protvista-uniprot 2.13.2 → 3.0.1

package/dist/es/tooltips/variationTooltip.js

@@ -0,0 +1,82 @@
+import groupBy from 'lodash-es/groupBy';
+import { formatXrefs, getEvidenceFromCodes } from './featureTooltip';
+const getDiseaseAssociations = (associations) => associations === null || associations === void 0 ? void 0 : associations.map((association) => `
+              <h4>Disease association</h4><p>${association.name}</p>
+              ${association.description
+    ? `<>${association.description}</p>`
+    : ''}
+              ${association.dbReferences
+    ? `<h5>Cross-references</h5>${formatXrefs(association.dbReferences)}`
+    : ''}
+              ${getEvidenceFromCodes(association.evidences)}
+          `).join('');
+const getDescriptions = (descriptions) => `<hr/><h5>Description</h5>${descriptions
+    .map((description) => `<p>${description.value}</p>`)
+    .join('')}
+  `;
+const getPopulationFrequencies = (popFrequencies) => `<hr/><h5>Population frequencies</h5>${popFrequencies
+    .map((freq) => `<p>${freq.frequency} - ${freq.populationName} (${freq.source})</p>`)
+    .join('')}`;
+const getEnsemblCovidLinks = (variant) => {
+    const shouldGenerateLink = variant.locations.some((location) => location.source === 'EnsemblViruses');
+    if (shouldGenerateLink) {
+        const xref = variant.xrefs.find((xref) => xref.name === 'ENA');
+        return xref.id
+            ? `<h5>Ensembl COVID-19</h5>
+          <p>
+          <a href="https://covid-19.ensembl.org/Sars_cov_2/Variation/Explore?v=${xref.id}" target="_blank" rel="noopener noreferrer">${xref.id}</a>
+        </p>`
+            : '';
+    }
+    return '';
+};
+const getPredictions = (predictions) => {
+    const groupedPredictions = groupBy(predictions, 'predAlgorithmNameType');
+    const counts = Object.keys(groupedPredictions).map((key) => {
+        const valueGroups = groupBy(groupedPredictions[key], 'predictionValType');
+        return {
+            algorithm: key,
+            values: Object.keys(valueGroups).map((valKey) => ({
+                name: valKey,
+                count: valueGroups[valKey].length,
+            })),
+        };
+    });
+    return counts
+        .map((countItem) => `<h6>${countItem.algorithm}</h6><ul class="no-bullet">${countItem.values
+        .map((countValue) => `<li>${countValue.name}</li>`)
+        .join('')}</ul>`)
+        .join('');
+};
+const formatTooltip = (variant) => {
+    var _a;
+    return `
+                <h5>Variant</h5><p>${variant.wildType} > ${variant.alternativeSequence || ''}</p>
+                ${variant.populationFrequencies
+        ? getPopulationFrequencies(variant.populationFrequencies)
+        : ''}
+                ${variant.consequenceType
+        ? `<h5>Consequence</h5><p>${variant.consequenceType}</p>`
+        : ``}
+                ${variant.somaticStatus
+        ? `<h5>Somatic</h5><p>${variant.somaticStatus === 0 ? 'No' : 'Yes'}</p>`
+        : ``}
+                ${((_a = variant.genomicLocation) === null || _a === void 0 ? void 0 : _a.length)
+        ? `<h5>Location</h5><p>${variant.genomicLocation.join(', ')}</p>`
+        : ``}
+                ${variant.ftId
+        ? `<h5>Feature ID</h5><p>${variant.ftId}</p>`
+        : ``}
+                ${variant.descriptions
+        ? getDescriptions(variant.descriptions)
+        : ''}
+                ${variant.association
+        ? getDiseaseAssociations(variant.association)
+        : ''}
+                ${variant.predictions ? getPredictions(variant.predictions) : ''}
+                ${getEnsemblCovidLinks(variant)}
+                
+        `;
+};
+export default formatTooltip;
+//# sourceMappingURL=variationTooltip.js.map

package/dist/es/tooltips/variationTooltip.js.map

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package/dist/es/utils.d.ts

@@ -0,0 +1,3 @@
+export declare const renameProperties: (features: any) => any;
+export declare const loadComponent: (name: string, elementConstructor: CustomElementConstructor) => void;
+export declare const fetchAll: (urls: string[], getUrl?: any) => Promise<any>;

package/dist/es/utils.js

@@ -0,0 +1,28 @@
+export const renameProperties = (features) => features.map((ft) => ({
+    ...ft,
+    start: ft.begin || undefined,
+}));
+export const loadComponent = (name, elementConstructor) => {
+    if (!customElements.get(name)) {
+        customElements.define(name, elementConstructor);
+    }
+};
+// Returns an object of the form url => payload json
+// getUrl optional function modifies url string
+export const fetchAll = async (urls, getUrl = null) => Object.fromEntries(await Promise.all(urls.map(async (url) => {
+    try {
+        const response = await fetch(getUrl ? getUrl(url) : url);
+        if (!response.ok) {
+            // TODO handle this better based on error code
+            // Fail silently for now
+            console.warn(`HTTP error status: ${response.status} at ${url}`);
+            return [url, null];
+        }
+        return [url, await response.json()];
+    }
+    catch (error) {
+        console.warn(`Failed to fetch or parse JSON from ${url}:`, error);
+        return [url, null]; // or handle error data as needed
+    }
+})));
+//# sourceMappingURL=utils.js.map

package/dist/es/utils.js.map

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