Merge branch 'staging' into yukthiw/world-efp

Author: mwkyuen

.github/workflows/deploy.yml

@@ -4,7 +4,7 @@ on:
     branches:
       - main
       - staging
-      
+
 permissions:
   contents: read
   pages: write
@@ -27,7 +27,9 @@ jobs:
       - run: npm ci
       - run: npm run build
         env:
-          BASE_URL: "/ePlant"
+          BASE_URL: '/ePlant'
+          VITE_MAPS_API_KEY: ${{ secrets.VITE_MAPS_API_KEY }}
+          VITE_MAPS_API_KEY: ${{ secrets.VITE_MAPS_ID }}
       - run: mv dist _site
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v2

CODE_OF_CONDUCT

@@ -0,0 +1,127 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces (including issues and pull requests), and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[INSERT CONTACT METHOD].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org),
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html](https://www.contributor-covenant.org/version/2/1/code_of_conduct.html).
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder](https://github.com/mozilla/diversity).
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq](https://www.contributor-covenant.org/faq). Translations are available at
+[https://www.contributor-covenant.org/translations](https://www.contributor-covenant.org/translations).

CONTRIBUTING.md

@@ -0,0 +1,98 @@
+# Contributing to ePlant
+
+First off, thank you for considering contributing to ePlant! By submitting your work, you
+agree that it can be shared under the terms of our license.
+
+### Code of Conduct
+Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
+
+## How to Contribute
+
+### Reporting Bugs
+
+If you find a bug, please create an issue on GitHub with the following information:
+
+- **Summary**: A brief summary of the bug.
+- **Steps to Reproduce**: Detailed steps to reproduce the bug.
+- **Expected Result**: What you expected to happen.
+- **Actual Result**: What actually happened.
+- **Screenshots**: Any screenshots that might help us understand the issue.
+
+### Feature Requests
+
+We welcome feature requests! To suggest a new feature, please open an issue on GitHub and provide:
+
+- **Summary**: A brief summary of the feature.
+- **Motivation**: Why you think this feature is needed.
+- **Use Cases**: How you expect the feature to be used.
+- **Workarounds (Optional)**: Any workaround that you currently use.
+
+### Getting started
+
+1. **Fork the repository**: [Click the "Fork" button](https://github.com/BioAnalyticResource/ePlant/fork) at the top of this repository to create your own copy of the project.
+
+2. **Clone the repository**: Go to the new fork. There is a big green button to clone.
+   ```bash
+   git clone <fork_address>
+   ```
+3. **Set upstream**: Set up the main ePlant project as your upstream branch.
+   ```bash
+   git remote add upstream https://github.com/BioAnalyticResource/ePlant
+   ```
+4. **Verify versions**: Most folks are working with _Node v18.0.0^ and npm 9.8.0^. [You can install Node from here.](https://nodejs.org/en/download/package-manager)
+   ```bash
+   node -v
+   npm -v
+   ```
+5. **Download all dependancies**:
+   ```bash
+   npm i
+   ```
+6. **Run the app locally**:
+   ```bash
+   npm run dev
+   ```
+
+### Submitting changes
+1. **Create a branch**
+   ```bash
+   git checkout -b your-branch-name
+   ```
+2. **Make changes**: Make changes in your forked repository.
+3.  **Test your changes**: Make sure your changes are working correctly.
+4. **Commit your changes**:
+   ```bash
+   git commit -m "Your commit message"
+   ```
+5. **Push to your own fork**:
+   ```bash
+   git push origin your-branch-name
+   ```
+6. **Submit a pull request**: Choose your fork as the head repository and https://github.com/BioAnalyticResource/ePlant/ as the base repository.
+
+#### PR templates
+
+Please include in the PR:
+
+- **Issue**: The issue(s) related to the work done.
+- **Previous behaviour**: A description of the behaviour was changed.
+- **Updated behaviour**: How the new changes affect the expected behaviour.
+- **Notes (Optional)**: Additional notes.
+
+### Code Style
+This is an abridged version of the [Google style guide](https://google.github.io/styleguide/tsguide.html) and [MS Typescript Coding guidelines](https://github.com/microsoft/TypeScript/wiki/Coding-guidelines), plus some tweaks to make it our own.
+
+Use Prettier and ESLint for code formatting. You may want to install the plugin for your IDE to get live feedback and you can configure your IDE to apply auto formatting when you save a file. Using the tsconfig.json file, you can customize the rules for type checking. Avoid removing and/or ignoring default rules as much as possible. If you feel strongly about a rule please outline the changes into a PR and we can discuss the merits of introducing a new change.
+
+All the new code must be written in typescript and all the types should be clearly defined in the project.
+
+### Documentation
+If your change affects any part of the documentation, please update the `README.md` accordingly.
+
+### Testing
+Make sure to run all tests before submitting your changes. If you add new functionality, please include tests for it.
+
+### Getting Help
+If you need help, feel free to ask questions by opening an issue. We appreciate your contributions!
+
+Thank you for contributing to ePlant!

Eplant/views/ChromosomeViewer/Viewer/Chromosome.tsx

@@ -1,9 +1,9 @@
 // -------
 // IMPORTS
 // -------
-import React, { FC, useEffect, useLayoutEffect, useState } from 'react'
+import React, { FC, useEffect, useState } from 'react'
 
-import { useCollections, useGeneticElements } from '@eplant/state'
+import { useCollections } from '@eplant/state'
 import { Unstable_Popup as Popup } from '@mui/base/Unstable_Popup'
 import ArrowLeft from '@mui/icons-material/ArrowLeft'
 import Box from '@mui/material/Box'
@@ -17,28 +17,32 @@ import {
   GeneAnnotationItem,
   GeneRange,
 } from '../types'
-
-import GeneAnnotation from './GeneAnnotation'
-import GeneList from './GeneList'
 import {
   getChromosomeSvg,
   getChromosomeXCoordinate,
-  getGeneAnnotation,
   pixelToBp,
-} from './utilities'
+} from '../utilities'
+
+import GeneAnnotation from './GeneAnnotation'
+import GeneList from './GeneList'
 
 //----------
 // TYPES
 //----------
 interface ChromosomeProps {
-  scale: number
   chromosome: ChromosomeItem
+  annotations: GeneAnnotationItem[]
+  scale: number
 }
 
 //----------
 // COMPONENT
 //----------
-const Chromosome: FC<ChromosomeProps> = ({ scale, chromosome }) => {
+const Chromosome: FC<ChromosomeProps> = ({
+  chromosome,
+  annotations,
+  scale,
+}) => {
   // State
   const [isHovered, setIsHovered] = useState<boolean>(false)
   const [anchorOrigin, setAnchorOrigin] = useState<number[]>([])
@@ -47,13 +51,7 @@ const Chromosome: FC<ChromosomeProps> = ({ scale, chromosome }) => {
     start: 0,
     end: 0,
   })
-  // Gene Annotation drawing
-  const [geneAnnotationArray, setGeneAnnotationArray] = useState<
-    GeneAnnotationItem[]
-  >([])
 
-  // Global State
-  const [geneticElements] = useGeneticElements()
   const [collections] = useCollections()
   const theme = useTheme()
 
@@ -73,45 +71,6 @@ const Chromosome: FC<ChromosomeProps> = ({ scale, chromosome }) => {
   // Gene List popover variables
   const openPopup = Boolean(anchorEl)
 
-  // Fire before paint, converts geneticElements into geneAnnotationArray
-  useLayoutEffect(() => {
-    // TODO: move this to top level to prevent uneccessary api calls
-    const poplar = false
-    const species = poplar ? 'Populus_trichocarpa' : 'Arabidopsis_thaliana'
-    let newGeneAnnotationArray: GeneAnnotationItem[] = []
-    geneticElements.map((gene) => {
-      // for each item in geneticElements, fetch it's gene information to add to it's geneAnnotation
-      fetch(
-        `https://bar.utoronto.ca/eplant${
-          poplar ? '_poplar' : ''
-        }/cgi-bin/querygene.cgi?species=${species}&term=${gene.id}`
-      )
-        .then((response) => response.json())
-        .then((geneItem) => {
-          if (geneItem.chromosome === chromosome.id) {
-            newGeneAnnotationArray = geneAnnotationArray
-            const geneAnnotation: GeneAnnotationItem =
-              getGeneAnnotation(geneItem)
-
-            // Make sure new geneAnnotation is not already in geneAnnotationArray
-            const isDuplicate = newGeneAnnotationArray.some((gene) => {
-              if (gene.id === geneAnnotation.id) {
-                return true
-              }
-              return false
-            })
-            if (!isDuplicate) {
-              newGeneAnnotationArray.push(geneAnnotation)
-              setGeneAnnotationArray(newGeneAnnotationArray)
-            }
-          }
-        })
-        .catch((err) => {
-          console.log(err)
-        })
-    })
-  }, [])
-
   // Execute on first render, after paint
   useEffect(() => {
     const svg: HTMLElement & SVGSVGElement = getChromosomeSvg(chromosome.id)
@@ -288,7 +247,7 @@ const Chromosome: FC<ChromosomeProps> = ({ scale, chromosome }) => {
         </g>
         {/* GENES ANNOTATION TAGS */}
         <g id={`${chromosome.id}_geneAnnotationTags`}>
-          {geneAnnotationArray.map((gene, i) => {
+          {annotations.map((gene, i) => {
             // Flatten collections into array of gene IDs - important for not drawing removed gene annotations
             const flatGeneCollection = collections.flatMap(
               (collection) => collection.genes