Add remaining Pubmed tables

dspinellis / alexandria3k

Local relational access to openly-available publication data sets

GNU General Public License v3.0

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Add remaining Pubmed tables #37

Closed BasVerlooy closed 6 months ago

BasVerlooy commented 6 months ago

This pull requests adds all remaining tables from Pubmed into the code, there are still 3 things that need to be done:

[ ] the affiliations table doesn't work yet, this table is nested in the author table and is currently still empty
[x] documentation needs to be updated, following the documentation the schema and python api still need to be updated
[x] rebase all commits into 1 commit

BasVerlooy commented 6 months ago

The last remaining issue is still the author_affiliations table, it looks like the parent_cursor from the author_affiliations table which refers to the ArticlesCursor is not the same cursor that is used when populating the authors table. This causes the parent_cursor.elements to always be empty. Have you had any experience which such issue before?

dspinellis commented 6 months ago

The last remaining issue is still the author_affiliations table, it looks like the parent_cursor from the author_affiliations table which refers to the ArticlesCursor is not the same cursor that is used when populating the authors table. This causes the parent_cursor.elements to always be empty. Have you had any experience which such issue before?

If I understand the problem correctly, we have the same issue in Crossref works authors and affiliations. The cursor is split into different parts for each table. Look at the code and let me know if you need further clarifications.

BasVerlooy commented 6 months ago

The option for nested tables is added and I think this was the last blocker for this pull request