BETYdb

Web-interface to the Biofuel Ecophysiological Traits and Yields Database.
https://github.com/PecanProject/bety

Category: Renewable Energy
Sub Category: Bioenergy

Keywords

agriculture crops database ecosystem-models pecan phenotyping plants postgis ruby trait

Keywords from Contributors

ecosystem-model ecosystem-science cyberinfrastructure data-assimilation meta-analysis national-science-foundation measur observation archiving ecology

Last synced: about 23 hours ago
JSON representation

Repository metadata

Web-interface to the Biofuel Ecophysiological Traits and Yields Database (used by PEcAn and TERRA REF)

Host: GitHub
URL: https://github.com/PecanProject/bety
Owner: PecanProject
License: bsd-3-clause
Created: 2012-11-25T21:09:46.000Z (over 12 years ago)
Default Branch: develop
Last Pushed: 2024-08-21T04:10:46.000Z (8 months ago)
Last Synced: 2025-04-10T05:41:09.322Z (17 days ago)
Topics: agriculture, crops, database, ecosystem-models, pecan, phenotyping, plants, postgis, ruby, trait
Language: Ruby
Homepage: https://www.betydb.org
Size: 37.4 MB
Stars: 17
Watchers: 36
Forks: 37
Open Issues: 174
Releases: 62
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION

BETYdb

This is the source code for the Biofuel Ecophysiological Traits and Yields database (BETYdb)

The website is primarily written in Ruby-on-Rails, and has a PostgreSQL backend.
BETYdb provides an interface for contributing and accessing data, and is the informatics backend for the Predictive Ecosystem Analyzer (PEcAn).

Running BETY using Docker

To get started with BETY you can use the docker-compose.yml file included. This will start the database (postgresql with postgis version 9.5) as well as the BETY container. If this is the first time you start it you will need to initialize the database, this can be done using the following commands:

docker-compose -p bety up -d postgres
docker run --rm --network bety_bety pecan/db

If you want to change the id of the database, you can use:

docker-compose run -e LOCAL_SERVER=77 bety fix

To add initial users you can use the following commands (this will add the guestuser as well as the carya demo user)

docker-compose run bety user 'guestuser' 'guestuser' 'Guest User' '[email protected]' 4 4
docker-compose run bety user 'carya' 'illinois' 'Demo User' '[email protected]' 1 1

Once bety finishes inializing the database, or to restart BETY, you can bring up the all the containers using:

docker-compose -p bety up -d

To change the path BETY runs under you can change the path using the environment variable RAILS_RELATIVE_URL_ROOT, for example to just run bety you can use the following command. This will precompile any of the static assets and run BETY.

docker run -e RAILS_RELATIVE_URL_ROOT="/bety" pecan/bety

Documentation.

Technical Documentation: https://pecanproject.github.io/bety-documentation/technical/
Data Entry: https://pecanproject.github.io/bety-documentation/dataentry/
Data Access: https://pecan.gitbook.io/betydb-data-access/

Citation (CITATION)

## Software

Scott Rohde; Carl Crott; Patrick Mulroony; Jeremy Kemball; David LeBauer; Jimmy Chen; Rob Kooper; Yilin Dong; Andrew Shirk; Zhengqi Yang; Uday Saraf; Michael Dietze. 
2014. BETYdb 3.2.3. [doi:10.5281/zenodo.11792](https://doi.org/10.5281/zenodo.11792)

## Data

LeBauer, David, Michael Dietze, Rob Kooper, Steven Long, Patrick Mulrooney, Gareth Scott Rohde, Dan Wang (2010).
Biofuel Ecophysiological Traits and Yields Database (BETYdb),
Energy Biosciences Institute, University of Illinois at Urbana-Champaign.
doi:10.13012/J8H41PB9

Owner metadata

Name: PEcAn Project
Login: PecanProject
Email:
Kind: organization
Description:
Website: http://pecanproject.org
Location:
Twitter:
Company:
Icon url: https://avatars.githubusercontent.com/u/2879854?v=4
Repositories: 22
Last ynced at: 2024-03-26T21:34:15.642Z
Profile URL: https://github.com/PecanProject

GitHub Events

Total

Watch event: 1
Pull request event: 2

Last Year

Watch event: 1
Pull request event: 2

Committers metadata

Last synced: 4 days ago

Total Commits: 2,254
Total Committers: 22
Avg Commits per committer: 102.455
Development Distribution Score (DDS): 0.403

Commits in past year: 14
Committers in past year: 4
Avg Commits per committer in past year: 3.5
Development Distribution Score (DDS) in past year: 0.5

Name	Email	Commits
Scott Rohde	s**e@i**u	1346
Rob Kooper	k**r@i**u	195
David LeBauer	d**r@g**m	159
Carl Crott	c**t@g**m	155
Patrick Mulrooney	m**y@g**m	115
Jeremy Kemball	j**l@g**m	89
yln	s**2@h**m	60
Jimmy Chen	c**y@g**m	45
dependabot[bot]	4****]	19
Andrew Shirk	s**k@i**u	17
robbenyang	r**g@g**m	10
Max Burnette	m**2@i**u	10
MarvinJ	h**3@i**u	8
udaysaraf	s**2@i**u	7
phenolphtalein	p****n	6
Chris Black	c**s@c**g	4
Chris Schnaufer	s**r@e**u	3
Jeremy Kemball	j**l@J**l	2
Katrin Leinweber	k**i@p**e	1
Shawn P. Serbin	s**n@b**v	1
The Gitter Badger	b**r@g**m	1
Haotian Jiang	i**t@g**m	1

Committer domains:

Issue and Pull Request metadata

Last synced: 2 days ago

Total issues: 454
Total pull requests: 312
Average time to close issues: 6 months
Average time to close pull requests: 2 months
Total issue authors: 30
Total pull request authors: 22
Average comments per issue: 3.2
Average comments per pull request: 2.09
Merged pull request: 208
Bot issues: 0
Bot pull requests: 39

Past year issues: 0
Past year pull requests: 12
Past year average time to close issues: N/A
Past year average time to close pull requests: about 24 hours
Past year issue authors: 0
Past year pull request authors: 5
Past year average comments per issue: 0
Past year average comments per pull request: 0.5
Past year merged pull request: 7
Past year bot issues: 0
Past year bot pull requests: 4

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/PecanProject/bety

Top Issue Authors

gsrohde (228)
dlebauer (99)
robkooper (25)
serbinsh (22)
Chris-Schnaufer (12)
mdietze (11)
zhangwenx (9)
echeng7 (6)
samsrabin (5)
bcow (4)
ashiklom (4)
abstewa2 (3)
infotroph (3)
craig-willis (3)
istfer (3)

Top Pull Request Authors

robkooper (77)
gsrohde (59)
dlebauer (50)
dependabot[bot] (39)
phenolphtalein (32)
MarvinJ (13)
kemball (9)
udaysaraf (6)
max-zilla (5)
zyang36 (5)
infotroph (4)
Chris-Schnaufer (2)
jschen3 (2)
KristinaRiemer (1)
gitter-badger (1)

Top Issue Labels

4 - Done (73)
constraints (36)
terraref (36)
help wanted (35)
PEcAn (34)
bug (32)
1 - Ready (32)
qaqc (26)
2 - Working (24)
enhancement (20)
data (20)
question (18)
needs feedback (17)
will be completed by AddUniquenessConstraints migration (11)
will be completed by migrations and other code in value_constraints_batch_1 branch (7)
3 - ready for release (7)
in progress (5)
UA (5)
0 - Backlog (4)
Epic (3)
Discussion (3)
3.5 Needs documenting only (2)
ready for review (2)
wontfix (2)
will be completed by TimeConstraints migration (1)
wll be completed by code in miscellaneous_constraints branch (1)
duplicate (1)

Top Pull Request Labels

dependencies (39)
in progress (20)
ready for review (19)
PEcAn (14)
1 - Ready (6)
needs feedback (6)
terraref (3)
enhancement (3)
2 - Working (3)
3 - ready for release (2)
Discussion (1)
wontfix (1)
4 - Done (1)

Dependencies

Gemfile rubygems

capybara ~> 2.8 development
capybara-webkit ~> 1.7 development
database_cleaner >= 0 development
pry >= 0 development
pry-byebug >= 0 development
pry-rails >= 0 development
rails-controller-testing >= 0 development
rspec-rails ~> 3.0 development
selenium-webdriver >= 0 development
unicorn >= 0 development
yard >= 0 development
activemodel-serializers-xml >= 0
activerecord-postgis-adapter >= 0
activerecord-session_store >= 0
apipie-rails = 0.5.6
bootstrap-will_paginate >= 0
choice = 0.1.6
coffee-rails >= 0
comma ~> 4.3.2
dynamic_form >= 0
jquery-rails >= 0
jquery-ui-rails >= 0
json >= 0
json-schema >= 0
memoist >= 0
multi_json >= 0
narray = 0.6.0.4
nokogiri >= 0
optimist >= 0
passenger >= 0
pg >= 0
protected_attributes_continued >= 0
rabl >= 0
railroad = 0.5.0
rails = 5.2.4.6
rails3-restful-authentication ~> 3.0.1
recaptcha = 4.8.0
rgeo >= 0
rspec_api_documentation >= 0
ruby-graphviz = 1.0.8
rubyzip ~> 1.3.0
safe_attributes >= 0
sass-rails >= 0
seer = 0.10.0
tzinfo >= 0
uglifier >= 0
will_paginate >= 0
yajl-ruby ~> 1.3.1

Gemfile.lock rubygems

111 dependencies

.github/workflows/ci.yml actions

actions/cache v1 composite
actions/checkout v2 composite
actions/setup-ruby v1 composite
mdillon/postgis 9.5 docker

.github/workflows/dbdump.yml actions

actions/checkout v2 composite
mdillon/postgis 9.5 docker

Dockerfile docker

ruby 2.6 build

docker-compose.yml docker

mdillon/postgis 9.5
pecan/bety ${BRANCH

initdb/Dockerfile docker

alpine latest build

.github/workflows/docker.yml actions

actions/checkout v4 composite
docker/build-push-action v5 composite
docker/login-action v3 composite
docker/metadata-action v5 composite
docker/setup-buildx-action v3 composite
docker/setup-qemu-action v3 composite

docker-compose.develop.yml docker

Score: 8.343315881404946

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README.md

BETYdb

Running BETY using Docker

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