@inflexa-ai/harness 0.2.0 → 0.3.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (80) hide show
  1. package/README.md +48 -0
  2. package/dist/agents/conversation-agent.d.ts +3 -0
  3. package/dist/agents/conversation-agent.js +2 -2
  4. package/dist/agents/sandbox/shared.d.ts +3 -0
  5. package/dist/agents/sandbox/shared.js +2 -2
  6. package/dist/app/chat-turn.d.ts +3 -0
  7. package/dist/app/chat-turn.js +3 -1
  8. package/dist/app/synthesize-run.d.ts +3 -0
  9. package/dist/app/synthesize-run.js +3 -1
  10. package/dist/execution/artifact-metadata.d.ts +3 -0
  11. package/dist/execution/artifact-metadata.js +8 -2
  12. package/dist/execution/artifact-registration.d.ts +2 -1
  13. package/dist/execution/artifact-registration.js +8 -2
  14. package/dist/execution/ephemeral-runner.d.ts +3 -0
  15. package/dist/execution/ephemeral-runner.js +8 -4
  16. package/dist/execution/post-step-pipeline.d.ts +3 -0
  17. package/dist/execution/post-step-pipeline.js +24 -4
  18. package/dist/execution/reconcile-manifest.d.ts +7 -0
  19. package/dist/execution/reconcile-manifest.js +19 -5
  20. package/dist/execution/report-runner.d.ts +3 -0
  21. package/dist/execution/report-runner.js +4 -4
  22. package/dist/execution/step-summary.d.ts +3 -0
  23. package/dist/execution/step-summary.js +4 -2
  24. package/dist/index.d.ts +3 -0
  25. package/dist/index.js +5 -0
  26. package/dist/lib/chrome.d.ts +4 -1
  27. package/dist/lib/chrome.js +10 -7
  28. package/dist/lib/console-logger.d.ts +19 -0
  29. package/dist/lib/console-logger.js +62 -0
  30. package/dist/lib/logger.d.ts +88 -0
  31. package/dist/lib/logger.js +37 -0
  32. package/dist/lib/otel.d.ts +2 -1
  33. package/dist/lib/otel.js +8 -3
  34. package/dist/runtime/boot.d.ts +2 -2
  35. package/dist/runtime/boot.js +1 -1
  36. package/dist/runtime/connection-budget.d.ts +2 -2
  37. package/dist/runtime/connection-budget.js +5 -3
  38. package/dist/runtime/dbos.d.ts +7 -7
  39. package/dist/runtime/dbos.js +14 -11
  40. package/dist/runtime/shutdown.d.ts +2 -2
  41. package/dist/runtime/shutdown.js +4 -3
  42. package/dist/sandbox/create-sandbox.d.ts +2 -2
  43. package/dist/sandbox/docker-client.d.ts +2 -2
  44. package/dist/sandbox/docker-client.js +4 -1
  45. package/dist/sandbox/k8s-client.d.ts +3 -0
  46. package/dist/sandbox/k8s-client.js +5 -4
  47. package/dist/sandbox/notification-sweep.d.ts +3 -3
  48. package/dist/sandbox/notification-sweep.js +4 -2
  49. package/dist/sandbox/reaper.d.ts +3 -3
  50. package/dist/sandbox/reaper.js +7 -4
  51. package/dist/sandbox/watchdog.d.ts +3 -3
  52. package/dist/sandbox/watchdog.js +8 -2
  53. package/dist/state/init.d.ts +2 -1
  54. package/dist/state/init.js +5 -6
  55. package/dist/tasks/data-profile.d.ts +5 -0
  56. package/dist/tasks/data-profile.js +24 -17
  57. package/dist/tools/bio/search-dgidb.d.ts +11 -1
  58. package/dist/tools/bio/search-dgidb.js +92 -78
  59. package/dist/tools/iterate-report.d.ts +3 -0
  60. package/dist/tools/iterate-report.js +3 -1
  61. package/dist/tools/research/literature-reviewer.d.ts +3 -0
  62. package/dist/tools/research/literature-reviewer.js +2 -2
  63. package/dist/tools/workspace/execute-command.d.ts +3 -0
  64. package/dist/tools/workspace/execute-command.js +3 -1
  65. package/dist/workflows/execute-analysis.d.ts +3 -0
  66. package/dist/workflows/execute-analysis.js +11 -7
  67. package/dist/workflows/execute-target-assessment.d.ts +3 -0
  68. package/dist/workflows/execute-target-assessment.js +19 -15
  69. package/dist/workflows/sandbox-step.d.ts +9 -0
  70. package/dist/workflows/sandbox-step.js +39 -17
  71. package/dist/workflows/target-assessment/lib/llm-step.d.ts +3 -0
  72. package/dist/workflows/target-assessment/lib/llm-step.js +3 -1
  73. package/dist/workflows/target-assessment/lib/structured-llm.d.ts +3 -0
  74. package/dist/workflows/target-assessment/lib/structured-llm.js +1 -0
  75. package/dist/workflows/target-assessment/phase5-persist.d.ts +3 -0
  76. package/dist/workflows/target-assessment/phase5-persist.js +8 -3
  77. package/dist/workflows/target-assessment/progress.d.ts +2 -1
  78. package/dist/workflows/target-assessment/progress.js +4 -3
  79. package/dist/workspace/filesystem.js +163 -74
  80. package/package.json +95 -96
package/package.json CHANGED
@@ -1,101 +1,100 @@
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  {
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- "name": "@inflexa-ai/harness",
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- "version": "0.2.0",
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- "description": "Host-agnostic bioinformatics agent harness — hand-rolled agent loop, DBOS-durable workflows, sandboxed compute.",
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- "license": "Apache-2.0",
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- "type": "module",
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- "main": "dist/index.js",
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- "types": "dist/index.d.ts",
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- "exports": {
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- ".": {
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- "types": "./dist/index.d.ts",
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- "import": "./dist/index.js"
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+ "name": "@inflexa-ai/harness",
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+ "version": "0.3.0",
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+ "description": "Host-agnostic bioinformatics agent harness \u2014 hand-rolled agent loop, DBOS-durable workflows, sandboxed compute.",
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+ "license": "Apache-2.0",
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+ "type": "module",
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+ "main": "dist/index.js",
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+ "types": "dist/index.d.ts",
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+ "exports": {
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+ ".": {
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+ "types": "./dist/index.d.ts",
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+ "import": "./dist/index.js"
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+ },
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+ "./*.js": {
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+ "types": "./dist/*.d.ts",
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+ "import": "./dist/*.js"
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+ },
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+ "./*": {
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+ "types": "./dist/*.d.ts",
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+ "import": "./dist/*.js"
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+ }
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  },
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- "./*.js": {
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- "types": "./dist/*.d.ts",
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- "import": "./dist/*.js"
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+ "files": [
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+ "dist",
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+ "NOTICE"
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+ ],
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+ "engines": {
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+ "node": ">=24"
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  },
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- "./*": {
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- "types": "./dist/*.d.ts",
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- "import": "./dist/*.js"
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+ "repository": {
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+ "type": "git",
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+ "url": "https://github.com/inflexa-ai/inflexa.git",
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+ "directory": "harness"
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+ },
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+ "scripts": {
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+ "build": "tsc -p tsconfig.json",
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+ "format": "prettier --write src/",
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+ "format:file": "prettier --write",
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+ "lint": "eslint .",
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+ "prepare": "tsc -p tsconfig.json",
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+ "prepublishOnly": "bun run build && bun run smoke",
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+ "smoke": "node scripts/smoke.mjs",
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+ "typecheck": "tsc --noEmit"
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+ },
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+ "dependencies": {
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+ "@ai-sdk/anthropic": "^4.0.15",
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+ "@ai-sdk/openai-compatible": "^3.0.10",
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+ "@ai-sdk/provider": "^4.0.3",
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+ "@anthropic-ai/sdk": "^0.107.0",
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+ "@dbos-inc/dbos-sdk": "^4.23.6",
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+ "@kubernetes/client-node": "^1.4.0",
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+ "@opentelemetry/api": "^1.9.1",
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+ "@opentelemetry/core": "^2.9.0",
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+ "@opentelemetry/exporter-metrics-otlp-http": "^0.219.0",
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+ "@opentelemetry/exporter-trace-otlp-proto": "^0.219.0",
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+ "@opentelemetry/resources": "^2.9.0",
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+ "@opentelemetry/sdk-metrics": "^2.9.0",
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+ "@opentelemetry/sdk-trace-base": "^2.9.0",
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+ "@opentelemetry/sdk-trace-node": "^2.9.0",
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+ "@opentelemetry/semantic-conventions": "^1.43.0",
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+ "ai": "^7.0.28",
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+ "cheerio": "^1.2.0",
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+ "dockerode": "^4.0.12",
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+ "fast-xml-parser": "^5.10.0",
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+ "hono": "^4.12.30",
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+ "js-tiktoken": "^1.0.21",
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+ "mime": "^4.1.0",
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+ "nanoid": "^5.1.16",
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+ "neverthrow": "^8.2.0",
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+ "nunjucks": "^3.2.4",
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+ "openai": "^4.104.0",
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+ "pdf-parse": "^2.4.5",
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+ "pg": "^8.22.0",
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+ "puppeteer-core": "^23.11.1",
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+ "zod": "^4.4.3"
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+ },
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+ "devDependencies": {
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+ "@eslint/js": "^10.0.1",
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+ "@types/bun": "latest",
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+ "@types/dockerode": "^3.3.47",
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+ "@types/node": "^24.13.3",
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+ "@types/nunjucks": "^3.2.6",
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+ "@types/pdf-parse": "^1.1.5",
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+ "@types/pg": "^8.20.0",
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+ "eslint": "^10.7.0",
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+ "eslint-plugin-neverthrow": "^1.1.4",
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+ "globals": "^17.7.0",
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+ "prettier": "^3.9.5",
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+ "testcontainers": "^10.28.0",
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+ "typescript": "^6.0.3",
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+ "typescript-eslint": "^8.64.0"
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+ },
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+ "publishConfig": {
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+ "access": "public",
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+ "registry": "https://registry.npmjs.org"
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+ },
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+ "patchedDependencies": {
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+ "eslint-plugin-neverthrow@1.1.4": "patches/eslint-plugin-neverthrow@1.1.4.patch"
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  }
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- },
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- "files": [
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- "dist",
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- "NOTICE"
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- ],
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- "engines": {
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- "node": ">=24"
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- },
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- "repository": {
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- "type": "git",
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- "url": "https://github.com/inflexa-ai/inflexa.git",
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- "directory": "harness"
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- },
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- "scripts": {
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- "build": "tsc -p tsconfig.json",
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- "format": "prettier --write src/",
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- "format:file": "prettier --write",
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- "lint": "eslint .",
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- "prepare": "tsc -p tsconfig.json",
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- "prepublishOnly": "bun run build && bun run smoke",
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- "smoke": "node scripts/smoke.mjs",
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- "typecheck": "tsc --noEmit"
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- },
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- "dependencies": {
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- "@ai-sdk/anthropic": "^4.0.15",
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- "@ai-sdk/openai-compatible": "^3.0.10",
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- "@ai-sdk/provider": "^4.0.3",
49
- "@anthropic-ai/sdk": "^0.107.0",
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- "@dbos-inc/dbos-sdk": "^4.23.6",
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- "@kubernetes/client-node": "^1.4.0",
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- "@opentelemetry/api": "^1.9.1",
53
- "@opentelemetry/core": "^2.9.0",
54
- "@opentelemetry/exporter-metrics-otlp-http": "^0.219.0",
55
- "@opentelemetry/exporter-trace-otlp-proto": "^0.219.0",
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- "@opentelemetry/resources": "^2.9.0",
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- "@opentelemetry/sdk-metrics": "^2.9.0",
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- "@opentelemetry/sdk-trace-base": "^2.9.0",
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- "@opentelemetry/sdk-trace-node": "^2.9.0",
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- "@opentelemetry/semantic-conventions": "^1.43.0",
61
- "ai": "^7.0.28",
62
- "cheerio": "^1.2.0",
63
- "dockerode": "^4.0.12",
64
- "fast-xml-parser": "^5.10.0",
65
- "hono": "^4.12.30",
66
- "js-tiktoken": "^1.0.21",
67
- "mime": "^4.1.0",
68
- "nanoid": "^5.1.16",
69
- "neverthrow": "^8.2.0",
70
- "nunjucks": "^3.2.4",
71
- "openai": "^4.104.0",
72
- "pdf-parse": "^2.4.5",
73
- "pg": "^8.22.0",
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- "pino": "^10.3.1",
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- "puppeteer-core": "^23.11.1",
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- "zod": "^4.4.3"
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- },
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- "devDependencies": {
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- "@eslint/js": "^10.0.1",
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- "@types/bun": "latest",
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- "@types/dockerode": "^3.3.47",
82
- "@types/node": "^24.13.3",
83
- "@types/nunjucks": "^3.2.6",
84
- "@types/pdf-parse": "^1.1.5",
85
- "@types/pg": "^8.20.0",
86
- "eslint": "^10.7.0",
87
- "eslint-plugin-neverthrow": "^1.1.4",
88
- "globals": "^17.7.0",
89
- "prettier": "^3.9.5",
90
- "testcontainers": "^10.28.0",
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- "typescript": "^6.0.3",
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- "typescript-eslint": "^8.64.0"
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- },
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- "publishConfig": {
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- "access": "public",
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- "registry": "https://registry.npmjs.org"
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- },
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- "patchedDependencies": {
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- "eslint-plugin-neverthrow@1.1.4": "patches/eslint-plugin-neverthrow@1.1.4.patch"
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- }
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  }