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carlos-alm merged 9 commits into from
Jul 20, 2026
Merged

fix(export): honor --functions for json and graphson formats #2141

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8c01783
fix(export): honor --functions for json and graphson formats
carlos-alm Jul 20, 2026
ad7c2b0
docs: add dogfood report for v3.16.0
carlos-alm Jul 20, 2026
14ce543
docs(dogfood-skill): fix stale benchmark script refs, add safety note…
carlos-alm Jul 20, 2026
0199ac7
Revert "docs(dogfood-skill): fix stale benchmark script refs, add saf…
carlos-alm Jul 20, 2026
c59b5c6
Revert "docs: add dogfood report for v3.16.0"
carlos-alm Jul 20, 2026
b5f6720
fix: close db handle in exportJSON function-level test to match sibli…
carlos-alm Jul 20, 2026
e302743
Merge branch 'main' into fix/export-functions-json-graphson
carlos-alm Jul 20, 2026
2348999
fix(export): align exportGraphSON function-level scope with other for…
carlos-alm Jul 20, 2026
e1da404
Merge branch 'main' into fix/export-functions-json-graphson
carlos-alm Jul 20, 2026
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233 changes: 163 additions & 70 deletions src/features/export.ts
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -331,26 +331,73 @@ export function exportJSON(
db: BetterSqlite3Database,
opts: ExportOpts = {},
): { nodes: unknown[]; edges: unknown[] } {
const fileLevel = opts.fileLevel !== false;
const noTests = opts.noTests || false;
const minConf = opts.minConfidence ?? DEFAULT_MIN_CONFIDENCE;

let nodes = db
.prepare(`
SELECT id, name, kind, file, line FROM nodes WHERE kind = 'file'
`)
.all() as Array<{ id: number; name: string; kind: string; file: string; line: number }>;
if (noTests) nodes = nodes.filter((n) => !isTestFile(n.file));

let edges = db
.prepare(`
SELECT DISTINCT n1.file AS source, n2.file AS target, e.kind, e.confidence
FROM edges e
JOIN nodes n1 ON e.source_id = n1.id
JOIN nodes n2 ON e.target_id = n2.id
WHERE n1.file != n2.file AND e.confidence >= ?
`)
.all(minConf) as Array<{ source: string; target: string; kind: string; confidence: number }>;
if (noTests) edges = edges.filter((e) => !isTestFile(e.source) && !isTestFile(e.target));
if (fileLevel) {
let nodes = db
.prepare(`
SELECT id, name, kind, file, line FROM nodes WHERE kind = 'file'
`)
.all() as Array<{ id: number; name: string; kind: string; file: string; line: number }>;
if (noTests) nodes = nodes.filter((n) => !isTestFile(n.file));

let edges = db
.prepare(`
SELECT DISTINCT n1.file AS source, n2.file AS target, e.kind, e.confidence
FROM edges e
JOIN nodes n1 ON e.source_id = n1.id
JOIN nodes n2 ON e.target_id = n2.id
WHERE n1.file != n2.file AND e.confidence >= ?
`)
.all(minConf) as Array<{ source: string; target: string; kind: string; confidence: number }>;
if (noTests) edges = edges.filter((e) => !isTestFile(e.source) && !isTestFile(e.target));

const base = { nodes, edges };
return paginateResult(base, 'edges', { limit: opts.limit, offset: opts.offset }) as {
nodes: unknown[];
edges: unknown[];
};
}

const { edges: fnEdges } = loadFunctionLevelEdges(db, {
noTests,
minConfidence: opts.minConfidence,
});
const nodeMap = new Map<
number,
{ id: number; name: string; kind: string; file: string; line: number; role: string | null }
>();
for (const e of fnEdges) {
if (!nodeMap.has(e.source_id)) {
nodeMap.set(e.source_id, {
id: e.source_id,
name: e.source_name,
kind: e.source_kind,
file: e.source_file,
line: e.source_line,
role: e.source_role,
});
}
if (!nodeMap.has(e.target_id)) {
nodeMap.set(e.target_id, {
id: e.target_id,
name: e.target_name,
kind: e.target_kind,
file: e.target_file,
line: e.target_line,
role: e.target_role,
});
}
}
const nodes = [...nodeMap.values()];
const edges = fnEdges.map((e) => ({
source: e.source_id,
target: e.target_id,
kind: e.edge_kind,
confidence: e.confidence,
}));

const base = { nodes, edges };
return paginateResult(base, 'edges', { limit: opts.limit, offset: opts.offset }) as {
Expand Down Expand Up @@ -384,64 +431,110 @@ export function exportGraphSON(
db: BetterSqlite3Database,
opts: ExportOpts = {},
): { vertices: unknown[]; edges: unknown[] } {
const fileLevel = opts.fileLevel !== false;
const noTests = opts.noTests || false;
const minConf = opts.minConfidence ?? DEFAULT_MIN_CONFIDENCE;

let nodes = db
.prepare(`
SELECT id, name, kind, file, line, role FROM nodes
WHERE kind IN ('function', 'method', 'class', 'interface', 'type', 'struct', 'enum', 'trait', 'record', 'module', 'constant', 'file')
`)
.all() as Array<{
id: number;
name: string;
kind: string;
file: string;
line: number | null;
role: string | null;
}>;
if (noTests) nodes = nodes.filter((n) => !isTestFile(n.file));

let edges = db
.prepare(`
SELECT e.rowid AS id, n1.id AS outV, n2.id AS inV, e.kind, e.confidence
FROM edges e
JOIN nodes n1 ON e.source_id = n1.id
JOIN nodes n2 ON e.target_id = n2.id
WHERE e.confidence >= ?
`)
.all(minConf) as Array<{
id: number;
outV: number;
inV: number;
kind: string;
confidence: number;
let vertices: Array<{ id: unknown; label: string; properties: Record<string, unknown> }>;
let gEdges: Array<{
id: unknown;
label: string;
inV: unknown;
outV: unknown;
properties: Record<string, unknown>;
}>;
if (noTests) {
const nodeIds = new Set(nodes.map((n) => n.id));
edges = edges.filter((e) => nodeIds.has(e.outV) && nodeIds.has(e.inV));
}

const vertices = nodes.map((n) => ({
id: n.id,
label: n.kind,
properties: {
name: [{ id: 0, value: n.name }],
file: [{ id: 0, value: n.file }],
...(n.line != null ? { line: [{ id: 0, value: n.line }] } : {}),
...(n.role ? { role: [{ id: 0, value: n.role }] } : {}),
},
}));
if (fileLevel) {
const { edges: fileEdges } = loadFileLevelEdges(db, {
noTests,
minConfidence: opts.minConfidence,
includeKind: true,
includeConfidence: true,
});
const filesInvolved = new Set<string>();
for (const e of fileEdges) {
filesInvolved.add(e.source);
filesInvolved.add(e.target);
}
const fileNodes = db
.prepare(`SELECT id, name, file, line FROM nodes WHERE kind = 'file'`)
.all() as Array<{ id: number; name: string; file: string; line: number | null }>;
const idByFile = new Map(
fileNodes.filter((n) => filesInvolved.has(n.file)).map((n) => [n.file, n]),
);

vertices = [...idByFile.values()].map((n) => ({
id: n.id,
label: 'file',
properties: {
name: [{ id: 0, value: n.name }],
file: [{ id: 0, value: n.file }],
...(n.line != null ? { line: [{ id: 0, value: n.line }] } : {}),
},
}));

const gEdges = edges.map((e) => ({
id: e.id,
label: e.kind,
inV: e.inV,
outV: e.outV,
properties: {
confidence: e.confidence,
},
}));
gEdges = fileEdges
.filter((e) => idByFile.has(e.source) && idByFile.has(e.target))
.map((e, i) => ({
id: i,
label: e.edge_kind ?? 'edge',
inV: idByFile.get(e.target)?.id,
outV: idByFile.get(e.source)?.id,
properties: { confidence: e.confidence },
}));
} else {
const { edges: fnEdges } = loadFunctionLevelEdges(db, {
noTests,
minConfidence: opts.minConfidence,
});

const nodeMap = new Map<
number,
{ id: number; name: string; kind: string; file: string; line: number; role: string | null }
>();
for (const e of fnEdges) {
if (!nodeMap.has(e.source_id)) {
nodeMap.set(e.source_id, {
id: e.source_id,
name: e.source_name,
kind: e.source_kind,
file: e.source_file,
line: e.source_line,
role: e.source_role,
});
}
if (!nodeMap.has(e.target_id)) {
nodeMap.set(e.target_id, {
id: e.target_id,
name: e.target_name,
kind: e.target_kind,
file: e.target_file,
line: e.target_line,
role: e.target_role,
});
}
}

vertices = [...nodeMap.values()].map((n) => ({
id: n.id,
label: n.kind,
properties: {
name: [{ id: 0, value: n.name }],
file: [{ id: 0, value: n.file }],
...(n.line != null ? { line: [{ id: 0, value: n.line }] } : {}),
...(n.role ? { role: [{ id: 0, value: n.role }] } : {}),
},
}));

gEdges = fnEdges.map((e, i) => ({
id: i,
label: e.edge_kind,
inV: e.target_id,
outV: e.source_id,
properties: {
confidence: e.confidence,
},
}));
}

const base = { vertices, edges: gEdges };
return paginateResult(base, 'edges', { limit: opts.limit, offset: opts.offset }) as {
Expand Down
76 changes: 73 additions & 3 deletions tests/graph/export.test.ts
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -258,6 +258,35 @@ describe('exportJSON', () => {
expect(data.edges.length).toBeGreaterThanOrEqual(1);
db.close();
});

it('returns function-level nodes and edges with fileLevel: false', () => {
const db = createTestDb();
const fn = insertNode(db, 'doWork', 'function', 'src/a.js', 5);
const fn2 = insertNode(db, 'helper', 'function', 'src/b.js', 10);
insertEdge(db, fn, fn2, 'calls');

const data = exportJSON(db, { fileLevel: false });
expect(data.nodes.every((n) => n.kind !== 'file')).toBe(true);
expect(data.nodes.some((n) => n.name === 'doWork')).toBe(true);
expect(data.edges.some((e) => e.source === fn && e.target === fn2)).toBe(true);
db.close();
});
Comment on lines +268 to +273

@greptile-apps greptile-apps Bot Jul 20, 2026

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P2 Missing db.close() in the first new JSON test leaves an open in-memory database handle. Every surrounding test does close its db; this one should too.

Suggested change
const data = exportJSON(db, { fileLevel: false });
expect(data.nodes.every((n) => n.kind !== 'file')).toBe(true);
expect(data.nodes.some((n) => n.name === 'doWork')).toBe(true);
expect(data.edges.some((e) => e.source === fn && e.target === fn2)).toBe(true);
});
const data = exportJSON(db, { fileLevel: false });
expect(data.nodes.every((n) => n.kind !== 'file')).toBe(true);
expect(data.nodes.some((n) => n.name === 'doWork')).toBe(true);
expect(data.edges.some((e) => e.source === fn && e.target === fn2)).toBe(true);
db.close();
});

Fix in Claude Code

@carlos-alm carlos-alm Jul 20, 2026

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Fixed — added the missing db.close() to this test to match its sibling tests.


it('produces different output for fileLevel vs functions', () => {
const db = createTestDb();
const a = insertNode(db, 'src/a.js', 'file', 'src/a.js', 0);
const b = insertNode(db, 'src/b.js', 'file', 'src/b.js', 0);
insertEdge(db, a, b, 'imports');
const fn = insertNode(db, 'doWork', 'function', 'src/a.js', 5);
const fn2 = insertNode(db, 'helper', 'function', 'src/b.js', 10);
insertEdge(db, fn, fn2, 'calls');

const fileLevel = exportJSON(db);
const functionLevel = exportJSON(db, { fileLevel: false });
expect(fileLevel.nodes.every((n) => n.kind === 'file')).toBe(true);
expect(functionLevel.nodes.some((n) => n.kind === 'function')).toBe(true);
db.close();
});
});

describe('exportGraphML', () => {
Expand Down Expand Up @@ -357,7 +386,7 @@ describe('exportGraphSON', () => {
const fn2 = insertNode(db, 'helper', 'function', 'src/b.js', 10);
insertEdge(db, fn, fn2, 'calls');

const data = exportGraphSON(db);
const data = exportGraphSON(db, { fileLevel: false });
const vertex = data.vertices.find((v) => v.properties.name[0].value === 'doWork');
expect(vertex).toBeDefined();
expect(vertex.properties.name).toEqual([{ id: 0, value: 'doWork' }]);
Expand All @@ -371,7 +400,7 @@ describe('exportGraphSON', () => {
const fn2 = insertNode(db, 'helper', 'function', 'src/b.js', 10);
insertEdge(db, fn, fn2, 'calls');

const data = exportGraphSON(db);
const data = exportGraphSON(db, { fileLevel: false });
expect(data.edges.length).toBeGreaterThanOrEqual(1);
const edge = data.edges[0];
expect(edge).toHaveProperty('inV');
Expand All @@ -387,12 +416,53 @@ describe('exportGraphSON', () => {
const fn2 = insertNode(db, 'helper', 'function', 'src/b.js', 10);
insertEdge(db, fn, fn2, 'calls');

const data = exportGraphSON(db);
const data = exportGraphSON(db, { fileLevel: false });
const edge = data.edges[0];
expect(edge.properties).toHaveProperty('confidence');
expect(edge.properties.confidence).toBe(1.0);
db.close();
});

it('produces different output for fileLevel vs functions', () => {
const db = createTestDb();
const a = insertNode(db, 'src/a.js', 'file', 'src/a.js', 0);
const b = insertNode(db, 'src/b.js', 'file', 'src/b.js', 0);
insertEdge(db, a, b, 'imports');
const fn = insertNode(db, 'doWork', 'function', 'src/a.js', 5);
const fn2 = insertNode(db, 'helper', 'function', 'src/b.js', 10);
insertEdge(db, fn, fn2, 'calls');

const fileLevel = exportGraphSON(db);
const functionLevel = exportGraphSON(db, { fileLevel: false });
expect(fileLevel.vertices.every((v) => v.label === 'file')).toBe(true);
expect(functionLevel.vertices.some((v) => v.label === 'function')).toBe(true);
expect(functionLevel.vertices.every((v) => v.label !== 'file')).toBe(true);
db.close();
});

it('function-level matches loadFunctionLevelEdges semantics: calls-only edges, no isolated nodes', () => {
const db = createTestDb();
const fnA = insertNode(db, 'doWork', 'function', 'src/a.js', 5);
const fnB = insertNode(db, 'helper', 'function', 'src/b.js', 10);
insertEdge(db, fnA, fnB, 'calls');
// A class that implements/extends another — should NOT appear as a graphson edge
// in function-level output, matching dot/mermaid/graphml/neo4j's calls-only scope.
const base = insertNode(db, 'Base', 'class', 'src/c.js', 1);
const impl = insertNode(db, 'Impl', 'class', 'src/d.js', 1);
insertEdge(db, impl, base, 'implements');
// An isolated function with no edges at all — should not appear as a vertex,
// matching loadFunctionLevelEdges (which only returns nodes that participate
// in a calls edge), not an independent "all matching-kind nodes" query.
insertNode(db, 'unreachable', 'function', 'src/e.js', 1);

const data = exportGraphSON(db, { fileLevel: false });

expect(data.edges.every((e) => e.label === 'calls')).toBe(true);
expect(data.vertices.some((v) => v.properties.name[0].value === 'unreachable')).toBe(false);
expect(data.vertices.some((v) => v.properties.name[0].value === 'Impl')).toBe(false);
expect(data.vertices.some((v) => v.properties.name[0].value === 'doWork')).toBe(true);
db.close();
});
});

describe('exportNeo4jCSV', () => {
Expand Down
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