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openbis2sqlite

https://github.com/bamresearch/openbis2sqlite

Science Score: 44.0%

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
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (2.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: BAMresearch
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 60.5 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 6
Created almost 3 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Citation

README.md

openBIS2SQLite

Scripts to convert openbis postgres dumps to a sqlite readable transaction

how to get dump file

  1. connect to postgres database
    1. docker
    2. start a shell in a running docker container (sudo docker exec -it <container> sh)
    3. generate dump with pg_dump --create --no-owner --inserts --attribute-inserts -Fc -U <user> -f <filename> openbis_prod, default user being postgres
    4. copy the created file from docker to local with sudo docker cp <container>:/home/openbis/openbis/servers/<filename> <destination>

Owner

  • Name: Bundesanstalt für Materialforschung und -prüfung
  • Login: BAMresearch
  • Kind: organization
  • Email: oss@bam.de
  • Location: Berlin/Germany

German Federal scientific research institute for materials testing and research

Citation (CITATION.cff) 

cff-version: 0.0.4
title: openBIS2SQLite
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
 - given-names: Cezary
    family-names: Kujath
    email: cezary.kujath@bam.de
    affiliation: Bundesanstalt für Materialforschung und -prüfung (BAM)
  - given-names: Annika
    family-names: Robens-Radermacher
    email: annika.robens-radermacher@bam.de
    affiliation: Bundesanstalt für Materialforschung und -prüfung (BAM)
    orcid: 'https://orcid.org/0000-0001-9653-6085'
repository-code: 'https://github.com/BAMresearch/PGDrome'
abstract: >-
  Scripts to convert openbis postgres dumps to a sqlite readable transaction
keywords:
  - openBIS
  - sqlite
license: MIT

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Dependencies

.github/workflows/publish_conda.yml actions
  • actions/checkout v3 composite
  • conda-incubator/setup-miniconda v2 composite
.github/workflows/run_tests.yml actions
  • actions/checkout v2 composite
  • conda-incubator/setup-miniconda v2 composite
pyproject.toml pypi
  • pgdumplib *
environment.yml conda
  • ca-certificates
  • openssl
  • pgdumplib
  • pytest
  • python 3.10.*