fix: specify explicit graph.json path in graph_explorer prompt - #1286
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✅ Factory Review: KEEP
Verdict: KEEP
Reason: QA: CLEAN — 5393 tests pass, 0 lint/type issues, code review 7/7 PASS, adversarial 10/10 VERIFIED. No eval baseline exists (factory self-repo) so precheck score_direction is N/A.
QA Analysis
Adversarial QA Report — PR #1286: Graph Explorer Path Fix
Date: 2026-08-17
Branch: fix/1256-graph-explorer-path
Detected project type: CLI / Library (Python)
Files changed: factory/workflow/definitions.py, factory/workflow/skill_export.py
Smoke Test
Status: VERIFIED
uv run pytest tests/ -k "graph_explorer or skill_export or graph" -vOutput: 191 passed, 4978 deselected, 1 warning in 3.23s
All existing tests related to graph, skill_export, and workflow definitions pass cleanly.
Acceptance Criteria (derived from PR commits)
AC1: Replace implicit graph.json references with explicit {project_path}/graph.json in graph_explorer prompt template
Status: VERIFIED
Evidence:
uv run python -c "
from factory.workflow.definitions import _GRAPH_EXPLORER_PROMPT
lines = _GRAPH_EXPLORER_PROMPT.split('\n')
for i, line in enumerate(lines):
if '{project_path}' in line:
print(f'Line {i}: {line}')
print()
print('Total occurrences:', _GRAPH_EXPLORER_PROMPT.count('{project_path}'))
"Output:
Line 4: ls {project_path}/graph.json
Line 7: If {project_path}/graph.json exists:
Line 8: 1. Run `factory graph query "{project_path}" "<focus from observations>" --depth 2` to find relevant nodes
Line 9: 2. Run `factory graph explain "{project_path}" "<key node>"` on the most important nodes...
Line 10: 3. Run `factory graph path "{project_path}" "<A>" "<B>"` to trace dependency paths...
Line 13: If {project_path}/graph.json does NOT exist, fall back to direct file exploration:
Total occurrences: 6
All 6 references use explicit {project_path}/graph.json paths. The old implicit "graph.json exists" / "graphify is NOT installed" patterns are gone.
AC2: Add {project_path} as first positional argument to factory graph CLI commands in prompt template
Status: VERIFIED
Evidence:
Verified the graph CLI accepts path as first positional argument:
uv run factory graph query --helpusage: factory graph query [-h] [--depth DEPTH] path question
uv run factory graph explain --helpusage: factory graph explain [-h] path node
uv run factory graph path --helpusage: factory graph path [-h] path source target
All three commands take path as the first positional arg, matching the prompt template format factory graph query "{project_path}" ....
AC3: In skill_export.py, replace {project_path} with $PROJECT_PATH when generating SKILL.md files
Status: VERIFIED
Evidence:
uv run python << 'PYEOF'
from factory.workflow.skill_export import _agent_to_instruction
from factory.workflow.definitions import _GRAPH_EXPLORER_PROMPT
from factory.workflow.primitives import AgentNode, AgentRole, Workflow
node = AgentNode(
id='graph_explorer',
role=AgentRole.RESEARCHER,
prompt_template=_GRAPH_EXPLORER_PROMPT,
reads={'.factory/strategy/observations.md', 'graph.json'},
writes={'.factory/strategy/graph-context.md'},
)
wf = Workflow(name='test', nodes={'graph_explorer': node}, edges=[], start_node='graph_explorer')
result = _agent_to_instruction(node, wf)
if '{project_path}' in result:
print('FAIL')
else:
print('PASS: No {project_path} found')
if '$PROJECT_PATH' in result:
print('PASS: $PROJECT_PATH is present')
PYEOFOutput:
PASS: No {project_path} found
PASS: $PROJECT_PATH is present
Feature Tests
FT1: Full skill export — no {project_path} leaks in any of 35 exported SKILL.md files
Status: VERIFIED
Evidence:
uv run python << 'PYEOF'
from factory.workflow.skill_export import export_all_skills
from pathlib import Path
import os, tempfile
with tempfile.TemporaryDirectory() as tmpdir:
export_all_skills(Path(tmpdir))
found_issues = []
checked = 0
for root, dirs, files in os.walk(tmpdir):
for f in files:
if f.endswith('.md'):
path = os.path.join(root, f)
content = open(path).read()
checked += 1
if '{project_path}' in content:
for i, line in enumerate(content.split('\n')):
if '{project_path}' in line:
rel = os.path.relpath(path, tmpdir)
found_issues.append(f'{rel}:{i}: {line.strip()}')
print(f'Checked {checked} exported SKILL.md files')
if found_issues:
print(f'FAIL: {len(found_issues)} lines with project_path')
else:
print('PASS: No {project_path} found in any exported SKILL.md files')
PYEOFOutput:
Checked 35 exported SKILL.md files
PASS: No {project_path} found in any exported SKILL.md files
FT2: $PROJECT_PATH correctly appears in graph commands within exported skills
Status: VERIFIED
Evidence:
Exported SKILL.md files for workflows containing graph_explorer show correct $PROJECT_PATH usage:
workflow-study/SKILL.md: $PROJECT_PATH=15, graph.json refs=4
Line 16: factory graph update $PROJECT_PATH
Line 36: ls $PROJECT_PATH/graph.json
Line 40: 1. Run `factory graph query "$PROJECT_PATH" "<focus from observations>" --depth 2`
Line 41: 2. Run `factory graph explain "$PROJECT_PATH" "<key node>"`
Line 42: 3. Run `factory graph path "$PROJECT_PATH" "<A>" "<B>"`
workflow-design/SKILL.md: $PROJECT_PATH=53, graph.json refs=4
Line 33: factory graph update $PROJECT_PATH
Line 53: ls $PROJECT_PATH/graph.json
Line 57: 1. Run `factory graph query "$PROJECT_PATH" ...`
Line 58: 2. Run `factory graph explain "$PROJECT_PATH" ...`
Line 59: 3. Run `factory graph path "$PROJECT_PATH" ...`
workflow-plan/SKILL.md: $PROJECT_PATH=46, graph.json refs=4
(same pattern)
FT3: graph_explorer reads field now includes graph.json
Status: VERIFIED
Evidence:
uv run python -c "
from factory.workflow.definitions import _study_subgraph
nodes, edges = _study_subgraph()
ge = nodes['graph_explorer']
print('reads:', ge.reads)
"Output:
reads: {'graph.json', '.factory/strategy/observations.md'}
Edge Case Tests
EC1: FnNode commands still use {project_path} (executor replaces those, NOT skill_export)
Status: VERIFIED
Evidence:
uv run python << 'PYEOF'
from factory.workflow.definitions import _study_subgraph
nodes, edges = _study_subgraph()
print('graph_update command:', nodes['graph_update'].command)
print('concat_study command:', nodes['concat_study'].command)
PYEOFOutput:
graph_update command: factory graph update {project_path}
concat_study command: cat {project_path}/.factory/strategy/observations.md {project_path}/.factory/strategy/graph-context.md > {project_path}/.factory/strategy/study-combined.md
FnNode commands correctly retain {project_path} — the executor handles substitution for these at runtime, not skill_export.
EC2: Only graph_explorer AgentNodes have {project_path} in prompt_template
Status: VERIFIED
Evidence:
Scanned all AgentNodes across all 21 workflow functions. Only 2 AgentNodes have {project_path} in their prompt_template:
design_workflow -> graph_explorer: 6 occurrencesstudy_standalone_workflow -> graph_explorer: 6 occurrences
Both are the same _GRAPH_EXPLORER_PROMPT constant and both are correctly replaced by _agent_to_instruction().
EC3: Multiple {project_path} occurrences all replaced (not just the first)
Status: VERIFIED
Evidence:
uv run python << 'PYEOF'
from factory.workflow.skill_export import _agent_to_instruction
from factory.workflow.primitives import AgentNode, AgentRole, Workflow
node = AgentNode(
id='test_multi', role=AgentRole.RESEARCHER,
prompt_template='Check {project_path}/a.json and {project_path}/b.json and {project_path}/c.json',
)
wf = Workflow(name='t', nodes={'test_multi': node}, edges=[], start_node='test_multi')
result = _agent_to_instruction(node, wf)
count = result.count('$PROJECT_PATH')
print(f'$PROJECT_PATH count: {count} (expected 3)')
has_old = '{project_path}' in result
print(f'Old placeholder present: {has_old} (expected False)')
PYEOFOutput:
$PROJECT_PATH count: 3 (expected 3)
Old placeholder present: False (expected False)
The .replace() call replaces all occurrences, not just the first.
EC4: $PROJECT_PATH is properly quoted in graph commands
Status: VERIFIED
Evidence:
All three graph commands in the exported prompt use "$PROJECT_PATH" (double-quoted):
factory graph query "$PROJECT_PATH" "<focus from observations>" --depth 2
factory graph explain "$PROJECT_PATH" "<key node>"
factory graph path "$PROJECT_PATH" "<A>" "<B>"
Proper quoting ensures paths with spaces are handled correctly at runtime.
Acceptance Criteria Verification Summary
| # | Criterion | Status |
|---|---|---|
| AC1 | Replace implicit graph.json with explicit {project_path}/graph.json |
VERIFIED |
| AC2 | Add {project_path} to factory graph CLI commands |
VERIFIED |
| AC3 | Replace {project_path} with $PROJECT_PATH in SKILL.md export |
VERIFIED |
| FT1 | No {project_path} leaks in any of 35 exported SKILL.md files |
VERIFIED |
| FT2 | $PROJECT_PATH correctly appears in graph commands in skills |
VERIFIED |
| FT3 | graph_explorer reads field includes graph.json |
VERIFIED |
| EC1 | FnNode commands unaffected (still use {project_path} for executor) |
VERIFIED |
| EC2 | Only graph_explorer AgentNodes affected (scoped fix) | VERIFIED |
| EC3 | All occurrences replaced (not just first) | VERIFIED |
| EC4 | $PROJECT_PATH properly quoted in generated commands |
VERIFIED |
Adversarial Verdict: PASS
All acceptance criteria verified with evidence. The fix correctly:
- Makes the graph explorer prompt explicit about where
graph.jsonlives - Adds the project path as the first positional argument to
factory graphCLI commands (matching their actual CLI signatures) - Replaces
{project_path}with$PROJECT_PATHat SKILL.md export time so the shell variable is used at runtime - Does not affect FnNode commands (which use executor-side substitution)
- Handles all occurrences (6 per prompt, across 2 workflows)
- All 191 related existing tests pass
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #1286 +/- ##
=======================================
Coverage 84.73% 84.74%
=======================================
Files 228 228
Lines 25448 25448
Branches 4091 4091
=======================================
+ Hits 21564 21565 +1
+ Misses 2914 2913 -1
Partials 970 970 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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✅ Factory Review: KEEP
Verdict: KEEP
Reason: QA: CLEAN — 5737 tests pass, 0 issues across 7 review categories, 8/8 adversarial criteria verified, composite score 0.9644
QA Analysis
Adversarial QA Report
PR: #1286 — fix: add graph.json to graph_explorer reads set
Project type: Library (Python CLI with workflow engine)
Date: 2026-08-18
Smoke Test
No project-specific smoke test defined. Used uv sync + import verification as baseline.
- Command:
uv sync - Output:
Resolved 168 packages in 0.89ms / Checked 148 packages in 2ms - Status: PASS
Test Plan
Derived from PR commit message and issue #1256:
- Verify
graph.jsonis present ingraph_explorer.readsset - Verify dependency alignment:
graph_update.writescoversgraph_explorer.readsforgraph.json - Verify fix works across all
_study_subgraphfocus variants (None, string, empty) - Verify fix propagates to all workflows containing
graph_explorer - Verify executor
_wait_for_readsbehavior: old reads would NOT detect missing dependency, new reads WILL - Verify prompt specifies explicit
{project_path}/graph.jsonpath - Verify serialization preserves the reads set
- Verify existing test suite passes
Acceptance Criteria
AC1: graph.json is in graph_explorer.reads set
Status: VERIFIED
Command:
uv run python -c "
from factory.workflow.definitions import _study_subgraph
nodes, edges = _study_subgraph()
ge = nodes['graph_explorer']
gu = nodes['graph_update']
print('graph_update writes:', gu.writes)
print('graph_explorer reads:', ge.reads)
assert 'graph.json' in ge.reads
assert '.factory/strategy/observations.md' in ge.reads
"
Output:
graph_update writes: {'graph.json'}
graph_explorer reads: {'.factory/strategy/observations.md', 'graph.json'}
Evidence: graph.json is present in the reads set alongside the existing observations.md.
AC2: Dependency alignment — graph_update.writes covers graph_explorer.reads for graph.json
Status: VERIFIED
Command:
uv run python -c "
from factory.workflow.definitions import _study_subgraph
nodes, edges = _study_subgraph()
gu = nodes['graph_update']
ge = nodes['graph_explorer']
graph_writes = {w for w in gu.writes if 'graph' in w}
graph_reads = {r for r in ge.reads if 'graph' in r}
assert graph_reads <= graph_writes
print('PASS: graph_explorer reads for graph.json are a subset of graph_update writes')
"
Output:
PASS: graph_explorer reads for graph.json are a subset of graph_update writes
AC3: Fix works across all focus variants
Status: VERIFIED
Command:
uv run python -c "
from factory.workflow.definitions import _study_subgraph
for label, focus in [('None', None), ('auth', 'auth'), ('empty', '')]:
nodes, _ = _study_subgraph(focus=focus if label != 'None' else None)
ge = nodes['graph_explorer']
assert 'graph.json' in ge.reads
print(f'{label}: PASS (reads={ge.reads})')
"
Output:
None: PASS (reads={'graph.json', '.factory/strategy/observations.md'})
auth: PASS (reads={'graph.json', '.factory/strategy/observations.md'})
empty: PASS (reads={'graph.json', '.factory/strategy/observations.md'})
AC4: Fix propagates to all workflows containing graph_explorer
Status: VERIFIED
Command:
uv run python -c "
from factory.workflow.definitions import (
improve_workflow, design_workflow, research_workflow,
study_standalone_workflow, meta_workflow, create_workflow,
discover_workflow
)
workflows = {
'improve': improve_workflow, 'design': design_workflow,
'research': research_workflow, 'study_standalone': study_standalone_workflow,
'meta': meta_workflow, 'create': create_workflow, 'discover': discover_workflow,
}
for name, wf_fn in workflows.items():
wf = wf_fn()
if 'graph_explorer' not in wf.nodes:
print(f'{name}: no graph_explorer node')
continue
ge = wf.nodes['graph_explorer']
assert 'graph.json' in ge.reads
assert '.factory/strategy/observations.md' in ge.reads
print(f'{name}: PASS (reads={ge.reads})')
"
Output:
improve: no graph_explorer node
design: PASS (reads={'graph.json', '.factory/strategy/observations.md'})
research: no graph_explorer node
study_standalone: PASS (reads={'graph.json', '.factory/strategy/observations.md'})
meta: no graph_explorer node
create: no graph_explorer node
discover: no graph_explorer node
Evidence: Both workflows with graph_explorer (design, study_standalone) have the fix. Other workflows don't use the study subgraph directly.
AC5: Executor _wait_for_reads would have failed without the fix
Status: VERIFIED
Command:
uv run python -c "
from factory.workflow.definitions import _study_subgraph
nodes, edges = _study_subgraph()
ge = nodes['graph_explorer']
study = nodes['study']
# Simulate: only study has completed, graph_update still running
completed_files_only_study = {'.factory/strategy/observations.md'}
old_reads = {'.factory/strategy/observations.md'}
new_reads = ge.reads
old_missing = old_reads - completed_files_only_study
new_missing = new_reads - completed_files_only_study
print(f'OLD reads missing: {old_missing} -> executor would NOT wait (bug!)')
print(f'NEW reads missing: {new_missing} -> executor WILL wait correctly')
assert not old_missing
assert new_missing == {'graph.json'}
print('PASS: Fix correctly makes executor aware of graph.json dependency')
"
Output:
OLD reads missing: set() → executor would NOT wait (bug!)
NEW reads missing: {'graph.json'} → executor WILL wait correctly
PASS: Fix correctly makes executor aware of graph.json dependency
Evidence: Without the fix, the executor's _wait_for_reads would see no missing dependencies and proceed immediately, even if graph_update hadn't produced graph.json yet. With the fix, the executor correctly waits.
AC6: Prompt specifies explicit {project_path}/graph.json path
Status: VERIFIED
Command:
uv run python -c "
from factory.workflow.definitions import _GRAPH_EXPLORER_PROMPT
assert '{project_path}/graph.json' in _GRAPH_EXPLORER_PROMPT
print('PASS: explicit path')
assert 'NOT inside' in _GRAPH_EXPLORER_PROMPT and '.factory' in _GRAPH_EXPLORER_PROMPT
print('PASS: .factory clarification')
assert 'test -f graph.json' in _GRAPH_EXPLORER_PROMPT
print('PASS: relative smoke check')
"
Output:
PASS: explicit path
PASS: .factory clarification
PASS: relative smoke check
AC7: Serialization preserves the reads set
Status: VERIFIED
Command:
uv run python -c "
from factory.workflow.definitions import _study_subgraph
nodes, _ = _study_subgraph()
ge = nodes['graph_explorer']
node_dict = ge.model_dump()
print('Serialized reads:', node_dict.get('reads'))
assert 'graph.json' in node_dict.get('reads', set())
print('PASS')
"
Output:
Serialized reads: {'.factory/strategy/observations.md', 'graph.json'}
PASS
AC8: Existing test suite passes
Status: VERIFIED
Command:
uv run pytest tests/test_workflow_definitions.py tests/test_plan_workflow.py -v --no-header
Output (summary):
206 passed in 1.22s
All 206 tests pass, including 6 tests specifically targeting graph_explorer and _study_subgraph.
Edge Case Tests
Edge 1: graph_explorer reads set is not accidentally shared/mutated across calls
Status: VERIFIED (via AC3)
Each call to _study_subgraph() produces independent node instances. Verified by calling with different focus values and checking reads are consistent.
Edge 2: No regression in concat_study reads
Status: VERIFIED
uv run python -c "
from factory.workflow.definitions import _study_subgraph
nodes, _ = _study_subgraph()
cs = nodes['concat_study']
print('concat_study reads:', cs.reads)
assert 'graph.json' not in cs.reads # concat_study should NOT read graph.json
print('PASS: concat_study does not incorrectly read graph.json')
"
Output: PASS: concat_study does not incorrectly read graph.json
Summary
| # | Criterion | Status |
|---|---|---|
| 1 | graph.json in graph_explorer.reads | VERIFIED |
| 2 | Dependency alignment with graph_update.writes | VERIFIED |
| 3 | All focus variants work | VERIFIED |
| 4 | Propagates to all workflows | VERIFIED |
| 5 | Executor wait behavior correct | VERIFIED |
| 6 | Explicit path in prompt | VERIFIED |
| 7 | Serialization preserves reads | VERIFIED |
| 8 | Existing test suite passes (206/206) | VERIFIED |
Adversarial Verdict: PASS
The fix is minimal, correct, and solves the stated problem. Adding graph.json to the graph_explorer.reads set ensures the headless executor's _wait_for_reads properly tracks the dependency on graph_update's output. Without this fix, the executor would not wait for graph.json to be produced before running graph_explorer, which could cause the agent to explore without graph data. The prompt already had the explicit {project_path}/graph.json path reference. All 206 existing tests pass.
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The headless executor uses the reads set for runtime dependency tracking (_wait_for_reads). Without graph.json declared, the executor's dependency tracker doesn't know graph_explorer depends on the graph_update output. Closes #1256
Factory Graph finds 19% more relevant files than raw Claude Code but Claude Code returns more precise line ranges (+22% precision). Study phase adds ~2% incremental lift over prompt-only.
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Summary
"graph.json"to thegraph_explorernode'sreadsset in_study_subgraph()readsfor runtime dependency tracking (_wait_for_reads) — without this, the executor's dependency tracker doesn't knowgraph_explorerdepends ongraph.json, even though edge ordering prevents an actual race todayskill_export.py{project_path}→$PROJECT_PATHreplacement were already merged via feat: Outer Loop v2 — evolutionary workflow search with E2E validation #1284Test plan
pytest -k "workflow or graph or definition"— 849 passedCloses #1256