Docker¶
The openbases python module is also available as a
Docker Image, meaning you don’t
need to install anything locally (other than having Docker). Hooray!
Running the container shows it’s entrypoints. It basically will direct you to the various modules provided by openbases:
$ docker run openbases/openbases
Usage:
This entrypoint connects you to the executables provided by openbases
Python within the container. You could just as easily exec one of these
commands to the container, but this entrypoint makes this easy to do
with just 'run':
ob-validate: validate a paper.md for an Open Journals submission
docker run <container> validate --help
docker run <container> validate
ob-icons: produce
docker run <container> icons --help
docker run <container> icons
ob-paper: generate a paper.pdf for an Open Journals submission
docker run <container> paper --help
docker run <container> paper
ob-badges: generate markdown badges!
docker run <container> badges --help
docker run <container> badges
or just ask to see this global help!
docker run <container> help
For each of the above, note that you can run the module and ask for additional --help
to get usage, and see more detailed usage on the usage page.
Validate¶
What options do we have?
$ docker run openbases/openbases validate --help
Open Bases Validator Python [v0.0.53]
usage: ob-validate [--version] [--repo [REPO]] [--basic] general usage ...
OpenBases Python Validator
optional arguments:
--version show openbases python version
--repo [REPO] repository base, if needed to check for files
--basic a basic validator, for custom usage
actions:
actions for openbases
general usage description
paper validate a paper.md
To validate a paper, we need to bind the entire repository directory to data, and then specify paths relative to it.
$ docker run -it -v $PWD/:/data openbases/openbases validate paper --infile /data/paper.md
For more detailed usage, see the usage page.
Paper¶
What options do we have?
$ docker run openbases/openbases validate --help
Open Bases Paper Python [v0.0.53]
usage: ob-paper [--debug] [--quiet] [--version] general usage ...
OpenBases Python Paper
optional arguments:
--debug, -d use verbose logging to debug.
--quiet, -q suppress all normal output
--version show openbases python version
actions:
actions for openbases
general usage description
get extract values from a paper.md
shell start an interactive shell with openbases paper
Here are a bunch of examples to try:
$ docker run -it -v $PWD:/data openbases/openbases paper get /data/paper.md
title: The Experiment Factory: Reproducible Experiment Containers
tags: ['containers', 'docker', 'psychology', 'reproducibility', 'Docker']
authors: [{'name': 'Vanessa Sochat', 'orcid': '0000-0002-4387-3819', 'affiliation': 1}]
affiliations: [{'name': 'Stanford University Research Computing', 'index': 1}]
date: 28 November 2017
bibliography: paper.bib
Get a specific field
$ docker run -it -v $PWD:/data openbases/openbases paper get /data/paper.md title
The Experiment Factory: Reproducible Experiment Containers
Get a list, render in comma separated list
$ docker run -it -v $PWD:/data openbases/openbases paper get /data/paper.md tags
containers,docker,psychology,reproducibility,Docker
Get more than one at once:
$ docker run -it -v $PWD:/data openbases/openbases paper get /data/paper.md title tags
The Experiment Factory: Reproducible Experiment Containers
containers,docker,psychology,reproducibility,Docker
Look up a subfield (e.g., authors –> name)
$ docker run -it -v $PWD:/data openbases/openbases paper get /data/paper.md authors:name
Vanessa Sochat
$ docker run -it -v $PWD:/data openbases/openbases paper get /data/paper.md authors:orcid
0000-0002-4387-3819
All together now!
$ docker run -it -v $PWD:/data openbases/openbases paper get /data/paper.md tags authors:name title
Icons¶
What options do we have?
$ docker run openbases/openbases icons --help
Open Bases Icons [v0.0.53]
usage: ob-icons [--version] [--regexp REGEXP] [--help] [--url URL] [--n N]
[--sep SEP]
OpenBases Python Icons
optional arguments:
--version show openbases python version
--regexp REGEXP regular expression filter for icon name
--help show openbases icons help
--url URL complete url for json list of icons
--n N, --N N number of icons to return
--sep SEP separator to print icons to screen (default newline)
Examples!
$ docker run openbases/openbases icons
https://openbases.github.io/openbases-icons/ic/flaticon/sea-life-collection/grampus.png
You can ask for more than 1, of course:
$ docker run openbases/openbases icons --n 2
https://openbases.github.io/openbases-icons/ic/flaticon/in-the-zoo/butterfly.png
https://openbases.github.io/openbases-icons/ic/flaticon/in-the-zoo/penguin.png
You can also filter the search to some term you like (regular expression):
$ docker run openbases/openbases icons --n 2 --regexp fish
https://openbases.github.io/openbases-icons/ic/flaticon/sea-life-collection/fish.png
https://openbases.github.io/openbases-icons/ic/flaticon/sea-life-collection/fish1.png
If you know the name of your logo, that would be how to find it!
docker run openbases/openbases icons --regexp joss
https://openbases.github.io/openbases-icons/ic/openjournals/joss-logo.png
Badges¶
What options do we have?
$ docker run openbases/openbases badges --help
Open Bases Badges Python [v0.0.53]
usage: ob-badge [--version] general usage ...
OpenBases Python Badges
optional arguments:
--version show openbases python version
actions:
actions for openbases
general usage description
view view options for style, labels, etc.
create extract values from a paper.md
Here are examples to get you started.
$ docker run openbases/openbases badges create experiment labjs
Notice if we change the base type, we get a different color:
$ docker run openbases/openbases badges create submission labjs
See the usage page for more details on how to see colors, badge types, and other settings.
Development¶
If you want to develop, you can build the container locally too.
docker build -t openbases/openbases .