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🔧 Make findClinicalUsage script more flexible + update arrange… #207

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merged 2 commits into from
Oct 11, 2024
Merged

🔧 Make findClinicalUsage script more flexible + update arrange… #207

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47c9559
:wrench: Make findClinicalUsage script more flexible + update arrange…
evans-g-crsj Oct 11, 2024
dc21b6d
:art: Simplify if cond in findClinicalIndicesUsage
evans-g-crsj Oct 11, 2024
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7 changes: 7 additions & 0 deletions admin/arrangerProjectConf.json
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Original file line number Diff line number Diff line change
Expand Up @@ -315,6 +315,13 @@
"isArray": true
}
},
{
"field": "study_meta_categories",
"graphqlField": "study",
"extendedFieldMappingInput": {
"isArray": true
}
},
{
"field": "clinvar.clin_sig",
"graphqlField": "variants",
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40 changes: 21 additions & 19 deletions admin/findClinicalIndicesUsage.mjs
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Original file line number Diff line number Diff line change
Expand Up @@ -29,16 +29,30 @@ const allAliases = await client.cat.aliases({

const clinicalAliases = allAliases.body.filter(cbKeepClinicalPlusTranscriptomicsIndicesOnly);

const makeReleaseToCreationDate = l =>
const formatTableContent = (l, standardRePattern = true) =>
l
.filter(x => x.index.includes('_re_'))
.filter(x => (standardRePattern ? x.index.includes('_re_') : !x.index.includes('_re_')))
.sort((a, b) => b['creation.date'] - a['creation.date'])
.map(x => ['re_' + x.index.split('re_')[1], x['creation.date.string'], isIndexNameFromTranscriptomics(x.index)])
.reduce((xs, x) => (xs.some(y => y[0] === x[0]) ? xs : [...xs, x]), [])
.map(x => {
if (standardRePattern) {
return [
're_' + x.index.split('re_')[1],
x['creation.date.string'],
isIndexNameFromTranscriptomics(x.index),
];
}
const release = x.index
.split('sd_')[1]
.split('_')
.slice(1)
.join('_');
return [release, x['creation.date.string'], isIndexNameFromTranscriptomics(x.index)];
})
.reduce((xs, x) => (xs.some(y => y[0] === x[0] && y[2] === x[2]) ? xs : [...xs, x]), [])
.map(x => ({ release: x[0], creation_date: x[1], transcriptomics: x[2] }));

const clinicalIndicesNotAliased = clinicalIndices.filter(x => clinicalAliases.every(a => a.index !== x.index));
const unaliasedClinicalIndicesWithCreationDate = makeReleaseToCreationDate(clinicalIndicesNotAliased);
const unaliasedClinicalIndicesWithCreationDate = formatTableContent(clinicalIndicesNotAliased);

console.log(`===== Not Aliased (pattern:re_*)`);
unaliasedClinicalIndicesWithCreationDate.length
Expand All @@ -58,24 +72,12 @@ const showIfOnlyCbtn = re => {

//======

const aliasedClinicalIndicesWithCreationDate = makeReleaseToCreationDate(clinicalIndicesAliased);
const aliasedClinicalIndicesWithCreationDate = formatTableContent(clinicalIndicesAliased);
aliasedClinicalIndicesWithCreationDate.length
? console.table(aliasedClinicalIndicesWithCreationDate.map(x => ({ ...x, release: showIfOnlyCbtn(x.release) })))
: console.log('None');

console.log(`===== Others (Clinical)`);
const othersClinical = clinicalIndices
.filter(x => !x.index.includes('_re_'))
.sort((a, b) => b['creation.date'] - a['creation.date'])
.map(x => {
const release = x.index
.split('sd_')[1]
.split('_')
.slice(1)
.join('_');
return [release, x['creation.date.string'], isIndexNameFromTranscriptomics(x.index)];
})
.reduce((xs, x) => (xs.some(y => y[0] === x[0]) ? xs : [...xs, x]), [])
.map(x => ({ release: x[0], creation_date: x[1], transcriptomics: x[2] }));
const othersClinical = formatTableContent(clinicalIndices, false);

othersClinical.length ? console.table(othersClinical) : console.log('None');
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