معرفی شرکت ها
baton-1.0.1
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشترتوضیحات
Python wrapper for baton.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | baton-1.0.1 |
| نام | baton |
| نسخه کتابخانه | 1.0.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Colin Nolan |
| ایمیل نویسنده | colin.nolan@sanger.ac.uk |
| آدرس صفحه اصلی | https://github.com/wtsi-hgi/python-baton-wrapper |
| آدرس اینترنتی | https://pypi.org/project/baton/ |
| مجوز | LGPL |
|Build Status| |codecov.io| # baton Python Wrapper
Introduction
------------
Python 3 Wrapper for `baton <https://github.com/wtsi-npg/baton>`__,
superseding a [previous implementation in metadata-check]
(https://github.com/wtsi-hgi/metadata-check/blob/9cd5c41b0f2e254fc1d6249a14752bd428587bb7/irods\_baton/baton\_wrapper.py).
The wrapper provides access to most of baton's functionality.
How to use
----------
Prerequisites
~~~~~~~~~~~~~
- Python >= 3.5.2
- baton >= 0.16.4
- iRODS >= 4.1.9
*Note: Although older version of baton/iRODS will probably work, the
library is only aimed at the versions specified above.*
Installation
~~~~~~~~~~~~
Stable releases can be installed via
`PyPI <https://pypi.python.org/pypi?name=baton&:action=display>`__:
.. code:: bash
$ pip3 install baton
Bleeding edge versions can be installed directly from GitHub:
.. code:: bash
$ pip3 install git+https://github.com/wtsi-hgi/python-baton-wrapper.git@<commit_id_or_branch_or_tag>#egg=baton
To declare this library as a dependency of your project, add it to your
``requirement.txt`` file.
API
~~~
Setup
^^^^^
To use the iRODS API, you must first define a "connection" to an iRODS
server:
.. code:: python
from baton.api import connect_to_irods_with_baton, Connection
# Setup connection to iRODS using baton
irods = connect_to_irods_with_baton("/where/baton/binaries/are/installed/", skip_baton_binaries_validation=False) # type: Connection
Data Objects and Collections
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The API provides the ability to retrieve models of the data objects and
collections stored on an iRODS server. Similarly to the JSON that baton
provides, the models do not contain the payloads. They do however
provide access to all of the information that baton can retrieve about
an entity, including Access Control Lists (ACLs), custom metadata
(AVUs), the content of collections and information about data object
replicas. All methods provide the option to not load AVUs.
.. code:: python
from baton.models import DataObject, Collection, SearchCriterion, ComparisonOperator
# Get models of data objects or collections at the given path(s) in iRODS
irods.data_object.get_by_path("/collection/data_object", load_metadata=False) # type: DataObject:
irods.collection.get_by_path(["/collection", "/other_collection"]) # type: Sequence[Collection]:
# Setup search for data objects or collections based on their metadata
search_criterion_1 = SearchCriterion("attribute", "match_value", ComparisonOperator.EQUALS)
search_criterion_2 = SearchCriterion("other_attribute", "other_match_value", ComparisonOperator.LESS_THAN)
# Do search to get models of data objects or collections
irods.data_object.get_by_metadata(search_criterion_1, zone="OptionalZoneRestriction") # type: Sequence[DataObject]
irods.collection.get_by_metadata([search_criterion_1, search_criterion_2], load_metadata=False) # type: Sequence[Collection]
# Get models of data objects or collections contained within a collection(s)
irods.collection.get_all_in_collection("/collection", load_metadata=False) # type: Sequence[Collection]
irods.data_object.get_all_in_collection(["/collection", "/other_collection"]) # type: Sequence[DataObject]
Metadata (AVUs)
^^^^^^^^^^^^^^^
The API provides the ability to both retrieve and manipulate the custom
metadata (AVUs) associated with data objects and collections.
*Warning: there is currently no support for reading/writing the unit
property of AVUs.*
Although the type of metadata is the same for both data objects and
collections, due to the way iRODS works, it is necessary to know the
type of entity that a path corresponds to in order to retrieve metadata.
.. code:: python
from baton.collections import IrodsMetadata
metadata_1 = IrodsMetadata({"key": {"value_1"}})
metadata_2 = IrodsMetadata({"another_key": {"value_1", "value_2"}})
# Metadata (methods available for both `data_object` and `collection`)
irods.data_object.metadata.get_all("/collection/data_object") # type: IrodsMetadata
irods.collection.metadata.get_all(["/collection", "/other_collection"]) # type: Sequence[IrodsMetadata]
# `metadata_1` is added to the data object with the first path in the list and `metadata_2` is added to the second
irods.data_object.metadata.add(["/collection/data_object", "/other_data_object"], [metadata_1, metadata_2])
irods.collection.metadata.add("/collection", metadata_1)
irods.data_object.metadata.set("/collection/data_object", metadata_1)
# `metadata_1` is added to both collections in the list
irods.collection.metadata.set(["/collection", "/other_collection"], metadata_1)
irods.data_object.metadata.remove(["/collection/data_object", "/other_data_object"], [metadata_1, metadata_2])
irods.collection.metadata.remove("/collection", metadata_1)
irods.data_object.metadata.remove_all("/collection/data_object")
irods.collection.metadata.remove_all(["/collection", "/other_collection"])
Access Control Lists (ACLs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
The API provides the ability to both retrieve and manipulate the access
control lists (ACLs) associated with data objects and collections.
.. code:: python
from baton.models import AccessControl
# ACLs. Note: it is implied that the owner is in the same zone as the entity to which the access control is applied
acl_examples = [
AccessControl(User("user_1", "zone_user_is_in"), AccessControl.Level.READ),
AccessControl(User("group_1", "zone_group_is_in"), AccessControl.Level.WRITE),
AccessControl("user_1#zone_user_is_in", AccessControl.Level.OWN)
]
irods.data_object.access_control.get_all("/collection/data_object") # type: Set[AccessControl]
irods.collection.access_control.get_all(["/collection", "/another/collection"]) # type: List[Set[AccessControl]]
irods.data_object.access_control.add_or_replace(["/collection/data_object", "/another/data_object"], acl_examples[0])
irods.collection.access_control.add_or_replace("/collection", acl_examples, recursive=True)
irods.data_object.access_control.set("/collection/data_object", acl_examples[1])
irods.collection.access_control.set(["/collection", "/another/collection"], acl_examples[0], recursive=False)
irods.data_object.access_control.revoke(["/collection/data_object", "/another/data_object"], acl_examples)
irods.collection.access_control.revoke("/collection", acl_examples[1], recursive=True)
irods.data_object.access_control.revoke_all(["/collection/data_object", "/another/data_object"])
irods.collection.access_control.revoke_all("/collection", recursive=True)
Custom objects via specific queries
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
iRODS supports specific queries which return new types of object. In
order to use such custom objects in iRODS via this library, a custom
model of the object should to be made. Then, a subclass of
``BatonCustomObjectMapper`` needs to be defined to specify how a
specific query (or number of specific queries) can be used to retrieve
from and/or modify the object in iRODS.
The API provides the ability to retrieve the queries that are installed
on an iRODS server (ironically, by use of a specific query!):
.. code:: python
from baton.models import SpecificQuery
# Get specific queries that have been installed on the iRODS server
irods.specific_query.get_all(zone="OptionalZoneRestriction") # type: Sequence[SpecificQuery]
JSON Serialization/Deserialization
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
There are JSON encoders and decoders for nearly all iRODS object models
in this library. These can be used to convert models to/from their baton
defined JSON representations. All serializers/deserializers extend
``JSONEncoder`` and ``JSONDecoder`` (most through use of the
`hgijson <https://github.com/wtsi-hgi/python-json/>`__ library) meaning
that they can be used with `Python's built in ``json``
package <https://docs.python.org/3/library/json.html>`__:
.. code:: python
import json
from baton.json import DataObjectJSONEncoder, DataObjectJSONDecoder, CollectionJSONEncoder, CollectionJSONDecoder, IrodsMetadataJSONEncoder, IrodsMetadataJSONDecoder, AccessControlJSONEncoder, AccessControlJSONDecoder
data_object_as_json_string = json.dumps(data_object, cls=DataObjectJSONEncoder) # type: str
data_object = json.loads(data_object_as_json_string, cls=DataObjectJSONDecoder) # type: DataObject
collection_as_json_string = json.dumps(collection, cls=CollectionJSONEncoder) # type: str
collection = json.loads(collection_as_json_string, cls=CollectionJSONDecoder) # type: Collection
metadata_as_json_string = json.dumps(metadata, cls=IrodsMetadataJSONEncoder) # type: str
metadata = json.loads(metadata_as_json_string, cls=IrodsMetadataJSONDecoder) # type: IrodsMetadata
acl_as_json_string = json.dumps(metadata, cls=AccessControlJSONEncoder) # type: str
acl = json.loads(acl_as_json_string, cls=AccessControlJSONDecoder) # type: List[AccessControl]
Development
-----------
Setup
~~~~~
Install both library dependencies and the dependencies needed for
testing:
.. code:: bash
$ pip3 install -q -r requirements.txt
$ pip3 install -q -r test_requirements.txt
*A baton installation is not required.*
Some tests use `Docker <https://www.docker.com>`__ therefore a Docker
daemon must be running on the test machine, with the environment
variables ``DOCKER_TLS_VERIFY``, ``DOCKER_HOST`` and
``DOCKER_CERT_PATH`` set.
Testing
~~~~~~~
Using nosetests, in the project directory, run:
.. code:: bash
$ nosetests -v --cover-inclusive --tests baton/tests, baton/tests/_baton
To generate a test coverage report with nosetests:
.. code:: bash
$ nosetests -v --with-coverage --cover-package=baton --cover-inclusive --tests baton/tests, baton/tests/_baton
License
-------
`LGPL license <LICENSE.txt>`__.
Copyright (c) 2015, 2016 Genome Research Limited
.. |Build Status| image:: https://travis-ci.org/wtsi-hgi/python-common.svg
:target: https://travis-ci.org/wtsi-hgi/python-baton-wrapper
.. |codecov.io| image:: https://codecov.io/gh/wtsi-hgi/python-baton-wrapper/graph/badge.svg
:target: https://codecov.io/github/wtsi-hgi/python-baton-wrapper
نحوه نصب
نصب پکیج whl baton-1.0.1:
pip install baton-1.0.1.whl
نصب پکیج tar.gz baton-1.0.1:
pip install baton-1.0.1.tar.gz