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Fixes for extension .lock database contention and tool improvements to avoid LLM use of grep (#119)
* Resolve database lock contention w/ vscode-codeql Resolves #117 Fixes a known compatibility issue for databases added, and therefore locked, via the GitHub.vscode-codeql extension. The vscode-codeql query server creates .lock files in the cache directory of every registered CodeQL database, preventing the ql-mcp server from running CLI commands (codeql_query_run, codeql_database_analyze) against those same databases. Add a DatabaseCopier that syncs databases from vscode-codeql storage into a managed directory under the `vscode-codeql-development-mcp-server` extension's globalStorage, stripping .lock files from the copy. The EnvironmentBuilder now sets CODEQL_DATABASES_BASE_DIRS to this managed directory by default (configurable via codeql-mcp.copyDatabases). - New DatabaseCopier class with incremental sync (skips unchanged databases) - StoragePaths.getManagedDatabaseStoragePath() for the managed databases/ dir - EnvironmentBuilder accepts injectable DatabaseCopierFactory for testability - codeql-mcp.copyDatabases setting (default: true) - 11 unit tests for DatabaseCopier (real filesystem operations) - 15 unit tests for EnvironmentBuilder (updated for copy mode + fallback) - 3 bridge integration tests (managed dir structure, no .lock files) - 4 E2E integration tests: inject .lock → copy → codeql_query_run + codeql_database_analyze succeed against the lock-free copy * Address PR review comments * Address more PR review comments * Add search_ql_code and codeql_resolve_files tools Add search_ql_code and codeql_resolve_files tools in order to eliminate grep/CLI dependencies. - New tools: search_ql_code (QL text/regex search) and codeql_resolve_files (file discovery by extension/glob) so LLMs never need shell access - Rewrite profile_codeql_query_from_logs with two-tier design: compact inline JSON + line-indexed detail file for targeted read_file access; parser now captures RA operations and pipeline-stage tuple progressions - Fix codeql_resolve_database to probe child directories for databases - Remove all grep/CLI references from prompts and resources - Cross-platform: normalize \r\n line endings in parser and search tool * Add "after" files for query evaluation integration tests * address Code Scanning TOCTOU race and PR review feedback - Eliminate filesystem race condition in search-ql-code.ts (read-then-check instead of stat-then-read) - Add symlink cycle detection using lstatSync and visited-path tracking - Fix tool description field names in profile-codeql-query-from-logs.ts ({startLine,endLine} → detailLines: {start,end}) - Fix monitoring-state.json fixtures to use standard sessions format - Rename find_qll_files → find_ql_files to match actual .ql extension * Stream large files instead of loading into memory - addresses latest review feedback for PR #119 - search-ql-code: check file size via lstatSync before reading; stream large files (>5 MB) line-by-line instead of skipping them - evaluator-log-parser: replace readFileSync with streaming async generator (createReadStream + readline) for brace-depth JSON parsing; parseEvaluatorLog now reads the file once instead of twice - profile-codeql-query: convert local parser to streaming with Map-based lookups instead of O(n) events.find() - database-copier: use lstat in removeLockFiles to skip symlinks; throw on fatal mkdir failures for proper fallback in EnvironmentBuilder - Validate contextLines/maxResults with schema bounds and clamping - Add environment-builder test for syncAll-throws fallback * Fix tool issues found during explain-codeql-query workflow testing - search_ql_code: add missing await in tool handler; skip .codeql, node_modules, and .git directories to avoid duplicate results from compiled pack caches - cli-tool-registry: extract resolveDatabasePath helper for multi-language DB root auto-resolution; apply to codeql_query_run, codeql_database_analyze, and codeql_resolve_database - environment-builder: route CODEQL_MCP_TMP_DIR to workspace-local .codeql/ql-mcp scratch directory (configurable via scratchDir setting); add CODEQL_MCP_WORKSPACE_FOLDERS env var - query-file-finder: add contextual hints array for missing tests, documentation, and expected results * [UPDATE PRIMITIVE] Fix transient HTTP 503 failures in install-packs.sh via exponential backoff retry (#121) * Initial plan * fix: add retry logic with exponential backoff to install-packs.sh The GitHub Actions integration test was failing on windows-latest with HTTP 503 "Egress is over the account limit" when downloading CodeQL packs from GHCR.io. Add a run_with_retry() helper function that retries a command up to 3 times with exponential backoff (10s, 20s, 40s). Both codeql pack install calls in install_packs() now use run_with_retry to handle transient network errors gracefully. Co-authored-by: data-douser <70299490+data-douser@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: data-douser <70299490+data-douser@users.noreply.github.com> * deterministic profiler output and search efficiency - addresses latest feedback for PR #119 ; - profile-codeql-query-from-logs: remove non-deterministic `Generated:` timestamp from detail file header to ensure reproducible output for integration test fixtures ; - search-ql-code: early-exit file processing once maxResults matches are collected; subsequent files are scanned cheaply for totalMatches count only, avoiding large array allocations and context extraction ; * Fix TOCTOU bug for search_ql_code tool * Stream-count large files & detect ambiguous DB paths - search-ql-code: use streaming (readline) for totalMatches counting on large files in the early-exit path; eliminates TOCTOU race from prior lstatSync check - cli-tool-registry: resolveDatabasePath now collects all candidate children and throws on ambiguity instead of silently picking the first - Add tests for cross-file totalMatches accuracy under truncation, single- child DB auto-resolve, and multi-child DB ambiguity error * Address latest PR review comments * Use fstatSync(fd) to avoid OOM w/ searchFile --------- Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
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‎.github/instructions/server_src_ts.instructions.md‎

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@@ -24,12 +24,9 @@ This file contains instructions for working with TypeScript source code files in
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- PREFER the import of functionality from `@modelcontextprotocol/sdk` over direct implementation, unless absolutely necessary.
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- PREFER to implement each MCP server primitive in its own file named after the primitive, e.g., `server/src/<lib-example>/<primitive-example>.ts`.
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- PREFER many simple MCP server primitives that each do one thing well over fewer complex MCP server primitives that do many things.
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- PREFER copying and/or adapting existing `*.prompt.md` files matching one of the following patterns:
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- `ql/.github/prompts/*.prompt.md`
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- `ql/languages/*/tools/dev/*.prompt.md`
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- `ql/resources/{codeql,qlt}/*.prompt.md`
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## CONTRAINTS
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- NEVER leave any trailing whitespace on any line.
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- NEVER guess at what a `codeql` or `qlt` CLI subcommand does; ALWAYS verify against the official `codeql <subcommand> -h -vv` or `qlt <subcommand> -h` documentation, respectively.
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- NEVER guess at what a `codeql` CLI subcommand does; ALWAYS verify against the official `codeql <subcommand> -h -vv` documentation.
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- **NEVER use stat/lstat followed by a separate read/open on the same path** — this is a TOCTOU (Time-of-Check-Time-of-Use) race condition (CWE-367). Instead, attempt the operation directly (e.g., `readFileSync`) within a try/catch block. If you need to know the file size before reading, read first and then check the buffer size — do NOT stat then read. For directory traversal, `lstatSync` is acceptable since it is the operation itself (checking entry type), not a precursor to a separate operation.

‎client/integration-tests/primitives/tools/codeql_resolve_files/find_ql_files/README.md‎

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# Integration Test: codeql_resolve_files/find_ql_files
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## Purpose
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Tests the `codeql_resolve_files` tool to ensure it can find QL query files by extension within a CodeQL pack directory.
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## Test Scenario
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This test validates that the `codeql_resolve_files` tool can:
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1. Accept a directory path and file extension filter
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2. Use the `codeql resolve files` CLI command to find matching files
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3. Return a list of file paths matching the specified criteria
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## Test Parameters
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- `dir`: "server/ql/javascript/examples/src"
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- `include-extension`: [".ql"]
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## Expected Behavior
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The tool should:
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1. Invoke `codeql resolve files` with the specified directory and extension filter
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2. Return file paths for all `.ql` files found in the directory tree
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3. Return a successful result with the file listing

‎client/integration-tests/primitives/tools/codeql_resolve_files/find_ql_files/after/monitoring-state.json‎

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{
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"sessions": [
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{
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"id": "integration_test_session",
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"calls": [
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{
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"tool": "codeql_resolve_files",
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"timestamp": "2025-09-25T16:06:00.000Z",
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"status": "success"
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}
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]
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}
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]
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}

‎client/integration-tests/primitives/tools/codeql_resolve_files/find_ql_files/before/monitoring-state.json‎

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{
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"sessions": [],
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"parameters": {
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"dir": "server/ql/javascript/examples/src",
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"include-extension": [".ql"]
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}
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}

‎client/integration-tests/primitives/tools/profile_codeql_query_from_logs/multi_query_raw_log/after/query-evaluation-detail.txt‎

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# CodeQL Evaluator Profile — Predicate Detail
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# Log format: raw
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# CodeQL version: 2.23.1
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# Use read_file with line ranges from the JSON response to access individual predicates.
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== Query: QueryA.ql ==
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Total: 200.00ms | Predicates evaluated: 2 | Cache hits: 1
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--- QueryA::source/0#abc123 ---
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Eval order: 1 of 2
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Duration: 65.00 ms
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Result: 5 tuples
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Strategy: SIMPLE_INTENSIONAL
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Position: /workspace/QueryA.ql:10,1-12,5
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Pipeline stages (1):
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[1] 50.00ms -> 5 tuples (counts=[5])
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--- QueryA::sink/0#def456 ---
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Eval order: 2 of 2
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Duration: 45.00 ms
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Result: 3 tuples
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Strategy: SIMPLE_INTENSIONAL
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Position: /workspace/QueryA.ql:14,1-16,5
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Dependencies (1):
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- QueryA::source/0#abc123
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Pipeline stages (1):
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[1] 30.00ms -> 3 tuples (counts=[3])
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== Query: QueryB.ql ==
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Total: 300.00ms | Predicates evaluated: 3 | Cache hits: 0
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--- QueryB::entryPoint/0#jkl012 ---
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Eval order: 1 of 3
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Duration: 95.00 ms
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Result: 8 tuples
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Strategy: EXTENSIONAL
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Position: /workspace/QueryB.ql:8,1-10,3
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Pipeline stages (1):
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[1] 80.00ms -> 8 tuples (counts=[8])
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--- QueryB::flowStep/2#mno345 ---
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Eval order: 2 of 3
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Duration: 95.00 ms
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Result: 12 tuples
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Strategy: SIMPLE_INTENSIONAL
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Position: /workspace/QueryB.ql:12,1-18,5
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Dependencies (1):
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- QueryB::entryPoint/0#jkl012
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Pipeline stages (1):
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[1] 80.00ms -> 12 tuples (counts=[12])
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--- QueryB::result/3#pqr678 ---
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Eval order: 3 of 3
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Duration: 45.00 ms
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Result: 2 tuples
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Strategy: SIMPLE_INTENSIONAL
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Position: /workspace/QueryB.ql:20,1-22,5
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Dependencies (2):
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- QueryB::flowStep/2#mno345
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- QueryB::entryPoint/0#jkl012
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Pipeline stages (1):
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[1] 30.00ms -> 2 tuples (counts=[2])

‎client/integration-tests/primitives/tools/profile_codeql_query_from_logs/multi_query_raw_log/after/query-evaluation-profile.json‎

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"resultSize": 5,
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"pipelineCount": 1,
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"evaluationStrategy": "SIMPLE_INTENSIONAL",
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"dependencies": []
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"dependencies": [],
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"pipelineStages": [
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{
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"durationMs": 50,
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"resultSize": 5,
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"counts": [
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5
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],
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"duplicationPercentages": [
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0
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]
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}
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]
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},
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{
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"predicateName": "QueryA::sink/0#def456",
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"evaluationStrategy": "SIMPLE_INTENSIONAL",
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"dependencies": [
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"QueryA::source/0#abc123"
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],
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"pipelineStages": [
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{
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"durationMs": 30,
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"resultSize": 3,
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"counts": [
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3
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],
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"duplicationPercentages": [
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0
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]
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}
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]
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}
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],
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"resultSize": 8,
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"pipelineCount": 1,
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"evaluationStrategy": "EXTENSIONAL",
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"dependencies": []
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"dependencies": [],
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"pipelineStages": [
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{
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"durationMs": 80,
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"resultSize": 8,
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"counts": [
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8
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],
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"duplicationPercentages": [
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0
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]
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}
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]
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},
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{
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"predicateName": "QueryB::flowStep/2#mno345",
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"evaluationStrategy": "SIMPLE_INTENSIONAL",
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"dependencies": [
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"QueryB::entryPoint/0#jkl012"
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],
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"pipelineStages": [
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{
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"durationMs": 80,
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"resultSize": 12,
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"counts": [
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12
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],
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"duplicationPercentages": [
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0
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]
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}
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]
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},
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{
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"dependencies": [
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"QueryB::flowStep/2#mno345",
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"QueryB::entryPoint/0#jkl012"
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],
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"pipelineStages": [
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{
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"durationMs": 30,
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"resultSize": 2,
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"counts": [
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2
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],
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"duplicationPercentages": [
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0
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]
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}
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]
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}
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],

‎client/integration-tests/primitives/tools/profile_codeql_query_from_logs/single_query_raw_log/after/query-evaluation-detail.txt‎

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# CodeQL Evaluator Profile — Predicate Detail
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# Log format: raw
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# CodeQL version: 2.23.1
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# Use read_file with line ranges from the JSON response to access individual predicates.
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== Query: ExampleQuery1.ql ==
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Total: 203.81ms | Predicates evaluated: 9 | Cache hits: 1
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--- Files::Container.splitAbsolutePath/2#dispred#43b82b7b_120#join_rhs ---
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Eval order: 2 of 9
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Duration: 58.52 ms
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Result: 27 tuples
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Strategy: SIMPLE_INTENSIONAL
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Position: /home/runner/.codeql/packages/codeql/util/2.0.18/codeql/util/FileSystem.qll:220,5-221,90
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Dependencies (1):
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- cached_Files::Container.splitAbsolutePath/2#dispred#43b82b7b
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RA operations (2 steps):
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{3} r1 = SCAN `cached_Files::Container.splitAbsolutePath/2#dispred#43b82b7b` OUTPUT In.1, In.2, In.0
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return r1
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Pipeline stages (1):
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[1] 27.98ms -> 27 tuples (counts=[27])
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--- files ---
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Eval order: 1 of 9
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Duration: 20.94 ms
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Result: 1 tuples
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Strategy: EXTENSIONAL
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Position: /home/runner/.codeql/packages/codeql/javascript-all/2.6.11/semmlecode.javascript.dbscheme:21,1-24,3
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--- Files::Impl::File.getURL/0#dispred#3f789d74#bf ---
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Eval order: 6 of 9
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Duration: 11.28 ms
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Result: 1 tuples
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Strategy: SIMPLE_INTENSIONAL
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Position: /home/runner/.codeql/packages/codeql/util/2.0.18/codeql/util/FileSystem.qll:220,5-221,90
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Dependencies (2):
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- m#Files::Impl::File.getURL/0#dispred#3f789d74#bf
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- Files::Container.getAbsolutePath/0#dispred#051b95e1#bf
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RA operations (3 steps):
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{4} r1 = JOIN `m#Files::Impl::File.getURL/0#dispred#3f789d74#bf` WITH `Files::Container.getAbsolutePath/0#dispred#051b95e1#bf` ON FIRST 1 OUTPUT Lhs.0, _, Rhs.1, _
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{2} | REWRITE WITH Tmp.1 := "file://", Tmp.3 := ":0:0:0:0", Out.1 := (Tmp.1 ++ In.2 ++ Tmp.3) KEEPING 2
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return r1
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Pipeline stages (1):
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[1] 6.74ms -> 1 tuples (counts=[1, 1])
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--- m#Files::Impl::File.getURL/0#dispred#3f789d74#bf ---
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Eval order: 3 of 9
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Duration: 9.62 ms
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Result: 1 tuples
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Strategy: SIMPLE_INTENSIONAL
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Position: /home/runner/.codeql/packages/codeql/util/2.0.18/codeql/util/FileSystem.qll:220,5-221,90
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Dependencies (2):
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- Files::Container.splitAbsolutePath/2#dispred#43b82b7b_120#join_rhs
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- files
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RA operations (4 steps):
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{2} r1 = CONSTANT(unique string, unique int)["ExampleQuery1.js",1]
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{1} | JOIN WITH `Files::Container.splitAbsolutePath/2#dispred#43b82b7b_120#join_rhs` ON FIRST 2 OUTPUT Rhs.2
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{1} | JOIN WITH files ON FIRST 1 OUTPUT Lhs.0
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return r1
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Pipeline stages (1):
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[1] 3.57ms -> 1 tuples (counts=[1, 1, 1])
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--- #select#query ---
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Eval order: 9 of 9
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Duration: 9.01 ms
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Result: 1 tuples
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Strategy: SIMPLE_INTENSIONAL
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Position: /home/runner/work/codeql-development-mcp-server/codeql-development-mcp-server/server/ql/javascript/examples/src/ExampleQuery1/ExampleQuery1.ql:13,1-15,80
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Dependencies (5):
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- m#Files::Impl::File.getURL/0#dispred#3f789d74#bf
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- Files::Container.getAbsolutePath/0#dispred#051b95e1#bf
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- Files::Container.getAbsolutePath/0#dispred#051b95e1#bf_0#antijoin_rhs
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- Files::Impl::File.getURL/0#dispred#3f789d74#bf
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- Files::Impl::File.getURL/0#dispred#3f789d74#bf_0#antijoin_rhs
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RA operations (21 steps):
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{2} r1 = JOIN `m#Files::Impl::File.getURL/0#dispred#3f789d74#bf` WITH `Files::Container.getAbsolutePath/0#dispred#051b95e1#bf` ON FIRST 1 OUTPUT Lhs.0, Rhs.1
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{1} r2 = `m#Files::Impl::File.getURL/0#dispred#3f789d74#bf` AND NOT `Files::Container.getAbsolutePath/0#dispred#051b95e1#bf_0#antijoin_rhs`(FIRST 1)
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{2} | SCAN OUTPUT In.0, _
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{2} | REWRITE WITH Out.1 := "(no string representation)"
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{2} r3 = r1 UNION r2
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{4} | JOIN WITH `Files::Impl::File.getURL/0#dispred#3f789d74#bf` ON FIRST 1 OUTPUT Lhs.0, Lhs.1, Rhs.1, _
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{4} | REWRITE WITH Out.3 := "Example test code file found for codeql_test_extract example query."
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{1} r4 = `m#Files::Impl::File.getURL/0#dispred#3f789d74#bf` AND NOT `Files::Container.getAbsolutePath/0#dispred#051b95e1#bf_0#antijoin_rhs`(FIRST 1)
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{2} | SCAN OUTPUT In.0, _
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{2} | REWRITE WITH Out.1 := "(no string representation)"
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{2} r5 = r1 UNION r4
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{2} | AND NOT `Files::Impl::File.getURL/0#dispred#3f789d74#bf_0#antijoin_rhs`(FIRST 1)
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{4} | SCAN OUTPUT In.0, In.1, _, _
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{4} | REWRITE WITH Out.2 := "", Out.3 := "Example test code file found for codeql_test_extract example query."
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{4} r6 = r3 UNION r5
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return r6
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Pipeline stages (1):
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[1] 4.21ms -> 1 tuples (counts=[1, -1, -1, 0, 0, -1, 1, 1, 1, -1, -1, 0, 0, -1, 1, -1, 0, 0, -1, 1])
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--- Files::Container.getAbsolutePath/0#dispred#051b95e1#bf ---
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Eval order: 5 of 9
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Duration: 4.14 ms
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Result: 1 tuples
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Strategy: SIMPLE_INTENSIONAL
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Position: /home/runner/.codeql/packages/codeql/util/2.0.18/codeql/util/FileSystem.qll:63,5-87,66
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Dependencies (2):
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- m#Files::Container.getAbsolutePath/0#dispred#051b95e1#bf
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- files
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RA operations (2 steps):
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{2} r1 = JOIN `m#Files::Container.getAbsolutePath/0#dispred#051b95e1#bf` WITH files ON FIRST 1 OUTPUT Lhs.0, Rhs.1
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return r1
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Pipeline stages (1):
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[1] 0.47ms -> 1 tuples (counts=[1])
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--- Files::Container.getAbsolutePath/0#dispred#051b95e1#bf_0#antijoin_rhs ---
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Eval order: 8 of 9
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Duration: 3.71 ms
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Result: 1 tuples
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Strategy: SIMPLE_INTENSIONAL
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Position: /home/runner/work/codeql-development-mcp-server/codeql-development-mcp-server/server/ql/javascript/examples/src/ExampleQuery1/ExampleQuery1.ql:13,1-15,80
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Dependencies (1):
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- Files::Container.getAbsolutePath/0#dispred#051b95e1#bf
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RA operations (2 steps):
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{1} r1 = SCAN `Files::Container.getAbsolutePath/0#dispred#051b95e1#bf` OUTPUT In.0
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return r1
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Pipeline stages (1):
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[1] 0.30ms -> 1 tuples (counts=[1])
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--- m#Files::Container.getAbsolutePath/0#dispred#051b95e1#bf ---
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Eval order: 4 of 9
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Duration: 2.81 ms
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Result: 1 tuples
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Strategy: SIMPLE_INTENSIONAL
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Position: /home/runner/.codeql/packages/codeql/util/2.0.18/codeql/util/FileSystem.qll:63,5-87,66
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Dependencies (1):
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- m#Files::Impl::File.getURL/0#dispred#3f789d74#bf
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RA operations (1 steps):
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return `m#Files::Impl::File.getURL/0#dispred#3f789d74#bf`
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Pipeline stages (1):
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[1] 2.43ms -> 1 tuples (counts=[])
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--- Files::Impl::File.getURL/0#dispred#3f789d74#bf_0#antijoin_rhs ---
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Eval order: 7 of 9
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Duration: 0.72 ms
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Result: 1 tuples
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Strategy: SIMPLE_INTENSIONAL
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Position: /home/runner/work/codeql-development-mcp-server/codeql-development-mcp-server/server/ql/javascript/examples/src/ExampleQuery1/ExampleQuery1.ql:13,1-15,80
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Dependencies (1):
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- Files::Impl::File.getURL/0#dispred#3f789d74#bf
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RA operations (2 steps):
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{1} r1 = SCAN `Files::Impl::File.getURL/0#dispred#3f789d74#bf` OUTPUT In.0
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return r1
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Pipeline stages (1):
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[1] 0.35ms -> 1 tuples (counts=[1])

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