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PubMedCentralDownloader

What it is​

A small utility class to locate and download a PubMed Central (PMC) PDF given a PMCID, using the local oa_file_list.txt mapping file and streaming/downloading from the NCBI PMC FTP endpoint.

Public API​

  • Class: PubMedCentralDownloader
    • find_pdf_path(pmcid: str, oa_file_list_path: str) -> str
      • Streams through the given OA file list to find the relative FTP path (PDF or .tar.gz) associated with a PMCID.
      • Raises FileNotFoundError if no matching entry is found.
    • open_pmc_pdf_stream(pmcid: str, oa_file_list_path: str = "oa_file_list.txt") -> BinaryIO
      • Returns an open binary stream containing the PMC PDF bytes.
      • If the OA entry points to a .pdf, returns the underlying HTTP raw stream.
      • If it points to a .tar.gz, downloads the archive content, extracts the first .pdf found, and returns a BytesIO stream.
      • Raises FileNotFoundError for missing PDFs or unsupported path types.
      • Caller is responsible for closing the returned stream.

Configuration/Dependencies​

  • External dependency: requests (imported dynamically via importlib.import_module("requests"))
  • Local input file: oa_file_list.txt (default name; path configurable via parameters)
  • Remote base URL constant: PMC_FTP_BASE = "https://ftp.ncbi.nlm.nih.gov/pub/pmc/"

Usage​

from naas_abi_marketplace.applications.pubmed.integrations.PubMedAPI.PubMedCentralDownloader import (
    PubMedCentralDownloader
)

downloader = PubMedCentralDownloader()

pmcid = "PMC1234567"
with downloader.open_pmc_pdf_stream(pmcid, oa_file_list_path="oa_file_list.txt") as pdf_stream:
    pdf_bytes = pdf_stream.read()

with open(f"{pmcid}.pdf", "wb") as f:
    f.write(pdf_bytes)

Caveats​

  • open_pmc_pdf_stream fully downloads .tar.gz archives into memory (response.content) before extracting a PDF.
  • find_pdf_path expects the OA file list to contain tab-delimited (or whitespace-delimited) lines where:
    • parts[0] is the relative path, and
    • one of parts[1:] equals the provided pmcid.
  • Network call uses a fixed timeout=60 and a hardcoded User-Agent string.