@inflexa-ai/harness 0.35.8 → 0.36.1

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Files changed (198) hide show
  1. package/dist/auth/types.d.ts +5 -14
  2. package/dist/auth/types.js +3 -10
  3. package/dist/billing/usage-recorder.d.ts +1 -1
  4. package/dist/contracts/analogy-report.d.ts +1 -1
  5. package/dist/contracts/analogy-report.js +1 -1
  6. package/dist/contracts/chat-parts.d.ts +2 -3
  7. package/dist/contracts/index.d.ts +0 -4
  8. package/dist/contracts/index.js +0 -2
  9. package/dist/index.d.ts +0 -7
  10. package/dist/index.js +0 -21
  11. package/dist/lib/metrics.d.ts +1 -1
  12. package/dist/lib/otel-spans.d.ts +0 -2
  13. package/dist/lib/otel-spans.js +0 -2
  14. package/dist/loop/genai-spans.d.ts +14 -0
  15. package/dist/loop/genai-spans.js +35 -0
  16. package/dist/loop/run-agent.d.ts +1 -1
  17. package/dist/loop/run-agent.js +37 -4
  18. package/dist/runtime/assemble.d.ts +0 -3
  19. package/dist/runtime/assemble.js +0 -3
  20. package/dist/state/index.d.ts +0 -2
  21. package/dist/state/index.js +0 -1
  22. package/dist/state/init.js +1 -60
  23. package/dist/state/purge-analysis.d.ts +1 -2
  24. package/dist/state/purge-analysis.js +1 -2
  25. package/dist/tasks/regulatory-corpus-boot-refresh.js +1 -1
  26. package/dist/tools/bio/gene-preclinical-profile.d.ts +1 -3
  27. package/dist/tools/bio/gene-preclinical-profile.js +1 -3
  28. package/dist/tools/lib/chembl-client.d.ts +1 -4
  29. package/dist/tools/lib/chembl-client.js +1 -4
  30. package/dist/tools/lib/clinical-benchmarks-client.d.ts +1 -1
  31. package/dist/tools/lib/clinical-benchmarks-client.js +1 -1
  32. package/dist/tools/lib/clinical-trials-client.d.ts +0 -3
  33. package/dist/tools/lib/clinical-trials-client.js +0 -3
  34. package/dist/tools/lib/identifier-resolver.d.ts +5 -7
  35. package/dist/tools/lib/identifier-resolver.js +5 -7
  36. package/dist/tools/lib/iuphar-client.d.ts +1 -3
  37. package/dist/tools/lib/iuphar-client.js +1 -3
  38. package/dist/tools/lib/opentargets-client.d.ts +1 -1
  39. package/dist/tools/lib/opentargets-client.js +1 -1
  40. package/dist/tools/lib/protein-family-normalize.d.ts +5 -7
  41. package/dist/tools/lib/protein-family-normalize.js +5 -7
  42. package/dist/tools/lib/uniprot-client.d.ts +0 -7
  43. package/dist/tools/lib/uniprot-client.js +2 -9
  44. package/package.json +1 -1
  45. package/dist/contracts/target-assessment-row.d.ts +0 -85
  46. package/dist/contracts/target-assessment-row.js +0 -37
  47. package/dist/contracts/target-dossier.d.ts +0 -12423
  48. package/dist/contracts/target-dossier.js +0 -1282
  49. package/dist/prompts/target-assessment/briefs/executive-recommendation.d.ts +0 -1
  50. package/dist/prompts/target-assessment/briefs/executive-recommendation.js +0 -85
  51. package/dist/prompts/target-assessment/briefs/index.d.ts +0 -4
  52. package/dist/prompts/target-assessment/briefs/index.js +0 -4
  53. package/dist/prompts/target-assessment/briefs/liability-bullets.d.ts +0 -1
  54. package/dist/prompts/target-assessment/briefs/liability-bullets.js +0 -114
  55. package/dist/prompts/target-assessment/briefs/target-organ-liabilities.d.ts +0 -1
  56. package/dist/prompts/target-assessment/briefs/target-organ-liabilities.js +0 -37
  57. package/dist/prompts/target-assessment/briefs/translational-commentary.d.ts +0 -1
  58. package/dist/prompts/target-assessment/briefs/translational-commentary.js +0 -23
  59. package/dist/prompts/target-assessment/drugs-in-class.d.ts +0 -1
  60. package/dist/prompts/target-assessment/drugs-in-class.js +0 -29
  61. package/dist/prompts/target-assessment/investigation/adversarial-critique.d.ts +0 -1
  62. package/dist/prompts/target-assessment/investigation/adversarial-critique.js +0 -67
  63. package/dist/prompts/target-assessment/investigation/claim-reverification.d.ts +0 -1
  64. package/dist/prompts/target-assessment/investigation/claim-reverification.js +0 -49
  65. package/dist/prompts/target-assessment/investigation/index.d.ts +0 -3
  66. package/dist/prompts/target-assessment/investigation/index.js +0 -3
  67. package/dist/prompts/target-assessment/investigation/mechanism-proposal.d.ts +0 -1
  68. package/dist/prompts/target-assessment/investigation/mechanism-proposal.js +0 -49
  69. package/dist/prompts/target-assessment/modulator-triage.d.ts +0 -1
  70. package/dist/prompts/target-assessment/modulator-triage.js +0 -31
  71. package/dist/prompts/target-assessment/off-target-annotator.d.ts +0 -1
  72. package/dist/prompts/target-assessment/off-target-annotator.js +0 -28
  73. package/dist/prompts/target-assessment/tox-voice/core.d.ts +0 -1
  74. package/dist/prompts/target-assessment/tox-voice/core.js +0 -74
  75. package/dist/prompts/target-assessment/tox-voice/critique.d.ts +0 -7
  76. package/dist/prompts/target-assessment/tox-voice/critique.js +0 -109
  77. package/dist/prompts/target-assessment/tox-voice/exemplars.d.ts +0 -8
  78. package/dist/prompts/target-assessment/tox-voice/exemplars.js +0 -24
  79. package/dist/prompts/target-assessment/tox-voice/index.d.ts +0 -4
  80. package/dist/prompts/target-assessment/tox-voice/index.js +0 -4
  81. package/dist/prompts/target-assessment/tox-voice/vocabulary.d.ts +0 -18
  82. package/dist/prompts/target-assessment/tox-voice/vocabulary.js +0 -61
  83. package/dist/state/target-assessments.d.ts +0 -68
  84. package/dist/state/target-assessments.js +0 -222
  85. package/dist/workflows/execute-target-assessment.d.ts +0 -118
  86. package/dist/workflows/execute-target-assessment.js +0 -631
  87. package/dist/workflows/target-assessment/assemblers/index.d.ts +0 -5
  88. package/dist/workflows/target-assessment/assemblers/index.js +0 -4
  89. package/dist/workflows/target-assessment/assemblers/literature.d.ts +0 -281
  90. package/dist/workflows/target-assessment/assemblers/literature.js +0 -971
  91. package/dist/workflows/target-assessment/assemblers/orchestrator.d.ts +0 -118
  92. package/dist/workflows/target-assessment/assemblers/orchestrator.js +0 -945
  93. package/dist/workflows/target-assessment/assemblers/safety.d.ts +0 -374
  94. package/dist/workflows/target-assessment/assemblers/safety.js +0 -1068
  95. package/dist/workflows/target-assessment/assemblers/trials.d.ts +0 -30
  96. package/dist/workflows/target-assessment/assemblers/trials.js +0 -75
  97. package/dist/workflows/target-assessment/collectors/index.d.ts +0 -114
  98. package/dist/workflows/target-assessment/collectors/index.js +0 -538
  99. package/dist/workflows/target-assessment/coverage.d.ts +0 -97
  100. package/dist/workflows/target-assessment/coverage.js +0 -86
  101. package/dist/workflows/target-assessment/decisions/index.d.ts +0 -86
  102. package/dist/workflows/target-assessment/decisions/index.js +0 -127
  103. package/dist/workflows/target-assessment/fanout/index.d.ts +0 -32
  104. package/dist/workflows/target-assessment/fanout/index.js +0 -156
  105. package/dist/workflows/target-assessment/investigation/index.d.ts +0 -97
  106. package/dist/workflows/target-assessment/investigation/index.js +0 -419
  107. package/dist/workflows/target-assessment/lib/approval-precedents.d.ts +0 -73
  108. package/dist/workflows/target-assessment/lib/approval-precedents.js +0 -185
  109. package/dist/workflows/target-assessment/lib/citation-validator.d.ts +0 -46
  110. package/dist/workflows/target-assessment/lib/citation-validator.js +0 -316
  111. package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.d.ts +0 -65
  112. package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.js +0 -174
  113. package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.d.ts +0 -44
  114. package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.js +0 -152
  115. package/dist/workflows/target-assessment/lib/compute-derived.d.ts +0 -20
  116. package/dist/workflows/target-assessment/lib/compute-derived.js +0 -261
  117. package/dist/workflows/target-assessment/lib/compute-selectivity.d.ts +0 -15
  118. package/dist/workflows/target-assessment/lib/compute-selectivity.js +0 -18
  119. package/dist/workflows/target-assessment/lib/dedup-modulators.d.ts +0 -37
  120. package/dist/workflows/target-assessment/lib/dedup-modulators.js +0 -157
  121. package/dist/workflows/target-assessment/lib/evidence-conflict-detector.d.ts +0 -17
  122. package/dist/workflows/target-assessment/lib/evidence-conflict-detector.js +0 -100
  123. package/dist/workflows/target-assessment/lib/expression-constants.d.ts +0 -21
  124. package/dist/workflows/target-assessment/lib/expression-constants.js +0 -21
  125. package/dist/workflows/target-assessment/lib/family-complex-supplement.d.ts +0 -20
  126. package/dist/workflows/target-assessment/lib/family-complex-supplement.js +0 -36
  127. package/dist/workflows/target-assessment/lib/fda-label-safety.d.ts +0 -72
  128. package/dist/workflows/target-assessment/lib/fda-label-safety.js +0 -166
  129. package/dist/workflows/target-assessment/lib/heterodimer-filter.d.ts +0 -30
  130. package/dist/workflows/target-assessment/lib/heterodimer-filter.js +0 -44
  131. package/dist/workflows/target-assessment/lib/hpo-organ-map.d.ts +0 -34
  132. package/dist/workflows/target-assessment/lib/hpo-organ-map.js +0 -63
  133. package/dist/workflows/target-assessment/lib/impc-organ-map.d.ts +0 -19
  134. package/dist/workflows/target-assessment/lib/impc-organ-map.js +0 -39
  135. package/dist/workflows/target-assessment/lib/intended-polypharm-filter.d.ts +0 -4
  136. package/dist/workflows/target-assessment/lib/intended-polypharm-filter.js +0 -24
  137. package/dist/workflows/target-assessment/lib/llm-step.d.ts +0 -80
  138. package/dist/workflows/target-assessment/lib/llm-step.js +0 -101
  139. package/dist/workflows/target-assessment/lib/meddra-organ-map.d.ts +0 -40
  140. package/dist/workflows/target-assessment/lib/meddra-organ-map.js +0 -138
  141. package/dist/workflows/target-assessment/lib/recommendation-quality-gates.d.ts +0 -17
  142. package/dist/workflows/target-assessment/lib/recommendation-quality-gates.js +0 -99
  143. package/dist/workflows/target-assessment/lib/recommendation-sanitizer.d.ts +0 -2
  144. package/dist/workflows/target-assessment/lib/recommendation-sanitizer.js +0 -51
  145. package/dist/workflows/target-assessment/lib/regulatory-actions.d.ts +0 -25
  146. package/dist/workflows/target-assessment/lib/regulatory-actions.js +0 -176
  147. package/dist/workflows/target-assessment/lib/safety-corroboration.d.ts +0 -44
  148. package/dist/workflows/target-assessment/lib/safety-corroboration.js +0 -273
  149. package/dist/workflows/target-assessment/lib/structured-llm.d.ts +0 -61
  150. package/dist/workflows/target-assessment/lib/structured-llm.js +0 -102
  151. package/dist/workflows/target-assessment/lib/target-identity-filter.d.ts +0 -59
  152. package/dist/workflows/target-assessment/lib/target-identity-filter.js +0 -95
  153. package/dist/workflows/target-assessment/lib/therapeutic-programs.d.ts +0 -20
  154. package/dist/workflows/target-assessment/lib/therapeutic-programs.js +0 -68
  155. package/dist/workflows/target-assessment/metrics.d.ts +0 -16
  156. package/dist/workflows/target-assessment/metrics.js +0 -30
  157. package/dist/workflows/target-assessment/phase4-assemble.d.ts +0 -3182
  158. package/dist/workflows/target-assessment/phase4-assemble.js +0 -39
  159. package/dist/workflows/target-assessment/phase5-persist.d.ts +0 -59
  160. package/dist/workflows/target-assessment/phase5-persist.js +0 -349
  161. package/dist/workflows/target-assessment/progress-stream.d.ts +0 -75
  162. package/dist/workflows/target-assessment/progress-stream.js +0 -110
  163. package/dist/workflows/target-assessment/progress.d.ts +0 -39
  164. package/dist/workflows/target-assessment/progress.js +0 -77
  165. package/dist/workflows/target-assessment/schemas.d.ts +0 -970
  166. package/dist/workflows/target-assessment/schemas.js +0 -318
  167. package/dist/workflows/target-assessment/steps/collectors/pathways.d.ts +0 -15
  168. package/dist/workflows/target-assessment/steps/collectors/pathways.js +0 -58
  169. package/dist/workflows/target-assessment/steps/fanout/aes-for-one-class-drug-step.d.ts +0 -34
  170. package/dist/workflows/target-assessment/steps/fanout/aes-for-one-class-drug-step.js +0 -31
  171. package/dist/workflows/target-assessment/steps/fanout/aes-for-one-trial-step.d.ts +0 -57
  172. package/dist/workflows/target-assessment/steps/fanout/aes-for-one-trial-step.js +0 -54
  173. package/dist/workflows/target-assessment/steps/fanout/faers-for-one-modulator-step.d.ts +0 -35
  174. package/dist/workflows/target-assessment/steps/fanout/faers-for-one-modulator-step.js +0 -32
  175. package/dist/workflows/target-assessment/steps/fanout/index.d.ts +0 -14
  176. package/dist/workflows/target-assessment/steps/fanout/index.js +0 -10
  177. package/dist/workflows/target-assessment/steps/fanout/polypharm-for-one-modulator-step.d.ts +0 -29
  178. package/dist/workflows/target-assessment/steps/fanout/polypharm-for-one-modulator-step.js +0 -29
  179. package/dist/workflows/target-assessment/steps/phase2-aggregate.d.ts +0 -657
  180. package/dist/workflows/target-assessment/steps/phase2-aggregate.js +0 -34
  181. package/dist/workflows/target-assessment/steps/phase3-aggregate.d.ts +0 -806
  182. package/dist/workflows/target-assessment/steps/phase3-aggregate.js +0 -16
  183. package/dist/workflows/target-assessment/steps/synthesis/diagnostics.d.ts +0 -28
  184. package/dist/workflows/target-assessment/steps/synthesis/diagnostics.js +0 -27
  185. package/dist/workflows/target-assessment/sub-workflows/index.d.ts +0 -15
  186. package/dist/workflows/target-assessment/sub-workflows/index.js +0 -11
  187. package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.d.ts +0 -41
  188. package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.js +0 -12
  189. package/dist/workflows/target-assessment/sub-workflows/per-modulator-faers.d.ts +0 -41
  190. package/dist/workflows/target-assessment/sub-workflows/per-modulator-faers.js +0 -12
  191. package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.d.ts +0 -37
  192. package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.js +0 -12
  193. package/dist/workflows/target-assessment/sub-workflows/per-trial-aes.d.ts +0 -66
  194. package/dist/workflows/target-assessment/sub-workflows/per-trial-aes.js +0 -12
  195. package/dist/workflows/target-assessment/synthesis/index.d.ts +0 -607
  196. package/dist/workflows/target-assessment/synthesis/index.js +0 -354
  197. package/dist/workflows/target-assessment/synthesis-probes.d.ts +0 -56
  198. package/dist/workflows/target-assessment/synthesis-probes.js +0 -320
@@ -1,77 +0,0 @@
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- /**
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- * Progress emission for the target-assessment DBOS workflow.
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- *
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- * Emits a typed `data-target-assessment-progress` part via
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- * `DBOS.writeStream("progress", part)` and updates `cortex_target_assessments.progress`.
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- * Both writes happen inside a `DBOS.runStep` so a recovered workflow does not
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- * duplicate the event.
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- *
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- * Wire shape: `TargetAssessmentProgressEventSchema` in
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- * `harness/src/contracts/target-dossier.ts`. The SSE route reads via
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- * `DBOS.readStream(workflowId, "progress")` and folds-on-read by `phase`.
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- */
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- import { DBOS } from "@dbos-inc/dbos-sdk";
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- import { describeDbError } from "../../lib/db-result.js";
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- import { updateProgress } from "../../state/target-assessments.js";
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- /** DBOS stream key the SSE route reads via `DBOS.readStream(wfId, "progress")`. */
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- export const TA_PROGRESS_STREAM_KEY = "progress";
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- export const PROGRESS_PERCENTS = {
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- resolving: 5,
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- collecting: 25,
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- deciding: 55,
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- fanning_out: 70,
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- assembling: 85,
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- synthesizing: 90,
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- completed: 100,
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- failed: 100,
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- suspended: 100,
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- };
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- export const PROGRESS_MESSAGES = {
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- resolving: "Resolving target identity",
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- collecting: "Collecting evidence from 14 data sources",
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- deciding: "Triaging modulators and classifying trials",
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- fanning_out: "Building per-modulator and per-trial detail",
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- assembling: "Assembling dossier sections",
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- synthesizing: "Drafting safety and translational commentary",
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- completed: "Completed",
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- failed: "Failed",
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- suspended: "Suspended — insufficient funds",
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- };
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- /**
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- * Emit one progress transition. MUST be called from inside the workflow
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- * body — the `DBOS.runStep` wrapper makes it replay-safe (DBOS persists
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- * the stream-write offset under `(workflowID, function_id)`; replay
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- * returns cached without re-writing the part).
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- *
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- * Best-effort: a DB or stream failure logs and continues — progress
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- * emission MUST NOT block the workflow.
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- */
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- export async function emitProgress(pool, logger, assessmentId, phase) {
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- const log = logger.named("ta-progress").with({ assessmentId, phase });
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- const message = PROGRESS_MESSAGES[phase];
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- const percent = PROGRESS_PERCENTS[phase];
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- await DBOS.runStep(async () => {
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- const part = {
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- type: "data-target-assessment-progress",
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- payload: { phase, message, percent, at: new Date().toISOString() },
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- };
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- try {
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- await DBOS.writeStream(TA_PROGRESS_STREAM_KEY, part);
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- }
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- catch (err) {
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- log.warn("writeStream failed", log.errorFields(err));
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- }
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- // The "suspended" phase is owned by the terminal handler
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- // (`markAssessmentSuspended` already set status + progress text). A
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- // row write here would either race or overwrite the suspended status.
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- if (phase !== "suspended") {
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- const rowStatus = phase === "completed" ? "completed" : phase === "failed" ? "failed" : "running";
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- // Best-effort: log a failed row write and continue — progress
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- // emission MUST NOT block the workflow. `updateProgress` returns
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- // its DB failure as an `Err`, so handle both branches here.
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- (await updateProgress(pool, assessmentId, message, rowStatus)).match(() => { }, (error) => {
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- log.warn("updateProgress failed", { err: describeDbError(error) });
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- });
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- }
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- }, { name: `ta-progress:${phase}` });
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- }