{"record":{"id":"07bdf18bc87af9b9","repo":"Graphify-Labs/graphify","slug":"error-graph-is-empty-extraction-produced-no-nod-07bdf1","errorCode":null,"errorMessage":"ERROR: Graph is empty - extraction produced no nodes.","messagePattern":"ERROR: Graph is empty - extraction produced no nodes\\.","errorType":"console","errorClass":"SystemExit","httpStatus":null,"severity":"error","filePath":"tools/skillgen/expected/graphify__skill-opencode.md","lineNumber":411,"sourceCode":"from graphify.build import build_from_json\nfrom graphify.cluster import cluster, score_all\nfrom graphify.analyze import god_nodes, surprising_connections, suggest_questions\nfrom graphify.report import generate\nfrom graphify.export import to_json\nfrom pathlib import Path\n\nextraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\\\"utf-8\\\"))\ndetection  = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\\\"utf-8\\\"))\n\n# root= mirrors the --update runbook (#1361): relativize source_file to the same\n# base so the full build and incremental --update never drift apart on re-extract.\nG = build_from_json(extraction, root='INPUT_PATH', directed=IS_DIRECTED)\n# Guard BEFORE any write: an empty extraction must not clobber a good graph.json /\n# GRAPH_REPORT.md / analysis sidecar. Check immediately after build (#1392).\nif G.number_of_nodes() == 0:\n    print('ERROR: Graph is empty - extraction produced no nodes.')\n    print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')\n    raise SystemExit(1)\ncommunities = cluster(G)\ncohesion = score_all(G, communities)\ntokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}\ngods = god_nodes(G)\nsurprises = surprising_connections(G, communities)\nlabels = {cid: 'Community ' + str(cid) for cid in communities}\n# Placeholder questions - regenerated with real labels in Step 5\nquestions = suggest_questions(G, communities, labels)\n\n# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing\n# nothing) when the new graph is smaller than the existing graph.json. Only write\n# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so\n# they never describe a graph that graph.json doesn't contain (#1392).\nwrote = to_json(G, communities, 'graphify-out/graph.json')\nif not wrote:\n    print('ERROR: refused to shrink graphify-out/graph.json (existing graph has more nodes; #479).')\n    print('If this shrink is intentional (you deleted files), re-run a full build with --force.')\n    raise SystemExit(1)","sourceCodeStart":393,"sourceCodeEnd":429,"githubUrl":"https://github.com/Graphify-Labs/graphify/blob/7fe58b0b0f3873be9a21c30106b8b8527c353aa6/tools/skillgen/expected/graphify__skill-opencode.md#L393-L429","documentation":"Empty-graph guard (#1392) in the graphify build pipeline. After build_from_json() turns .graphify_extract.json into a networkx graph, a zero node count triggers this ERROR and SystemExit(1) before any file is written, shielding existing graph.json / GRAPH_REPORT.md / sidecar from an empty overwrite.","triggerScenarios":"G.number_of_nodes() == 0 after build_from_json(extraction, root='INPUT_PATH', directed=IS_DIRECTED): no nodes in the extract, all files skipped, binary-only corpus, or root relativization dropping every node.","commonSituations":"Extraction step failed or wrote nothing; wrong input path; over-matching ignore rules; INPUT_PATH mismatch with stored source_file paths.","solutions":["Examine .graphify_extract.json for nodes; fix extraction if empty.","Confirm input path and its file types.","Check skip/ignore configuration.","Re-run extraction then build — the guard left old artifacts safe."],"exampleFix":null,"handlingStrategy":"validation","validationCode":"import json\nfrom pathlib import Path\n\nextraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding='utf-8'))\nassert any(f.get('nodes') for f in extraction.get('files', [])), 'no extracted nodes - re-run extraction'","typeGuard":null,"tryCatchPattern":null,"preventionTips":["Pre-check the extract sidecar before building.","Match root= to the extraction-time base path.","Investigate extraction runs that extract zero files.","Keep binary-only or empty directories out of the input root."],"tags":["graphify","extraction","empty-graph","fail-fast","build"],"backgroundTag":null,"analyzedSha":"7fe58b0b0f3873be9a21c30106b8b8527c353aa6","analyzedAt":"2026-08-14T19:23:21.323Z","schemaVersion":2},"datasetVersion":"2026-08-15T17:31:12.345Z"}