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SampleDB

SampleDB: A sample and measurement metadata database - Published in JOSS (2021)

https://github.com/sciapp/sampledb

Science Score: 98.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ✓
    Committers with academic emails
    15 of 18 committers (83.3%) from academic institutions
  • ✓
    Institutional organization owner
    Organization sciapp has institutional domain (pgi-jcns.fz-juelich.de)
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Scientific Fields

Mathematics Computer Science - 84% confidence
Last synced: 6 months ago · JSON representation

Repository

Sample and Measurement Metadata Database

Basic Info
Statistics
  • Stars: 29
  • Watchers: 8
  • Forks: 12
  • Open Issues: 14
  • Releases: 53
Created over 6 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License

README.md

SampleDB

MIT license DOI DOI

SampleDB is a web-based sample and measurement metadata database.

Documentation

You can find the documentation for the current release at https://scientific-it-systems.iffgit.fz-juelich.de/SampleDB/.

Getting Started

We recommend using our pre-built Docker images for setting up SampleDB. You will need two containers, one for a PostgreSQL database and another for SampleDB itself, and a directory to store all files in.

If you would like to set up a development version of SampleDB instead, please see the contribution guide.

If you do not have Docker installed yet, please install Docker.

Using docker-compose

First, get the docker-compose.yml configuration file. You can git clone this repo or just get the file:

bash curl https://raw.githubusercontent.com/sciapp/sampledb/develop/docker-compose.yml.dist --output docker-compose.yml

Then simply bring everything up with:

bash docker compose up -d

Using docker commands

First, start your database container:

bash docker run \ -d \ -e POSTGRES_PASSWORD=password \ -e PGDATA=/var/lib/postgresql/data/pgdata \ -v `pwd`/pgdata:/var/lib/postgresql/data/pgdata:rw \ --restart=always \ --name sampledb-postgres \ postgres:15

Next, start the SampleDB container:

bash docker run \ -d \ --link sampledb-postgres \ -e SAMPLEDB_CONTACT_EMAIL=sampledb@example.com \ -e SAMPLEDB_MAIL_SERVER=mail.example.com \ -e SAMPLEDB_MAIL_SENDER=sampledb@example.com \ -e SAMPLEDB_ADMIN_PASSWORD=password \ -e SAMPLEDB_SQLALCHEMY_DATABASE_URI=postgresql+psycopg2://postgres:password@sampledb-postgres:5432/postgres \ --restart=always \ --name sampledb \ -p 8000:8000 \ sciapp/sampledb:0.31.1

Once it's started

This will start a minimal SampleDB installation at http://localhost:8000 and allow you to sign in with the username admin and the password password (which you should change immediately after signing in).

To learn how to further set up SampleDB, please follow the rest of the Getting Started guide.

Contributing

If you want to improve SampleDB, please read the contribution guide for a few notes on how to report issues or submit changes.

Support

If you run into any issues setting up or running SampleDB, please open an issue on GitHub.

You can also subscribe to the SampleDB mailing list to learn about new features and to discuss any questions regarding SampleDB.

Owner

  • Name: Scientific Applications
  • Login: sciapp
  • Kind: organization
  • Location: Jülich, North Rhine-Westphalia, Germany

JOSS Publication

SampleDB: A sample and measurement metadata database
Published
February 10, 2021
DOI
Volume 6, Issue 58, Page 2107
Authors
Florian Rhiem ORCID
PGI/JCNS-TA, Forschungszentrum Jülich
Editor
Arfon Smith ORCID
Tags
sample management research data management
View PDF Review Thread Software Archive

GitHub Events

Total
  • Create event: 3
  • Issues event: 2
  • Release event: 1
  • Watch event: 7
  • Issue comment event: 33
  • Push event: 71
  • Pull request review comment event: 34
  • Pull request review event: 36
  • Pull request event: 18
  • Fork event: 1
Last Year
  • Create event: 3
  • Issues event: 2
  • Release event: 1
  • Watch event: 7
  • Issue comment event: 33
  • Push event: 71
  • Pull request review comment event: 34
  • Pull request review event: 36
  • Pull request event: 18
  • Fork event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 2,268
  • Total Committers: 18
  • Avg Commits per committer: 126.0
  • Development Distribution Score (DDS): 0.187
Past Year
  • Commits: 155
  • Committers: 6
  • Avg Commits per committer: 25.833
  • Development Distribution Score (DDS): 0.31
Top Committers
Name Email Commits
Florian Rhiem f****m@f****e 1,844
Malte Deckers m****s@f****e 231
Dorothea Henkel d****l@f****e 58
Jannik Streitberg j****g@f****e 36
b.mayer b****r@f****e 25
Tim Hallmann t****n@f****e 16
Rene Noffke r****e@a****e 13
Nicolas CARPi n****t@d****l 11
rnoffke r****e@f****e 10
peters@iff242 f****s@f****e 5
Maximilian Heuwes m****s@f****e 4
Lukas Engering l****g@f****e 4
Daniel Kaiser d****r@f****e 3
Torben Moll t****l@f****e 3
Nils Cedric Holle n****s@h****e 2
Moritz Velde m****e@f****e 1
Moritz Hannemann m****n@f****e 1
knguyen k****1@a****e 1
Committer Domains (Top 20 + Academic)
fz-juelich.de: 13 alumni.fh-aachen.de: 2 hollemail.de: 1 fzj-juelich.de: 1 deltablot.email: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 40
  • Total pull requests: 41
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 16 days
  • Total issue authors: 15
  • Total pull request authors: 5
  • Average comments per issue: 2.53
  • Average comments per pull request: 2.39
  • Merged pull requests: 29
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 20
  • Average time to close issues: 6 days
  • Average time to close pull requests: 3 days
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 3.0
  • Average comments per pull request: 1.9
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • NilsWeber98 (9)
  • nilsholle (7)
  • NicolasCARPi (4)
  • link89 (3)
  • dvanic (3)
  • ju-bar (2)
  • stuartcampbell (2)
  • ivandga (2)
  • dnlsch (2)
  • theo-martel (1)
  • chsaikeerthi (1)
  • michaelosthege (1)
  • ischmahl (1)
  • ReimarBauer (1)
  • johannes-michael (1)
Pull Request Authors
  • timhallmann (21)
  • MayerBjoern (9)
  • NicolasCARPi (6)
  • rnoffke (4)
  • nilsholle (2)
Top Labels
Issue Labels
enhancement (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 49 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 45
  • Total maintainers: 1
pypi.org: sampledb

A sample and measurement metadata database

  • Versions: 45
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 49 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 11.4%
Stargazers count: 13.7%
Average: 14.6%
Downloads: 16.3%
Dependent repos count: 21.6%
Maintainers (1)
FlorianRhiem
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • APScheduler ==3.9.1
  • Babel ==2.10.3
  • Brotli ==1.0.9
  • CherryPy ==18.6.1
  • Flask ==2.1.2
  • Flask-Babel ==2.0.0
  • Flask-HTTPAuth ==4.7.0
  • Flask-Login ==0.6.1
  • Flask-Mail ==0.9.1
  • Flask-MonitoringDashboard ==3.1.1
  • Flask-RESTful ==0.3.9
  • Flask-SQLAlchemy ==2.5.1
  • Flask-WTF ==1.0.1
  • Jinja2 ==3.1.2
  • Markdown ==3.3.7
  • MarkupSafe ==2.1.1
  • Pillow ==9.1.1
  • Pint ==0.19.2
  • PySocks ==1.7.1
  • Pygments ==2.12.0
  • SQLAlchemy ==1.4.37
  • Sphinx ==5.0.2
  • WTForms ==3.0.1
  • Werkzeug ==2.1.2
  • alabaster ==0.7.12
  • aniso8601 ==9.0.1
  • async-generator ==1.10
  • attrs ==21.4.0
  • bcrypt ==3.2.2
  • beautifulsoup4 ==4.11.1
  • bleach ==5.0.0
  • blinker ==1.4
  • certifi ==2022.6.15
  • cffi ==1.15.0
  • charset-normalizer ==2.0.12
  • cheroot ==8.6.0
  • chromedriver-binary-auto ==0.1.2
  • click ==8.1.3
  • colorhash ==1.0.4
  • configparser ==5.2.0
  • coverage ==6.4.1
  • cryptography ==37.0.3
  • cssselect2 ==0.6.0
  • dnspython ==2.2.1
  • docutils ==0.18.1
  • email-validator ==1.2.1
  • execnet ==1.9.0
  • fonttools ==4.33.3
  • greenlet ==1.1.2
  • h11 ==0.13.0
  • html5lib ==1.1
  • idna ==3.3
  • imagesize ==1.3.0
  • iniconfig ==1.1.1
  • itsdangerous ==2.1.2
  • jaraco.classes ==3.2.1
  • jaraco.collections ==3.5.1
  • jaraco.context ==4.1.1
  • jaraco.functools ==3.5.0
  • jaraco.text ==3.8.0
  • jsonschema ==4.6.0
  • kaleido ==0.2.1
  • ldap3 ==2.9.1
  • lxml ==4.9.0
  • more-itertools ==8.13.0
  • numpy ==1.22.4
  • outcome ==1.2.0
  • packaging ==21.3
  • plotly ==5.8.2
  • pluggy ==1.0.0
  • portend ==3.1.0
  • psutil ==5.9.1
  • psycopg2-binary ==2.9.3
  • py ==1.11.0
  • pyOpenSSL ==22.0.0
  • pyasn1 ==0.4.8
  • pycparser ==2.21
  • pydyf ==0.2.0
  • pyotp ==2.6.0
  • pyparsing ==3.0.9
  • pyphen ==0.12.0
  • pyrsistent ==0.18.1
  • pytest ==7.1.2
  • pytest-cov ==3.0.0
  • pytest-forked ==1.4.0
  • pytest-xdist ==2.5.0
  • pytz ==2022.1
  • qrcode ==7.3.1
  • reportlab ==3.6.10
  • requests ==2.28.0
  • requests-mock ==1.9.3
  • scipy ==1.8.1
  • selenium ==4.2.0
  • six ==1.16.0
  • sniffio ==1.2.0
  • snowballstemmer ==2.2.0
  • sortedcontainers ==2.4.0
  • soupsieve ==2.3.2.post1
  • sphinxcontrib-applehelp ==1.0.2
  • sphinxcontrib-devhelp ==1.0.2
  • sphinxcontrib-htmlhelp ==2.0.0
  • sphinxcontrib-httpdomain ==1.8.0
  • sphinxcontrib-jsmath ==1.0.1
  • sphinxcontrib-qthelp ==1.0.3
  • sphinxcontrib-serializinghtml ==1.1.5
  • tempora ==5.0.1
  • tenacity ==8.0.1
  • tinycss2 ==1.1.1
  • tomli ==2.0.1
  • trio ==0.21.0
  • trio-websocket ==0.9.2
  • tzlocal ==2.0.0
  • urllib3 ==1.26.9
  • vcversioner ==2.16.0.0
  • weasyprint ==55.0
  • webencodings ==0.5.1
  • wsproto ==1.1.0
  • zc.lockfile ==2.0
  • zopfli ==0.2.1
Dockerfile docker
  • python 3.10-slim-bullseye build