From 7549d5d7ea188530e32e6709cd5e733d44dbf3ec Mon Sep 17 00:00:00 2001
From: Celine Pelletier <cpelletier@ferlab.bio>
Date: Tue, 2 Apr 2024 13:14:53 -0400
Subject: [PATCH] feat: SKFP-000 add indices usage script for genomic indices

---
 admin/findGenomicIndicesUsage.mjs | 70 +++++++++++++++++++++++++++++++
 1 file changed, 70 insertions(+)
 create mode 100644 admin/findGenomicIndicesUsage.mjs

diff --git a/admin/findGenomicIndicesUsage.mjs b/admin/findGenomicIndicesUsage.mjs
new file mode 100644
index 0000000..17c303b
--- /dev/null
+++ b/admin/findGenomicIndicesUsage.mjs
@@ -0,0 +1,70 @@
+/**
+(WIP) Helper script to find unused genomic indices
+ * */
+import assert from 'node:assert/strict';
+import { Client } from '@elastic/elasticsearch';
+import { esHost } from '../dist/src/env.js';
+
+const client = new Client({ node: esHost });
+
+const catCentricIndicesResponse = await client.cat.indices({
+    index: `*centric*`,
+    h: 'index,creation.date,creation.date.string',
+    format: 'json',
+});
+
+const catSuggestionsIndicesResponse = await client.cat.indices({
+    index: `*suggestions*`,
+    h: 'index,creation.date,creation.date.string',
+    format: 'json',
+});
+
+if (catCentricIndicesResponse.statusCode !== 200) {
+    console.error('Received bad response', catCentricIndicesResponse, ' Terminating.');
+    process.exit(1);
+}
+
+if (catSuggestionsIndicesResponse.statusCode !== 200) {
+    console.error('Received bad response', catSuggestionsIndicesResponse, ' Terminating.');
+    process.exit(1);
+}
+
+const cbKeepGenomicIndicesOnly = x => ['variant', 'gene'].some(stem => x.index.includes(stem));
+
+const genomicCentricIndices = catCentricIndicesResponse.body.filter(cbKeepGenomicIndicesOnly);
+assert(Array.isArray(genomicCentricIndices) && genomicCentricIndices.length > 0, 'No index found. Terminating');
+
+const genomicSuggestionsIndices = catSuggestionsIndicesResponse.body.filter(cbKeepGenomicIndicesOnly);
+assert(Array.isArray(genomicSuggestionsIndices) && genomicSuggestionsIndices.length > 0, 'No index found. Terminating');
+
+const genomicIndices = genomicCentricIndices.concat(genomicSuggestionsIndices);
+
+const allAliases = await client.cat.aliases({
+    h: 'alias,index',
+    format: 'json',
+});
+
+const genomicAliases = allAliases.body.filter(cbKeepGenomicIndicesOnly);
+
+const makeReleaseToCreationDate = l =>
+    l
+        .filter(x => 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']])
+        .reduce((xs, x) => (xs.some(y => y[0] === x[0]) ? xs : [...xs, x]), [])
+        .map(x => ({ release: x[0], creation_date: x[1] }));
+
+const genomicIndicesNotAliased = genomicIndices.filter(x => genomicAliases.every(a => a.index !== x.index));
+const unaliasedGenomicIndicesWithCreationDate = makeReleaseToCreationDate(genomicIndicesNotAliased);
+console.log(`===== Not Aliased`);
+
+unaliasedGenomicIndicesWithCreationDate.length
+    ? console.table(unaliasedGenomicIndicesWithCreationDate)
+    : console.log('None');
+
+console.log(`===== Aliased`);
+const genomicIndicesAliased = genomicIndices.filter(x => genomicAliases.some(a => a.index === x.index));
+const aliasedGenomicIndicesWithCreationDate = makeReleaseToCreationDate(genomicIndicesAliased);
+aliasedGenomicIndicesWithCreationDate.length
+    ? console.table(aliasedGenomicIndicesWithCreationDate)
+    : console.log('None');