feat(serve): add multi-graph support to MCP server (#581) by YanisGuerault · Pull Request #2099 · Graphify-Labs/graphify

YanisGuerault · 2026-07-22T10:16:46Z

Summary

Enable serving multiple knowledge graphs from a single MCP endpoint via --graphs-dir flag or GRAPHS_DIR env var
Always registry-based architecture: single graph = 1-entry registry, multi-graph = directory scan — no separate code path
Resolve issue MCP server must work with multiple repos #581

Changes

Add GraphContext dataclass + GraphRegistry (from_path, from_directory, hot-reload via rescan)
Refactor _build_server to accept GraphRegistry with per-call context resolution (_get_ctx)
Tool visibility keyed on registry size: list_graphs/use_graph when >1, PR tools when ==1
New graph param on all tool schemas (replaces project_path)
--graphs-dir CLI flag forces HTTP transport with daemon rescan thread

🤖 Generated with Claude Code

Enable serving multiple knowledge graphs from a single MCP endpoint. Always registry-based: single graph = 1-entry registry, multi-graph = directory scan via --graphs-dir flag or GRAPHS_DIR env var. - Add GraphContext dataclass + GraphRegistry (from_path, from_directory) - Refactor _build_server to accept GraphRegistry with per-call resolution - Tool visibility keyed on registry size: list_graphs/use_graph when >1, PR tools when ==1. New graph param on all tool schemas. - Add --graphs-dir CLI flag forcing HTTP transport with auto-rescan - Remove multi_serve.py and graphify-multi-mcp entry point (consolidated) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

graphify-labs

Graphify reviewed this change.

Worth a look — the grounded gate found no coupling regressions or blocking issues, but 5 advisory finding(s) below merit a look before merge.

Formal verification. No changes could be formally verified in this run.

Graphify review — findings

Adds a multi-graph MCP server mode alongside the existing single-graph one: a new GraphRegistry loads either a single graph.json or every <name>/graph.json under a directory, rescans on an interval to pick up file changes (dropping graphs whose files vanish or fail to load), and _resolve_graph selects a target by explicit graph param, session default, or the sole loaded graph. Reworks _build_server to route all tool handlers through the registry and expose list_graphs/use_graph, and returns its handler dict for testing. Ships a multi Docker target driven by GRAPHS_DIR/SCAN_INTERVAL/PORT env vars plus a docker-compose.multi.yml and README docs, leaving the default single-graph image and entrypoint unchanged.

Worth a look

Default Docker build now produces multi-graph image instead of existing single-graph image — Dockerfile:28 · Escalate · high
- agreed by 2 of 2 members but NOT verified (no proof, no reproducing execution) — consensus is not a verdict; needs human review
Multi-graph compose publishes unauthenticated MCP service by default — docker-compose.multi.yml:11 · Escalate · medium
- agreed by 2 of 2 members but NOT verified (no proof, no reproducing execution) — consensus is not a verdict; needs human review
except (OSError, SystemExit, Exception) swallows SystemExit and all errors, deleting graph — graphify/serve.py · Escalate · medium
- agreed by 2 of 2 members but NOT verified (no proof, no reproducing execution) — consensus is not a verdict; needs human review
GraphRegistry.get/names read shared _graphs without lock — graphify/serve.py · Escalate · medium
- agreed by 2 of 2 members but NOT verified (no proof, no reproducing execution) — consensus is not a verdict; needs human review
Non-atomic single-graph resolution can return None during concurrent rescan — graphify/serve.py:146 · Escalate · medium
- agreed by 2 of 2 members but NOT verified (no proof, no reproducing execution) — consensus is not a verdict; needs human review

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 1850 functions depend on the 1647 functions this change touches.

Health — this change adds coupling hotspots:

new: dispatch_command() — 2 callers, 122 callees
new: _build_server() — 12 callers, 17 callees
new: _query_graph_text() — 20 callers, 10 callees
new: _score_query() — 15 callers, 6 callees
new: _build_http_app() — 19 callers, 4 callees
new: _query_terms() — 20 callers, 3 callees
new: _subgraph_to_text() — 20 callers, 3 callees
new: _main() — 8 callers, 7 callees
…and 14 more — each is listed as a finding

Verification — 1850 functions in the blast radius were not formally verified this run (proofs are advisory here).

Gate & verification

graphify gate

PASS — objectively clean (no health regressions, tests not run — proofs not run this pass (advisory)). Grounded, not self-assessed.

Advisory (not blocking):

verification_scope: 1689 function(s) in the blast radius were not formally verified this run

Formal verification

Could not verify: Could not verify \_\_init\_\_.

The verifier did not have enough to check \_\_init\_\_, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: signature changed: no shared positional arity

Could not verify: Could not verify \_build\_http\_app.

The verifier did not have enough to check \_build\_http\_app, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: not verifiable: all 24 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly SystemExit — names the real obstacle, not a sampling gap)

Could not verify: Could not verify \_build\_server.

The verifier did not have enough to check \_build\_server, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: not verifiable: all 54 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly AttributeError — names the real obstacle, not a sampling gap)

Could not verify: Could not verify \_\_init\_\_.

The verifier did not have enough to check \_\_init\_\_, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: signature changed: no shared positional arity

Could not verify: Could not verify \_\_init\_\_.

The verifier did not have enough to check \_\_init\_\_, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: signature changed: no shared positional arity

Verification did not run: Verification did not run for \_main.

The verification could not execute (an environment/toolchain issue, not a statement about the code).

Guarantee: No guarantee, the check itself did not complete.

Note: Detail: harness produced no verdict (rc=1): error: Graph path must be a .json file, got: '/workspace/job-a1e2a6c2baa84ce596d72365c42bb445/head/a' error: Graph path

Could not verify: Could not verify \_\_init\_\_.

The verifier did not have enough to check \_\_init\_\_, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: signature changed: no shared positional arity

Verification did not run: Verification did not run for serve.

The verification could not execute (an environment/toolchain issue, not a statement about the code).

Guarantee: No guarantee, the check itself did not complete.

Note: Detail: harness produced no verdict (rc=1): error: Graph path must be a .json file, got: '/workspace/job-a1e2a6c2baa84ce596d72365c42bb445/head/a longer string' erro

Verification did not run: Verification did not run for serve\_http.

The verification could not execute (an environment/toolchain issue, not a statement about the code).

Guarantee: No guarantee, the check itself did not complete.

Note: Detail: harness produced no verdict (rc=124): timeout after 30s

· 9 grounded finding(s) anchored inline below; 13 more finding(s) on lines outside this diff (see the check run).

graphify-labs · 2026-08-25T14:11:52Z

+    )
+
+
 def _load_graph(graph_path: str) -> nx.Graph:


⚠️ Health regression — _load_graph()

12 callers depend on it (afferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T14:11:52Z



-def _build_server(graph_path: str):
+def _build_server(registry: GraphRegistry, *, session_state: dict | None = None):


⚠️ Health regression — _build_server()

fans out to 17 callees (efferent coupling); 12 callers depend on it (afferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T14:11:52Z

-        path = _resolve_graph_path(project_path)
-        G, communities = _load_ctx(path)
-        active_graph_path = str(Path(path).resolve())
+    def _get_ctx(arguments: dict) -> GraphContext:


⚠️ Health regression — _get_ctx()

9 callers depend on it (afferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T14:11:52Z

@@ -1781,6 +1919,8 @@ def _tool_get_node(arguments: dict) -> str:
        ])

    def _tool_get_neighbors(arguments: dict) -> str:


⚠️ Health regression — _tool_get_neighbors()

fans out to 8 callees (efferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T14:11:53Z

@@ -1884,6 +2035,8 @@ def _tool_list_prs(arguments: dict) -> str:
        return format_prs_text(prs, base)

    def _tool_get_pr_impact(arguments: dict) -> str:


⚠️ Health regression — _tool_get_pr_impact()

fans out to 6 callees (efferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T14:11:53Z

@@ -1990,17 +2174,33 @@ async def list_resources() -> list[types.Resource]:
        ]

    async def read_resource(uri: AnyUrl) -> str:


⚠️ Health regression — read_resource()

fans out to 6 callees (efferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T14:11:53Z

+    return server, _handlers


 def serve(graph_path: str | None = None) -> None:


⚠️ Health regression — serve()

fans out to 6 callees (efferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T14:11:53Z

@@ -2175,8 +2374,9 @@ async def __call__(self, scope, receive, send) -> None:


 def _build_http_app(


⚠️ Health regression — _build_http_app()

19 callers depend on it (afferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T14:11:53Z

        assert "Nodes: 2" in _call_tool(client, headers, "graph_stats", {}, rid=3)


 def test_corrupt_project_graph_is_a_tool_error_without_killing_server(tmp_path):


⚠️ Health regression — test_corrupt_project_graph_is_a_tool_error_without_killing_server()

fans out to 7 callees (efferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

Replace directory discovery with explicit repository paths and remove the legacy multi-MCP deployment workflow.

graphify-labs

Graphify reviewed this change.

Worth a look — the grounded gate found no coupling regressions or blocking issues, but 5 advisory finding(s) below merit a look before merge.

Formal verification. 2 change(s) tested, no difference found (not proven).

Graphify review — findings

Adds a public graphify <repo>... --mcp CLI path that serves one or more existing repository graphs over MCP, parsed by _run_mcp_cli and dispatched to stdio via serve or HTTP via serve_http, rejecting duplicate repo basenames, missing graphify-out/graph.json, and malformed transport/host/port/api-key options. Introduces GraphRegistry and GraphContext to hold multiple named graphs, with from_paths skipping the learning overlay and project-path access, and exposes list_graphs/use_graph tools plus an optional per-tool graph parameter so callers can target a specific graph or set a session default. Retools the Dockerfile and adds docker-compose.multi.yml to run the public CLI against a mounted repo tree instead of baking a graph into the image.

Worth a look

HTTP transport binds to 0.0.0.0 without requiring API key — graphify/__main__.py:519 · Escalate · high
- agreed by 2 of 2 members but NOT verified (no proof, no reproducing execution) — consensus is not a verdict; needs human review
CLI allows unauthenticated non-loopback HTTP MCP binding — graphify/__main__.py:584 · Escalate · high
- agreed by 2 of 2 members but NOT verified (no proof, no reproducing execution) — consensus is not a verdict; needs human review
GraphRegistry.get/names read shared dict without holding the lock while rescan mutates it — graphify/serve.py · Escalate · high
- agreed by 2 of 2 members but NOT verified (no proof, no reproducing execution) — consensus is not a verdict; needs human review
Per-call project_path graph selection removed from tool dispatch — graphify/serve.py · Escalate · high
- agreed by 2 of 2 members but NOT verified (no proof, no reproducing execution) — consensus is not a verdict; needs human review
MCP tool calls no longer honor project_path routing — graphify/serve.py:2080 · Escalate · high
- agreed by 2 of 2 members but NOT verified (no proof, no reproducing execution) — consensus is not a verdict; needs human review

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 839 functions depend on the 570 functions this change touches.

Health — this change adds coupling hotspots:

new: dispatch_command() — 2 callers, 122 callees
new: _build_server() — 14 callers, 17 callees
new: _query_graph_text() — 20 callers, 10 callees
new: _score_query() — 15 callers, 6 callees
new: _build_http_app() — 20 callers, 4 callees
new: render() — 13 callers, 5 callees
new: _get_ctx() — 9 callers, 7 callees
new: _query_terms() — 20 callers, 3 callees
…and 21 more — each is listed as a finding

Verification — 839 functions in the blast radius were not formally verified this run (proofs are advisory here).

Gate & verification

graphify gate

PASS — objectively clean (no health regressions, tests not run — proofs not run this pass (advisory)). Grounded, not self-assessed.

Advisory (not blocking):

verification_scope: 827 function(s) in the blast radius were not formally verified this run

Formal verification

No difference found (not proven): No behavior difference found in \_run\_cli (not a proof).

The verifier ran both versions of \_run\_cli on many inputs and saw identical behavior every time. Strong evidence the change is safe, but evidence, not a proof.

Guarantee: Empirical: differential testing (both versions run on many generated inputs). A divergence on an untested input remains possible, so this is 'no counterexample found', not 'proven equivalent'.

Note: An input the sampler did not try could still differ.

Could not verify: Could not verify \_\_init\_\_.

The verifier did not have enough to check \_\_init\_\_, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: signature changed: no shared positional arity

Could not verify: Could not verify \_build\_http\_app.

The verifier did not have enough to check \_build\_http\_app, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: not verifiable: all 24 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly SystemExit — names the real obstacle, not a sampling gap)

Could not verify: Could not verify \_build\_server.

The verifier did not have enough to check \_build\_server, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: not verifiable: all 54 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly AttributeError — names the real obstacle, not a sampling gap)

Could not verify: Could not verify \_\_init\_\_.

The verifier did not have enough to check \_\_init\_\_, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: signature changed: no shared positional arity

Could not verify: Could not verify \_\_init\_\_.

The verifier did not have enough to check \_\_init\_\_, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: signature changed: no shared positional arity

Could not verify: Could not verify \_load\_graph.

The verifier did not have enough to check \_load\_graph, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: not verifiable: all 23 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly SystemExit — names the real obstacle, not a sampling gap)

Verification did not run: Verification did not run for \_main.

The verification could not execute (an environment/toolchain issue, not a statement about the code).

Guarantee: No guarantee, the check itself did not complete.

Note: Detail: harness produced no verdict (rc=1): error: Graph path must be a .json file, got: '/workspace/job-7af6d2a6766b4d54bd60987fc9155ca7/head/a' error: Graph path

Could not verify: Could not verify \_\_init\_\_.

The verifier did not have enough to check \_\_init\_\_, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: signature changed: no shared positional arity

Verification did not run: Verification did not run for serve.

The verification could not execute (an environment/toolchain issue, not a statement about the code).

Guarantee: No guarantee, the check itself did not complete.

Note: Detail: harness produced no verdict (rc=1): error: Graph path must be a .json file, got: '/workspace/job-7af6d2a6766b4d54bd60987fc9155ca7/head/a longer string' erro

Verification did not run: Verification did not run for serve\_http.

The verification could not execute (an environment/toolchain issue, not a statement about the code).

Guarantee: No guarantee, the check itself did not complete.

Note: Detail: harness produced no verdict (rc=124): timeout after 30s

No difference found (not proven): No behavior difference found in monolith\_roundtrip (not a proof).

The verifier ran both versions of monolith\_roundtrip on many inputs and saw identical behavior every time. Strong evidence the change is safe, but evidence, not a proof.

Guarantee: Empirical: differential testing (both versions run on many generated inputs). A divergence on an untested input remains possible, so this is 'no counterexample found', not 'proven equivalent'.

Note: An input the sampler did not try could still differ.

· 11 grounded finding(s) anchored inline below; 18 more finding(s) on lines outside this diff (see the check run).

graphify-labs · 2026-08-25T15:14:21Z

+    serve(registry=registry)
+
+
+def _serve_mcp_repositories(


⚠️ Health regression — _serve_mcp_repositories()

6 callers depend on it (afferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T15:14:21Z

+    return True
+
+
 def _run_cli() -> None:


⚠️ Health regression — _run_cli()

high coupling complexity (Ca·Ce = 15).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T15:14:21Z

+    )
+
+
+def _load_graph(graph_path: str, *, load_learning_overlay: bool = True) -> nx.Graph:


⚠️ Health regression — _load_graph()

12 callers depend on it (afferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T15:14:21Z



-def _build_server(graph_path: str):
+def _build_server(registry: GraphRegistry, *, session_state: dict | None = None):


⚠️ Health regression — _build_server()

fans out to 17 callees (efferent coupling); 14 callers depend on it (afferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T15:14:21Z

+            return fallback_session_state
+        return session_states.setdefault(session, {})
+
+    def _get_ctx(arguments: dict) -> GraphContext:


⚠️ Health regression — _get_ctx()

fans out to 7 callees (efferent coupling); 9 callers depend on it (afferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T15:14:21Z

@@ -1884,6 +2023,8 @@ def _tool_list_prs(arguments: dict) -> str:
        return format_prs_text(prs, base)

    def _tool_get_pr_impact(arguments: dict) -> str:


⚠️ Health regression — _tool_get_pr_impact()

fans out to 6 callees (efferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T15:14:21Z

@@ -1990,17 +2164,34 @@ async def list_resources() -> list[types.Resource]:
        ]

    async def read_resource(uri: AnyUrl) -> str:


⚠️ Health regression — read_resource()

fans out to 8 callees (efferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T15:14:21Z



-def serve(graph_path: str | None = None) -> None:
+def serve(graph_path: str | None = None, *, registry: GraphRegistry | None = None) -> None:


⚠️ Health regression — serve()

fans out to 6 callees (efferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T15:14:21Z

@@ -2175,8 +2366,9 @@ async def __call__(self, scope, receive, send) -> None:


 def _build_http_app(


⚠️ Health regression — _build_http_app()

20 callers depend on it (afferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

graphify-labs · 2026-08-25T15:14:21Z

        assert "Nodes: 2" in _call_tool(client, headers, "graph_stats", {}, rid=3)


 def test_corrupt_project_graph_is_a_tool_error_without_killing_server(tmp_path):


⚠️ Health regression — test_corrupt_project_graph_is_a_tool_error_without_killing_server()

fans out to 7 callees (efferent coupling).

Grounded coupling-delta finding (deterministic), not an LLM guess.

YanisGuerault force-pushed the feat/add-multi-graph-support branch from 12f436c to 6d020bd Compare July 22, 2026 10:24

YanisGuerault changed the title ~~feat(serve): add multi-graph support to MCP server~~ feat(serve): add multi-graph support to MCP server (#581) Jul 22, 2026

YanisGuerault force-pushed the feat/add-multi-graph-support branch from 6d020bd to 2e39ab0 Compare August 25, 2026 13:56

graphify-labs Bot reviewed Aug 25, 2026

View reviewed changes

refactor(mcp): move multi-graph serving to --mcp

70194e1

Replace directory discovery with explicit repository paths and remove the legacy multi-MCP deployment workflow.

YanisGuerault force-pushed the feat/add-multi-graph-support branch from 3e02e0a to 70194e1 Compare August 25, 2026 15:02

graphify-labs Bot reviewed Aug 25, 2026

View reviewed changes



		def _build_server(graph_path: str):
		def _build_server(registry: GraphRegistry, *, session_state: dict \| None = None):

		@@ -1781,6 +1919,8 @@ def _tool_get_node(arguments: dict) -> str:
		])

		def _tool_get_neighbors(arguments: dict) -> str:

		@@ -1884,6 +2035,8 @@ def _tool_list_prs(arguments: dict) -> str:
		return format_prs_text(prs, base)

		def _tool_get_pr_impact(arguments: dict) -> str:

		@@ -1990,17 +2174,33 @@ async def list_resources() -> list[types.Resource]:
		]

		async def read_resource(uri: AnyUrl) -> str:

		return server, _handlers


		def serve(graph_path: str \| None = None) -> None:

		@@ -2175,8 +2374,9 @@ async def __call__(self, scope, receive, send) -> None:


		def _build_http_app(

		assert "Nodes: 2" in _call_tool(client, headers, "graph_stats", {}, rid=3)


		def test_corrupt_project_graph_is_a_tool_error_without_killing_server(tmp_path):

		)


		def _load_graph(graph_path: str, *, load_learning_overlay: bool = True) -> nx.Graph:

		@@ -1884,6 +2023,8 @@ def _tool_list_prs(arguments: dict) -> str:
		return format_prs_text(prs, base)

		def _tool_get_pr_impact(arguments: dict) -> str:

		@@ -1990,17 +2164,34 @@ async def list_resources() -> list[types.Resource]:
		]

		async def read_resource(uri: AnyUrl) -> str:



		def serve(graph_path: str \| None = None) -> None:
		def serve(graph_path: str \| None = None, *, registry: GraphRegistry \| None = None) -> None:

		@@ -2175,8 +2366,9 @@ async def __call__(self, scope, receive, send) -> None:


		def _build_http_app(

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Graphify review — findings

Impact & health

Graphify review

Gate & verification

graphify gate

Formal verification

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Graphify review — findings

Impact & health

Graphify review

Gate & verification

graphify gate

Formal verification

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YanisGuerault commented Jul 22, 2026 •

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