getpaper 0.4.9

getpaper - papers download made easy!

getpaper

Paper downloader

WARNING: temporally broken with last update

getting started

Install the library with:

pip install getpaper

If you want to edit getpaper repository consider installing it locally:

pip install -e .

On linux systems you sometimes need to check that build essentials are installed:

sudo apt install build-essential.

It is also recommended to use micromamba, conda, anaconda or other environments to avoid bloating system python with too many dependencies.

Usage

Downloading papers

After the installation you can either import the library into your python code or you can use the console scripts.

If you install from pip calling download will mean calling getpaper/download.py , for parse - getpaper/parse.py , for index - getpaper/index.py

download download_pubmed --pubmed 22266545 --folder "data/output/test/papers" --name pmid

Downloads the paper with pubmed id into the folder 'papers' and uses the pubmed id as name

download download_doi --doi 10.1038/s41597-020-00710-z --folder "data/output/test/papers"

Downloads the paper with DOI into the folder papers, as --name is not specified doi is used as name

It is also possible to download many papers in parallel with download_papers(dois: List[str], destination: Path, threads: int) function, for example:

from pathlib import Path
from typing import List
from getpaper.download import download_papers
dois: List[str] = ["10.3390/ijms22031073", "10.1038/s41597-020-00710-z", "wrong"]
destination: Path = Path("./data/output/test/papers").absolute().resolve()
threads: int = 5
results = download_papers(dois, destination, threads)
successful = results[0]
failed = results[1]

Here results will be OrderedDict[str, Path] with successfully downloaded doi->paper_path and List[str] with failed dois, in current example:

(OrderedDict([('10.3390/ijms22031073',
               PosixPath('/home/antonkulaga/sources/getpaper/notebooks/data/output/test/papers/10.3390/ijms22031073.pdf')),
              ('10.1038/s41597-020-00710-z',
               PosixPath('/home/antonkulaga/sources/getpaper/notebooks/data/output/test/papers/10.1038/s41597-020-00710-z.pdf'))]),
 ['wrong'])

Same function can be called from the command line:

download download_papers --dois "10.3390/ijms22031073" --dois "10.1038/s41597-020-00710-z" --dois "wrong" --folder "data/output/test/papers" --threads 5

You can also call download.py script directly:

python getpaper/download.py download_papers --dois "10.3390/ijms22031073" --dois "10.1038/s41597-020-00710-z" --dois "wrong" --folder "data/output/test/papers" --threads 5

Parsing the papers

You can parse the downloaded papers with the unstructured library. For example if the papers are in the folder test, you can run:

getpaper/parse.py parse_folder --folder data/output/test/papers --cores 5

You can also switch between different PDF parsers:

getpaper/parse.py parse_folder --folder data/output/test/papers --parser pdf_miner --cores 5

You can also parse papers on a per-file basis, for example:

getpaper/parse.py parse_paper --paper data/output/test/papers/10.3390/ijms22031073.pdf

Combining parsing and downloading

getpaper/parse.py download_and_parse --doi 10.1038/s41597-020-00710-z

Count tokens

To evaluate how much you want to split texts and how much embeddings will cost you it is useful to compute token number:

getpaper/parse.py count_tokens --path /home/antonkulaga/sources/non-animal-models/data/inputs/datasets

Examples

You can run examples.py to see usage examples

Additional requirements

index.py has local dependencies on other modules, for this reason if you are running it inside getpaper project folder consider having it installed locally:

pip install -e .

Detectron2 is required for using models from the layoutparser model zoo but is not automatically installed with this package. For macOS and Linux, build from source with:

pip install 'git+https://github.com/facebookresearch/detectron2.git@e2ce8dc#egg=detectron2'

Note

Since 0.3.0 version all indexing features were moved to indexpaper library