@murphai/murph 0.1.15 → 0.1.17

package/node_modules/@murphai/core/dist/genetics/api.js

@@ -0,0 +1,226 @@
+import { CONTRACT_SCHEMA_VERSION, FRONTMATTER_DOC_TYPES, extractHealthEntityRegistryLinks, geneticsRegistryEntityDefinition, contractIdMaxLength, GENETIC_VARIANT_LIMITS, ID_PREFIXES, } from "@murphai/contracts";
+import { VaultError } from "../errors.js";
+import { generateRecordId } from "../ids.js";
+import { createMarkdownRegistryApi } from "../registry/api.js";
+import { bulletList, maybeSection, normalizeId, normalizeSlug, optionalEnum, optionalString, requireString, validateSortedStringList, } from "../history/shared.js";
+import { VARIANT_SIGNIFICANCES, VARIANT_ZYGOSITIES, } from "./types.js";
+const GENETICS_DIRECTORY = geneticsRegistryEntityDefinition.registry.directory;
+const GENETIC_TITLE_MAX_LENGTH = GENETIC_VARIANT_LIMITS.title;
+const GENETIC_GENE_MAX_LENGTH = GENETIC_VARIANT_LIMITS.gene;
+const GENETIC_INHERITANCE_MAX_LENGTH = GENETIC_VARIANT_LIMITS.inheritance;
+const GENETIC_NOTE_MAX_LENGTH = GENETIC_VARIANT_LIMITS.note;
+const GENETIC_FAMILY_ID_MAX_LENGTH = contractIdMaxLength(ID_PREFIXES.family);
+function parseGeneticVariantFrontmatter(attributes) {
+    const schema = geneticsRegistryEntityDefinition.registry.frontmatterSchema;
+    if (!schema) {
+        throw new Error("Genetics registry definition is missing a frontmatter schema.");
+    }
+    const result = schema.safeParse(attributes);
+    if (!result.success) {
+        throw new VaultError("VAULT_INVALID_GENETIC_VARIANT", "Genetics registry document has an unexpected shape.");
+    }
+    return result.data;
+}
+function sortGeneticRecords(records) {
+    records.sort((left, right) => left.entity.gene.localeCompare(right.entity.gene) ||
+        left.entity.title.localeCompare(right.entity.title) ||
+        left.entity.variantId.localeCompare(right.entity.variantId));
+}
+function buildBody(record) {
+    const relations = canonicalizeGeneticRelations(record);
+    return [
+        `# ${record.title}`,
+        "",
+        `Gene: ${record.gene}`,
+        "",
+        "## Source Family Members",
+        "",
+        bulletList(relations.sourceFamilyMemberIds),
+        "",
+        maybeSection("Notes", record.note),
+        "",
+    ].join("\n");
+}
+function normalizeGeneticLinkType(value) {
+    return value === "source_family_member" ? value : null;
+}
+function compareGeneticLinks(left, right) {
+    return left.targetId.localeCompare(right.targetId);
+}
+function buildGeneticLinksFromFields(input) {
+    return (input.sourceFamilyMemberIds ?? []).map((targetId) => ({
+        type: "source_family_member",
+        targetId,
+    }));
+}
+function normalizeGeneticLinks(rawLinks) {
+    const sortedLinks = [...rawLinks].sort(compareGeneticLinks);
+    const links = [];
+    const seen = new Set();
+    for (const link of sortedLinks) {
+        const dedupeKey = `${link.type}:${link.targetId}`;
+        if (seen.has(dedupeKey)) {
+            continue;
+        }
+        seen.add(dedupeKey);
+        links.push(link);
+    }
+    return links;
+}
+function parseGeneticLinks(attributes) {
+    return normalizeGeneticLinks(extractHealthEntityRegistryLinks("genetics", attributes).flatMap((link) => {
+        const type = normalizeGeneticLinkType(link.type);
+        return type ? [{ type, targetId: link.targetId }] : [];
+    }));
+}
+function geneticRelationsFromLinks(links) {
+    const sourceFamilyMemberIds = links.map((link) => link.targetId);
+    return {
+        sourceFamilyMemberIds: sourceFamilyMemberIds.length > 0 ? sourceFamilyMemberIds : undefined,
+        links: [...links],
+    };
+}
+function canonicalizeGeneticRelations(input) {
+    const links = normalizeGeneticLinks(input.links !== undefined
+        ? [...input.links]
+        : buildGeneticLinksFromFields({
+            sourceFamilyMemberIds: input.sourceFamilyMemberIds,
+        }));
+    return geneticRelationsFromLinks(links);
+}
+function recordFromParts(attributes, relativePath, markdown) {
+    const frontmatter = parseGeneticVariantFrontmatter(attributes);
+    const relations = canonicalizeGeneticRelations({
+        links: parseGeneticLinks(attributes),
+    });
+    const entity = {
+        ...frontmatter,
+        zygosity: optionalEnum(frontmatter.zygosity, VARIANT_ZYGOSITIES, "zygosity"),
+        significance: optionalEnum(frontmatter.significance, VARIANT_SIGNIFICANCES, "significance"),
+        inheritance: optionalString(frontmatter.inheritance, "inheritance", GENETIC_INHERITANCE_MAX_LENGTH),
+        sourceFamilyMemberIds: relations.sourceFamilyMemberIds,
+        note: optionalString(frontmatter.note, "note", GENETIC_NOTE_MAX_LENGTH),
+        links: relations.links,
+    };
+    return {
+        entity,
+        document: {
+            relativePath,
+            markdown,
+        },
+    };
+}
+const geneticsRegistryApi = createMarkdownRegistryApi({
+    directory: GENETICS_DIRECTORY,
+    recordFromParts,
+    isExpectedRecord: () => true,
+    invalidCode: "VAULT_INVALID_GENETIC_VARIANT",
+    invalidMessage: "Genetics registry document has an unexpected shape.",
+    sortRecords: sortGeneticRecords,
+    getRecordId: (record) => record.entity.variantId,
+    getRecordSlug: (record) => record.entity.slug,
+    getRecordRelativePath: (record) => record.document.relativePath,
+    conflictCode: "VAULT_GENETIC_VARIANT_CONFLICT",
+    conflictMessage: "variantId and slug resolve to different variants.",
+    readMissingCode: "VAULT_GENETIC_VARIANT_MISSING",
+    readMissingMessage: "Genetic variant was not found.",
+    createRecordId: () => generateRecordId("var"),
+    operationType: "genetics_upsert",
+    summary: (recordId) => `Upsert genetic variant ${recordId}`,
+    audit: {
+        action: "genetics_upsert",
+        commandName: "core.upsertGeneticVariant",
+        summary: (created) => `${created ? "Created" : "Updated"} genetic variant registry record.`,
+    },
+});
+function buildAttributes(input) {
+    const relations = canonicalizeGeneticRelations(input);
+    return Object.fromEntries(Object.entries({
+        schemaVersion: CONTRACT_SCHEMA_VERSION.geneticVariantFrontmatter,
+        docType: FRONTMATTER_DOC_TYPES.geneticVariant,
+        variantId: input.variantId,
+        slug: input.slug,
+        title: input.title,
+        gene: input.gene,
+        zygosity: input.zygosity,
+        significance: input.significance,
+        inheritance: input.inheritance,
+        sourceFamilyMemberIds: relations.sourceFamilyMemberIds,
+        links: relations.links.length > 0 ? relations.links : undefined,
+        note: input.note,
+    }).filter(([, value]) => value !== undefined));
+}
+export async function upsertGeneticVariant(input) {
+    const normalizedVariantId = normalizeId(input.variantId, "variantId", "var");
+    const selectorSlug = (input.slug ? normalizeSlug(input.slug, "slug") : undefined) ??
+        (input.gene && input.title
+            ? normalizeSlug(undefined, "slug", `${input.gene}-${input.title}`)
+            : undefined);
+    const existingRecord = await geneticsRegistryApi.resolveExistingRecord({
+        vaultRoot: input.vaultRoot,
+        recordId: normalizedVariantId,
+        slug: selectorSlug,
+    });
+    const existingEntity = existingRecord?.entity;
+    const title = requireString(input.title ?? existingEntity?.title, "title", GENETIC_TITLE_MAX_LENGTH);
+    const gene = requireString(input.gene ?? existingEntity?.gene, "gene", GENETIC_GENE_MAX_LENGTH);
+    const sourceFamilyMemberIds = input.sourceFamilyMemberIds === undefined
+        ? existingEntity?.sourceFamilyMemberIds
+        : validateSortedStringList(input.sourceFamilyMemberIds, "sourceFamilyMemberIds", "familyMemberId", 24, GENETIC_FAMILY_ID_MAX_LENGTH);
+    const usesRelationInputs = input.links !== undefined ||
+        input.sourceFamilyMemberIds !== undefined;
+    const relations = canonicalizeGeneticRelations({
+        links: input.links !== undefined ? input.links : usesRelationInputs ? undefined : existingEntity?.links,
+        sourceFamilyMemberIds,
+    });
+    const note = input.note === undefined
+        ? existingEntity?.note
+        : optionalString(input.note, "note", GENETIC_NOTE_MAX_LENGTH);
+    return geneticsRegistryApi.upsertRecord({
+        vaultRoot: input.vaultRoot,
+        existingRecord,
+        recordId: normalizedVariantId,
+        requestedSlug: selectorSlug,
+        defaultSlug: normalizeSlug(undefined, "slug", `${gene}-${title}`),
+        buildDocument: (target) => ({
+            attributes: buildAttributes({
+                variantId: target.recordId,
+                slug: target.slug,
+                title,
+                gene,
+                zygosity: input.zygosity === undefined
+                    ? existingEntity?.zygosity
+                    : optionalEnum(input.zygosity, VARIANT_ZYGOSITIES, "zygosity"),
+                significance: input.significance === undefined
+                    ? existingEntity?.significance
+                    : optionalEnum(input.significance, VARIANT_SIGNIFICANCES, "significance"),
+                inheritance: input.inheritance === undefined
+                    ? existingEntity?.inheritance
+                    : optionalString(input.inheritance, "inheritance", GENETIC_INHERITANCE_MAX_LENGTH),
+                sourceFamilyMemberIds: relations.sourceFamilyMemberIds,
+                links: relations.links,
+                note,
+            }),
+            body: buildBody({
+                gene,
+                title,
+                sourceFamilyMemberIds: relations.sourceFamilyMemberIds,
+                links: relations.links,
+                note,
+            }),
+        }),
+    });
+}
+export async function listGeneticVariants(vaultRoot) {
+    return geneticsRegistryApi.listRecords(vaultRoot);
+}
+export async function readGeneticVariant({ vaultRoot, variantId, slug, }) {
+    const normalizedVariantId = normalizeId(variantId, "variantId", "var");
+    const normalizedSlug = slug ? normalizeSlug(slug, "slug") : undefined;
+    return geneticsRegistryApi.readRecord({
+        vaultRoot,
+        recordId: normalizedVariantId,
+        slug: normalizedSlug,
+    });
+}
+//# sourceMappingURL=api.js.map

package/node_modules/@murphai/core/dist/genetics/api.js.map

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package/node_modules/@murphai/core/dist/genetics/index.d.ts

@@ -0,0 +1,3 @@
+export * from "./api.ts";
+export * from "./types.ts";
+//# sourceMappingURL=index.d.ts.map

package/node_modules/@murphai/core/dist/genetics/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/genetics/index.ts"],"names":[],"mappings":"AAAA,cAAc,UAAU,CAAC;AACzB,cAAc,YAAY,CAAC"}

package/node_modules/@murphai/core/dist/genetics/index.js

@@ -0,0 +1,3 @@
+export * from "./api.js";
+export * from "./types.js";
+//# sourceMappingURL=index.js.map

package/node_modules/@murphai/core/dist/genetics/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/genetics/index.ts"],"names":[],"mappings":"AAAA,cAAc,UAAU,CAAC;AACzB,cAAc,YAAY,CAAC"}

package/node_modules/@murphai/core/dist/genetics/types.d.ts

@@ -0,0 +1,40 @@
+import { type GeneticVariantFrontmatter } from "@murphai/contracts";
+import type { StoredMarkdownRegistryEntity } from "../bank/types.ts";
+export declare const VARIANT_ZYGOSITIES: readonly ["heterozygous", "homozygous", "compound_heterozygous", "unknown"];
+export declare const VARIANT_SIGNIFICANCES: readonly ["pathogenic", "likely_pathogenic", "risk_factor", "vus", "benign", "unknown"];
+export type VariantZygosity = (typeof VARIANT_ZYGOSITIES)[number];
+export type VariantSignificance = (typeof VARIANT_SIGNIFICANCES)[number];
+export type VariantInheritance = string;
+export type GeneticVariantLinkType = "source_family_member";
+export interface GeneticVariantLink {
+    type: GeneticVariantLinkType;
+    targetId: string;
+}
+export interface GeneticVariantEntity extends GeneticVariantFrontmatter {
+    links: GeneticVariantLink[];
+}
+export type GeneticVariantStoredDocument = StoredMarkdownRegistryEntity<GeneticVariantEntity>;
+export interface UpsertGeneticVariantInput {
+    vaultRoot: string;
+    variantId?: string;
+    slug?: string;
+    gene?: string;
+    title?: string;
+    zygosity?: VariantZygosity;
+    significance?: VariantSignificance;
+    inheritance?: VariantInheritance;
+    sourceFamilyMemberIds?: string[];
+    links?: GeneticVariantLink[];
+    note?: string;
+}
+export interface UpsertGeneticVariantResult {
+    created: boolean;
+    auditPath: string;
+    record: GeneticVariantStoredDocument;
+}
+export interface ReadGeneticVariantInput {
+    vaultRoot: string;
+    variantId?: string;
+    slug?: string;
+}
+//# sourceMappingURL=types.d.ts.map

package/node_modules/@murphai/core/dist/genetics/types.d.ts.map

@@ -0,0 +1 @@
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package/node_modules/@murphai/core/dist/genetics/types.js

@@ -0,0 +1,4 @@
+import { VARIANT_SIGNIFICANCES as CONTRACT_VARIANT_SIGNIFICANCES, VARIANT_ZYGOSITIES as CONTRACT_VARIANT_ZYGOSITIES, } from "@murphai/contracts";
+export const VARIANT_ZYGOSITIES = CONTRACT_VARIANT_ZYGOSITIES;
+export const VARIANT_SIGNIFICANCES = CONTRACT_VARIANT_SIGNIFICANCES;
+//# sourceMappingURL=types.js.map

package/node_modules/@murphai/core/dist/genetics/types.js.map

@@ -0,0 +1 @@
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package/node_modules/@murphai/core/dist/history/api.d.ts

@@ -0,0 +1,7 @@
+import type { AppendBloodTestInput, AppendBloodTestResult, AppendHistoryEventInput, AppendHistoryEventResult, HistoryEventRecord, ListHistoryEventsInput, ReadHistoryEventInput, ReadHistoryEventResult, TestHistoryEventRecord } from "./types.ts";
+export declare function appendHistoryEvent(input: AppendHistoryEventInput): Promise<AppendHistoryEventResult>;
+export declare function appendBloodTest(input: AppendBloodTestInput): Promise<AppendBloodTestResult>;
+export declare function listHistoryEvents({ vaultRoot, kinds, source, from, to, order, limit, }: ListHistoryEventsInput): Promise<HistoryEventRecord[]>;
+export declare function readHistoryEvent({ vaultRoot, eventId, }: ReadHistoryEventInput): Promise<ReadHistoryEventResult>;
+export declare function isBloodTestHistoryRecord(record: Pick<TestHistoryEventRecord, "kind" | "testCategory" | "specimenType">): boolean;
+//# sourceMappingURL=api.d.ts.map

package/node_modules/@murphai/core/dist/history/api.d.ts.map

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