@inflexa-ai/harness 0.35.8 → 0.36.0

package/dist/workflows/target-assessment/schemas.js

@@ -1,318 +0,0 @@
-/**
- * Shared schemas for target-assessment workflow inter-step contracts.
- *
- * The workflow input/output schemas, the resolved-target shape used by
- * every Phase-1 collector, and the keyed Phase-1/2/3 bundle shapes.
- */
-import { z } from "zod";
-import { EvidenceItemSchema } from "@inflexa-ai/harness/contracts/target-dossier.js";
-import { withCoverage } from "./coverage.js";
-export const TargetAssessmentInputSchema = z.object({
-    /** UUID of the target_assessments row already inserted by the trigger route. */
-    assessmentId: z.string().uuid(),
-    /** Free-form target identifier (gene symbol, alias, UniProt accession, ENSG, CHEMBL\d+). */
-    target: z.string().min(1),
-    /** Optional reviewer goal (carried into the dossier header). */
-    goal: z.string().nullable().optional(),
-    /** Organization id — used for scoping & billing. */
-    organizationId: z.string(),
-    /** Requesting user id (identity sub claim). */
-    requestedBy: z.string(),
-});
-export const ResolvedTargetSchema = z.object({
-    assessmentId: z.string().uuid(),
-    goal: z.string().nullable(),
-    canonicalId: z.string(),
-    canonicalOntology: z.enum(["hgnc", "ensembl"]),
-    geneSymbol: z.string(),
-    approvedName: z.string(),
-    ids: z.object({
-        hgnc: z.string().nullable(),
-        ensembl: z.string().nullable(),
-        uniprot: z.string().nullable(),
-        chembl: z.string().nullable(),
-        entrez: z.string().nullable(),
-    }),
-    synonyms: z.array(z.string()),
-    proteinSynonyms: z.array(z.string()),
-    proteinFamily: z.string().nullable(),
-    resolutionCoverage: z.object({
-        hgnc: z.boolean(),
-        uniprot: z.boolean(),
-        ensembl: z.boolean(),
-        chembl: z.boolean(),
-    }),
-});
-// ── Phase-1 collector output schemas ─────────────────────────────────
-const AssociationSchema = z.object({
-    diseaseId: z.string(),
-    diseaseName: z.string(),
-    score: z.number(),
-    geneticAssociationScore: z.number().nullable(),
-    knownDrugScore: z.number().nullable(),
-    literatureScore: z.number().nullable(),
-    animalModelScore: z.number().nullable().default(null),
-    somaticMutationScore: z.number().nullable().default(null),
-    literaturePmids: z.array(z.string()).default([]),
-});
-export const OpenTargetsBundleSchema = z.object({
-    ensemblId: z.string(),
-    approvedSymbol: z.string(),
-    approvedName: z.string(),
-    tractability: z
-        .object({
-        smallMolecule: z.boolean().nullable(),
-        antibody: z.boolean().nullable(),
-        otherModalities: z.boolean().nullable(),
-    })
-        .nullable(),
-    associations: z.array(AssociationSchema),
-    safetyLiabilities: z.array(z.object({
-        event: z.string(),
-        biosamples: z.array(z.string()),
-        effects: z.string().nullable(),
-        source: z.string(),
-    })),
-    // One target carries rows of more than one datasource, and each datasource has
-    // its own unit. Thus `datasourceId` rides with the row, because a reader that
-    // compares two rows without it compares a TPM against a CPM. The
-    // `baselineExpression` surface carries no protein measurement, thus the bundle
-    // makes no protein claim.
-    baselineExpression: z.array(z.object({
-        tissueId: z.string(),
-        tissueLabel: z.string(),
-        organSystem: z.string().nullable(),
-        datasourceId: z.string(),
-        rna: z.object({ value: z.number(), unit: z.string() }).nullable(),
-    })),
-});
-export const ChemblModulatorsBundleSchema = z.object({
-    targetChemblId: z.string().nullable(),
-    modulators: z.array(z.object({
-        moleculeChemblId: z.string(),
-        parentChemblId: z.string().nullable(),
-        preferredName: z.string().nullable(),
-        maxPhase: z.number().nullable(),
-        moleculeType: z.string().nullable(),
-        firstApproval: z.number().nullable(),
-        /** Present only for entries discovered via the activity-table secondary path. */
-        evidence_source: z.literal("chembl_activity").optional(),
-    })),
-});
-export const CtgovInterventionSchema = z.object({
-    name: z.string(),
-    type: z.string().nullable(),
-    description: z.string().nullable(),
-    otherNames: z.array(z.string()),
-});
-export const CtgovTrialSchema = z.object({
-    nctId: z.string(),
-    title: z.string(),
-    officialTitle: z.string().nullable(),
-    status: z.string(),
-    phase: z.string().nullable(),
-    studyType: z.string().nullable(),
-    primaryPurpose: z.string().nullable(),
-    conditions: z.array(z.string()),
-    interventions: z.array(z.string()),
-    interventionDetails: z.array(CtgovInterventionSchema),
-    enrollmentCount: z.number().nullable(),
-    startDate: z.string().nullable(),
-    primaryCompletionDate: z.string().nullable(),
-    whyStopped: z.string().nullable(),
-    briefSummary: z.string().nullable(),
-    detailedDescription: z.string().nullable(),
-    sponsor: z.string().nullable(),
-    collection_query: z.string().optional(),
-    collection_channel: z.enum(["target_symbol", "class_modulator", "therapeutic_program", "biomarker_context", "failed_intervention"]).optional(),
-});
-export const CtgovBundleSchema = z.object({
-    active: z.array(CtgovTrialSchema),
-    failed: z.array(CtgovTrialSchema),
-});
-export const FaersByTargetBundleSchema = z.object({
-    drugProbed: z.string(),
-    totalReports: z.number().nullable(),
-    topReactions: z.array(z.object({ reaction: z.string(), count: z.number() })),
-    seriousness: z
-        .object({
-        totalReports: z.number(),
-        fatalCount: z.number(),
-        hospitalizationCount: z.number(),
-        lifeThreateningCount: z.number(),
-        disablingCount: z.number(),
-        congenitalAnomalyCount: z.number().default(0),
-        otherSeriousCount: z.number().default(0),
-    })
-        .nullable(),
-});
-// The rows come from the Open Targets `baselineExpression` surface, which carries
-// no protein measurement. Thus a row states an RNA value only.
-export const ExpressionHumanBundleSchema = z.object({
-    source: z.enum(["gtex", "hpa_consensus", "hpa_rna_tissue"]),
-    unit: z.enum(["tpm", "ntpm", "consensus_normalized"]),
-    normalization_notes: z.string().min(1),
-    tissues: z.array(z.object({
-        tissueLabel: z.string(),
-        organSystem: z.string().nullable(),
-        value: z.number().nullable(),
-    })),
-});
-export const ExpressionMultiSpeciesBundleSchema = z.object({
-    geneSymbol: z.string(),
-    humanEnsemblId: z.string().nullable(),
-    bySpecies: z.array(z.object({
-        species: z.string(),
-        taxonId: z.number(),
-        ensemblId: z.string(),
-        source: z.string(),
-        unit: z.string(),
-        normalization_notes: z.string(),
-        tissues: z.array(z.object({
-            tissue: z.string(),
-            rank: z.enum(["absent", "low", "medium", "high"]),
-            expressionScore: z.number().nullable(),
-        })),
-    })),
-    notFound: z.array(z.string()),
-});
-export const ClinvarBundleSchema = z.object({
-    totalFound: z.number(),
-    variants: z.array(z.object({
-        variationId: z.string(),
-        title: z.string(),
-        clinicalSignificance: z.string(),
-        reviewStatus: z.string(),
-        conditions: z.array(z.string()),
-        molecularConsequence: z.string(),
-        accession: z.string(),
-    })),
-});
-export const CbioportalBundleSchema = z.object({
-    entrezGeneId: z.number().nullable(),
-    rows: z.array(z.object({
-        cancerTypeId: z.string(),
-        cancerTypeName: z.string(),
-        totalSamples: z.number(),
-        mutatedSamples: z.number(),
-        frequency: z.number(),
-        studies: z.array(z.string()),
-    })),
-});
-export const ImpcBundleSchema = z.object({
-    mouseMarkerSymbol: z.string().nullable(),
-    mgiAccessionId: z.string().nullable(),
-    viability: z.enum(["lethal_pre_weaning", "subviable", "viable"]).nullable(),
-    viabilityCalls: z.array(z.object({
-        zygosity: z.string(),
-        parameterStableId: z.string(),
-        mpTerm: z.object({ id: z.string(), name: z.string() }).nullable(),
-    })),
-    mpTerms: z.array(z.object({ id: z.string(), term: z.string(), bestPValue: z.number().nullable() })),
-    organSystems: z.array(z.string()),
-    sexDimorphic: z.boolean(),
-    phenotypeCount: z.number(),
-});
-export const PubmedIndexBundleSchema = z.object({
-    totalFound: z.number(),
-    topPmids: z.array(z.string()),
-    results: z.array(z.object({
-        pmid: z.string(),
-        title: z.string(),
-        journal: z.string(),
-        year: z.string(),
-        authors: z.string(),
-    })),
-});
-export const PathwaysBundleSchema = z.object({
-    pathways: z.array(z.object({
-        id: z.string(),
-        name: z.string(),
-        source: z.enum(["kegg", "reactome"]),
-        url: z.string().optional(),
-        entity_uniprots: z.array(z.string()).optional(),
-        metadata: z.object({ species_present: z.array(z.string()).optional() }).optional(),
-    })),
-});
-export const StringPpiBundleSchema = z.object({
-    partners: z.array(z.object({
-        proteinA: z.string(),
-        proteinB: z.string(),
-        score: z.number(),
-        experimentalScore: z.number().optional(),
-        databaseScore: z.number().optional(),
-        textminingScore: z.number().optional(),
-    })),
-});
-/**
- * Heterodimer / receptor-accessory complex inventory for the assessment
- * target, sourced from IUPHAR Guide to Pharmacology. Drives runtime
- * heterodimer-name detection (no hardcoded RAMP/MRAP/RGS regex) and the
- * obligate-cofactor supplement in the off-target panel.
- */
-export const FamilyComplexesBundleSchema = z.object({
-    primaryTargetGene: z.string(),
-    primaryTargetUniprot: z.string().nullable(),
-    accessoryProteinNames: z.array(z.string()),
-    complexes: z.array(z.object({
-        complexName: z.string(),
-        complexId: z.number().nullable(),
-        accessoryNames: z.array(z.string()),
-        subunitNames: z.array(z.string()),
-    })),
-});
-export const TherapeuticProgramsBundleSchema = z.object({
-    programs: z.array(z.object({
-        programId: z.string(),
-        name: z.string(),
-        targetSymbol: z.string(),
-        targetUniprot: z.string().nullable(),
-        modality: z.string(),
-        sponsor: z.string().nullable(),
-        mechanism: z.string(),
-        status: z.string(),
-        nctIds: z.array(z.string()),
-        pmids: z.array(z.string()),
-        evidence: z.array(EvidenceItemSchema),
-        confidence: z.enum(["high", "medium", "low"]),
-    })),
-});
-/**
- * Curated human phenotype and causal-disease evidence from Monarch.
- *
- * `ancestorIds` is the HPO ancestor closure, carried through so the consumer
- * resolves a phenotype onto an organ by identifier rather than by its label.
- */
-export const MonarchBundleSchema = z.object({
-    geneCurie: z.string(),
-    phenotypes: z.array(z.object({
-        hpoId: z.string(),
-        label: z.string(),
-        ancestorIds: z.array(z.string()),
-        publications: z.array(z.string()),
-        diseaseContext: z.string().nullable(),
-        frequencyPercent: z.number().nullable(),
-        primaryKnowledgeSource: z.string().nullable(),
-    })),
-});
-// ── Phase-1 keyed bundle (output of phase1Aggregate) ─────────────────
-export const Phase1BundleSchema = z.object({
-    resolved: ResolvedTargetSchema,
-    collectors: z.object({
-        opentargets: withCoverage(OpenTargetsBundleSchema),
-        chemblModulators: withCoverage(ChemblModulatorsBundleSchema),
-        ctgov: withCoverage(CtgovBundleSchema),
-        faersByTarget: withCoverage(FaersByTargetBundleSchema),
-        expressionHuman: withCoverage(ExpressionHumanBundleSchema),
-        expressionMultiSpecies: withCoverage(ExpressionMultiSpeciesBundleSchema),
-        clinvar: withCoverage(ClinvarBundleSchema),
-        cbioportal: withCoverage(CbioportalBundleSchema),
-        impc: withCoverage(ImpcBundleSchema),
-        pubmedIndex: withCoverage(PubmedIndexBundleSchema),
-        pathways: withCoverage(PathwaysBundleSchema),
-        stringPpi: withCoverage(StringPpiBundleSchema),
-        familyComplexes: withCoverage(FamilyComplexesBundleSchema),
-        monarch: withCoverage(MonarchBundleSchema),
-        therapeuticPrograms: withCoverage(TherapeuticProgramsBundleSchema).optional(),
-    }),
-});

package/dist/workflows/target-assessment/steps/collectors/pathways.d.ts

@@ -1,15 +0,0 @@
-export type PathwayRow = {
-    id: string;
-    name: string;
-    source: "reactome" | "kegg";
-    url: string;
-    entity_uniprots?: string[];
-    metadata?: {
-        species_present?: string[];
-    };
-};
-export declare function stripHtml(s: string): string;
-export declare function dedupPathwaysAcrossSpecies(rows: PathwayRow[], opts?: {
-    geneSymbolEchoFilter?: string;
-    assessmentUniprot?: string;
-}): PathwayRow[];

package/dist/workflows/target-assessment/steps/collectors/pathways.js

@@ -1,58 +0,0 @@
-import { stripHtmlAndCollapseWs } from "../../../../tools/lib/pathway-client.js";
-const REACTOME_ID_RE = /^R-([A-Z]+)-(\d+)/;
-export function stripHtml(s) {
-    return stripHtmlAndCollapseWs(s);
-}
-export function dedupPathwaysAcrossSpecies(rows, opts = {}) {
-    // Group Reactome rows by stable suffix; KEGG/other sources pass through.
-    const reactomeGroups = new Map();
-    const others = [];
-    for (const r of rows) {
-        if (r.source !== "reactome") {
-            others.push(r);
-            continue;
-        }
-        const m = REACTOME_ID_RE.exec(r.id);
-        if (!m) {
-            others.push(r);
-            continue;
-        }
-        const suffix = m[2];
-        const arr = reactomeGroups.get(suffix) ?? [];
-        arr.push(r);
-        reactomeGroups.set(suffix, arr);
-    }
-    const collapsed = [];
-    for (const group of reactomeGroups.values()) {
-        const withSpecies = group.map((r) => ({
-            r,
-            species: REACTOME_ID_RE.exec(r.id)[1],
-        }));
-        const human = withSpecies.find((x) => x.species === "HSA");
-        const winner = (human ?? withSpecies[0]).r;
-        const species_present = withSpecies.map((x) => x.species);
-        collapsed.push({
-            ...winner,
-            metadata: { ...(winner.metadata ?? {}), species_present },
-        });
-    }
-    const merged = [...collapsed, ...others];
-    let filtered = merged;
-    if (opts.assessmentUniprot) {
-        filtered = filtered.filter((r) => {
-            if (r.source !== "reactome")
-                return true; // only Reactome carries entity_uniprots
-            if (!r.entity_uniprots || r.entity_uniprots.length === 0)
-                return true; // graceful fallback when fetch failed
-            return r.entity_uniprots.includes(opts.assessmentUniprot);
-        });
-    }
-    if (opts.geneSymbolEchoFilter) {
-        const echo = opts.geneSymbolEchoFilter.toLowerCase();
-        filtered = filtered.filter((r) => r.name.toLowerCase() !== echo);
-    }
-    return filtered;
-}
-// `stripHtmlAndCollapseWs` is the underlying helper — kept in scope so the
-// `stripHtml` re-export above stays callable.
-void stripHtmlAndCollapseWs;

package/dist/workflows/target-assessment/steps/fanout/aes-for-one-class-drug-step.d.ts

@@ -1,34 +0,0 @@
-/**
- * Per-class-drug AE — fan-out item schemas.
- *
- * The DBOS-driven implementation lives in `target-assessment/fanout/index.ts`
- * (`aesForOneClassDrug`); this module is retained for its input/output
- * schemas and inferred item types.
- */
-import { z } from "zod";
-export declare const ClassDrugItemSchema: z.ZodObject<{
-    moleculeChemblId: z.ZodString;
-    preferredName: z.ZodString;
-    maxPhase: z.ZodNullable<z.ZodNumber>;
-    firstApproval: z.ZodNullable<z.ZodNumber>;
-}, z.core.$strip>;
-export type ClassDrugItem = z.infer<typeof ClassDrugItemSchema>;
-export declare const PerClassDrugAEsItemSchema: z.ZodObject<{
-    moleculeChemblId: z.ZodString;
-    preferredName: z.ZodString;
-    totalReports: z.ZodNullable<z.ZodNumber>;
-    topReactions: z.ZodArray<z.ZodObject<{
-        reaction: z.ZodString;
-        count: z.ZodNumber;
-    }, z.core.$strip>>;
-    seriousness: z.ZodNullable<z.ZodObject<{
-        totalReports: z.ZodNumber;
-        fatalCount: z.ZodNumber;
-        hospitalizationCount: z.ZodNumber;
-        lifeThreateningCount: z.ZodNumber;
-        disablingCount: z.ZodNumber;
-        congenitalAnomalyCount: z.ZodDefault<z.ZodNumber>;
-        otherSeriousCount: z.ZodDefault<z.ZodNumber>;
-    }, z.core.$strip>>;
-}, z.core.$strip>;
-export type PerClassDrugAEsItem = z.infer<typeof PerClassDrugAEsItemSchema>;

package/dist/workflows/target-assessment/steps/fanout/aes-for-one-class-drug-step.js

@@ -1,31 +0,0 @@
-/**
- * Per-class-drug AE — fan-out item schemas.
- *
- * The DBOS-driven implementation lives in `target-assessment/fanout/index.ts`
- * (`aesForOneClassDrug`); this module is retained for its input/output
- * schemas and inferred item types.
- */
-import { z } from "zod";
-export const ClassDrugItemSchema = z.object({
-    moleculeChemblId: z.string(),
-    preferredName: z.string(),
-    maxPhase: z.number().nullable(),
-    firstApproval: z.number().nullable(),
-});
-export const PerClassDrugAEsItemSchema = z.object({
-    moleculeChemblId: z.string(),
-    preferredName: z.string(),
-    totalReports: z.number().nullable(),
-    topReactions: z.array(z.object({ reaction: z.string(), count: z.number() })),
-    seriousness: z
-        .object({
-        totalReports: z.number(),
-        fatalCount: z.number(),
-        hospitalizationCount: z.number(),
-        lifeThreateningCount: z.number(),
-        disablingCount: z.number(),
-        congenitalAnomalyCount: z.number().default(0),
-        otherSeriousCount: z.number().default(0),
-    })
-        .nullable(),
-});

package/dist/workflows/target-assessment/steps/fanout/aes-for-one-trial-step.d.ts

@@ -1,57 +0,0 @@
-/**
- * Per-trial AE — fan-out item schemas.
- *
- * The DBOS-driven implementation lives in `target-assessment/fanout/index.ts`
- * (`aesForOneTrial`); this module is retained for its input/output schemas
- * and inferred item types.
- */
-import { z } from "zod";
-export declare const TrialItemSchema: z.ZodObject<{
-    nctId: z.ZodString;
-    title: z.ZodString;
-}, z.core.$strip>;
-export type TrialItem = z.infer<typeof TrialItemSchema>;
-export declare const PerTrialAEsItemSchema: z.ZodObject<{
-    nctId: z.ZodString;
-    title: z.ZodString;
-    whyStopped: z.ZodNullable<z.ZodString>;
-    outcomes: z.ZodDefault<z.ZodArray<z.ZodObject<{
-        type: z.ZodEnum<{
-            other: "other";
-            primary: "primary";
-            secondary: "secondary";
-        }>;
-        measure: z.ZodString;
-        description: z.ZodNullable<z.ZodString>;
-        timeFrame: z.ZodNullable<z.ZodString>;
-        effect: z.ZodDiscriminatedUnion<[z.ZodObject<{
-            kind: z.ZodLiteral<"quantitative">;
-            value: z.ZodNumber;
-            units: z.ZodString;
-            ci_low: z.ZodOptional<z.ZodNumber>;
-            ci_high: z.ZodOptional<z.ZodNumber>;
-        }, z.core.$strip>, z.ZodObject<{
-            kind: z.ZodLiteral<"not_extracted">;
-            reason: z.ZodEnum<{
-                ctgov_no_numeric_result: "ctgov_no_numeric_result";
-                ctgov_no_result_groups: "ctgov_no_result_groups";
-            }>;
-        }, z.core.$strip>], "kind">;
-    }, z.core.$strip>>>;
-    groups: z.ZodArray<z.ZodObject<{
-        groupId: z.ZodString;
-        title: z.ZodString;
-        description: z.ZodNullable<z.ZodString>;
-    }, z.core.$strip>>;
-    events: z.ZodArray<z.ZodObject<{
-        serious: z.ZodBoolean;
-        term: z.ZodString;
-        organSystem: z.ZodNullable<z.ZodString>;
-        counts: z.ZodArray<z.ZodObject<{
-            groupId: z.ZodString;
-            numAffected: z.ZodNullable<z.ZodNumber>;
-            numAtRisk: z.ZodNullable<z.ZodNumber>;
-        }, z.core.$strip>>;
-    }, z.core.$strip>>;
-}, z.core.$strip>;
-export type PerTrialAEsItem = z.infer<typeof PerTrialAEsItemSchema>;

package/dist/workflows/target-assessment/steps/fanout/aes-for-one-trial-step.js

@@ -1,54 +0,0 @@
-/**
- * Per-trial AE — fan-out item schemas.
- *
- * The DBOS-driven implementation lives in `target-assessment/fanout/index.ts`
- * (`aesForOneTrial`); this module is retained for its input/output schemas
- * and inferred item types.
- */
-import { z } from "zod";
-export const TrialItemSchema = z.object({
-    nctId: z.string(),
-    title: z.string(),
-});
-const OutcomeEffectSchema = z.discriminatedUnion("kind", [
-    z.object({
-        kind: z.literal("quantitative"),
-        value: z.number(),
-        units: z.string(),
-        ci_low: z.number().optional(),
-        ci_high: z.number().optional(),
-    }),
-    z.object({
-        kind: z.literal("not_extracted"),
-        reason: z.enum(["ctgov_no_numeric_result", "ctgov_no_result_groups"]),
-    }),
-]);
-export const PerTrialAEsItemSchema = z.object({
-    nctId: z.string(),
-    title: z.string(),
-    whyStopped: z.string().nullable(),
-    outcomes: z
-        .array(z.object({
-        type: z.enum(["primary", "secondary", "other"]),
-        measure: z.string(),
-        description: z.string().nullable(),
-        timeFrame: z.string().nullable(),
-        effect: OutcomeEffectSchema,
-    }))
-        .default([]),
-    groups: z.array(z.object({
-        groupId: z.string(),
-        title: z.string(),
-        description: z.string().nullable(),
-    })),
-    events: z.array(z.object({
-        serious: z.boolean(),
-        term: z.string(),
-        organSystem: z.string().nullable(),
-        counts: z.array(z.object({
-            groupId: z.string(),
-            numAffected: z.number().nullable(),
-            numAtRisk: z.number().nullable(),
-        })),
-    })),
-});

package/dist/workflows/target-assessment/steps/fanout/faers-for-one-modulator-step.d.ts

@@ -1,35 +0,0 @@
-/**
- * Per-modulator FAERS — fan-out item schemas.
- *
- * The DBOS-driven implementation lives in `target-assessment/fanout/index.ts`
- * (`faersForOneModulator`); this module is retained for its input/output
- * schemas and inferred item types.
- */
-import { z } from "zod";
-export declare const ModulatorItemSchema: z.ZodObject<{
-    moleculeChemblId: z.ZodString;
-    preferredName: z.ZodString;
-    maxPhase: z.ZodNullable<z.ZodNumber>;
-    firstApproval: z.ZodNullable<z.ZodNumber>;
-    rationale: z.ZodString;
-}, z.core.$strip>;
-export type ModulatorItem = z.infer<typeof ModulatorItemSchema>;
-export declare const PerModulatorFaersItemSchema: z.ZodObject<{
-    moleculeChemblId: z.ZodString;
-    preferredName: z.ZodString;
-    totalReports: z.ZodNullable<z.ZodNumber>;
-    topReactions: z.ZodArray<z.ZodObject<{
-        reaction: z.ZodString;
-        count: z.ZodNumber;
-    }, z.core.$strip>>;
-    seriousness: z.ZodNullable<z.ZodObject<{
-        totalReports: z.ZodNumber;
-        fatalCount: z.ZodNumber;
-        hospitalizationCount: z.ZodNumber;
-        lifeThreateningCount: z.ZodNumber;
-        disablingCount: z.ZodNumber;
-        congenitalAnomalyCount: z.ZodDefault<z.ZodNumber>;
-        otherSeriousCount: z.ZodDefault<z.ZodNumber>;
-    }, z.core.$strip>>;
-}, z.core.$strip>;
-export type PerModulatorFaersItem = z.infer<typeof PerModulatorFaersItemSchema>;

package/dist/workflows/target-assessment/steps/fanout/faers-for-one-modulator-step.js

@@ -1,32 +0,0 @@
-/**
- * Per-modulator FAERS — fan-out item schemas.
- *
- * The DBOS-driven implementation lives in `target-assessment/fanout/index.ts`
- * (`faersForOneModulator`); this module is retained for its input/output
- * schemas and inferred item types.
- */
-import { z } from "zod";
-export const ModulatorItemSchema = z.object({
-    moleculeChemblId: z.string(),
-    preferredName: z.string(),
-    maxPhase: z.number().nullable(),
-    firstApproval: z.number().nullable(),
-    rationale: z.string(),
-});
-export const PerModulatorFaersItemSchema = z.object({
-    moleculeChemblId: z.string(),
-    preferredName: z.string(),
-    totalReports: z.number().nullable(),
-    topReactions: z.array(z.object({ reaction: z.string(), count: z.number() })),
-    seriousness: z
-        .object({
-        totalReports: z.number(),
-        fatalCount: z.number(),
-        hospitalizationCount: z.number(),
-        lifeThreateningCount: z.number(),
-        disablingCount: z.number(),
-        congenitalAnomalyCount: z.number().default(0),
-        otherSeriousCount: z.number().default(0),
-    })
-        .nullable(),
-});

package/dist/workflows/target-assessment/steps/fanout/index.d.ts

@@ -1,14 +0,0 @@
-/**
- * Phase-3 fan-out item schemas. Each schema describes one work item (one
- * modulator, one trial, one class drug) and its coverage-tagged payload.
- * The harness DBOS implementation lives in
- * `../../fanout/index.ts` — these schemas are the shared type contract.
- */
-export { ModulatorItemSchema, PerModulatorFaersItemSchema } from "./faers-for-one-modulator-step.js";
-export type { ModulatorItem, PerModulatorFaersItem } from "./faers-for-one-modulator-step.js";
-export { TrialItemSchema, PerTrialAEsItemSchema } from "./aes-for-one-trial-step.js";
-export type { TrialItem, PerTrialAEsItem } from "./aes-for-one-trial-step.js";
-export { PolypharmInputItemSchema, PerModulatorPolypharmItemSchema } from "./polypharm-for-one-modulator-step.js";
-export type { PolypharmInputItem, PerModulatorPolypharmItem } from "./polypharm-for-one-modulator-step.js";
-export { ClassDrugItemSchema, PerClassDrugAEsItemSchema } from "./aes-for-one-class-drug-step.js";
-export type { ClassDrugItem, PerClassDrugAEsItem } from "./aes-for-one-class-drug-step.js";

package/dist/workflows/target-assessment/steps/fanout/index.js

@@ -1,10 +0,0 @@
-/**
- * Phase-3 fan-out item schemas. Each schema describes one work item (one
- * modulator, one trial, one class drug) and its coverage-tagged payload.
- * The harness DBOS implementation lives in
- * `../../fanout/index.ts` — these schemas are the shared type contract.
- */
-export { ModulatorItemSchema, PerModulatorFaersItemSchema } from "./faers-for-one-modulator-step.js";
-export { TrialItemSchema, PerTrialAEsItemSchema } from "./aes-for-one-trial-step.js";
-export { PolypharmInputItemSchema, PerModulatorPolypharmItemSchema } from "./polypharm-for-one-modulator-step.js";
-export { ClassDrugItemSchema, PerClassDrugAEsItemSchema } from "./aes-for-one-class-drug-step.js";