cellmaps-imagedownloader 0.3.0
A tool to download specified image data from the Human Protein Atlas website using CSV file or to copy data from CM4AI dataset
License: MIT license
Keywords: cellmaps_imagedownloader

=============================================
Cell Maps ImmunoFluorescent Image Downloader
=============================================
The Cell Maps Image Downloader is part of the Cell Mapping Toolkit

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        :target: https://pypi.python.org/pypi/cellmaps_imagedownloader

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        :target: https://zenodo.org/doi/10.5281/zenodo.10607371
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Downloads ImmunoFluorescent image data from `Human Protein Atlas <https://www.proteinatlas.org/>`__
or from a `CM4AI RO-Crate <https://cm4ai.org>`__


* Free software: MIT license
* Documentation: https://cellmaps-imagedownloader.readthedocs.io.


Dependencies
------------

* `cellmaps_utils <https://pypi.org/project/cellmaps-utils>`__
* `requests <https://pypi.org/project/requests>`__
* `mygene <https://pypi.org/project/mygene>`__
* `tqdm <https://pypi.org/project/tqdm>`__

Compatibility
-------------

* Python 3.8 - 3.11

Installation
------------

.. code-block::

    pip install cellmaps_imagedownloader

**Or directly from source:**

.. code-block::

   git clone https://github.com/idekerlab/cellmaps_imagedownloader
   cd cellmaps_imagedownloader
   pip install -r requirements_dev.txt
   make dist
   pip install dist/cellmaps_imagedownloader*whl


Run **make** command with no arguments to see other build/deploy options including creation of Docker image

.. code-block::

   make

Output:

.. code-block::

   clean                remove all build, test, coverage and Python artifacts
   clean-build          remove build artifacts
   clean-pyc            remove Python file artifacts
   clean-test           remove test and coverage artifacts
   lint                 check style with flake8
   test                 run tests quickly with the default Python
   test-all             run tests on every Python version with tox
   coverage             check code coverage quickly with the default Python
   docs                 generate Sphinx HTML documentation, including API docs
   servedocs            compile the docs watching for changes
   testrelease          package and upload a TEST release
   release              package and upload a release
   dist                 builds source and wheel package
   install              install the package to the active Python's site-packages
   dockerbuild          build docker image and store in local repository
   dockerpush           push image to dockerhub

Before running tests, please install ``pip install -r requirements_dev.txt``.


Needed files
------------

* samples file: CSV file with list of IF images to download (see sample samples file in examples folder)
* unique file: CSV file of unique samples (see sample unique file in examples folder)
* provenance: file containing provenance information about input files in JSON format (see sample provenance file in examples folder)

Usage
-----

For information invoke :code:`cellmaps_imagedownloadercmd.py -h`

**Example usage**


.. code-block::

    cellmaps_imagedownloadercmd.py ./cellmaps_imagedownloader_outdir  --samples examples/samples.csv --unique examples/unique.csv --provenance examples/provenance.json


Via Docker
~~~~~~~~~~~~~~~~~~~~~~

**Example usage**


.. code-block::

   Coming soon...

Credits
-------

This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
.. _NDEx: http://www.ndexbio.org


=======
History
=======

0.3.0 (2025-05-02)
-------------------

* Updated to work with 0.6 release of CM4AI dataset by
  supporting format in `manifest.csv`

* Added `r` prefix to regex strings with escape sequences to remove
  deprecation warnings that show up in python 3.11

* Updated to PEP 517 compliant build system

0.2.1 (2025-03-18)
------------------

* Add version bounds for required packages.

0.2.0 (2024-11-22)
------------------

* Added `--protein_list` and `--cell_line` flags that will fetch images from HPA for specific proteins and/or cell line.

* Bug fixes in fairscape registration.

0.1.1 (2024-08-26)
------------------

* Bug fix in adding gene node attributes. The bug was resulting in duplicate entries and
  missing gene names, related to ambiguous antibodies.

0.1.0 (2024-01-01)
------------------

* First release on PyPI.