import { pgTable, text, integer, bigserial, index, uniqueIndex, boolean, jsonb, real, timestamp } from 'drizzle-orm/pg-core';
import { ciId, createdAt, updatedAt } from './_common.js';

/** Knowledge graph edge with mandatory context and provenance (CLAUDE.md §28-29, §244). */
export const knowledgeEdges = pgTable(
  'knowledge_edges',
  {
    id: bigserial('id', { mode: 'number' }).primaryKey(),
    sourceEntityType: text('source_entity_type').notNull(), // cancer | gene | variant | drug | biomarker | trial | publication | pathway | risk_factor
    sourceEntityId: text('source_entity_id').notNull(),
    targetEntityType: text('target_entity_type').notNull(),
    targetEntityId: text('target_entity_id').notNull(),
    relationshipType: text('relationship_type').notNull(), // HAS_SUBTYPE | OCCURS_IN | ASSOCIATED_WITH | HAS_VARIANT | HAS_BIOMARKER | TREATED_BY | STUDIED_IN | DESCRIBED_BY | TARGETS | APPROVED_FOR | INVESTIGATED_FOR | PREDICTS_RESPONSE_TO | CONFERS_RESISTANCE_TO | PREDISPOSES_TO | PROGNOSTIC_IN | DIAGNOSTIC_OF
    cancerContextIds: text('cancer_context_ids').array().notNull().default([]),
    predictive: boolean('predictive'),
    prognostic: boolean('prognostic'),
    diagnostic: boolean('diagnostic'),
    predisposing: boolean('predisposing'),
    direction: text('direction'), // supports | resistance | sensitivity | neutral | unknown
    evidenceLevel: text('evidence_level'), // source-native level (e.g. CIViC A-E) — never re-scaled silently
    evidenceScore: real('evidence_score'),
    evidenceCategory: text('evidence_category').notNull().default('curated_evidence'), // observed_data | published_evidence | curated_evidence | regulatory_status | clinical_guideline | computed_metric
    status: text('status').notNull().default('active'), // active | candidate | superseded | retracted_basis
    sourceId: ciId('source_id').notNull(),
    sourceRecordId: text('source_record_id'),
    provenanceIds: integer('provenance_ids').array().notNull().default([]),
    supportCount: integer('support_count').notNull().default(1),
    firstSeenAt: timestamp('first_seen_at', { withTimezone: true }).notNull().defaultNow(),
    lastSeenAt: timestamp('last_seen_at', { withTimezone: true }).notNull().defaultNow(),
  },
  (t) => [
    uniqueIndex('knowledge_edges_uq').on(t.sourceEntityType, t.sourceEntityId, t.targetEntityType, t.targetEntityId, t.relationshipType, t.sourceId, t.sourceRecordId),
    index('knowledge_edges_source_idx').on(t.sourceEntityType, t.sourceEntityId, t.relationshipType),
    index('knowledge_edges_target_idx').on(t.targetEntityType, t.targetEntityId, t.relationshipType),
  ],
);

/** CIViC evidence items kept in their native structure (CLAUDE.md §10.9). */
export const civicEvidenceItems = pgTable(
  'civic_evidence_items',
  {
    id: bigserial('id', { mode: 'number' }).primaryKey(),
    civicId: integer('civic_id').notNull(),
    name: text('name'),
    molecularProfileId: integer('molecular_profile_id'),
    molecularProfileName: text('molecular_profile_name'),
    geneSymbols: text('gene_symbols').array().notNull().default([]),
    geneIds: text('gene_ids').array().notNull().default([]),
    variantIds: text('variant_ids').array().notNull().default([]),
    civicVariantIds: integer('civic_variant_ids').array().notNull().default([]),
    diseaseName: text('disease_name'),
    doid: text('doid'),
    cancerId: ciId('cancer_id'),
    cancerMatchType: text('cancer_match_type'),
    therapyNames: text('therapy_names').array().notNull().default([]),
    therapyIds: text('therapy_ids').array().notNull().default([]), // CI-DRUG-…
    therapyInteractionType: text('therapy_interaction_type'),
    evidenceType: text('evidence_type'), // PREDICTIVE | PROGNOSTIC | DIAGNOSTIC | PREDISPOSING | ONCOGENIC | FUNCTIONAL
    evidenceLevel: text('evidence_level'), // A-E
    evidenceDirection: text('evidence_direction'), // SUPPORTS | DOES_NOT_SUPPORT
    significance: text('significance'), // SENSITIVITYRESPONSE | RESISTANCE | …
    evidenceRating: integer('evidence_rating'),
    status: text('status'), // ACCEPTED | SUBMITTED | REJECTED
    description: text('description'),
    pmid: text('pmid'),
    sourceCitation: text('source_citation'),
    phenotypes: text('phenotypes').array().notNull().default([]),
    provenanceId: integer('provenance_id').notNull(),
    ingestRunId: text('ingest_run_id'),
    updatedAt: updatedAt(),
  },
  (t) => [uniqueIndex('civic_evidence_uq').on(t.civicId), index('civic_evidence_cancer_idx').on(t.cancerId), index('civic_evidence_gene_idx').on(t.geneSymbols)],
);

/** Risk factors / carcinogens as first-class entities (CLAUDE.md §74, §133). */
export const riskFactors = pgTable(
  'risk_factors',
  {
    id: bigserial('id', { mode: 'number' }).primaryKey(),
    slug: text('slug').notNull(),
    name: text('name').notNull(),
    kind: text('kind').notNull(), // behavioral | infectious | environmental | occupational | genetic | hormonal | demographic | carcinogen
    classificationAuthority: text('classification_authority'),
    classification: text('classification'),
    description: text('description'),
    createdAt: createdAt(),
  },
  (t) => [uniqueIndex('risk_factors_slug_uq').on(t.slug)],
);