Add Pubmed data source main table

dspinellis / alexandria3k

Local relational access to openly-available publication data sets

GNU General Public License v3.0

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Add Pubmed data source main table #31

Closed BasVerlooy closed 6 months ago

BasVerlooy commented 8 months ago

Add the main table for the Pubmed datasource
Create a new xml method which allows you to get an element in an array by the value of it's attribute
Move some code from CrossRef into the data_source.py as the code is also being used by pubmed now and removes code duplication. Also add the option to check for file extensions when loading files, MacOS will often create .DS_Store files and this caused the loading to fail.
Add tests for the new pubmed datasource
Add a test for the new XML method

dspinellis commented 8 months ago

Thank you for your contribution! I think it addresses two topics: PubMed data source and progress bar. In order to help me review it, please do the following.

[ ] Split the PR into one for each separate feature, so that they can be individually merged
[ ] Squash the commits into one commit for each PR (git-rebase is your friend)
[ ] Remember to start each commit message with an uppercase letter
[ ] Add an option to disable the progress bar output (make the program silent / quiet)
[ ] Ensure the progress bar works correctly with the files-read debug option and Python API invocation (it should not appear)

BasVerlooy commented 7 months ago

The progress bar has been removed from this branch and will have it's own PR, it will also have a setting to disable it and work correctly with the debug option and Python API invocation.

Furthermore the commits have been squashed into 1 commit, for future commit I'll take into account that the messages should start with a capital.

dspinellis commented 6 months ago

Great, well done!