Identifier Table

[joshlawrimore]

See this article for examples of PMID, PMCID, and DOI. Create an identifier table with the following columns:

Core_id: Primary key for identifier table. Integer
PMID: Pubmed identifier for paper abstract and citation. Integer
PMCID: PubMed Central identifier. String
DOI: Digital object identifier. String
Document ID: Foreign key for documents table, document hash. BYTEA
Provenance ID: Foreign key for provenance table. Records what script generated the core_id and when. Integer.
created_at: datetime

Update the upload_pdfs.py to create an entry in the identifier table for PMID if the user specifies the title of the paper is PMID. Also allow user to input a dictionary or point to a JSON file that allows users to provide PMID, PMCID, and/or DOI identifiers for file paths. JSON should have structure like this:

{
    "/home/user/documents/research/articles": {
        "pdfs": [
            {
                "filepath": "/home/user/documents/research/articles/first_article.pdf",
                "PMID": "34567890",
                "DOI": "10.1038/s41586-023-06521-2",
                "PMCID": "PMC9876543"
            },
            {
                "filepath": "/home/user/documents/research/articles/second_article.pdf",
                "PMID": "45678901",
                "DOI": "",
                "PMCID": "PMC1234567"
            },
            {
                "filepath": "/home/user/documents/research/articles/third_article.pdf",
                "PMID": "56789012",
                "DOI": "10.1126/science.abg5610",
                "PMCID": ""
            }
        ]
    }
}