@inflexa-ai/harness 0.12.0 → 0.14.0

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Files changed (207) hide show
  1. package/dist/agents/conversation-agent.d.ts +9 -15
  2. package/dist/agents/conversation-agent.js +32 -31
  3. package/dist/agents/sandbox/cheminformatics-agent.js +1 -1
  4. package/dist/agents/sandbox/chromatin-agent.js +1 -1
  5. package/dist/agents/sandbox/dna-methylation-agent.js +1 -1
  6. package/dist/agents/sandbox/drug-repurposing-agent.js +5 -10
  7. package/dist/agents/sandbox/enrichment-agent.js +1 -1
  8. package/dist/agents/sandbox/genomic-variant-agent.js +1 -11
  9. package/dist/agents/sandbox/immune-profiling-agent.js +1 -1
  10. package/dist/agents/sandbox/index.js +0 -3
  11. package/dist/agents/sandbox/multi-omics-integration-agent.js +1 -1
  12. package/dist/agents/sandbox/network-agent.js +1 -1
  13. package/dist/agents/sandbox/pkpd-clinical-response-agent.js +3 -6
  14. package/dist/agents/sandbox/scientific-executor.js +1 -1
  15. package/dist/agents/sandbox/shared.d.ts +2 -2
  16. package/dist/agents/sandbox/shared.js +8 -14
  17. package/dist/agents/sandbox/translational-safety-agent.js +4 -7
  18. package/dist/agents/sandbox/types.d.ts +5 -5
  19. package/dist/agents/sandbox/types.js +4 -4
  20. package/dist/app/chat-turn.js +4 -1
  21. package/dist/app/message-assembly.d.ts +5 -2
  22. package/dist/app/message-assembly.js +7 -2
  23. package/dist/app/run-activity.d.ts +13 -0
  24. package/dist/app/run-activity.js +51 -0
  25. package/dist/config/resource-limits.d.ts +0 -7
  26. package/dist/config/resource-limits.js +0 -1
  27. package/dist/contracts/target-dossier.d.ts +10 -10
  28. package/dist/execution/dbos-run-launcher.js +1 -26
  29. package/dist/execution/report-runner.js +1 -1
  30. package/dist/execution/run-authorizer.d.ts +1 -1
  31. package/dist/execution/run-authorizer.js +1 -1
  32. package/dist/execution/run-event-parts.d.ts +44 -0
  33. package/dist/execution/run-event-parts.js +0 -0
  34. package/dist/execution/run-event-stream.d.ts +91 -0
  35. package/dist/execution/run-event-stream.js +212 -0
  36. package/dist/execution/run-launcher.d.ts +2 -18
  37. package/dist/execution/run-launcher.js +2 -4
  38. package/dist/execution/run-synthesis.js +1 -1
  39. package/dist/index.d.ts +7 -4
  40. package/dist/index.js +23 -6
  41. package/dist/input-sanitization.d.ts +14 -4
  42. package/dist/input-sanitization.js +27 -4
  43. package/dist/lib/storage.js +4 -1
  44. package/dist/loop/budget-exceeded.d.ts +18 -2
  45. package/dist/loop/budget-exceeded.js +49 -2
  46. package/dist/loop/run-agent.d.ts +22 -1
  47. package/dist/loop/run-agent.js +51 -5
  48. package/dist/loop/run-to-terminal.d.ts +0 -2
  49. package/dist/loop/run-to-terminal.js +8 -1
  50. package/dist/memory/ai-sdk-message-storage.d.ts +37 -4
  51. package/dist/memory/ai-sdk-message-storage.js +45 -4
  52. package/dist/memory/content-to-cortex.js +19 -3
  53. package/dist/memory/message-backfill.js +1 -1
  54. package/dist/memory/reconstruct-cards.d.ts +1 -1
  55. package/dist/memory/reconstruct-cards.js +7 -5
  56. package/dist/memory/thread-history.js +72 -8
  57. package/dist/prompts/conversation.d.ts +1 -1
  58. package/dist/prompts/conversation.js +41 -15
  59. package/dist/prompts/literature-reviewer.d.ts +1 -1
  60. package/dist/prompts/literature-reviewer.js +16 -14
  61. package/dist/prompts/planner.d.ts +3 -0
  62. package/dist/prompts/planner.js +16 -21
  63. package/dist/prompts/sandbox/drug-repurposing-agent.d.ts +1 -1
  64. package/dist/prompts/sandbox/drug-repurposing-agent.js +31 -22
  65. package/dist/prompts/sandbox/multi-omics-integration-agent.d.ts +1 -1
  66. package/dist/prompts/sandbox/multi-omics-integration-agent.js +9 -10
  67. package/dist/prompts/sandbox/pkpd-clinical-response-agent.d.ts +1 -1
  68. package/dist/prompts/sandbox/pkpd-clinical-response-agent.js +8 -7
  69. package/dist/prompts/sandbox/translational-safety-agent.d.ts +1 -1
  70. package/dist/prompts/sandbox/translational-safety-agent.js +20 -14
  71. package/dist/prompts/sandbox-standards.d.ts +4 -4
  72. package/dist/prompts/sandbox-standards.js +5 -5
  73. package/dist/prompts/synthesis-agent.d.ts +1 -1
  74. package/dist/prompts/synthesis-agent.js +7 -7
  75. package/dist/providers/errors.d.ts +7 -0
  76. package/dist/providers/errors.js +88 -3
  77. package/dist/runtime/assemble.d.ts +5 -10
  78. package/dist/runtime/assemble.js +0 -4
  79. package/dist/runtime/boot.d.ts +2 -2
  80. package/dist/runtime/boot.js +1 -1
  81. package/dist/runtime/dbos.d.ts +4 -5
  82. package/dist/runtime/dbos.js +6 -7
  83. package/dist/runtime/pools.d.ts +15 -1
  84. package/dist/runtime/pools.js +15 -1
  85. package/dist/sandbox/mount-plan.d.ts +1 -1
  86. package/dist/sandbox/sandbox-error.d.ts +1 -1
  87. package/dist/sandbox/sandbox-error.js +1 -1
  88. package/dist/sandbox/sandbox-step-translate.d.ts +15 -2
  89. package/dist/sandbox/sandbox-step-translate.js +17 -2
  90. package/dist/sandbox/types.d.ts +1 -1
  91. package/dist/schemas/validate-plan.d.ts +1 -1
  92. package/dist/schemas/workflow-state.d.ts +2 -2
  93. package/dist/schemas/workflow-state.js +2 -2
  94. package/dist/state/data-profile.d.ts +53 -1
  95. package/dist/state/data-profile.js +66 -6
  96. package/dist/state/index.d.ts +6 -6
  97. package/dist/state/index.js +4 -4
  98. package/dist/state/init.js +37 -2
  99. package/dist/state/plans.js +1 -1
  100. package/dist/state/runs.d.ts +49 -0
  101. package/dist/state/runs.js +150 -0
  102. package/dist/tasks/data-profile-activity.d.ts +87 -0
  103. package/dist/tasks/data-profile-activity.js +56 -0
  104. package/dist/tasks/data-profile.js +66 -4
  105. package/dist/tools/__fixtures__/tool-context.js +1 -0
  106. package/dist/tools/ad-hoc-router.d.ts +31 -0
  107. package/dist/tools/ad-hoc-router.js +132 -0
  108. package/dist/tools/analysis-invocation.d.ts +4 -0
  109. package/dist/tools/analysis-invocation.js +17 -0
  110. package/dist/tools/bio/chembl.d.ts +1 -1
  111. package/dist/tools/bio/chembl.js +51 -54
  112. package/dist/tools/bio/comptox.js +35 -33
  113. package/dist/tools/bio/drug-gene-interactions.d.ts +76 -0
  114. package/dist/tools/bio/drug-gene-interactions.js +175 -0
  115. package/dist/tools/bio/gene-disease-evidence.d.ts +61 -0
  116. package/dist/tools/bio/gene-disease-evidence.js +187 -0
  117. package/dist/tools/bio/gene-preclinical-profile.d.ts +58 -0
  118. package/dist/tools/bio/gene-preclinical-profile.js +125 -0
  119. package/dist/tools/bio/index.d.ts +23 -16
  120. package/dist/tools/bio/index.js +29 -22
  121. package/dist/tools/bio/keys.d.ts +16 -9
  122. package/dist/tools/bio/keys.js +22 -13
  123. package/dist/tools/bio/lookup-annotation.d.ts +48 -0
  124. package/dist/tools/bio/lookup-annotation.js +173 -0
  125. package/dist/tools/bio/opentargets.d.ts +7 -11
  126. package/dist/tools/bio/opentargets.js +24 -35
  127. package/dist/tools/bio/pubchem.js +6 -4
  128. package/dist/tools/bio/pubmed.d.ts +15 -7
  129. package/dist/tools/bio/pubmed.js +79 -20
  130. package/dist/tools/bio/search-clinical-trials.d.ts +20 -1
  131. package/dist/tools/bio/search-clinical-trials.js +26 -5
  132. package/dist/tools/bio/search-faers.js +9 -3
  133. package/dist/tools/bio/search-gene.d.ts +0 -1
  134. package/dist/tools/bio/search-gene.js +4 -5
  135. package/dist/tools/bio/search-geo-datasets.js +10 -4
  136. package/dist/tools/bio/search-interactions.d.ts +8 -4
  137. package/dist/tools/bio/search-interactions.js +28 -12
  138. package/dist/tools/bio/target-safety.d.ts +59 -0
  139. package/dist/tools/bio/target-safety.js +191 -0
  140. package/dist/tools/define-tool.d.ts +6 -2
  141. package/dist/tools/define-tool.js +1 -1
  142. package/dist/tools/execute-analysis.d.ts +44 -0
  143. package/dist/tools/execute-analysis.js +252 -0
  144. package/dist/tools/iterate-report.js +7 -6
  145. package/dist/tools/lib/dgidb-client.d.ts +49 -0
  146. package/dist/tools/lib/dgidb-client.js +168 -0
  147. package/dist/tools/lib/disgenet-client.d.ts +56 -0
  148. package/dist/tools/lib/disgenet-client.js +59 -0
  149. package/dist/tools/lib/drugbank-client.d.ts +83 -0
  150. package/dist/tools/lib/drugbank-client.js +95 -0
  151. package/dist/tools/lib/ensembl-client.d.ts +4 -1
  152. package/dist/tools/lib/ensembl-client.js +5 -3
  153. package/dist/tools/lib/gwas-catalog-client.d.ts +60 -0
  154. package/dist/tools/lib/gwas-catalog-client.js +136 -0
  155. package/dist/tools/lib/pharmgkb-client.d.ts +22 -0
  156. package/dist/tools/lib/pharmgkb-client.js +32 -0
  157. package/dist/tools/lib/pubmed-client.d.ts +57 -4
  158. package/dist/tools/lib/pubmed-client.js +57 -3
  159. package/dist/tools/lib/string-client.d.ts +25 -4
  160. package/dist/tools/lib/string-client.js +22 -5
  161. package/dist/tools/research/generate-plan.d.ts +16 -9
  162. package/dist/tools/research/generate-plan.js +116 -70
  163. package/dist/tools/research/inspect-data-profile.d.ts +31 -6
  164. package/dist/tools/research/inspect-data-profile.js +23 -7
  165. package/dist/tools/research/inspect-run.d.ts +33 -15
  166. package/dist/tools/research/inspect-run.js +155 -66
  167. package/dist/tools/research/literature-reviewer.js +7 -11
  168. package/dist/workflows/execute-analysis.d.ts +68 -5
  169. package/dist/workflows/execute-analysis.js +76 -7
  170. package/dist/workflows/sandbox-step.js +1 -11
  171. package/dist/workflows/target-assessment/decisions/index.d.ts +1 -1
  172. package/dist/workflows/target-assessment/phase4-assemble.d.ts +1 -1
  173. package/dist/workflows/target-assessment/steps/phase2-aggregate.d.ts +2 -2
  174. package/dist/workflows/target-assessment/steps/phase3-aggregate.d.ts +1 -1
  175. package/package.json +1 -1
  176. package/dist/agents/sandbox/ephemeral-executor.d.ts +0 -9
  177. package/dist/agents/sandbox/ephemeral-executor.js +0 -20
  178. package/dist/execution/ephemeral-runner.d.ts +0 -98
  179. package/dist/execution/ephemeral-runner.js +0 -189
  180. package/dist/prompts/sandbox/ephemeral-executor.d.ts +0 -1
  181. package/dist/prompts/sandbox/ephemeral-executor.js +0 -66
  182. package/dist/tools/bio/check-safety-panel.d.ts +0 -35
  183. package/dist/tools/bio/check-safety-panel.js +0 -76
  184. package/dist/tools/bio/get-impc-ko-profile.d.ts +0 -9
  185. package/dist/tools/bio/get-impc-ko-profile.js +0 -23
  186. package/dist/tools/bio/lookup-go-term.d.ts +0 -31
  187. package/dist/tools/bio/lookup-go-term.js +0 -116
  188. package/dist/tools/bio/search-bgee-expression.d.ts +0 -10
  189. package/dist/tools/bio/search-bgee-expression.js +0 -30
  190. package/dist/tools/bio/search-clinvar.d.ts +0 -13
  191. package/dist/tools/bio/search-clinvar.js +0 -28
  192. package/dist/tools/bio/search-dgidb.d.ts +0 -53
  193. package/dist/tools/bio/search-dgidb.js +0 -213
  194. package/dist/tools/bio/search-disgenet.d.ts +0 -30
  195. package/dist/tools/bio/search-disgenet.js +0 -84
  196. package/dist/tools/bio/search-drugbank.d.ts +0 -38
  197. package/dist/tools/bio/search-drugbank.js +0 -109
  198. package/dist/tools/bio/search-gwas-catalog.d.ts +0 -33
  199. package/dist/tools/bio/search-gwas-catalog.js +0 -172
  200. package/dist/tools/bio/search-pathway.d.ts +0 -12
  201. package/dist/tools/bio/search-pathway.js +0 -32
  202. package/dist/tools/bio/search-pharmgkb.d.ts +0 -17
  203. package/dist/tools/bio/search-pharmgkb.js +0 -52
  204. package/dist/tools/execute-plan.d.ts +0 -64
  205. package/dist/tools/execute-plan.js +0 -211
  206. package/dist/tools/run-ephemeral.d.ts +0 -33
  207. package/dist/tools/run-ephemeral.js +0 -65
@@ -15,6 +15,7 @@
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  * re-authenticating fixes it — which is a different remedy from every other
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  * non-retryable 4xx, so it is a different kind.
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  */
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+ import { redactSecrets } from "../input-sanitization.js";
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  /**
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  * Structural guard for an already-constructed `ProviderError` value. A
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  * `ProviderError` is a plain object, not an `Error`, so it cannot be
@@ -71,7 +72,67 @@ export function toProviderError(e, workload) {
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  cause: e,
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  };
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  }
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- return { type: "provider", retryable, message: detail, cause: e };
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+ // The `provider` arm composes like its three siblings rather than forwarding
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+ // the SDK message verbatim. It has to: when a 4xx body does not parse against
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+ // the configured provider's error schema, the AI SDK falls back to
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+ // `response.statusText`, so the "detail" is a bare HTTP reason phrase —
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+ // `"Bad Request"` — that names neither the call nor the cause, while the
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+ // status, the workload, and the body the SDK captured are all still on the
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+ // `cause` chain right here.
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+ //
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+ // Composed strictly AFTER `classifyProviderError` has returned, so message
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+ // text can never become a classification input: the harness-providers spec
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+ // fixes classification on the HTTP status alone.
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+ const status = extractStatus(e);
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+ const lead = status === undefined ? `Provider call failed for ${workload}` : `Provider call failed for ${workload} (HTTP ${status})`;
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+ // A transport that carries no reason phrase (an HTTP/2 hop yields
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+ // `statusText === ""`) leaves `detail` empty; appending it regardless would
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+ // trail a bare `": "` on an otherwise complete message.
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+ const reason = detail.trim();
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+ const diagnosed = reason ? `${lead}: ${reason}` : lead;
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+ const body = extractResponseBody(e);
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+ return {
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+ type: "provider",
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+ retryable,
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+ // The excerpt trails deliberately — workload and status lead, so a
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+ // downstream truncation (`profileFailureReason` cuts the line at 200)
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+ // eats the least diagnostic content first.
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+ message: body ? `${diagnosed} — response body: ${excerptResponseBody(body)}` : diagnosed,
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+ cause: e,
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+ };
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+ }
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+ /**
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+ * Max characters of a captured provider response body carried in a message.
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+ *
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+ * Derived, not picked: the tightest downstream consumer (`profileFailureReason`,
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+ * `tasks/data-profile.ts`) truncates the whole line at 200, and the lead this
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+ * excerpt trails — a workload label plus `HTTP <status>` plus a reason phrase —
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+ * runs to roughly 80. 120 is therefore the largest round value that cannot evict
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+ * that lead.
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+ *
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+ * Deliberately NOT shared with that consumer's `PROFILE_ERROR_MAX_LEN`: that one
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+ * bounds a `varchar` ledger column, this one bounds a message many non-ledger
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+ * consumers read, and coupling them would make either one unmovable.
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+ */
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+ const PROVIDER_BODY_EXCERPT_MAX_LEN = 120;
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+ /**
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+ * Single-lined, secret-redacted, length-capped rendering of a captured response body. Bounding happens
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+ * here rather than at a consumer because most `ProviderError` consumers truncate nothing at all, and the
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+ * one that does would let an unbounded body crowd out the workload and status ahead of it.
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+ *
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+ * The body is an UNTRUSTED upstream/proxy payload, and this excerpt lands verbatim in the ledger's
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+ * `data_profile_error` (surfaced to the UI) and the logs, whereas the composed lead does not — so
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+ * secrets are redacted here and nowhere else on the message. Redaction runs on the FULL body before
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+ * truncation: a token straddling the cut would otherwise be sliced into an unmatchable fragment that
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+ * leaks. `redactSecrets` matches only prefixed formats (API keys, JWTs, bearer tokens, connection
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+ * strings) and is safe on biological data, so a legitimate error body passes through intact.
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+ */
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+ function excerptResponseBody(body) {
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+ const singleLine = redactSecrets(body).replace(/\s+/g, " ").trim();
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+ // Slice by CODE POINT, not UTF-16 unit: a raw byte body can carry astral characters, and a plain
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+ // `.slice` could bisect a surrogate pair into a lone half that renders as U+FFFD.
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+ const chars = [...singleLine];
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+ return chars.length > PROVIDER_BODY_EXCERPT_MAX_LEN ? chars.slice(0, PROVIDER_BODY_EXCERPT_MAX_LEN - 1).join("") + "…" : singleLine;
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  }
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  /** Max links walked on the `cause` chain looking for a structured status. */
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  const MAX_CAUSE_HOPS = 5;
@@ -88,8 +149,13 @@ const CONNECTION_ERROR_CODES = new Set([
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  "UND_ERR_SOCKET",
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  ]);
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  const CONNECTION_ERROR_PATTERN = /fetch failed|socket hang up|network error|connection (?:refused|reset|error|closed)|econnrefused|enotfound|etimedout|terminated/i;
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- /** Walk the `cause` chain for the first numeric HTTP status. */
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- function extractStatus(err) {
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+ /**
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+ * Walk the `cause` chain for the first numeric HTTP status. The single status
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+ * walker: `classifyProviderError` keys on what this returns, so a caller asking
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+ * "did the provider layer have a status to classify on?" must ask it here rather
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+ * than re-implement the traversal.
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+ */
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+ export function extractStatus(err) {
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  let cursor = err;
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  for (let i = 0; i < MAX_CAUSE_HOPS && cursor; i++) {
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  const e = cursor;
@@ -101,6 +167,25 @@ function extractStatus(err) {
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  }
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  return undefined;
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  }
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+ /**
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+ * Walk the `cause` chain for the first captured provider response body.
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+ *
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+ * This is what recovers a proxy-minted or otherwise non-conforming error body:
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+ * the AI SDK keeps the raw bytes on `APICallError.responseBody` even when its
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+ * own parse against the provider's error schema fails and its `message` degrades
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+ * to the HTTP reason phrase. A blank body is treated as absent — an empty
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+ * `— response body:` segment says less than no segment at all.
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+ */
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+ function extractResponseBody(err) {
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+ let cursor = err;
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+ for (let i = 0; i < MAX_CAUSE_HOPS && cursor; i++) {
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+ const e = cursor;
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+ if (typeof e.responseBody === "string" && e.responseBody.trim() !== "")
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+ return e.responseBody;
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+ cursor = e.cause;
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+ }
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+ return undefined;
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+ }
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  /** Does any link of the `cause` chain look like a transport-level failure? */
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  function looksLikeConnectionError(err) {
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  let cursor = err;
@@ -21,11 +21,10 @@ import { type ExecuteAnalysisDeps, type ExecuteAnalysisInput, type ExecuteAnalys
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  import { type SandboxStepDeps, type SandboxStepInput, type SandboxStepResult } from "../workflows/sandbox-step.js";
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  import { type ExecuteTargetAssessmentDeps, type ExecuteTargetAssessmentInput, type ExecuteTargetAssessmentResult } from "../workflows/execute-target-assessment.js";
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  import { type DataProfileDeps, type DataProfileWorkflowInput } from "../tasks/data-profile.js";
24
- import { type EphemeralDeps, type EphemeralResult, type EphemeralWorkflowInput } from "../execution/ephemeral-runner.js";
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  /** Registered child sandbox-step callable the parent's child dispatch closes over. */
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  export type SandboxStepCallable = (input: SandboxStepInput) => Promise<SandboxStepResult>;
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  /**
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- * Deps bundles for the five durable workflows. `executeAnalysis` is a builder
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+ * Deps bundles for the durable workflows. `executeAnalysis` is a builder
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  * because its `sandboxStepCallable` is the registered sandbox-step callable,
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  * which does not exist until registration runs inside `assembleCoreRuntime`.
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  */
@@ -34,7 +33,6 @@ export interface CoreWorkflowDeps {
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  readonly buildExecuteAnalysis: (sandboxStep: SandboxStepCallable) => ExecuteAnalysisDeps;
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  readonly executeTargetAssessment: ExecuteTargetAssessmentDeps;
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  readonly dataProfile: DataProfileDeps;
37
- readonly ephemeral: Omit<EphemeralDeps, "resourcePolicy">;
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  }
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  /** The registered, callable workflow handles. */
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  export interface RegisteredWorkflows {
@@ -42,22 +40,19 @@ export interface RegisteredWorkflows {
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  readonly sandboxStep: SandboxStepCallable;
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  readonly executeTargetAssessment: (input: ExecuteTargetAssessmentInput) => Promise<ExecuteTargetAssessmentResult>;
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  readonly dataProfile: (input: DataProfileWorkflowInput) => Promise<void>;
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- readonly ephemeral: (input: EphemeralWorkflowInput) => Promise<EphemeralResult>;
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  }
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  /**
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- * Conversation-agent deps minus the two workflow callables and the resource
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+ * Conversation-agent deps minus the workflow callable and the resource
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  * policy — `assembleCoreRuntime` supplies those itself so a caller cannot wire
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  * a stale callable or a policy that diverges from the one the workflows see.
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  */
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- export type ConversationAssemblyDeps = Omit<ConversationAgentDeps, "executeAnalysisWorkflow" | "ephemeralWorkflow" | "resourcePolicy">;
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+ export type ConversationAssemblyDeps = Omit<ConversationAgentDeps, "executeAnalysisWorkflow" | "resourcePolicy">;
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  export interface CoreRuntimeDeps {
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  readonly conversation: ConversationAssemblyDeps;
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  readonly workflows: CoreWorkflowDeps;
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  /**
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- * Host resource policy — per-step ceilings, machine budget, ephemeral
58
- * sizing. One supply point: assembly distributes it to the planner tools,
59
- * `execute_plan` (budget snapshot into workflow input), and the ephemeral
60
- * runner. Absent, every consumer keeps its legacy behavior.
54
+ * Host resource policy — per-step ceilings and machine budget. One supply
55
+ * point for planner/routing guidance and workflow-input budget snapshots.
61
56
  */
62
57
  readonly resourcePolicy?: ResourcePolicy;
63
58
  }
@@ -19,18 +19,15 @@ import { registerExecuteAnalysis } from "../workflows/execute-analysis.js";
19
19
  import { registerSandboxStep } from "../workflows/sandbox-step.js";
20
20
  import { registerExecuteTargetAssessment, } from "../workflows/execute-target-assessment.js";
21
21
  import { registerDataProfileWorkflow } from "../tasks/data-profile.js";
22
- import { registerEphemeralWorkflow } from "../execution/ephemeral-runner.js";
23
22
  export function assembleCoreRuntime(deps) {
24
23
  const { conversation, workflows: wf, resourcePolicy } = deps;
25
24
  const sandboxStep = registerSandboxStep(wf.sandboxStep);
26
25
  const executeAnalysis = registerExecuteAnalysis(wf.buildExecuteAnalysis(sandboxStep));
27
26
  const executeTargetAssessment = registerExecuteTargetAssessment(wf.executeTargetAssessment);
28
27
  const dataProfile = registerDataProfileWorkflow(wf.dataProfile);
29
- const ephemeral = registerEphemeralWorkflow({ ...wf.ephemeral, resourcePolicy });
30
28
  const conversationAgent = createConversationAgent({
31
29
  ...conversation,
32
30
  executeAnalysisWorkflow: executeAnalysis,
33
- ephemeralWorkflow: ephemeral,
34
31
  resourcePolicy,
35
32
  });
36
33
  return {
@@ -40,7 +37,6 @@ export function assembleCoreRuntime(deps) {
40
37
  sandboxStep,
41
38
  executeTargetAssessment,
42
39
  dataProfile,
43
- ephemeral,
44
40
  },
45
41
  };
46
42
  }
@@ -22,7 +22,7 @@
22
22
  * builds the conversation agent (register-before-launch invariant).
23
23
  * 6. `beforeLaunch()` — embedder hook for host-specific pre-launch work that
24
24
  * must attach before DBOS launch re-emits events (scheduled sweeps, an
25
- * ephemeral-workflow reap, an agent-switch install). Runs after registration
25
+ * legacy-workflow reap, an agent-switch install). Runs after registration
26
26
  * so it may close over the registered callables.
27
27
  * 7. `launchDbos(...)` — the last registration-dependent step.
28
28
  *
@@ -49,7 +49,7 @@ export interface BootHarnessDeps {
49
49
  readonly logger: Logger;
50
50
  /**
51
51
  * Host-specific work that must run AFTER workflow registration and BEFORE
52
- * DBOS launch (scheduled sweeps, ephemeral reap, agent-switch install). The
52
+ * DBOS launch (scheduled sweeps, legacy-row reap, agent-switch install). The
53
53
  * booted runtime is not returned until after launch, so this hook captures
54
54
  * whatever it needs from the embedder's own composition root.
55
55
  */
@@ -22,7 +22,7 @@
22
22
  * builds the conversation agent (register-before-launch invariant).
23
23
  * 6. `beforeLaunch()` — embedder hook for host-specific pre-launch work that
24
24
  * must attach before DBOS launch re-emits events (scheduled sweeps, an
25
- * ephemeral-workflow reap, an agent-switch install). Runs after registration
25
+ * legacy-workflow reap, an agent-switch install). Runs after registration
26
26
  * so it may close over the registered callables.
27
27
  * 7. `launchDbos(...)` — the last registration-dependent step.
28
28
  *
@@ -67,11 +67,10 @@ export declare function shutdownDbos({ logger: injected }: {
67
67
  logger: Logger;
68
68
  }): Promise<void>;
69
69
  /**
70
- * Cancel any `ephemeral:`-prefixed PENDING workflow this executor owns —
71
- * called BEFORE `launchDbos`, whose recovery would otherwise re-dispatch them.
72
- *
73
- * Ephemeral runs are turn-scoped: a run whose pod died mid-flight has no live
74
- * awaiter and must never re-execute. DBOS has no "zero recovery" knob, and
70
+ * Cancel any legacy `ephemeral:`-prefixed PENDING workflow this executor owns
71
+ * before `launchDbos`, whose recovery would otherwise re-dispatch rows created
72
+ * by older releases. No current workflow creates this prefix. DBOS has no
73
+ * "zero recovery" knob, and
75
74
  * `launch()` starts recovery itself, so there is no post-launch window to
76
75
  * cancel from — the only race-free point is a direct system-DB UPDATE before
77
76
  * launch. A CANCELLED row is excluded from the recovery query (which selects
@@ -109,11 +109,10 @@ export async function shutdownDbos({ logger: injected }) {
109
109
  }
110
110
  }
111
111
  /**
112
- * Cancel any `ephemeral:`-prefixed PENDING workflow this executor owns —
113
- * called BEFORE `launchDbos`, whose recovery would otherwise re-dispatch them.
114
- *
115
- * Ephemeral runs are turn-scoped: a run whose pod died mid-flight has no live
116
- * awaiter and must never re-execute. DBOS has no "zero recovery" knob, and
112
+ * Cancel any legacy `ephemeral:`-prefixed PENDING workflow this executor owns
113
+ * before `launchDbos`, whose recovery would otherwise re-dispatch rows created
114
+ * by older releases. No current workflow creates this prefix. DBOS has no
115
+ * "zero recovery" knob, and
117
116
  * `launch()` starts recovery itself, so there is no post-launch window to
118
117
  * cancel from — the only race-free point is a direct system-DB UPDATE before
119
118
  * launch. A CANCELLED row is excluded from the recovery query (which selects
@@ -134,7 +133,7 @@ export async function sweepEphemeralWorkflows({ pool, logger: injectedLogger, ex
134
133
  values: [Date.now(), executorID],
135
134
  });
136
135
  if (rowCount && rowCount > 0) {
137
- logger.info("swept orphaned ephemeral workflows", { executorID, swept: rowCount });
136
+ logger.info("swept legacy ephemeral workflow rows", { executorID, swept: rowCount });
138
137
  }
139
138
  }
140
139
  catch (err) {
@@ -142,7 +141,7 @@ export async function sweepEphemeralWorkflows({ pool, logger: injectedLogger, ex
142
141
  if (err && typeof err === "object" && "code" in err && err.code === "42P01") {
143
142
  return;
144
143
  }
145
- logger.error("ephemeral sweep failed", { executorID, ...logger.errorFields(err) });
144
+ logger.error("legacy ephemeral-row sweep failed", { executorID, ...logger.errorFields(err) });
146
145
  }
147
146
  }
148
147
  /** Snapshot of DBOS lifecycle state — read by the readiness probe. */
@@ -1,5 +1,6 @@
1
1
  /**
2
- * Per-pod Postgres pool sizing — the single source of truth.
2
+ * Per-pod Postgres pool sizing and acquisition bounds — the single source of
3
+ * truth.
3
4
  *
4
5
  * Cortex runs two pools per pod against the same cluster (see the postgres-storage-backend spec): the
5
6
  * application pool (`lib/storage.ts::createPool()`) and the DBOS system-DB
@@ -21,5 +22,18 @@ export declare const DEFAULT_APP_POOL_SIZE = 12;
21
22
  * overlap during DBOS recovery, replication / monitoring users.
22
23
  */
23
24
  export declare const SAFETY_MARGIN = 5;
25
+ /**
26
+ * How long a caller may wait for a connection from the app pool before the
27
+ * acquisition fails.
28
+ *
29
+ * The driver waits forever by default, which leaves a caller on a saturated
30
+ * pool with no failure mode at all — only an indefinite hang, indistinguishable
31
+ * from work still in progress and therefore able to stall the caller's own
32
+ * in-flight guard permanently. A bound turns that silent stall into a surfaced
33
+ * error the caller can degrade on. 30s is long enough that a healthy pool under
34
+ * burst never trips it, and short enough that a wedged caller surfaces well
35
+ * inside a human's patience.
36
+ */
37
+ export declare const APP_POOL_ACQUIRE_TIMEOUT_MS = 30000;
24
38
  /** Resolve the app pool size from the optional `DB_POOL_MAX` override. */
25
39
  export declare function resolveAppPoolSize(dbPoolMax: string | undefined): number;
@@ -1,5 +1,6 @@
1
1
  /**
2
- * Per-pod Postgres pool sizing — the single source of truth.
2
+ * Per-pod Postgres pool sizing and acquisition bounds — the single source of
3
+ * truth.
3
4
  *
4
5
  * Cortex runs two pools per pod against the same cluster (see the postgres-storage-backend spec): the
5
6
  * application pool (`lib/storage.ts::createPool()`) and the DBOS system-DB
@@ -21,6 +22,19 @@ export const DEFAULT_APP_POOL_SIZE = 12;
21
22
  * overlap during DBOS recovery, replication / monitoring users.
22
23
  */
23
24
  export const SAFETY_MARGIN = 5;
25
+ /**
26
+ * How long a caller may wait for a connection from the app pool before the
27
+ * acquisition fails.
28
+ *
29
+ * The driver waits forever by default, which leaves a caller on a saturated
30
+ * pool with no failure mode at all — only an indefinite hang, indistinguishable
31
+ * from work still in progress and therefore able to stall the caller's own
32
+ * in-flight guard permanently. A bound turns that silent stall into a surfaced
33
+ * error the caller can degrade on. 30s is long enough that a healthy pool under
34
+ * burst never trips it, and short enough that a wedged caller surfaces well
35
+ * inside a human's patience.
36
+ */
37
+ export const APP_POOL_ACQUIRE_TIMEOUT_MS = 30_000;
24
38
  /** Resolve the app pool size from the optional `DB_POOL_MAX` override. */
25
39
  export function resolveAppPoolSize(dbPoolMax) {
26
40
  if (dbPoolMax === undefined || dbPoolMax === "")
@@ -24,7 +24,7 @@ export interface MountPlanCoords {
24
24
  /**
25
25
  * Enforced read-only: emit no read-write step mount. The container sees only
26
26
  * the read-only analysis tree (plus container-local `/tmp`). Used by the
27
- * ephemeral executor, whose prompt promises it physically cannot write files.
27
+ * a generic read-only agent that must not mutate analysis files.
28
28
  */
29
29
  readOnly?: boolean;
30
30
  }
@@ -32,7 +32,7 @@
32
32
  * step and throws directly, so the seam forwards its `Promise<void>` as-is.)
33
33
  * Workflow consumers (`sandbox-step.ts`) already wrap each seam call in
34
34
  * `DBOS.runStep`, so the re-thrown error records the step as failed;
35
- * non-workflow consumers (`reaper`, `watchdog`, `ephemeral-runner`,
35
+ * non-workflow consumers (`reaper`, `watchdog`,
36
36
  * `data-profile`, `run-exec`) already handle a thrown failure. They are
37
37
  * untouched by this wave.
38
38
  */
@@ -32,7 +32,7 @@
32
32
  * step and throws directly, so the seam forwards its `Promise<void>` as-is.)
33
33
  * Workflow consumers (`sandbox-step.ts`) already wrap each seam call in
34
34
  * `DBOS.runStep`, so the re-thrown error records the step as failed;
35
- * non-workflow consumers (`reaper`, `watchdog`, `ephemeral-runner`,
35
+ * non-workflow consumers (`reaper`, `watchdog`,
36
36
  * `data-profile`, `run-exec`) already handle a thrown failure. They are
37
37
  * untouched by this wave.
38
38
  */
@@ -1,10 +1,23 @@
1
1
  /**
2
2
  * Pure translation between the agent-loop / sandbox event stream and the
3
3
  * typed per-step parts the frontend renders. No DBOS, no per-run state — just the
4
- * label mapping, the file-tree delta extraction/fold, and the chat-data-part
5
- * narrowing the `sandbox-step` workflow body composes into its emitters.
4
+ * reconciliation-id construction, the label mapping, the file-tree delta
5
+ * extraction/fold, and the chat-data-part narrowing a workflow body composes
6
+ * into its emitters.
6
7
  */
7
8
  import type { ChatDataPart, EmitFn } from "../loop/types.js";
9
+ /**
10
+ * Stable reconciliation id for a step's reconciling parts
11
+ * (`data-step-activity`, `data-step-file-tree`). One id per (runId, stepId)
12
+ * so the run-stream fold collapses every phase transition latest-wins onto
13
+ * a single frame. The client keys these by `stepId`, but the server fold
14
+ * keys by part `id`, so the id MUST be unique per step within the run.
15
+ *
16
+ * Every producer of these parts mints its ids here: the id is a
17
+ * reconciliation contract, and the fold collapses correctly only while all
18
+ * producers construct it identically.
19
+ */
20
+ export declare function stepPartId(kind: string, runId: string, stepId: string): string;
8
21
  export declare function activityForTool(name: string, input?: unknown): string;
9
22
  /** On-change working-tree delta the sandbox executor posts per exec (paths
10
23
  * only; the executor skips directories). */
@@ -1,9 +1,24 @@
1
1
  /**
2
2
  * Pure translation between the agent-loop / sandbox event stream and the
3
3
  * typed per-step parts the frontend renders. No DBOS, no per-run state — just the
4
- * label mapping, the file-tree delta extraction/fold, and the chat-data-part
5
- * narrowing the `sandbox-step` workflow body composes into its emitters.
4
+ * reconciliation-id construction, the label mapping, the file-tree delta
5
+ * extraction/fold, and the chat-data-part narrowing a workflow body composes
6
+ * into its emitters.
6
7
  */
8
+ /**
9
+ * Stable reconciliation id for a step's reconciling parts
10
+ * (`data-step-activity`, `data-step-file-tree`). One id per (runId, stepId)
11
+ * so the run-stream fold collapses every phase transition latest-wins onto
12
+ * a single frame. The client keys these by `stepId`, but the server fold
13
+ * keys by part `id`, so the id MUST be unique per step within the run.
14
+ *
15
+ * Every producer of these parts mints its ids here: the id is a
16
+ * reconciliation contract, and the fold collapses correctly only while all
17
+ * producers construct it identically.
18
+ */
19
+ export function stepPartId(kind, runId, stepId) {
20
+ return `${kind}-${runId}-${stepId}`;
21
+ }
7
22
  /** Friendly live-activity label per sandbox tool id. Falls back to the raw
8
23
  * tool name so a newly added tool still reads sensibly. */
9
24
  const TOOL_ACTIVITY = {
@@ -241,7 +241,7 @@ export interface CreateSandboxMeta {
241
241
  * a sandbox with none. */
242
242
  resources: ResourceSpec;
243
243
  /** Enforced read-only: provision with no read-write step mount, only the
244
- * read-only analysis tree. Used by the ephemeral executor. */
244
+ * read-only analysis tree for generic read-only agents. */
245
245
  readOnly?: boolean;
246
246
  }
247
247
  /**
@@ -22,7 +22,7 @@ export interface ValidatePlanOptions {
22
22
  * Host per-step resource ceilings. When present, a step whose declared
23
23
  * `resources` exceed them is an error — the planner gets actionable
24
24
  * feedback at plan time instead of a silent clamp at sandbox creation.
25
- * The plan-generation path passes this; `execute_plan` deliberately does
25
+ * The plan-generation path passes this; `execute_analysis` plan mode deliberately does
26
26
  * not, so stored plans that predate the policy keep running (the
27
27
  * sandbox-creation clamp remains their backstop).
28
28
  */
@@ -7,8 +7,8 @@
7
7
  import { z } from "zod";
8
8
  /**
9
9
  * A step of an analysis plan. `PlanStepSchema` (schemas/plan-schemas.ts) narrows
10
- * this into the planner's output contract and emits it as the `validate_plan` /
11
- * `submit_plan` arg schema — so each field's meaning belongs in `.describe()`,
10
+ * this into the planner's output contract and emits it as the `submit_plan`
11
+ * arg schema — so each field's meaning belongs in `.describe()`,
12
12
  * not in a comment the model never sees.
13
13
  */
14
14
  export declare const AnalysisStepSchema: z.ZodObject<{
@@ -8,8 +8,8 @@ import { z } from "zod";
8
8
  // ── Plan structures ─────────────────────────────────────────────────
9
9
  /**
10
10
  * A step of an analysis plan. `PlanStepSchema` (schemas/plan-schemas.ts) narrows
11
- * this into the planner's output contract and emits it as the `validate_plan` /
12
- * `submit_plan` arg schema — so each field's meaning belongs in `.describe()`,
11
+ * this into the planner's output contract and emits it as the `submit_plan`
12
+ * arg schema — so each field's meaning belongs in `.describe()`,
13
13
  * not in a comment the model never sees.
14
14
  */
15
15
  export const AnalysisStepSchema = z.object({
@@ -101,6 +101,13 @@ export interface DataProfileStatus {
101
101
  startedAt: string | null;
102
102
  completedAt: string | null;
103
103
  result: DataProfileResult | null;
104
+ /**
105
+ * The DBOS workflow id of the profile attempt that owns this row — the durable
106
+ * event stream a consumer subscribes to for this profile's activity. `null` means
107
+ * this profile's stream is not addressable (see
108
+ * {@link recordDataProfileWorkflowId}).
109
+ */
110
+ workflowId: string | null;
104
111
  seedInputFileIds: string[] | null;
105
112
  }
106
113
  /**
@@ -117,14 +124,59 @@ export interface DataProfileStatus {
117
124
  * unseeded — neither is an error, both stay in the ok channel.
118
125
  */
119
126
  export declare function tryStartDataProfile(pool: Querier, analysisId: string): ResultAsync<boolean, DbError>;
120
- /** Claim a `failed` row back into `running` (the deliberate-retry route). Carries {@link SEEDED}. */
127
+ /**
128
+ * Claim a `failed` row back into `running` (the deliberate-retry route). Carries {@link SEEDED}.
129
+ *
130
+ * Clears `data_profile_workflow_id`, because the claim IS the moment a new attempt takes the row
131
+ * and the prior attempt's workflow is finished. Left in place it would leave the row `running`
132
+ * while naming a stream that has already drained, so a consumer would subscribe and observe
133
+ * nothing without knowing why; NULL says "not addressable yet", which is exactly true until the
134
+ * new body records its own id (see {@link recordDataProfileWorkflowId}).
135
+ */
121
136
  export declare function tryRetryDataProfile(pool: Querier, analysisId: string): ResultAsync<boolean, DbError>;
122
137
  /**
123
138
  * Claim a `completed` row back into `running` (the re-profile route). `data_profile_result`
124
139
  * is deliberately preserved so a consumer can keep serving the prior profile while the new
125
140
  * one runs. Carries {@link SEEDED}.
141
+ *
142
+ * `data_profile_workflow_id` is NOT preserved alongside it, and the asymmetry is the point: the
143
+ * result is CONTENT that stays valid until replaced, while the id is a POINTER to a live stream
144
+ * whose workflow is now finished. Keeping it would leave the row `running` while naming a drained
145
+ * stream — see {@link tryRetryDataProfile} for the same reasoning.
126
146
  */
127
147
  export declare function tryRerunDataProfile(pool: Querier, analysisId: string): ResultAsync<boolean, DbError>;
148
+ /**
149
+ * Record the DBOS workflow id of the attempt that owns a claimed-`running` row, so a
150
+ * consumer resolves which durable event stream carries this profile's activity from the
151
+ * ledger row alone — no durability-engine query, no id reconstructed from the workflow-id
152
+ * string format. The workflow BODY calls this, never the trigger: the claim CAS runs
153
+ * before the workflow id is minted, so only the body can report the id of the attempt
154
+ * that actually started.
155
+ *
156
+ * `AND data_profile_status = 'running'` buys exactly one thing: a write that lands late
157
+ * cannot stamp a row that has already settled, which would otherwise point a consumer at
158
+ * a workflow for a profile that is already finished. What it does NOT buy is
159
+ * disambiguation between two attempts that each believe they are the running one — the
160
+ * stale-expiry claim admits precisely that, since a row whose `data_profile_started_at`
161
+ * has aged past the timeout can be claimed by a second attempt while the first body is
162
+ * still alive but has not completed its first step, and that first step then overwrites
163
+ * the second's id.
164
+ *
165
+ * That residue is deliberately left open rather than closed. Its worst outcome is already
166
+ * a specified-normal state: a consumer subscribed to a superseded workflow reads a stream
167
+ * that has already drained, so it observes no activity — indistinguishable from "running,
168
+ * nothing reported yet". A missing activity line for one profile is acceptable; a wrong
169
+ * one would not be. And closing it costs more than it buys: either the three claim
170
+ * functions widen their `Result<boolean>` returns to carry the id — their callers branch
171
+ * on truthiness (`if (!retried)`), so an object return makes every such branch
172
+ * always-taken, a silent behaviour change in the embedder's recovery path — or the
173
+ * embedder mints the workflow ids, putting a harness-internal construction in a
174
+ * consumer's hands.
175
+ *
176
+ * `ok(true)` when this call stamped the row; `ok(false)` when the CAS refused it — a
177
+ * normal in-band outcome, not an error.
178
+ */
179
+ export declare function recordDataProfileWorkflowId(pool: Querier, analysisId: string, workflowId: string): ResultAsync<boolean, DbError>;
128
180
  /**
129
181
  * Stamp a claimed-`running` row `completed` and record its result — a terminal
130
182
  * write CAS'd on `data_profile_status = 'running'`.