@inflexa-ai/harness 0.28.1 → 0.30.0

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 (168) hide show
  1. package/dist/agents/conversation-agent.js +7 -4
  2. package/dist/agents/report-session-agent.js +1 -1
  3. package/dist/agents/sandbox/data-profiler.js +0 -1
  4. package/dist/agents/sandbox/immune-profiling-agent.js +3 -1
  5. package/dist/agents/sandbox/network-agent.js +0 -1
  6. package/dist/agents/sandbox/types.d.ts +1 -1
  7. package/dist/agents/sandbox/types.js +1 -1
  8. package/dist/app/data-profile-orientation.d.ts +52 -27
  9. package/dist/app/data-profile-orientation.js +331 -92
  10. package/dist/app/data-profile-view.d.ts +70 -0
  11. package/dist/app/data-profile-view.js +123 -0
  12. package/dist/app/synthesize-run.js +1 -1
  13. package/dist/config/resource-limits.d.ts +1 -1
  14. package/dist/config/resource-limits.js +1 -1
  15. package/dist/contracts/data-profile.d.ts +276 -25
  16. package/dist/contracts/index.d.ts +3 -1
  17. package/dist/contracts/index.js +1 -0
  18. package/dist/contracts/profile-vocabulary.d.ts +103 -0
  19. package/dist/contracts/profile-vocabulary.js +449 -0
  20. package/dist/contracts/schemas/chat-parts.d.ts +12 -12
  21. package/dist/contracts/severity.d.ts +2 -2
  22. package/dist/contracts/target-dossier.d.ts +91 -91
  23. package/dist/data/safety-panel-schema.d.ts +4 -4
  24. package/dist/execution/input-signature.d.ts +16 -3
  25. package/dist/execution/input-signature.js +0 -0
  26. package/dist/execution/post-step-pipeline.js +1 -1
  27. package/dist/execution/staged-input.d.ts +4 -4
  28. package/dist/index.d.ts +7 -2
  29. package/dist/index.js +14 -0
  30. package/dist/input-scan/clustering.d.ts +63 -0
  31. package/dist/input-scan/clustering.js +208 -0
  32. package/dist/input-scan/companions.d.ts +30 -0
  33. package/dist/input-scan/companions.js +138 -0
  34. package/dist/input-scan/decoder/container_readout.py +171 -0
  35. package/dist/input-scan/detect-sets.d.ts +24 -0
  36. package/dist/input-scan/detect-sets.js +279 -0
  37. package/dist/input-scan/enrich.d.ts +62 -19
  38. package/dist/input-scan/enrich.js +132 -187
  39. package/dist/input-scan/formats.d.ts +13 -5
  40. package/dist/input-scan/formats.js +13 -5
  41. package/dist/input-scan/index.d.ts +10 -4
  42. package/dist/input-scan/index.js +7 -4
  43. package/dist/input-scan/markers.d.ts +21 -0
  44. package/dist/input-scan/markers.js +89 -0
  45. package/dist/input-scan/menu.d.ts +127 -0
  46. package/dist/input-scan/menu.js +0 -0
  47. package/dist/input-scan/quarantine.d.ts +17 -0
  48. package/dist/input-scan/quarantine.js +69 -0
  49. package/dist/input-scan/readout-budget.d.ts +32 -0
  50. package/dist/input-scan/readout-budget.js +61 -0
  51. package/dist/input-scan/readout.d.ts +33 -0
  52. package/dist/input-scan/readout.js +336 -0
  53. package/dist/input-scan/scan.d.ts +5 -4
  54. package/dist/input-scan/scan.js +5 -5
  55. package/dist/input-scan/set-types.d.ts +209 -0
  56. package/dist/input-scan/set-types.js +15 -0
  57. package/dist/input-scan/templates.d.ts +93 -0
  58. package/dist/input-scan/templates.js +369 -0
  59. package/dist/input-scan/tokens.d.ts +94 -0
  60. package/dist/input-scan/tokens.js +267 -0
  61. package/dist/input-scan/tuning.d.ts +55 -0
  62. package/dist/input-scan/tuning.js +55 -0
  63. package/dist/input-scan/types.d.ts +2 -2
  64. package/dist/loop/run-agent.d.ts +13 -1
  65. package/dist/loop/run-agent.js +2 -1
  66. package/dist/prompts/SOUL.d.ts +2 -2
  67. package/dist/prompts/SOUL.js +17 -1
  68. package/dist/prompts/conversation.d.ts +1 -1
  69. package/dist/prompts/conversation.js +45 -71
  70. package/dist/prompts/planner.js +57 -10
  71. package/dist/prompts/report-session.d.ts +1 -1
  72. package/dist/prompts/report-session.js +3 -2
  73. package/dist/prompts/sandbox/bulk-transcriptomics-agent.d.ts +1 -1
  74. package/dist/prompts/sandbox/bulk-transcriptomics-agent.js +3 -1
  75. package/dist/prompts/sandbox/data-profiler.d.ts +10 -1
  76. package/dist/prompts/sandbox/data-profiler.js +197 -53
  77. package/dist/prompts/sandbox/dna-methylation-agent.d.ts +1 -1
  78. package/dist/prompts/sandbox/dna-methylation-agent.js +18 -12
  79. package/dist/prompts/sandbox/immune-profiling-agent.d.ts +1 -1
  80. package/dist/prompts/sandbox/immune-profiling-agent.js +6 -2
  81. package/dist/prompts/sandbox/metabolomics-agent.d.ts +1 -1
  82. package/dist/prompts/sandbox/metabolomics-agent.js +8 -4
  83. package/dist/prompts/sandbox/microbiome-agent.d.ts +1 -1
  84. package/dist/prompts/sandbox/microbiome-agent.js +12 -6
  85. package/dist/prompts/sandbox/network-agent.d.ts +1 -1
  86. package/dist/prompts/sandbox/network-agent.js +9 -6
  87. package/dist/prompts/sandbox/spatial-omics-agent.d.ts +1 -1
  88. package/dist/prompts/sandbox/spatial-omics-agent.js +4 -2
  89. package/dist/prompts/sandbox-standards.d.ts +1 -1
  90. package/dist/prompts/sandbox-standards.js +10 -7
  91. package/dist/providers/ai-sdk.js +34 -1
  92. package/dist/providers/reasoning.d.ts +65 -0
  93. package/dist/providers/reasoning.js +81 -0
  94. package/dist/providers/types.d.ts +14 -0
  95. package/dist/schemas/data-profile-schemas.d.ts +947 -84
  96. package/dist/schemas/data-profile-schemas.js +300 -115
  97. package/dist/schemas/run-synthesis.d.ts +4 -4
  98. package/dist/state/data-profile.d.ts +1 -1
  99. package/dist/state/index.d.ts +1 -1
  100. package/dist/state/vector-store.d.ts +13 -0
  101. package/dist/state/vector-store.js +8 -0
  102. package/dist/tasks/data-profile-absorb.d.ts +78 -0
  103. package/dist/tasks/data-profile-absorb.js +285 -0
  104. package/dist/tasks/data-profile-index.d.ts +34 -25
  105. package/dist/tasks/data-profile-index.js +160 -59
  106. package/dist/tasks/data-profile-resolve.d.ts +72 -0
  107. package/dist/tasks/data-profile-resolve.js +639 -0
  108. package/dist/tasks/data-profile.d.ts +16 -5
  109. package/dist/tasks/data-profile.js +270 -131
  110. package/dist/tools/bio/chembl.d.ts +1 -1
  111. package/dist/tools/bio/chembl.js +15 -10
  112. package/dist/tools/bio/comptox.js +5 -1
  113. package/dist/tools/bio/drug-gene-interactions.js +5 -2
  114. package/dist/tools/bio/gene-disease-evidence.d.ts +19 -9
  115. package/dist/tools/bio/gene-disease-evidence.js +78 -22
  116. package/dist/tools/bio/gene-preclinical-profile.d.ts +33 -13
  117. package/dist/tools/bio/gene-preclinical-profile.js +63 -22
  118. package/dist/tools/bio/lookup-annotation.d.ts +1 -0
  119. package/dist/tools/bio/lookup-annotation.js +28 -10
  120. package/dist/tools/bio/opentargets.d.ts +10 -2
  121. package/dist/tools/bio/opentargets.js +42 -13
  122. package/dist/tools/bio/pubchem.js +5 -2
  123. package/dist/tools/bio/pubmed.js +9 -3
  124. package/dist/tools/bio/search-clinical-trials.d.ts +25 -25
  125. package/dist/tools/bio/search-clinical-trials.js +56 -18
  126. package/dist/tools/bio/search-faers.d.ts +26 -6
  127. package/dist/tools/bio/search-faers.js +70 -18
  128. package/dist/tools/bio/search-gene.d.ts +19 -3
  129. package/dist/tools/bio/search-gene.js +69 -12
  130. package/dist/tools/bio/search-geo-datasets.js +4 -1
  131. package/dist/tools/bio/search-interactions.js +6 -2
  132. package/dist/tools/bio/target-safety.d.ts +2 -2
  133. package/dist/tools/bio/target-safety.js +3 -2
  134. package/dist/tools/lib/cbioportal-client.js +25 -6
  135. package/dist/tools/lib/chembl-client.d.ts +3 -1
  136. package/dist/tools/lib/chembl-client.js +6 -1
  137. package/dist/tools/lib/gwas-catalog-client.d.ts +7 -6
  138. package/dist/tools/lib/gwas-catalog-client.js +18 -6
  139. package/dist/tools/lib/openfda-client.d.ts +7 -5
  140. package/dist/tools/lib/openfda-client.js +17 -9
  141. package/dist/tools/lib/opentargets-client.d.ts +20 -0
  142. package/dist/tools/lib/opentargets-client.js +45 -0
  143. package/dist/tools/lib/pathway-client.d.ts +7 -0
  144. package/dist/tools/lib/pathway-client.js +68 -1
  145. package/dist/tools/research/context7-docs.js +3 -3
  146. package/dist/tools/research/generate-analogy-report.js +2 -2
  147. package/dist/tools/research/generate-plan.d.ts +3 -0
  148. package/dist/tools/research/generate-plan.js +64 -5
  149. package/dist/tools/research/inspect-data-profile.d.ts +48 -22
  150. package/dist/tools/research/inspect-data-profile.js +73 -54
  151. package/dist/tools/research/resolve-citation.js +8 -3
  152. package/dist/tools/research/search-arxiv.js +8 -3
  153. package/dist/tools/research/search-semantic-scholar.js +10 -4
  154. package/dist/tools/workspace/scan-inputs.d.ts +4 -4
  155. package/dist/tools/workspace/scan-inputs.js +13 -14
  156. package/dist/tools/workspace/workspace-search.d.ts +11 -2
  157. package/dist/tools/workspace/workspace-search.js +44 -16
  158. package/dist/workflows/sandbox-step.d.ts +6 -0
  159. package/dist/workflows/sandbox-step.js +31 -14
  160. package/dist/workflows/target-assessment/assemblers/safety.d.ts +1 -1
  161. package/dist/workflows/target-assessment/phase4-assemble.d.ts +38 -38
  162. package/dist/workflows/target-assessment/schemas.d.ts +12 -12
  163. package/dist/workflows/target-assessment/steps/phase2-aggregate.d.ts +6 -6
  164. package/dist/workflows/target-assessment/steps/phase3-aggregate.d.ts +6 -6
  165. package/dist/workflows/target-assessment/synthesis/index.d.ts +12 -12
  166. package/package.json +5 -3
  167. package/dist/input-scan/coverage.d.ts +0 -22
  168. package/dist/input-scan/coverage.js +0 -85
@@ -1,85 +0,0 @@
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- /**
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- * Profile coverage — how much of the scanned tree the agent's kinds actually describe.
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- *
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- * Measured against the SUBMITTED kinds, never against the scan's own shapes. Computed
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- * from the shapes it would report only whether the scan grouped its own observations,
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- * which is always yes; measured against the kinds it is a real check, and it is the
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- * check that was missing when a profile covering 49 of 3513 files read as complete and
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- * fresh.
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- *
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- * Deterministic by construction: matching declared patterns against a known file set
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- * requires no judgement, and a coverage figure a model self-reported would not be a
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- * check at all.
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- */
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- /** Unmatched paths carried on the snapshot, so a shortfall names examples rather than a bare count. */
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- const MAX_UNMATCHED_SAMPLE = 10;
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- /**
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- * Compile a kind's path pattern to a matcher.
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- *
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- * `**` crosses directory separators, `*` and `?` do not, and `<0>`-style placeholders —
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- * the syntax the manifest renders variable positions in, which an agent may reasonably
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- * copy — match one token. Everything else is literal.
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- */
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- function compilePattern(pattern) {
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- let out = "";
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- for (let i = 0; i < pattern.length; i++) {
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- const char = pattern[i];
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- if (char === "*") {
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- if (pattern[i + 1] === "*") {
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- out += ".*";
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- i++;
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- // `**/` should also match zero directories, so the slash is optional.
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- if (pattern[i + 1] === "/")
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- i++;
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- continue;
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- }
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- out += "[^/]*";
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- continue;
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- }
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- if (char === "?") {
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- out += "[^/]";
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- continue;
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- }
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- if (char === "<") {
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- const close = pattern.indexOf(">", i);
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- if (close > i) {
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- out += "[^/]*";
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- i = close;
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- continue;
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- }
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- }
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- out += char.replace(/[.+^${}()|[\]\\]/g, "\\$&");
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- }
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- return new RegExp(`^${out}$`);
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- }
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- function normalize(path) {
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- return path.replace(/^\.\//, "").replace(/^\/+/, "").replace(/\/+/g, "/");
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- }
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- /**
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- * Whether a path falls under a pattern. A pattern naming a directory covers everything
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- * beneath it — agents write `data/inputs/vcf` as often as `data/inputs/vcf/*.vcf.gz`,
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- * and reading the first as a zero-file kind would report a coverage failure that is an
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- * artefact of notation.
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- */
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- function matches(path, pattern, compiled) {
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- if (compiled.test(path))
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- return true;
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- const bare = pattern.replace(/\/+$/, "");
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- return bare.length > 0 && !/[*?<]/.test(bare) && path.startsWith(`${bare}/`);
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- }
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- /** Coverage of a scanned file set by a set of declared kind patterns. */
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- export function computeCoverage(paths, patterns) {
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- const compiled = patterns.map((pattern) => ({ pattern, regex: compilePattern(pattern) }));
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- const unmatchedSample = [];
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- let matched = 0;
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- for (const raw of paths) {
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- const path = normalize(raw);
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- if (compiled.some(({ pattern, regex }) => matches(path, pattern, regex))) {
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- matched++;
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- continue;
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- }
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- if (unmatchedSample.length < MAX_UNMATCHED_SAMPLE)
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- unmatchedSample.push(path);
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- }
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- return { matched, unmatched: paths.length - matched, total: paths.length, unmatchedSample };
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- }