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Tripal v4 Development Team

The objective of this is to document the work, progress and efforts of the team during the Codefest. Members of the team should be able to check in to this document to find project details, instructions, design descriptions, etc. as needed for the Codefest activities.

Team Lead

Name Organization Contact Time Zone
Lacey Sanderson Univ. of Saskatchewan lacey.sanderson@usask.ca Regina, Canada

Members

Name Organization Contact Time Zone
Risharde Ramnath Univ. of Connecticut & Washington State Univ. risharde@gmail.com Atlantic
Josh Burns Washington State Univ. josh.burns@wsu.edu US Pacific
Sean Buehler Univ. of Tennessee & i5K & Univ. of Connecticut sean.buehler@uconn.edu US Eastern
Blake Inderski United States Swine Pathogen Database blake.inderski@usda.gov US Central
Carolyn Caron Univ. of Saskatchewan carolyn.caron@usask.ca Regina, Canada
Katheryn Buble Washington State Univ. katheryn.buble@wsu.edu US Pacific
Reynold Tan Univ. of Saskatchewan rlt002@mail.usask.ca Regina, Canada
Yichao Shen Univ. of Saskatchewan yis412@mail.usask.ca Regina, Canada
Peter Richter Univ. of Connecticut peter.richter@uconn.edu US Eastern

Schedule

Team leaders should reach out prior to Jan 11-15th to schedule team meetings when members can meet to discuss project objectives and divide work.

Date Time Where
Everyday this week 17:00 UTC GatherTown Tripal4 Room

Scheduling Preference

Please add your name beside which you prefer.

  • Equally scheduled time every day (e.g. 2hrs each day to work together; drop-in style)
    • Prefer this option:
  • Focus on a couple days with longer scheduled time (e.g 4hrs on Tues and Thurs to work together; drop-in style)
    • Prefer this option:
  • Happy with both options
    • Prefer this option: Lacey, Carolyn, Sean, Rish, Yichao, Reynold, Josh, Peter

Availability

Add your availability and the amount of time you have to devote to this working group.

  • Lacey: available 9am CST (3pm UTC) to 5pm CST (11pm UTC) all days with 8+ hours to devote to this working groupx.
  • Sean: available 9am EST (2pm UTC) to 4pm EST (9pm UTC) ^^ also except for Tripal Galaxy team (TBD)
  • Carolyn: same as Lacey minus scheduling for Tripal Galaxy team
  • Rish: Mostly afternoons around this time is good (1PM AST and up)
  • Reynold: available 9am CST (3pm UTC) to 5pm CST (11pm UTC) all days
  • Josh: available Tue,Thu,Fri 4pm UTC to 10pm UTC Mon 4pm UTC to 6pm UTC Wed 6pm UTC to 10pm UTC
  • Peter: available 9am EST (2pm UTC) to 5pm EST (10pm UTC)

Preparation

You should have a recent Drupal 8, Tripal 4 development site available for development. I highly recommend using the TripalDocker! Instructions for installation are here: https://tripal4.readthedocs.io/en/latest/install/docker.html

1. Install Docker for your system. I highly recommend Docker Desktop (I use the one for Mac OS X).

2. Clone the most recent version of Tripal 4 keeping track of where you cloned it.

mkdir ~/Dockers
cd ~/Dockers
git clone https://github.com/tripal/t4d8

3. Create a docker container based on the most recent TripalDocker image with your cloned version of Tripal4 mounted inside it.

cd t4d8
docker run --publish=9000:80 --name=t4d8 -tid --volume=`pwd`:/var/www/drupal8/web/modules/contrib/tripal tripalproject/tripaldocker:latest

The first time you run this command you will see Unable to find image 'tripalproject/tripaldocker:latest' locally. This is not an error! It's just a warning and the command will automatically pull the image from the docker cloud :-)

So, what does this command mean? I'll try to explain the parts below for users new to docker :-) If you are familar with docker, feel free to ignore the next points!

  • The docker run command creates a container from a docker image. You can think of a dockerfile as instructions, an image as an OS and a container as a running machine.
  • The --name=t4d8 is how you will access the container later using docker exec commands as shown in the usage section.
  • The -tid part runs the container in the background with an interactive terminal ready to be accessed using exec.
  • The --publish=9000:80 opens port 9000 on your computer and ensures when you access localhost:9000 you will see the website inside the container.
  • The --volume=[localpath]:[containerpath] ensures that your local changes will be sync'd with that directory inside the container. This makes development in the container a lot easier!

The command above was written for linux or mac users. Here is some information for Windows users.

  • For Windows users the above command will not works as written. Sprecifically, the pwd needs to be replaced with the absolute path in including the t4d8 directory. For example: docker run --publish=9000:80 --name=t4d8 -tid --volume=C:\Users\yourusername\Dockers\t4d8:/var/www/drupal8/web/modules/contrib/tripal tripalproject/tripaldocker:latest

4. Start the PostgreSQL database.

docker exec t4d8 service postgresql start

This will create a persistent Drupal/Tripal site for you to play with! Data is stored even when your computer restarts and Tripal will already be enabled with Chado installed.

Furthermore, the --volume part of the run command ensures any changes made in your local directory are automatically copied into the docker container so you can live edit your website.

TripalDocker
URL http://localhost:9000
Administrative User drupaladmin
Administrative Password some_admin_password

Useful Commands:

Run Drupal Core PHP Unit Tests:

docker exec t4d8 drush trp-prep-tests
docker exec --workdir=/var/www/drupal8/web/modules/contrib/tripal t4d8 phpunit

Run Drush to rebuild the cache

docker exec t4d8 drush cr

Query the database

docker exec -it t4d8 drush sql:cli

Open a terminal to look inside the container

docker exec -it t4d8 bash

Wipe the container

docker rm --force t4d8

Upgrading your branch to match new changes

Since Tripal 4 is under rapid development, there will likely be changes to the main branch during the course of your development on a single task. It is recommended that you pull these changed into your branch to ensure there will not be merge conflicts and that you are working with the most recent version.

How do you do this?

git checkout 9.x-4.x
git pull
git checkout yourbranch
git merge 9.x-4.x

The above commands pull the most recent changes from github into your clone focused on the 9.x-4.x branch. Then you checkout your branch again and merge the changes into it.

When merging you will likely get a vi window pop-up asking for a commit message -the default message is fine.

Always use git status after a merge to make sure there are no merge conflicts. If there are merge conflicts, check out this guide for how to resolve them and ask for help if in doubt!

NOTE: We are not currently making upgrade hooks to keep development rapid. As such you should check the recent changes to see if you need to uninstall and reinstall any of the modules. If you do, use docker exec -it t4d8 drush pm-uninstall tripal_chado to uninstall and docker exec -it t4d8 drush en tripal_chado to reinstall.

Plans

Core Objectives

  • Help you get involved with Tripal 4 development!
  • Finish off the last items necessary for a Tripal 4 Alpha Release!

Roadmap

Troubleshoot developer environments as needed

Add any questions/errors you come across while setting up your environment here -Even if you find the fix yourself! This will help others get their environments up and running and could help us find bugs that need fixing!

Carolyn: For some reason I had trouble using git on my Mac, received the error xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools)..., but running sudo xcode-select --reset fixed it :)

Orientation for resources

Open up lines of communication and encourages questions/collaboration

Start working on Issues

Pick a topic below to work on by adding your name after the item!
Feel free to team up :-)

High Priority
  • #81: Chado integration for Tripal Vocabularies –Lacey DONE
  • #28: Chado integration for Tripal Fields –Lacey
  • #89: Prepare Chado by creating entities (Dependant on #81) –Peter
  • #27: Upgrade the Entity API –Sean, Katheryn
  • #63: Bug in Tripal Content Types listing/add form –Rish DONE
  • #88: Create Icons for the Tripal Toolbar –Reynold DONE
  • #50: Publish Entities from Chado (Dependant on #28)
  • #91: Improve performance of chado_insert_cvterm() involved in TripalTerm creation. –Rish
  • Check functionality (play around and look for bugs!) –Carolyn
  • Start the sitebuilding guide with the instructions for creating vocabularies/idspaces/term through the UI. –Carolyn DONE
  • Tokens used for titles and urls (Dependant on #28)
Needed eventually but not for release
  • #83: Test Coverage using github actions
  • #39: Automated Testing for Entities
  • #78: Automated Testing for Permissions
  • #70: Automated Testing for Job Management System –Yichao
  • #77: Dismiss notifications on Dashboard

Accomplishments

Once the Codefest week is over, here is where the team documents the accomplishments that were made during the week!

  • PR #90: Add troubleshooting docs for tripaldocker. (Valentin)
  • PR #92: Basic code for #63 to instruct users to begin by creating vocabulary when there are no tripal content types. Added functional test. (Rish)
  • PR #93: Completed integration of Tripal Vocabularies, IDSpaces and Terms with Chado cv, db, cvterm, dbxref including documentation! This completes Issue #81 and includes documentation for the Tripal > Chado mapping as well as for alternate data storage backends! (Lacey)
  • PR #96: Restructure documentation and add stubs for the core guides. (Lacey)
  • PR #97: Fix term listing to use IDSpaces. (Lacey)
  • PR #98: Performance for chado_insert_cvterm() and fix cvterm tests. (Rish)
  • PR #99: Tripal Toolbar Icons! (Reynold)
  • PR #101: Review of Developer Docs (Josh)
  • PR #102: Ensure tests are run on 8.9.x, 9.0.x and 9.1.x and fix associated deprecation notices. (Lacey)
  • PR #104: Add documentation for how to create vocabularies, IDSpaces and terms (Carolyn)
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The objective of this is to document the work, progress and efforts of the team during the Codefest. Members of the team should be able to check in to this document to find project details, instructions, design descriptions, etc. as needed fo the Codefest activities. Team Lead Name Organization Contact Time Zone Stephen Ficklin

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