dserver-direct-mongo-plugin 0.4.0

This plugin allows to submit mongo queries and aggregation pipelines directly an underlying MongoDB.

• GitHub: https://github.com/livMatS/dserver-direct-mongo-plugin

• PyPI: https://pypi.org/project/dserver-direct-mongo-plugin/

• Free software: MIT License

Features

• Query datasets via mongo language

• Funnel datasets through aggregation pipelines

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.

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

This plugin allows to submit plain mongo queries and aggregation pipelines directly to the lookup server.

Configuration

Inform this plugin about the Mongo database to use by setting the environment variables

export DSERVER_MONGO_URI="mongodb://localhost:27017/"
export DSERVER_MONGO_DB="dserver"
export DSERVER_MONGO_COLLECTION="metadata"

If the Mongo search and retrieve plugins are used, then you may use the same database, but must use a different collection.

Use

export DSERVER_ALLOW_DIRECT_QUERY=true
export DSERVER_ALLOW_DIRECT_AGGREGATION=false

to enable or disable direct mongo query and aggregation on this plugin.

ATTENTION: While direct queries respect user-wise access rights to database entries on the lookup server level, there is no guarantee for aggregation pipelines to do so per design. Don not enable direct aggregation in a production environment.

Authentication

The dtool lookup server 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 following curl command samples

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

Refer to the core dcumentation of dservercore for more information.

Direct query

To look for a sepcific field key2: 42 in a dataset’s README.yml (provided the file is properly YAML-formatted), use

$ curl -H "$HEADER" -H "Content-Type: application/json" -X POST \
    -d '{"query": {"readme.key2": 42}}' http://localhost:5000/mongo/query

Response content:

[
  {
    "base_uri": "s3://test-bucket",
    "created_at": 1683797360.056,
    "creator_username": "jotelha",
    "dtoolcore_version": "3.18.2",
    "frozen_at": 1683797362.855,
    "name": "test_dataset_2",
    "number_of_items": 1,
    "size_in_bytes": 19347,
    "tags": [],
    "type": "dataset",
    "uri": "s3://test-bucket/26785c2a-e8f8-46bf-82a1-cec92dbdf28f",
    "uuid": "26785c2a-e8f8-46bf-82a1-cec92dbdf28f"
  }
]

Next to the content of the README.yml, other fields of the database-internal dataset representation returned in the example above are directly queryable as well. All queries are formulated in the MongoDB language. The MongoDB documenatation offers information on how to formulate queries. The list of available query operators is particularly useful. The following illustrates a few other possible JSON-like query documents.

'{"base_uri":{"$regex":"^s3"}}' will find all datasets whose base URI matches the provided regular expression, here any s3-prefixed string.

{"readme.owners.name": {"$regex": "Testing User"}} will match any dataset with a README field that contains the sub string Testing User, such as

owners:
- name: A user who does not match the search pattern
  username: test_user
- name: Another Testing User matches the search pattern
  username: another_test_user

The query

{
  "creator_username": "jotelha",
  "readme.parameters.temperature": 298
}

will match all datasets created by user jotelha and annotated with:

parameters:
  temperature: 298

in its README.yml.

Direct aggregation

The following example of an aggregation pipeline identifies and counts instances of the same dataset at different base URIs:

$ curl -H "$HEADER" -H "Content-Type: application/json" -X POST \
    -d '{"aggregation": [
            {
                "$sort": {"base_uri": 1}
            }, {
                "$group":  {
                    "_id": "$name",
                    "count": {"$sum": 1},
                    "available_at": {"$push": "$base_uri"}
                }
            }, {
                "$project": {
                    "name": "$_id",
                    "count": true,
                    "available_at": true,
                    "_id": false
                }
            }, {
                "$sort": {"name": 1}
            }
        ]
    }' http://localhost:5000/mongo/aggregate

Response content:

[
  {
    "available_at": [
      "s3://test-bucket"
    ],
    "count": 1,
    "name": "test_dataset_1"
  },
  {
    "available_at": [
      "s3://test-bucket",
      "smb://test-share"
    ],
    "count": 2,
    "name": "test_dataset_2"
  }
]

Testing

Running unit tests with pytest requires a healthy lookup server installation and the availability of required services such as databases. Please refer to the core dservercore for setup instructions.