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.

Build and run

You need first to install and start the grobid service, latest stable version, see the documentation. 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.

Requirements

This client has been developed and tested with Python 3.5 and should work with any higher 3.* versions. It does not require any dependencies beyond the standard python ones.

Install

Get the github repo:

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

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

Usage and options

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]

optional arguments:
  -h, --help            show this help message and exit
  --input INPUT         path to the directory containing PDF 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
  --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 (.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 (.tei.xml), using 20 concurrent workers.

By default if an existing .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.

The file example.py gives an example of usage 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.

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:

n	runtime (s)	s/PDF	PDF/s
1	209.0	1.54	0.65
2	112.0	0.82	1.21
3	80.4	0.59	1.69
5	62.9	0.46	2.16
8	55.7	0.41	2.44
10	55.3	0.40	2.45

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).

Todo

Benchmarking with many more files (e.g. million PDFs). Also implement existing GROBID services for text input (date, name, affiliation/address, raw bibliographical references, etc.). Better support for parameters.

License and contact

Distributed under Apache 2.0 license.

Main author and contact: Patrice Lopez ([email protected])