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Update snaps
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@cmdcolin
cmdcolin committed Sep 11, 2024
1 parent 1e588ae commit 884e638
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Showing 14 changed files with 22 additions and 34 deletions.
1 change: 1 addition & 0 deletions component_tests/cgv/package.json
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Expand Up @@ -42,6 +42,7 @@
"@jbrowse/plugin-variants": "file:./packed/jbrowse-plugin-variants.tgz",
"@jbrowse/plugin-wiggle": "file:./packed/jbrowse-plugin-wiggle.tgz",
"@jbrowse/product-core": "file:./packed/jbrowse-product-core.tgz",
"@jbrowse/sv-core": "file:./packed/jbrowse-sv-core.tgz",
"@jbrowse/embedded-core": "file:./packed/jbrowse-embedded-core.tgz",
"@jbrowse/react-linear-genome-view": "file:./packed/jbrowse-react-linear-genome-view.tgz",
"@jbrowse/react-circular-genome-view": "file:./packed/jbrowse-react-circular-genome-view.tgz"
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1 change: 1 addition & 0 deletions component_tests/lgv/package.json
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Expand Up @@ -42,6 +42,7 @@
"@jbrowse/plugin-variants": "file:./packed/jbrowse-plugin-variants.tgz",
"@jbrowse/plugin-wiggle": "file:./packed/jbrowse-plugin-wiggle.tgz",
"@jbrowse/product-core": "file:./packed/jbrowse-product-core.tgz",
"@jbrowse/sv-core": "file:./packed/jbrowse-sv-core.tgz",
"@jbrowse/embedded-core": "file:./packed/jbrowse-embedded-core.tgz",
"@jbrowse/react-linear-genome-view": "file:./packed/jbrowse-react-linear-genome-view.tgz"
},
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1 change: 1 addition & 0 deletions component_tests/react-app/package.json
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Expand Up @@ -55,6 +55,7 @@
"@jbrowse/plugin-spreadsheet-view": "file:./packed/jbrowse-plugin-spreadsheet-view.tgz",
"@jbrowse/plugin-sv-inspector": "file:./packed/jbrowse-plugin-sv-inspector.tgz",
"@jbrowse/app-core": "file:./packed/jbrowse-app-core.tgz",
"@jbrowse/sv-core": "file:./packed/jbrowse-sv-core.tgz",
"@jbrowse/product-core": "file:./packed/jbrowse-product-core.tgz",
"@jbrowse/web-core": "file:./packed/jbrowse-web-core.tgz"
},
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18 changes: 9 additions & 9 deletions plugins/variants/src/VariantFeatureWidget/VariantFeatureWidget.tsx
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Expand Up @@ -69,7 +69,7 @@ const VariantFeatureWidget = observer(function (props: {
const { model } = props
const { featureData, descriptions } = model
const feat = JSON.parse(JSON.stringify(featureData))
const { samples, ALT, ...rest } = feat
const { samples, ALT, type = '', ...rest } = feat

return (
<Paper data-testid="variant-side-drawer">
Expand All @@ -81,7 +81,7 @@ const VariantFeatureWidget = observer(function (props: {
<CsqPanel feature={rest} descriptions={descriptions} />
<AnnPanel feature={rest} descriptions={descriptions} />
<Suspense fallback={null}>
{feat.type === 'breakend' ? (
{type === 'breakend' ? (
<LaunchBreakendPanel
feature={feat}
locStrings={feat.ALT.map(
Expand All @@ -90,25 +90,25 @@ const VariantFeatureWidget = observer(function (props: {
model={model}
/>
) : null}
{feat.type === 'translocation' ? (
{type === 'translocation' ? (
<LaunchBreakendPanel
feature={feat}
model={model}
locStrings={[`${feat.INFO.CHR2[0]}:${feat.INFO.END}`]}
/>
) : null}
{feat.type === 'paired_feature' ? (
{type === 'paired_feature' ? (
<LaunchBreakendPanel
feature={feat}
model={model}
locStrings={[`${feat.mate.refName}:${feat.mate.start}`]}
/>
) : null}
{feat.type.includes('inversion') ||
feat.type.includes('deletion') ||
feat.type.includes('duplication') ||
feat.type.includes('cnv') ||
feat.type.includes('sv') ? (
{type.includes('inversion') ||
type.includes('deletion') ||
type.includes('duplication') ||
type.includes('cnv') ||
type.includes('sv') ? (
<LaunchBreakendPanel
feature={{
uniqueId: 'random',
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18 changes: 0 additions & 18 deletions plugins/variants/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.tsx.snap
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Expand Up @@ -140,24 +140,6 @@ exports[`renders with just the required model elements 1`] = `
</span>
</div>
</div>
<div
class="css-1m8nxnb-field"
>
<div
aria-label="alternate base(s): Comma-separated list of alternate non-reference alleles"
class="css-167enf1-fieldDescription-fieldName"
data-mui-internal-clone-element="true"
>
ALT
</div>
<div
class="css-xb19vs-fieldValue"
>
<span>
&lt;TRA&gt;
</span>
</div>
</div>
<div
class="css-1m8nxnb-field"
>
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2 changes: 1 addition & 1 deletion plugins/variants/src/VcfFeature/util.ts
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Expand Up @@ -5,7 +5,7 @@ const altTypeToSO: Record<string, string> = {
INS: 'insertion',
DUP: 'duplication',
INV: 'inversion',
INVDUP: 'inverted duplication',
INVDUP: 'inverted_duplication',
CNV: 'copy_number_variation',
TRA: 'translocation',
'DUP:TANDEM': 'tandem_duplication',
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Binary file modified ...-arcs-test-tsx-toggle-short-read-arc-display-use-out-of-view-pairing-1-snap.png
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Binary file modified ..._snapshots__/alignment-arcs-test-tsx-toggle-short-read-cloud-display-1-snap.png
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2 changes: 1 addition & 1 deletion ...ts/jbrowse-web/src/tests/__image_snapshots__/breakpoint_split_view_snapshot.svg
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6 changes: 4 additions & 2 deletions products/jbrowse-web/src/tests/__snapshots__/BreakpointSplitView.test.tsx.snap
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Expand Up @@ -4,17 +4,19 @@ exports[`breakpoint split view 1`] = `
<g
data-testid="pacbio_hg002_breakpoints-loaded"
fill="none"
stroke="#000000"
stroke-opacity="0.38"
>
<path
d="M 407.99312656000257 75.5 C 607.9931265600026 75.5 203.41868021525443 84.5 403.4186802152544 84.5"
data-testid="r1"
stroke="#000000"
stroke-opacity="0.38"
stroke-width="1"
/>
<path
d="M 660.4186802152544 84.5 C 860.4186802152544 84.5 206.99312656000257 48.5 406.99312656000257 48.5"
data-testid="r1"
stroke="#000000"
stroke-opacity="0.38"
stroke-width="1"
/>
</g>
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2 changes: 1 addition & 1 deletion products/jbrowse-web/src/tests/__snapshots__/ExportSvgBreakpointSplitView.test.tsx.snap
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2 changes: 1 addition & 1 deletion test_data/volvox/trix/volvox-rev-del_meta.json
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@@ -1,5 +1,5 @@
{
"dateCreated": "2023-09-07T19:05:43.767Z",
"dateCreated": "2024-09-11T21:23:34.442Z",
"tracks": [
{
"trackId": "volvox-rev-del-annotations",
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1 change: 1 addition & 0 deletions test_data/volvox/trix/volvox.ix
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Expand Up @@ -77,6 +77,7 @@ ig-like ["ctgA%3A33325..35791"|"gff3tabix_genes"|"m04"|"Ig-like"],1
inv133 ["ctgA%3A1..1000"|"volvox.inv.vcf"|"inv133"],1
inv134 ["ctgA%3A2700..10000"|"volvox.inv.vcf"|"inv134"],1
inv135 ["ctgA%3A6000..9000"|"volvox.inv.vcf"|"inv135"],1 ["ctgA%3A6000..9000"|"volvox.inv.vcf"|"inv135"],2
inv136 ["ctgA%3A19848..30074"|"volvox.inv.vcf"|"inv136"],1
inv9000 ["ctgA%3A6000..9000"|"volvox.inv.vcf"|"inv9000"],1
is ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],2 ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],3 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],4 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],5
kinase ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN"|"EDEN"|"protein%20kinase"],1 ["ctgA%3A11911..15561"|"gff3tabix_genes"|"m11"|"kinase"],2 ["ctgA%3A14731..17239"|"gff3tabix_genes"|"m14"|"kinase"],3 ["ctgA%3A21748..25612"|"gff3tabix_genes"|"m12"|"kinase"],4 ["ctgA%3A46012..48851"|"gff3tabix_genes"|"m09"|"kinase"],5
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2 changes: 1 addition & 1 deletion test_data/volvox/trix/volvox_meta.json
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@@ -1,5 +1,5 @@
{
"dateCreated": "2023-09-07T19:05:43.740Z",
"dateCreated": "2024-09-11T21:23:34.423Z",
"tracks": [
{
"trackId": "volvox_sv_test",
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