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Foundation for wave 3: intelligence schema (trial_intelligence, trial_site_country_counts, drug_pipeline, drug_codes, research_gap_components; migration 0002), trial intervention→drug reconciliation (alias/salt-stripped/probabilistic), new metric definitions (trial growth, termination share, sponsor HHI, per-1000-deaths, gap ratios), maintenance.intel job, API route stubs (epidemiology/approvals/graph/intelligence), navigation restructure

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Simon-Pierre Boucher committed 13 days ago (Sep 11, 2026) parent 718f988

27 changed files +8,980 −12

modified apps/api/src/app.ts +12 −0
@@ -26,6 +26,10 @@ import { sourceRoutes } from './routes/sources.js';
26 26 import { statsRoutes } from './routes/stats.js';
27 27 import { changeRoutes } from './routes/changes.js';
28 28 import { adminRoutes } from './routes/admin.js';
29 +import { graphRoutes } from './routes/graph.js';
30 +import { epidemiologyRoutes } from './routes/epidemiology.js';
31 +import { approvalRoutes } from './routes/approvals.js';
32 +import { intelligenceRoutes } from './routes/intelligence.js';
29 33
30 34 export interface BuildOptions {
31 35 db?: Database;
@@ -103,6 +107,10 @@ export async function buildApp(opts: BuildOptions = {}): Promise<FastifyInstance
103 107 { name: 'sources', description: 'Source registry, licenses, connector health' },
104 108 { name: 'stats' },
105 109 { name: 'changes' },
110 + { name: 'epidemiology', description: 'Time-aware incidence/mortality/prevalence observations with provenance (Data Explorer)' },
111 + { name: 'approvals', description: 'Jurisdiction-aware regulatory approvals and the drug development pipeline' },
112 + { name: 'graph', description: 'Cancer–gene–variant–drug–trial knowledge graph (contextual neighbourhoods)' },
113 + { name: 'intelligence', description: 'Derived clinical-trial intelligence and research-gap components (computed metrics with formula versions)' },
106 114 { name: 'admin', description: 'Operator endpoints (x-admin-token)' },
107 115 { name: 'system' },
108 116 ],
@@ -152,6 +160,10 @@ export async function buildApp(opts: BuildOptions = {}): Promise<FastifyInstance
152 160 await v1.register(sourceRoutes);
153 161 await v1.register(statsRoutes);
154 162 await v1.register(changeRoutes);
163 + await v1.register(epidemiologyRoutes);
164 + await v1.register(approvalRoutes);
165 + await v1.register(graphRoutes);
166 + await v1.register(intelligenceRoutes);
155 167 await v1.register(adminRoutes, { prefix: '/admin' });
156 168 },
157 169 { prefix: '/v1' },
modified apps/api/src/lib/queue.ts +1 −0
@@ -8,6 +8,7 @@ export const JOBS = {
8 8 connectorRun: 'connector.run',
9 9 counters: 'maintenance.counters',
10 10 rank: 'maintenance.rank',
11 + intel: 'maintenance.intel',
11 12 healthProbe: 'health.probe',
12 13 } as const;
13 14 export type JobName = (typeof JOBS)[keyof typeof JOBS];
added apps/api/src/routes/approvals.ts +10 −0
@@ -0,0 +1,10 @@
1 +import type { FastifyPluginAsyncZod } from 'fastify-type-provider-zod';
2 +
3 +/**
4 + * Regulatory routes (SPEC §13-15, §63): `GET /approvals` (jurisdiction-aware, dated, filterable by
5 + * authority, cancer, drug, date range), `GET /approvals/recent`, `GET /pipeline` (drug development
6 + * stages). Filled by the Approvals & Pipeline work package.
7 + */
8 +export const approvalRoutes: FastifyPluginAsyncZod = async (_app) => {
9 + /* routes added by the approvals work package */
10 +};
added apps/api/src/routes/epidemiology.ts +10 −0
@@ -0,0 +1,10 @@
1 +import type { FastifyPluginAsyncZod } from 'fastify-type-provider-zod';
2 +
3 +/**
4 + * Epidemiology routes (SPEC §20, §63, §110): `GET /epidemiology` → observations filtered by metric,
5 + * cancer, geography, sex, age group and year range; `GET /epidemiology/coverage` → which
6 + * metric × geography × year combinations exist. Filled by the Data Explorer work package.
7 + */
8 +export const epidemiologyRoutes: FastifyPluginAsyncZod = async (_app) => {
9 + /* routes added by the data-explorer work package */
10 +};
added apps/api/src/routes/graph.ts +10 −0
@@ -0,0 +1,10 @@
1 +import type { FastifyPluginAsyncZod } from 'fastify-type-provider-zod';
2 +
3 +/**
4 + * Knowledge-graph routes (SPEC §18, §80): `GET /graph/:type/:id` → contextual neighbours of one
5 + * entity (cancer | gene | variant | drug | biomarker | trial) with relationship type, cancer context,
6 + * evidence level and provenance on every edge. Filled by the Knowledge Graph work package.
7 + */
8 +export const graphRoutes: FastifyPluginAsyncZod = async (_app) => {
9 + /* routes added by the knowledge-graph work package */
10 +};
added apps/api/src/routes/intelligence.ts +18 −0
@@ -0,0 +1,18 @@
1 +import type { FastifyPluginAsyncZod } from 'fastify-type-provider-zod';
2 +
3 +/**
4 + * Intelligence routes (SPEC §10-11, §34): `GET /trials/intelligence` (per-cancer trial metrics),
5 + * `GET /trials/sites` (country/city aggregates for the map), `GET /research-gap` (components and
6 + * ratios per scope). Filled by the Trial Intelligence and Research Gap work packages
7 + * (each adds its own routes to this file; keep route groups in separate functions).
8 + */
9 +export const intelligenceRoutes: FastifyPluginAsyncZod = async (app) => {
10 + await app.register(trialIntelligenceRoutes);
11 + await app.register(researchGapRoutes);
12 +};
13 +
14 +/** Filled by the Trial Intelligence work package. */
15 +export const trialIntelligenceRoutes: FastifyPluginAsyncZod = async (_app) => {};
16 +
17 +/** Filled by the Research Gap work package. */
18 +export const researchGapRoutes: FastifyPluginAsyncZod = async (_app) => {};
modified apps/web/src/components/layout/mobile-nav.tsx +2 −2
@@ -1,6 +1,6 @@
1 1 import Link from 'next/link';
2 2 import { Menu } from 'lucide-react';
3 −import { NAV, FOOTER_NAV } from '@/lib/site';
3 +import { NAV, MORE_NAV, FOOTER_NAV } from '@/lib/site';
4 4
5 5 /** CSS-only disclosure menu for small screens (no client JS). */
6 6 export function MobileNav() {
@@ -16,7 +16,7 @@ export function MobileNav() {
16 16 </Link>
17 17 ))}
18 18 <div className="my-1 border-t border-rule" />
19 − {FOOTER_NAV.filter((f) => !NAV.some((n) => n.href === f.href)).map((n) => (
19 + {[...MORE_NAV, ...FOOTER_NAV.filter((f) => !NAV.some((n) => n.href === f.href) && !MORE_NAV.some((m) => m.href === f.href))].map((n) => (
20 20 <Link key={n.href} href={n.href} className="block px-3 py-1.5 text-[13px] text-ink-2 no-underline hover:bg-paper-2">
21 21 {n.label}
22 22 </Link>
modified apps/web/src/lib/site.ts +20 −5
@@ -7,13 +7,24 @@ export const CONTACT_EMAIL = 'corrections@cancerindex.io';
7 7
8 8 export const NAV = [
9 9 { href: '/cancers', label: 'Cancers' },
10 − { href: '/taxonomy', label: 'Taxonomy' },
10 + { href: '/explore', label: 'Data' },
11 + { href: '/trials', label: 'Trials' },
12 + { href: '/drugs', label: 'Drugs' },
13 + { href: '/genes', label: 'Genes' },
14 + { href: '/approvals', label: 'Approvals' },
11 15 { href: '/rankings', label: 'Rankings' },
16 + { href: '/research-gap', label: 'Research gap' },
17 + { href: '/graph', label: 'Graph' },
18 +] as const;
19 +
20 +/** Secondary navigation (mobile menu + footer): everything not in the primary bar. */
21 +export const MORE_NAV = [
22 + { href: '/taxonomy', label: 'Taxonomy' },
12 23 { href: '/countries', label: 'Countries' },
13 24 { href: '/compare', label: 'Compare' },
14 − { href: '/genes', label: 'Genes' },
15 − { href: '/drugs', label: 'Drugs' },
16 − { href: '/trials', label: 'Trials' },
25 + { href: '/trials/intelligence', label: 'Trial intelligence' },
26 + { href: '/trials/map', label: 'Trial map' },
27 + { href: '/pipeline', label: 'Drug pipeline' },
17 28 { href: '/sources', label: 'Sources' },
18 29 { href: '/methodology', label: 'Methodology' },
19 30 ] as const;
@@ -21,10 +32,14 @@ export const NAV = [
21 32 export const FOOTER_NAV = [
22 33 { href: '/about', label: 'About' },
23 34 { href: '/trust', label: 'Trust & policies' },
35 + { href: '/explore', label: 'Data explorer' },
24 36 { href: '/data', label: 'Data downloads' },
25 − { href: '/developers', label: 'Developers' },
37 + { href: '/developers', label: 'Developers (API)' },
26 38 { href: '/sources', label: 'Sources' },
27 39 { href: '/methodology', label: 'Methodology' },
40 + { href: '/taxonomy', label: 'Taxonomy' },
41 + { href: '/countries', label: 'Countries' },
42 + { href: '/compare', label: 'Compare' },
28 43 ] as const;
29 44
30 45 /** External identifier browsers (chips on cancer pages link out to the authority). */
added packages/connectors/src/connectors/clinicaltrials/drugs.test.ts +39 −0
@@ -0,0 +1,39 @@
1 +import { describe, expect, it } from 'vitest';
2 +import { stripToMolecule, NON_DRUG_RE } from './drugs.js';
3 +
4 +describe('stripToMolecule (trial intervention → molecule)', () => {
5 + it('strips leading registry labels', () => {
6 + expect(stripToMolecule('Drug: Cisplatin')).toBe('cisplatin');
7 + expect(stripToMolecule('Biological: Pembrolizumab')).toBe('pembrolizumab');
8 + });
9 + it('strips salts and esters', () => {
10 + expect(stripToMolecule('Doxorubicin Hydrochloride')).toBe('doxorubicin');
11 + expect(stripToMolecule('Gemcitabine Hydrochloride Injection')).toBe('gemcitabine');
12 + expect(stripToMolecule('Imatinib Mesylate')).toBe('imatinib');
13 + expect(stripToMolecule('Vincristine Sulfate')).toBe('vincristine');
14 + });
15 + it('strips doses, routes and parentheticals', () => {
16 + expect(stripToMolecule('Pembrolizumab 200 mg IV')).toBe('pembrolizumab');
17 + expect(stripToMolecule('Pembrolizumab (MK-3475)')).toBe('pembrolizumab');
18 + expect(stripToMolecule('Oral capecitabine 1000 mg/m2')).toBe('capecitabine');
19 + });
20 + it('returns null when nothing changes (pass 1 already covered it)', () => {
21 + expect(stripToMolecule('Pembrolizumab')).toBeNull();
22 + expect(stripToMolecule('nab-paclitaxel')).toBeNull();
23 + });
24 + it('never collapses a distinct product to its parent molecule', () => {
25 + // "protein bound" is not a salt/formulation token: the qualifier is kept, so the label is either
26 + // unchanged (null → stays in pass 1 territory) or only loses its dose.
27 + expect(stripToMolecule('Paclitaxel protein-bound')).toBeNull();
28 + expect(stripToMolecule('Paclitaxel protein-bound 100 mg/m2')).toBe('paclitaxel protein bound');
29 + });
30 +});
31 +
32 +describe('NON_DRUG_RE', () => {
33 + it('flags placebo / procedures / care as non-drugs', () => {
34 + for (const s of ['Placebo', 'placebo matching pembrolizumab', 'Standard of care', 'Best Supportive Care', 'Surgery', 'Radiation therapy']) expect(NON_DRUG_RE.test(s)).toBe(true);
35 + });
36 + it('lets molecule names through', () => {
37 + for (const s of ['Cisplatin', 'Dexamethasone', 'Placebo-controlled nivolumab']) expect(NON_DRUG_RE.test(s)).toBe(false);
38 + });
39 +});
added packages/connectors/src/connectors/clinicaltrials/drugs.ts +265 −0
@@ -0,0 +1,265 @@
1 +import { sql } from 'drizzle-orm';
2 +import type { Database } from '@cancerindex/database';
3 +import { normalizeLabel } from '@cancerindex/shared';
4 +
5 +/**
6 + * Trial intervention → canonical drug reconciliation (CLAUDE.md §69, §221; SPEC §9, §97).
7 + *
8 + * Registrants type intervention names freely ("Pembrolizumab", "MK-3475", "Keytruda 200 mg",
9 + * "Drug: cisplatin", "Doxorubicin Hydrochloride"). We reconcile in three deterministic passes, each
10 + * recorded as its own `match_type` so the UI can show how a link was made:
11 + *
12 + * 1. ALIAS — normalized name equals a `drug_aliases.normalized` (generic, brand,
13 + * development code or synonym) that maps to exactly one drug.
14 + * 2. ALIAS — the same after stripping registry noise: a leading "drug:"/"biological:"
15 + * label, dose/route suffixes ("200 mg", "iv", "tablets"), and a trailing salt
16 + * or ester ("hydrochloride", "sulfate", "acetate"…). Stored with `via` in the
17 + * normalized form so the strip is auditable.
18 + * 3. PROBABILISTIC — the first word of a multi-word name is itself an unambiguous generic alias
19 + * (e.g. "paclitaxel protein bound" → paclitaxel is *not* accepted here because
20 + * nab-paclitaxel is a distinct product; the pass is limited to names whose
21 + * remaining words are dose/route/formulation tokens only).
22 + *
23 + * Aliases that point to several drugs are skipped (ambiguous) — never guessed. Placebo, "standard
24 + * of care", procedures and classes are left UNRESOLVED on purpose; they are not drugs.
25 + *
26 + * Everything is set-based SQL (fast on ~250 k rows) and idempotent: rows already mapped are left
27 + * untouched unless `remap` is requested (after an alias-set change).
28 + */
29 +
30 +/** Salts / esters / counter-ions that name the same molecule (trailing tokens). */
31 +export const SALT_TOKENS = [
32 + 'hydrochloride',
33 + 'dihydrochloride',
34 + 'hcl',
35 + 'sulfate',
36 + 'sulphate',
37 + 'acetate',
38 + 'sodium',
39 + 'disodium',
40 + 'potassium',
41 + 'calcium',
42 + 'magnesium',
43 + 'mesylate',
44 + 'mesilate',
45 + 'dimesylate',
46 + 'citrate',
47 + 'tartrate',
48 + 'bitartrate',
49 + 'maleate',
50 + 'malate',
51 + 'fumarate',
52 + 'phosphate',
53 + 'diphosphate',
54 + 'succinate',
55 + 'tosylate',
56 + 'besylate',
57 + 'bromide',
58 + 'chloride',
59 + 'lactate',
60 + 'gluconate',
61 + 'pamoate',
62 + 'trihydrate',
63 + 'dihydrate',
64 + 'monohydrate',
65 + 'hydrate',
66 + 'anhydrous',
67 + 'ditosylate',
68 + 'camsylate',
69 + 'hemihydrate',
70 + 'hydrobromide',
71 + 'nitrate',
72 + 'oxalate',
73 + 'propionate',
74 + 'valerate',
75 + 'decanoate',
76 + 'enanthate',
77 + 'undecanoate',
78 + 'cypionate',
79 + 'pivalate',
80 + 'isethionate',
81 + 'trifluoroacetate',
82 +];
83 +
84 +/** Formulation / dose / route tokens that never change the molecule. */
85 +export const FORMULATION_TOKENS = [
86 + 'mg',
87 + 'mcg',
88 + 'ug',
89 + 'g',
90 + 'ml',
91 + 'iu',
92 + 'units',
93 + 'unit',
94 + 'tablet',
95 + 'tablets',
96 + 'capsule',
97 + 'capsules',
98 + 'injection',
99 + 'injections',
100 + 'infusion',
101 + 'solution',
102 + 'suspension',
103 + 'oral',
104 + 'iv',
105 + 'intravenous',
106 + 'subcutaneous',
107 + 'sc',
108 + 'im',
109 + 'intramuscular',
110 + 'topical',
111 + 'cream',
112 + 'gel',
113 + 'patch',
114 + 'kg',
115 + 'm2',
116 + 'daily',
117 + 'weekly',
118 + 'bid',
119 + 'qd',
120 + 'dose',
121 + 'doses',
122 + 'low',
123 + 'high',
124 + 'standard',
125 + 'extended',
126 + 'release',
127 + 'er',
128 + 'xr',
129 + 'sr',
130 + 'depot',
131 + 'vial',
132 + 'for',
133 + 'per',
134 + 'x',
135 +];
136 +
137 +const LEADING_LABEL = /^(drug|biological|biologic|medication|agent|intervention|treatment|arm [a-z0-9]+|experimental|active comparator|placebo comparator)\s*:\s*/i;
138 +
139 +/**
140 + * Pure normalizer for pass 2: label → salt/formulation-stripped normalized string, or null when
141 + * nothing changes (so pass 2 never repeats pass 1) or when the result is empty.
142 + */
143 +export function stripToMolecule(label: string): string | null {
144 + let s = label.replace(LEADING_LABEL, '');
145 + s = s.replace(/\([^)]*\)/g, ' '); // parentheticals: "(MK-3475)", "(200 mg)"
146 + s = s.replace(/\[[^\]]*\]/g, ' ');
147 + s = s.replace(/\b\d+(\.\d+)?\s*(mg|mcg|ug|g|ml|iu|units?)(\s*\/\s*(kg|m2|ml|day|d|week|wk|dose))?\b/gi, ' '); // doses
148 + s = s.replace(/\b\d+(\.\d+)?\s*%/g, ' ');
149 + let norm = normalizeLabel(s);
150 + if (!norm) return null;
151 + const tokens = norm.split(' ');
152 + // strip trailing salt / formulation tokens (repeat: "doxorubicin hydrochloride injection")
153 + while (tokens.length > 1) {
154 + const last = tokens[tokens.length - 1]!;
155 + if (SALT_TOKENS.includes(last) || FORMULATION_TOKENS.includes(last) || /^\d+(\.\d+)?$/.test(last)) tokens.pop();
156 + else break;
157 + }
158 + // strip leading formulation tokens ("oral capecitabine", "iv cisplatin")
159 + while (tokens.length > 1) {
160 + const first = tokens[0]!;
161 + if (FORMULATION_TOKENS.includes(first)) tokens.shift();
162 + else break;
163 + }
164 + norm = tokens.join(' ').trim();
165 + if (!norm || norm === normalizeLabel(label)) return null;
166 + return norm;
167 +}
168 +
169 +/** Names that are never a drug entity (kept UNRESOLVED without being queued as drug labels). */
170 +export const NON_DRUG_RE = /^(placebo|placebos|saline|normal saline|sham|vehicle|standard of care|standard care|best supportive care|supportive care|observation|no intervention|no treatment|control|usual care|chemotherapy|radiotherapy|radiation|radiation therapy|surgery|questionnaire|survey|blood draw|blood sample|biopsy|imaging|mri|ct scan|pet scan|exercise|diet|counseling|education|physical therapy|acupuncture|massage|yoga|music therapy|hypnosis|dexamethasone placebo)( .*)?$/i;
171 +
172 +export interface DrugReconcileResult {
173 + pass1: number;
174 + pass2: number;
175 + pass3: number;
176 + ambiguousSkipped: number;
177 + remainingUnresolved: number;
178 + distinctUnresolved: number;
179 +}
180 +
181 +/**
182 + * Set-based reconciliation of `trial_interventions` (DRUG/BIOLOGICAL rows) to `drugs`.
183 + * `remap = true` resets ALIAS/PROBABILISTIC rows first (after alias changes); default only fills
184 + * UNRESOLVED rows.
185 + */
186 +export async function reconcileInterventionDrugs(db: Database, opts: { remap?: boolean } = {}): Promise<DrugReconcileResult> {
187 + if (opts.remap) {
188 + await db.execute(sql`UPDATE trial_interventions SET drug_id = NULL, match_type = 'UNRESOLVED' WHERE intervention_type IN ('DRUG','BIOLOGICAL') AND match_type IN ('ALIAS','PROBABILISTIC')`);
189 + }
190 + // Unambiguous alias map: normalized → drug_id (aliases shared by several drugs are excluded).
191 + await db.execute(sql`CREATE TEMP TABLE IF NOT EXISTS _alias_map (normalized text PRIMARY KEY, drug_id varchar(32) NOT NULL)`);
192 + await db.execute(sql`TRUNCATE _alias_map`);
193 + await db.execute(sql`
194 + INSERT INTO _alias_map (normalized, drug_id)
195 + SELECT normalized, min(drug_id) FROM drug_aliases WHERE length(normalized) >= 3
196 + GROUP BY normalized HAVING count(DISTINCT drug_id) = 1`);
197 + const [amb] = await db.execute<{ n: string }>(sql`SELECT count(*)::text AS n FROM (SELECT normalized FROM drug_aliases GROUP BY normalized HAVING count(DISTINCT drug_id) > 1) x`);
198 +
199 + // Pass 1: exact normalized alias.
200 + const p1 = await db.execute<{ n: string }>(sql`
201 + WITH u AS (
202 + UPDATE trial_interventions ti SET drug_id = m.drug_id, match_type = 'ALIAS'
203 + FROM _alias_map m
204 + WHERE ti.intervention_type IN ('DRUG','BIOLOGICAL') AND ti.match_type = 'UNRESOLVED' AND ti.normalized = m.normalized
205 + RETURNING 1)
206 + SELECT count(*)::text AS n FROM u`);
207 +
208 + // Pass 2: salt/dose/label-stripped form. Distinct labels are stripped in JS (pure function) then
209 + // matched in one statement.
210 + const remaining = await db.execute<{ normalized: string; name: string }>(sql`
211 + SELECT normalized, min(name) AS name FROM trial_interventions
212 + WHERE intervention_type IN ('DRUG','BIOLOGICAL') AND match_type = 'UNRESOLVED' GROUP BY normalized`);
213 + const stripped: Array<[string, string]> = [];
214 + for (const r of remaining) {
215 + if (NON_DRUG_RE.test(r.name)) continue;
216 + const m = stripToMolecule(r.name);
217 + if (m) stripped.push([r.normalized, m]);
218 + }
219 + let p2 = 0;
220 + for (let i = 0; i < stripped.length; i += 2000) {
221 + const chunk = stripped.slice(i, i + 2000);
222 + const res = await db.execute<{ n: string }>(sql`
223 + WITH s(normalized, molecule) AS (SELECT * FROM unnest(${sql.param(chunk.map((c) => c[0]))}::text[], ${sql.param(chunk.map((c) => c[1]))}::text[])),
224 + u AS (
225 + UPDATE trial_interventions ti SET drug_id = m.drug_id, match_type = 'ALIAS'
226 + FROM s JOIN _alias_map m ON m.normalized = s.molecule
227 + WHERE ti.intervention_type IN ('DRUG','BIOLOGICAL') AND ti.match_type = 'UNRESOLVED' AND ti.normalized = s.normalized
228 + RETURNING 1)
229 + SELECT count(*)::text AS n FROM u`);
230 + p2 += Number(res[0]?.n ?? 0);
231 + }
232 +
233 + // Pass 3 (PROBABILISTIC): "<generic> <formulation words only>" where the generic is a *generic*
234 + // alias (not brand/synonym) — e.g. "cisplatin 75 mg/m2 iv d1" already handled by pass 2; this
235 + // catches "pembrolizumab injection solution" style remainders whose extra tokens are all
236 + // formulation tokens. Names with any non-formulation extra token stay UNRESOLVED.
237 + const rem2 = await db.execute<{ normalized: string; name: string }>(sql`
238 + SELECT normalized, min(name) AS name FROM trial_interventions
239 + WHERE intervention_type IN ('DRUG','BIOLOGICAL') AND match_type = 'UNRESOLVED' GROUP BY normalized`);
240 + const heads: Array<[string, string]> = [];
241 + for (const r of rem2) {
242 + if (NON_DRUG_RE.test(r.name)) continue;
243 + const tokens = r.normalized.split(' ');
244 + if (tokens.length < 2) continue;
245 + const rest = tokens.slice(1);
246 + if (rest.every((t) => FORMULATION_TOKENS.includes(t) || SALT_TOKENS.includes(t) || /^\d+(\.\d+)?$/.test(t))) heads.push([r.normalized, tokens[0]!]);
247 + }
248 + let p3 = 0;
249 + for (let i = 0; i < heads.length; i += 2000) {
250 + const chunk = heads.slice(i, i + 2000);
251 + const res = await db.execute<{ n: string }>(sql`
252 + WITH s(normalized, head) AS (SELECT * FROM unnest(${sql.param(chunk.map((c) => c[0]))}::text[], ${sql.param(chunk.map((c) => c[1]))}::text[])),
253 + g AS (SELECT a.normalized, min(a.drug_id) AS drug_id FROM drug_aliases a WHERE a.alias_type = 'generic' GROUP BY a.normalized HAVING count(DISTINCT a.drug_id) = 1),
254 + u AS (
255 + UPDATE trial_interventions ti SET drug_id = g.drug_id, match_type = 'PROBABILISTIC'
256 + FROM s JOIN g ON g.normalized = s.head
257 + WHERE ti.intervention_type IN ('DRUG','BIOLOGICAL') AND ti.match_type = 'UNRESOLVED' AND ti.normalized = s.normalized
258 + RETURNING 1)
259 + SELECT count(*)::text AS n FROM u`);
260 + p3 += Number(res[0]?.n ?? 0);
261 + }
262 +
263 + const [left] = await db.execute<{ n: string; d: string }>(sql`SELECT count(*)::text AS n, count(DISTINCT normalized)::text AS d FROM trial_interventions WHERE intervention_type IN ('DRUG','BIOLOGICAL') AND match_type = 'UNRESOLVED'`);
264 + return { pass1: Number(p1[0]?.n ?? 0), pass2: p2, pass3: p3, ambiguousSkipped: Number(amb?.n ?? 0), remainingUnresolved: Number(left?.n ?? 0), distinctUnresolved: Number(left?.d ?? 0) };
265 +}
modified packages/connectors/src/connectors/clinicaltrials/index.ts +4 −0
@@ -8,10 +8,12 @@ import { manifest } from './manifest.js';
8 8 import { ONCOLOGY_EXPRESSION, STUDY_FIELDS, normalizeStudy, trimStudyPayload, type ApiPage, type ApiStudy, type ApiVersion, type NormalizedTrial } from './normalize.js';
9 9 import { reconcileConditions, type ConditionMapping, type ResolverLike } from './reconcile.js';
10 10 import { refreshTrialPulse } from './pulse.js';
11 +import { reconcileInterventionDrugs } from './drugs.js';
11 12
12 13 export { ONCOLOGY_EXPRESSION, STUDY_FIELDS, normalizeStudy, trimStudyPayload } from './normalize.js';
13 14 export { reconcileConditions, conditionCandidates } from './reconcile.js';
14 15 export { refreshTrialPulse } from './pulse.js';
16 +export { reconcileInterventionDrugs, stripToMolecule, NON_DRUG_RE } from './drugs.js';
15 17
16 18 export const PAGE_SIZE = 1000;
17 19 /** Trigram suggestions are computed for at most this many unresolved labels per run (curation aid only). */
@@ -200,6 +202,8 @@ export class ClinicalTrialsConnector extends Connector {
200 202 const re = await this.rereconcileUnresolved(ctx, resolver);
201 203 const pulse = await refreshTrialPulse(ctx.db);
202 204 ctx.info(`re-reconciled ${re.labels} unresolved labels → ${re.rows} trial_conditions rows updated; trial_pulse rows ${pulse}`);
205 + const dr = await reconcileInterventionDrugs(ctx.db);
206 + ctx.info(`interventions → drugs: alias ${dr.pass1}, stripped ${dr.pass2}, probabilistic ${dr.pass3}; ambiguous aliases skipped ${dr.ambiguousSkipped}; still unresolved ${dr.remainingUnresolved} rows (${dr.distinctUnresolved} distinct labels)`);
203 207 }
204 208 const pct = agg.conditionsTotal ? Math.round((agg.conditionsResolved / agg.conditionsTotal) * 1000) / 10 : 0;
205 209 const top = [...agg.unresolved.values()].sort((a, b) => b.count - a.count).slice(0, 15).map((u) => `${u.sourceText} (${u.count})`);
modified packages/connectors/src/index.ts +1 −0
@@ -3,3 +3,4 @@ export * from './registry.js';
3 3 export * from './sources-sync.js';
4 4 export * from './planned.js';
5 5 export * from './ops/index.js';
6 +export { reconcileInterventionDrugs, stripToMolecule, NON_DRUG_RE, SALT_TOKENS, FORMULATION_TOKENS } from './connectors/clinicaltrials/drugs.js';
added packages/database/migrations/0002_dizzy_pete_wisdom.sql +126 −0
@@ -0,0 +1,126 @@
1 +CREATE TABLE "drug_codes" (
2 + "id" bigserial PRIMARY KEY NOT NULL,
3 + "drug_id" varchar(32) NOT NULL,
4 + "system" text NOT NULL,
5 + "code" text NOT NULL,
6 + "label" text,
7 + "match_type" text DEFAULT 'EXACT_IDENTIFIER' NOT NULL,
8 + "source_id" varchar(32)
9 +);
10 +--> statement-breakpoint
11 +CREATE TABLE "drug_pipeline" (
12 + "id" bigserial PRIMARY KEY NOT NULL,
13 + "drug_id" varchar(32) NOT NULL,
14 + "cancer_id" varchar(32),
15 + "stage" text NOT NULL,
16 + "max_phase" text,
17 + "active_trials" integer DEFAULT 0 NOT NULL,
18 + "recruiting_trials" integer DEFAULT 0 NOT NULL,
19 + "phase3_trials" integer DEFAULT 0 NOT NULL,
20 + "total_trials" integer DEFAULT 0 NOT NULL,
21 + "approvals" integer DEFAULT 0 NOT NULL,
22 + "jurisdictions" text[] DEFAULT '{}' NOT NULL,
23 + "first_approval_date" text,
24 + "latest_approval_date" text,
25 + "first_trial_date" text,
26 + "formula_version" text NOT NULL,
27 + "inputs" jsonb DEFAULT '{}'::jsonb NOT NULL,
28 + "updated_at" timestamp with time zone DEFAULT now() NOT NULL
29 +);
30 +--> statement-breakpoint
31 +CREATE TABLE "research_gap_components" (
32 + "id" bigserial PRIMARY KEY NOT NULL,
33 + "cancer_id" varchar(32) NOT NULL,
34 + "geography" text NOT NULL,
35 + "year" integer NOT NULL,
36 + "sex" text DEFAULT 'all' NOT NULL,
37 + "burden_source_id" varchar(32) NOT NULL,
38 + "deaths" double precision,
39 + "incidence" double precision,
40 + "active_trials" integer DEFAULT 0 NOT NULL,
41 + "phase3_trials" integer DEFAULT 0 NOT NULL,
42 + "publications_5y" integer DEFAULT 0 NOT NULL,
43 + "approved_drugs" integer DEFAULT 0 NOT NULL,
44 + "death_share" real,
45 + "trial_share" real,
46 + "publication_share" real,
47 + "trial_gap_ratio" real,
48 + "research_gap_ratio" real,
49 + "trials_per_1000_deaths" real,
50 + "publications_per_1000_deaths" real,
51 + "eligible" boolean DEFAULT true NOT NULL,
52 + "ineligible_reason" text,
53 + "formula_version" text NOT NULL,
54 + "inputs" jsonb DEFAULT '{}'::jsonb NOT NULL,
55 + "updated_at" timestamp with time zone DEFAULT now() NOT NULL
56 +);
57 +--> statement-breakpoint
58 +CREATE TABLE "trial_intelligence" (
59 + "id" bigserial PRIMARY KEY NOT NULL,
60 + "cancer_id" varchar(32) NOT NULL,
61 + "entity_level" text DEFAULT 'all' NOT NULL,
62 + "total_trials" integer DEFAULT 0 NOT NULL,
63 + "active_trials" integer DEFAULT 0 NOT NULL,
64 + "recruiting_trials" integer DEFAULT 0 NOT NULL,
65 + "phase1_active" integer DEFAULT 0 NOT NULL,
66 + "phase2_active" integer DEFAULT 0 NOT NULL,
67 + "phase3_active" integer DEFAULT 0 NOT NULL,
68 + "phase3_recruiting" integer DEFAULT 0 NOT NULL,
69 + "phase4_active" integer DEFAULT 0 NOT NULL,
70 + "completed_trials" integer DEFAULT 0 NOT NULL,
71 + "terminated_trials" integer DEFAULT 0 NOT NULL,
72 + "withdrawn_trials" integer DEFAULT 0 NOT NULL,
73 + "suspended_trials" integer DEFAULT 0 NOT NULL,
74 + "with_results" integer DEFAULT 0 NOT NULL,
75 + "new_trials_12m" integer DEFAULT 0 NOT NULL,
76 + "new_trials_prior_12m" integer DEFAULT 0 NOT NULL,
77 + "trial_growth_yoy" real,
78 + "avg_enrollment" real,
79 + "median_enrollment" real,
80 + "total_enrollment_active" integer,
81 + "distinct_sponsors" integer DEFAULT 0 NOT NULL,
82 + "industry_share" real,
83 + "sponsor_hhi" real,
84 + "top_sponsor" text,
85 + "top_sponsor_share" real,
86 + "distinct_countries" integer DEFAULT 0 NOT NULL,
87 + "us_share" real,
88 + "top_country" text,
89 + "top_country_share" real,
90 + "country_hhi" real,
91 + "termination_share" real,
92 + "why_stopped_breakdown" jsonb DEFAULT '{}'::jsonb NOT NULL,
93 + "trials_per_1000_deaths" real,
94 + "trials_per_100k_cases" real,
95 + "burden_geography" text,
96 + "burden_year" integer,
97 + "burden_source_id" varchar(32),
98 + "formula_version" text NOT NULL,
99 + "inputs" jsonb DEFAULT '{}'::jsonb NOT NULL,
100 + "updated_at" timestamp with time zone DEFAULT now() NOT NULL
101 +);
102 +--> statement-breakpoint
103 +CREATE TABLE "trial_site_country_counts" (
104 + "id" bigserial PRIMARY KEY NOT NULL,
105 + "cancer_id" varchar(32),
106 + "phase" text,
107 + "recruiting_only" boolean DEFAULT false NOT NULL,
108 + "country" text NOT NULL,
109 + "iso3" text,
110 + "sites" integer NOT NULL,
111 + "trials" integer NOT NULL,
112 + "formula_version" text NOT NULL,
113 + "updated_at" timestamp with time zone DEFAULT now() NOT NULL
114 +);
115 +--> statement-breakpoint
116 +CREATE UNIQUE INDEX "drug_codes_uq" ON "drug_codes" USING btree ("drug_id","system","code");--> statement-breakpoint
117 +CREATE INDEX "drug_codes_lookup_idx" ON "drug_codes" USING btree ("system","code");--> statement-breakpoint
118 +CREATE UNIQUE INDEX "drug_pipeline_uq" ON "drug_pipeline" USING btree ("drug_id","cancer_id");--> statement-breakpoint
119 +CREATE INDEX "drug_pipeline_stage_idx" ON "drug_pipeline" USING btree ("stage");--> statement-breakpoint
120 +CREATE INDEX "drug_pipeline_cancer_idx" ON "drug_pipeline" USING btree ("cancer_id","stage");--> statement-breakpoint
121 +CREATE UNIQUE INDEX "research_gap_components_uq" ON "research_gap_components" USING btree ("cancer_id","geography","year","sex","burden_source_id");--> statement-breakpoint
122 +CREATE INDEX "research_gap_scope_idx" ON "research_gap_components" USING btree ("geography","year","sex");--> statement-breakpoint
123 +CREATE UNIQUE INDEX "trial_intelligence_uq" ON "trial_intelligence" USING btree ("cancer_id","entity_level");--> statement-breakpoint
124 +CREATE INDEX "trial_intelligence_active_idx" ON "trial_intelligence" USING btree ("entity_level","active_trials");--> statement-breakpoint
125 +CREATE UNIQUE INDEX "trial_site_country_uq" ON "trial_site_country_counts" USING btree ("cancer_id","phase","recruiting_only","country");--> statement-breakpoint
126 +CREATE INDEX "trial_site_country_lookup_idx" ON "trial_site_country_counts" USING btree ("cancer_id","phase","recruiting_only");
\ No newline at end of file
added packages/database/migrations/meta/0002_snapshot.json +8029 −0
@@ -0,0 +1,8029 @@
1 +{
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3 + "prevId": "dc7abeda-b455-4b0f-86ae-e01f476fb4f0",
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87 + "type": "text",
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133 + }
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150 + },
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155 + "nulls": "last"
156 + }
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160 + "method": "btree",
161 + "with": {}
162 + }
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167 + "policies": {},
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554 + },
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558 + "primaryKey": false,
559 + "notNull": true,
560 + "default": "'[]'::jsonb"
561 + },
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7700 + "type": "integer",
7701 + "primaryKey": false,
7702 + "notNull": false
7703 + },
7704 + "distinct_sponsors": {
7705 + "name": "distinct_sponsors",
7706 + "type": "integer",
7707 + "primaryKey": false,
7708 + "notNull": true,
7709 + "default": 0
7710 + },
7711 + "industry_share": {
7712 + "name": "industry_share",
7713 + "type": "real",
7714 + "primaryKey": false,
7715 + "notNull": false
7716 + },
7717 + "sponsor_hhi": {
7718 + "name": "sponsor_hhi",
7719 + "type": "real",
7720 + "primaryKey": false,
7721 + "notNull": false
7722 + },
7723 + "top_sponsor": {
7724 + "name": "top_sponsor",
7725 + "type": "text",
7726 + "primaryKey": false,
7727 + "notNull": false
7728 + },
7729 + "top_sponsor_share": {
7730 + "name": "top_sponsor_share",
7731 + "type": "real",
7732 + "primaryKey": false,
7733 + "notNull": false
7734 + },
7735 + "distinct_countries": {
7736 + "name": "distinct_countries",
7737 + "type": "integer",
7738 + "primaryKey": false,
7739 + "notNull": true,
7740 + "default": 0
7741 + },
7742 + "us_share": {
7743 + "name": "us_share",
7744 + "type": "real",
7745 + "primaryKey": false,
7746 + "notNull": false
7747 + },
7748 + "top_country": {
7749 + "name": "top_country",
7750 + "type": "text",
7751 + "primaryKey": false,
7752 + "notNull": false
7753 + },
7754 + "top_country_share": {
7755 + "name": "top_country_share",
7756 + "type": "real",
7757 + "primaryKey": false,
7758 + "notNull": false
7759 + },
7760 + "country_hhi": {
7761 + "name": "country_hhi",
7762 + "type": "real",
7763 + "primaryKey": false,
7764 + "notNull": false
7765 + },
7766 + "termination_share": {
7767 + "name": "termination_share",
7768 + "type": "real",
7769 + "primaryKey": false,
7770 + "notNull": false
7771 + },
7772 + "why_stopped_breakdown": {
7773 + "name": "why_stopped_breakdown",
7774 + "type": "jsonb",
7775 + "primaryKey": false,
7776 + "notNull": true,
7777 + "default": "'{}'::jsonb"
7778 + },
7779 + "trials_per_1000_deaths": {
7780 + "name": "trials_per_1000_deaths",
7781 + "type": "real",
7782 + "primaryKey": false,
7783 + "notNull": false
7784 + },
7785 + "trials_per_100k_cases": {
7786 + "name": "trials_per_100k_cases",
7787 + "type": "real",
7788 + "primaryKey": false,
7789 + "notNull": false
7790 + },
7791 + "burden_geography": {
7792 + "name": "burden_geography",
7793 + "type": "text",
7794 + "primaryKey": false,
7795 + "notNull": false
7796 + },
7797 + "burden_year": {
7798 + "name": "burden_year",
7799 + "type": "integer",
7800 + "primaryKey": false,
7801 + "notNull": false
7802 + },
7803 + "burden_source_id": {
7804 + "name": "burden_source_id",
7805 + "type": "varchar(32)",
7806 + "primaryKey": false,
7807 + "notNull": false
7808 + },
7809 + "formula_version": {
7810 + "name": "formula_version",
7811 + "type": "text",
7812 + "primaryKey": false,
7813 + "notNull": true
7814 + },
7815 + "inputs": {
7816 + "name": "inputs",
7817 + "type": "jsonb",
7818 + "primaryKey": false,
7819 + "notNull": true,
7820 + "default": "'{}'::jsonb"
7821 + },
7822 + "updated_at": {
7823 + "name": "updated_at",
7824 + "type": "timestamp with time zone",
7825 + "primaryKey": false,
7826 + "notNull": true,
7827 + "default": "now()"
7828 + }
7829 + },
7830 + "indexes": {
7831 + "trial_intelligence_uq": {
7832 + "name": "trial_intelligence_uq",
7833 + "columns": [
7834 + {
7835 + "expression": "cancer_id",
7836 + "isExpression": false,
7837 + "asc": true,
7838 + "nulls": "last"
7839 + },
7840 + {
7841 + "expression": "entity_level",
7842 + "isExpression": false,
7843 + "asc": true,
7844 + "nulls": "last"
7845 + }
7846 + ],
7847 + "isUnique": true,
7848 + "concurrently": false,
7849 + "method": "btree",
7850 + "with": {}
7851 + },
7852 + "trial_intelligence_active_idx": {
7853 + "name": "trial_intelligence_active_idx",
7854 + "columns": [
7855 + {
7856 + "expression": "entity_level",
7857 + "isExpression": false,
7858 + "asc": true,
7859 + "nulls": "last"
7860 + },
7861 + {
7862 + "expression": "active_trials",
7863 + "isExpression": false,
7864 + "asc": true,
7865 + "nulls": "last"
7866 + }
7867 + ],
7868 + "isUnique": false,
7869 + "concurrently": false,
7870 + "method": "btree",
7871 + "with": {}
7872 + }
7873 + },
7874 + "foreignKeys": {},
7875 + "compositePrimaryKeys": {},
7876 + "uniqueConstraints": {},
7877 + "policies": {},
7878 + "checkConstraints": {},
7879 + "isRLSEnabled": false
7880 + },
7881 + "public.trial_site_country_counts": {
7882 + "name": "trial_site_country_counts",
7883 + "schema": "",
7884 + "columns": {
7885 + "id": {
7886 + "name": "id",
7887 + "type": "bigserial",
7888 + "primaryKey": true,
7889 + "notNull": true
7890 + },
7891 + "cancer_id": {
7892 + "name": "cancer_id",
7893 + "type": "varchar(32)",
7894 + "primaryKey": false,
7895 + "notNull": false
7896 + },
7897 + "phase": {
7898 + "name": "phase",
7899 + "type": "text",
7900 + "primaryKey": false,
7901 + "notNull": false
7902 + },
7903 + "recruiting_only": {
7904 + "name": "recruiting_only",
7905 + "type": "boolean",
7906 + "primaryKey": false,
7907 + "notNull": true,
7908 + "default": false
7909 + },
7910 + "country": {
7911 + "name": "country",
7912 + "type": "text",
7913 + "primaryKey": false,
7914 + "notNull": true
7915 + },
7916 + "iso3": {
7917 + "name": "iso3",
7918 + "type": "text",
7919 + "primaryKey": false,
7920 + "notNull": false
7921 + },
7922 + "sites": {
7923 + "name": "sites",
7924 + "type": "integer",
7925 + "primaryKey": false,
7926 + "notNull": true
7927 + },
7928 + "trials": {
7929 + "name": "trials",
7930 + "type": "integer",
7931 + "primaryKey": false,
7932 + "notNull": true
7933 + },
7934 + "formula_version": {
7935 + "name": "formula_version",
7936 + "type": "text",
7937 + "primaryKey": false,
7938 + "notNull": true
7939 + },
7940 + "updated_at": {
7941 + "name": "updated_at",
7942 + "type": "timestamp with time zone",
7943 + "primaryKey": false,
7944 + "notNull": true,
7945 + "default": "now()"
7946 + }
7947 + },
7948 + "indexes": {
7949 + "trial_site_country_uq": {
7950 + "name": "trial_site_country_uq",
7951 + "columns": [
7952 + {
7953 + "expression": "cancer_id",
7954 + "isExpression": false,
7955 + "asc": true,
7956 + "nulls": "last"
7957 + },
7958 + {
7959 + "expression": "phase",
7960 + "isExpression": false,
7961 + "asc": true,
7962 + "nulls": "last"
7963 + },
7964 + {
7965 + "expression": "recruiting_only",
7966 + "isExpression": false,
7967 + "asc": true,
7968 + "nulls": "last"
7969 + },
7970 + {
7971 + "expression": "country",
7972 + "isExpression": false,
7973 + "asc": true,
7974 + "nulls": "last"
7975 + }
7976 + ],
7977 + "isUnique": true,
7978 + "concurrently": false,
7979 + "method": "btree",
7980 + "with": {}
7981 + },
7982 + "trial_site_country_lookup_idx": {
7983 + "name": "trial_site_country_lookup_idx",
7984 + "columns": [
7985 + {
7986 + "expression": "cancer_id",
7987 + "isExpression": false,
7988 + "asc": true,
7989 + "nulls": "last"
7990 + },
7991 + {
7992 + "expression": "phase",
7993 + "isExpression": false,
7994 + "asc": true,
7995 + "nulls": "last"
7996 + },
7997 + {
7998 + "expression": "recruiting_only",
7999 + "isExpression": false,
8000 + "asc": true,
8001 + "nulls": "last"
8002 + }
8003 + ],
8004 + "isUnique": false,
8005 + "concurrently": false,
8006 + "method": "btree",
8007 + "with": {}
8008 + }
8009 + },
8010 + "foreignKeys": {},
8011 + "compositePrimaryKeys": {},
8012 + "uniqueConstraints": {},
8013 + "policies": {},
8014 + "checkConstraints": {},
8015 + "isRLSEnabled": false
8016 + }
8017 + },
8018 + "enums": {},
8019 + "schemas": {},
8020 + "sequences": {},
8021 + "roles": {},
8022 + "policies": {},
8023 + "views": {},
8024 + "_meta": {
8025 + "columns": {},
8026 + "schemas": {},
8027 + "tables": {}
8028 + }
8029 +}
\ No newline at end of file
modified packages/database/migrations/meta/_journal.json +7 −0
@@ -15,6 +15,13 @@
15 15 "when": 1788872445984,
16 16 "tag": "0001_jazzy_arclight",
17 17 "breakpoints": true
18 + },
19 + {
20 + "idx": 2,
21 + "version": "7",
22 + "when": 1789100478898,
23 + "tag": "0002_dizzy_pete_wisdom",
24 + "breakpoints": true
18 25 }
19 26 ]
20 27 }
\ No newline at end of file
modified packages/database/src/schema/index.ts +1 −0
@@ -8,3 +8,4 @@ export * from './evidence.js';
8 8 export * from './epidemiology.js';
9 9 export * from './rankings.js';
10 10 export * from './ext-ops.js';
11 +export * from './intelligence.js';
added packages/database/src/schema/intelligence.ts +164 −0
@@ -0,0 +1,164 @@
1 +import { pgTable, text, integer, bigserial, index, uniqueIndex, real, jsonb, doublePrecision, boolean } from 'drizzle-orm/pg-core';
2 +import { ciId, updatedAt } from './_common.js';
3 +
4 +/**
5 + * Derived layer — "intelligence" tables (SPEC §10, §15, §33-34, §115). Every row is recomputed
6 + * deterministically from canonical relations, carries a `formula_version` and keeps its inputs so a
7 + * number can be traced ("Why 542 active trials?"). Nothing here is an observation: the claim
8 + * category of every value is `computed_metric`.
9 + */
10 +
11 +/** Per-cancer clinical-trial intelligence (SPEC §10): counts, growth, sponsor & geographic concentration, failures. */
12 +export const trialIntelligence = pgTable(
13 + 'trial_intelligence',
14 + {
15 + id: bigserial('id', { mode: 'number' }).primaryKey(),
16 + cancerId: ciId('cancer_id').notNull(),
17 + /** top = mutually exclusive registry set (§246-247); all = every active malignant entity. */
18 + entityLevel: text('entity_level').notNull().default('all'),
19 + // --- counts (interventional studies over the entity and its descendants) ---
20 + totalTrials: integer('total_trials').notNull().default(0),
21 + activeTrials: integer('active_trials').notNull().default(0),
22 + recruitingTrials: integer('recruiting_trials').notNull().default(0),
23 + phase1Active: integer('phase1_active').notNull().default(0),
24 + phase2Active: integer('phase2_active').notNull().default(0),
25 + phase3Active: integer('phase3_active').notNull().default(0),
26 + phase3Recruiting: integer('phase3_recruiting').notNull().default(0),
27 + phase4Active: integer('phase4_active').notNull().default(0),
28 + completedTrials: integer('completed_trials').notNull().default(0),
29 + terminatedTrials: integer('terminated_trials').notNull().default(0),
30 + withdrawnTrials: integer('withdrawn_trials').notNull().default(0),
31 + suspendedTrials: integer('suspended_trials').notNull().default(0),
32 + withResults: integer('with_results').notNull().default(0),
33 + // --- growth (registration date = first_posted_date) ---
34 + newTrials12m: integer('new_trials_12m').notNull().default(0),
35 + newTrialsPrior12m: integer('new_trials_prior_12m').notNull().default(0),
36 + trialGrowthYoy: real('trial_growth_yoy'), // (new_12m − prior_12m) / prior_12m; null when prior < threshold
37 + // --- enrollment ---
38 + avgEnrollment: real('avg_enrollment'),
39 + medianEnrollment: real('median_enrollment'),
40 + totalEnrollmentActive: integer('total_enrollment_active'),
41 + // --- sponsors ---
42 + distinctSponsors: integer('distinct_sponsors').notNull().default(0),
43 + industryShare: real('industry_share'), // share of active trials with lead_sponsor_class = INDUSTRY
44 + sponsorHhi: real('sponsor_hhi'), // Herfindahl–Hirschman index of lead sponsors over active trials (0..1)
45 + topSponsor: text('top_sponsor'),
46 + topSponsorShare: real('top_sponsor_share'),
47 + // --- geography ---
48 + distinctCountries: integer('distinct_countries').notNull().default(0),
49 + usShare: real('us_share'), // share of active trials with ≥ 1 US site
50 + topCountry: text('top_country'),
51 + topCountryShare: real('top_country_share'),
52 + countryHhi: real('country_hhi'),
53 + // --- failures ---
54 + terminationShare: real('termination_share'), // (terminated + withdrawn) / (completed + terminated + withdrawn), studies first posted ≥ 2010
55 + whyStoppedBreakdown: jsonb('why_stopped_breakdown').$type<Record<string, number>>().notNull().default({}),
56 + // --- burden-normalized (US, latest year with both counts) ---
57 + trialsPer1000Deaths: real('trials_per_1000_deaths'),
58 + trialsPer100kCases: real('trials_per_100k_cases'),
59 + burdenGeography: text('burden_geography'),
60 + burdenYear: integer('burden_year'),
61 + burdenSourceId: ciId('burden_source_id'),
62 + formulaVersion: text('formula_version').notNull(),
63 + inputs: jsonb('inputs').$type<Record<string, unknown>>().notNull().default({}),
64 + computedAt: updatedAt(),
65 + },
66 + (t) => [uniqueIndex('trial_intelligence_uq').on(t.cancerId, t.entityLevel), index('trial_intelligence_active_idx').on(t.entityLevel, t.activeTrials)],
67 +);
68 +
69 +/**
70 + * Country-level trial site aggregates for the trial map (SPEC §11). `cancer_id` null = all oncology
71 + * trials; otherwise a top-level cancer (descendants included). `phase` null = any phase.
72 + */
73 +export const trialSiteCountryCounts = pgTable(
74 + 'trial_site_country_counts',
75 + {
76 + id: bigserial('id', { mode: 'number' }).primaryKey(),
77 + cancerId: ciId('cancer_id'),
78 + phase: text('phase'),
79 + recruitingOnly: boolean('recruiting_only').notNull().default(false),
80 + country: text('country').notNull(),
81 + iso3: text('iso3'),
82 + sites: integer('sites').notNull(),
83 + trials: integer('trials').notNull(),
84 + formulaVersion: text('formula_version').notNull(),
85 + computedAt: updatedAt(),
86 + },
87 + (t) => [uniqueIndex('trial_site_country_uq').on(t.cancerId, t.phase, t.recruitingOnly, t.country), index('trial_site_country_lookup_idx').on(t.cancerId, t.phase, t.recruitingOnly)],
88 +);
89 +
90 +/**
91 + * Drug development pipeline (SPEC §15, §114, §119): per drug (and optionally per cancer) the highest
92 + * development stage supported by registered trials and jurisdiction-aware approvals.
93 + */
94 +export const drugPipeline = pgTable(
95 + 'drug_pipeline',
96 + {
97 + id: bigserial('id', { mode: 'number' }).primaryKey(),
98 + drugId: ciId('drug_id').notNull(),
99 + cancerId: ciId('cancer_id'), // null = across all cancers
100 + /** preclinical | phase1 | phase2 | phase3 | phase4 | approved | withdrawn */
101 + stage: text('stage').notNull(),
102 + maxPhase: text('max_phase'), // highest phase among interventional trials (PHASE1..PHASE4)
103 + activeTrials: integer('active_trials').notNull().default(0),
104 + recruitingTrials: integer('recruiting_trials').notNull().default(0),
105 + phase3Trials: integer('phase3_trials').notNull().default(0),
106 + totalTrials: integer('total_trials').notNull().default(0),
107 + approvals: integer('approvals').notNull().default(0),
108 + jurisdictions: text('jurisdictions').array().notNull().default([]),
109 + firstApprovalDate: text('first_approval_date'),
110 + latestApprovalDate: text('latest_approval_date'),
111 + firstTrialDate: text('first_trial_date'),
112 + formulaVersion: text('formula_version').notNull(),
113 + inputs: jsonb('inputs').$type<Record<string, unknown>>().notNull().default({}),
114 + computedAt: updatedAt(),
115 + },
116 + (t) => [uniqueIndex('drug_pipeline_uq').on(t.drugId, t.cancerId), index('drug_pipeline_stage_idx').on(t.stage), index('drug_pipeline_cancer_idx').on(t.cancerId, t.stage)],
117 +);
118 +
119 +/** Cross-reference codes for drugs (CLAUDE.md §347): ATC, UNII, RxCUI, DIN, ChEMBL… searchable, never buried in JSON. */
120 +export const drugCodes = pgTable(
121 + 'drug_codes',
122 + {
123 + id: bigserial('id', { mode: 'number' }).primaryKey(),
124 + drugId: ciId('drug_id').notNull(),
125 + system: text('system').notNull(), // atc | unii | rxcui | din | chembl | drugbank | pubchem_cid | ncit | civic_therapy | hc_drug_code | ema_product | mhra | tga
126 + code: text('code').notNull(),
127 + label: text('label'), // e.g. ATC class name, brand for a DIN
128 + matchType: text('match_type').notNull().default('EXACT_IDENTIFIER'),
129 + sourceId: ciId('source_id'),
130 + },
131 + (t) => [uniqueIndex('drug_codes_uq').on(t.drugId, t.system, t.code), index('drug_codes_lookup_idx').on(t.system, t.code)],
132 +);
133 +
134 +/** Research-gap components per cancer and burden scope (SPEC §34, §113): shares and log-ratios with their inputs. */
135 +export const researchGapComponents = pgTable(
136 + 'research_gap_components',
137 + {
138 + id: bigserial('id', { mode: 'number' }).primaryKey(),
139 + cancerId: ciId('cancer_id').notNull(),
140 + geography: text('geography').notNull(), // ISO3 or WORLD
141 + year: integer('year').notNull(),
142 + sex: text('sex').notNull().default('all'),
143 + burdenSourceId: ciId('burden_source_id').notNull(),
144 + deaths: doublePrecision('deaths'),
145 + incidence: doublePrecision('incidence'),
146 + activeTrials: integer('active_trials').notNull().default(0),
147 + phase3Trials: integer('phase3_trials').notNull().default(0),
148 + publications5y: integer('publications_5y').notNull().default(0),
149 + approvedDrugs: integer('approved_drugs').notNull().default(0),
150 + deathShare: real('death_share'),
151 + trialShare: real('trial_share'),
152 + publicationShare: real('publication_share'),
153 + trialGapRatio: real('trial_gap_ratio'), // log2(deathShare / trialShare)
154 + researchGapRatio: real('research_gap_ratio'), // log2(deathShare / publicationShare)
155 + trialsPer1000Deaths: real('trials_per_1000_deaths'),
156 + publicationsPer1000Deaths: real('publications_per_1000_deaths'),
157 + eligible: boolean('eligible').notNull().default(true),
158 + ineligibleReason: text('ineligible_reason'),
159 + formulaVersion: text('formula_version').notNull(),
160 + inputs: jsonb('inputs').$type<Record<string, unknown>>().notNull().default({}),
161 + computedAt: updatedAt(),
162 + },
163 + (t) => [uniqueIndex('research_gap_components_uq').on(t.cancerId, t.geography, t.year, t.sex, t.burdenSourceId), index('research_gap_scope_idx').on(t.geography, t.year, t.sex)],
164 +);
modified packages/database/src/seed-data/metrics.ts +122 −0
@@ -282,4 +282,126 @@ export const METRIC_CATALOG: MetricSeed[] = [
282 282 eligibility: { requires: ['mortality_count', 'publications_5y'], entityLevel: 'top' },
283 283 experimental: false,
284 284 },
285 +
286 + // --- Clinical-trial intelligence (SPEC §10; computed in packages/ranking/src/trial-intelligence.ts) ---
287 + {
288 + slug: 'phase3_recruiting_trials',
289 + name: 'Recruiting Phase III trials',
290 + description: 'Interventional studies with PHASE3 among their phases and overall status RECRUITING, mapped to this cancer or its descendants.',
291 + formula: 'COUNT(DISTINCT trial) … overall_status = RECRUITING AND PHASE3 = ANY(phases) AND study_type = INTERVENTIONAL',
292 + formulaVersion: 'ci-phase3-recruiting-v1',
293 + unit: 'count',
294 + higherIsWorse: false,
295 + aggregation: 'descendants',
296 + validDimensions: ['entity_level'],
297 + sourceSlugs: ['clinicaltrials'],
298 + category: 'trials',
299 + eligibility: { entityLevel: 'any' },
300 + experimental: false,
301 + },
302 + {
303 + slug: 'trial_growth_yoy',
304 + name: 'Trial registration growth (year over year)',
305 + description: 'Relative change in the number of interventional studies first posted in the last 12 months versus the preceding 12 months, over the cancer and its descendants. Requires at least 20 studies in the prior window so small denominators do not produce spurious growth.',
306 + formula: '(new_trials_12m − new_trials_prior_12m) / new_trials_prior_12m (first_posted_date windows; interventional; descendants)',
307 + formulaVersion: 'ci-trial-growth-v1',
308 + unit: 'ratio',
309 + higherIsWorse: null,
310 + aggregation: 'descendants',
311 + validDimensions: ['entity_level'],
312 + sourceSlugs: ['clinicaltrials'],
313 + category: 'trend',
314 + eligibility: { entityLevel: 'any', minPriorTrials: 20 },
315 + experimental: false,
316 + },
317 + {
318 + slug: 'trial_termination_share',
319 + name: 'Trial termination share',
320 + description: 'Share of interventional studies first posted since 2010 that ended TERMINATED or WITHDRAWN among those that reached a terminal status (COMPLETED, TERMINATED, WITHDRAWN). Registrant-reported statuses; reasons are shown as posted and never inferred. Requires ≥ 30 terminal studies.',
321 + formula: '(terminated + withdrawn) / (completed + terminated + withdrawn) WHERE first_posted_date ≥ 2010-01-01 AND study_type = INTERVENTIONAL',
322 + formulaVersion: 'ci-trial-termination-v1',
323 + unit: 'ratio',
324 + higherIsWorse: true,
325 + aggregation: 'descendants',
326 + validDimensions: ['entity_level'],
327 + sourceSlugs: ['clinicaltrials'],
328 + category: 'trials',
329 + eligibility: { entityLevel: 'any', minTerminalTrials: 30 },
330 + experimental: false,
331 + },
332 + {
333 + slug: 'sponsor_concentration',
334 + name: 'Sponsor concentration (HHI)',
335 + description: 'Herfindahl–Hirschman index of lead sponsors over active interventional studies (sum of squared sponsor shares; 1 = a single sponsor). Requires ≥ 10 active studies.',
336 + formula: 'Σ (active_trials_by_lead_sponsor / active_trials)² over the cancer and its descendants',
337 + formulaVersion: 'ci-sponsor-hhi-v1',
338 + unit: 'index',
339 + higherIsWorse: null,
340 + aggregation: 'descendants',
341 + validDimensions: ['entity_level'],
342 + sourceSlugs: ['clinicaltrials'],
343 + category: 'trials',
344 + eligibility: { entityLevel: 'any', minActiveTrials: 10 },
345 + experimental: false,
346 + },
347 + {
348 + slug: 'trials_per_1000_deaths',
349 + name: 'Active trials per 1,000 annual deaths',
350 + description: 'Active interventional studies divided by annual deaths (thousands) in the same population scope. A burden-normalized measure of clinical-research intensity; it depends on the epidemiology source of the scope and on how registrants phrase conditions.',
351 + formula: 'active_trials / (mortality_count / 1000) (same geography, year, sex, source family; deaths ≥ 100)',
352 + formulaVersion: 'ci-trials-per-deaths-v1',
353 + unit: 'per_1000_deaths',
354 + higherIsWorse: false,
355 + aggregation: 'none',
356 + validDimensions: ['geography', 'year'],
357 + sourceSlugs: ['clinicaltrials', 'cdc-wonder', 'cdc-uscs', 'seer', 'iarc-globocan'],
358 + category: 'unmet_need',
359 + eligibility: { requires: ['mortality_count', 'active_trials'], minDeaths: 100, entityLevel: 'top' },
360 + experimental: false,
361 + },
362 + {
363 + slug: 'publications_per_1000_deaths',
364 + name: 'Publications (5 y) per 1,000 annual deaths',
365 + description: 'PubMed records over the last 5 years divided by annual deaths (thousands) in the same population scope. A burden-normalized measure of research output.',
366 + formula: 'publications_5y / (mortality_count / 1000) (same geography, year, sex, source family; deaths ≥ 100)',
367 + formulaVersion: 'ci-pubs-per-deaths-v1',
368 + unit: 'per_1000_deaths',
369 + higherIsWorse: false,
370 + aggregation: 'none',
371 + validDimensions: ['geography', 'year'],
372 + sourceSlugs: ['pubmed', 'cdc-wonder', 'cdc-uscs', 'seer', 'iarc-globocan'],
373 + category: 'unmet_need',
374 + eligibility: { requires: ['mortality_count', 'publications_5y'], minDeaths: 100, entityLevel: 'top' },
375 + experimental: false,
376 + },
377 + {
378 + slug: 'trial_gap_ratio',
379 + name: 'Trial Gap Ratio',
380 + description: 'log₂ of a cancer’s share of deaths divided by its share of active interventional trials, both computed over the eligible top-level cancers of the scope. 0 = trial share matches death share; +1 = twice as many deaths as trials would suggest; −1 = half. Scale-free, so it can be compared across scopes, unlike the percentile-based Trial Gap Index.',
381 + formula: 'log2( (deaths / Σ deaths) / (active_trials / Σ active_trials) ) over eligible top-level cancers (deaths ≥ 100, active_trials ≥ 1)',
382 + formulaVersion: 'ci-trial-gap-ratio-v1',
383 + unit: 'log2_ratio',
384 + higherIsWorse: true,
385 + aggregation: 'none',
386 + validDimensions: ['geography', 'year'],
387 + sourceSlugs: ['clinicaltrials', 'cdc-wonder', 'cdc-uscs', 'seer', 'iarc-globocan'],
388 + category: 'unmet_need',
389 + eligibility: { requires: ['mortality_count', 'active_trials'], minDeaths: 100, entityLevel: 'top' },
390 + experimental: false,
391 + },
392 + {
393 + slug: 'research_gap_ratio',
394 + name: 'Research Gap Ratio',
395 + description: 'log₂ of a cancer’s share of deaths divided by its share of publications (last 5 years), both over the eligible top-level cancers of the scope. 0 = literature share matches death share; positive values flag comparatively under-published cancers. Caveat: literature counts are query-based per entity and not aggregated over descendants.',
396 + formula: 'log2( (deaths / Σ deaths) / (publications_5y / Σ publications_5y) ) over eligible top-level cancers (deaths ≥ 100, publications_5y ≥ 1)',
397 + formulaVersion: 'ci-research-gap-ratio-v1',
398 + unit: 'log2_ratio',
399 + higherIsWorse: true,
400 + aggregation: 'none',
401 + validDimensions: ['geography', 'year'],
402 + sourceSlugs: ['pubmed', 'cdc-wonder', 'cdc-uscs', 'seer', 'iarc-globocan'],
403 + category: 'unmet_need',
404 + eligibility: { requires: ['mortality_count', 'publications_5y'], minDeaths: 100, entityLevel: 'top' },
405 + experimental: false,
406 + },
285 407 ];
added packages/ranking/src/drug-pipeline.ts +16 −0
@@ -0,0 +1,16 @@
1 +import type { Database } from '@cancerindex/database';
2 +
3 +export const DRUG_PIPELINE_FORMULA_VERSION = 'ci-drug-pipeline-v1';
4 +
5 +export interface DrugPipelineResult {
6 + rows: number;
7 +}
8 +
9 +/**
10 + * STUB — implemented by the Approvals & Pipeline work package.
11 + * Recomputes `drug_pipeline` (per drug, and per drug × cancer) from trial_interventions ×
12 + * trial_conditions × clinical_trials and drug_approvals.
13 + */
14 +export async function computeDrugPipeline(_db: Database): Promise<DrugPipelineResult> {
15 + return { rows: 0 };
16 +}
modified packages/ranking/src/engine.ts +1 −1
@@ -135,7 +135,7 @@ export async function computeAllRankings(db: Database): Promise<RankingResult[]>
135 135 return results;
136 136 }
137 137
138 −async function persistSnapshot(db: Database, def: typeof metricDefinitions.$inferSelect, scope: Scope, items: RankInput[], opts: { descending: boolean; sourceIds: string[] }): Promise<RankingResult> {
138 +export async function persistSnapshot(db: Database, def: typeof metricDefinitions.$inferSelect, scope: Scope, items: RankInput[], opts: { descending: boolean; sourceIds: string[] }): Promise<RankingResult> {
139 139 const key = scopeKey(scope);
140 140 const ranked = rankEntities(items, { descending: def.higherIsWorse === false ? opts.descending : opts.descending });
141 141 const hash = await inputsHash(items);
modified packages/ranking/src/index.ts +4 −0
@@ -2,3 +2,7 @@ export * from './rank.js';
2 2 export * from './counters.js';
3 3 export * from './engine.js';
4 4 export * from './trace.js';
5 +export * from './intelligence.js';
6 +export * from './trial-intelligence.js';
7 +export * from './drug-pipeline.js';
8 +export * from './research-gap.js';
added packages/ranking/src/intelligence.ts +48 −0
@@ -0,0 +1,48 @@
1 +import type { Database } from '@cancerindex/database';
2 +import { computeTrialIntelligence } from './trial-intelligence.js';
3 +import { computeDrugPipeline } from './drug-pipeline.js';
4 +import { computeResearchGap } from './research-gap.js';
5 +
6 +export interface IntelligenceResult {
7 + trialIntelligenceRows: number;
8 + trialSiteCountryRows: number;
9 + drugPipelineRows: number;
10 + researchGapRows: number;
11 + ms: number;
12 +}
13 +
14 +/**
15 + * Derived "intelligence" layer (SPEC §10-11, §15, §34): recomputed after counters, before rankings.
16 + * Each part is independent and deterministic; a failure in one part is reported, not hidden, and
17 + * does not prevent the others from running.
18 + */
19 +export async function computeIntelligence(db: Database, log: (msg: string, extra?: Record<string, unknown>) => void = () => {}): Promise<IntelligenceResult> {
20 + const t0 = Date.now();
21 + const out: IntelligenceResult = { trialIntelligenceRows: 0, trialSiteCountryRows: 0, drugPipelineRows: 0, researchGapRows: 0, ms: 0 };
22 + const errors: string[] = [];
23 + try {
24 + const r = await computeTrialIntelligence(db);
25 + out.trialIntelligenceRows = r.rows;
26 + out.trialSiteCountryRows = r.siteCountryRows;
27 + log('trial intelligence computed', { ...r });
28 + } catch (e) {
29 + errors.push(`trial-intelligence: ${(e as Error).message}`);
30 + }
31 + try {
32 + const r = await computeDrugPipeline(db);
33 + out.drugPipelineRows = r.rows;
34 + log('drug pipeline computed', { ...r });
35 + } catch (e) {
36 + errors.push(`drug-pipeline: ${(e as Error).message}`);
37 + }
38 + try {
39 + const r = await computeResearchGap(db);
40 + out.researchGapRows = r.rows;
41 + log('research gap components computed', { ...r });
42 + } catch (e) {
43 + errors.push(`research-gap: ${(e as Error).message}`);
44 + }
45 + out.ms = Date.now() - t0;
46 + if (errors.length) throw new Error(`intelligence partially failed: ${errors.join(' | ')}`);
47 + return out;
48 +}
added packages/ranking/src/research-gap.ts +18 −0
@@ -0,0 +1,18 @@
1 +import type { Database } from '@cancerindex/database';
2 +
3 +export const RESEARCH_GAP_FORMULA_VERSION = 'ci-research-gap-components-v1';
4 +
5 +export interface ResearchGapResult {
6 + rows: number;
7 + scopes: number;
8 +}
9 +
10 +/**
11 + * STUB — implemented by the Research Gap Index work package.
12 + * Recomputes `research_gap_components` per (cancer, geography, year, sex, burden source) and the
13 + * burden-normalized ranking snapshots (trials_per_1000_deaths, publications_per_1000_deaths,
14 + * trial_gap_ratio, research_gap_ratio).
15 + */
16 +export async function computeResearchGap(_db: Database): Promise<ResearchGapResult> {
17 + return { rows: 0, scopes: 0 };
18 +}
added packages/ranking/src/trial-intelligence.ts +17 −0
@@ -0,0 +1,17 @@
1 +import type { Database } from '@cancerindex/database';
2 +
3 +export const TRIAL_INTELLIGENCE_FORMULA_VERSION = 'ci-trial-intel-v1';
4 +export const TRIAL_SITE_COUNTRY_FORMULA_VERSION = 'ci-trial-sites-v1';
5 +
6 +export interface TrialIntelligenceResult {
7 + rows: number;
8 + siteCountryRows: number;
9 +}
10 +
11 +/**
12 + * STUB — implemented by the Clinical Trial Intelligence work package.
13 + * Recomputes `trial_intelligence` (per cancer × entity level) and `trial_site_country_counts`.
14 + */
15 +export async function computeTrialIntelligence(_db: Database): Promise<TrialIntelligenceResult> {
16 + return { rows: 0, siteCountryRows: 0 };
17 +}
modified scripts/ci.ts +13 −1
@@ -106,6 +106,18 @@ async function main() {
106 106 console.log(`[counters] refreshed ${n} entities`);
107 107 break;
108 108 }
109 + case 'intel': {
110 + const { computeIntelligence } = await import('@cancerindex/ranking');
111 + const r = await computeIntelligence(db, (m, extra) => console.log(`[intel] ${m}`, extra ?? ''));
112 + console.log(`[intel] trial_intelligence=${r.trialIntelligenceRows} site_countries=${r.trialSiteCountryRows} drug_pipeline=${r.drugPipelineRows} research_gap=${r.researchGapRows} (${r.ms} ms)`);
113 + break;
114 + }
115 + case 'reconcile-drugs': {
116 + const { reconcileInterventionDrugs } = await import('@cancerindex/connectors');
117 + const r = await reconcileInterventionDrugs(db, { remap: !!flags.remap });
118 + console.log('[reconcile-drugs]', r);
119 + break;
120 + }
109 121 case 'rank': {
110 122 const { computeAllRankings } = await import('@cancerindex/ranking');
111 123 const res = await computeAllRankings(db);
@@ -148,7 +160,7 @@ async function main() {
148 160 break;
149 161 }
150 162 default:
151 − console.log('usage: pnpm cix <connectors|run|run-all|health|sources:sync|counters|rank|stats|trace|doctor|alerts>');
163 + console.log('usage: pnpm cix <connectors|run|run-all|health|sources:sync|counters|intel|reconcile-drugs [--remap]|rank|stats|trace|doctor|alerts>');
152 164 }
153 165 } finally {
154 166 await closeDb();
modified workers/lib/env.ts +2 −0
@@ -27,6 +27,7 @@ export const JOBS = {
27 27 connectorRun: 'connector.run',
28 28 counters: 'maintenance.counters',
29 29 rank: 'maintenance.rank',
30 + intel: 'maintenance.intel',
30 31 healthProbe: 'health.probe',
31 32 } as const;
32 33 export type JobName = (typeof JOBS)[keyof typeof JOBS];
@@ -34,6 +35,7 @@ export type JobName = (typeof JOBS)[keyof typeof JOBS];
34 35 /** Daily maintenance (UTC): counters after the nightly connector windows, rankings after counters. */
35 36 export const SCHEDULES = {
36 37 counters: '0 6 * * *',
38 + intel: '15 6 * * *',
37 39 rank: '30 6 * * *',
38 40 healthProbe: '15 * * * *',
39 41 } as const;
modified workers/main.ts +20 −3
@@ -3,6 +3,7 @@
3 3 *
4 4 * connector.run {id, mode?, maxMinutes?, maxRecords?, resetCursor?} singleton per connector
5 5 * maintenance.counters {thenRank?} refreshCounters
6 + * maintenance.intel {thenRank?} computeIntelligence (trial intelligence, drug pipeline, research gap)
6 7 * maintenance.rank {} computeAllRankings
7 8 * health.probe {} healthCheck per connector → connector_cursors.health
8 9 *
@@ -15,7 +16,7 @@ import { sql } from 'drizzle-orm';
15 16 import { logger } from '@cancerindex/shared';
16 17 import { getDb, closeDb, raiseAlertSafe, resolveAlerts } from '@cancerindex/database';
17 18 import { ALERT_KINDS, CONNECTORS, getConnector, humanDuration, isStale, runConnector, RunContext, type RunMode } from '@cancerindex/connectors';
18 −import { refreshCounters, computeAllRankings } from '@cancerindex/ranking';
19 +import { refreshCounters, computeAllRankings, computeIntelligence } from '@cancerindex/ranking';
19 20
20 21 const log = logger.child({ component: 'worker' });
21 22 const db = getDb();
@@ -76,9 +77,10 @@ async function registerSchedules(): Promise<void> {
76 77 const skipped = CONNECTORS.filter((c) => !wanted.has(c.manifest.id)).map((c) => `${c.manifest.id}(${c.manifest.status}${c.manifest.schedule ? '' : ',no-schedule'})`);
77 78 if (skipped.length) log.info({ skipped }, 'connectors without schedule');
78 79 await boss.schedule(JOBS.counters, SCHEDULES.counters, { thenRank: false, requestedBy: 'schedule' }, { key: 'daily', singletonKey: 'counters', tz: 'UTC' });
80 + await boss.schedule(JOBS.intel, SCHEDULES.intel, { thenRank: false, requestedBy: 'schedule' }, { key: 'daily', singletonKey: 'intel', tz: 'UTC' });
79 81 await boss.schedule(JOBS.rank, SCHEDULES.rank, { requestedBy: 'schedule' }, { key: 'daily', singletonKey: 'rank', tz: 'UTC' });
80 82 await boss.schedule(JOBS.healthProbe, SCHEDULES.healthProbe, { requestedBy: 'schedule' }, { key: 'hourly', singletonKey: 'health', tz: 'UTC' });
81 − log.info({ counters: SCHEDULES.counters, rank: SCHEDULES.rank, health: SCHEDULES.healthProbe }, 'maintenance schedules registered (UTC)');
83 + log.info({ counters: SCHEDULES.counters, intel: SCHEDULES.intel, rank: SCHEDULES.rank, health: SCHEDULES.healthProbe }, 'maintenance schedules registered (UTC)');
82 84 }
83 85
84 86 async function handleConnectorRun([job]: Job<ConnectorRunData>[]): Promise<void> {
@@ -111,7 +113,20 @@ async function handleCounters([job]: Job<{ thenRank?: boolean; requestedBy?: str
111 113 const t0 = Date.now();
112 114 const n = await refreshCounters(db);
113 115 log.info({ entities: n, ms: Date.now() - t0, requestedBy: job!.data.requestedBy }, 'counters refreshed');
114 − if (job!.data.thenRank) await boss.send(JOBS.rank, { requestedBy: 'counters' }, { singletonKey: 'rank' });
116 + // Derived intelligence follows counters; rankings follow intelligence (chained by handleIntel).
117 + await boss.send(JOBS.intel, { thenRank: !!job!.data.thenRank, requestedBy: 'counters' }, { singletonKey: 'intel' });
118 +}
119 +
120 +async function handleIntel([job]: Job<{ thenRank?: boolean; requestedBy?: string }>[]): Promise<void> {
121 + try {
122 + const r = await computeIntelligence(db, (msg, extra) => log.info({ ...extra }, msg));
123 + log.info({ ...r, requestedBy: job!.data.requestedBy }, 'intelligence recomputed');
124 + } catch (err) {
125 + log.error({ err }, 'intelligence failed (partial results kept)');
126 + await raiseAlertSafe(db, { kind: 'intelligence_failure', severity: 'warn', message: `intelligence recompute failed: ${(err as Error).message.slice(0, 300)}` });
127 + } finally {
128 + if (job!.data.thenRank) await boss.send(JOBS.rank, { requestedBy: 'intel' }, { singletonKey: 'rank' });
129 + }
115 130 }
116 131
117 132 async function handleRank([job]: Job<{ requestedBy?: string }>[]): Promise<void> {
@@ -167,12 +182,14 @@ async function main(): Promise<void> {
167 182 await boss.start();
168 183 await ensureQueue(JOBS.connectorRun, (CI_MAX_RUN_MINUTES + 20) * 60);
169 184 await ensureQueue(JOBS.counters, 30 * 60);
185 + await ensureQueue(JOBS.intel, 60 * 60);
170 186 await ensureQueue(JOBS.rank, 60 * 60);
171 187 await ensureQueue(JOBS.healthProbe, 10 * 60);
172 188 await registerSchedules();
173 189
174 190 await boss.work<ConnectorRunData>(JOBS.connectorRun, { batchSize: 1, localConcurrency: WORKER_CONCURRENCY, pollingIntervalSeconds: 5 }, handleConnectorRun);
175 191 await boss.work(JOBS.counters, { batchSize: 1, pollingIntervalSeconds: 5 }, handleCounters);
192 + await boss.work(JOBS.intel, { batchSize: 1, pollingIntervalSeconds: 5 }, handleIntel);
176 193 await boss.work(JOBS.rank, { batchSize: 1, pollingIntervalSeconds: 5 }, handleRank);
177 194 await boss.work(JOBS.healthProbe, { batchSize: 1, pollingIntervalSeconds: 30 }, handleHealthProbe);
178 195 log.info({ concurrency: WORKER_CONCURRENCY, maxRunMinutes: CI_MAX_RUN_MINUTES, connectors: CONNECTORS.map((c) => c.manifest.id) }, 'worker ready');
179 196