🗑️ remove next prefix

admin/checkAliasWithRelease.mjs

@@ -15,10 +15,7 @@ const rAllAliases = await client.cat.aliases({
 assert(rAllAliases.statusCode === 200);
 
 const allAliases = rAllAliases.body;
-const hasNext = allAliases.some(x => x.alias.includes('next_'));
-const clinicalAliases = allAliases
-    .filter(cbKeepClinicalIndicesOnly)
-    .filter(x => (hasNext ? x.alias.includes('next_') : x));
+const clinicalAliases = allAliases.filter(cbKeepClinicalIndicesOnly);
 
 const aliasToReleases = clinicalAliases.reduce((xs, x) => {
     const r = 're' + x.index.split('_re_')[1];
@@ -34,9 +31,9 @@ const { all, ...entities } = aliasToReleases;
 console.log(`\n`);
 
 //not the best test but it should suffice
-const ok = hasNext ? all.length === 1 : all.length <= 2
+const ok = all.length <= 2;
 if (!ok) {
-    console.warn('Check if the clinical aliases are ok - There might be a problem')
+    console.warn('Check if the clinical aliases are ok - There might be a problem');
 }
 console.log(`Release(s) found: ${all}`);
 console.log(entities);

admin/confKfNext.json

@@ -2,31 +2,31 @@
   "indices": [
     {
       "graphqlField": "biospecimen",
-      "esIndex": "next_biospecimen_centric"
+      "esIndex": "biospecimen_centric"
     },
     {
       "graphqlField": "file",
-      "esIndex": "next_file_centric"
+      "esIndex": "file_centric"
     },
     {
       "graphqlField": "genes",
-      "esIndex": "next_gene_centric"
+      "esIndex": "gene_centric"
     },
     {
       "graphqlField": "members",
       "esIndex": "members-public"
     },
     {
       "graphqlField": "participant",
-      "esIndex": "next_participant_centric"
+      "esIndex": "participant_centric"
     },
     {
       "graphqlField": "study",
-      "esIndex": "next_study_centric"
+      "esIndex": "study_centric"
     },
     {
       "graphqlField": "variants",
-      "esIndex": "next_variant_centric"
+      "esIndex": "variant_centric"
     }
   ],
   "extendedMappingMutations": [

admin/postReleaseIndicesToAliasesHelper.mjs

@@ -4,7 +4,7 @@
  *
  *  npm run post-re-alias-helper -- release:re_test_023 action:remove
  *
- *   npm run post-re-alias-helper -- release:re_test_023 action:remove test
+ *   npm run post-re-alias-helper -- release:re_test_023 action:remove
  *
  * */
 import assert from 'node:assert/strict';
@@ -31,9 +31,6 @@ assert(
     }"`,
 );
 
-const testArgument = args.find(a => a.startsWith('test')) ?? '';
-const isTest = !!testArgument;
-
 const userReadline = readline.createInterface({
     input: process.stdin,
     output: process.stdout,
@@ -86,37 +83,18 @@ await displayIndicesQuestion();
 
 const INDICES_PREFIXES = ['biospecimen_centric', 'participant_centric', 'study_centric', 'file_centric'];
 
-const allAliases = await client.cat.aliases({
-    h: 'alias',
-    format: 'json',
-});
-
-//At this point, KF next uses the prefix next.
-const isNextFormat = allAliases.body
-    .map(x => x.alias)
-    .some(
-        x =>
-            x.startsWith('next_study_centric') ||
-            x.startsWith('next_participant_centric') ||
-            x.startsWith('next_biospecimen_centric') ||
-            x.startsWith('next_variant_centric') ||
-            x.startsWith('next_gene_centric') ||
-            x.startsWith('next_file_centric'),
-    );
-
 const actions = releaseIndices.reduce((xs, x) => {
     const prefix = INDICES_PREFIXES.find(p => x.startsWith(p));
     if (!prefix) {
         // Must never happen
         return xs;
     }
-    const alias = isNextFormat ? `next_${prefix}` : prefix;
     return [
         ...xs,
         {
             [aliasAction]: {
                 index: x,
-                alias: isTest ? `${alias}_test` : alias,
+                alias: prefix,
             },
         },
     ];
@@ -126,7 +104,7 @@ assert(actions.length === releaseIndices.length);
 const allIndexTargetsCorrectAlias = actions.every(a => {
     const index = a[aliasAction].index;
     const alias = a[aliasAction].alias;
-    return index.startsWith(alias.replace('next_', ''));
+    return index.startsWith(alias);
 });
 assert(allIndexTargetsCorrectAlias);
 

admin/run.mjs

@@ -1,5 +1,5 @@
 // docker run -u node -it --rm --network host -v ${PWD}:/code --workdir /code node:20-alpine3.18 sh
-// examples: npm run admin-project p:include e:include test OR npm run admin-project p:next_prd (will default to kf)
+// examples: npm run admin-project p:include e:include OR npm run admin-project p:prd (will default to kf)
 //kf-api-arranger/node_modules/@arranger/mapping-utils/dist/extendMapping.js change  rangeStep: ['double', 'float', 'half_float', 'scaled_float'].includes(type) ? 0.01 : 1 to rangeStep: 1.0
 /* eslint-disable no-console */
 import 'regenerator-runtime/runtime.js';
@@ -10,7 +10,6 @@ import { countNOfDocs, createIndexIfNeeded } from '../dist/src/esUtils.js';
 import { ArrangerApi } from './arrangerApi.mjs';
 import { projectsConfig } from './projectsConfig.mjs';
 import { esHost } from '../dist/src/env.js';
-import { clinicalIndexStems, isClinicalIndex } from './releaseStatsUtils.mjs';
 
 const hasProjectArrangerMetadataIndex = async (esClient, projectName) => {
     const r = await esClient.indices.exists({
@@ -40,7 +39,7 @@ const ENV = {
 const args = process.argv.slice(2);
 
 //de-hardcode when possible
-const SUPPORTED_PROJECT_NAMES = ['next_prd', 'next_qa', 'include', 'test'];
+const SUPPORTED_PROJECT_NAMES = ['prd', 'qa', 'include'];
 const projectArg = args.find(a => a.startsWith('p:'))?.split(':')[1];
 if (!projectArg || !SUPPORTED_PROJECT_NAMES.some(sp => sp === projectArg)) {
     console.warn(
@@ -73,35 +72,16 @@ console.info(`admin-project-script - Project value is=${envVal}`);
 console.debug(`admin-project-script - Reaching to ElasticSearch at ${esHost}`);
 const client = await EsInstance.default.getInstance();
 
-const isTest = args.some(a => a === 'test');
-const appendTestIfNeeded = x => (isTest && isClinicalIndex(x) ? `${x}_test` : x);
-if (isTest) {
-    const allAliases = await client.cat.aliases({
-        h: 'alias',
-        format: 'json',
-    });
-    const clinicalTestAliases = allAliases.body
-        .filter(x => isClinicalIndex(x.alias) && x.alias.endsWith('_test'))
-        .map(x => x.alias);
-    if (!clinicalTestAliases || !clinicalIndexStems.every(s => clinicalTestAliases.some(x => x.includes(s)))) {
-        console.debug(
-            `admin-project-script - Terminating. When creating a test, all clinical entities must be aliased with _test suffix`,
-        );
-        console.debug(`admin-project-script - received test aliases: `);
-        console.debug(clinicalTestAliases);
-        process.exit(1);
-    }
-}
 //values are hardcoded for now, but as soon as possible, we should use env var from env.ts
-const kfNext = [
-    'next_participant_centric',
-    'next_study_centric',
-    'next_biospecimen_centric',
-    'next_file_centric',
-    'next_variant_centric',
-    'next_gene_centric',
+const kf = [
+    'participant_centric',
+    'study_centric',
+    'biospecimen_centric',
+    'file_centric',
+    'variant_centric',
+    'gene_centric',
     'members-public',
-].map(x => (isTest && isClinicalIndex(x) ? appendTestIfNeeded(x) : x));
+];
 
 const include = [
     'participant_centric',
@@ -110,10 +90,10 @@ const include = [
     'file_centric',
     'variant_centric',
     'gene_centric',
-].map(x => (isTest && isClinicalIndex(x) ? appendTestIfNeeded(x) : x));
+];
 
 const envToIndicesPrefixes = {
-    kf: kfNext,
+    kf: kf,
     include: include,
 };
 
@@ -134,7 +114,7 @@ const projectName = projectArg;
 const allProjectsConf = projectsConfig(projectName, envVal);
 
 const projectsConf = allProjectsConf
-    .map(x => ({ ...x, indices: x.indices.map(i => ({ ...i, esIndex: appendTestIfNeeded(i.esIndex) })) }))
+    .map(x => ({ ...x, indices: x.indices.map(i => ({ ...i, esIndex: i.esIndex })) }))
     .filter(p => {
         const indicesInConf = p.indices.map(i => i.esIndex);
         // indices in conf are the same as target indices from env vars?
@@ -200,9 +180,9 @@ if (updateConditions.every(b => b)) {
     );
     if (nOfDocsInProjectMetadata === projectConf.indices.length) {
         console.debug(`admin-project-script - Applying extended mapping mutations.`);
-        console.time("fixExtendedMapping")
+        console.time('fixExtendedMapping');
         await ArrangerApi.fixExtendedMapping(client, projectConf.extendedMappingMutations);
-        console.timeEnd("fixExtendedMapping")
+        console.timeEnd('fixExtendedMapping');
     }
 }