cellmaps-imagedownloader

============================================= Cell Maps ImmunoFluorescent Image Downloader

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

.. image:: https://img.shields.io/pypi/v/cellmaps_imagedownloader.svg :target: https://pypi.python.org/pypi/cellmaps_imagedownloader

.. image:: https://app.travis-ci.com/idekerlab/cellmaps_imagedownloader.svg?branch=main :target: https://app.travis-ci.com/idekerlab/cellmaps_imagedownloader

.. image:: https://readthedocs.org/projects/cellmaps-imagedownloader/badge/?version=latest :target: https://cellmaps-imagedownloader.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status

.. image:: https://zenodo.org/badge/635992073.svg :target: https://zenodo.org/doi/10.5281/zenodo.10607371 :alt: Zenodo DOI badge

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.