Data

Tools

Indexes

Applications

Experiments

Open Source Science

arxiv-publication-metadata

A Snakemake workflow to produce accessible datasets for ArXiv publication metadata

https://github.com/sdruskat/arxiv-publication-metadata

Science Score: 64.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 1 committers (100.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.3%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

A Snakemake workflow to produce accessible datasets for ArXiv publication metadata

Basic Info
  • Host: GitHub
  • Owner: sdruskat
  • Language: Python
  • Default Branch: main
  • Size: 52.7 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created almost 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

Snakemake
Project Status: Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.

Snakemake workflow: Extract LUTs from ArXiv OAI-PMH XML

Snakemake workflow to extract metadata from ArXiv OAI-PMH XML harvested with metha, and write it to JSON lookup tables for better accessibility.

Documentation

The technical documentation and description of outputs is in workflow/documentation.md.

Running the workflow

You need to have conda installed to create and activate a new environment.

bash conda env create -n arxiv-metadata --file conda-environment.yaml conda activate arxiv-metadata

You also need to get an access token from Zenodo and set it to the following two environment variables:

shell export SNAKEMAKE_STORAGE_ZENODO_ACCESS_TOKEN=<Your Zenodo access token> export SNAKEMAKE_STORAGE_ZENODO_RESTRICTED_ACCESS_TOKEN=<Your Zenodo access token>

Run with -–keep-storage-local-copies to avoid downloading resources over and over again. Also run with --software-deployment-method conda to use global conda packages.

shell snakemake --keep-storage-local-copies --software-deployment-method conda -c <number-of-cores-to-use>

You can use run.sh to run the workflow this way, and with 12 cores.

Citation

If you use this workflow in your work, please cite it using the metadata provided in CITATION.cff.

License

This work is licensed as specific in the REUSE 3.0 Specification. Please consult the single file licenses.

Owner

  • Name: Stephan Druskat
  • Login: sdruskat
  • Kind: user
  • Location: Berlin
  • Company: German Aerospace Center (DLR)

Software Engineering PhD candidate @DLR-SC, Research Software Engineer (https://hexatomic.github.io)

Citation (CITATION.cff) 

# SPDX-FileCopyrightText: 2024 German Aerospace Center (DLR)
# SPDX-FileContributor: Stephan Druskat <stephan.druskat@dlr.de>
#
# SPDX-License-Identifier: CC0-1.0

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: ArXiv metadata extraction workflow
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Stephan
    family-names: Druskat
    email: stephan.druskat@dlr.de
    affiliation: German Aerospace Center (DLR)
    orcid: 'https://orcid.org/0000-0003-4925-7248'
abstract: >-
  A Snakemake workflow for extracting metadata for ArXiv
  publication versions from OAI-PMH2 metadata.
license: MIT
version: 0.1.0
date-released: '2024-04-29'

GitHub Events

Total
Last Year

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 48
  • Total Committers: 1
  • Avg Commits per committer: 48.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Stephan Druskat s****t@d****e 48
Committer Domains (Top 20 + Academic)
dlr.de: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels