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Merged
Char-Al merged 9 commits into from
Aug 22, 2025
Merged

Update dev #86

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f0371a6
Merge pull request #85 from mobidic/dev
Char-Al Aug 20, 2025
1a42e77
Fix : scheduler when import another VCF
Char-Al Aug 21, 2025
d900276
Remove log development messages
Char-Al Aug 21, 2025
66a5026
Remove log development messages
Char-Al Aug 21, 2025
b016472
Fix: comma at the end of datatable
Char-Al Aug 21, 2025
72bfafb
Fix: sorting on column 'Gene'
Char-Al Aug 21, 2025
f9a80a3
Add external links
Char-Al Aug 21, 2025
fdae73c
Fix: Return values for predictions scores (filter and export columns)
Char-Al Aug 21, 2025
b4bb9aa
Fix: change orgin-data for MaxEntScan (bug with SearchBuilder)
Char-Al Aug 21, 2025
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9 changes: 6 additions & 3 deletions seal/schedulers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -449,14 +449,15 @@ def importvcf():
app.logger.error(f'Path does not exist for : {vcf_path}')
path_locker.unlink()
return

status_final = False
if "add_caller" in data and data["add_caller"] == True:
sample = get_sample(data)
if not sample:
app.logger.error(f'Sample does not found')
path_locker.unlink()
return
msg = "Add new caller"
status_final = sample.status
else:
sample = create_sample(data)
msg = "Import Sample"
Expand Down Expand Up @@ -493,7 +494,8 @@ def importvcf():
app.logger.info("------ END VEP ------")
except CommandFailedError as e:
app.logger.info(f"{type(e).__name__} : {e}")
sample.status = -1
if not status_final:
sample.status = -1
path_locker.unlink()
db.session.commit()
error_file = current_file.with_suffix('.error')
Expand Down Expand Up @@ -678,7 +680,8 @@ def importvcf():
date=datetime.now(),
action=f"Sample Imported")
db.session.add(history)
sample.status = 1
if not status_final:
sample.status = status
db.session.commit()


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17 changes: 0 additions & 17 deletions seal/static/seal/analysis/sample.js
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Original file line number Diff line number Diff line change
Expand Up @@ -360,7 +360,6 @@ function BaseConditionsFilterSelect(values_options, condition="==", sort=true) {
}
if (sort) {
options.sort((a, b) => {
console.log(a.val())
if (a.val().toLowerCase() < b.val().toLowerCase()) {
return -1;
} else if (a.val().toLowerCase() > b.val().toLowerCase()) {
Expand Down Expand Up @@ -408,14 +407,6 @@ function BaseConditionsFilterSelect(values_options, condition="==", sort=true) {
case "isTrue":
conditionName = "Is True";
search = function (value) {
console.log("t");
console.log((value === false ||
value === "false" ||
value === "0" ||
value === null ||
value === undefined ||
value === "" ||
(typeof value === 'number' && isNaN(value))))
return value === true ||
value === "true" ||
value === "1" ||
Expand All @@ -426,14 +417,6 @@ function BaseConditionsFilterSelect(values_options, condition="==", sort=true) {
case "isFalse":
conditionName = "Is False";
search = function (value) {
console.log("f");
console.log((value === false ||
value === "false" ||
value === "0" ||
value === null ||
value === undefined ||
value === "" ||
(typeof value === 'number' && isNaN(value))))
return value === false ||
value === "false" ||
value === "0" ||
Expand Down
85 changes: 43 additions & 42 deletions seal/templates/analysis/sample.html
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Original file line number Diff line number Diff line change
Expand Up @@ -548,6 +548,9 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
data: "annotations",
myTitleFn: (data) => formatNA(data.SYMBOL),
renderConfig: {
default: (data) => {
return data.SYMBOL
},
display: (data) => {
return data.SYMBOL == null
? "<i>NA</i>"
Expand All @@ -560,44 +563,45 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
// Nomenclature Column
createColumn({
id: "visible-Nomenclature",
data: "annotations",
data: null,
className: 'w3-border-right',
myTitleFn: (data) => {
if (data == null) return "<i>NA</i>";
if (data.annotations == null) return "<i>NA</i>";

let response = data.preferred ? " (selected)" : "";
response += data.canonical ? " (canonical)" : "";
let response = data.annotations.preferred ? " (selected)" : "";
response += data.annotations.canonical ? " (canonical)" : "";

const HGVSg = formatNA(data.HGVSg, "NA");
const HGVSc = formatNA(data.HGVSc, "NA");
const HGVSp = formatNA(data.HGVSp, "NA");
const HGVSg = formatNA(data.annotations.HGVSg, "NA");
const HGVSc = formatNA(data.annotations.HGVSc, "NA");
const HGVSp = formatNA(data.annotations.HGVSp, "NA");

return `${HGVSg}\n${HGVSc}${response}\n${HGVSp}`;
},
renderConfig: {
display: (data) => {
if (data == null) return "<i>NA</i>";
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">
if (data.annotations == null) return "<i>NA</i>";
const genome = "{{ genome_version }}".toLowerCase() == "grch38" ? "hg38" : "hg19";
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">
<span class="fa-layers do-not-select">
<i class="fa-solid fa-square do-not-select" data-fa-transform="grow-11"></i>
<span class="fa-layers-text fa-inverse do-not-select" data-fa-transform="shrink-3" style="font-weight:900">MD</span>
</span>
</span></a><br />` : "";
const genebe = `<a target="_blank" title="GeneBe" href="https://genebe.net/variant/hg38/${data.HGVSg}" class="w3-text-flat-emerald w3-hover-text-flat-pumpkin do-not-select" style="cursor: pointer;"><span class="fa-layers fa-fw do-not-select">
const genebe = `<a target="_blank" title="GeneBe" href="https://genebe.net/variant/${genome}/${data.annotations.HGVSg}" class="w3-text-flat-emerald w3-hover-text-flat-pumpkin do-not-select" style="cursor: pointer;"><span class="fa-layers fa-fw do-not-select">
<span class="fa-layers do-not-select">
<i class="fa-solid fa-square do-not-select" data-fa-transform="grow-11"></i>
<span class="fa-layers-text fa-inverse do-not-select" data-fa-transform="shrink-3" style="font-weight:900">GB</span>
</span>
</span></a><br />`;
const franklin = `<a target="_blank" title="Franklin" href="https://franklin.genoox.com/clinical-db/variant/snp/${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">
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">
<span class="fa-layers do-not-select">
<i class="fa-solid fa-square do-not-select" data-fa-transform="grow-11"></i>
<span class="fa-layers-text fa-inverse do-not-select" data-fa-transform="shrink-3" style="font-weight:900">F</span>
</span>
</span></a>`;

const color = data.preferred ? "w3-text-flat-peter-river" : "";
const starIcon = data.canonical
const color = data.annotations.preferred ? "w3-text-flat-peter-river" : "";
const starIcon = data.annotations.canonical
? `<i class="${color} fas fa-star w3-tiny"></i>`
: `<i class="${color} far fa-star w3-tiny"></i>`;

Expand All @@ -607,9 +611,9 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
${starIcon}
</div>
<div class="w3-container w3-cell" style="padding: 0px !important;">
<p style="width: 180px;margin:0;white-space: nowrap;overflow: hidden;text-overflow: ellipsis;">${formatNA(data.HGVSg, "<i>NA</i>")}</p>
<p style="width: 180px;margin:0;white-space: nowrap;overflow: hidden;text-overflow: ellipsis;">${formatNA(data.HGVSc, "<i>NA</i>")}</p>
<p style="width: 180px;margin:0;white-space: nowrap;overflow: hidden;text-overflow: ellipsis;">${formatNA(data.HGVSp, "<i>NA</i>")}</p>
<p style="width: 180px;margin:0;white-space: nowrap;overflow: hidden;text-overflow: ellipsis;">${formatNA(data.annotations.HGVSg, "<i>NA</i>")}</p>
<p style="width: 180px;margin:0;white-space: nowrap;overflow: hidden;text-overflow: ellipsis;">${formatNA(data.annotations.HGVSc, "<i>NA</i>")}</p>
<p style="width: 180px;margin:0;white-space: nowrap;overflow: hidden;text-overflow: ellipsis;">${formatNA(data.annotations.HGVSp, "<i>NA</i>")}</p>
</div>
<div class="w3-center w3-container w3-cell" style="vertical-align: middle;padding: 0px !important;">
${mobidetails}${genebe}${franklin}
Expand All @@ -618,9 +622,9 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
`;
},
sort: (data) => {
if (!data || !data.HGVSg) return -1;
if (!data.annotations || !data.annotations.HGVSg) return -1;

const matches = data.HGVSg.match(/(chr|cen|pter|qter|sup)?([0-9XYMt]+):[gmno]\.([0-9]+)(_[0-9]+)?([ACGT]+>)?(dup|ins|del|inv|[ACGT]+)?/);
const matches = data.annotations.HGVSg.match(/(chr|cen|pter|qter|sup)?([0-9XYMt]+):[gmno]\.([0-9]+)(_[0-9]+)?([ACGT]+>)?(dup|ins|del|inv|[ACGT]+)?/);
if (!matches) return -1;

const zero = "000000000";
Expand Down Expand Up @@ -896,10 +900,6 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
const clinvar = data.clinvar || {};
const phenotypes = data.phenotypes || {};
const star = (clinvar.CLNREVSTAT == null) ? 0 : clinvar_stars[clinvar.CLNREVSTAT];
if(clinvar.CLNREVSTAT == null){
console.log(`${clinvar_stars[clinvar.CLNREVSTAT]} - ${clinvar.CLNREVSTAT}`)
}

let stat = '';
if (clinvar.CLNREVSTAT) {
stat = ` (${star}/4)`;
Expand Down Expand Up @@ -951,7 +951,6 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
color = "peter-river";
colorHover = "belize-hole";
if (/pathogenic|establish/i.test(clinvar.CLNSIGCONF)) {
console.log(clinvar.CLNREVSTAT)
color = "carrot";
colorHover = "pumpkin";
}
Expand Down Expand Up @@ -1474,25 +1473,28 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
}),
createColumn({
id: "export-filter-clinvar_revstat",
data: "clinvar.CLNSIG",
data: null,
searchBuilderTitle:"ClinVar",
visible: false,
type: "clinvar",
renderConfig: {
default: (data) => {
const clinvar = data || {};
const clinvar = data.clinvar || {};
let value = "2 - NA";

if (clinvar) {
if (/benign/i.test(clinvar)) value = "0 - Benign/Likely Benign";
else if (/uncertain/i.test(clinvar)) value = "3 - Uncertain significance";
else if (/pathogenic|establish/i.test(clinvar)) value = "5 - Pathogenic/Likely Pathogenic";
else if (/conflicting/i.test(clinvar)) {
value = "1 - Conflicting (without Pathogenic)";
if (/pathogenic|establish/i.test(clinvar)) {
value = "4 - Conflicting (with Pathogenic)";
if (clinvar.CLNSIG) {
if (/benign/i.test(clinvar.CLNSIG)) {
value = "0 - Benign/Likely Benign"
} else if (/uncertain/i.test(clinvar.CLNSIG)) {
value = "3 - Uncertain significance"
} else if (/conflicting/i.test(clinvar.CLNSIG)) {
value = "1 - Conflicting (without Pathogenic)"
if (/pathogenic|establish/i.test(clinvar.CLNSIGCONF)) {
value = "4 - Conflicting (with Pathogenic)"
}
}
} else if (/pathogenic|establish/i.test(clinvar.CLNSIG)) {
value = "5 - Pathogenic/Likely Pathogenic"
}
}
return value;
},
Expand Down Expand Up @@ -1539,16 +1541,16 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
}),
createColumn({
id: "export-filter-MES",
data: "annotations",
data: null,
searchBuilderTitle:"Prediction - MaxEntScan",
visible: false,
renderConfig: {
default: (data, type) => {
const alt = parseFloat(data.MaxEntScan_alt || 0).toFixed(2);
const ref = parseFloat(data.MaxEntScan_ref || 0).toFixed(2);
const alt = parseFloat(data.annotations.MaxEntScan_alt || 0).toFixed(2);
const ref = parseFloat(data.annotations.MaxEntScan_ref || 0).toFixed(2);
const mes_var = (((alt - ref) / Math.abs(ref)) * 100).toFixed(2);
d = isNaN(parseFloat(mes_var)) ? null: parseFloat(mes_var).toFixed(2);
return type === 'export' && d=== null? '' : data;
return type === 'export' && d=== null? '' : Math.abs(d);
},
}
}),
Expand All @@ -1560,7 +1562,7 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
renderConfig: {
default: (data, type) => {
d = isNaN(parseFloat(data)) ? null: parseFloat(data).toFixed(2);
return type === 'export' && d=== null? '' : data;
return type === 'export' && d=== null? '' : d;
},
}
}),
Expand All @@ -1572,8 +1574,7 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
renderConfig: {
default: (data, type) => {
d = isNaN(parseFloat(data)) ? null: parseFloat(data).toFixed(2);
return type === 'export' && d=== null? '' : data;
return isNaN(parseFloat(data)) ? null: parseFloat(data).toFixed(2);
return type === 'export' && d=== null? '' : d;
},
}
}),
Expand Down Expand Up @@ -1658,7 +1659,7 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
return `[${family.filter}] ${af} (${family.allelic_depth}/${family.depth})`;
},
}
})
}),
{% endfor %}
];

Expand Down
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