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Creating a new Repository with the Ontology Development Kit

This is instructions on how to create an ontology repository in GitHub. This will only need to be done once per project. You may need assistance from someone with basic unix knowledge in following instructions here.

We will walk you though the steps to make a new ontology project

1. Install requirements

  • docker: Install Docker and make sure its runnning properly, for example by typing docker ps in your terminal or command line (CMD). If all is ok, you should be seeing something like:
CONTAINER ID   IMAGE     COMMAND   CREATED   STATUS    PORTS     NAMES

2. Download the wrapper script and pull latest ODK version

  • Linux/Mac: seed-via-docker.sh
  • PC: seed-via-docker.bat
  • Make sure to save the wrapper script in your working directory and that the filetype is correct.
  • You should have git installed - for the repo command to work perfectly, it requires a .gitconfig file in your user directory!
  • First, make sure you have Docker running (you will see the Docker whale in your toolbar on a Mac)
  • To make sure you have the latest version of the ODK installed, run in the command line

    docker pull obolibrary/odkfull

NOTE The very first time you run this it may be slow, while docker downloads necessary images. Don't worry, subsequent runs should be much faster!

NOTE Windows users, occasionally it has been reported that files downloaded on a Windows machine get a wrong file ending, for example seed-via-docker.bat.txt instead of seed-via-docker.bat, or, as we will see later, project.yaml.txt instead of project.yaml. If you have problems, double check your files are named correctly after the download!

3. Run the wrapper script

You can either pass in a configuration file in YAML format that specifies your ontology project setup, or you can pass arguments on the command line. You can use dir in your command line on PC to ensure that your wrapper script, .gitconfig, and project.yaml (if you so choose) are all in the correct directory before running the wrapper script.

Unix (Max, Linux)

Passing arguments on the command line:

./seed-via-docker.sh -d po -d ro -d pato -u cmungall -t "Triffid Behavior ontology" triffo

Using a the predefined project.yaml file:

./seed-via-docker.sh -C examples/triffo/project.yaml

Windows

Passing arguments on the command line:

seed-via-docker.bat -d po -d ro -d pato -u cmungall -t "Triffid Behavior ontology" triffo

Using a the predefined project.yaml config file:

seed-via-docker.bat -C project.yaml

General instructions for both Linux and Windows

  • Instead of -u cmungall you should be using your own username (i.e. -u nico), for example for your GitHub or GitLab hosting sites.
  • You can add a -c (lowercase) just before the -C (capital c) in the command to first delete any previous attempt to generate your ontology with the ODK, and then replaces it with a completely new one. So, -c stands for clean or "clean up previous attempts before running again" and -C stands for "the next parameter is the relative path to my config file".
  • In general, we now always recommend the use of config files. The ODK has a rich set of configuration options, most of which can only be set through the config file, but in general the config also serves as documentation and will help with updating your ontology at later stages. To create a config file, you can download for example project.yaml by clicking on the link and then typing command+s on Mac or ctrl+s on Windows to save it in the same directory as your seed-via-docker script. Then you can open the file with a text editor like Notepad++, Atom, Sublime or even nano, and adapt it to your project. Other more comprehensive examples can be found here.

This will create your starter files in target/triffid-behavior-ontology. It will also prepare an initial release and initialize a local repository (not yet pushed to your Git host site such as GitHub or GitLab).

Problems?

There are three frequently encountered problems at this stage:

  1. No .gitconfig in user directory
  2. Spaces is user path
  3. During download, your filenames got changed (Windows)

No .gitconfig in user directory

The seed-via-docker script requires a .gitconfig file in your user directory. If your .gitconfig is in a different directory, you need to change the path in the downloaded seed-via-docker script. For example on Windows (look at seed-via-docker.bat):

docker run -v %userprofile%/.gitconfig:/root/.gitconfig -v %cd%:/work -w /work --rm -ti obolibrary/odkfull /tools/odk.py seed %*

%userprofile%/.gitconfig should be changed to the correct path of your local .gitconfig file.

Spaces is user path

We have had reports of users having trouble if there paths (say, D:\data) contain a space symbol, like D:/Dropbox (Personal) or similar. In this case, we recommend to find a directory you can work in that does not contain a space symbol.

You can customize at this stage, but we recommend to first push the changes to you Git hosting site (see next steps).

During download, your filenames got changed (Windows)

Windows users, occasionally it has been reported that files downloaded on a Windows machine get a wrong file ending, for example seed-via-docker.bat.txt instead of seed-via-docker.bat, or, as we will see later, project.yaml.txt instead of project.yaml. If you have problems, double check your files are named correctly after the download!

4. Push to Git hosting website

The development kit will automatically initialize a git project, add all files and commit.

You will need to create a project on you Git hosting site.

For GitHub:

  1. Go to: https://github.com/new
  2. The owner MUST be the org you selected with the -u option. The name MUST be the one you set with -t, just with lower case letters and dashes instead of spaces. In our example above, the name "Triffid Behavior Ontology" translates to triffid-behavior-ontology.
  3. Do not initialize with a README (you already have one)
  4. Click Create
  5. See the section under "…or push an existing repository from the command line"

For GitLab:

  1. Go to: https://gitlab.com/projects/new
  2. The owner MUST be the org you selected with the -u option. The name MUST be the one you set with -t.
  3. Do not initialize with a README (you already have one)
  4. Click 'Create project'
  5. See the section under "Push an existing Git repository"

Follow the instructions there. E.g. (make sure the location of your remote is exactly correct!).

cd target/triffo
git remote add origin https://github.com/matentzn/triffid-behavior-ontology.git
git branch -M main
git push -u origin main

Note: you can now mv target/triffid-behavior-ontology to anywhere you like in your home directory. Or you can do a fresh checkout from github.

Alternative recommendation for GitHub by @matentzn

I generally feel its easier and less error prone to deviate from the standard instructions above. I keep having problems with git, passwords, typose etc, so I tend to do it, inofficially, as follows:

  1. When my repo is created I go to my GitHub Desktop
  2. I then do File > Add local repository, and select the directory which contains my newly created repo (e.g. target/triffo).
  3. I then Click on "Publish repository".
  4. If I want the code to be public, I deselect "Keep this code private". By default, the repo will be uploaded to my own user profile on GitHub, but I can also select another Organization I have access to in the respective Dropdown menu.
  5. NOTE: there seem to be some issues with pushing a GitHub Workflow file recently - you may be asked by GitHub Desktop to provide an additional permission to push the Workflow file.

Next Steps: Edit and release cycle

In your repo you will see a README-editors.md file that has been customized for your project. Follow these instructions.

OBO Library metadata

The assumption here is that you are adhering to OBO principles and want to eventually submit to OBO. Your repo will contain stub metadata files to help you do this.

You can create pull requests for your ontology on the OBO Foundry. See the src/metadata file for more details.

For more documentation, see http://obofoundry.org

Additional

You will want to also:

  • enable GitHub actions

See the README-editors.md file that has been generated for your project.