Changelog and reformat additions

Clinical-Genomics · Oct 25, 2024 · 49c49f5 · 49c49f5
1 parent dcac8f7
commit 49c49f5
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Showing 4 changed files with 99 additions and 81 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,13 +10,16 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - `--force` flag prints a warning to stderr when overwriting an existing sample.
 - `gens delete sample` command
 - Height ordering for variants track.
+### Changed
+- Prettier for code formatting
 ### Fixed
-- Pan able to exit chrosome when using genome build 17 
+- Pan able to exit chromosome when using genome build 37 
 - `--force` flag `update_one` call not being called properly
 - Incorrect total sample count on home page.
 - Some typos and documentation.
 - Labels often not being visible on larger variants.
 
+
 ## [2.3]
 ### Added
 - Link out to Scout: introduce config variable for base URL
@@ -104,7 +107,6 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
  - Reinstated tooltips to display additional information on genetic elements
 ### Changed
  - Use popper for positioning tooltips
- - Prettier for code formatting
 ### Fixed
 
 ## [1.2.0]

diff --git a/assets/js/gens.js b/assets/js/gens.js
@@ -111,7 +111,7 @@ export function initCanvases({
 }
 
 // Make hard link and copy link to clipboard
-export function copyPermalink (genomeBuild, region) {
+export function copyPermalink(genomeBuild, region) {
   // create element and add url to it
   const tempElement = document.createElement("input");
   const loc = window.location;

diff --git a/assets/js/interactive.js b/assets/js/interactive.js
@@ -68,7 +68,7 @@ export class InteractiveCanvas extends BaseScatterTrack {
       yStart: 2.0, // Start value for y axis
       yEnd: -2.0, // End value for y axis
       step: 0.5, // Step value for drawing ticks along y-axis
-      color: "#000000" // Viz color
+      color: "#000000", // Viz color
     };
 
     // Setup draw canvas
@@ -229,41 +229,51 @@ export class InteractiveCanvas extends BaseScatterTrack {
         });
       }
       // reset dragging behaviour
-      this.markingRegion = false
-      this.drag = false
-    })
+      this.markingRegion = false;
+      this.drag = false;
+    });
     // when user asks for Y zoom
-    this.staticCanvas.addEventListener('zoomY', event => {
+    this.staticCanvas.addEventListener("zoomY", (event) => {
       // clear with old coord context
-      this.clearStaticContent()
+      this.clearStaticContent();
       // also needs to clear for track draw
-      if (event.detail.direction === 'out') {
-        this.log2.yStart += 1
-        this.log2.yEnd -= 1
+      if (event.detail.direction === "out") {
+        this.log2.yStart += 1;
+        this.log2.yEnd -= 1;
         if (this.log2.yStart > 2) {
-          this.log2.step = 1
+          this.log2.step = 1;
         }
       }
-      if (event.detail.direction === 'in' && this.log2.yStart > 1) {
-        this.log2.yStart -= 1
-        this.log2.yEnd += 1
+      if (event.detail.direction === "in" && this.log2.yStart > 1) {
+        this.log2.yStart -= 1;
+        this.log2.yEnd += 1;
         if (this.log2.yStart <= 2) {
-          this.log2.step = 0.5
+          this.log2.step = 0.5;
         }
       }
       // then draw new with new coords
-      this.drawStaticContent()
-      drawTrack({ ...readInputField(), force: true, displayLoading: false, drawTitle: false })
-    })
+      this.drawStaticContent();
+      drawTrack({
+        ...readInputField(),
+        force: true,
+        displayLoading: false,
+        drawTitle: false,
+      });
+    });
   }
 
   // clear static content
-  async clearStaticContent () {
-    const linePadding = 2
-    const staticContext = this.staticCanvas.getContext('2d')
+  async clearStaticContent() {
+    const linePadding = 2;
+    const staticContext = this.staticCanvas.getContext("2d");
     // Fill background colour
-    staticContext.fillStyle = '#F7F9F9'
-    staticContext.fillRect(0, 0, this.staticCanvas.width, this.staticCanvas.height)
+    staticContext.fillStyle = "#F7F9F9";
+    staticContext.fillRect(
+      0,
+      0,
+      this.staticCanvas.width,
+      this.staticCanvas.height,
+    );
     // Make content area visible
     // content window
     staticContext.clearRect(
@@ -273,14 +283,19 @@ export class InteractiveCanvas extends BaseScatterTrack {
       this.staticCanvas.height,
     );
     // area for ticks above content area
-    staticContext.clearRect(0, 0, this.staticCanvas.width, this.y + linePadding)
+    staticContext.clearRect(
+      0,
+      0,
+      this.staticCanvas.width,
+      this.y + linePadding,
+    );
     // Transfer image to visible canvas
-    staticContext.drawImage(this.drawCanvas, 0, 0)
+    staticContext.drawImage(this.drawCanvas, 0, 0);
   }
 
   // Draw static content for interactive canvas
-  async drawStaticContent () {
-    const staticContext = this.staticCanvas.getContext('2d')
+  async drawStaticContent() {
+    const staticContext = this.staticCanvas.getContext("2d");
     // Draw rotated y-axis legends
     drawRotatedText(
       staticContext,
@@ -464,33 +479,38 @@ export class InteractiveCanvas extends BaseScatterTrack {
       .catch((error) => {
         this.allowDraw = true;
 
-      // Transfer image to visible canvas
-      this.blitInteractiveCanvas({ start, end })
-      // Draw chromosome title on the content canvas as a blitting
-      // work around
-      this.titleYPos = result.y_pos - this.titleMargin
-      if (drawTitle) {
-        this.titleBbox !== null && this.blitChromName(
-          { textPosition: this.titleBbox, clearOnly: true })
-        this.titleBbox = this.drawTitle(`Chromosome ${result.chrom}`)
-        this.blitChromName({ textPosition: this.titleBbox })
-      }
+        // Transfer image to visible canvas
+        this.blitInteractiveCanvas({ start, end });
+        // Draw chromosome title on the content canvas as a blitting
+        // work around
+        this.titleYPos = result.y_pos - this.titleMargin;
+        if (drawTitle) {
+          this.titleBbox !== null &&
+            this.blitChromName({
+              textPosition: this.titleBbox,
+              clearOnly: true,
+            });
+          this.titleBbox = this.drawTitle(`Chromosome ${result.chrom}`);
+          this.blitChromName({ textPosition: this.titleBbox });
+        }
 
-      return result
-    }).then((result) => {
-      if (displayLoading) {
-        this.loadingDiv.style.display = 'none'
-      } else {
-        document.getElementsByTagName('body')[0].style.cursor = 'auto'
-      }
-      this.allowDraw = true
-    }).catch(error => {
-      this.allowDraw = true
+        return result;
+      })
+      .then((result) => {
+        if (displayLoading) {
+          this.loadingDiv.style.display = "none";
+        } else {
+          document.getElementsByTagName("body")[0].style.cursor = "auto";
+        }
+        this.allowDraw = true;
+      })
+      .catch((error) => {
+        this.allowDraw = true;
 
-      this.inputField.dispatchEvent(
-        new CustomEvent('error', { detail: { error: error } })
-      )
-    })
+        this.inputField.dispatchEvent(
+          new CustomEvent("error", { detail: { error: error } }),
+        );
+      });
   }
 
   drawTitle(title) {

diff --git a/assets/js/navigation.js b/assets/js/navigation.js
@@ -2,13 +2,13 @@ import { get } from "./fetch.js";
 import { CHROMOSOMES } from "./track.js";
 import { chromSizes } from "./helper.js";
 
-function redrawEvent ({ region, exclude = [], ...kwargs }) {
-  return new CustomEvent(
-    'draw', { detail: { region: region, exclude: exclude, ...kwargs } }
-  )
+function redrawEvent({ region, exclude = [], ...kwargs }) {
+  return new CustomEvent("draw", {
+    detail: { region: region, exclude: exclude, ...kwargs },
+  });
 }
 
-function drawEventManager ({ target, throttleTime }) {
+function drawEventManager({ target, throttleTime }) {
   const tracks = [
     ...target.querySelectorAll(".track-container"),
     target.querySelector("#cytogenetic-ideogram"),
@@ -221,28 +221,24 @@ export function zoomOut() {
 }
 
 // Handle zoom in Y button click
-export function zoomInY () {
-  console.log('dispatching zoom in Y')
-  const zoomYEvent = new CustomEvent(
-    'zoomY', { detail: { direction: 'in' } }
-  )
-  document.getElementById('interactive-static').dispatchEvent(zoomYEvent)
+export function zoomInY() {
+  console.log("dispatching zoom in Y");
+  const zoomYEvent = new CustomEvent("zoomY", { detail: { direction: "in" } });
+  document.getElementById("interactive-static").dispatchEvent(zoomYEvent);
 }
 
 // Handle zoom out Y button click
-export function zoomOutY () {
-  console.log('dispatching zoom out Y')
-  const zoomYEvent = new CustomEvent(
-    'zoomY', { detail: { direction: 'out' } }
-  )
-  document.getElementById('interactive-static').dispatchEvent(zoomYEvent)
+export function zoomOutY() {
+  console.log("dispatching zoom out Y");
+  const zoomYEvent = new CustomEvent("zoomY", { detail: { direction: "out" } });
+  document.getElementById("interactive-static").dispatchEvent(zoomYEvent);
 }
 
 // Dispatch dispatch an event to draw a given region
 // Redraw events can be limited to certain tracks or include all tracks
 class KeyLogger {
   // Records keypress combinations
-  constructor (bufferSize = 10) {
+  constructor(bufferSize = 10) {
     // Setup variables
     this.bufferSize = bufferSize;
     this.lastKeyTime = Date.now();
@@ -270,7 +266,7 @@ class KeyLogger {
     });
   }
 
-  recentKeys (timeWindow) {
+  recentKeys(timeWindow) {
     // get keys pressed within a window of time.
     const currentTime = Date.now();
     return this.keyBuffer.filter(
@@ -327,14 +323,14 @@ document.addEventListener("keyevent", (event) => {
       case "d":
         panTracks("right", 0.7);
         break;
-      case '?':
-      case 'W':
-        zoomInY()
-        break
-      case 'S':
-      case '_':
-        zoomOutY()
-        break
+      case "?":
+      case "W":
+        zoomInY();
+        break;
+      case "S":
+      case "_":
+        zoomOutY();
+        break;
       case "ArrowUp":
       case "w":
       case "+":