@genspectrum/dashboard-components 1.16.0 → 1.18.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/custom-elements.json +7 -7
- package/dist/components.d.ts +145 -45
- package/dist/components.js +524 -291
- package/dist/components.js.map +1 -1
- package/dist/util.d.ts +215 -55
- package/package.json +1 -1
- package/src/preact/MutationAnnotationsContext.spec.tsx +82 -10
- package/src/preact/MutationAnnotationsContext.tsx +93 -45
- package/src/preact/components/annotated-mutation.stories.tsx +31 -0
- package/src/preact/components/annotated-mutation.tsx +5 -5
- package/src/preact/components/csv-download-button.tsx +22 -14
- package/src/preact/components/features-over-time-grid.tsx +189 -43
- package/src/preact/components/mutations-over-time-mutations-filter.stories.tsx +1 -1
- package/src/preact/components/mutations-over-time-mutations-filter.tsx +1 -1
- package/src/preact/mutationsOverTime/__mockData__/aminoAcidMutationsByDay/aminoAcidMutationsOverTimePage1.json +52 -0
- package/src/preact/mutationsOverTime/__mockData__/byWeek/mutationsOverTimePage1.json +76 -0
- package/src/preact/mutationsOverTime/__mockData__/defaultMockData/mockDefaultMutationsOverTimeWithFilter.json +43 -0
- package/src/preact/mutationsOverTime/__mockData__/defaultMockData/mutationsOverTimePage1.json +126 -0
- package/src/preact/mutationsOverTime/__mockData__/defaultMockData/mutationsOverTimePage2.json +116 -0
- package/src/preact/mutationsOverTime/__mockData__/defaultMockData/mutationsOverTimePageSize20.json +216 -0
- package/src/preact/mutationsOverTime/getFilteredMutationCodes.spec.ts +236 -0
- package/src/preact/mutationsOverTime/{getFilteredMutationsOverTimeData.ts → getFilteredMutationCodes.ts} +34 -49
- package/src/preact/mutationsOverTime/mutations-over-time.stories.tsx +128 -23
- package/src/preact/mutationsOverTime/mutations-over-time.tsx +139 -74
- package/src/preact/mutationsOverTime/useMutationsOverTimePageData.ts +111 -0
- package/src/preact/shared/tanstackTable/pagination-context.tsx +5 -2
- package/src/preact/shared/tanstackTable/pagination.tsx +11 -9
- package/src/preact/shared/tanstackTable/tanstackTable.tsx +7 -4
- package/src/preact/wastewater/mutationsOverTime/wastewater-mutations-over-time.tsx +1 -1
- package/src/query/queryMutationsOverTime.spec.ts +187 -662
- package/src/query/queryMutationsOverTime.ts +46 -33
- package/src/utils/useControlledState.ts +15 -0
- package/src/web-components/gs-app.ts +8 -4
- package/src/web-components/mutation-annotations-context.ts +13 -5
- package/src/web-components/mutationAnnotations.mdx +29 -0
- package/src/web-components/visualization/gs-mutations-over-time.stories.ts +78 -22
- package/standalone-bundle/dashboard-components.js +6914 -6701
- package/standalone-bundle/dashboard-components.js.map +1 -1
- package/src/preact/mutationsOverTime/__mockData__/aminoAcidMutationsByDay/aminoAcidMutationsOverTime.json +0 -5496
- package/src/preact/mutationsOverTime/__mockData__/byWeek/mutationsOverTime.json +0 -7100
- package/src/preact/mutationsOverTime/__mockData__/defaultMockData/mutationsOverTime.json +0 -12646
- package/src/preact/mutationsOverTime/getFilteredMutationsOverTime.spec.ts +0 -417
package/dist/components.js
CHANGED
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@@ -11,7 +11,7 @@ import { Chart, registerables, Scale, BarController } from "chart.js";
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import { VennDiagramController, ArcSlice, extractSets } from "chartjs-chart-venn";
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import { autoUpdate, computePosition, offset, shift, flip } from "@floating-ui/dom";
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import { BarWithErrorBarsController, BarWithErrorBar } from "chartjs-chart-error-bars";
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import { createTable,
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import { createTable, getPaginationRowModel, getCoreRowModel, createColumnHelper } from "@tanstack/table-core";
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import { map, geoJson } from "leaflet";
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import * as topojson from "topojson-client";
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import flatpickr from "flatpickr";
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@@ -332,15 +332,22 @@ function n$1(t2) {
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})(t2, e2, o2);
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}
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const lapisContext = createContext("lapis-context");
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const
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const mutationEntrySchema = z$2.union([
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z$2.string(),
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z$2.object({ mutation: z$2.string(), name: z$2.string().optional(), description: z$2.string().optional() })
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]);
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const positionEntrySchema = z$2.union([
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z$2.string(),
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z$2.object({ position: z$2.string(), name: z$2.string().optional(), description: z$2.string().optional() })
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]);
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const mutationAnnotationSchema = z$2.object({
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name: z$2.string(),
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description: z$2.string(),
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symbol: z$2.string(),
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nucleotideMutations:
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nucleotidePositions:
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aminoAcidMutations:
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aminoAcidPositions:
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nucleotideMutations: z$2.array(mutationEntrySchema).optional(),
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nucleotidePositions: z$2.array(positionEntrySchema).optional(),
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aminoAcidMutations: z$2.array(mutationEntrySchema).optional(),
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aminoAcidPositions: z$2.array(positionEntrySchema).optional()
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});
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const mutationAnnotationsSchema = z$2.array(mutationAnnotationSchema, {
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errorMap: () => ({ message: "invalid mutation annotations" })
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@@ -2070,7 +2077,7 @@ function replaceCssProperties(styleSheet2) {
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}
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}
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const tailwindStyle = `/*! tailwindcss v4.1.11 | MIT License | https://tailwindcss.com */
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--tw-outline-style{syntax:"*";inherits:false;initial-value:solid}@property --tw-blur{syntax:"*";inherits:false}@property --tw-brightness{syntax:"*";inherits:false}@property --tw-contrast{syntax:"*";inherits:false}@property --tw-grayscale{syntax:"*";inherits:false}@property --tw-hue-rotate{syntax:"*";inherits:false}@property --tw-invert{syntax:"*";inherits:false}@property --tw-opacity{syntax:"*";inherits:false}@property --tw-saturate{syntax:"*";inherits:false}@property --tw-sepia{syntax:"*";inherits:false}@property --tw-drop-shadow{syntax:"*";inherits:false}@property --tw-drop-shadow-color{syntax:"*";inherits:false}@property --tw-drop-shadow-alpha{syntax:"<percentage>";inherits:false;initial-value:100%}@property --tw-drop-shadow-size{syntax:"*";inherits:false}@property --tw-duration{syntax:"*";inherits:false}@property --tw-scale-x{syntax:"*";inherits:false;initial-value:1}@property --tw-scale-y{syntax:"*";inherits:false;initial-value:1}@property --tw-scale-z{syntax:"*";inherits:false;initial-value:1}
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repeatCount='indefinite'/%3E%3C/circle%3E%3C/g%3E%3C/svg%3E")}.p-0{padding:calc(var(--spacing)*0)}.p-1{padding:calc(var(--spacing)*1)}.p-1\\.5{padding:calc(var(--spacing)*1.5)}.p-2{padding:calc(var(--spacing)*2)}.p-4{padding:calc(var(--spacing)*4)}.px-1{padding-inline:calc(var(--spacing)*1)}.px-2{padding-inline:calc(var(--spacing)*2)}.px-3{padding-inline:calc(var(--spacing)*3)}.px-4{padding-inline:calc(var(--spacing)*4)}.py-0\\.5{padding-block:calc(var(--spacing)*.5)}.py-1{padding-block:calc(var(--spacing)*1)}.py-2{padding-block:calc(var(--spacing)*2)}.py-16{padding-block:calc(var(--spacing)*16)}.pr-14{padding-right:calc(var(--spacing)*14)}.text-center{text-align:center}.text-justify{text-align:justify}.text-left{text-align:left}.text-right{text-align:right}.text-2xl{font-size:var(--text-2xl);line-height:var(--tw-leading,var(--text-2xl--line-height))}.text-base{font-size:var(--text-base);line-height:var(--tw-leading,var(--text-base--line-height))}.text-lg{font-size:var(--text-lg);line-height:var(--tw-leading,var(--text-lg--line-height))}.text-sm{font-size:var(--text-sm);line-height:var(--tw-leading,var(--text-sm--line-height))}.text-xl{font-size:var(--text-xl);line-height:var(--tw-leading,var(--text-xl--line-height))}.text-xs{font-size:var(--text-xs);line-height:var(--tw-leading,var(--text-xs--line-height))}.select-sm{--size:calc(var(--size-field,.25rem)*8);font-size:.75rem}.select-xs{--size:calc(var(--size-field,.25rem)*6);font-size:.6875rem}.leading-5{--tw-leading:calc(var(--spacing)*5);line-height:calc(var(--spacing)*5)}.font-bold{--tw-font-weight:var(--font-weight-bold);font-weight:var(--font-weight-bold)}.font-medium{--tw-font-weight:var(--font-weight-medium);font-weight:var(--font-weight-medium)}.font-normal{--tw-font-weight:var(--font-weight-normal);font-weight:var(--font-weight-normal)}.text-nowrap{text-wrap:nowrap}.text-wrap{text-wrap:wrap}.break-words{overflow-wrap:break-word}.whitespace-nowrap{white-space:nowrap}.whitespace-pre-wrap{white-space:pre-wrap}.text-\\[\\#606060\\]{color:#606060}.text-black{color:var(--color-black)}.text-blue-600{color:var(--color-blue-600)}.text-gray-500{color:var(--color-gray-500)}.text-gray-600{color:var(--color-gray-600)}.text-gray-700{color:var(--color-gray-700)}.text-neutral-500{color:var(--color-neutral-500)}.text-red-600{color:var(--color-red-600)}.text-red-700{color:var(--color-red-700)}.text-white{color:var(--color-white)}.capitalize{text-transform:capitalize}.lowercase{text-transform:lowercase}.underline{text-decoration-line:underline}.decoration-red-600{text-decoration-color:var(--color-red-600)}.shadow{--tw-shadow:0 1px 3px 0 var(--tw-shadow-color,#0000001a),0 1px 2px -1px var(--tw-shadow-color,#0000001a);box-shadow:var(--tw-inset-shadow),var(--tw-inset-ring-shadow),var(--tw-ring-offset-shadow),var(--tw-ring-shadow),var(--tw-shadow)}.shadow-lg{--tw-shadow:0 10px 15px -3px var(--tw-shadow-color,#0000001a),0 4px 6px -4px var(--tw-shadow-color,#0000001a);box-shadow:var(--tw-inset-shadow),var(--tw-inset-ring-shadow),var(--tw-ring-offset-shadow),var(--tw-ring-shadow),var(--tw-shadow)}.shadow-md{--tw-shadow:0 4px 6px -1px var(--tw-shadow-color,#0000001a),0 2px 4px -2px var(--tw-shadow-color,#0000001a);box-shadow:var(--tw-inset-shadow),var(--tw-inset-ring-shadow),var(--tw-ring-offset-shadow),var(--tw-ring-shadow),var(--tw-shadow)}.shadow-sm{--tw-shadow:0 1px 3px 0 var(--tw-shadow-color,#0000001a),0 1px 2px -1px var(--tw-shadow-color,#0000001a);box-shadow:var(--tw-inset-shadow),var(--tw-inset-ring-shadow),var(--tw-ring-offset-shadow),var(--tw-ring-shadow),var(--tw-shadow)}.shadow-xs{--tw-shadow:0 1px 2px 0 var(--tw-shadow-color,#0000000d);box-shadow:var(--tw-inset-shadow),var(--tw-inset-ring-shadow),var(--tw-ring-offset-shadow),var(--tw-ring-shadow),var(--tw-shadow)}.outline{outline-style:var(--tw-outline-style);outline-width:1px}.btn-ghost:not(.btn-active,:hover,:active:focus,:focus-visible){--btn-shadow:"";--btn-bg:#0000;--btn-border:#0000;--btn-noise:none}.btn-ghost:not(.btn-active,:hover,:active:focus,:focus-visible):not(:disabled,[disabled],.btn-disabled){--btn-fg:currentColor;outline-color:currentColor}@media (hover:none){.btn-ghost:hover:not(.btn-active,:active,:focus-visible,:disabled,[disabled],.btn-disabled){--btn-shadow:"";--btn-bg:#0000;--btn-border:#0000;--btn-noise:none;--btn-fg:currentColor}}.blur{--tw-blur:blur(8px);filter:var(--tw-blur,)var(--tw-brightness,)var(--tw-contrast,)var(--tw-grayscale,)var(--tw-hue-rotate,)var(--tw-invert,)var(--tw-saturate,)var(--tw-sepia,)var(--tw-drop-shadow,)}.filter{filter:var(--tw-blur,)var(--tw-brightness,)var(--tw-contrast,)var(--tw-grayscale,)var(--tw-hue-rotate,)var(--tw-invert,)var(--tw-saturate,)var(--tw-sepia,)var(--tw-drop-shadow,)}.transition-colors{transition-property:color,background-color,border-color,outline-color,text-decoration-color,fill,stroke,--tw-gradient-from,--tw-gradient-via,--tw-gradient-to;transition-timing-function:var(--tw-ease,var(--default-transition-timing-function));transition-duration:var(--tw-duration,var(--default-transition-duration))}.duration-150{--tw-duration:.15s;transition-duration:.15s}.btn-outline:not(.btn-active,:hover,:active:focus,:focus-visible,:disabled,[disabled],.btn-disabled,:checked){--btn-shadow:"";--btn-bg:#0000;--btn-fg:var(--btn-color);--btn-border:var(--btn-color);--btn-noise:none}@media (hover:none){.btn-outline:hover:not(.btn-active,:active,:focus-visible,:disabled,[disabled],.btn-disabled,:checked){--btn-shadow:"";--btn-bg:#0000;--btn-fg:var(--btn-color);--btn-border:var(--btn-color);--btn-noise:none}}.btn-sm{--fontsize:.75rem;--btn-p:.75rem;--size:calc(var(--size-field,.25rem)*8)}.btn-xs{--fontsize:.6875rem;--btn-p:.5rem;--size:calc(var(--size-field,.25rem)*6)}.select-text{-webkit-user-select:text;-moz-user-select:text;user-select:text}.input-error,.input-error:focus,.input-error:focus-within{--input-color:var(--color-error)}.mdi--chevron-left{--svg:url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 24 24' width='24' height='24'%3E%3Cpath fill='black' d='M15.41 16.58L10.83 12l4.58-4.59L14 6l-6 6l6 6z'/%3E%3C/svg%3E")}.mdi--chevron-left-first{--svg:url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 24 24' width='24' height='24'%3E%3Cpath fill='black' d='M18.41 16.59L13.82 12l4.59-4.59L17 6l-6 6l6 6zM6 6h2v12H6z'/%3E%3C/svg%3E")}.mdi--chevron-right{--svg:url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 24 24' width='24' height='24'%3E%3Cpath fill='black' d='M8.59 16.58L13.17 12L8.59 7.41L10 6l6 6l-6 6z'/%3E%3C/svg%3E")}.mdi--chevron-right-last{--svg:url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 24 24' width='24' height='24'%3E%3Cpath fill='black' d='M5.59 7.41L10.18 12l-4.59 4.59L7 18l6-6l-6-6zM16 6h2v12h-2z'/%3E%3C/svg%3E")}.mdi--fullscreen{--svg:url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 24 24' width='24' height='24'%3E%3Cpath fill='black' d='M5 5h5v2H7v3H5zm9 0h5v5h-2V7h-3zm3 9h2v5h-5v-2h3zm-7 3v2H5v-5h2v3z'/%3E%3C/svg%3E")}.mdi--fullscreen-exit{--svg:url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 24 24' width='24' height='24'%3E%3Cpath fill='black' d='M14 14h5v2h-3v3h-2zm-9 0h5v5H8v-3H5zm3-9h2v5H5V8h3zm11 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*){visibility:visible}.hover\\:scale-90:hover{--tw-scale-x:90%;--tw-scale-y:90%;--tw-scale-z:90%;scale:var(--tw-scale-x)var(--tw-scale-y)}.hover\\:scale-110:hover{--tw-scale-x:110%;--tw-scale-y:110%;--tw-scale-z:110%;scale:var(--tw-scale-x)var(--tw-scale-y)}.hover\\:bg-gray-100:hover{background-color:var(--color-gray-100)}.hover\\:font-bold:hover{--tw-font-weight:var(--font-weight-bold);font-weight:var(--font-weight-bold)}.hover\\:text-blue-700:hover{color:var(--color-blue-700)}.hover\\:text-blue-800:hover{color:var(--color-blue-800)}.hover\\:text-gray-400:hover{color:var(--color-gray-400)}.hover\\:text-gray-700:hover{color:var(--color-gray-700)}.hover\\:text-red-600:hover{color:var(--color-red-600)}.hover\\:underline:hover{text-decoration-line:underline}.hover\\:opacity-80:hover{opacity:.8}}.focus\\:ring-2:focus{--tw-ring-shadow:var(--tw-ring-inset,)0 0 0 calc(2px + var(--tw-ring-offset-width))var(--tw-ring-color,currentcolor);box-shadow:var(--tw-inset-shadow),var(--tw-inset-ring-shadow),var(--tw-ring-offset-shadow),var(--tw-ring-shadow),var(--tw-shadow)}.focus\\:ring-blue-300:focus{--tw-ring-color:var(--color-blue-300)}.focus\\:outline-none:focus{--tw-outline-style:none;outline-style:none}.focus-visible\\:underline:focus-visible{text-decoration-line:underline}@media (min-width:40rem){.sm\\:modal-middle{place-items:center}.sm\\:modal-middle :where(.modal-box){--modal-tl:var(--radius-box);--modal-tr:var(--radius-box);--modal-bl:var(--radius-box);--modal-br:var(--radius-box);width:91.6667%;max-width:32rem;height:auto;max-height:calc(100vh - 5em);translate:0 2%;scale:98%}.sm\\:max-w-5xl{max-width:var(--container-5xl)}.sm\\:flex-row{flex-direction:row}.sm\\:text-4xl{font-size:var(--text-4xl);line-height:var(--tw-leading,var(--text-4xl--line-height))}}@container (min-width:2rem){.\\@\\[2rem\\]\\:visible{visibility:visible}}@container (min-width:6rem){.\\@\\[6rem\\]\\:visible{visibility:visible}}@container (min-width:14rem){.\\@4xs\\:flex-row{flex-direction:row}.\\@4xs\\:rounded-l-none{border-top-left-radius:0;border-bottom-left-radius:0}.\\@4xs\\:rounded-tr-none{border-top-right-radius:0}.\\@4xs\\:rounded-bl-md{border-bottom-left-radius:var(--radius-md)}}@container (min-width:28rem){.\\@md\\:flex-row{flex-direction:row}.\\@md\\:rounded-l-md{border-top-left-radius:var(--radius-md);border-bottom-left-radius:var(--radius-md)}.\\@md\\:rounded-l-none{border-top-left-radius:0;border-bottom-left-radius:0}.\\@md\\:rounded-r-md{border-top-right-radius:var(--radius-md);border-bottom-right-radius:var(--radius-md)}.\\@md\\:rounded-r-none{border-top-right-radius:0;border-bottom-right-radius:0}}@container (min-width:36rem){.\\@xl\\:block{display:block}.\\@xl\\:justify-end{justify-content:flex-end}}}@keyframes progress{50%{background-position-x:-115%}}@keyframes rating{0%,40%{filter:brightness(1.05)contrast(1.05);scale:1.1}}@keyframes skeleton{0%{background-position:150%}to{background-position:-50%}}@keyframes dropdown{0%{opacity:0}}@keyframes radio{0%{padding:5px}50%{padding:3px}}@keyframes toast{0%{opacity:0;scale:.9}to{opacity:1;scale:1}}@property --tw-translate-x{syntax:"*";inherits:false;initial-value:0}@property --tw-translate-y{syntax:"*";inherits:false;initial-value:0}@property --tw-translate-z{syntax:"*";inherits:false;initial-value:0}@property --tw-rotate-x{syntax:"*";inherits:false}@property --tw-rotate-y{syntax:"*";inherits:false}@property --tw-rotate-z{syntax:"*";inherits:false}@property --tw-skew-x{syntax:"*";inherits:false}@property --tw-skew-y{syntax:"*";inherits:false}@property --tw-border-style{syntax:"*";inherits:false;initial-value:solid}@property --tw-leading{syntax:"*";inherits:false}@property --tw-font-weight{syntax:"*";inherits:false}@property --tw-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-shadow-color{syntax:"*";inherits:false}@property --tw-shadow-alpha{syntax:"<percentage>";inherits:false;initial-value:100%}@property --tw-inset-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-inset-shadow-color{syntax:"*";inherits:false}@property --tw-inset-shadow-alpha{syntax:"<percentage>";inherits:false;initial-value:100%}@property --tw-ring-color{syntax:"*";inherits:false}@property --tw-ring-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-inset-ring-color{syntax:"*";inherits:false}@property --tw-inset-ring-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-ring-inset{syntax:"*";inherits:false}@property --tw-ring-offset-width{syntax:"<length>";inherits:false;initial-value:0}@property --tw-ring-offset-color{syntax:"*";inherits:false;initial-value:#fff}@property --tw-ring-offset-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-outline-style{syntax:"*";inherits:false;initial-value:solid}@property --tw-blur{syntax:"*";inherits:false}@property --tw-brightness{syntax:"*";inherits:false}@property --tw-contrast{syntax:"*";inherits:false}@property --tw-grayscale{syntax:"*";inherits:false}@property --tw-hue-rotate{syntax:"*";inherits:false}@property --tw-invert{syntax:"*";inherits:false}@property --tw-opacity{syntax:"*";inherits:false}@property --tw-saturate{syntax:"*";inherits:false}@property --tw-sepia{syntax:"*";inherits:false}@property --tw-drop-shadow{syntax:"*";inherits:false}@property --tw-drop-shadow-color{syntax:"*";inherits:false}@property --tw-drop-shadow-alpha{syntax:"<percentage>";inherits:false;initial-value:100%}@property --tw-drop-shadow-size{syntax:"*";inherits:false}@property --tw-duration{syntax:"*";inherits:false}@property --tw-scale-x{syntax:"*";inherits:false;initial-value:1}@property --tw-scale-y{syntax:"*";inherits:false;initial-value:1}@property --tw-scale-z{syntax:"*";inherits:false;initial-value:1}
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const parseResult = T$1(() => mutationAnnotationsSchema.safeParse(value), [value]);
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const contextValue = T$1(
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const nucleotidePositionMap = /* @__PURE__ */ new Map();
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|
+
function resolve(annotation, entry) {
|
|
2215
|
+
const overrides = typeof entry === "object" ? entry : void 0;
|
|
2216
|
+
return {
|
|
2217
|
+
annotation,
|
|
2218
|
+
name: (overrides == null ? void 0 : overrides.name) ?? annotation.name,
|
|
2219
|
+
description: (overrides == null ? void 0 : overrides.description) ?? annotation.description
|
|
2190
2220
|
};
|
|
2191
2221
|
}
|
|
2192
|
-
function
|
|
2193
|
-
const
|
|
2194
|
-
map2.set(code.toUpperCase(), [...
|
|
2222
|
+
function addToMap(map2, code, resolved) {
|
|
2223
|
+
const existing = map2.get(code.toUpperCase()) ?? [];
|
|
2224
|
+
map2.set(code.toUpperCase(), [...existing, resolved]);
|
|
2195
2225
|
}
|
|
2196
2226
|
function useRawMutationAnnotations() {
|
|
2197
2227
|
return x$1(MutationAnnotationsContext).rawAnnotations;
|
|
2198
2228
|
}
|
|
2199
2229
|
function useMutationAnnotationsProvider() {
|
|
2200
2230
|
const mutationAnnotations = x$1(MutationAnnotationsContext);
|
|
2201
|
-
return getMutationAnnotationsProvider(mutationAnnotations);
|
|
2231
|
+
return T$1(() => getMutationAnnotationsProvider(mutationAnnotations), [mutationAnnotations]);
|
|
2202
2232
|
}
|
|
2203
2233
|
function getMutationAnnotationsProvider(mutationAnnotations) {
|
|
2204
2234
|
return (mutation, sequenceType) => {
|
|
2205
2235
|
const position = mutation.segment === void 0 ? `${mutation.position}` : `${mutation.segment.toUpperCase()}:${mutation.position}`;
|
|
2206
|
-
const
|
|
2207
|
-
const
|
|
2208
|
-
const
|
|
2209
|
-
const
|
|
2210
|
-
return
|
|
2211
|
-
if (
|
|
2236
|
+
const exactMatches = mutationAnnotations[sequenceType].mutation.get(mutation.code.toUpperCase());
|
|
2237
|
+
const positionMatches = mutationAnnotations[sequenceType].position.get(position);
|
|
2238
|
+
const combined = exactMatches && positionMatches ? [...exactMatches, ...positionMatches] : exactMatches ?? positionMatches;
|
|
2239
|
+
const seenNames = /* @__PURE__ */ new Set();
|
|
2240
|
+
return combined == null ? void 0 : combined.filter((resolved) => {
|
|
2241
|
+
if (seenNames.has(resolved.annotation.name)) {
|
|
2212
2242
|
return false;
|
|
2213
2243
|
}
|
|
2214
|
-
|
|
2244
|
+
seenNames.add(resolved.annotation.name);
|
|
2215
2245
|
return true;
|
|
2216
2246
|
});
|
|
2217
2247
|
};
|
|
@@ -2339,10 +2369,10 @@ const AnnotatedMutationWithoutContext = ({
|
|
|
2339
2369
|
"Annotations for ",
|
|
2340
2370
|
mutation.code
|
|
2341
2371
|
] }),
|
|
2342
|
-
mutationAnnotations.map((
|
|
2343
|
-
/* @__PURE__ */ u$1(InfoHeadline2, { children:
|
|
2344
|
-
/* @__PURE__ */ u$1(InfoParagraph, { children: /* @__PURE__ */ u$1("div", { dangerouslySetInnerHTML: { __html: DOMPurify.sanitize(
|
|
2345
|
-
] }, annotation.name))
|
|
2372
|
+
mutationAnnotations.map((resolved) => /* @__PURE__ */ u$1(Fragment, { children: [
|
|
2373
|
+
/* @__PURE__ */ u$1(InfoHeadline2, { children: resolved.name }),
|
|
2374
|
+
/* @__PURE__ */ u$1(InfoParagraph, { children: /* @__PURE__ */ u$1("div", { dangerouslySetInnerHTML: { __html: DOMPurify.sanitize(resolved.description) } }) })
|
|
2375
|
+
] }, resolved.annotation.name))
|
|
2346
2376
|
] });
|
|
2347
2377
|
return /* @__PURE__ */ u$1(Fragment, { children: [
|
|
2348
2378
|
innerLabel,
|
|
@@ -2352,7 +2382,7 @@ const AnnotatedMutationWithoutContext = ({
|
|
|
2352
2382
|
buttonClassName: "select-text cursor-pointer",
|
|
2353
2383
|
modalContent,
|
|
2354
2384
|
modalRef,
|
|
2355
|
-
children: /* @__PURE__ */ u$1("sup", { className: "hover:underline focus-visible:underline decoration-red-600", children: mutationAnnotations.map((
|
|
2385
|
+
children: /* @__PURE__ */ u$1("sup", { className: "hover:underline focus-visible:underline decoration-red-600", children: mutationAnnotations.map((resolved) => resolved.annotation.symbol).map((symbol, index) => /* @__PURE__ */ u$1(Fragment, { children: [
|
|
2356
2386
|
/* @__PURE__ */ u$1("span", { className: "text-red-600", children: symbol }),
|
|
2357
2387
|
index !== mutationAnnotations.length - 1 && ","
|
|
2358
2388
|
] }, symbol)) })
|
|
@@ -2874,18 +2904,24 @@ const CsvDownloadButton = ({
|
|
|
2874
2904
|
getData,
|
|
2875
2905
|
className
|
|
2876
2906
|
}) => {
|
|
2877
|
-
const
|
|
2878
|
-
|
|
2879
|
-
|
|
2880
|
-
|
|
2881
|
-
|
|
2882
|
-
|
|
2883
|
-
|
|
2884
|
-
|
|
2885
|
-
|
|
2907
|
+
const [isDownloading, setIsDownloading] = d(false);
|
|
2908
|
+
const download = async () => {
|
|
2909
|
+
setIsDownloading(true);
|
|
2910
|
+
try {
|
|
2911
|
+
const content = await getDownloadContent();
|
|
2912
|
+
const blob = new Blob([content], { type: "text/csv" });
|
|
2913
|
+
const url = URL.createObjectURL(blob);
|
|
2914
|
+
const a2 = document.createElement("a");
|
|
2915
|
+
a2.href = url;
|
|
2916
|
+
a2.download = filename;
|
|
2917
|
+
a2.click();
|
|
2918
|
+
URL.revokeObjectURL(url);
|
|
2919
|
+
} finally {
|
|
2920
|
+
setIsDownloading(false);
|
|
2921
|
+
}
|
|
2886
2922
|
};
|
|
2887
|
-
const getDownloadContent = () => {
|
|
2888
|
-
const data = getData();
|
|
2923
|
+
const getDownloadContent = async () => {
|
|
2924
|
+
const data = await getData();
|
|
2889
2925
|
const keys = getDataKeys(data);
|
|
2890
2926
|
const header = keys.join(",");
|
|
2891
2927
|
const rows = data.map((row) => keys.map((key) => row[key]).join(",")).join("\n");
|
|
@@ -2900,7 +2936,7 @@ ${rows}
|
|
|
2900
2936
|
}, /* @__PURE__ */ new Set());
|
|
2901
2937
|
return [...keysSet];
|
|
2902
2938
|
};
|
|
2903
|
-
return /* @__PURE__ */ u$1("button", { className, onClick: download, children: label });
|
|
2939
|
+
return /* @__PURE__ */ u$1("button", { className, onClick: () => void download(), disabled: isDownloading, children: isDownloading ? "Downloading..." : label });
|
|
2904
2940
|
};
|
|
2905
2941
|
const Fullscreen = () => {
|
|
2906
2942
|
const element = A$1(null);
|
|
@@ -7236,6 +7272,107 @@ __decorateClass$b([
|
|
|
7236
7272
|
NumberSequencesOverTimeComponent = __decorateClass$b([
|
|
7237
7273
|
t$3("gs-number-sequences-over-time")
|
|
7238
7274
|
], NumberSequencesOverTimeComponent);
|
|
7275
|
+
const displayMutationsSchema = z$2.array(z$2.string(), {
|
|
7276
|
+
errorMap: () => ({ message: `invalid display mutations` })
|
|
7277
|
+
});
|
|
7278
|
+
function getFilteredMutationCodes({
|
|
7279
|
+
overallMutationData,
|
|
7280
|
+
displayedSegments,
|
|
7281
|
+
displayedMutationTypes,
|
|
7282
|
+
proportionInterval,
|
|
7283
|
+
mutationFilterValue,
|
|
7284
|
+
sequenceType,
|
|
7285
|
+
annotationProvider
|
|
7286
|
+
}) {
|
|
7287
|
+
return overallMutationData.filter((entry) => {
|
|
7288
|
+
if (entry.proportion < proportionInterval.min || entry.proportion > proportionInterval.max) {
|
|
7289
|
+
return false;
|
|
7290
|
+
}
|
|
7291
|
+
if (displayedSegments.some((segment) => segment.segment === entry.mutation.segment && !segment.checked)) {
|
|
7292
|
+
return false;
|
|
7293
|
+
}
|
|
7294
|
+
if (mutationOrAnnotationDoNotMatchFilter(
|
|
7295
|
+
entry.mutation,
|
|
7296
|
+
sequenceType,
|
|
7297
|
+
mutationFilterValue,
|
|
7298
|
+
annotationProvider
|
|
7299
|
+
)) {
|
|
7300
|
+
return false;
|
|
7301
|
+
}
|
|
7302
|
+
return !displayedMutationTypes.some(
|
|
7303
|
+
(mutationType2) => mutationType2.type === entry.mutation.type && !mutationType2.checked
|
|
7304
|
+
);
|
|
7305
|
+
}).map((e2) => e2.mutation.code);
|
|
7306
|
+
}
|
|
7307
|
+
function mutationOrAnnotationDoNotMatchFilter(mutation, sequenceType, mutationFilter, annotationProvider) {
|
|
7308
|
+
return !(mutationOrAnnotationMatchesTextFilter(mutation, sequenceType, mutationFilter.textFilter, annotationProvider) && mutationMatchesAnnotationFilter(mutation, sequenceType, mutationFilter.annotationNameFilter, annotationProvider));
|
|
7309
|
+
}
|
|
7310
|
+
function mutationOrAnnotationMatchesTextFilter(mutation, sequenceType, textFilter, annotationProvider) {
|
|
7311
|
+
if (textFilter === "") {
|
|
7312
|
+
return true;
|
|
7313
|
+
}
|
|
7314
|
+
if (mutation.code.includes(textFilter)) {
|
|
7315
|
+
return true;
|
|
7316
|
+
}
|
|
7317
|
+
const mutationAnnotations = annotationProvider(mutation, sequenceType);
|
|
7318
|
+
if (mutationAnnotations === void 0 || mutationAnnotations.length === 0) {
|
|
7319
|
+
return false;
|
|
7320
|
+
}
|
|
7321
|
+
return mutationAnnotations.some(
|
|
7322
|
+
(resolved) => resolved.annotation.description.includes(textFilter) || resolved.annotation.name.includes(textFilter) || resolved.annotation.symbol.includes(textFilter)
|
|
7323
|
+
);
|
|
7324
|
+
}
|
|
7325
|
+
function mutationMatchesAnnotationFilter(mutation, sequenceType, annotationNameFilter, annotationProvider) {
|
|
7326
|
+
if (annotationNameFilter.size === 0) {
|
|
7327
|
+
return true;
|
|
7328
|
+
}
|
|
7329
|
+
const mutationAnnotations = annotationProvider(mutation, sequenceType);
|
|
7330
|
+
if (mutationAnnotations === void 0 || mutationAnnotations.length === 0) {
|
|
7331
|
+
return false;
|
|
7332
|
+
}
|
|
7333
|
+
return mutationAnnotations.some((resolved) => annotationNameFilter.has(resolved.annotation.name));
|
|
7334
|
+
}
|
|
7335
|
+
async function queryDatesInDataset(lapisFilter, lapis, granularity, lapisDateField, signal) {
|
|
7336
|
+
const { dateFrom, dateTo } = getDateRangeFromFilter(lapisFilter, lapisDateField, granularity);
|
|
7337
|
+
if (dateFrom !== null && dateTo !== null) {
|
|
7338
|
+
return generateAllInRange(dateFrom, dateTo);
|
|
7339
|
+
}
|
|
7340
|
+
const { content: availableDates } = await queryAvailableDates(
|
|
7341
|
+
lapisFilter,
|
|
7342
|
+
lapis,
|
|
7343
|
+
granularity,
|
|
7344
|
+
lapisDateField,
|
|
7345
|
+
signal
|
|
7346
|
+
);
|
|
7347
|
+
const { min, max } = getMinMaxTemporal(availableDates);
|
|
7348
|
+
return generateAllInRange(dateFrom ?? min, dateTo ?? max);
|
|
7349
|
+
}
|
|
7350
|
+
function getDateRangeFromFilter(lapisFilter, lapisDateField, granularity) {
|
|
7351
|
+
const valueFromFilter = lapisFilter[lapisDateField];
|
|
7352
|
+
if (valueFromFilter) {
|
|
7353
|
+
return {
|
|
7354
|
+
dateFrom: parseDateStringToTemporal(valueFromFilter, granularity),
|
|
7355
|
+
dateTo: parseDateStringToTemporal(valueFromFilter, granularity)
|
|
7356
|
+
};
|
|
7357
|
+
}
|
|
7358
|
+
const minFromFilter = lapisFilter[`${lapisDateField}From`];
|
|
7359
|
+
const maxFromFilter = lapisFilter[`${lapisDateField}To`];
|
|
7360
|
+
return {
|
|
7361
|
+
dateFrom: minFromFilter ? parseDateStringToTemporal(minFromFilter, granularity) : null,
|
|
7362
|
+
dateTo: maxFromFilter ? parseDateStringToTemporal(maxFromFilter, granularity) : null
|
|
7363
|
+
};
|
|
7364
|
+
}
|
|
7365
|
+
function queryAvailableDates(lapisFilter, lapis, granularity, lapisDateField, signal) {
|
|
7366
|
+
return fetchAndPrepareDates(lapisFilter, granularity, lapisDateField).evaluate(lapis, signal);
|
|
7367
|
+
}
|
|
7368
|
+
function fetchAndPrepareDates(filter, granularity, lapisDateField) {
|
|
7369
|
+
const fetchData = new FetchAggregatedOperator(filter, [lapisDateField]);
|
|
7370
|
+
const dataWithFixedDateKey = new RenameFieldOperator(fetchData, lapisDateField, "date");
|
|
7371
|
+
const mapData = new MapOperator(dataWithFixedDateKey, (data) => mapDateToGranularityRange(data, granularity));
|
|
7372
|
+
const groupByData = new GroupByAndSumOperator(mapData, "dateRange", "count");
|
|
7373
|
+
const sortData = new SortOperator(groupByData, dateRangeCompare);
|
|
7374
|
+
return new MapOperator(sortData, (data) => data.dateRange);
|
|
7375
|
+
}
|
|
7239
7376
|
class Map2dBase {
|
|
7240
7377
|
constructor(serializeFirstAxis, serializeSecondAxis, initialContent) {
|
|
7241
7378
|
this.serializeFirstAxis = serializeFirstAxis;
|
|
@@ -7386,116 +7523,6 @@ class Map2dView {
|
|
|
7386
7523
|
};
|
|
7387
7524
|
}
|
|
7388
7525
|
}
|
|
7389
|
-
const displayMutationsSchema = z$2.array(z$2.string(), {
|
|
7390
|
-
errorMap: () => ({ message: `invalid display mutations` })
|
|
7391
|
-
});
|
|
7392
|
-
function getFilteredMutationOverTimeData$1({
|
|
7393
|
-
data,
|
|
7394
|
-
overallMutationData,
|
|
7395
|
-
displayedSegments,
|
|
7396
|
-
displayedMutationTypes,
|
|
7397
|
-
proportionInterval,
|
|
7398
|
-
hideGaps,
|
|
7399
|
-
mutationFilterValue,
|
|
7400
|
-
sequenceType,
|
|
7401
|
-
annotationProvider
|
|
7402
|
-
}) {
|
|
7403
|
-
const filteredData = new Map2dView(data);
|
|
7404
|
-
const mutationsToFilterOut = overallMutationData.filter((entry) => {
|
|
7405
|
-
if (entry.proportion < proportionInterval.min || entry.proportion > proportionInterval.max) {
|
|
7406
|
-
return true;
|
|
7407
|
-
}
|
|
7408
|
-
if (displayedSegments.some((segment) => segment.segment === entry.mutation.segment && !segment.checked)) {
|
|
7409
|
-
return true;
|
|
7410
|
-
}
|
|
7411
|
-
if (mutationOrAnnotationDoNotMatchFilter(entry.mutation, sequenceType, mutationFilterValue, annotationProvider)) {
|
|
7412
|
-
return true;
|
|
7413
|
-
}
|
|
7414
|
-
return displayedMutationTypes.some(
|
|
7415
|
-
(mutationType2) => mutationType2.type === entry.mutation.type && !mutationType2.checked
|
|
7416
|
-
);
|
|
7417
|
-
});
|
|
7418
|
-
mutationsToFilterOut.forEach((entry) => {
|
|
7419
|
-
filteredData.deleteRow(entry.mutation);
|
|
7420
|
-
});
|
|
7421
|
-
if (hideGaps) {
|
|
7422
|
-
const dateRangesToFilterOut = filteredData.getSecondAxisKeys().filter((dateRange2) => {
|
|
7423
|
-
const vals = filteredData.getColumn(dateRange2);
|
|
7424
|
-
return !vals.some((v2) => ((v2 == null ? void 0 : v2.type) === "value" || (v2 == null ? void 0 : v2.type) === "valueWithCoverage") && v2.totalCount > 0);
|
|
7425
|
-
});
|
|
7426
|
-
dateRangesToFilterOut.forEach((dateRange2) => filteredData.deleteColumn(dateRange2));
|
|
7427
|
-
}
|
|
7428
|
-
return filteredData;
|
|
7429
|
-
}
|
|
7430
|
-
function mutationOrAnnotationDoNotMatchFilter(mutation, sequenceType, mutationFilter, annotationProvider) {
|
|
7431
|
-
return !(mutationOrAnnotationMatchesTextFilter(mutation, sequenceType, mutationFilter.textFilter, annotationProvider) && mutationMatchesAnnotationFilter(mutation, sequenceType, mutationFilter.annotationNameFilter, annotationProvider));
|
|
7432
|
-
}
|
|
7433
|
-
function mutationOrAnnotationMatchesTextFilter(mutation, sequenceType, textFilter, annotationProvider) {
|
|
7434
|
-
if (textFilter === "") {
|
|
7435
|
-
return true;
|
|
7436
|
-
}
|
|
7437
|
-
if (mutation.code.includes(textFilter)) {
|
|
7438
|
-
return true;
|
|
7439
|
-
}
|
|
7440
|
-
const mutationAnnotations = annotationProvider(mutation, sequenceType);
|
|
7441
|
-
if (mutationAnnotations === void 0 || mutationAnnotations.length === 0) {
|
|
7442
|
-
return false;
|
|
7443
|
-
}
|
|
7444
|
-
return mutationAnnotations.some(
|
|
7445
|
-
(annotation) => annotation.description.includes(textFilter) || annotation.name.includes(textFilter) || annotation.symbol.includes(textFilter)
|
|
7446
|
-
);
|
|
7447
|
-
}
|
|
7448
|
-
function mutationMatchesAnnotationFilter(mutation, sequenceType, annotationNameFilter, annotationProvider) {
|
|
7449
|
-
if (annotationNameFilter.size === 0) {
|
|
7450
|
-
return true;
|
|
7451
|
-
}
|
|
7452
|
-
const mutationAnnotations = annotationProvider(mutation, sequenceType);
|
|
7453
|
-
if (mutationAnnotations === void 0 || mutationAnnotations.length === 0) {
|
|
7454
|
-
return false;
|
|
7455
|
-
}
|
|
7456
|
-
return mutationAnnotations.some((annotation) => annotationNameFilter.has(annotation.name));
|
|
7457
|
-
}
|
|
7458
|
-
async function queryDatesInDataset(lapisFilter, lapis, granularity, lapisDateField, signal) {
|
|
7459
|
-
const { dateFrom, dateTo } = getDateRangeFromFilter(lapisFilter, lapisDateField, granularity);
|
|
7460
|
-
if (dateFrom !== null && dateTo !== null) {
|
|
7461
|
-
return generateAllInRange(dateFrom, dateTo);
|
|
7462
|
-
}
|
|
7463
|
-
const { content: availableDates } = await queryAvailableDates(
|
|
7464
|
-
lapisFilter,
|
|
7465
|
-
lapis,
|
|
7466
|
-
granularity,
|
|
7467
|
-
lapisDateField,
|
|
7468
|
-
signal
|
|
7469
|
-
);
|
|
7470
|
-
const { min, max } = getMinMaxTemporal(availableDates);
|
|
7471
|
-
return generateAllInRange(dateFrom ?? min, dateTo ?? max);
|
|
7472
|
-
}
|
|
7473
|
-
function getDateRangeFromFilter(lapisFilter, lapisDateField, granularity) {
|
|
7474
|
-
const valueFromFilter = lapisFilter[lapisDateField];
|
|
7475
|
-
if (valueFromFilter) {
|
|
7476
|
-
return {
|
|
7477
|
-
dateFrom: parseDateStringToTemporal(valueFromFilter, granularity),
|
|
7478
|
-
dateTo: parseDateStringToTemporal(valueFromFilter, granularity)
|
|
7479
|
-
};
|
|
7480
|
-
}
|
|
7481
|
-
const minFromFilter = lapisFilter[`${lapisDateField}From`];
|
|
7482
|
-
const maxFromFilter = lapisFilter[`${lapisDateField}To`];
|
|
7483
|
-
return {
|
|
7484
|
-
dateFrom: minFromFilter ? parseDateStringToTemporal(minFromFilter, granularity) : null,
|
|
7485
|
-
dateTo: maxFromFilter ? parseDateStringToTemporal(maxFromFilter, granularity) : null
|
|
7486
|
-
};
|
|
7487
|
-
}
|
|
7488
|
-
function queryAvailableDates(lapisFilter, lapis, granularity, lapisDateField, signal) {
|
|
7489
|
-
return fetchAndPrepareDates(lapisFilter, granularity, lapisDateField).evaluate(lapis, signal);
|
|
7490
|
-
}
|
|
7491
|
-
function fetchAndPrepareDates(filter, granularity, lapisDateField) {
|
|
7492
|
-
const fetchData = new FetchAggregatedOperator(filter, [lapisDateField]);
|
|
7493
|
-
const dataWithFixedDateKey = new RenameFieldOperator(fetchData, lapisDateField, "date");
|
|
7494
|
-
const mapData = new MapOperator(dataWithFixedDateKey, (data) => mapDateToGranularityRange(data, granularity));
|
|
7495
|
-
const groupByData = new GroupByAndSumOperator(mapData, "dateRange", "count");
|
|
7496
|
-
const sortData = new SortOperator(groupByData, dateRangeCompare);
|
|
7497
|
-
return new MapOperator(sortData, (data) => data.dateRange);
|
|
7498
|
-
}
|
|
7499
7526
|
class BaseMutationOverTimeDataMap extends Map2dBase {
|
|
7500
7527
|
constructor(initialContent) {
|
|
7501
7528
|
super(serializeSubstitutionOrDeletion, serializeTemporal$1, initialContent);
|
|
@@ -7540,12 +7567,11 @@ async function queryOverallMutationData({
|
|
|
7540
7567
|
lapisFilter,
|
|
7541
7568
|
sequenceType,
|
|
7542
7569
|
lapis,
|
|
7543
|
-
granularity,
|
|
7544
7570
|
lapisDateField,
|
|
7545
7571
|
includeMutations,
|
|
7572
|
+
requestedDateRanges,
|
|
7546
7573
|
signal
|
|
7547
7574
|
}) {
|
|
7548
|
-
const requestedDateRanges = await queryDatesInDataset(lapisFilter, lapis, granularity, lapisDateField, signal);
|
|
7549
7575
|
if (requestedDateRanges.length === 0) {
|
|
7550
7576
|
if (includeMutations) {
|
|
7551
7577
|
return {
|
|
@@ -7575,7 +7601,7 @@ async function queryOverallMutationData({
|
|
|
7575
7601
|
}
|
|
7576
7602
|
return dataPromise;
|
|
7577
7603
|
}
|
|
7578
|
-
async function
|
|
7604
|
+
async function queryMutationsOverTimeMetadata(lapisFilter, sequenceType, lapis, lapisDateField, granularity, displayMutations, signal) {
|
|
7579
7605
|
const requestedDateRanges = await queryDatesInDataset(lapisFilter, lapis, granularity, lapisDateField, signal);
|
|
7580
7606
|
if (requestedDateRanges.length > MAX_NUMBER_OF_GRID_COLUMNS$1) {
|
|
7581
7607
|
throw new UserFacingError(
|
|
@@ -7589,10 +7615,20 @@ async function queryMutationsOverTimeData(lapisFilter, sequenceType, lapis, lapi
|
|
|
7589
7615
|
lapis,
|
|
7590
7616
|
lapisDateField,
|
|
7591
7617
|
includeMutations: displayMutations,
|
|
7592
|
-
|
|
7618
|
+
requestedDateRanges,
|
|
7619
|
+
signal
|
|
7593
7620
|
}).then((r2) => r2.content);
|
|
7594
7621
|
overallMutationData.sort((a2, b2) => sortSubstitutionsAndDeletions(a2.mutation, b2.mutation));
|
|
7595
|
-
|
|
7622
|
+
return { overallMutationData, requestedDateRanges };
|
|
7623
|
+
}
|
|
7624
|
+
async function queryMutationsOverTimePage(lapisFilter, lapis, lapisDateField, sequenceType, requestedDateRanges, includeMutationCodes, signal) {
|
|
7625
|
+
if (includeMutationCodes.length === 0 || requestedDateRanges.length === 0) {
|
|
7626
|
+
return new BaseMutationOverTimeDataMap({
|
|
7627
|
+
keysFirstAxis: /* @__PURE__ */ new Map(),
|
|
7628
|
+
keysSecondAxis: new Map(requestedDateRanges.map((date) => [date.dateString, date])),
|
|
7629
|
+
data: /* @__PURE__ */ new Map()
|
|
7630
|
+
});
|
|
7631
|
+
}
|
|
7596
7632
|
const apiResult = await fetchMutationsOverTime(
|
|
7597
7633
|
lapis,
|
|
7598
7634
|
{
|
|
@@ -7601,33 +7637,17 @@ async function queryMutationsOverTimeData(lapisFilter, sequenceType, lapis, lapi
|
|
|
7601
7637
|
dateFrom: date.firstDay.toString(),
|
|
7602
7638
|
dateTo: date.lastDay.toString()
|
|
7603
7639
|
})),
|
|
7604
|
-
includeMutations,
|
|
7640
|
+
includeMutations: includeMutationCodes,
|
|
7605
7641
|
dateField: lapisDateField
|
|
7606
7642
|
},
|
|
7607
7643
|
sequenceType,
|
|
7608
7644
|
signal
|
|
7609
7645
|
);
|
|
7646
|
+
return buildMutationOverTimeDataMap(apiResult, requestedDateRanges);
|
|
7647
|
+
}
|
|
7648
|
+
function buildMutationOverTimeDataMap(apiResult, requestedDateRanges) {
|
|
7610
7649
|
const totalCounts = apiResult.data.totalCountsByDateRange;
|
|
7611
7650
|
const responseMutations = apiResult.data.mutations.map(parseMutationCode);
|
|
7612
|
-
const mutationEntries = responseMutations.map((mutation, i2) => {
|
|
7613
|
-
const numbers = {
|
|
7614
|
-
count: overallMutationData[i2].count,
|
|
7615
|
-
proportion: overallMutationData[i2].proportion
|
|
7616
|
-
};
|
|
7617
|
-
if (mutation.type === "deletion") {
|
|
7618
|
-
return {
|
|
7619
|
-
type: "deletion",
|
|
7620
|
-
mutation,
|
|
7621
|
-
...numbers
|
|
7622
|
-
};
|
|
7623
|
-
} else {
|
|
7624
|
-
return {
|
|
7625
|
-
type: "substitution",
|
|
7626
|
-
mutation,
|
|
7627
|
-
...numbers
|
|
7628
|
-
};
|
|
7629
|
-
}
|
|
7630
|
-
});
|
|
7631
7651
|
const mutationOverTimeData = {
|
|
7632
7652
|
keysFirstAxis: new Map(responseMutations.map((mutation) => [mutation.code, mutation])),
|
|
7633
7653
|
keysSecondAxis: new Map(requestedDateRanges.map((date) => [date.dateString, date])),
|
|
@@ -7665,10 +7685,7 @@ async function queryMutationsOverTimeData(lapisFilter, sequenceType, lapis, lapi
|
|
|
7665
7685
|
])
|
|
7666
7686
|
)
|
|
7667
7687
|
};
|
|
7668
|
-
return
|
|
7669
|
-
mutationOverTimeData: new BaseMutationOverTimeDataMap(mutationOverTimeData),
|
|
7670
|
-
overallMutationData: mutationEntries
|
|
7671
|
-
};
|
|
7688
|
+
return new BaseMutationOverTimeDataMap(mutationOverTimeData);
|
|
7672
7689
|
}
|
|
7673
7690
|
function parseMutationCode(code) {
|
|
7674
7691
|
const maybeDeletion = DeletionClass.parse(code);
|
|
@@ -7943,6 +7960,13 @@ function calculateTooltipPosition(triggerRect, tooltipRect, position) {
|
|
|
7943
7960
|
}
|
|
7944
7961
|
return { top, left };
|
|
7945
7962
|
}
|
|
7963
|
+
function useControlledState(initialState) {
|
|
7964
|
+
const [state, setState] = d(initialState);
|
|
7965
|
+
y2(() => {
|
|
7966
|
+
setState(initialState);
|
|
7967
|
+
}, [initialState]);
|
|
7968
|
+
return [state, setState];
|
|
7969
|
+
}
|
|
7946
7970
|
const pageSizeContext = createContext$1({
|
|
7947
7971
|
pageSize: -1,
|
|
7948
7972
|
setPageSize: () => {
|
|
@@ -7953,34 +7977,36 @@ function usePageSizeContext() {
|
|
|
7953
7977
|
return x$1(pageSizeContext);
|
|
7954
7978
|
}
|
|
7955
7979
|
const PageSizeContextProvider = ({ children, pageSizes }) => {
|
|
7956
|
-
const [pageSize, setPageSize] =
|
|
7980
|
+
const [pageSize, setPageSize] = useControlledState(
|
|
7981
|
+
typeof pageSizes === "number" ? pageSizes : pageSizes.at(0) ?? 10
|
|
7982
|
+
);
|
|
7957
7983
|
return /* @__PURE__ */ u$1(pageSizeContext.Provider, { value: { pageSize, setPageSize }, children });
|
|
7958
7984
|
};
|
|
7959
7985
|
const pageSizesSchema = z$2.union([z$2.array(z$2.number()), z$2.number()]);
|
|
7960
7986
|
function Pagination({
|
|
7961
7987
|
table,
|
|
7962
|
-
pageSizes
|
|
7988
|
+
pageSizes,
|
|
7989
|
+
totalRows
|
|
7963
7990
|
}) {
|
|
7964
7991
|
return /* @__PURE__ */ u$1("div", { className: "@container", children: /* @__PURE__ */ u$1("div", { className: "flex items-center gap-x-6 gap-y-2 flex-wrap @xl:justify-end justify-center", children: [
|
|
7965
7992
|
/* @__PURE__ */ u$1(PageSizeSelector, { table, pageSizes }),
|
|
7966
|
-
/* @__PURE__ */ u$1(PageIndicator, { table }),
|
|
7967
|
-
/* @__PURE__ */ u$1("div", { className: "@xl:block hidden", children: /* @__PURE__ */ u$1(GotoPageSelector, { table }) }),
|
|
7993
|
+
/* @__PURE__ */ u$1(PageIndicator, { table, totalRows }),
|
|
7994
|
+
/* @__PURE__ */ u$1("div", { className: "@xl:block hidden", children: /* @__PURE__ */ u$1(GotoPageSelector, { table, totalRows }) }),
|
|
7968
7995
|
/* @__PURE__ */ u$1(SelectPageButtons, { table })
|
|
7969
7996
|
] }) });
|
|
7970
7997
|
}
|
|
7971
|
-
function PageIndicator({ table }) {
|
|
7972
|
-
if (table.
|
|
7998
|
+
function PageIndicator({ table, totalRows }) {
|
|
7999
|
+
if (table.getPaginationRowModel().rows.length <= 1 && totalRows <= 1) {
|
|
7973
8000
|
return null;
|
|
7974
8001
|
}
|
|
7975
8002
|
const minRow = table.getState().pagination.pageIndex * table.getState().pagination.pageSize + 1;
|
|
7976
|
-
const maxRow = minRow + table.
|
|
7977
|
-
const numRows = table.getCoreRowModel().rows.length;
|
|
8003
|
+
const maxRow = minRow + table.getPaginationRowModel().rows.length - 1;
|
|
7978
8004
|
return /* @__PURE__ */ u$1("span", { className: "text-sm", children: [
|
|
7979
8005
|
minRow,
|
|
7980
8006
|
" - ",
|
|
7981
8007
|
maxRow,
|
|
7982
8008
|
" of ",
|
|
7983
|
-
|
|
8009
|
+
totalRows
|
|
7984
8010
|
] });
|
|
7985
8011
|
}
|
|
7986
8012
|
const heightForSmallerLines = "h-[calc(var(--size)*0.7)]";
|
|
@@ -8015,8 +8041,8 @@ function PageSizeSelector({
|
|
|
8015
8041
|
)
|
|
8016
8042
|
] });
|
|
8017
8043
|
}
|
|
8018
|
-
function GotoPageSelector({ table }) {
|
|
8019
|
-
if (table.getRowModel().rows.length === 0) {
|
|
8044
|
+
function GotoPageSelector({ table, totalRows }) {
|
|
8045
|
+
if (table.getRowModel().rows.length === 0 && totalRows === 0) {
|
|
8020
8046
|
return null;
|
|
8021
8047
|
}
|
|
8022
8048
|
return /* @__PURE__ */ u$1("label", { className: "items-center flex", children: [
|
|
@@ -8086,6 +8112,7 @@ function flexRender(Comp, props) {
|
|
|
8086
8112
|
return !Comp ? null : typeof Comp === "function" ? /* @__PURE__ */ u$1(Comp, { ...props }) : Comp;
|
|
8087
8113
|
}
|
|
8088
8114
|
function usePreactTable(options2) {
|
|
8115
|
+
var _a;
|
|
8089
8116
|
const resolvedOptions = {
|
|
8090
8117
|
state: {},
|
|
8091
8118
|
onStateChange: () => {
|
|
@@ -8105,17 +8132,20 @@ function usePreactTable(options2) {
|
|
|
8105
8132
|
...options2.state
|
|
8106
8133
|
},
|
|
8107
8134
|
onStateChange: (updater) => {
|
|
8108
|
-
var
|
|
8135
|
+
var _a2;
|
|
8109
8136
|
setState(updater);
|
|
8110
|
-
(
|
|
8137
|
+
(_a2 = options2.onStateChange) == null ? void 0 : _a2.call(options2, updater);
|
|
8111
8138
|
}
|
|
8112
8139
|
}));
|
|
8140
|
+
const isControlled = options2.manualPagination === true && ((_a = options2.state) == null ? void 0 : _a.pagination) !== void 0;
|
|
8113
8141
|
const { pageSize } = usePageSizeContext();
|
|
8114
8142
|
y2(
|
|
8115
8143
|
() => {
|
|
8116
|
-
|
|
8144
|
+
if (!isControlled) {
|
|
8145
|
+
tableRef.current.setPageSize(pageSize);
|
|
8146
|
+
}
|
|
8117
8147
|
},
|
|
8118
|
-
[pageSize]
|
|
8148
|
+
[pageSize, isControlled]
|
|
8119
8149
|
// eslint-disable-line react-hooks/exhaustive-deps -- only run this when the pageSize changes
|
|
8120
8150
|
);
|
|
8121
8151
|
return tableRef.current;
|
|
@@ -8135,17 +8165,86 @@ function FeaturesOverTimeGrid({
|
|
|
8135
8165
|
featureRenderer,
|
|
8136
8166
|
tooltipPortalTarget
|
|
8137
8167
|
}) {
|
|
8138
|
-
const tableData =
|
|
8139
|
-
|
|
8140
|
-
|
|
8141
|
-
|
|
8142
|
-
|
|
8143
|
-
|
|
8144
|
-
|
|
8145
|
-
|
|
8146
|
-
|
|
8168
|
+
const tableData = useGridTableData(data, customColumns, featureRenderer);
|
|
8169
|
+
const columns = useGridColumns(
|
|
8170
|
+
data.getSecondAxisKeys(),
|
|
8171
|
+
rowLabelHeader,
|
|
8172
|
+
customColumns,
|
|
8173
|
+
colorScale,
|
|
8174
|
+
tooltipPortalTarget,
|
|
8175
|
+
featureRenderer
|
|
8176
|
+
);
|
|
8177
|
+
const { pageSize } = usePageSizeContext();
|
|
8178
|
+
const table = usePreactTable({
|
|
8179
|
+
data: tableData,
|
|
8180
|
+
columns,
|
|
8181
|
+
getCoreRowModel: getCoreRowModel(),
|
|
8182
|
+
getPaginationRowModel: getPaginationRowModel(),
|
|
8183
|
+
initialState: {
|
|
8184
|
+
pagination: { pageIndex: 0, pageSize }
|
|
8185
|
+
}
|
|
8186
|
+
});
|
|
8187
|
+
return /* @__PURE__ */ u$1(FeaturesOverTimeGridDisplay, { table, pageSizes });
|
|
8188
|
+
}
|
|
8189
|
+
function FeaturesOverTimeGridServerPaginated({
|
|
8190
|
+
rowLabelHeader,
|
|
8191
|
+
data,
|
|
8192
|
+
isLoading,
|
|
8193
|
+
loadingRowLabels,
|
|
8194
|
+
requestedDateRanges,
|
|
8195
|
+
colorScale,
|
|
8196
|
+
pageSizes,
|
|
8197
|
+
pageIndex,
|
|
8198
|
+
totalRows,
|
|
8199
|
+
onPageChange,
|
|
8200
|
+
customColumns = EMPTY_COLUMNS,
|
|
8201
|
+
featureRenderer,
|
|
8202
|
+
tooltipPortalTarget
|
|
8203
|
+
}) {
|
|
8204
|
+
const tableData = useGridTableData(data, customColumns, featureRenderer);
|
|
8205
|
+
const columns = useGridColumns(
|
|
8206
|
+
(data == null ? void 0 : data.getSecondAxisKeys()) ?? requestedDateRanges,
|
|
8207
|
+
rowLabelHeader,
|
|
8208
|
+
customColumns,
|
|
8209
|
+
colorScale,
|
|
8210
|
+
tooltipPortalTarget,
|
|
8211
|
+
featureRenderer
|
|
8212
|
+
);
|
|
8213
|
+
const { pageSize, setPageSize } = usePageSizeContext();
|
|
8214
|
+
const table = usePreactTable({
|
|
8215
|
+
data: tableData,
|
|
8216
|
+
columns,
|
|
8217
|
+
getCoreRowModel: getCoreRowModel(),
|
|
8218
|
+
// getPaginationRowModel not needed with manualPagination: true
|
|
8219
|
+
manualPagination: true,
|
|
8220
|
+
pageCount: Math.ceil(totalRows / pageSize),
|
|
8221
|
+
state: {
|
|
8222
|
+
pagination: { pageIndex, pageSize }
|
|
8223
|
+
},
|
|
8224
|
+
onPaginationChange: (updater) => {
|
|
8225
|
+
const current = { pageIndex, pageSize };
|
|
8226
|
+
const next = typeof updater === "function" ? updater(current) : updater;
|
|
8227
|
+
if (next.pageIndex !== current.pageIndex) {
|
|
8228
|
+
onPageChange(next.pageIndex);
|
|
8229
|
+
}
|
|
8230
|
+
if (next.pageSize !== current.pageSize) {
|
|
8231
|
+
setPageSize(next.pageSize);
|
|
8232
|
+
}
|
|
8233
|
+
}
|
|
8234
|
+
});
|
|
8235
|
+
return /* @__PURE__ */ u$1(
|
|
8236
|
+
FeaturesOverTimeGridDisplay,
|
|
8237
|
+
{
|
|
8238
|
+
table,
|
|
8239
|
+
pageSizes,
|
|
8240
|
+
loadingState: { isLoading, loadingRowLabels },
|
|
8241
|
+
totalRows
|
|
8242
|
+
}
|
|
8243
|
+
);
|
|
8244
|
+
}
|
|
8245
|
+
function useGridColumns(dates, rowLabelHeader, customColumns, colorScale, tooltipPortalTarget, featureRenderer) {
|
|
8246
|
+
return T$1(() => {
|
|
8147
8247
|
const columnHelper = createColumnHelper();
|
|
8148
|
-
const dates = data.getSecondAxisKeys();
|
|
8149
8248
|
const featureHeader = columnHelper.accessor((row) => row.feature, {
|
|
8150
8249
|
id: "feature",
|
|
8151
8250
|
header: () => /* @__PURE__ */ u$1("span", { children: rowLabelHeader }),
|
|
@@ -8165,13 +8264,13 @@ function FeaturesOverTimeGrid({
|
|
|
8165
8264
|
return columnHelper.accessor((row) => row.values[index], {
|
|
8166
8265
|
id: `date-${index}`,
|
|
8167
8266
|
header: () => /* @__PURE__ */ u$1("div", { className: "@container min-w-[0.05rem]", children: /* @__PURE__ */ u$1("p", { ...styleGridHeader(index, dates.length), children: date.dateString }) }),
|
|
8168
|
-
cell: ({ getValue, row, column, table
|
|
8267
|
+
cell: ({ getValue, row, column, table }) => {
|
|
8169
8268
|
const valueRaw = getValue();
|
|
8170
8269
|
const value = valueRaw ?? null;
|
|
8171
8270
|
const rowIndex = row.index;
|
|
8172
8271
|
const columnIndex = column.getIndex();
|
|
8173
|
-
const numberOfRows =
|
|
8174
|
-
const numberOfColumns =
|
|
8272
|
+
const numberOfRows = table.getRowModel().rows.length;
|
|
8273
|
+
const numberOfColumns = table.getAllColumns().length;
|
|
8175
8274
|
if (valueRaw === void 0) {
|
|
8176
8275
|
console.error(
|
|
8177
8276
|
`Found undefined value for ${row.original.feature} - ${date.dateString}. This shouldn't happen.`
|
|
@@ -8184,7 +8283,7 @@ function FeaturesOverTimeGrid({
|
|
|
8184
8283
|
value: value ?? null,
|
|
8185
8284
|
tooltip: tooltip2,
|
|
8186
8285
|
tooltipPosition: getTooltipPosition(
|
|
8187
|
-
rowIndex -
|
|
8286
|
+
rowIndex - table.getState().pagination.pageIndex * table.getState().pagination.pageSize,
|
|
8188
8287
|
numberOfRows,
|
|
8189
8288
|
columnIndex,
|
|
8190
8289
|
numberOfColumns
|
|
@@ -8197,29 +8296,48 @@ function FeaturesOverTimeGrid({
|
|
|
8197
8296
|
});
|
|
8198
8297
|
});
|
|
8199
8298
|
return [featureHeader, ...customColumnHeaders, ...dateHeaders];
|
|
8200
|
-
}, [colorScale,
|
|
8201
|
-
|
|
8202
|
-
|
|
8203
|
-
|
|
8204
|
-
|
|
8205
|
-
|
|
8206
|
-
getPaginationRowModel: getPaginationRowModel(),
|
|
8207
|
-
initialState: {
|
|
8208
|
-
pagination: {
|
|
8209
|
-
pageIndex: 0,
|
|
8210
|
-
pageSize
|
|
8211
|
-
}
|
|
8299
|
+
}, [colorScale, dates, customColumns, tooltipPortalTarget, featureRenderer, rowLabelHeader]);
|
|
8300
|
+
}
|
|
8301
|
+
function useGridTableData(data, customColumns, featureRenderer) {
|
|
8302
|
+
return T$1(() => {
|
|
8303
|
+
if (!data) {
|
|
8304
|
+
return [];
|
|
8212
8305
|
}
|
|
8213
|
-
|
|
8306
|
+
const firstAxisKeys = data.getFirstAxisKeys();
|
|
8307
|
+
return data.getAsArray().map((row, index) => {
|
|
8308
|
+
const firstAxisKey = firstAxisKeys[index];
|
|
8309
|
+
const customValues = customColumns.map((col) => col.values[featureRenderer.asString(firstAxisKey)]);
|
|
8310
|
+
return { feature: firstAxisKey, values: [...row], customValues };
|
|
8311
|
+
});
|
|
8312
|
+
}, [data, customColumns, featureRenderer]);
|
|
8313
|
+
}
|
|
8314
|
+
function FeaturesOverTimeGridDisplay({
|
|
8315
|
+
table,
|
|
8316
|
+
pageSizes,
|
|
8317
|
+
loadingState,
|
|
8318
|
+
totalRows
|
|
8319
|
+
}) {
|
|
8320
|
+
const displayedTotalRows = totalRows ?? table.getCoreRowModel().rows.length;
|
|
8214
8321
|
return /* @__PURE__ */ u$1("div", { className: "w-full", children: [
|
|
8215
8322
|
/* @__PURE__ */ u$1("table", { className: "w-full", children: [
|
|
8216
8323
|
/* @__PURE__ */ u$1("thead", { children: table.getHeaderGroups().map((headerGroup) => /* @__PURE__ */ u$1("tr", { children: headerGroup.headers.map((header) => /* @__PURE__ */ u$1("th", { colSpan: header.colSpan, style: { width: `${header.getSize()}px` }, children: header.isPlaceholder ? null : flexRender(header.column.columnDef.header, header.getContext()) }, header.id)) }, headerGroup.id)) }),
|
|
8217
|
-
/* @__PURE__ */ u$1("tbody", { children: [
|
|
8324
|
+
/* @__PURE__ */ u$1("tbody", { children: (loadingState == null ? void 0 : loadingState.isLoading) ? loadingState.loadingRowLabels.map((label, rowIndex) => /* @__PURE__ */ u$1("tr", { children: [
|
|
8325
|
+
/* @__PURE__ */ u$1("td", { className: "text-center", children: label }),
|
|
8326
|
+
rowIndex === 0 && /* @__PURE__ */ u$1(
|
|
8327
|
+
"td",
|
|
8328
|
+
{
|
|
8329
|
+
rowSpan: loadingState.loadingRowLabels.length,
|
|
8330
|
+
colSpan: table.getFlatHeaders().length - 1,
|
|
8331
|
+
className: "text-center",
|
|
8332
|
+
children: /* @__PURE__ */ u$1("span", { className: "loading loading-spinner loading-sm" })
|
|
8333
|
+
}
|
|
8334
|
+
)
|
|
8335
|
+
] }, label)) : /* @__PURE__ */ u$1(Fragment, { children: [
|
|
8218
8336
|
table.getRowModel().rows.map((row) => /* @__PURE__ */ u$1("tr", { children: row.getVisibleCells().map((cell) => /* @__PURE__ */ u$1("td", { children: flexRender(cell.column.columnDef.cell, cell.getContext()) }, cell.id)) }, row.id)),
|
|
8219
|
-
table.getRowModel().rows.length === 0 && /* @__PURE__ */ u$1("td", { colSpan: table.getFlatHeaders().length, children: /* @__PURE__ */ u$1("div", { className: "text-center", children: "No data available for your filters." }) })
|
|
8220
|
-
] })
|
|
8337
|
+
table.getRowModel().rows.length === 0 && /* @__PURE__ */ u$1("tr", { children: /* @__PURE__ */ u$1("td", { colSpan: table.getFlatHeaders().length, children: /* @__PURE__ */ u$1("div", { className: "text-center", children: "No data available for your filters." }) }) })
|
|
8338
|
+
] }) })
|
|
8221
8339
|
] }),
|
|
8222
|
-
/* @__PURE__ */ u$1("div", { className: "mt-2", children: /* @__PURE__ */ u$1(Pagination, { table, pageSizes }) })
|
|
8340
|
+
/* @__PURE__ */ u$1("div", { className: "mt-2", children: /* @__PURE__ */ u$1(Pagination, { table, pageSizes, totalRows: displayedTotalRows }) })
|
|
8223
8341
|
] });
|
|
8224
8342
|
}
|
|
8225
8343
|
function styleGridHeader(columnIndex, numDateColumns) {
|
|
@@ -8347,6 +8465,64 @@ const AnnotationCheckboxes = ({ value, setFilterValue }) => {
|
|
|
8347
8465
|
] })
|
|
8348
8466
|
] });
|
|
8349
8467
|
};
|
|
8468
|
+
function useMutationsOverTimePageData(filteredMutationCodes, pageIndex, pageSize, lapisFilter, lapis, lapisDateField, sequenceType, requestedDateRanges, hideGaps) {
|
|
8469
|
+
const pageMutationCodes = T$1(
|
|
8470
|
+
() => filteredMutationCodes.slice(pageIndex * pageSize, (pageIndex + 1) * pageSize),
|
|
8471
|
+
[filteredMutationCodes, pageIndex, pageSize]
|
|
8472
|
+
);
|
|
8473
|
+
const cache = A$1(/* @__PURE__ */ new Map());
|
|
8474
|
+
y2(() => {
|
|
8475
|
+
cache.current = /* @__PURE__ */ new Map();
|
|
8476
|
+
}, [lapisFilter, lapis, lapisDateField, sequenceType, requestedDateRanges]);
|
|
8477
|
+
const {
|
|
8478
|
+
data: pageData,
|
|
8479
|
+
error,
|
|
8480
|
+
isLoading
|
|
8481
|
+
} = useQuery(async () => {
|
|
8482
|
+
const cacheKey = JSON.stringify({
|
|
8483
|
+
lapisFilter,
|
|
8484
|
+
lapis,
|
|
8485
|
+
lapisDateField,
|
|
8486
|
+
sequenceType,
|
|
8487
|
+
requestedDateRanges,
|
|
8488
|
+
pageMutationCodes
|
|
8489
|
+
});
|
|
8490
|
+
const cachedData = cache.current.get(cacheKey);
|
|
8491
|
+
if (cachedData !== void 0) {
|
|
8492
|
+
return cachedData;
|
|
8493
|
+
}
|
|
8494
|
+
const newData = await queryMutationsOverTimePage(
|
|
8495
|
+
lapisFilter,
|
|
8496
|
+
lapis,
|
|
8497
|
+
lapisDateField,
|
|
8498
|
+
sequenceType,
|
|
8499
|
+
requestedDateRanges,
|
|
8500
|
+
pageMutationCodes
|
|
8501
|
+
);
|
|
8502
|
+
cache.current.set(cacheKey, newData);
|
|
8503
|
+
return newData;
|
|
8504
|
+
}, [lapisFilter, lapis, lapisDateField, sequenceType, requestedDateRanges, pageMutationCodes]);
|
|
8505
|
+
if (error) {
|
|
8506
|
+
throw error;
|
|
8507
|
+
}
|
|
8508
|
+
return T$1(() => {
|
|
8509
|
+
if (isLoading) {
|
|
8510
|
+
return { isLoading: true, data: null, pageMutationCodes };
|
|
8511
|
+
}
|
|
8512
|
+
return { isLoading: false, data: handleHideGaps(pageData, hideGaps), pageMutationCodes };
|
|
8513
|
+
}, [pageData, hideGaps, isLoading, pageMutationCodes]);
|
|
8514
|
+
}
|
|
8515
|
+
function handleHideGaps(data, hideGaps) {
|
|
8516
|
+
if (!hideGaps) {
|
|
8517
|
+
return data;
|
|
8518
|
+
}
|
|
8519
|
+
const view = new Map2dView(data);
|
|
8520
|
+
view.getSecondAxisKeys().filter((dateRange2) => {
|
|
8521
|
+
const vals = view.getColumn(dateRange2);
|
|
8522
|
+
return !vals.some((v2) => ((v2 == null ? void 0 : v2.type) === "value" || (v2 == null ? void 0 : v2.type) === "valueWithCoverage") && v2.totalCount > 0);
|
|
8523
|
+
}).forEach((dateRange2) => view.deleteColumn(dateRange2));
|
|
8524
|
+
return view;
|
|
8525
|
+
}
|
|
8350
8526
|
const mutationsOverTimeViewSchema = z$2.literal(views.grid);
|
|
8351
8527
|
const meanProportionIntervalSchema$1 = z$2.object({
|
|
8352
8528
|
min: z$2.number().min(0).max(1),
|
|
@@ -8373,35 +8549,52 @@ const MutationsOverTime = (componentProps) => {
|
|
|
8373
8549
|
};
|
|
8374
8550
|
const MutationsOverTimeInner = ({ ...componentProps }) => {
|
|
8375
8551
|
const lapis = useLapisUrl();
|
|
8376
|
-
const { lapisFilter, sequenceType, granularity, lapisDateField, displayMutations } = componentProps;
|
|
8377
|
-
const
|
|
8378
|
-
|
|
8379
|
-
|
|
8380
|
-
|
|
8381
|
-
|
|
8552
|
+
const { lapisFilter, sequenceType, granularity, lapisDateField, displayMutations, pageSizes } = componentProps;
|
|
8553
|
+
const [pageIndex, setPageIndex] = d(0);
|
|
8554
|
+
const {
|
|
8555
|
+
data: metadata,
|
|
8556
|
+
error: metadataError,
|
|
8557
|
+
isLoading: metadataLoading
|
|
8558
|
+
} = useQuery(() => {
|
|
8559
|
+
setPageIndex(0);
|
|
8560
|
+
return queryMutationsOverTimeMetadata(
|
|
8561
|
+
lapisFilter,
|
|
8562
|
+
sequenceType,
|
|
8563
|
+
lapis,
|
|
8564
|
+
lapisDateField,
|
|
8565
|
+
granularity,
|
|
8566
|
+
displayMutations
|
|
8567
|
+
);
|
|
8568
|
+
}, [granularity, lapis, lapisDateField, lapisFilter, sequenceType, displayMutations]);
|
|
8569
|
+
if (metadataLoading) {
|
|
8382
8570
|
return /* @__PURE__ */ u$1(LoadingDisplay, {});
|
|
8383
8571
|
}
|
|
8384
|
-
if (
|
|
8385
|
-
throw
|
|
8572
|
+
if (metadataError) {
|
|
8573
|
+
throw metadataError;
|
|
8386
8574
|
}
|
|
8387
|
-
if (
|
|
8575
|
+
if (metadata.overallMutationData.length === 0) {
|
|
8388
8576
|
return /* @__PURE__ */ u$1(NoDataDisplay, {});
|
|
8389
8577
|
}
|
|
8390
|
-
|
|
8391
|
-
return /* @__PURE__ */ u$1(
|
|
8578
|
+
return /* @__PURE__ */ u$1(PageSizeContextProvider, { pageSizes, children: /* @__PURE__ */ u$1(
|
|
8392
8579
|
MutationsOverTimeTabs$1,
|
|
8393
8580
|
{
|
|
8394
|
-
|
|
8395
|
-
|
|
8396
|
-
|
|
8581
|
+
metadata,
|
|
8582
|
+
originalComponentProps: componentProps,
|
|
8583
|
+
pageIndex,
|
|
8584
|
+
setPageIndex
|
|
8397
8585
|
}
|
|
8398
|
-
);
|
|
8586
|
+
) });
|
|
8399
8587
|
};
|
|
8400
8588
|
const MutationsOverTimeTabs$1 = ({
|
|
8401
|
-
|
|
8589
|
+
metadata,
|
|
8402
8590
|
originalComponentProps,
|
|
8403
|
-
|
|
8591
|
+
pageIndex,
|
|
8592
|
+
setPageIndex
|
|
8404
8593
|
}) => {
|
|
8594
|
+
const lapis = useLapisUrl();
|
|
8595
|
+
const { lapisFilter, sequenceType, lapisDateField } = originalComponentProps;
|
|
8596
|
+
const { overallMutationData, requestedDateRanges } = metadata;
|
|
8597
|
+
const { pageSize } = usePageSizeContext();
|
|
8405
8598
|
const tabsRef = useDispatchFinishedLoadingEvent();
|
|
8406
8599
|
const tooltipPortalTargetRef = A$1(null);
|
|
8407
8600
|
const [tooltipPortalTarget, setTooltipPortalTarget] = d(null);
|
|
@@ -8422,34 +8615,53 @@ const MutationsOverTimeTabs$1 = ({
|
|
|
8422
8615
|
]);
|
|
8423
8616
|
const [hideGaps, setHideGaps] = d(originalComponentProps.hideGaps ?? false);
|
|
8424
8617
|
y2(() => setHideGaps(originalComponentProps.hideGaps ?? false), [originalComponentProps.hideGaps]);
|
|
8425
|
-
const
|
|
8426
|
-
|
|
8427
|
-
data: mutationOverTimeData,
|
|
8618
|
+
const filteredMutationCodes = T$1(
|
|
8619
|
+
() => getFilteredMutationCodes({
|
|
8428
8620
|
overallMutationData,
|
|
8429
8621
|
displayedSegments,
|
|
8430
8622
|
displayedMutationTypes,
|
|
8431
8623
|
proportionInterval,
|
|
8432
|
-
hideGaps,
|
|
8433
8624
|
mutationFilterValue,
|
|
8434
8625
|
sequenceType: originalComponentProps.sequenceType,
|
|
8435
8626
|
annotationProvider
|
|
8436
|
-
})
|
|
8437
|
-
|
|
8438
|
-
|
|
8439
|
-
|
|
8440
|
-
|
|
8441
|
-
|
|
8442
|
-
|
|
8443
|
-
|
|
8444
|
-
|
|
8445
|
-
|
|
8446
|
-
|
|
8447
|
-
|
|
8448
|
-
|
|
8449
|
-
|
|
8450
|
-
|
|
8451
|
-
|
|
8452
|
-
|
|
8627
|
+
}),
|
|
8628
|
+
[
|
|
8629
|
+
overallMutationData,
|
|
8630
|
+
displayedSegments,
|
|
8631
|
+
displayedMutationTypes,
|
|
8632
|
+
proportionInterval,
|
|
8633
|
+
originalComponentProps.sequenceType,
|
|
8634
|
+
mutationFilterValue,
|
|
8635
|
+
annotationProvider
|
|
8636
|
+
]
|
|
8637
|
+
);
|
|
8638
|
+
y2(() => {
|
|
8639
|
+
setPageIndex(0);
|
|
8640
|
+
}, [filteredMutationCodes, setPageIndex]);
|
|
8641
|
+
const totalFilteredRows = filteredMutationCodes.length;
|
|
8642
|
+
const {
|
|
8643
|
+
isLoading: isPageLoading,
|
|
8644
|
+
data: pageData,
|
|
8645
|
+
pageMutationCodes
|
|
8646
|
+
} = useMutationsOverTimePageData(
|
|
8647
|
+
filteredMutationCodes,
|
|
8648
|
+
pageIndex,
|
|
8649
|
+
pageSize,
|
|
8650
|
+
lapisFilter,
|
|
8651
|
+
lapis,
|
|
8652
|
+
lapisDateField,
|
|
8653
|
+
sequenceType,
|
|
8654
|
+
requestedDateRanges,
|
|
8655
|
+
hideGaps
|
|
8656
|
+
);
|
|
8657
|
+
const mutationRenderer = T$1(
|
|
8658
|
+
() => ({
|
|
8659
|
+
asString: (value) => value.code,
|
|
8660
|
+
renderRowLabel: (value) => /* @__PURE__ */ u$1("div", { className: "text-center", children: /* @__PURE__ */ u$1(AnnotatedMutation, { mutation: value, sequenceType: originalComponentProps.sequenceType }) }),
|
|
8661
|
+
renderTooltip: (value, temporal, proportionValue) => /* @__PURE__ */ u$1(MutationsOverTimeGridTooltip, { mutation: value, date: temporal, value: proportionValue })
|
|
8662
|
+
}),
|
|
8663
|
+
[originalComponentProps.sequenceType]
|
|
8664
|
+
);
|
|
8453
8665
|
const getTab = (view) => {
|
|
8454
8666
|
switch (view) {
|
|
8455
8667
|
// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition -- for extensibility
|
|
@@ -8457,12 +8669,18 @@ const MutationsOverTimeTabs$1 = ({
|
|
|
8457
8669
|
return {
|
|
8458
8670
|
title: "Grid",
|
|
8459
8671
|
content: /* @__PURE__ */ u$1(
|
|
8460
|
-
|
|
8672
|
+
FeaturesOverTimeGridServerPaginated,
|
|
8461
8673
|
{
|
|
8462
8674
|
rowLabelHeader: "Mutation",
|
|
8463
|
-
data:
|
|
8675
|
+
data: pageData,
|
|
8676
|
+
isLoading: isPageLoading,
|
|
8677
|
+
loadingRowLabels: pageMutationCodes,
|
|
8678
|
+
requestedDateRanges,
|
|
8464
8679
|
colorScale,
|
|
8465
8680
|
pageSizes: originalComponentProps.pageSizes,
|
|
8681
|
+
pageIndex,
|
|
8682
|
+
totalRows: totalFilteredRows,
|
|
8683
|
+
onPageChange: setPageIndex,
|
|
8466
8684
|
customColumns: originalComponentProps.customColumns,
|
|
8467
8685
|
featureRenderer: mutationRenderer,
|
|
8468
8686
|
tooltipPortalTarget
|
|
@@ -8484,15 +8702,16 @@ const MutationsOverTimeTabs$1 = ({
|
|
|
8484
8702
|
setProportionInterval,
|
|
8485
8703
|
hideGaps,
|
|
8486
8704
|
setHideGaps,
|
|
8487
|
-
filteredData,
|
|
8488
8705
|
colorScale,
|
|
8489
8706
|
setColorScale,
|
|
8490
8707
|
originalComponentProps,
|
|
8491
8708
|
setFilterValue: setMutationFilterValue,
|
|
8492
|
-
mutationFilterValue
|
|
8709
|
+
mutationFilterValue,
|
|
8710
|
+
filteredMutationCodes,
|
|
8711
|
+
metadata
|
|
8493
8712
|
}
|
|
8494
8713
|
);
|
|
8495
|
-
return /* @__PURE__ */ u$1("div", { ref: tooltipPortalTargetRef, children: /* @__PURE__ */ u$1(
|
|
8714
|
+
return /* @__PURE__ */ u$1("div", { ref: tooltipPortalTargetRef, children: /* @__PURE__ */ u$1(Tabs, { ref: tabsRef, tabs, toolbar }) });
|
|
8496
8715
|
};
|
|
8497
8716
|
const Toolbar$3 = ({
|
|
8498
8717
|
activeTab,
|
|
@@ -8504,13 +8723,27 @@ const Toolbar$3 = ({
|
|
|
8504
8723
|
setProportionInterval,
|
|
8505
8724
|
hideGaps,
|
|
8506
8725
|
setHideGaps,
|
|
8507
|
-
filteredData,
|
|
8508
8726
|
colorScale,
|
|
8509
8727
|
setColorScale,
|
|
8510
8728
|
originalComponentProps,
|
|
8511
8729
|
setFilterValue,
|
|
8512
|
-
mutationFilterValue
|
|
8730
|
+
mutationFilterValue,
|
|
8731
|
+
filteredMutationCodes,
|
|
8732
|
+
metadata
|
|
8513
8733
|
}) => {
|
|
8734
|
+
const lapis = useLapisUrl();
|
|
8735
|
+
const { lapisFilter, sequenceType, lapisDateField } = originalComponentProps;
|
|
8736
|
+
const getDownloadDataAsync = async () => {
|
|
8737
|
+
const pageData = await queryMutationsOverTimePage(
|
|
8738
|
+
lapisFilter,
|
|
8739
|
+
lapis,
|
|
8740
|
+
lapisDateField,
|
|
8741
|
+
sequenceType,
|
|
8742
|
+
metadata.requestedDateRanges,
|
|
8743
|
+
filteredMutationCodes
|
|
8744
|
+
);
|
|
8745
|
+
return getDownloadData$1(handleHideGaps(pageData, hideGaps));
|
|
8746
|
+
};
|
|
8514
8747
|
return /* @__PURE__ */ u$1(Fragment, { children: [
|
|
8515
8748
|
/* @__PURE__ */ u$1(MutationsOverTimeMutationsFilter, { setFilterValue, value: mutationFilterValue }),
|
|
8516
8749
|
/* @__PURE__ */ u$1(
|
|
@@ -8551,7 +8784,7 @@ const Toolbar$3 = ({
|
|
|
8551
8784
|
CsvDownloadButton,
|
|
8552
8785
|
{
|
|
8553
8786
|
className: "btn btn-xs",
|
|
8554
|
-
getData:
|
|
8787
|
+
getData: getDownloadDataAsync,
|
|
8555
8788
|
filename: "mutations_over_time.csv"
|
|
8556
8789
|
}
|
|
8557
8790
|
),
|