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feat: add standards-based hybrid file ontology - #28

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seonghobae wants to merge 16 commits into
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codex/standards-file-ontology
Open

feat: add standards-based hybrid file ontology#28
seonghobae wants to merge 16 commits into
mainfrom
codex/standards-file-ontology

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@seonghobae

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What changed

  • Adds an international-standards-based hybrid file ontology that separates content identity from storage location.
  • Adds read-only adapters for local/Synology filesystems, S3, S3-compatible storage, and Azure Blob.
  • Adds evidence-backed semantic extraction through Contextual Orchestrator, including confidence, chunk hashes, offsets, and fail-closed structured-output handling.
  • Adds SHACL validation, semantic search/indexing, CLI workflows, documentation, and the Hyosung Heavy Industries VOC pilot path.

Why

Business documents became difficult to locate after storage cleanup because folder paths alone did not preserve their semantic relationships. The index must remain usable when Synology is absent and the backing storage changes to S3-compatible or Azure Blob.

Impact

Validation

  • PYTHONPATH=src py -m pytest -q — 190 passed, 8 skipped
  • py -m sdp.demo_smoke — ready
  • Live VOC pilot — 12 files, 10 assets, 12 distributions, 286 semantic assertions, all extracted
  • Direct pySHACL validation — 10/10 assets conform
  • Evidence/confidence/hash/offset and secret-marker audits — clean
  • Codegraph index synced and verified current
  • Independent review — Critical 0, Important 0, Minor 0

Comment thread src/sdp/file_ontology.py Fixed
Comment thread src/sdp/document_semantics.py Fixed
Comment thread src/sdp/document_semantics.py Fixed
Comment thread src/sdp/file_pilot.py Fixed
Comment thread src/sdp/file_pilot.py Fixed
Comment thread src/sdp/storage_readers.py Fixed
Comment thread src/sdp/storage_readers.py Fixed
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coderabbitai Bot commented Aug 3, 2026

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Review details
⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 5aa7de3f-d60b-47d0-b1f6-244b8c43f0df

📥 Commits

Reviewing files that changed from the base of the PR and between e48aa13 and 5e4b11c.

📒 Files selected for processing (32)
  • README.md
  • docs/disksage-copy-lineage-erd.md
  • docs/implementation-compliance.md
  • docs/superpowers/plans/2026-07-21-semantic-file-ontology.md
  • docs/superpowers/specs/2026-07-21-semantic-file-ontology-design.md
  • migrations/0002_file_copy_lineage.sql
  • ontology/cwl-file-profile.ttl
  • ontology/cwl-file-shapes.ttl
  • pyproject.toml
  • requirements-dev.txt
  • requirements-test.in
  • requirements-test.txt
  • requirements.txt
  • src/sdp/api.py
  • src/sdp/catalog.py
  • src/sdp/config.py
  • src/sdp/disksage_catalog.py
  • src/sdp/document_semantics.py
  • src/sdp/file_ontology.py
  • src/sdp/file_pilot.py
  • src/sdp/graph_models.py
  • src/sdp/graph_store.py
  • src/sdp/policy.py
  • src/sdp/resources/cwl-file-profile.ttl
  • src/sdp/resources/cwl-file-shapes.ttl
  • src/sdp/storage_readers.py
  • tests/fuzz/test_fuzz_properties.py
  • tests/test_api.py
  • tests/test_file_knowledge.py
  • tests/test_graph_engine.py
  • tests/test_graph_security.py
  • tests/test_migrations.py

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Pull request overview

OpenCode cannot approve yet because required coverage evidence did not pass.

Review outcome

1. HIGH .github/workflows/opencode-review.yml:1 - Coverage evidence did not prove required test/docstring evidence

  • Problem: The required coverage-evidence job result was failure, so OpenCode cannot establish approval sufficiency for this head.

  • Root cause: Automated approval is only valid when the same-head coverage-evidence job proves supported repository test suites passed and configured docstring gates passed or were advisory, or reports not applicable because no supported source files or package manifests exist. Missing, failed, skipped, unavailable, or unsupported-tooling test evidence is a blocker.

  • Fix: Install or configure the repository test/docstring evidence tooling when source files or package manifests exist, rerun the current-head coverage-evidence job, and approve only after it reports success with required evidence or explicit no-source not-applicable evidence.

  • Regression test: Keep the approval branch checking needs.coverage-evidence.result == success before posting APPROVE, and publish REQUEST_CHANGES when coverage-evidence blocker states such as cancelled, skipped, failed, unsupported-tooling, or below-100 evidence are present.

  • Result: REQUEST_CHANGES

  • Reason: coverage-evidence result was failure, so required test/docstring evidence was not proven for current head 247489f6e4f7d5ae285c6c3a7d6f8ec9b6244ba3.

  • Head SHA: 247489f6e4f7d5ae285c6c3a7d6f8ec9b6244ba3

  • Workflow run: 30806544206

  • Workflow attempt: 1

Coverage evidence

Coverage Decision

  • Result: FAIL
  • Test evidence: not proven passing
  • Docstring evidence: not proven passing when configured
  • Failure count: 1

Changed-File Evidence Map

flowchart LR
  PR["PR changed files"] --> Evidence["OpenCode bounded evidence"]
  Evidence --> S1["Changed file (22 files)"]
  S1 --> I1["repository behavior"]
  I1 --> R1["Review risk: Changed file (22 files)"]
  R1 --> V1["required checks"]
  Evidence --> S2["Docs (3 files)"]
  S2 --> I2["operator or user guidance"]
  I2 --> R2["Review risk: Docs (3 files)"]
  R2 --> V2["docs review"]
  Evidence --> S3["Test (5 files)"]
  S3 --> I3["regression suite"]
  I3 --> R3["Review risk: Test (5 files)"]
  R3 --> V3["targeted test run"]
Loading

@opencode-agent

opencode-agent Bot commented Aug 3, 2026

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OpenCode Review Overview

  • Head SHA: 5e4b11ca013701fd43a82e2a7d070d5ab062a16e
  • Workflow run: 32261446230
  • Workflow attempt: 1
  • Gate result: REQUEST_CHANGES (approval step)

Pull request overview

OpenCode cannot approve yet because required coverage evidence did not pass.

Review outcome

1. HIGH .github/workflows/opencode-review.yml:1 - Coverage evidence did not prove required test/docstring evidence

  • Problem: The required coverage-evidence job result was failure, so OpenCode cannot establish approval sufficiency for this head.

  • Root cause: Automated approval is only valid when the same-head coverage-evidence job proves supported repository test suites passed and configured docstring gates passed or were advisory, or reports not applicable because no supported source files or package manifests exist. Missing, failed, skipped, unavailable, or unsupported-tooling test evidence is a blocker.

  • Fix: Install or configure the repository test/docstring evidence tooling when source files or package manifests exist, rerun the current-head coverage-evidence job, and approve only after it reports success with required evidence or explicit no-source not-applicable evidence.

  • Regression test: Keep the approval branch checking needs.coverage-evidence.result == success before posting APPROVE, and publish REQUEST_CHANGES when coverage-evidence blocker states such as cancelled, skipped, failed, unsupported-tooling, or below-100 evidence are present.

  • Result: REQUEST_CHANGES

  • Reason: coverage-evidence result was failure, so required test/docstring evidence was not proven for current head 5e4b11ca013701fd43a82e2a7d070d5ab062a16e.

  • Head SHA: 5e4b11ca013701fd43a82e2a7d070d5ab062a16e

  • Workflow run: 32261446230

  • Workflow attempt: 1

Coverage evidence

Coverage Decision

  • Result: FAIL
  • Test evidence: not proven passing
  • Docstring evidence: not proven passing when configured
  • Failure count: 1

Changed-File Evidence Map

flowchart LR
  PR["PR changed files"] --> Evidence["OpenCode bounded evidence"]
  Evidence --> S1["Changed file (22 files)"]
  S1 --> I1["repository behavior"]
  I1 --> R1["Review risk: Changed file (22 files)"]
  R1 --> V1["required checks"]
  Evidence --> S2["Docs (4 files)"]
  S2 --> I2["operator or user guidance"]
  I2 --> R2["Review risk: Docs (4 files)"]
  R2 --> V2["docs review"]
  Evidence --> S3["Test (6 files)"]
  S3 --> I3["regression suite"]
  I3 --> R3["Review risk: Test (6 files)"]
  R3 --> V3["targeted test run"]
Loading

* feat: preview DiskSage catalog candidates safely

* feat: model DiskSage post-copy lineage

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Pull request overview

OpenCode cannot approve yet because required coverage evidence did not pass.

Review outcome

1. HIGH .github/workflows/opencode-review.yml:1 - Coverage evidence did not prove required test/docstring evidence

  • Problem: The required coverage-evidence job result was failure, so OpenCode cannot establish approval sufficiency for this head.

  • Root cause: Automated approval is only valid when the same-head coverage-evidence job proves supported repository test suites passed and configured docstring gates passed or were advisory, or reports not applicable because no supported source files or package manifests exist. Missing, failed, skipped, unavailable, or unsupported-tooling test evidence is a blocker.

  • Fix: Install or configure the repository test/docstring evidence tooling when source files or package manifests exist, rerun the current-head coverage-evidence job, and approve only after it reports success with required evidence or explicit no-source not-applicable evidence.

  • Regression test: Keep the approval branch checking needs.coverage-evidence.result == success before posting APPROVE, and publish REQUEST_CHANGES when coverage-evidence blocker states such as cancelled, skipped, failed, unsupported-tooling, or below-100 evidence are present.

  • Result: REQUEST_CHANGES

  • Reason: coverage-evidence result was failure, so required test/docstring evidence was not proven for current head 19028a981f84a135243221ca9708650273b0c87e.

  • Head SHA: 19028a981f84a135243221ca9708650273b0c87e

  • Workflow run: 30888091310

  • Workflow attempt: 1

Coverage evidence

Coverage Decision

  • Result: FAIL
  • Test evidence: not proven passing
  • Docstring evidence: not proven passing when configured
  • Failure count: 1

Changed-File Evidence Map

flowchart LR
  PR["PR changed files"] --> Evidence["OpenCode bounded evidence"]
  Evidence --> S1["Changed file (24 files)"]
  S1 --> I1["repository behavior"]
  I1 --> R1["Review risk: Changed file (24 files)"]
  R1 --> V1["required checks"]
  Evidence --> S2["Docs (4 files)"]
  S2 --> I2["operator or user guidance"]
  I2 --> R2["Review risk: Docs (4 files)"]
  R2 --> V2["docs review"]
  Evidence --> S3["Test (6 files)"]
  S3 --> I3["regression suite"]
  I3 --> R3["Review risk: Test (6 files)"]
  R3 --> V3["targeted test run"]
Loading

# Conflicts:
#	src/sdp/authz.py
#	src/sdp/graph_store.py
#	src/sdp/observability.py
@seonghobae
seonghobae enabled auto-merge August 13, 2026 20:03
Comment thread requirements.txt
--hash=sha256:850ba148bd908d7e2411587e247a1e4f0327839c40e2e5e6d05a007ecc69911d \
--hash=sha256:c777f4d763f140633dcb6d8a3eda953bf7a214dc4eff598413c070bcdc117cbc
# via rdflib
pypdf==6.14.2 \
Comment thread requirements.txt
--hash=sha256:850ba148bd908d7e2411587e247a1e4f0327839c40e2e5e6d05a007ecc69911d \
--hash=sha256:c777f4d763f140633dcb6d8a3eda953bf7a214dc4eff598413c070bcdc117cbc
# via rdflib
pypdf==6.14.2 \
@opencode-agent
opencode-agent Bot disabled auto-merge August 13, 2026 22:19

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Pull request overview

OpenCode cannot approve yet because required coverage evidence did not pass.

Review outcome

1. HIGH .github/workflows/opencode-review.yml:1 - Coverage evidence did not prove required test/docstring evidence

  • Problem: The required coverage-evidence job result was failure, so OpenCode cannot establish approval sufficiency for this head.

  • Root cause: Automated approval is only valid when the same-head coverage-evidence job proves supported repository test suites passed and configured docstring gates passed or were advisory, or reports not applicable because no supported source files or package manifests exist. Missing, failed, skipped, unavailable, or unsupported-tooling test evidence is a blocker.

  • Fix: Install or configure the repository test/docstring evidence tooling when source files or package manifests exist, rerun the current-head coverage-evidence job, and approve only after it reports success with required evidence or explicit no-source not-applicable evidence.

  • Regression test: Keep the approval branch checking needs.coverage-evidence.result == success before posting APPROVE, and publish REQUEST_CHANGES when coverage-evidence blocker states such as cancelled, skipped, failed, unsupported-tooling, or below-100 evidence are present.

  • Result: REQUEST_CHANGES

  • Reason: coverage-evidence result was failure, so required test/docstring evidence was not proven for current head 5e4b11ca013701fd43a82e2a7d070d5ab062a16e.

  • Head SHA: 5e4b11ca013701fd43a82e2a7d070d5ab062a16e

  • Workflow run: 32261446230

  • Workflow attempt: 1

Coverage evidence

Coverage Decision

  • Result: FAIL
  • Test evidence: not proven passing
  • Docstring evidence: not proven passing when configured
  • Failure count: 1

Changed-File Evidence Map

flowchart LR
  PR["PR changed files"] --> Evidence["OpenCode bounded evidence"]
  Evidence --> S1["Changed file (22 files)"]
  S1 --> I1["repository behavior"]
  I1 --> R1["Review risk: Changed file (22 files)"]
  R1 --> V1["required checks"]
  Evidence --> S2["Docs (4 files)"]
  S2 --> I2["operator or user guidance"]
  I2 --> R2["Review risk: Docs (4 files)"]
  R2 --> V2["docs review"]
  Evidence --> S3["Test (6 files)"]
  S3 --> I3["regression suite"]
  I3 --> R3["Review risk: Test (6 files)"]
  R3 --> V3["targeted test run"]
Loading

@opencode-agent opencode-agent Bot added priority: medium Normal-priority or P2 work status: needs-review Open pull request requiring current-head review or checks type: feature New or expanded product capability labels Aug 22, 2026
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