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dtool-lookup-api-0.6.0
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مشاهده بیشترتوضیحات
This package offers both synchronous and asynchronous implementations of a standardized Python API to communicate with the dtool lookup server.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | dtool-lookup-api-0.6.0 |
| نام | dtool-lookup-api |
| نسخه کتابخانه | 0.6.0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Johannes Laurin Hoermann |
| ایمیل نویسنده | johannes.hoermann@imtek.uni-freiburg.de |
| آدرس صفحه اصلی | https://github.com/IMTEK-Simulation/dtool-lookup-api |
| آدرس اینترنتی | https://pypi.org/project/dtool-lookup-api/ |
| مجوز | MIT |
README
======
|PyPI| |github tag| |github tests|
Python API for interacting with dtool lookup server.
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.
.. code-block:: bash
pip install dtool_lookup_api
This package depends on a `dtool-lookup-server
<https://github.com/jic-dtool/dtool-lookup-server>`_ instance to talk to.
Configuration
-------------
The API needs to know the URL of the lookup server
.. code-block:: bash
export DTOOL_LOOKUP_SERVER_URL=https://localhost:5000
You may also need specify an access token generated on the server
.. code-block:: bash
export DTOOL_LOOKUP_SERVER_TOKEN=$(flask user token testuser)
Instead of specifying the access token directly, it is also possible to provide
.. code-block:: bash
export DTOOL_LOOKUP_SERVER_TOKEN_GENERATOR_URL=https://localhost:5001
export DTOOL_LOOKUP_SERVER_USERNAME=my-username
export DTOOL_LOOKUP_SERVER_PASSWORD=my-password
for the API to request a token. This, however, is intended only for testing
purposes and strongly discouraged in a production environment, as your password
would reside within environment variables or the dtool config file as clear text.
Our recommended setup is a combination of
.. code-block:: bash
export DTOOL_LOOKUP_SERVER_URL=https://localhost:5000
export DTOOL_LOOKUP_SERVER_TOKEN_GENERATOR_URL=https://localhost:5001
in the config. If used interactively, the API will then ask for your
credentials at the first interaction and cache the provided values for this
session, i.e.
.. code-block::
In [1]: from dtool_lookup_api import query
...: res = query(
...: {
...: 'readme.owners.name': {'$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
.. code-block::
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
.. code-block:: bash
export DTOOL_LOOKUP_SERVER_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``
.. code-block:: bash
{
"DTOOL_LOOKUP_SERVER_TOKEN_GENERATOR_URL": "https://localhost:5001/token",
"DTOOL_LOOKUP_SERVER_URL": "https://localhost:5000"
}
List all datasets
-----------------
To list all registered datasets
.. code-block::
In [1]: from dtool_lookup_api import all
...: res = all()
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
.. code-block::
In [1]: from dtool_lookup_api import lookup
...: uuid = "1a1f9fad-8589-413e-9602-5bbd66bfe675"
...: res = lookup(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"
.. code-block::
In [1]: from dtool_lookup_api import search
...: res = search("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
.. code-block::
In [1]: from dtool_lookup_api import manifest
...: uri = 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675'
...: res = 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 cotent of a particular dataset by URI
.. code-block::
In [1]: from dtool_lookup_api import readme
..: res = readme('smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675')
In [2]: 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': 'testing@test.edu',
'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
.. code-block::
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
.. code-block::
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 `dtool-lookup-server-direct-mongo-plugin
<https://github.com/IMTEK-Simulation/dtool-lookup-server-direct-mongo-plugin>`_.
TODO: Response from server-side direct mongo plugin still yields dates as strings.
Fix within https://github.com/IMTEK-Simulation/dtool-lookup-server-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
.. code-block:: python
import dtool_lookup_api.asynchronous as dl
res = await dl.query({
'base_uri': 'smb://test-share',
'name': {'$regex': 'test'},
})
The drawback of the above approach is that the same code doesn't work in python and in jupyter (`await` outsite of a function is a syntax error in non-interactive python context).
The code below can be executed in both contexts:
.. code-block:: python
import dtool_lookup_api.asynchronous as dl
if asyncio.get_event_loop().is_running():
# then we are in jupyter notebook
# this allows nested event loops, i.e. calls to asyncio.run inside the notebook as well
# This way, the same code works in notebook and python
import nest_asyncio
nest_asyncio.apply()
def query(query_dict):
return asyncio.run(dl.query(query_dict))
query({
'base_uri': 'smb://test-share',
'name': {'$regex': 'test'},
})
See https://github.com/jupyter/notebook/issues/3397#issuecomment-419386811, https://ipython.readthedocs.io/en/stable/interactive/autoawait.html
Testing
-------
Tests require the presence of a working dtool lookup server ecosystem.
The testing workflow within :code:`.github/workflows/test.yml` uses the
`dtool-lookup-server-container-composition
<https://github.com/jotelha/dtool-lookup-server-container-composition>`_
to provide a mock ecosystem. It is possible to run the workflow locally
with the help of `docker <https://www.docker.com/>`_ and
`act <https://github.com/nektos/act>`_.
After `installing and configuring act <https://github.com/nektos/act#installation>`_, run
.. code-block:: bash
act -P ubuntu-latest=catthehacker/ubuntu:full-latest -s GITHUB_TOKEN=$GITHUB_TOKEN -W .github/workflows/test.yml --bind
from within this repository. :code:`$GITHUB_TOKEN` must hold a valid
`access token <https://github.com/settings/tokens>`_.
The user must be member of the :code:`docker` group.
The :code:`--bind` option avoids quirky permission errors by running
the test in the current directory. This will however result in the
local creation of two subdirectories :code:`dtool-lookup-server-container-composition`
and :code:`workflow` during testing, which may be removed with
.. code-block:: bash
rm -rf dtool-lookup-server-container-composition
sudo rm -rf workflow
eventually. All tests have been confirmed to work with the
:code:`catthehacker/ubuntu:full-20.04` `runner <https://github.com/nektos/act#runners>`_.
.. |PyPI| image:: https://img.shields.io/pypi/v/dtool-lookup-api
:alt: PyPI
:target: https://pypi.org/project/dtool-lookup-api/
.. |github tag| image:: https://img.shields.io/github/v/tag/IMTEK-Simulation/dtool-lookup-api
:alt: GitHub tag (latest by date)
:target: https://github.com/IMTEK-Simulation/dtool-lookup-api/tags
.. |github tests| image:: https://img.shields.io/github/actions/workflow/status/livMatS/dtool-lookup-api/test.yml?branch=master
:alt: GitHub Workflow Status
:target: https://github.com/livMatS/dtool-lookup-api/actions/workflows/test.yml
نیازمندی
| مقدار | نام |
|---|---|
| - | asgiref |
| - | aiohttp |
| >=3.9.0 | dtoolcore |
| - | PyYAML |
| - | pytest |
| - | pytest-cov |
| - | pytest-ordering |
نحوه نصب
نصب پکیج whl dtool-lookup-api-0.6.0:
pip install dtool-lookup-api-0.6.0.whl
نصب پکیج tar.gz dtool-lookup-api-0.6.0:
pip install dtool-lookup-api-0.6.0.tar.gz