o2r-meta

Metadata toolsuite for an extract-map-validate workflow supporting reproducible research

https://github.com/o2r-project/o2r-meta

Science Score: 77.0%

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
Found 6 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
6 of 12 committers (50.0%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (17.9%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Metadata toolsuite for an extract-map-validate workflow supporting reproducible research

Basic Info

Host: GitHub
Owner: o2r-project
License: apache-2.0
Language: HTML
Default Branch: master
Homepage:
Size: 17.8 MB

Statistics

Stars: 2
Watchers: 2
Forks: 3
Open Issues: 13
Releases: 1

Created over 9 years ago · Last pushed over 3 years ago

Metadata Files

Readme License Citation Authors Codemeta

README.md

o2r meta

This is python library with a set of tools for extract-map-validate workflows as part of the o2r project:

schema & documentation of the o2r metadata
extract - collect meta information from files in a workspace
broker - translate metadata from o2r to third party schemas
validate - check if metadata set is valid to the schema
harvest - collect metadata from external sources via OAI-PMH
adding new parsers to the program

For their role within o2r, please refer to o2r-architecture.

Getting started

The full functionality of o2r-meta, including building the documentation and running the tests, requires Python >= 3.7.

Installation from source code

bash git clone https://github.com/o2r-project/o2r-meta.git cd o2r-meta pip install -r requirements.txt pip install -e .

Common pitfall: pygdal version has to match the system GDAL version. Verify the system GDAL version like this:

bash gdal-config --version

and, if necessary, force pygdal version to be installed as following: bash pip install pygdal==x.x.x.x

Installation with Docker

Another way of installation is provided by the Dockerfile. Build it like this:

bash git clone https://github.com/o2r-project/o2r-meta.git cd o2r-meta docker build -t meta .

And start a tool of o2r-meta like this:

bash docker run --rm -v $(pwd)/extract/tests/:/testdata:ro meta -debug extract -i /testdata -s

Build the documentation

To familiarise with the use of o2r-meta and get access to the How-to guide, we recommend the installation of the documentation before using the tool.

bash cd docs/ pip install -r requirements-docs.txt make html

This will create directory build/html under docs, which contains the documentation. The entry point is file index.html.

Run the tests

The o2r-meta tests use pytest. To install the necessary packages:

bash pip install -U pytest pip install -U pytest-console-scripts

To run the tests: bash cd tests pytest

How to cite

To cite this software please use

Nüst, Daniel, 2018. Reproducibility Service for Executable Research Compendia: Technical Specifications and Reference Implementation. Zenodo. doi:10.5281/zenodo.2203843

License

Owner

Name: Opening Reproducible Research
Login: o2r-project
Kind: organization
Email: daniel.nuest@uni-muenster.de
Location: Münster

Website: http://o2r.info
Repositories: 52
Profile: https://github.com/o2r-project

Citation (CITATION.cff)

cff-version: 1.1.0
message: "If you use this software, please cite it as 'Nüst, Daniel, 2018. Reproducibility Service for Executable Research Compendia: Technical Specifications and Reference Implementation. Zenodo. https://doi.org/10.5281/zenodo.2203843'."
authors:
  - family-names: Schutzeichel
    given-names: Marc
    affiliation: University of Münster, Münster, Germany
  - family-names: Nüst
    given-names: Daniel
    orcid: https://orcid.org/0000-0002-0024-5046
    affiliation: Opening Reproducible Research, University of Münster, Münster, Germany
    email: daniel.nuest@uni-muenster.de
    website: https://nuest.staff.ifgi.de/
  - family-names: Konkol
    given-names: Markus
    affiliation: Opening Reproducible Research, University of Münster, Münster, Germany
    website: https://github.com/Timmimim
  - family-names: Suleiman
    given-names: Jan
    affiliation: Opening Reproducible Research, University of Münster, Münster, Germany
    website: https://github.com/jansule
  - family-names: Garzon
    given-names: Sebastian
    orcid: https://orcid.org/0000-0002-8335-9312
    affiliation: Opening Reproducible Research, University of Münster, Münster, Germany
    website: https://github.com/sbastiangarzon

title: "o2r-meta"
version: 0.1.0
date-released: 2020-07-02
license: Apache-2.0
url: https://github.com/o2r-project/o2r-meta/
commit: 1447d43a660e1a38add5736d0b0dc52e6860c0e0
abstract: "Python library for extracting, mapping, and validating metadata for reproducible workflows in scholarly communication."
repository-code: https://github.com/o2r-project/o2r-meta/releases/tag/v0.1.0
identifiers:
  - type: "swh"
    value: "swh:1:rev:fb1a32f9819aef9ff37af4984048ab5b0a85e81f"

CodeMeta (codemeta.json)

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "@type": "SoftwareSourceCode",
  "license": "https://spdx.org/licenses/Apache-2.0",
  "codeRepository": "git+https://github.com/o2r-project/o2r-meta.git",
  "contIntegration": "https://travis-ci.org/o2r-project/o2r-meta",
  "dateCreated": "2019-08-16",
  "datePublished": "2020-07-02",
  "dateModified": "2020-07-02",
  "issueTracker": "https://github.com/o2r-project/o2r-meta/issues",
  "name": "geoextent",
  "version": "0.1.0",
  "identifier": "https://doi.org/10.5281/zenodo.3925693",
  "description": "Python library for extracting, mapping, and validating metadata for reproducible workflows in scholarly communication; part of the DFG-funded research project Opening Reproducible Research (o2r, https://o2r.info).",
  "applicationCategory": "Geoinformatics",
  "funding": "PE 1632/10-1, KR 3930/3-1, TR 864/6-1, PE 1632/17-1, KR 3930/8-1, TR 864/12-1",
  "developmentStatus": "active",
  "isPartOf": "https://o2r.info/",
  "funder": {
    "@type": "Organization",
    "name": "DFG"
  },
  "keywords": [
    "spatial data",
    "metadata",
    "discovery",
    "scholarly communiation",
    "scientific publishing"
  ],
  "programmingLanguage": [
    "Python 3"
  ],
  "operatingSystem": [
    "OS independent"
  ],
  "relatedLink": [
    "https://o2r.info/"
  ],
  "author": [
    {
      "@type": "Person",
      "givenName": "Marc",
      "familyName": "Schutzeichel",
      "affiliation": {
        "@type": "Organization",
        "name": "University of Mnster, Mnster, Germany"
      }
    },
    {
      "@type": "Person",
      "@id": "https://orcid.org/0000-0002-0024-5046",
      "givenName": "Daniel",
      "familyName": "Nst",
      "email": "daniel.nuest@uni-muenster.de",
      "affiliation": {
        "@type": "Organization",
        "name": "Opening Reproducible Research, University of Mnster, Mnster, Germany"
      }
    },
    {
      "@type": "Person",
      "@id": "https://orcid.org/0000-0001-6651-0976",
      "givenName": "Markus",
      "familyName": "Konkol",
      "affiliation": {
        "@type": "Organization",
        "name": "Opening Reproducible Research, University of Mnster, Mnster, Germany"
      }
    },
    {
      "@type": "Person",
      "givenName": "Jan",
      "familyName": "Suleiman",
      "affiliation": {
        "@type": "Organization",
        "name": "Opening Reproducible Research, University of Mnster, Mnster, Germany"
      }
    }
  ]
}

GitHub Events

Total

Last Year

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 271
Total Committers: 12
Avg Commits per committer: 22.583
Development Distribution Score (DDS): 0.509

Top Committers

Name	Email	Commits
7048730	m**l@u**e	133
nuest	d**t@u**e	52
m-schu	m**0@u**e	27
Sebastian Garzón	j**8@u**o	25
MarkusKonk	m**1@u**e	9
7048730	7**2@w**e	7
Markus	m**l@a**e	5
7048730	7**0@u**m	4
jansule	j**2@u**e	3
EftyK	e**i@g**m	3
Sebastian Garzon	s****n	2
Fmazin	4**n@u**m	1

Committer Domains (Top 20 + Academic)

uni-muenster.de: 4 arcor.de: 1 wwu.de: 1 uniandes.edu.co: 1 ulbnet.uni-muenster.de: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time

Total issues: 71
Total pull requests: 29
Average time to close issues: 2 months
Average time to close pull requests: 5 days
Total issue authors: 6
Total pull request authors: 4
Average comments per issue: 1.99
Average comments per pull request: 0.52
Merged pull requests: 27
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

nuest (25)
ghost (25)
jansule (10)
MarkusKonk (8)
Timmimim (2)
LukasLohoff (1)

Pull Request Authors

nuest (14)
ghost (13)
EftyK (1)
Fmazin (1)

Top Labels

Issue Labels

extractor (18) enhancement (12) bug (8) broker (7) schema (2) question (2) help wanted (1) wontfix (1) harvester (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 5 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 1
Total maintainers: 1

pypi.org: o2r-meta

A package to extract metadata from files and directories

Homepage: https://github.com/o2r-project/o2r-meta
Documentation: https://o2r-meta.readthedocs.io/
License: MIT
Latest release: 1.1.0
published over 3 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 5 Last month

Rankings

Dependent packages count: 6.6%

Forks count: 17.3%

Stargazers count: 28.2%

Average: 28.7%

Dependent repos count: 30.6%

Downloads: 61.0%

Maintainers (1)

eftyk

Last synced: 6 months ago

Dependencies

docs/requirements-docs.txt pypi

furo *
sphinx-issues *
sphinxcontrib.autoprogram *

requirements-dev.txt pypi

pytest >=5 development
pytest-console-scripts * development

requirements-opt.txt pypi

fiona *
rpy2 *

requirements.txt pypi

PyYAML *
StringDist *
dicttoxml *
filelock *
geoextent *
guess_language-spirit *
jsonschema *
lxml *
netCDF4 *
pygeoj *
python-dateutil *
requests *

setup.py pypi

PyYAML *
StringDist *
dicttoxml *
filelock *
geoextent *
guess_language-spirit *
jsonschema *
lxml *
netCDF4 *
pygdal *
pygeoj *
python-dateutil *
requests *