diff --git a/data/STRchive-citations.json b/data/STRchive-citations.json index 64e04bfd..85c0de53 100644 --- a/data/STRchive-citations.json +++ b/data/STRchive-citations.json @@ -165701,6 +165701,24 @@ "language": "eng", "note": "PMID: 20301686\nThis CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: url:https://www.ncbi.nlm.nih.gov/books/NBK1513" }, +{ + "id": "genereviews:NBK1229", + "manubot_success": true, + "link": "http://www.ncbi.nlm.nih.gov/books/NBK1229/", + "title": "Genetic Prion Disease", + "type": "chapter", + "doi": "", + "authors": [ + ["Inga", "Zerr"], + ["Matthias", "Schmitz"] + ], + "publisher": "GeneReviews\u00ae", + "issn": "", + "date": "1993-01-01", + "abstract": "Genetic prion disease generally manifests with cognitive difficulties, ataxia, and myoclonus (abrupt jerking movements of muscle groups and/or entire limbs). The order of appearance and/or predominance of these features and other associated neurologic and psychiatric findings vary. The three major phenotypes of genetic prion disease are genetic Creutzfeldt-Jakob disease (gCJD), fatal familial insomnia (FFI), and Gerstmann-Str\u00e4ussler-Scheinker (GSS) syndrome. Although these phenotypes display overlapping clinical and pathologic features, recognition of these phenotypes can be useful when providing affected individuals and their families with information about the expected clinical course. The age at onset typically ranges from 50 to 60 years. The disease course ranges from a few months in gCJD and FFI to a few (up to 4, and in rare cases up to 10) years in GSS syndrome., The diagnosis of genetic prion disease is established in a proband with suggestive findings and a heterozygous PRNP pathogenic variant identified by molecular genetic testing., Treatment of manifestations: No treatment of the underlying cause of genetic prion disease is available. Supportive care by a multidisciplinary team of specialists including neurologists, psychiatrists, physical therapists, occupational therapists, speech and language therapists, and social workers is recommended. Surveillance: Because of very rapid disease progression, close periodic monitoring by the multidisciplinary team is needed, typically every 14 days to evaluate needs for symptomatic treatment., Genetic prion disease is inherited in an autosomal dominant manner. Some individuals diagnosed with genetic prion disease may have a parent who is heterozygous for a PRNP pathogenic variant (some of whom may be asymptomatic because of reduced penetrance). Other individuals with genetic prion disease may have the disorder as the result of a de novo PRNP pathogenic variant. Each child of an individual with a PRNP pathogenic variant has a 50% chance of inheriting the variant. Although predictive testing (i.e., testing of asymptomatic at-risk adults) is possible, the capabilities and limitations of predictive testing as well as possible socioeconomic and medical care issues should be discussed in the context of formal genetic counseling prior to testing. Predictive testing in minors (i.e., testing of asymptomatic at-risk individuals younger than age 18 years) is considered inappropriate.", + "language": "eng", + "note": "PMID: 20301407\nThis CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: url:https://www.ncbi.nlm.nih.gov/books/NBK1229" +}, { "id": "omim:309548", "manubot_success": false, @@ -165959,12 +165977,6 @@ "link": "https://www.ncbi.nlm.nih.gov/books/NBK1305", "note": "WARNING: Manubot could not generate citation: Command '['manubot', 'cite', 'url:https://www.ncbi.nlm.nih.gov/books/NBK1305']' timed out after 3 seconds" }, -{ - "id": "genereviews:NBK1229", - "manubot_success": false, - "link": "https://www.ncbi.nlm.nih.gov/books/NBK1229", - "note": "WARNING: Manubot could not generate citation: Command '['manubot', 'cite', 'url:https://www.ncbi.nlm.nih.gov/books/NBK1229']' timed out after 3 seconds" -}, { "id": "isbn:978-3-031-66932-3", "manubot_success": false, diff --git a/data/criTRia-curations.schema.json b/data/criTRia-curations.schema.json index a41521da..840c5573 100644 --- a/data/criTRia-curations.schema.json +++ b/data/criTRia-curations.schema.json @@ -67,6 +67,7 @@ "title": "Description", "description": "Overall description of the evidence used for curation and any relevant notes e.g. rationale for classification, caveats, etc.", "type": ["string", "null"], + "in_text_citations": true, "multiline": true }, "Source": { @@ -139,6 +140,7 @@ "title": "Evidence Detail", "description": "Detailed description of the evidence", "type": ["string", "null"], + "in_text_citations": true, "multiline": true }, "evidence_category": { @@ -212,6 +214,7 @@ "title": "Evidence Detail", "description": "Detailed description of the evidence", "type": ["string", "null"], + "in_text_citations": true, "multiline": true }, "evidence_category": { diff --git a/site/bun.lock b/site/bun.lock index 03240630..b3171dfe 100644 --- a/site/bun.lock +++ b/site/bun.lock @@ -29,7 +29,6 @@ "react-dom": "^19.2.7", "string-strip-html": "^13.5.3", "tailwindcss": "^4.3.1", - 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"dot-case/tslib": ["tslib@2.8.1", "", {}, "sha512-oJFu94HQb+KVduSUQL7wnpmqnfmLsOA/nAh6b6EH0wCEoK0/mPeXU6c3wKDV83MkOuHPRHtSXKKU99IBazS/2w=="], - "eslint-plugin-astro/globals": ["globals@16.5.0", "", {}, "sha512-c/c15i26VrJ4IRt5Z89DnIzCGDn9EcebibhAOjw5ibqEHsE1wLUgkPn9RDmNcUKyU87GeaL633nyJ+pplFR2ZQ=="], "eslint-plugin-jsx-a11y/minimatch": ["minimatch@3.1.5", "", { "dependencies": { "brace-expansion": "^1.1.7" } }, "sha512-VgjWUsnnT6n+NUk6eZq77zeFdpW2LWDzP6zFGrCbHXiYNul5Dzqk2HHQ5uFH2DNW5Xbp8+jVzaeNt94ssEEl4w=="], @@ -1813,14 +1806,10 @@ "is-inside-container/is-docker": ["is-docker@3.0.0", "", { "bin": { "is-docker": "cli.js" } }, "sha512-eljcgEDlEns/7AXFosB5K/2nCM4P7FQPkGc/DWLy5rmFEWvZayGrik1d9/QIY5nJ4f9YsVvBkA6kJpHn9rISdQ=="], - "lower-case/tslib": ["tslib@2.8.1", "", {}, "sha512-oJFu94HQb+KVduSUQL7wnpmqnfmLsOA/nAh6b6EH0wCEoK0/mPeXU6c3wKDV83MkOuHPRHtSXKKU99IBazS/2w=="], - "mdast-util-find-and-replace/escape-string-regexp": ["escape-string-regexp@5.0.0", "", {}, "sha512-/veY75JbMK4j1yjvuUxuVsiS/hr/4iHs9FTT6cgTexxdE0Ly/glccBAkloH/DofkjRbZU3bnoj38mOmhkZ0lHw=="], "micromatch/picomatch": ["picomatch@2.3.2", "", {}, "sha512-V7+vQEJ06Z+c5tSye8S+nHUfI51xoXIXjHQ99cQtKUkQqqO1kO/KCJUfZXuB47h/YBlDhah2H3hdUGXn8ie0oA=="], - "no-case/tslib": ["tslib@2.8.1", "", {}, "sha512-oJFu94HQb+KVduSUQL7wnpmqnfmLsOA/nAh6b6EH0wCEoK0/mPeXU6c3wKDV83MkOuHPRHtSXKKU99IBazS/2w=="], - "p-locate/p-limit": ["p-limit@3.1.0", "", { "dependencies": { "yocto-queue": "^0.1.0" } }, "sha512-TYOanM3wGwNGsZN2cVTYPArw454xnXj5qmWF1bEoAc4+cU/ol7GVh7odevjp1FNHduHc3KZMcFduxU5Xc6uJRQ=="], "parse-entities/@types/unist": ["@types/unist@2.0.11", "", {}, "sha512-CmBKiL6NNo/OqgmMn95Fk9Whlp2mtvIv+KNpQKN2F4SjvrEesubTRWGYSg+BnWZOnlCaSTU1sMpsBOzgbYhnsA=="], @@ -1831,8 +1820,6 @@ "path-scurry/lru-cache": ["lru-cache@10.4.3", "", {}, "sha512-JNAzZcXrCt42VGLuYz0zfAzDfAvJWW6AfYlDBQyDV5DClI2m5sAmK+OIO7s59XfsRsWHp02jAJrRadPRGTt6SQ=="], - "snake-case/tslib": ["tslib@2.8.1", "", {}, "sha512-oJFu94HQb+KVduSUQL7wnpmqnfmLsOA/nAh6b6EH0wCEoK0/mPeXU6c3wKDV83MkOuHPRHtSXKKU99IBazS/2w=="], - "string-width/emoji-regex": ["emoji-regex@10.6.0", "", {}, "sha512-toUI84YS5YmxW219erniWD0CIVOo46xGKColeNQRgOzDorgBi1v4D71/OFzgD9GO2UGKIv1C3Sp8DAn0+j5w7A=="], "string-width-cjs/emoji-regex": ["emoji-regex@8.0.0", "", {}, "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A=="], diff --git a/site/package.json b/site/package.json index e054d54e..c12ceddc 100755 --- a/site/package.json +++ b/site/package.json @@ -41,7 +41,6 @@ "react-dom": "^19.2.7", "string-strip-html": "^13.5.3", "tailwindcss": "^4.3.1", - "tippy.js": "^6.3.7", "ua-parser-js": "^2.0.10" }, "devDependencies": { diff --git a/site/src/components/Table.tsx b/site/src/components/Table.tsx index f8a22430..1f0230db 100644 --- a/site/src/components/Table.tsx +++ b/site/src/components/Table.tsx @@ -29,6 +29,7 @@ import { useReactTable, } from "@tanstack/react-table"; import clsx from "clsx"; +import { clamp } from "lodash-es"; declare module "@tanstack/react-table" { // eslint-disable-next-line @@ -175,7 +176,7 @@ export default function Table({ /> {/* pagination */} -
+
diff --git a/site/src/components/TableOfContents.tsx b/site/src/components/TableOfContents.tsx index c1aaa321..1cfa47a0 100644 --- a/site/src/components/TableOfContents.tsx +++ b/site/src/components/TableOfContents.tsx @@ -1,6 +1,10 @@ import { useCallback, useEffect, useRef, useState } from "react"; import { firstInView } from "@/util/dom"; -import { useEventListener, useMutationObserver } from "@reactuses/core"; +import { + useEventListener, + useMutationObserver, + useWindowSize, +} from "@reactuses/core"; import { IconMenu2, IconX } from "@tabler/icons-react"; import Button from "./Button"; @@ -14,8 +18,16 @@ const headingSelector = "h1[id], h2[id], h3[id], h4[id]"; export default function TableOfContents() { const list = useRef(null); + /** available screen width */ + const { width } = useWindowSize(); + /** open/closed state */ - const [open, setOpen] = useState(window.innerWidth > 1600); + const [open, setOpen] = useState(width > 1600); + + useEffect(() => { + // eslint-disable-next-line + setOpen(width > 1600); + }, [width]); type Heading = { element: Element; diff --git a/site/src/data/index.ts b/site/src/data/index.ts index 723dbc30..0d10fda4 100644 --- a/site/src/data/index.ts +++ b/site/src/data/index.ts @@ -130,6 +130,7 @@ export const loci = rawLoci.map((locus) => { age_onset: extractCitations(locus.age_onset, references), details: extractCitations(locus.details, references), mechanism_detail: extractCitations(locus.mechanism_detail, references), + detection: extractCitations(locus.detection, references), year: extractCitations(locus.year, references), /** map references */ diff --git a/site/src/pages/loci/[id].astro b/site/src/pages/loci/[id].astro index e76da4e6..81fc16ce 100644 --- a/site/src/pages/loci/[id].astro +++ b/site/src/pages/loci/[id].astro @@ -348,7 +348,7 @@ const title = `Locus ${locus.id.replaceAll("_", " ")}`; } -
+
Details {locus.details && } @@ -370,13 +370,13 @@ const title = `Locus ${locus.id.replaceAll("_", " ")}`;
-
+
Detection - {locus.detection &&
{locus.detection}
} +
+ {locus.detection && } +
-
-
- Pathogenic (gene) Pathogen. (gene) Pathogenic motif, gene orientation @@ -528,7 +528,7 @@ const title = `Locus ${locus.id.replaceAll("_", " ")}`;
- Interruption (gene) Interrup. (gene) Interruption motif, gene orientation