Awesome

Simple python client for GROBID REST services

This Python client can be used to process in an efficient concurrent manner a set of PDF in a given directory by the GROBID service. It includes a command line for processing PDF on a file system and write results in a given output directory and a library for import in other python scripts. The client can also process similarly a list of files with reference strings (one per line) and patents in XML ST36 formats.

Before you start

Please be aware that, at the moment, grobid does not support Windows. If you are a Windows user, don't worry. You can still run grobid via Docker.

Build and run

You need first a running grobid service, latest stable version, see the documentation for installation. By default, it is assumed that the server will run on the address http://localhost:8070. You can change the server address by editing the file config.json, see below.

Requirements

This client has been developed and was tested with Python 3.5-3.9 and should work with any higher 3.* versions. It uses requests as dependency beyond the Standard Python Library.

Install

The client can be installed with any of the following ways:

• Install latest stable release from PyPI:

python3 -m pip install grobid-client-python

• Install current master development version from GitHub:

python3 -m pip install git+https://github.com/kermitt2/grobid_client_python.git

• Install and build from a clone of the repo (current master development version):

git clone https://github.com/kermitt2/grobid_client_python
cd grobid_client_python
python3 setup.py install

There is nothing more needed to start using the python command lines, see the next section.

Usage and options

The call to the script can normally be realized interchangeably with python3 -m grobid_client.grobid_client or simply grobid_client.

usage: grobid_client [-h] [--input INPUT] [--output OUTPUT] [--config CONFIG]
                     [--n N] [--generateIDs] [--consolidate_header]
                     [--consolidate_citations] [--include_raw_citations]
                     [--include_raw_affiliations] [--force] [--teiCoordinates]
                     [--verbose]
                     service

Client for GROBID services

positional arguments:
  service               one of ['processFulltextDocument',
                        'processHeaderDocument', 'processReferences',
                        'processCitationList','processCitationPatentST36',
                        'processCitationPatentPDF']

optional arguments:
  -h, --help            show this help message and exit
  --input INPUT         path to the directory containing PDF files or .txt
                        (for processCitationList only, one reference per line)
                        to process
  --output OUTPUT       path to the directory where to put the results
                        (optional)
  --config CONFIG       path to the config file, default is ./config.json
  --n N                 concurrency for service usage
  --generateIDs         generate random xml:id to textual XML elements of the
                        result files
  --consolidate_header  call GROBID with consolidation of the metadata
                        extracted from the header
  --consolidate_citations
                        call GROBID with consolidation of the extracted
                        bibliographical references
  --include_raw_citations
                        call GROBID requesting the extraction of raw citations
  --include_raw_affiliations
                        call GROBID requestiong the extraciton of raw
                        affiliations
  --force               force re-processing pdf input files when tei output
                        files already exist
  --teiCoordinates      add the original PDF coordinates (bounding boxes) to
                        the extracted elements
  --segmentSentences    segment sentences in the text content of the document
                        with additional <s> elements
  --verbose             print information about processed files in the console

Examples:

> grobid_client --input ~/tmp/in2 --output ~/tmp/out processFulltextDocument

This command will process all the PDF files present under the input directory recursively (files with extension .pdf only) with the processFulltextDocument service of GROBID, and write the resulting XML TEI files under the output directory, reusing the file name with a different file extension (.grobid.tei.xml), using the default 10 concurrent workers.

If --output is omitted, the resulting XML TEI documents will be produced alongside the PDF in the --input directory.

> grobid_client --input ~/tmp/in2 --output ~/tmp/out --n 20 processHeaderDocument

This command will process all the PDF files present in the input directory (files with extension .pdf only) with the processHeaderDocument service of GROBID, and write the resulting XML TEI files under the output directory, reusing the file name with a different file extension (.grobid.tei.xml), using 20 concurrent workers.

By default if an existing .grobid.tei.xml file is present in the output directory corresponding to a PDF in the input directory, this PDF will be skipped to avoid reprocessing several times the same PDF. To force the processing of PDF and over-write of existing TEI files, use the parameter --force.

processCitationList does not take a repertory of PDF as input, but a repertory of .txt files, with one reference raw string per line, for example:

> grobid_client --input resources/test_txt/ --output resources/test_out/ --n 20 processCitationList

The following command example will process all the PDF files present in the input directory and add bounding box coordinates (--teiCoordinates) relative to the original PDFs for the elements listed in the config file. It will also segment the sentences (--segmentSentences, this is a "layout aware" sentence segmentation) in the identified paragraphs with bounding box coordinates for the sentences.

> grobid_client --input ~/tmp/in2 --output ~/tmp/out --teiCoordinates --segmentSentences processFulltextDocument

The file example.py gives an example of usage as a library, from a another python script.

Using the client in your python

Import and call the client as follow:

from grobid_client.grobid_client import GrobidClient

client = GrobidClient(config_path="./config.json")
client.process("processFulltextDocument", "/mnt/data/covid/pdfs", n=20)

See also example.py.

Configuration of the client

There are a few parameters that can be set with the config.json file.

• grobid_server indicates the URL of the GROBID server to be used by the client.

• batch_size is the the size of the pool of threads used by ThreadPoolExecutor, you normally don't want to change this. This should be a high number (default 1000) - but not too high to protect the memory on the machine running the client. This should not be confused with the concurrency parameter n which indicates how many parallel requests can be send to GROBID.

• sleep_time indicates in seconds the time to wait for sending a new request to GROBID when the server indicates that all its threads are currently used. The client need to re-send the query after a wait time that will allow the server to free some threads. This wait time usually depends on the service and the capacities of the server, we suggest 5-10 seconds for the processFulltextDocument service and 2 seconds for processHeaderDocument service.

• timeout is a client side timeout - the process on server side will still be running until the server finished the task or the server timeout is reached.

• coordinates indicates the structure XML elements that should contains PDF coordinates when the parameters --teiCoordinates is used see here for more details.

Here is the default config.json file for the client:

{
    "grobid_server": "http://localhost:8070",
    "batch_size": 1000,
    "sleep_time": 5,
    "timeout": 60,
    "coordinates": [ "persName", "figure", "ref", "biblStruct", "formula", "s" ]
}

Benchmarking

Full text processing of 136 PDF (total 3443 pages, in average 25 pages per PDF) on Intel Core i7-4790K CPU 4.00GHz, 4 cores (8 threads), 16GB memory, n being the concurrency parameter:

As complementary info, GROBID processing of header of the 136 PDF and with n=10 takes 3.74 s (15 times faster than the complete full text processing because only the two first pages of the PDF are considered), 36 PDF/s.

In similar conditions, extraction and structuring of bibliographical references takes 26.9 s (5.1 PDF/s).

Processing of 3500 raw bibliographical take 4.3 s with n=10 (814 references parsed per second).

License and contact

Distributed under Apache 2.0 license.

Main author and contact: Patrice Lopez (patrice.lopez@science-miner.com)