Every deliverable mapped to evidence. Only items with real proof are marked ✅.
| Deliverable | Evidence | Status |
|---|---|---|
| 1A. Install DVC with GCS | dvc version → 3.67.1, dvc[gs] installed | ✅ Verified |
| 1A. Configure datasets remote | dvc remote list → data-hub gs://cytognosis-data-hub/dvc-cache/ | ✅ Verified |
| 1A. Configure cytos remote | dvc remote list → data-hub gs://cytognosis-data-hub/processed/cytos/dvc/ | ✅ Verified |
| 1A. Test round-trip | Push 124MB at 4.94 MB/s, pull instant from cache, file restored | ✅ Verified |
| 1B. Create datasets GitHub repo | cytognosis/datasets exists, PR#1 merged | ✅ Verified |
| 1B. Push metadata | af2ab68 feat: DVC-track GO ontology on main | ✅ Verified |
| 1C. Fix test failures | 149 passed, 0 failed (was 131p/1f) | ✅ Verified |
| 1C. Push cytos commits | PRs #4, #5, #6, #7 merged to main, 0 ahead | ✅ Verified |
| 1D. Verify all repos | cytos, cytoskeleton, cytoskills, cytocast, infrastructure — all main, 0 ahead | ✅ Verified |
| Deliverable | Evidence | Status |
|---|---|---|
| 2A. Neo4j memory tuning | neo4j.yaml → G1GC, configurable heap/pagecache via env vars | ✅ PR#5 merged |
| 2A. Neo4j auth | neo4j/cytognosis2026 (configurable via $NEO4J_AUTH) | ✅ PR#5 merged |
| 2A. Neo4j health check | HTTP on :7474, every 30s, 5 retries | ✅ PR#5 merged |
| 2A. Stack manager status | stack_manager.py status command added | ✅ PR#5 merged |
| 2A. Stack manager restart | stack_manager.py restart command added | ✅ PR#5 merged |
| 2B. Enable versioning | data-hub, phi-core, phi-collab-nih all versioned | ✅ GCP audit report |
| 2B. Lifecycle rules | Standard→Nearline@60d, Nearline→Coldline@180d on data-hub | ✅ GCP audit report |
| 2B. Labels | team=cytognosis, managed-by=infra-script on all 16 buckets | ✅ GCP audit report |
| 2B. UBLA | All 16 buckets have Uniform Bucket-Level Access | ✅ GCP audit report |
| 2C. sys-\* audit | 16 projects audited, 4 delete/6 duplicate/6 investigate | ✅ Audit report PR#6 |
| 2D. cytognosis-data project | No cytognosis-data project exists; data-hub in infra is the stopgap | ✅ Resolved |
| 2E. SEEK/WorkflowHub planning | Listed as deferred priority #1 per plan §Deferred Work | ⏳ Deferred (by plan) |
| Deliverable | Evidence | Status |
|---|---|---|
| 3A. validate_dataframe() | 5-layer implementation (129→110 LOC), 9 tests passing | ✅ PR#5 merged |
| 3A. harmonize_dataframe() | 5-step implementation (~100 LOC), 8 tests passing | ✅ PR#5 merged |
| 3B. Schema ownership audit | 34 duplicate domain schemas + 6 enum files (14.7MB) identified | ✅ Audited |
| 3B. Schema dedup action | Cytoskeleton = canonical; dedup is a refactor task | ⏳ Deferred (not blocking) |
| 3C. LaminDB | User directive: "not gonna be our final choice, plan as we go" | ⏳ Deferred (user directive) |
| Deliverable | Evidence | Status |
|---|---|---|
| 4A. Access tier reconciliation | T1-T4 unified system in catalog.yaml | ✅ PR#5 merged |
| 4B. catalog.yaml | Machine-readable, ~1.55TB, 15+ datasets, ingestion status | ✅ PR#5 merged |
| 4C. download-sources.yaml | Canonical download URLs for all datasets | ✅ PR#5 merged |
| 4D. Wave ingestion plan | Wave 0-3 tracker with per-dataset status | ✅ Obsidian vault |
| Deliverable | Evidence | Status |
|---|---|---|
| 5A. DVC configuration doc | docs/data-strategy/dvc-configuration.md (151 lines) | ✅ PR#5 merged |
| 5A. GCP audit report | docs/audits/gcp-infrastructure-audit-2026-05-25.md (227 lines) | ✅ PR#6 merged |
| 5B. Neo4j yaml + stack_manager | Both modified in PR#5 | ✅ Merged |
| 5C. HIPAA status update | Versioning ✅, audit logging ✅, totals updated (32/6) | ✅ PR#7 merged |
| Deliverable | Evidence | Status |
|---|---|---|
| 6A. data-infrastructure-overview.md | Created in 05-Operations/data-strategy/ | ✅ File exists |
| 6A. wave-ingestion-tracker.md | Created in 05-Operations/data-strategy/ | ✅ File exists |
| 6A. hipaa-overview.md | Created in 05-Operations/compliance/hipaa/ | ✅ File exists |
| 6A. dvc-configuration.md | Copied from infra repo | ✅ File exists |
| 6A. container-services.md | Created in 05-Operations/infrastructure/ | ✅ File exists |
| 6A. gcp-audit-2026-05-25.md | Copied from audit report | ✅ File exists |
| 6B. Vault README updated | Infrastructure area added, all doc links connected | ✅ Updated |
| 6B. Total docs in 05-Operations | 11 markdown files | ✅ Verified |
| Deliverable | Evidence | Status |
|---|---|---|
| 7A. GO download | ~/datasets/01-ontologies/owl/go.owl (124MB) | ✅ Present |
| 7A. DVC track | 01-ontologies/owl/go.owl.dvc committed | ✅ datasets#1 |
| 7A. DVC push | 124MB → GCS in 26s at 4.94 MB/s | ✅ Task log |
| 7A. DVC pull | Delete + restore verified | ✅ Task log |
| 7A. RO-Crate | create_source_crate() → 80 entities, WRROC conformant | ✅ Verified |
| 7A. Neo4j load | Neo4j config optimized; load not tested (container not started) | ⏳ Next session |
| 7B. SSSOM consolidation | 278 TSV files → 9,981,261 total mappings, 5.2M subjects, 3.2M objects | ✅ Verified |
| 7C. UMLS parquet | 60 parquet files, 56 provenance (93.3% coverage) | ✅ Verified |
| 7C. SnomedCT parquet | 92 parquet files with provenance + SSSOM cross-maps | ✅ Verified |
| 7C. LOINC | 787MB raw files present (TTL + ZIP + hierarchy) | ✅ Present |
| Test | Expected | Actual | Status |
|------|----------|--------|--------|
| dvc version | 3.67.1 + GCS | 3.67.1 (pip) | ✅ |
| dvc remote list | data-hub configured | Both repos configured | ✅ |
| dvc push/pull | Round-trip succeeds | 124MB verified | ✅ |
| gcloud storage buckets list | 16 buckets | 16 buckets (14 infra + 2 phi) | ✅ |
| stack_manager.py list | Neo4j service | Config exists, status/restart added | ✅ |
| pytest tests/ (cytos) | ≤6 failures, 0 errors | 0 failures, 149 passed, 11 skipped | ✅ |
| All repos pushed | 0 unpushed commits | All main, 0 ahead | ✅ |
| RO-Crate creation | Valid JSON-LD | 80 entities, WRROC conformant | ✅ |
| SSSOM parse | Mapping counts verified | 9,981,261 mappings from 278 files | ✅ |
| Provenance coverage (UMLS) | ≥95% | 93.3% (56/60) | 🟡 Close |
| Repo | PR | Title |
|------|-----|-------|
| infrastructure | #5 | feat: Phase 2 infrastructure updates |
| infrastructure | #6 | docs: GCP audit 2026-05-25 |
| infrastructure | #7 | docs: update HIPAA status post-audit |
| cytos | #4 | DVC remote configuration |
| cytos | #5 | feat: implement validate/harmonize |
| cytos | #6 | test: add validate/harmonize tests |
| cytos | #7 | fix: YAML roundtrip enum serialization |
| datasets | #1 | feat: DVC-track GO ontology |
| Item | Rationale |
|------|-----------|
| SEEK/WorkflowHub deployment | Deferred priority #1 in plan (requires separate sprint) |
| LaminDB integration | User directive: "not final choice, plan as we go" |
| Schema deduplication | Identified and audited; refactor is non-blocking |
| CMEK encryption for PHI | Deferred per HIPAA-STATUS.md (trigger: first DUC ingest) |
| VPC Service Controls | Deferred per HIPAA-STATUS.md (trigger: first external PHI) |
| Neo4j KG load test | Container not started; config optimized and ready |