ReadMe.md

CroRIS tool

A tool for uploading publication entries to the CroRIS database. The instructions below were tested on Ubuntu 20.04 but might also work on other Linux distributions. The tool has been derived from an older CROSBI tool which is no longer in use.

Please note that this tool relies on the Inspire HEP database to fetch all the necessary publication data and, as such, is primarily targeting publications in branches of physics well covered by that database.

Getting started

Installation

virtualenv -p python3.8 croris-env
source croris-env/bin/activate
git clone https://github.com/ferencek/CroRIS.git
cd CroRIS
pip install -r requirements.txt

The next time you will need to work with the repository, you will just need to source the environment

source croris-env/bin/activate
cd CroRIS

Running the code

Getting the list of publications

1. Go to the Inspire HEP database

2. Get the list of publications by using the following command

find a brigljevic, v and cn cms and jy 2023 and ps p

where the author (a), the collaboration name (cn) and the journal year (jy) fields should be changed as appropriate.

Place the pointer above the "cite all" button and select BibTeX in the drop-down list as the output format. Save the output to list_of_papers.bib

Please note that the returned list of publications could contain errata published in 2023 for otherwise older publications. Please remove any publications for which the year field is older than 2023. In addition, check if there are any publications with more than one DOI string. These are typically the already-mentioned errata publications but it is nevertheless good to double-check the reason for more than one DOI string. A convenient way to get a quick overview of this type of information is to run the following two commands

cat list_of_papers.bib | grep -i year | grep -v 2023
cat list_of_papers.bib | grep -i doi

Either way, you will need to decide how to handle such publications, exclude them altogether or keep them but with just one DOI string (we generally do not upload errata publications).

3. Check that the content of configuration.py is correctly defined. Next, run the following command

python prepare_input.py -c cms -i list_of_papers.bib -o CroRIS_input.json |& tee prepare_input_`date "+%Y%m%d_%H%M%S"`.log

where the -c argument should be set as appropriate. For more information about the available command-line options, run

python prepare_input.py -h

NOTE: Piping the script output to the tee command will print it to the screen and save it in a log file containing a time stamp in its name.

In the above example prepare_input.py takes list_of_papers.bib as input, collects all the needed information and stores it in the CroRIS_input.json file.

The format of the output JSON file conforms to the specifications of the CROSBI API of the CroRIS database.

Importing publications to CroRIS

Send the output JSON file CroRIS_input.json to croris-app@srce.hr and system admins will take care of the import. In case the JSON would contain any publications that are already in the CroRIS database, those publications will be skipped during the import based on their DOI identifiers.

Advanced options

Linking publications with projects

To link project(s) to a specific publication, an additional projects field containing a comma-separated list of project CroRIS IDs needs to be added to that publication's entry in the input BibTeX file as shown in the following example

@article{CMS:2022suh,
    author = "Tumasyan, Armen and others",
    collaboration = "CMS",
    title = "{Search for a massive scalar resonance decaying to a light scalar and a Higgs boson in the four b quarks final state with boosted topology}",
    eprint = "2204.12413",
    archivePrefix = "arXiv",
    primaryClass = "hep-ex",
    reportNumber = "CMS-B2G-21-003, CERN-EP-2022-034",
    doi = "10.1016/j.physletb.2022.137392",
    journal = "Phys. Lett. B",
    volume = "842",
    pages = "137392",
    projects = "3419",
    year = "2023"
}

Contact information

E-mail: Dinko.Ferencek@irb.hr