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Development

Prerequisites

  • Git for version management. Git How To provides an introduction into working with Git. Also there is a helpful Git Cheat Sheet.
  • Please make sure you changed your Protégé settings to numerical identifiers and got a personal ID to add new classes.

Contribution of OEO content

Please read the OEO best practices carefully.

Emoji ... ... symbolizes tool ... ...which is used for ...
🔶
orange diamond		 git keeping code in sync between your PC and online-repository
🐙 
octopus		 github discussions and reviews
📙 
orange book		 protégé changing the ontology
📝 
memo		 text editor changing the ontology as well as other files

Workflow

The workflow for contributing to this project has been inspired by the workflow described by Vincent Driessen.

Discussion

  1. 🐙 Create an issue on the GitHub repository describing the problem and proposed solution.

    Choose the right issue type from among the available choices:

    A) Adding a new entity to the ontology. Ideally, each issue should correspond to only one new term (with only a few subclasses, if needed)

    B) Restructuring existing parts of the ontology

    C) Updating definitions of existing entities in the ontology

    D) Other issue

    Assign a project (default "Issues") to the issue

    Discussion about the implementation should take place within the issue. Important: Please discuss the proposal within the issue thread before starting to work on a solution. For minor changes, which include small changes to improve clarity of definitions and the addition of clarifying annotations, at least one other person from the project team should agree to the proposed change before it is implemented. For major changes, which include adding new entities and restructuring the ontology, at least two other members of the project team need to agree to the change before it is implemented, which should include at least one domain expert and at least one ontology expert. Issues which are contentious, for which it is difficult to reach agreement, should be added to the agenda of the next ontology working group teleconference for discussion to reach agreement amongst the full working group. Subsequent to such discussion, the issue's first thread should be updated with a documented record of the conclusions reached.

Implementation

  1. 🔶 Once a solution has been agreed, create a branch from dev to work on your issue (see below, the "Conventions for git and GitHub" section)

    Checkout the latest stand of dev

    git checkout dev
    git pull

    Branch from dev (see also section "Conventions for git and GitHub" below)

    git checkout -b feature-issueNumber-myfeature

    It is best to merge one's changes as fast as possible (i.e. do not wait for 2 weeks) to avoid merging conflicts

  2. 📙 or 📝 Open Protégé (version 5.6.1) or a text editor and work on the ontology. If you haven't already, make sure you change your protégé settings to use numeric identifiers. Please choose the right module of the oeo to do your changes, oeo.omn is in most cases not the right file to change. Refer to this article for detailed explanations on working with protégé.

    One can also edit the files in a text editor

  3. 📙 Before committing your changes, open the oeo.omn file with Protégé and save the file from Protégé. You should also check if you included inconsistencies by following this ontology test procedure

    See the "Conventions" section below for commit messages format tips

  4. 🔶 Get your changes online

    stage the files you changed

    git add [file_name]

    🔎 Quick Tip: Changes in catalog.xml-files do NOT have to be staged, UNLESS something in the file structure has changed (e.g. adding/rearranging files, see 🔗)

    commit your changes

    git commit [-m " <commit_message> "]

    push your branch to the remote server

    git push

    If your branch does not exist on the remote server yet, git will provide you with instructions, simply follow them.

    Hint: You can create a draft pull request directly after your first commit 🐙, see 7.). Then you get the pull request number and 📙 implement the term tracker items in Protégé. Only after finishing the implementations you can assign reviewers and thus change the state of the PR. Using that workflow, it is clear whether a PR is actually ready for review.

  5. 🐙 Make sure that all automated tests are successful. This will be indicated by a green or red icon next to your most recent commit. In case an error occured that you don't know how to solve, write a comment in the PR and ask for help from the ontology-expert-team.

Review

  1. 🐙 Submit a pull request (PR)

    • Follow the steps of the github help to create the PR.
    • Please note that your PR should be directed from your branch (for example myfeature) towards the branch dev
    • To make reviewing easier, briefly describe the changes you have made in the pull request and summarise the discussion and conclusions in the associated issue.
    • Write the corresponding issue number in the pull request so that they are linked. Write it with one of the special keywords so that the issue will be automatically closed when the PR is merged (example: Closes #<your issue number>)
    • Add appropriate labels. See wiki for more information.

  2. 📝 Describe briefly (i.e. in one or two lines) what you changed in the CHANGELOG.md file. End the description by the number in parenthesis (#<your PR number>)

  3. 📙 Add term tracker items to the main changed classes of the ontology

    img

  4. 🔶 stage, commit and push the changes of steps 7 and 8

  5. 🐙 Ask for review of your PR.
    As the issue will have been discussed and agreed on prior to implementation, the purpose of the review step post-implementation is to check that the implementation has been faithful to what was agreed. One or two reviewers may be needed depending on the nature of the change that has been made. If the change involves adding content (A), a domain expert should review the issue. If the change involves restructuring the ontology (B), an ontology expert should review. If the change involves both changes to content and restructuring (B and C), it is best to ask both an ontology expert and a domain expert to review. See the section "Teams tag" of the README for more information about the expertise of the different team members.

Merge

  1. 🐙 Check that, after this whole process, your branch does not have conflicts with dev (GitHub will prevent you from merging if there are conflicts). In case of conflicts you are responsible for fixing them on your branch before you merge (see below "Fixing merge conflicts" section). If you need help, write a comment in the PR and ask for help from the ontology-expert-team.

  2. 🐙 Once approved, merge the PR into dev and delete the branch on which you were working. In the merge message on github, you can notify people who are currently working on other branches that you just merged into dev, so they know they have to check for potential conflicts with dev

Fixing merge conflicts in git

Avoid large merge conflicts by merging the updated dev versions in your branch. In case of conflicts between your branch and dev you must solve them either online via the "resolve conflicts" button (🐙) or locally (🔶+📝).

  1. 🔶 Get the latest version of dev

    git checkout dev
    git pull

  2. Switch to your branch

    git checkout <your branch>

  3. Merge dev into your branch

    git merge dev

  4. 📝 The conflicts have to be manually resolved

Conventions for git and GitHub

🔶 Naming convention for branches

Follow the best-practices for git branching naming convention. The convention is type-issue-nr-short-description

type

  • master / main / stable - includes the current stable version
  • dev - includes all current developments
  • feature - includes the feature that will be implemented
  • release - includes the current version to be released

The majority of the ontology development will be done in feature branches.

issue-nr

Add the issue number where you describe, discuss and document your development.

short-description

Describe shortly what the branch is about. Avoid long and short descriptive names for branches, 2-4 words are optimal.

Other hints:

  • Separate words with - (minus)
  • Do not put your name to the branch name, it's a collaborative project
  • Avoid using numbers only
  • Branch names should be precise and informative
  • Avoid using capital letters

Examples of branch names : feature-43-add-new-ontology-class or feature-711-branch-naming-convention

🔶 Commit messages

Try to follow esxisting conventions for commit messages:

You can use the command

git commit --amend

to edit the commit message of your latest commit (provided it is not already pushed on the remote server).
With --amend you can even add/modify changes to the commit.

Communicate

Feel free to ask the community if you need help. We are happy to support you.