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Fix check for "hasSubSubfeatures" in svg feature rendering (#4600)
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@cmdcolin
cmdcolin authored Oct 14, 2024
1 parent 825a135 commit d62f7a8
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Showing 37 changed files with 2,702 additions and 2,683 deletions.
1 change: 1 addition & 0 deletions eslint.config.mjs
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Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,7 @@ export default tseslint.config(
'react/no-is-mounted': 'off',
'react/prop-types': 'off',

'unicorn/prefer-global-this': 'off',
'unicorn/prefer-structured-clone': 'off',
'unicorn/no-new-array': 'off',
'unicorn/no-empty-file': 'off',
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4 changes: 2 additions & 2 deletions package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -105,10 +105,10 @@
"electron-mock-ipc": "^0.3.8",
"eslint": "^9.0.0",
"eslint-plugin-react": "^7.33.2",
"eslint-plugin-react-hooks": "^5.1.0-rc-d48603a5-20240813",
"eslint-plugin-react-hooks": "^5.0.0",
"eslint-plugin-react-refresh": "^0.4.3",
"eslint-plugin-tsdoc": "^0.3.0",
"eslint-plugin-unicorn": "^55.0.0",
"eslint-plugin-unicorn": "^56.0.0",
"express": "^4.0.0",
"express-basic-auth": "^1.2.1",
"find-yarn-workspace-root": "^2.0.0",
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36 changes: 18 additions & 18 deletions packages/core/BaseFeatureWidget/__snapshots__/index.test.tsx.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -3,31 +3,31 @@
exports[`open up a widget 1`] = `
<div>
<div
class="MuiPaper-root MuiPaper-elevation MuiPaper-rounded MuiPaper-elevation1 MuiAccordion-root MuiAccordion-rounded Mui-expanded css-fgq1ej-MuiPaper-root-MuiAccordion-root"
class="MuiPaper-root MuiPaper-elevation MuiPaper-rounded MuiPaper-elevation1 MuiAccordion-root MuiAccordion-rounded Mui-expanded css-9g9pc9-MuiPaper-root-MuiAccordion-root"
style="--Paper-shadow: 0px 2px 1px -1px rgba(0,0,0,0.2),0px 1px 1px 0px rgba(0,0,0,0.14),0px 1px 3px 0px rgba(0,0,0,0.12);"
>
<h3
class="MuiAccordion-heading css-rolk5j-MuiAccordion-heading"
class="MuiAccordion-heading css-cy7rkm-MuiAccordion-heading"
>
<div
aria-expanded="true"
class="MuiButtonBase-root MuiAccordionSummary-root Mui-expanded css-1yigmdy-MuiButtonBase-root-MuiAccordionSummary-root"
class="MuiButtonBase-root MuiAccordionSummary-root Mui-expanded css-t1q4kr-MuiButtonBase-root-MuiAccordionSummary-root"
role="button"
tabindex="0"
>
<div
class="MuiAccordionSummary-content Mui-expanded css-1rhnrrr-MuiAccordionSummary-content"
class="MuiAccordionSummary-content Mui-expanded css-rof4d7-MuiAccordionSummary-content"
>
<span
class="MuiTypography-root MuiTypography-button css-xin9dq-MuiTypography-root"
class="MuiTypography-root MuiTypography-button css-l5w3u1-MuiTypography-root"
/>
</div>
<div
class="MuiAccordionSummary-expandIconWrapper Mui-expanded css-yw020d-MuiAccordionSummary-expandIconWrapper"
class="MuiAccordionSummary-expandIconWrapper Mui-expanded css-1wqf3nl-MuiAccordionSummary-expandIconWrapper"
>
<svg
aria-hidden="true"
class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-1u842hp-MuiSvgIcon-root-icon"
class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-1qtxdat-MuiSvgIcon-root-icon"
data-testid="ExpandMoreIcon"
focusable="false"
viewBox="0 0 24 24"
Expand All @@ -40,24 +40,24 @@ exports[`open up a widget 1`] = `
</div>
</h3>
<div
class="MuiCollapse-root MuiCollapse-vertical MuiCollapse-entered css-wz2cs5-MuiCollapse-root"
class="MuiCollapse-root MuiCollapse-vertical MuiCollapse-entered css-qr6njo-MuiCollapse-root"
style="min-height: 0px;"
>
<div
class="MuiCollapse-wrapper MuiCollapse-vertical css-smkl36-MuiCollapse-wrapper"
class="MuiCollapse-wrapper MuiCollapse-vertical css-1x6hinx-MuiCollapse-wrapper"
>
<div
class="MuiCollapse-wrapperInner MuiCollapse-vertical css-9l5vo-MuiCollapse-wrapperInner"
class="MuiCollapse-wrapperInner MuiCollapse-vertical css-1i4ywhz-MuiCollapse-wrapperInner"
>
<div
class="MuiAccordion-region"
role="region"
>
<div
class="MuiAccordionDetails-root css-mz6w4y-MuiAccordionDetails-root-expansionPanelDetails"
class="MuiAccordionDetails-root css-1eji0yd-MuiAccordionDetails-root-expansionPanelDetails"
>
<p
class="MuiTypography-root MuiTypography-body1 css-1ptewxf-MuiTypography-root"
class="MuiTypography-root MuiTypography-body1 css-1xfjy4j-MuiTypography-root"
>
Core details
</p>
Expand Down Expand Up @@ -92,10 +92,10 @@ exports[`open up a widget 1`] = `
</div>
</div>
<hr
class="MuiDivider-root MuiDivider-fullWidth css-9mgopn-MuiDivider-root"
class="MuiDivider-root MuiDivider-fullWidth css-1jpc804-MuiDivider-root"
/>
<p
class="MuiTypography-root MuiTypography-body1 css-1ptewxf-MuiTypography-root"
class="MuiTypography-root MuiTypography-body1 css-1xfjy4j-MuiTypography-root"
>
Attributes
</p>
Expand All @@ -120,24 +120,24 @@ exports[`open up a widget 1`] = `
class="css-57ilie-container"
>
<div
class="MuiFormControl-root MuiFormControl-marginDense css-1pquc22-MuiFormControl-root-formControl"
class="MuiFormControl-root MuiFormControl-marginDense css-h2948o-MuiFormControl-root-formControl"
>
<button
class="MuiButtonBase-root MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeSmall MuiButton-containedSizeSmall MuiButton-colorPrimary MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeSmall MuiButton-containedSizeSmall MuiButton-colorPrimary css-qy5lo8-MuiButtonBase-root-MuiButton-root"
class="MuiButtonBase-root MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeSmall MuiButton-containedSizeSmall MuiButton-colorPrimary MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeSmall MuiButton-containedSizeSmall MuiButton-colorPrimary css-12qtcjg-MuiButtonBase-root-MuiButton-root"
tabindex="0"
type="button"
>
Show feature sequence
</button>
</div>
<button
class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-16y463b-MuiButtonBase-root-MuiIconButton-root"
class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-1thuchg-MuiButtonBase-root-MuiIconButton-root"
tabindex="0"
type="button"
>
<svg
aria-hidden="true"
class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-l9ansn-MuiSvgIcon-root"
class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-14500qs-MuiSvgIcon-root"
data-testid="HelpIcon"
focusable="false"
viewBox="0 0 24 24"
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8 changes: 4 additions & 4 deletions packages/core/rpc/BaseRpcDriver.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ export interface RpcDriverConstructorArgs {
config: AnyConfigurationModel
}

function isClonable(thing: unknown) {
function isCloneable(thing: unknown) {
return !(typeof thing === 'function') && !(thing instanceof Error)
}

Expand Down Expand Up @@ -110,11 +110,11 @@ export default abstract class BaseRpcDriver {
this.config = args.config
}

// filter the given object and just remove any non-clonable things from it
// filter the given object and just remove any non-cloneable things from it
filterArgs<THING_TYPE>(thing: THING_TYPE, sessionId: string): THING_TYPE {
if (Array.isArray(thing)) {
return thing
.filter(thing => isClonable(thing))
.filter(thing => isCloneable(thing))
.map(t => this.filterArgs(t, sessionId)) as unknown as THING_TYPE
}
if (typeof thing === 'object' && thing !== null) {
Expand All @@ -138,7 +138,7 @@ export default abstract class BaseRpcDriver {

return Object.fromEntries(
Object.entries(thing)
.filter(e => isClonable(e[1]))
.filter(e => isCloneable(e[1]))
.map(([k, v]) => [k, this.filterArgs(v, sessionId)]),
) as THING_TYPE
}
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4 changes: 2 additions & 2 deletions packages/core/util/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -1320,15 +1320,15 @@ export function localStorageSetItem(str: string, item: string) {
export function max(arr: number[], init = Number.NEGATIVE_INFINITY) {
let max = init
for (const entry of arr) {
max = entry > max ? entry : max
max = Math.max(entry, max)
}
return max
}

export function min(arr: number[], init = Number.POSITIVE_INFINITY) {
let min = init
for (const entry of arr) {
min = entry < min ? entry : min
min = Math.min(entry, min)
}
return min
}
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38 changes: 19 additions & 19 deletions plugins/alignments/src/AlignmentsFeatureDetail/__snapshots__/index.test.tsx.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -3,38 +3,38 @@
exports[`open up a widget 1`] = `
<div>
<div
class="MuiPaper-root MuiPaper-elevation MuiPaper-rounded MuiPaper-elevation1 css-1dtoofl-MuiPaper-root"
class="MuiPaper-root MuiPaper-elevation MuiPaper-rounded MuiPaper-elevation1 css-1gtchvp-MuiPaper-root"
data-testid="alignment-side-drawer"
style="--Paper-shadow: 0px 2px 1px -1px rgba(0,0,0,0.2),0px 1px 1px 0px rgba(0,0,0,0.14),0px 1px 3px 0px rgba(0,0,0,0.12);"
>
<div
class="MuiPaper-root MuiPaper-elevation MuiPaper-rounded MuiPaper-elevation1 MuiAccordion-root MuiAccordion-rounded Mui-expanded css-fgq1ej-MuiPaper-root-MuiAccordion-root"
class="MuiPaper-root MuiPaper-elevation MuiPaper-rounded MuiPaper-elevation1 MuiAccordion-root MuiAccordion-rounded Mui-expanded css-9g9pc9-MuiPaper-root-MuiAccordion-root"
style="--Paper-shadow: 0px 2px 1px -1px rgba(0,0,0,0.2),0px 1px 1px 0px rgba(0,0,0,0.14),0px 1px 3px 0px rgba(0,0,0,0.12);"
>
<h3
class="MuiAccordion-heading css-rolk5j-MuiAccordion-heading"
class="MuiAccordion-heading css-cy7rkm-MuiAccordion-heading"
>
<div
aria-expanded="true"
class="MuiButtonBase-root MuiAccordionSummary-root Mui-expanded css-1yigmdy-MuiButtonBase-root-MuiAccordionSummary-root"
class="MuiButtonBase-root MuiAccordionSummary-root Mui-expanded css-t1q4kr-MuiButtonBase-root-MuiAccordionSummary-root"
role="button"
tabindex="0"
>
<div
class="MuiAccordionSummary-content Mui-expanded css-1rhnrrr-MuiAccordionSummary-content"
class="MuiAccordionSummary-content Mui-expanded css-rof4d7-MuiAccordionSummary-content"
>
<span
class="MuiTypography-root MuiTypography-button css-xin9dq-MuiTypography-root"
class="MuiTypography-root MuiTypography-button css-l5w3u1-MuiTypography-root"
>
ctgA_3_555_0:0:0_2:0... - match
</span>
</div>
<div
class="MuiAccordionSummary-expandIconWrapper Mui-expanded css-yw020d-MuiAccordionSummary-expandIconWrapper"
class="MuiAccordionSummary-expandIconWrapper Mui-expanded css-1wqf3nl-MuiAccordionSummary-expandIconWrapper"
>
<svg
aria-hidden="true"
class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-1u842hp-MuiSvgIcon-root-icon"
class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-1qtxdat-MuiSvgIcon-root-icon"
data-testid="ExpandMoreIcon"
focusable="false"
viewBox="0 0 24 24"
Expand All @@ -47,24 +47,24 @@ exports[`open up a widget 1`] = `
</div>
</h3>
<div
class="MuiCollapse-root MuiCollapse-vertical MuiCollapse-entered css-wz2cs5-MuiCollapse-root"
class="MuiCollapse-root MuiCollapse-vertical MuiCollapse-entered css-qr6njo-MuiCollapse-root"
style="min-height: 0px;"
>
<div
class="MuiCollapse-wrapper MuiCollapse-vertical css-smkl36-MuiCollapse-wrapper"
class="MuiCollapse-wrapper MuiCollapse-vertical css-1x6hinx-MuiCollapse-wrapper"
>
<div
class="MuiCollapse-wrapperInner MuiCollapse-vertical css-9l5vo-MuiCollapse-wrapperInner"
class="MuiCollapse-wrapperInner MuiCollapse-vertical css-1i4ywhz-MuiCollapse-wrapperInner"
>
<div
class="MuiAccordion-region"
role="region"
>
<div
class="MuiAccordionDetails-root css-mz6w4y-MuiAccordionDetails-root-expansionPanelDetails"
class="MuiAccordionDetails-root css-1eji0yd-MuiAccordionDetails-root-expansionPanelDetails"
>
<p
class="MuiTypography-root MuiTypography-body1 css-1ptewxf-MuiTypography-root"
class="MuiTypography-root MuiTypography-body1 css-1xfjy4j-MuiTypography-root"
>
Core details
</p>
Expand Down Expand Up @@ -131,10 +131,10 @@ exports[`open up a widget 1`] = `
</div>
</div>
<hr
class="MuiDivider-root MuiDivider-fullWidth css-9mgopn-MuiDivider-root"
class="MuiDivider-root MuiDivider-fullWidth css-1jpc804-MuiDivider-root"
/>
<p
class="MuiTypography-root MuiTypography-body1 css-1ptewxf-MuiTypography-root"
class="MuiTypography-root MuiTypography-body1 css-1xfjy4j-MuiTypography-root"
>
Attributes
</p>
Expand Down Expand Up @@ -289,24 +289,24 @@ exports[`open up a widget 1`] = `
class="css-57ilie-container"
>
<div
class="MuiFormControl-root MuiFormControl-marginDense css-1pquc22-MuiFormControl-root-formControl"
class="MuiFormControl-root MuiFormControl-marginDense css-h2948o-MuiFormControl-root-formControl"
>
<button
class="MuiButtonBase-root MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeSmall MuiButton-containedSizeSmall MuiButton-colorPrimary MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeSmall MuiButton-containedSizeSmall MuiButton-colorPrimary css-qy5lo8-MuiButtonBase-root-MuiButton-root"
class="MuiButtonBase-root MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeSmall MuiButton-containedSizeSmall MuiButton-colorPrimary MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeSmall MuiButton-containedSizeSmall MuiButton-colorPrimary css-12qtcjg-MuiButtonBase-root-MuiButton-root"
tabindex="0"
type="button"
>
Show feature sequence
</button>
</div>
<button
class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-16y463b-MuiButtonBase-root-MuiIconButton-root"
class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-1thuchg-MuiButtonBase-root-MuiIconButton-root"
tabindex="0"
type="button"
>
<svg
aria-hidden="true"
class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-l9ansn-MuiSvgIcon-root"
class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-14500qs-MuiSvgIcon-root"
data-testid="HelpIcon"
focusable="false"
viewBox="0 0 24 24"
Expand Down
2 changes: 1 addition & 1 deletion plugins/alignments/src/PileupRenderer/renderMismatches.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -151,7 +151,7 @@ export function renderMismatches({
ctx,
Math.max(0, leftPx),
topPx + heightPx / 2 - 1,
adjustPx + (leftPx < 0 ? leftPx : 0),
adjustPx + Math.min(leftPx, 0),
2,
canvasWidth,
'#333',
Expand Down
4 changes: 2 additions & 2 deletions plugins/circular-view/src/CircularView/models/__snapshots__/slices.test.ts.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -41,14 +41,14 @@ exports[`two slices 1`] = `
"bpPerRadian": 3183.098861837907,
"endRadians": 6.288185307179586,
"flipped": false,
"key": "{wow}teest:1..10,000",
"key": "{wow}test:1..10,000",
"offsetRadians": 3.146592653589793,
"radianWidth": 3.146592653589793,
"region": {
"assemblyName": "wow",
"elided": true,
"end": 10000,
"refName": "teest",
"refName": "test",
"start": 0,
"widthBp": 10000,
},
Expand Down
2 changes: 1 addition & 1 deletion plugins/circular-view/src/CircularView/models/slices.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ test('two slices', () => {
{
elided: true,
assemblyName: 'wow',
refName: 'teest',
refName: 'test',
start: 0,
end: 10000,
widthBp: 10000,
Expand Down
8 changes: 4 additions & 4 deletions plugins/comparative-adapters/src/DeltaAdapter/util.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -77,10 +77,10 @@ export function paf_delta2paf(buffer: Buffer) {
const t3 = +t[3]!
const t4 = +t[4]!
strand = (t0 < t1 && t2 < t3) || (t0 > t1 && t2 > t3) ? 1 : -1
rs = +(t0 < t1 ? t0 : t1) - 1
re = +(t1 > t0 ? t1 : t0)
qs = +(t2 < t3 ? t2 : t3) - 1
qe = +(t3 > t2 ? t3 : t2)
rs = +Math.min(t0, t1) - 1
re = +Math.max(t1, t0)
qs = +Math.min(t2, t3) - 1
qe = +Math.max(t3, t2)
x = y = 0
NM = t4
cigar = []
Expand Down
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