<TODO: Create package art in Illustrator>
License: MIT
Feel free to fork and continue work on this python package, it is licensed under the MIT license to promote collaboration, extension, and inheritance of the scrapemed package.
Make sure to create a conda environment and install the necessary requirements before developing this package.
ie: $ conda create --name myenv --file requirements.txt
Now an overview of the package structure:
Under notebooks you can find some example work using the scrapemed modules, which may provide some insight into usage possibilities.
Under notebooks/data you will find some example downloaded date (XML from Pubmed Central). It is recommended that any time you download data while working out of the notebooks, it go here. Downloads will also go here by default when passing download=True to the scrapemed module functions which allow you to do so.
Under scrapemed/data you will find IMPORTANT data which affects module functionality. The supported_tag_list.txt contains all tags currently supported by the scrapemed module. The supported_xml_html.csv file contains all tag,attr,value combos currently supported by the scrapemed module, for tags which contain one or more attributes. The supported_xml_html.json file contains the same information in a json/dict format. The tag_descriptions.csv file contains descriptions of all supported tag types (TODO).
Under scrapemed/tests you will find several python scripts which can be run using pytest. If you also clone the nlp/.github/workflows/test-scrapemed.yml, these tests will be automatically run on any PR/ push to your github repo. Under scrapemed/test/testdata are some XML data crafted for the purpose of testing scrapemed. This data is necessary to run the testing scripts.
Each of the scrapemed python modules has a docstring at the top describing its general purpose and usage. All functions should also have descriptive docstrings and descriptions of input/output. Please contact me if any documentation is unclear.