating the permissions on a base URI

An admin user can update the permissions on a base URI simply by another PUT request:

$ curl -H "$HEADER" -H "Content-Type: application/json"  \
    -X PUT -d '{
      "base_uri": "s3://another-bucket",
      "users_with_search_permissions": ["joe", "olssont"],
      "users_with_register_permissions": ["olssont"]
    }' http://localhost:5000/base-uris/s3/another-bucket

Note that the request below can be used to clear all existing permissions:

$ curl -H "$HEADER" -H "Content-Type: application/json"  \
    -X PUT -d '{
      "base_uri": "s3://another-bucket",
      "users_with_register_permissions": [],
      "users_with_search_permissions": []}'  \
    http://localhost:5000/base-uris/s3/another-bucket

Getting information about the permissions on a base URI

An admin user can get information about the permissions on a base URI:

$ curl -H "$HEADER" -H "Content-Type: application/json"  \
    http://localhost:5000/base-uris/s3/another-bucket

Response content:

{
  "base_uri": "s3://another-bucket",
  "users_with_register_permissions": [],
  "users_with_search_permissions": []
}

Querying server configuration

The request:

$ curl -H "$HEADER" http://localhost:5000/config/info

will return the current server configuration with all keys in lowercase, i.e.:

{
  "config": {
    "allow_access_from": "0.0.0.0/0",
    "allow_direct_aggregation": true,
    "allow_direct_query": true,
    ...
  }
}

The request:

$ curl http://localhost:5000/config/versions

will return all components, i.e. server core, search, retrieve and extension plugins with their versions, i.e.:

{
  "versions": {
    "dservercore": "0.17.2",
    "dserver_retrieve_plugin_mongo": "0.1.0",
    "dserver_search_plugin_mongo": "0.1.0"
  }
}

This request does not require any authorization.

Creating a plugin

It is possible to create add plugins to this system. This is achieved by creating a separate Python package containing a Flask blueprint.

A basic plugin could consist of a single __init__ and a setup.py or pyproject.toml file in the directory structure below:

.
|-- my_plugin
|   `-- __init__.py
`-- setup.py

The __init__.py file could contain the code below. Importantly, the plugin has to implement a derivative of dtoolcore.ExtensionABC.

from flask_smorest import Blueprint
from dtoolcore import ExtensionABC

my_plugin_bp = Blueprint('my_plugin', __name__, url_prefix="/my_plugin")

@my_plugin_bp.route('/', methods=["GET"])
@my_plugin_bp.response(200)
def show(page):
    return "My plugin content"

class NotificationExtension(ExtensionABC):

    def register_dataset(self, dataset_info):
        """Register or update a dataset entry by replacing a possibly existing entry."""
        pass

    def get_blueprint(self):
        """Return the Flask blueprint to be used for the extension."""
        return my_plugin_bp

Classes adhering to the interface of the dservercore.ExtensionABC abstract base class need to be associated with the dservercore.extension entrypoint in the Python package setup.py file or pyproject.toml. The setup.py file would need to look something along the lines of the below.

from setuptools import setup

setup(
    name="my-plugin",
    packages=["my_plugin"],
    install_requires=[
        "dservercore",
    ],
    entry_points={
        "dservercore.extension": [
            "my_plugin=my_plugin:my_plugin_bp",
        ],
    }
)

A respective entry in a pyproject.toml would look as follows.

[project.entry-points."dservercore.extension"]
"MyExtension" = "dserver_extension_module:MyExtension"

Examples of actual plugins include:

• dserver-direct-mongo-plugin

• dserver-dependency-graph-plugin

• dserver-notification-plugin