PubMed Data Set Query Option Missing in PyPI Version of Alexandria3k

[panos-span]

Environment:

• OS : Ubuntu 22.04 (Windows Subsystem for Linux 2)
• Python Version : 3.11.5

Alexandria3k Version: 3.1.2

Issue Description:

When attempting to perform a query on the pubmed-data using the alexandria3k CLI, the system returns an error indicating that 'pubmed-data' is not a valid choice for data_name and it doesn't seem like there is a choice for 'pubmed-data' in general. This occurs despite the package documentation suggesting that PubMed data set queries are supported.

Command Attempted:

panaspanakis@hpc:~$ a3k query pubmed-data 'pubmed_data' --query 'SELECT DOI, title FROM pubmed_articles WHERE published_year > 2020 AND title LIKE "%Machine Learning%"'

Error Received:

usage: a3k query [-h] [-a ATTACH_DATABASES [ATTACH_DATABASES ...]] [-E OUTPUT_ENCODING] [-F FIELD_SEPARATOR] [-H] [-o OUTPUT] [-P] (-Q QUERY_FILE | -q QUERY) [-s SAMPLE]
                 {orcid,doaj,asjcs,journal-names,uspto,crossref,ror,funder-names} [data_location]
a3k query: error: argument data_name: invalid choice: 'pubmed-data' (choose from 'orcid', 'doaj', 'asjcs', 'journal-names', 'uspto', 'crossref', 'ror', 'funder-names')

Here is also a screenshot of the described issue below:

[dspinellis]

😃

[dspinellis]

Fixed by releasing version 3.2.0.