dtool-lookup-api 0.10.1

This package offers both synchronous and asynchronous implementations of a standardized Python API to communicate with dserver.

Python API for interacting with dserver.

This package offers a class-based asynchronous lookup API within dtool_lookup_api.core.LookupClient, a simple class-less wrapper around it at dtool_lookup_api.asynchronous, and a synchronous interface on top at dtool_lookup_api.synchronous.

Direct imports of utility functions from dtool_lookup_api in the examples below forward to the synchronous API variant.

Installation

To install the dtool_lookup_api package.

pip install dtool_lookup_api

This package depends on a dserver instance to talk to.

Configuration

The API needs to know the URL of the lookup server

export DSERVER_URL=https://localhost:5000

You may also need specify an access token generated on the server

export DSERVER_TOKEN=$(flask user token testuser)

Instead of specifying the access token directly, it is also possible to provide

export DSERVER_TOKEN_GENERATOR_URL=https://localhost:5001
export DSERVER_USERNAME=my-username
export DSERVER_PASSWORD=my-password

for the API to request a token. This, however, is intended only for testing purposes and strongly discouraged in a production environment, as your password would reside within environment variables or the dtool config file as clear text.

Our recommended setup is a combination of

export DSERVER_URL=https://localhost:5000
export DSERVER_TOKEN_GENERATOR_URL=https://localhost:5001

in the config. If used interactively, the API will then ask for your credentials at the first interaction and cache the provided values for this session, i.e.

In [1]: from dtool_lookup_api import query
   ...: res = query(
   ...:     {
   ...:         'readme.owners.name': {'$regex': '^Testing User$'},
   ...:     }
   ...: )
Authentication URL https://localhost:5001/token username:my-username
Authentication URL https://localhost:5001/token password:

In [2]: res
Out[2]:
[{'base_uri': 'smb://test-share',
  'created_at': 'Sun, 08 Nov 2020 18:38:40 GMT',
  'creator_username': 'jotelha',
  'dtoolcore_version': '3.17.0',
  'frozen_at': 'Wed, 11 Nov 2020 17:20:30 GMT',
  'name': 'simple_test_dataset',
  'tags': [],
  'type': 'dataset',
  'uri': 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675',
  'uuid': '1a1f9fad-8589-413e-9602-5bbd66bfe675'}]

In [3]: from dtool_lookup_api import all
   ...: all()
Out[4]:
[{'base_uri': 'smb://test-share',
  'created_at': 1604860720.736269,
  'creator_username': 'jotelha',
  'frozen_at': 1604921621.719575,
  'name': 'simple_test_dataset',
  'uri': 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675',
  'uuid': '1a1f9fad-8589-413e-9602-5bbd66bfe675'}]

Credentials caching and interactive prompting are turned off with

In [1]: import dtool_lookup_api.core.config
   ...: dtool_lookup_api.core.config.Config.interactive = False
   ...: dtool_lookup_api.core.config.Config.cache = False

In [2]: from dtool_lookup_api import all
   ...: all()
...
RuntimeError: Authentication failed

For testing purposes, it is possible to disable SSL certificates validation with

export DSERVER_VERIFY_SSL=false

As usual, these settings may be specified within the default dtool configuration file as well, i.e. at ~/.config/dtool/dtool.json

{
    "DSERVER_TOKEN_GENERATOR_URL": "https://localhost:5001/token",
    "DSERVER_URL": "https://localhost:5000"
}

List all datasets

To list all registered datasets

In [1]: from dtool_lookup_api import get_datasets
   ...: res = get_datasets()

In [2]: res
Out[2]:
[{'base_uri': 'smb://test-share',
'created_at': 1604860720.736269,
'creator_username': 'jotelha',
'frozen_at': 1604921621.719575,
'name': 'simple_test_dataset',
'uri': 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675',
'uuid': '1a1f9fad-8589-413e-9602-5bbd66bfe675'}]

Looking up datasets by UUID

To lookup URIs from a dataset UUID within Python

In [1]: from dtool_lookup_api import get_datasets_by_uuid
   ...: uuid = "1a1f9fad-8589-413e-9602-5bbd66bfe675"
   ...: res = get_datasets_by_uuid(uuid)

In [2]: res
Out[2]:
[{'base_uri': 'smb://test-share',
  'created_at': 1604860720.736269,
  'creator_username': 'jotelha',
  'frozen_at': 1604921621.719575,
  'name': 'simple_test_dataset',
  'uri': 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675',
  'uuid': '1a1f9fad-8589-413e-9602-5bbd66bfe675'}]

Full text searching

Full text search for the word “test”

In [1]: from dtool_lookup_api import get_datasets
    ...: res = get_datasets(free_text="test")

In [2]: res
Out[2]:
[{'base_uri': 'smb://test-share',
  'created_at': 1604860720.736,
  'creator_username': 'jotelha',
  'dtoolcore_version': '3.17.0',
  'frozen_at': 1605027357.308,
  'name': 'simple_test_dataset',
  'tags': [],
  'type': 'dataset',
  'uri': 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675',
  'uuid': '1a1f9fad-8589-413e-9602-5bbd66bfe675'}]

Manifest

Request the manifest of a particular dataset by URI

In [1]: from dtool_lookup_api import get_manifest
   ...: uri = 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675'
   ...: res = get_manifest(uri)

In [2]: res
Out[2]:
{'dtoolcore_version': '3.17.0',
 'hash_function': 'md5sum_hexdigest',
 'items': {'eb58eb70ebcddf630feeea28834f5256c207edfd': {'hash': '2f7d9c3e0cfd47e8fcab0c12447b2bf0',
   'relpath': 'simple_text_file.txt',
   'size_in_bytes': 17,
   'utc_timestamp': 1605027357.284966}}}

Readme

Request the readme content of a particular dataset by URI

In [1]: from dtool_lookup_api import get_readme
    ..: res = get_readme('smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675')

In [2]: import yaml
    ..: yaml.safe_load(res)
Out[2]:
{'creation_date': '2020-11-08',
'description': 'testing description',
'expiration_date': '2022-11-08',
'funders': [{'code': 'testing_code',
 'organization': 'testing_organization',
 'program': 'testing_program'}],
'owners': [{'email': '[e-mail]',
 'name': 'Testing User',
 'orcid': 'testing_orcid',
 'username': 'testing_user'}],
'project': 'testing project'}

Direct mongo language queries

To list all datasets at a certain base URI with their name matching some regular expression pattern, send a direct mongo language query to the server with

In [15]: from dtool_lookup_api import query
    ...: res = query(
    ...:     {
    ...:         'base_uri': 'smb://test-share',
    ...:         'name': {'$regex': 'test'},
    ...:     }
    ...: )

In [16]: res
Out[16]:
[{'base_uri': 'smb://test-share',
'created_at': 'Sun, 08 Nov 2020 18:38:40 GMT',
'creator_username': 'jotelha',
'dtoolcore_version': '3.17.0',
'frozen_at': 'Tue, 10 Nov 2020 16:55:57 GMT',
'name': 'simple_test_dataset',
'tags': [],
'type': 'dataset',
'uri': 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675',
'uuid': '1a1f9fad-8589-413e-9602-5bbd66bfe675'}]

It is possible to search readme content via

In [21]: from dtool_lookup_api import query
    ...: res = query(
    ...:     {
    ...:         'readme.owners.name': {'$regex': '^Testing User$'},
    ...:     }
    ...: )

In [22]: res
Out[22]:
[{'base_uri': 'smb://test-share',
  'created_at': 'Sun, 08 Nov 2020 18:38:40 GMT',
  'creator_username': 'jotelha',
  'dtoolcore_version': '3.17.0',
  'frozen_at': 'Tue, 10 Nov 2020 16:55:57 GMT',
  'name': 'simple_test_dataset',
  'tags': [],
  'type': 'dataset',
  'uri': 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675',
  'uuid': '1a1f9fad-8589-413e-9602-5bbd66bfe675'}]

This requires the server-side dserver-direct-mongo-plugin.

TODO: Response from server-side direct mongo plugin still yields dates as strings. Fix within https://github.com/IMTEK-Simulation/dserver-direct-mongo-plugin.

Usage on Jupyter notebook

The current implementation via asgiref.async_to_sync (https://github.com/django/asgiref) hinders the use of the synchronous interface within Jupyter notebooks. Directly use the asynchronous api instead

import dtool_lookup_api.asynchronous as dl
res = await dl.query({
    'base_uri': 'smb://test-share',
    'name': {'$regex': 'test'},
})

The drawback of the above approach is that the same code doesn’t work in python and in jupyter (await outsite of a function is a syntax error in non-interactive python context). The code below can be executed in both contexts:

import dtool_lookup_api.asynchronous as dl
if asyncio.get_event_loop().is_running():
    # then we are in jupyter notebook
    # this allows nested event loops, i.e. calls to asyncio.run inside the notebook as well
    # This way, the same code works in notebook and python
    import nest_asyncio
    nest_asyncio.apply()

def query(query_dict):
    return asyncio.run(dl.query(query_dict))

query({
    'base_uri': 'smb://test-share',
    'name': {'$regex': 'test'},
})

See https://github.com/jupyter/notebook/issues/3397#issuecomment-419386811, https://ipython.readthedocs.io/en/stable/interactive/autoawait.html

Testing

Install editable with testing requirements with

pip install -e .[test]

By default, tests rely on the demo.dtool.dev demonstrator instance.

This can be changed by configuring

DSERVER_ADDRESS_AND_CREDENTIALS = {
    "DSERVER_URL": "https://demo.dtool.dev/lookup",
    "DSERVER_TOKEN_GENERATOR_URL": "https://demo.dtool.dev/token",
    "DSERVER_USERNAME": "testuser",
    "DSERVER_PASSWORD": "test_password",
    "DSERVER_VERIFY_SSL": False,
}

within tests/conftest.py.