@murphai/murph 1.2.0 → 1.2.4

package/node_modules/@murphai/vault-usecases/dist/usecases/experiment-journal-vault.d.ts

@@ -3,16 +3,16 @@ import { z } from 'zod';
 import { type ExperimentAssistantSupportOptions, type ExperimentOnboardingCaptureOptions } from '../experiment-onboarding-options.js';
 import type { JsonObject } from '../health-cli-method-types.js';
 declare const experimentStatusSchema: z.ZodEnum<{
-    paused: "paused";
-    completed: "completed";
     abandoned: "abandoned";
-    planned: "planned";
     active: "active";
+    completed: "completed";
+    paused: "paused";
+    planned: "planned";
 }>;
 type ExperimentStatusValue = z.infer<typeof experimentStatusSchema>;
 declare const experimentSignalDirectionSchema: z.ZodEnum<{
-    increase: "increase";
     decrease: "decrease";
+    increase: "increase";
     stabilize: "stabilize";
 }>;
 export interface ApplyExperimentOnboardingRecordInput extends ExperimentOnboardingCaptureOptions, ExperimentAssistantSupportOptions {
@@ -108,7 +108,7 @@ export declare function startExperimentFromPlanRecord(input: StartExperimentFrom
         lookupId: string;
         slug: string;
         experimentPath: string;
-        status: "paused" | "completed" | "abandoned" | "planned" | "active";
+        status: "abandoned" | "active" | "completed" | "paused" | "planned";
         created: boolean;
         updated: true;
     };
@@ -119,7 +119,7 @@ export declare function applyExperimentOnboardingRecord(input: ApplyExperimentOn
     lookupId: string;
     slug: string;
     experimentPath: string;
-    status: "paused" | "completed" | "abandoned" | "planned" | "active";
+    status: "abandoned" | "active" | "completed" | "paused" | "planned";
     updated: true;
 }>;
 export declare function updateExperimentRecord(input: {
@@ -146,7 +146,7 @@ export declare function updateExperimentRecord(input: {
     lookupId: string;
     slug: string;
     experimentPath: string;
-    status: "paused" | "completed" | "abandoned" | "planned" | "active";
+    status: "abandoned" | "active" | "completed" | "paused" | "planned";
     updated: true;
 }>;
 export declare function checkpointExperimentRecord(input: {
@@ -161,7 +161,7 @@ export declare function checkpointExperimentRecord(input: {
     lookupId: string;
     slug: string;
     experimentPath: string;
-    status: "paused" | "completed" | "abandoned" | "planned" | "active";
+    status: "abandoned" | "active" | "completed" | "paused" | "planned";
     eventId: string;
     ledgerFile: string;
     updated: true;
@@ -175,7 +175,7 @@ export declare function checkpointExperimentRecordFromInput(input: {
     lookupId: string;
     slug: string;
     experimentPath: string;
-    status: "paused" | "completed" | "abandoned" | "planned" | "active";
+    status: "abandoned" | "active" | "completed" | "paused" | "planned";
     eventId: string;
     ledgerFile: string;
     updated: true;
@@ -191,7 +191,7 @@ export declare function stopExperimentRecord(input: {
     lookupId: string;
     slug: string;
     experimentPath: string;
-    status: "paused" | "completed" | "abandoned" | "planned" | "active";
+    status: "abandoned" | "active" | "completed" | "paused" | "planned";
     eventId: string;
     ledgerFile: string;
     updated: true;
@@ -224,7 +224,7 @@ export declare function listExperimentRecords(input: {
 }): Promise<{
     vault: string;
     filters: {
-        status: "paused" | "completed" | "abandoned" | "planned" | "active" | null;
+        status: "abandoned" | "active" | "completed" | "paused" | "planned" | null;
         limit: number;
     };
     items: import("@murphai/operator-config/vault-cli-contracts").ListEntity[];
@@ -243,7 +243,7 @@ export declare function logExperimentSessionRecordFromInput(input: {
     eventId: string;
     ledgerFile: string;
     created: boolean;
-    kind: "intervention_session";
+    kind: 'intervention_session';
 }>;
 export declare function logExperimentSessionRecord(input: {
     vault: string;
@@ -271,7 +271,7 @@ export declare function logExperimentSessionRecord(input: {
     eventId: string;
     ledgerFile: string;
     created: boolean;
-    kind: "intervention_session";
+    kind: 'intervention_session';
 }>;
 export declare function logExperimentContextRecordFromInput(input: {
     vault: string;
@@ -285,7 +285,7 @@ export declare function logExperimentContextRecordFromInput(input: {
     eventId: string;
     ledgerFile: string;
     created: boolean;
-    kind: "note" | "supplement_intake" | "experiment_context";
+    kind: "experiment_context" | "note" | "supplement_intake";
 }>;
 export declare function attachExperimentSessionRecord(input: {
     vault: string;
@@ -294,11 +294,6 @@ export declare function attachExperimentSessionRecord(input: {
     replace?: boolean;
     allowOutOfWindow?: boolean;
 }): Promise<{
-    eventId: string;
-    lookupId: string;
-    experimentId: string;
-    experimentSlug: string;
-    linked: true;
     vault: string;
     entity: {
         id: string;
@@ -318,16 +313,16 @@ export declare function attachExperimentSessionRecord(input: {
             queryable: boolean;
         }[];
     };
+    eventId: string;
+    lookupId: string;
+    experimentId: string;
+    experimentSlug: string;
+    linked: true;
 }>;
 export declare function detachExperimentSessionRecord(input: {
     vault: string;
     eventId: string;
 }): Promise<{
-    eventId: string;
-    lookupId: string;
-    experimentId: null;
-    experimentSlug: null;
-    linked: false;
     vault: string;
     entity: {
         id: string;
@@ -347,6 +342,11 @@ export declare function detachExperimentSessionRecord(input: {
             queryable: boolean;
         }[];
     };
+    eventId: string;
+    lookupId: string;
+    experimentId: null;
+    experimentSlug: null;
+    linked: false;
 }>;
 export declare function logExperimentContextRecord(input: {
     vault: string;
@@ -370,7 +370,7 @@ export declare function logExperimentContextRecord(input: {
     eventId: string;
     ledgerFile: string;
     created: boolean;
-    kind: "note" | "supplement_intake" | "experiment_context";
+    kind: "experiment_context" | "note" | "supplement_intake";
 }>;
 export declare function showExperimentProgress(input: {
     vault: string;
@@ -399,7 +399,7 @@ export declare function showExperimentProgressCard(input: {
     slug: string;
     asOf: string;
     card: {
-        v: 1;
+        v: 2;
         title: string;
         asOf: string;
         phase: {
@@ -408,6 +408,7 @@ export declare function showExperimentProgressCard(input: {
         };
         sessions: {
             logged: number;
+            assumed?: number | undefined;
             target: number | null;
         };
         weeks: {
@@ -420,8 +421,8 @@ export declare function showExperimentProgressCard(input: {
             value: string;
             unit: string | null;
             delta: string;
-            direction: "down" | "up" | "neutral";
-            sentiment: "neutral" | "negative" | "positive";
+            direction: "down" | "neutral" | "up";
+            sentiment: "negative" | "neutral" | "positive";
         }[];
         confounders: {
             date: string;
@@ -460,10 +461,13 @@ export declare function writeExperimentOutcomeRecord(input: {
     lookup: string;
     asOf?: string;
 }): Promise<{
+    vault: string;
+    experimentId: string;
+    lookupId: string;
+    slug: string;
+    asOf: string;
     outcome: {
-        outcomeId: string;
-        generatedAt: string;
-        schema: "murph.experiment-outcome.v1";
+        schemaVersion: "murph.experiment-outcome.v1";
         adherenceSummary: {
             adherenceLevel?: "unknown" | "low" | "partial" | "good";
             completedSessions: number;
@@ -493,15 +497,12 @@ export declare function writeExperimentOutcomeRecord(input: {
         metricResults: import("@murphai/query").ExperimentMetricResult[];
         protocolRef: import("@murphai/query").ExperimentProtocolProjectionFields["protocolRef"];
         windows: import("@murphai/query").ExperimentProgressSummary["windows"];
-        schemaVersion: "murph.experiment-outcome.v1";
+        outcomeId: string;
+        generatedAt: string;
+        schema: "murph.experiment-outcome.v1";
     };
     outcomePath: string;
     updatedExperiment: boolean;
-    vault: string;
-    experimentId: string;
-    lookupId: string;
-    slug: string;
-    asOf: string;
 }>;
 export declare function ensureJournalRecord(input: {
     vault: string;

package/node_modules/@murphai/vault-usecases/dist/usecases/experiment-journal-vault.d.ts.map

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package/node_modules/@murphai/vault-usecases/dist/usecases/experiment-journal-vault.js

@@ -11,7 +11,7 @@ import { compactObject, inferVaultLinkKind, isVaultQueryableRecordId, normalizeI
 import { normalizeExperimentMeasurementAnchorFlagOption, normalizeExperimentPlannedMeasurementFlagOption, } from '../option-utils.js';
 import { buildExperimentAssistantSupportFromOptions, buildExperimentOnboardingCaptureFromOptions, normalizeRequiredTextOption, normalizeStableIdListOption, normalizeStableIdOption, normalizeTextListOption, } from '../experiment-onboarding-options.js';
 import { upsertEventRecord } from './provider-event.js';
-import { attachInterventionSessionToExperiment, detachInterventionSessionFromExperiment, } from './intervention-experiment-link.js';
+import { assertExperimentMatchesIntervention, attachInterventionSessionToExperiment, detachInterventionSessionFromExperiment, } from './intervention-experiment-link.js';
 const experimentStatusSchema = z.enum(EXPERIMENT_STATUSES);
 const experimentSignalDirectionSchema = z.enum(['increase', 'decrease', 'stabilize']);
 const experimentSelectorPayloadSchema = z
@@ -303,7 +303,7 @@ function hydrateRunPlanAdherenceTargets(runPlan) {
         return runPlan;
     }
     const [adherenceTarget] = synthesizeLegacySessionAdherenceTargets({ runPlan });
-    if (!adherenceTarget) {
+    if (!adherenceTarget?.calendar) {
         return runPlan;
     }
     return experimentRunPlanSchema.parse({
@@ -552,12 +552,28 @@ export async function logExperimentSessionRecordFromInput(input) {
 export async function logExperimentSessionRecord(input) {
     const experiment = await requireEntityFamily(input.vault, input.lookup, 'experiment');
     const frontmatter = requireExperimentFrontmatter(experiment);
-    const interventionType = slugifyExperimentValue(input.interventionType) ??
-        slugifyExperimentValue(frontmatter.runPlan?.modality) ??
+    const explicitInterventionType = slugifyExperimentValue(input.interventionType);
+    const derivedInterventionType = slugifyExperimentValue(frontmatter.runPlan?.modality) ??
         inferExperimentInterventionType(frontmatter.commonsProtocolRef?.key);
+    const interventionType = explicitInterventionType ??
+        derivedInterventionType;
     if (!interventionType) {
         throw new VaultCliError('invalid_payload', 'Experiment session logging requires interventionType or runPlan.modality.');
     }
+    if (input.interventionType !== undefined &&
+        explicitInterventionType !== null &&
+        derivedInterventionType !== null &&
+        explicitInterventionType !== derivedInterventionType) {
+        assertExperimentMatchesIntervention({
+            experiment: {
+                entity: experiment,
+                experimentId: frontmatter.experimentId,
+                experimentSlug: frontmatter.slug,
+                frontmatter,
+            },
+            interventionType: input.interventionType,
+        });
+    }
     const title = normalizeOptionalText(input.title) ?? buildExperimentSessionTitle({
         durationMinutes: input.durationMinutes,
         interventionType,
@@ -821,14 +837,27 @@ export async function showExperimentProgressCard(input) {
         lookup: input.lookup,
         vault: input.vault,
     });
+    const frontmatter = requireExperimentFrontmatter(entity);
     const metricPoints = await readExperimentJournalMetricPoints({
         asOf: input.asOf,
-        frontmatter: requireExperimentFrontmatter(entity),
+        frontmatter,
         query,
         vault: input.vault,
     });
+    const healthCommons = await loadHealthCommonsBiomarkerDirectionRuntime();
+    const biomarkerKeys = [
+        frontmatter.analysisPlan?.primaryBiomarkerKey ?? null,
+        ...(frontmatter.analysisPlan?.secondaryBiomarkerKeys ?? []),
+    ].filter((biomarkerKey) => biomarkerKey !== null);
+    const biomarkerDesiredDirections = uniqueStrings(biomarkerKeys).flatMap((biomarkerKey) => {
+        const desiredDirection = healthCommons.resolveGeneratedHealthCommonsBiomarkerDesiredDirection(biomarkerKey);
+        return desiredDirection === null
+            ? []
+            : [{ biomarkerKey, desiredDirection }];
+    });
     const { card, warnings } = query.buildExperimentProgressCard(readModel, slug, {
         asOf: input.asOf,
+        biomarkerDesiredDirections,
         confounders: input.confounders,
         metricPoints,
     });
@@ -1748,6 +1777,9 @@ function normalizeExpectedDirectionEntriesOption(values, existing) {
     }
     return experimentExpectedDirectionsSchema.parse([...next].map(([biomarkerKey, direction]) => ({ biomarkerKey, direction })));
 }
+async function loadHealthCommonsBiomarkerDirectionRuntime() {
+    return loadRuntimeModule('@murphai/health-commons/runtime');
+}
 function normalizeSha256RevisionOption(value, optionName) {
     const normalized = normalizeRequiredTextOption(value, optionName);
     if (!/^sha256:[a-f0-9]{64}$/u.test(normalized)) {