Tripal v4 Development Team

--- tags: Tripal v4 Team --- # 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. - [Schedule](https://hackmd.io/e-e5K9zlRrW85ypHDZANmA#Schedule) - [Preparation for Codefest](https://hackmd.io/e-e5K9zlRrW85ypHDZANmA#Preparation) - [Useful Commands for TripalDocker](https://hackmd.io/e-e5K9zlRrW85ypHDZANmA#Useful-Commands) - [The Plan](https://hackmd.io/e-e5K9zlRrW85ypHDZANmA#Preparation) - [Core Objectives](https://hackmd.io/e-e5K9zlRrW85ypHDZANmA#Start-working-on-Issues) - [Troubleshoot Environments](https://hackmd.io/e-e5K9zlRrW85ypHDZANmA#Troubleshoot-developer-environments-as-needed) - [Resources](https://hackmd.io/e-e5K9zlRrW85ypHDZANmA#Orientation-for-resources) - [Communication](https://hackmd.io/e-e5K9zlRrW85ypHDZANmA#Open-up-lines-of-communication-and-encourages-questionscollaboration) - [Issues to work on](https://hackmd.io/e-e5K9zlRrW85ypHDZANmA#Start-working-on-Issues) - [Accomplishments](https://hackmd.io/e-e5K9zlRrW85ypHDZANmA#Accomplishments) ## 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](https://docs.docker.com/get-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? ```bash 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](https://docs.github.com/en/free-pro-team@latest/github/collaborating-with-issues-and-pull-requests/resolving-a-merge-conflict-using-the-command-line) 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 - Repository: https://github.com/tripal/t4d8 - Current Tripal Docs: https://tripal4.readthedocs.io/en/latest/ - Official Tripal4 -Help for upgrading a module: https://tripal4.readthedocs.io/en/latest/dev_guide/module_dev/upgrading.html - HackMd with common functions: https://hackmd.io/foMDA3SfSRyL1kZwL2ZoGw - Drupal 8 Docs: https://www.drupal.org/docs - Drupal 8 -Upgrading Drupal 7 modules: https://www.drupal.org/docs/upgrading-and-converting-drupal-7-modules - Drupal Change log (great for finding function specific upgrade info): https://www.drupal.org/list-changes/drupal #### Open up lines of communication and encourages questions/collaboration - **GatherTown**: When active in the Codefest, either in scheduled meetings or during group or solo coding time please stay connected in our GatherTown space: https://gather.town/app/9ug9mJSbtnueZqP3/TripalCofest - Try to hang out on gather.town even when solo coding as you may not be the only one. - **Tripal Slack**: Invite link is good until 1/16/2021: https://join.slack.com/t/tripal-project/shared_invite/zt-590q4q2f-YlO6xn7ri5UiCUZVx9M_lg - Feel free to send messages privately or in the group `#code-dev` channel. - **T4D8 Issue Queue**: Task specific updates and questions can also go in the linked issues below. #### 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](https://github.com/tripal/t4d8/issues/81): Chado integration for Tripal Vocabularies **--Lacey**~~ **DONE** - [#28](https://github.com/tripal/t4d8/issues/28): Chado integration for Tripal Fields **--Lacey** - [#89](https://github.com/tripal/t4d8/issues/89): Prepare Chado by creating entities (Dependant on #81) **--Peter** - [#27](https://github.com/tripal/t4d8/issues/27): Upgrade the Entity API **--Sean, Katheryn** - ~~[#63](https://github.com/tripal/t4d8/issues/63): Bug in Tripal Content Types listing/add form **--Rish**~~ **DONE** - ~~[#88](https://github.com/tripal/t4d8/issues/88): Create Icons for the Tripal Toolbar **--Reynold**~~ **DONE** - [#50](https://github.com/tripal/t4d8/issues/50): Publish Entities from Chado (Dependant on #28) - [#91](https://github.com/tripal/t4d8/issues/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](https://github.com/tripal/t4d8/issues/94#issuecomment-759647275). **--Carolyn**~~ **DONE** - Tokens used for titles and urls (Dependant on #28) ##### Needed eventually but not for release - [#83](https://github.com/tripal/t4d8/issues/83): Test Coverage using github actions - [#39](https://github.com/tripal/t4d8/issues/39): Automated Testing for Entities - [#78](https://github.com/tripal/t4d8/issues/78): Automated Testing for Permissions - [#70](https://github.com/tripal/t4d8/issues/70): Automated Testing for Job Management System **--Yichao** - [#77](https://github.com/tripal/t4d8/issues/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](https://github.com/tripal/t4d8/pull/90): Add troubleshooting docs for tripaldocker. (Valentin) - [PR #92](https://github.com/tripal/t4d8/pull/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](https://github.com/tripal/t4d8/pull/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](https://github.com/tripal/t4d8/pull/96): Restructure documentation and add stubs for the core guides. (Lacey) - [PR #97](https://github.com/tripal/t4d8/pull/97): Fix term listing to use IDSpaces. (Lacey) - [PR #98](https://github.com/tripal/t4d8/pull/98): Performance for chado_insert_cvterm() and fix cvterm tests. (Rish) - [PR #99](https://github.com/tripal/t4d8/pull/99): Tripal Toolbar Icons! (Reynold) - [PR #101](https://github.com/tripal/t4d8/pull/101): Review of Developer Docs (Josh) - [PR #102](https://github.com/tripal/t4d8/pull/102): Ensure tests are run on 8.9.x, 9.0.x and 9.1.x and fix associated deprecation notices. (Lacey) - [PR #104](https://github.com/tripal/t4d8/pull/104): Add documentation for how to create vocabularies, IDSpaces and terms (Carolyn)

Syntax	Example	Reference
# Header	Header	基本排版
- Unordered List	Unordered List
1. Ordered List	Ordered List
- [ ] Todo List	Todo List
> Blockquote	Blockquote
Bold font	Bold font
Italics font	Italics font
~~Strikethrough~~	~~Strikethrough~~
19^th^	19^th
H~2~O	H₂O
++Inserted text++	Inserted text
==Marked text==	Marked text
[link text](https:// "title")	Link
![image alt](https:// "title")	Image
`Code`	`Code`	在筆記中貼入程式碼
```javascript var i = 0; ```	`var i = 0;`
:smile:		Emoji list
{%youtube youtube_id %}	Externals
$L^aT_eX$	L^aT_eX
:::info This is a alert area. :::	This is a alert area.