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Char-AlChar-Al
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Add external links
1 parent 72bfafb commit f9a80a3

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Lines changed: 29 additions & 11 deletions

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‎seal/templates/analysis/sample.html‎

Lines changed: 29 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -575,32 +575,50 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
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const HGVSc = formatNA(data.HGVSc, "NA");
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const HGVSp = formatNA(data.HGVSp, "NA");
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578+
return `${HGVSg}\n${HGVSc}${response}\n${HGVSp}`;
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},
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// Nomenclature Column
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createColumn({
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id: "visible-Nomenclature",
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data: null,
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className: 'w3-border-right',
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myTitleFn: (data) => {
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if (data.annotations == null) return "<i>NA</i>";
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let response = data.annotations.preferred ? " (selected)" : "";
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response += data.annotations.canonical ? " (canonical)" : "";
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const HGVSg = formatNA(data.annotations.HGVSg, "NA");
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const HGVSc = formatNA(data.annotations.HGVSc, "NA");
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const HGVSp = formatNA(data.annotations.HGVSp, "NA");
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return `${HGVSg}\n${HGVSc}${response}\n${HGVSp}`;
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},
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renderConfig: {
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display: (data) => {
582-
if (data == null) return "<i>NA</i>";
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const mobidetails = (current_user_api_key_md !== "None") ? `<a target="_blank" title="MobiDetails" href="https://mobidetails.chu-montpellier.fr/api/variant/create?variant_chgvs=${encodeURIComponent(data.HGVSc)}&caller=browser&api_key=${current_user_api_key_md}" class="w3-text-flat-peter-river w3-hover-text-flat-carrot do-not-select" style="cursor: pointer;"><span class="fa-layers fa-fw do-not-select">
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if (data.annotations == null) return "<i>NA</i>";
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const genome = "{{ genome_version }}".toLowerCase() == "grch38" ? "hg38" : "hg19";
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const mobidetails = (current_user_api_key_md !== "None") ? `<a target="_blank" title="MobiDetails" href="https://mobidetails.chu-montpellier.fr/api/variant/create?variant_chgvs=${encodeURIComponent(data.annotations.HGVSc)}&caller=browser&api_key=${current_user_api_key_md}" class="w3-text-flat-peter-river w3-hover-text-flat-carrot do-not-select" style="cursor: pointer;"><span class="fa-layers fa-fw do-not-select">
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<span class="fa-layers do-not-select">
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<i class="fa-solid fa-square do-not-select" data-fa-transform="grow-11"></i>
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<span class="fa-layers-text fa-inverse do-not-select" data-fa-transform="shrink-3" style="font-weight:900">MD</span>
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</span>
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</span></a><br />` : "";
589-
const genebe = `<a target="_blank" title="GeneBe" href="https://genebe.net/variant/hg38/${data.HGVSg}" class="w3-text-flat-emerald w3-hover-text-flat-pumpkin do-not-select" style="cursor: pointer;"><span class="fa-layers fa-fw do-not-select">
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const genebe = `<a target="_blank" title="GeneBe" href="https://genebe.net/variant/${genome}/${data.annotations.HGVSg}" class="w3-text-flat-emerald w3-hover-text-flat-pumpkin do-not-select" style="cursor: pointer;"><span class="fa-layers fa-fw do-not-select">
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<span class="fa-layers do-not-select">
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<i class="fa-solid fa-square do-not-select" data-fa-transform="grow-11"></i>
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<span class="fa-layers-text fa-inverse do-not-select" data-fa-transform="shrink-3" style="font-weight:900">GB</span>
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</span>
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</span></a><br />`;
595-
const franklin = `<a target="_blank" title="Franklin" href="https://franklin.genoox.com/clinical-db/variant/snp/${data.HGVSg}" class="w3-text-flat-midnight-blue w3-hover-text-flat-turquoise do-not-select" style="cursor: pointer;"><span class="fa-layers fa-fw do-not-select">
613+
const franklin = `<a target="_blank" title="Franklin" href="https://franklin.genoox.com/clinical-db/variant/snp/${data.id}-${genome}" class="w3-text-flat-midnight-blue w3-hover-text-flat-turquoise do-not-select" style="cursor: pointer;"><span class="fa-layers fa-fw do-not-select">
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<span class="fa-layers do-not-select">
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<i class="fa-solid fa-square do-not-select" data-fa-transform="grow-11"></i>
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<span class="fa-layers-text fa-inverse do-not-select" data-fa-transform="shrink-3" style="font-weight:900">F</span>
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</span>
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</span></a>`;
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602-
const color = data.preferred ? "w3-text-flat-peter-river" : "";
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const starIcon = data.canonical
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const color = data.annotations.preferred ? "w3-text-flat-peter-river" : "";
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const starIcon = data.annotations.canonical
604622
? `<i class="${color} fas fa-star w3-tiny"></i>`
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: `<i class="${color} far fa-star w3-tiny"></i>`;
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@@ -610,9 +628,9 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
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${starIcon}
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</div>
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<div class="w3-container w3-cell" style="padding: 0px !important;">
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<p style="width: 180px;margin:0;white-space: nowrap;overflow: hidden;text-overflow: ellipsis;">${formatNA(data.HGVSg, "<i>NA</i>")}</p>
614-
<p style="width: 180px;margin:0;white-space: nowrap;overflow: hidden;text-overflow: ellipsis;">${formatNA(data.HGVSc, "<i>NA</i>")}</p>
615-
<p style="width: 180px;margin:0;white-space: nowrap;overflow: hidden;text-overflow: ellipsis;">${formatNA(data.HGVSp, "<i>NA</i>")}</p>
631+
<p style="width: 180px;margin:0;white-space: nowrap;overflow: hidden;text-overflow: ellipsis;">${formatNA(data.annotations.HGVSg, "<i>NA</i>")}</p>
632+
<p style="width: 180px;margin:0;white-space: nowrap;overflow: hidden;text-overflow: ellipsis;">${formatNA(data.annotations.HGVSc, "<i>NA</i>")}</p>
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<p style="width: 180px;margin:0;white-space: nowrap;overflow: hidden;text-overflow: ellipsis;">${formatNA(data.annotations.HGVSp, "<i>NA</i>")}</p>
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</div>
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<div class="w3-center w3-container w3-cell" style="vertical-align: middle;padding: 0px !important;">
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${mobidetails}${genebe}${franklin}
@@ -621,9 +639,9 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
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`;
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},
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sort: (data) => {
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if (!data || !data.HGVSg) return -1;
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if (!data.annotations || !data.annotations.HGVSg) return -1;
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626-
const matches = data.HGVSg.match(/(chr|cen|pter|qter|sup)?([0-9XYMt]+):[gmno]\.([0-9]+)(_[0-9]+)?([ACGT]+>)?(dup|ins|del|inv|[ACGT]+)?/);
644+
const matches = data.annotations.HGVSg.match(/(chr|cen|pter|qter|sup)?([0-9XYMt]+):[gmno]\.([0-9]+)(_[0-9]+)?([ACGT]+>)?(dup|ins|del|inv|[ACGT]+)?/);
627645
if (!matches) return -1;
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629647
const zero = "000000000";

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