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Parthenon v1.0.8 — Publish, Library Lifecycle, and Agentic Copilots

· 5 min read
Sanjay M. Udoshi MD
Creator, Parthenon

v1.0.8 — Publish, Library Lifecycle, and Agentic Copilots​

After the v1.0.7 platform/architecture release (CE/EE fork, extension points, AGPLv3), v1.0.8 returns to the research surface and lands three intertwined feature lines at once: the Publish module for authoring and sharing study write-ups, Library Lifecycle management that gives every cohort, concept set, and analysis a draft → active → archived state machine plus an admin console, and the first two Claude Agent SDK copilots — a Study Designer and a Publication assistant — gated behind a single runtime toggle.

Publish module​

A full authoring surface for turning a study into a shareable write-up, persisted server-side with no "lost work" failure modes:

  • Server-side drafts — PublishPage loads and saves drafts through the API rather than browser state, with a stable documentHash for autosave deduplication
  • Debounced autosave with retry and a beforeunload guard, surfaced via a SaveStatusIndicator, SaveDraftButton, and a HybridPromptModal that prompts to save on first edit
  • Snapshots — PublicationSnapshotService with create/list/revert endpoints under optimistic locking, wired into CreateSnapshotModal, RevertSnapshotDialog, and a SnapshotsPanel
  • Study-scoped sharing — PublicationDraftPolicy, per-draft visibility and updated_by_user_id, a VisibilityBadge, a ShareDropdown, and a read-only wizard mode for viewer collaborators (Study::scopeAccessibleBy)
  • Publication library — /publish/library route + PublicationLibraryPage

Shipped across PR #339 (Phase 1) and PR #347.

Library Lifecycle management​

Every library artifact — cohort definitions, concept sets, and the eight analysis types — now carries a lifecycle state, with the plumbing to manage it at both user and admin scale.

Model + API (Phases A–B)

  • HasLibraryLifecycle trait with draft / active / archived transitions, reapplied to 9 models
  • Lifecycle columns on concept_sets, cohort_definitions, and 8 analyses tables (folding in the prior deprecated_at)
  • Owner + super-admin lifecycle policies
  • promote / archive / restore endpoints plus bulk-archive and bulk-restore
  • RequiresPromotionException → 409 contract, with an auto-promote flow when a draft artifact is attached to a study
  • Default scope hides drafts (for non-owners) and archived items

List-page UX (Phase B7–B9)

  • Status tabs with live counts on the cohort-definitions, concept-sets, and analyses list pages
  • Super-admin scope=all on list endpoints with an AllUsersToggle (D1–D2)

Admin console (Phase D3–D9)

  • /admin/library unified index across all artifact types (D3)
  • Hard-delete with attachment preflight + audit (D4) — preflight matches analyses by fully-qualified class name
  • Nightly 30-day purge of soft-deleted items (D5)
  • Owner reassignment with permission check + audit (D6)
  • Bulk delete, reassign, and trash on the admin page (D7)
  • library:backfill-lifecycle command for existing rows (D8)
  • One-time lifecycle notice toast for end users (D9)

Cleanup suggestions (Phase C1–C3)

  • Nightly SuggestLibraryCleanupJob (C1), a cache table + model, an API endpoint (C2), and a suggestions page + banner (C3) surfacing unused artifacts

33 feat(library) commits, landed across PR #339 and the D-phase series.

Claude Agent SDK copilots​

The first two agentic copilots, built on the Claude Agent SDK and gated so they can be turned off entirely:

  • Study Designer (PR #343) — a read-only slice (Phase 0+1) that assists study design from inside the Studies workspace
  • Publication agent (PR #347) — assists manuscript drafting in the Publish module, shipped as a read-only Phase 1 and a write/approval Phase 2
  • Generalized agent core (PR #346) — the agent core was refactored for multi-profile use so both copilots share one engine (Phase B)
  • Runtime AI Agents toggle (PR #348) — a single admin switch that gates both copilots, replacing the earlier publish.agent feature flag

Studies v2​

  • Compiler Workbench v2 promoted to default, with v1 fidelity restored
  • Create wizard shell with an 8-step stepper (Phase 3) and a version popover wired to the wizard footer
  • Post-flip audit closeout (H1–H5, M1–M19, L3–L4) plus 204 new i18n keys
  • Study::scopeAccessibleBy for collaborator lookups

Hypertension v3 outcomes study​

The Hypertension v3 study was redesigned and run end-to-end on the Acumenus OMOP CDM as a real-world exercise of the new surfaces:

  • v3 cohort redesign + manuscript update
  • 12 OHDSI negative controls with empirical-null calibration
  • End-to-end study run on the Acumenus OMOP CDM (1M patients)

Dependencies​

  • Documented all directly-imported Python dependencies in the AI service requirements
  • umap-learn >=0.5.0 → >=0.5.12; python-multipart >=0.0.27 → >=0.0.29 (PRs #330, #331, #344)

Upgrade notes​

  • git pull && ./deploy.sh is sufficient for most environments. The lifecycle columns are added by idempotent migrations; run ./deploy.sh --db to apply them.
  • Run php artisan library:backfill-lifecycle once to set lifecycle state on pre-existing library rows.
  • AI Agents (Study Designer + Publication assistant) are off by default — enable them from the admin AI Agents toggle. The legacy publish.agent flag is no longer read.
  • The nightly purge and cleanup-suggestion jobs are scheduled automatically; no action required.

By the numbers​

  • 205 commits since v1.0.7 over 18 days
  • 33 feat(library), 31 feat(publish), 11 feat(studies), plus the agent-core and copilot work
  • 3 feature lines landed together: Publish, Library Lifecycle, and Agentic Copilots

Contributors​

Claude Code + @sudoshi