| Name | fileformats JSON |
| Version |
0.11.2
JSON |
| download |
| home_page | None |
| Summary | Classes for representing different file formats in Python classes for use in type hinting in data workflows |
| upload_time | 2024-04-09 01:42:56 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
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| keywords |
mime
data
file extension
file-formats
filetype
magic numbers
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
|
FileFormats
===========
.. image:: https://github.com/arcanaframework/fileformats/actions/workflows/ci-cd.yml/badge.svg
:target: https://github.com/arcanaframework/fileformats/actions/workflows/ci-cd.yml
.. image:: https://codecov.io/gh/arcanaframework/fileformats/branch/main/graph/badge.svg?token=UIS0OGPST7
:target: https://codecov.io/gh/arcanaframework/fileformats
.. image:: https://img.shields.io/pypi/pyversions/fileformats.svg
:target: https://pypi.python.org/pypi/fileformats/
:alt: Supported Python versions
.. image:: https://img.shields.io/pypi/v/fileformats.svg
:target: https://pypi.python.org/pypi/fileformats/
:alt: Latest Version
.. image:: https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat
:target: https://arcanaframework.github.io/fileformats/
:alt: Documentation Status
*Fileformats* provides a library of file-format types implemented as Python classes.
The file-format types are designed to be used in type validation during the construction
of data workflows (e.g. Pydra_, Fastr_), and also provide some basic data handling methods
(e.g. loading data to dictionaries) and conversions between some equivalent types When
the "extended" install option is provided.
File-format types are typically identified by a combination of file extension
and "magic numbers" where applicable, however, unlike many other file-type Python packages,
*FileFormats*, supports multi-file data formats ("file sets") often found in scientific
workflows, e.g. with separate header/data files. *FileFormats* also provides a flexible
framework to add custom identification routines for exotic file formats, e.g.
formats that require inspection of headers to locate data files, directories containing
certain file types, or to peek at metadata fields to define specific sub-types
(e.g. functional MRI DICOM file set).
See the `extension template <https://github.com/ArcanaFramework/fileformats-extension-template>`__
for instructions on how to design *FileFormats* extensions modules to augment the
standard file-types implemented in the main repository with custom domain/vendor-specific
file-format types.
Notes on MIME-type coverage
---------------------------
Support for all non-vendor standard MIME types (i.e. ones not matching ``*/vnd.*`` or ``*/x-*``) has been
added to *FileFormats* by semi-automatically scraping the `IANA MIME types`_ website for file
extensions and magic numbers. As such, many of the formats in the library have not been properly
tested on real data and so should be treated with some caution. If you encounter any issues with an implemented file
type, please raise an issue in the `GitHub tracker <https://github.com/ArcanaFramework/fileformats/issues>`__.
Adding support for vendor formats will be relatively straightforward, it just requires someone to do the job
of manually curating the scraped data (a days work or so). Please get in touch if you are interested in helping out
with this.
Installation
------------
*FileFormats* can be installed for Python >= 3.7 from PyPI with
.. code-block:: bash
$ python3 -m pip fileformats
Support for converter methods between a few select formats can be installed by
passing the 'extended' install extra, e.g
.. code-block:: bash
$ python3 -m pip install fileformats[extended]
Examples
--------
Using the ``WithMagicNumber`` mixin class, the ``Png`` format can be defined concisely as
.. code-block:: python
from fileformats.generic import File
from fileformats.core.mixin import WithMagicNumber
class Png(WithMagicNumber, File):
binary = True
ext = ".png"
iana_mime = "image/png"
magic_number = b".PNG"
Files can then be checked to see whether they are of PNG format by
.. code-block:: python
png = Png("/path/to/image/file.png") # Checks the extension and magic number
which will raise a ``FormatMismatchError`` if initialisation or validation fails, or
for a boolean method that checks the validation use ``matches``
.. code-block:: python
if Png.matches(a_path_to_a_file):
... handle case ...
Format Conversion
-----------------
While not implemented in the main File-formats itself, file-formats provides hooks for other packages to implement extra behaviour such as format conversion. The `fileformats-extras <https://github.com/ArcanaFramework/fileformats-extras>`__ implements a number of converters between standard file-format types, e.g. archive types to/from generic file/directories, which if installed can be called using the `convert()` method.
.. code-block:: python
from fileformats.application import Zip
from fileformats.generic import Directory
zip_file = Zip.convert(Directory("/path/to/a/directory"))
extracted = Directory.convert(zip_file)
copied = extracted.copy_to("/path/to/output")
The converters are implemented in the Pydra_ dataflow framework, and can be linked into
wider Pydra_ workflows by creating a converter task
.. code-block:: python
import pydra
from pydra.tasks.mypackage import MyTask
from fileformats.application import Json, Yaml
wf = pydra.Workflow(name="a_workflow", input_spec=["in_json"])
wf.add(
Yaml.get_converter(Json, name="json2yaml", in_file=wf.lzin.in_json)
)
wf.add(
MyTask(
name="my_task",
in_file=wf.json2yaml.lzout.out_file,
)
)
...
Alternatively, the conversion can be executed outside of a Pydra_ workflow with
.. code-block:: python
json_file = Json("/path/to/file.json")
yaml_file = Yaml.convert(json_file)
License
-------
This work is licensed under a
`Creative Commons Attribution 4.0 International License <http://creativecommons.org/licenses/by/4.0/>`_
.. image:: https://i.creativecommons.org/l/by/4.0/88x31.png
:target: http://creativecommons.org/licenses/by/4.0/
:alt: Creative Commons Attribution 4.0 International License
.. _Pydra: https://pydra.readthedocs.io
.. _Fastr: https://gitlab.com/radiology/infrastructure/fastr
.. _`IANA MIME types`: https://www.iana_mime.org/assignments/media-types/media-types.xhtml
Raw data
{
"_id": null,
"home_page": null,
"name": "fileformats",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.8",
"maintainer_email": "\"Thomas G. Close\" <tom.g.close@gmail.com>",
"keywords": "MIME, data, file extension, file-formats, filetype, magic numbers",
"author": null,
"author_email": "\"Thomas G. Close\" <tom.g.close@gmail.com>",
"download_url": "https://files.pythonhosted.org/packages/19/ac/77576a481935cc6ae750c49415701c9c0ff1ce3e02e0ae5329ce7257f2ef/fileformats-0.11.2.tar.gz",
"platform": null,
"description": "FileFormats\n===========\n.. image:: https://github.com/arcanaframework/fileformats/actions/workflows/ci-cd.yml/badge.svg\n :target: https://github.com/arcanaframework/fileformats/actions/workflows/ci-cd.yml\n.. image:: https://codecov.io/gh/arcanaframework/fileformats/branch/main/graph/badge.svg?token=UIS0OGPST7\n :target: https://codecov.io/gh/arcanaframework/fileformats\n.. image:: https://img.shields.io/pypi/pyversions/fileformats.svg\n :target: https://pypi.python.org/pypi/fileformats/\n :alt: Supported Python versions\n.. image:: https://img.shields.io/pypi/v/fileformats.svg\n :target: https://pypi.python.org/pypi/fileformats/\n :alt: Latest Version\n.. image:: https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat\n :target: https://arcanaframework.github.io/fileformats/\n :alt: Documentation Status\n\n\n*Fileformats* provides a library of file-format types implemented as Python classes.\nThe file-format types are designed to be used in type validation during the construction\nof data workflows (e.g. Pydra_, Fastr_), and also provide some basic data handling methods\n(e.g. loading data to dictionaries) and conversions between some equivalent types When\nthe \"extended\" install option is provided.\n\nFile-format types are typically identified by a combination of file extension\nand \"magic numbers\" where applicable, however, unlike many other file-type Python packages,\n*FileFormats*, supports multi-file data formats (\"file sets\") often found in scientific\nworkflows, e.g. with separate header/data files. *FileFormats* also provides a flexible\nframework to add custom identification routines for exotic file formats, e.g.\nformats that require inspection of headers to locate data files, directories containing\ncertain file types, or to peek at metadata fields to define specific sub-types\n(e.g. functional MRI DICOM file set).\n\nSee the `extension template <https://github.com/ArcanaFramework/fileformats-extension-template>`__\nfor instructions on how to design *FileFormats* extensions modules to augment the\nstandard file-types implemented in the main repository with custom domain/vendor-specific\nfile-format types.\n\nNotes on MIME-type coverage\n---------------------------\n\nSupport for all non-vendor standard MIME types (i.e. ones not matching ``*/vnd.*`` or ``*/x-*``) has been\nadded to *FileFormats* by semi-automatically scraping the `IANA MIME types`_ website for file\nextensions and magic numbers. As such, many of the formats in the library have not been properly\ntested on real data and so should be treated with some caution. If you encounter any issues with an implemented file\ntype, please raise an issue in the `GitHub tracker <https://github.com/ArcanaFramework/fileformats/issues>`__.\n\nAdding support for vendor formats will be relatively straightforward, it just requires someone to do the job\nof manually curating the scraped data (a days work or so). Please get in touch if you are interested in helping out\nwith this.\n\n\nInstallation\n------------\n\n*FileFormats* can be installed for Python >= 3.7 from PyPI with\n\n.. code-block:: bash\n\n $ python3 -m pip fileformats\n\n\nSupport for converter methods between a few select formats can be installed by\npassing the 'extended' install extra, e.g\n\n.. code-block:: bash\n\n $ python3 -m pip install fileformats[extended]\n\n\nExamples\n--------\n\nUsing the ``WithMagicNumber`` mixin class, the ``Png`` format can be defined concisely as\n\n.. code-block:: python\n\n from fileformats.generic import File\n from fileformats.core.mixin import WithMagicNumber\n\n class Png(WithMagicNumber, File):\n binary = True\n ext = \".png\"\n iana_mime = \"image/png\"\n magic_number = b\".PNG\"\n\n\nFiles can then be checked to see whether they are of PNG format by\n\n.. code-block:: python\n\n png = Png(\"/path/to/image/file.png\") # Checks the extension and magic number\n\nwhich will raise a ``FormatMismatchError`` if initialisation or validation fails, or\nfor a boolean method that checks the validation use ``matches``\n\n.. code-block:: python\n\n if Png.matches(a_path_to_a_file):\n ... handle case ...\n\nFormat Conversion\n-----------------\n\nWhile not implemented in the main File-formats itself, file-formats provides hooks for other packages to implement extra behaviour such as format conversion. The `fileformats-extras <https://github.com/ArcanaFramework/fileformats-extras>`__ implements a number of converters between standard file-format types, e.g. archive types to/from generic file/directories, which if installed can be called using the `convert()` method.\n\n.. code-block:: python\n\n from fileformats.application import Zip\n from fileformats.generic import Directory\n\n zip_file = Zip.convert(Directory(\"/path/to/a/directory\"))\n extracted = Directory.convert(zip_file)\n copied = extracted.copy_to(\"/path/to/output\")\n\nThe converters are implemented in the Pydra_ dataflow framework, and can be linked into\nwider Pydra_ workflows by creating a converter task\n\n.. code-block:: python\n\n import pydra\n from pydra.tasks.mypackage import MyTask\n from fileformats.application import Json, Yaml\n\n wf = pydra.Workflow(name=\"a_workflow\", input_spec=[\"in_json\"])\n wf.add(\n Yaml.get_converter(Json, name=\"json2yaml\", in_file=wf.lzin.in_json)\n )\n wf.add(\n MyTask(\n name=\"my_task\",\n in_file=wf.json2yaml.lzout.out_file,\n )\n )\n ...\n\nAlternatively, the conversion can be executed outside of a Pydra_ workflow with\n\n.. code-block:: python\n\n json_file = Json(\"/path/to/file.json\")\n yaml_file = Yaml.convert(json_file)\n\n\n\nLicense\n-------\n\nThis work is licensed under a\n`Creative Commons Attribution 4.0 International License <http://creativecommons.org/licenses/by/4.0/>`_\n\n.. image:: https://i.creativecommons.org/l/by/4.0/88x31.png\n :target: http://creativecommons.org/licenses/by/4.0/\n :alt: Creative Commons Attribution 4.0 International License\n\n.. _Pydra: https://pydra.readthedocs.io\n.. _Fastr: https://gitlab.com/radiology/infrastructure/fastr\n.. _`IANA MIME types`: https://www.iana_mime.org/assignments/media-types/media-types.xhtml\n",
"bugtrack_url": null,
"license": "Creative Commons Attribution 4.0 International Public License By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution 4.0 International Public License (\"Public License\"). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions. Section 1 \u2013 Definitions. Adapted Material means material subject to Copyright and Similar Rights that is derived from or based upon the Licensed Material and in which the Licensed Material is translated, altered, arranged, transformed, or otherwise modified in a manner requiring permission under the Copyright and Similar Rights held by the Licensor. For purposes of this Public License, where the Licensed Material is a musical work, performance, or sound recording, Adapted Material is always produced where the Licensed Material is synched in timed relation with a moving image. Adapter's License means the license You apply to Your Copyright and Similar Rights in Your contributions to Adapted Material in accordance with the terms and conditions of this Public License. Copyright and Similar Rights means copyright and/or similar rights closely related to copyright including, without limitation, performance, broadcast, sound recording, and Sui Generis Database Rights, without regard to how the rights are labeled or categorized. For purposes of this Public License, the rights specified in Section 2(b)(1)-(2) are not Copyright and Similar Rights. Effective Technological Measures means those measures that, in the absence of proper authority, may not be circumvented under laws fulfilling obligations under Article 11 of the WIPO Copyright Treaty adopted on December 20, 1996, and/or similar international agreements. Exceptions and Limitations means fair use, fair dealing, and/or any other exception or limitation to Copyright and Similar Rights that applies to Your use of the Licensed Material. Licensed Material means the artistic or literary work, database, or other material to which the Licensor applied this Public License. Licensed Rights means the rights granted to You subject to the terms and conditions of this Public License, which are limited to all Copyright and Similar Rights that apply to Your use of the Licensed Material and that the Licensor has authority to license. Licensor means the individual(s) or entity(ies) granting rights under this Public License. Share means to provide material to the public by any means or process that requires permission under the Licensed Rights, such as reproduction, public display, public performance, distribution, dissemination, communication, or importation, and to make material available to the public including in ways that members of the public may access the material from a place and at a time individually chosen by them. Sui Generis Database Rights means rights other than copyright resulting from Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, as amended and/or succeeded, as well as other essentially equivalent rights anywhere in the world. You means the individual or entity exercising the Licensed Rights under this Public License. Your has a corresponding meaning. Section 2 \u2013 Scope. License grant. Subject to the terms and conditions of this Public License, the Licensor hereby grants You a worldwide, royalty-free, non-sublicensable, non-exclusive, irrevocable license to exercise the Licensed Rights in the Licensed Material to: reproduce and Share the Licensed Material, in whole or in part; and produce, reproduce, and Share Adapted Material. Exceptions and Limitations. For the avoidance of doubt, where Exceptions and Limitations apply to Your use, this Public License does not apply, and You do not need to comply with its terms and conditions. Term. The term of this Public License is specified in Section 6(a). Media and formats; technical modifications allowed. The Licensor authorizes You to exercise the Licensed Rights in all media and formats whether now known or hereafter created, and to make technical modifications necessary to do so. The Licensor waives and/or agrees not to assert any right or authority to forbid You from making technical modifications necessary to exercise the Licensed Rights, including technical modifications necessary to circumvent Effective Technological Measures. For purposes of this Public License, simply making modifications authorized by this Section 2(a)(4) never produces Adapted Material. Downstream recipients. Offer from the Licensor \u2013 Licensed Material. Every recipient of the Licensed Material automatically receives an offer from the Licensor to exercise the Licensed Rights under the terms and conditions of this Public License. No downstream restrictions. You may not offer or impose any additional or different terms or conditions on, or apply any Effective Technological Measures to, the Licensed Material if doing so restricts exercise of the Licensed Rights by any recipient of the Licensed Material. No endorsement. 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