packagepoa 0.3.0

Generate, transform and assemble files for a PoA article.

package-poa

Generate, transform and assemble files for a PoA article.

This library is used to transform a zip file input to produce output consisting of a reformatted zip file and to help produce a PDF file with its coverage page removed.

The transform procedure in summary follows these steps:

• get an article DOI from the manifest.xml file inside the input zip file
• get the zip's list of files and their titles, also by reading the manifest.xml
• rename files and add them into a new zip file, not including the PDF or the manifest.xml
• coordinate removing the cover page from the PDF file by relying on an external executable to modify the PDF

The PDF cover page is removed with the code in https://github.com/elifesciences/strip-coverletter

The output files generated by this library can then be accompanied with a Publish on Accept (PoA) research article JATS XML file, and all together can be bundled up and sent to journal publishing ingestion workflow.

Requirements and install

a) Install from pypi package index

pip install packagepoa

b) Install locally

Clone the git repo

git clone https://github.com/elifesciences/package-poa.git

Create a python virtual environment and activate it

python3 -m venv venv
source venv/bin/activate

Install it locally

pip install -r requirements.txt
python setup.py install

In order to run the transform function as written, it will require strip-coverletter to be installed and ready to run locally, which will also require Docker to be installed and running.

Configuration

The packagepoa.cfg configuration file provided in this repository can be changed in order specify different output file naming, depending on the journal, and to configure the temporary folder path and the location of the PDF strip coverletter executable.

Example usage

This library is meant to be integrated into another operational system, where the input zip file can be downloaded from an S3 bucket and then processed. The following example illustrates how it might be invoked using interactive Python:

>>> from packagepoa import transform
>>> from packagepoa.conf import raw_config, parse_raw_config
>>> config = parse_raw_config(raw_config('elife'))
>>> transform.process_zipfile("tests/test_data/18022_1_supp_mat_highwire_zip_268991_x75s4v.zip", config)

Run code tests

Use pytest for testing, install it if missing:

pip install pytest

Run tests

pytest

Run tests with coverage

coverage run -m pytest

then report on code coverage

converage report -m

License

Licensed under MIT.