helixlife-expert-cli 0.1.0

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 (523) hide show
  1. package/README.md +159 -0
  2. package/cli/bin/helixlife-expert.js +3 -0
  3. package/cli/dist/core/api/client.d.ts +31 -0
  4. package/cli/dist/core/api/client.d.ts.map +1 -0
  5. package/cli/dist/core/api/client.js +183 -0
  6. package/cli/dist/core/api/client.js.map +1 -0
  7. package/cli/dist/core/api/http.d.ts +3 -0
  8. package/cli/dist/core/api/http.d.ts.map +1 -0
  9. package/cli/dist/core/api/http.js +22 -0
  10. package/cli/dist/core/api/http.js.map +1 -0
  11. package/cli/dist/core/api/response.d.ts +48 -0
  12. package/cli/dist/core/api/response.d.ts.map +1 -0
  13. package/cli/dist/core/api/response.js +84 -0
  14. package/cli/dist/core/api/response.js.map +1 -0
  15. package/cli/dist/core/api/sse.d.ts +6 -0
  16. package/cli/dist/core/api/sse.d.ts.map +1 -0
  17. package/cli/dist/core/api/sse.js +60 -0
  18. package/cli/dist/core/api/sse.js.map +1 -0
  19. package/cli/dist/core/auth/index.d.ts +35 -0
  20. package/cli/dist/core/auth/index.d.ts.map +1 -0
  21. package/cli/dist/core/auth/index.js +150 -0
  22. package/cli/dist/core/auth/index.js.map +1 -0
  23. package/cli/dist/core/env-config.d.ts +16 -0
  24. package/cli/dist/core/env-config.d.ts.map +1 -0
  25. package/cli/dist/core/env-config.js +80 -0
  26. package/cli/dist/core/env-config.js.map +1 -0
  27. package/cli/dist/core/errors.d.ts +20 -0
  28. package/cli/dist/core/errors.d.ts.map +1 -0
  29. package/cli/dist/core/errors.js +28 -0
  30. package/cli/dist/core/errors.js.map +1 -0
  31. package/cli/dist/core/index.d.ts +16 -0
  32. package/cli/dist/core/index.d.ts.map +1 -0
  33. package/cli/dist/core/index.js +16 -0
  34. package/cli/dist/core/index.js.map +1 -0
  35. package/cli/dist/core/interactive.d.ts +18 -0
  36. package/cli/dist/core/interactive.d.ts.map +1 -0
  37. package/cli/dist/core/interactive.js +74 -0
  38. package/cli/dist/core/interactive.js.map +1 -0
  39. package/cli/dist/core/output/index.d.ts +29 -0
  40. package/cli/dist/core/output/index.d.ts.map +1 -0
  41. package/cli/dist/core/output/index.js +153 -0
  42. package/cli/dist/core/output/index.js.map +1 -0
  43. package/cli/dist/core/parse.d.ts +9 -0
  44. package/cli/dist/core/parse.d.ts.map +1 -0
  45. package/cli/dist/core/parse.js +31 -0
  46. package/cli/dist/core/parse.js.map +1 -0
  47. package/cli/dist/core/paths.d.ts +21 -0
  48. package/cli/dist/core/paths.d.ts.map +1 -0
  49. package/cli/dist/core/paths.js +65 -0
  50. package/cli/dist/core/paths.js.map +1 -0
  51. package/cli/dist/core/sse-utils.d.ts +49 -0
  52. package/cli/dist/core/sse-utils.d.ts.map +1 -0
  53. package/cli/dist/core/sse-utils.js +181 -0
  54. package/cli/dist/core/sse-utils.js.map +1 -0
  55. package/cli/dist/core/terminal.d.ts +2 -0
  56. package/cli/dist/core/terminal.d.ts.map +1 -0
  57. package/cli/dist/core/terminal.js +6 -0
  58. package/cli/dist/core/terminal.js.map +1 -0
  59. package/cli/dist/core/token/index.d.ts +5 -0
  60. package/cli/dist/core/token/index.d.ts.map +1 -0
  61. package/cli/dist/core/token/index.js +26 -0
  62. package/cli/dist/core/token/index.js.map +1 -0
  63. package/cli/dist/core/types/config.d.ts +8 -0
  64. package/cli/dist/core/types/config.d.ts.map +1 -0
  65. package/cli/dist/core/types/config.js +30 -0
  66. package/cli/dist/core/types/config.js.map +1 -0
  67. package/cli/dist/core/version.d.ts +2 -0
  68. package/cli/dist/core/version.d.ts.map +1 -0
  69. package/cli/dist/core/version.js +10 -0
  70. package/cli/dist/core/version.js.map +1 -0
  71. package/cli/dist/index.d.ts +2 -0
  72. package/cli/dist/index.d.ts.map +1 -0
  73. package/cli/dist/index.js +23 -0
  74. package/cli/dist/index.js.map +1 -0
  75. package/cli/dist/modules/analysis/constants.d.ts +3 -0
  76. package/cli/dist/modules/analysis/constants.d.ts.map +1 -0
  77. package/cli/dist/modules/analysis/constants.js +3 -0
  78. package/cli/dist/modules/analysis/constants.js.map +1 -0
  79. package/cli/dist/modules/analysis/index.d.ts +3 -0
  80. package/cli/dist/modules/analysis/index.d.ts.map +1 -0
  81. package/cli/dist/modules/analysis/index.js +23 -0
  82. package/cli/dist/modules/analysis/index.js.map +1 -0
  83. package/cli/dist/modules/auth/index.d.ts +3 -0
  84. package/cli/dist/modules/auth/index.d.ts.map +1 -0
  85. package/cli/dist/modules/auth/index.js +76 -0
  86. package/cli/dist/modules/auth/index.js.map +1 -0
  87. package/cli/dist/modules/expert-scaffold.d.ts +27 -0
  88. package/cli/dist/modules/expert-scaffold.d.ts.map +1 -0
  89. package/cli/dist/modules/expert-scaffold.js +25 -0
  90. package/cli/dist/modules/expert-scaffold.js.map +1 -0
  91. package/cli/dist/modules/fund/clinical/apps.d.ts +19 -0
  92. package/cli/dist/modules/fund/clinical/apps.d.ts.map +1 -0
  93. package/cli/dist/modules/fund/clinical/apps.js +14 -0
  94. package/cli/dist/modules/fund/clinical/apps.js.map +1 -0
  95. package/cli/dist/modules/fund/clinical/command-utils.d.ts +4 -0
  96. package/cli/dist/modules/fund/clinical/command-utils.d.ts.map +1 -0
  97. package/cli/dist/modules/fund/clinical/command-utils.js +40 -0
  98. package/cli/dist/modules/fund/clinical/command-utils.js.map +1 -0
  99. package/cli/dist/modules/fund/clinical/commands/article-create.d.ts +9 -0
  100. package/cli/dist/modules/fund/clinical/commands/article-create.d.ts.map +1 -0
  101. package/cli/dist/modules/fund/clinical/commands/article-create.js +99 -0
  102. package/cli/dist/modules/fund/clinical/commands/article-create.js.map +1 -0
  103. package/cli/dist/modules/fund/clinical/commands/article-download.d.ts +30 -0
  104. package/cli/dist/modules/fund/clinical/commands/article-download.d.ts.map +1 -0
  105. package/cli/dist/modules/fund/clinical/commands/article-download.js +153 -0
  106. package/cli/dist/modules/fund/clinical/commands/article-download.js.map +1 -0
  107. package/cli/dist/modules/fund/clinical/commands/four-elements-create.d.ts +7 -0
  108. package/cli/dist/modules/fund/clinical/commands/four-elements-create.d.ts.map +1 -0
  109. package/cli/dist/modules/fund/clinical/commands/four-elements-create.js +81 -0
  110. package/cli/dist/modules/fund/clinical/commands/four-elements-create.js.map +1 -0
  111. package/cli/dist/modules/fund/clinical/commands/four-elements-precheck.d.ts +7 -0
  112. package/cli/dist/modules/fund/clinical/commands/four-elements-precheck.d.ts.map +1 -0
  113. package/cli/dist/modules/fund/clinical/commands/four-elements-precheck.js +76 -0
  114. package/cli/dist/modules/fund/clinical/commands/four-elements-precheck.js.map +1 -0
  115. package/cli/dist/modules/fund/clinical/commands/four-elements-update.d.ts +16 -0
  116. package/cli/dist/modules/fund/clinical/commands/four-elements-update.d.ts.map +1 -0
  117. package/cli/dist/modules/fund/clinical/commands/four-elements-update.js +108 -0
  118. package/cli/dist/modules/fund/clinical/commands/four-elements-update.js.map +1 -0
  119. package/cli/dist/modules/fund/clinical/commands/sample-size.d.ts +14 -0
  120. package/cli/dist/modules/fund/clinical/commands/sample-size.d.ts.map +1 -0
  121. package/cli/dist/modules/fund/clinical/commands/sample-size.js +164 -0
  122. package/cli/dist/modules/fund/clinical/commands/sample-size.js.map +1 -0
  123. package/cli/dist/modules/fund/clinical/commands/topic-evaluation-create.d.ts +25 -0
  124. package/cli/dist/modules/fund/clinical/commands/topic-evaluation-create.d.ts.map +1 -0
  125. package/cli/dist/modules/fund/clinical/commands/topic-evaluation-create.js +228 -0
  126. package/cli/dist/modules/fund/clinical/commands/topic-evaluation-create.js.map +1 -0
  127. package/cli/dist/modules/fund/clinical/commands/topic-evaluation-parameters.d.ts +45 -0
  128. package/cli/dist/modules/fund/clinical/commands/topic-evaluation-parameters.d.ts.map +1 -0
  129. package/cli/dist/modules/fund/clinical/commands/topic-evaluation-parameters.js +211 -0
  130. package/cli/dist/modules/fund/clinical/commands/topic-evaluation-parameters.js.map +1 -0
  131. package/cli/dist/modules/fund/clinical/constants.d.ts +85 -0
  132. package/cli/dist/modules/fund/clinical/constants.d.ts.map +1 -0
  133. package/cli/dist/modules/fund/clinical/constants.js +161 -0
  134. package/cli/dist/modules/fund/clinical/constants.js.map +1 -0
  135. package/cli/dist/modules/fund/clinical/form-rules.d.ts +56 -0
  136. package/cli/dist/modules/fund/clinical/form-rules.d.ts.map +1 -0
  137. package/cli/dist/modules/fund/clinical/form-rules.js +542 -0
  138. package/cli/dist/modules/fund/clinical/form-rules.js.map +1 -0
  139. package/cli/dist/modules/fund/clinical/four-elements.d.ts +46 -0
  140. package/cli/dist/modules/fund/clinical/four-elements.d.ts.map +1 -0
  141. package/cli/dist/modules/fund/clinical/four-elements.js +190 -0
  142. package/cli/dist/modules/fund/clinical/four-elements.js.map +1 -0
  143. package/cli/dist/modules/fund/clinical/index.d.ts +3 -0
  144. package/cli/dist/modules/fund/clinical/index.d.ts.map +1 -0
  145. package/cli/dist/modules/fund/clinical/index.js +176 -0
  146. package/cli/dist/modules/fund/clinical/index.js.map +1 -0
  147. package/cli/dist/modules/fund/clinical/parameters.d.ts +51 -0
  148. package/cli/dist/modules/fund/clinical/parameters.d.ts.map +1 -0
  149. package/cli/dist/modules/fund/clinical/parameters.js +145 -0
  150. package/cli/dist/modules/fund/clinical/parameters.js.map +1 -0
  151. package/cli/dist/modules/fund/clinical/sample-size.d.ts +130 -0
  152. package/cli/dist/modules/fund/clinical/sample-size.d.ts.map +1 -0
  153. package/cli/dist/modules/fund/clinical/sample-size.js +356 -0
  154. package/cli/dist/modules/fund/clinical/sample-size.js.map +1 -0
  155. package/cli/dist/modules/fund/clinical/session-cache.d.ts +25 -0
  156. package/cli/dist/modules/fund/clinical/session-cache.d.ts.map +1 -0
  157. package/cli/dist/modules/fund/clinical/session-cache.js +100 -0
  158. package/cli/dist/modules/fund/clinical/session-cache.js.map +1 -0
  159. package/cli/dist/modules/fund/clinical/sse-utils.d.ts +22 -0
  160. package/cli/dist/modules/fund/clinical/sse-utils.d.ts.map +1 -0
  161. package/cli/dist/modules/fund/clinical/sse-utils.js +80 -0
  162. package/cli/dist/modules/fund/clinical/sse-utils.js.map +1 -0
  163. package/cli/dist/modules/fund/constants.d.ts +3 -0
  164. package/cli/dist/modules/fund/constants.d.ts.map +1 -0
  165. package/cli/dist/modules/fund/constants.js +3 -0
  166. package/cli/dist/modules/fund/constants.js.map +1 -0
  167. package/cli/dist/modules/fund/index.d.ts +3 -0
  168. package/cli/dist/modules/fund/index.d.ts.map +1 -0
  169. package/cli/dist/modules/fund/index.js +28 -0
  170. package/cli/dist/modules/fund/index.js.map +1 -0
  171. package/cli/dist/modules/fund/nsfc/apps.d.ts +54 -0
  172. package/cli/dist/modules/fund/nsfc/apps.d.ts.map +1 -0
  173. package/cli/dist/modules/fund/nsfc/apps.js +76 -0
  174. package/cli/dist/modules/fund/nsfc/apps.js.map +1 -0
  175. package/cli/dist/modules/fund/nsfc/article-cache.d.ts +14 -0
  176. package/cli/dist/modules/fund/nsfc/article-cache.d.ts.map +1 -0
  177. package/cli/dist/modules/fund/nsfc/article-cache.js +79 -0
  178. package/cli/dist/modules/fund/nsfc/article-cache.js.map +1 -0
  179. package/cli/dist/modules/fund/nsfc/commands/article-create.d.ts +8 -0
  180. package/cli/dist/modules/fund/nsfc/commands/article-create.d.ts.map +1 -0
  181. package/cli/dist/modules/fund/nsfc/commands/article-create.js +108 -0
  182. package/cli/dist/modules/fund/nsfc/commands/article-create.js.map +1 -0
  183. package/cli/dist/modules/fund/nsfc/commands/article-download.d.ts +42 -0
  184. package/cli/dist/modules/fund/nsfc/commands/article-download.d.ts.map +1 -0
  185. package/cli/dist/modules/fund/nsfc/commands/article-download.js +189 -0
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  187. package/cli/dist/modules/fund/nsfc/commands/format-convert.d.ts +9 -0
  188. package/cli/dist/modules/fund/nsfc/commands/format-convert.d.ts.map +1 -0
  189. package/cli/dist/modules/fund/nsfc/commands/format-convert.js +98 -0
  190. package/cli/dist/modules/fund/nsfc/commands/format-convert.js.map +1 -0
  191. package/cli/dist/modules/fund/nsfc/commands/hypothesis-analyze.d.ts +12 -0
  192. package/cli/dist/modules/fund/nsfc/commands/hypothesis-analyze.d.ts.map +1 -0
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  194. package/cli/dist/modules/fund/nsfc/commands/hypothesis-analyze.js.map +1 -0
  195. package/cli/dist/modules/fund/nsfc/commands/hypothesis-create.d.ts +21 -0
  196. package/cli/dist/modules/fund/nsfc/commands/hypothesis-create.d.ts.map +1 -0
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  198. package/cli/dist/modules/fund/nsfc/commands/hypothesis-create.js.map +1 -0
  199. package/cli/dist/modules/fund/nsfc/commands/hypothesis-figure.d.ts +9 -0
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  202. package/cli/dist/modules/fund/nsfc/commands/hypothesis-figure.js.map +1 -0
  203. package/cli/dist/modules/fund/nsfc/commands/hypothesis-genes-select.d.ts +11 -0
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  207. package/cli/dist/modules/fund/nsfc/commands/hypothesis-pick.d.ts +11 -0
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  211. package/cli/dist/modules/fund/nsfc/commands/outline-confirm.d.ts +9 -0
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  219. package/cli/dist/modules/fund/nsfc/commands/research-path-confirm.d.ts +9 -0
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  223. package/cli/dist/modules/fund/nsfc/commands/tech-roadmap.d.ts +9 -0
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  227. package/cli/dist/modules/fund/nsfc/constants.d.ts +96 -0
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  231. package/cli/dist/modules/fund/nsfc/graph-render.d.ts +25 -0
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  235. package/cli/dist/modules/fund/nsfc/index.d.ts +4 -0
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  243. package/cli/dist/modules/fund/nsfc/parse-hypothesis.d.ts +76 -0
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  279. package/cli/dist/modules/fund/nsfc/validate.d.ts +30 -0
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  283. package/cli/dist/modules/literature/commands/workflow-list.d.ts +5 -0
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@@ -0,0 +1,351 @@
1
+ // Step2①:按 nextSubStep 跑首个分析工作流
2
+ import { readFile } from "node:fs/promises";
3
+ import { helixlifeError, helixlifeErrorCode, printOutput, createFormatLogger, resolveUserPath, } from "../../../../core/index.js";
4
+ import { wrapWorkbenchResult } from "../../../shared/result-wrapper.js";
5
+ import { buildNsfcExecuteBody, createNsfcOrder, extractNsfcOrderId, } from "../apps.js";
6
+ import { NSFC_APP_NAMES, NSFC_EXECUTE_API_PATH, NSFC_HYPOTHESIS_APP_IDS, NSFC_PROVINCE_PROGRAM, parseNsfcHasHypothesis, parseNsfcNextSubStep, resolveOutlineAppSuffix, resolvePickNoPriorAppId, resolveResearchPathAppId, } from "../constants.js";
7
+ import { articleContentToJsonArrayString, buildGeneSelectionOptions, buildHypothesisSelectionOptions, buildMissingInfoBlockSelectionOptions, buildNsfcV2GenePreResultsText, getResearchPathReportText, parseMissingInfoFromAnalysisResult, parseNsfcV2ArticleWorkflowResult, tryParseHypothesisList, } from "../parse-hypothesis.js";
8
+ import { saveNsfcSessionCache } from "../session-cache.js";
9
+ import { formatElapsedHint, streamNsfcWorkflow } from "../sse-utils.js";
10
+ function extractFileContent(inputs, key) {
11
+ const arr = inputs[key];
12
+ if (!Array.isArray(arr) || !arr[0])
13
+ return "";
14
+ const first = arr[0];
15
+ return String(first.content ?? "");
16
+ }
17
+ async function readJsonFile(path) {
18
+ const filePath = resolveUserPath(path);
19
+ try {
20
+ const raw = await readFile(filePath, "utf8");
21
+ const parsed = JSON.parse(raw);
22
+ if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) {
23
+ throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, `--inputs-file 须为 JSON 对象: ${path}`);
24
+ }
25
+ return parsed;
26
+ }
27
+ catch (error) {
28
+ if (error instanceof helixlifeError)
29
+ throw error;
30
+ throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, `无法读取 --inputs-file: ${path}`);
31
+ }
32
+ }
33
+ async function resolveQuery(options) {
34
+ if (options.query?.trim() && options.queryFile?.trim()) {
35
+ throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "--query 与 --query-file 互斥");
36
+ }
37
+ if (options.queryFile?.trim()) {
38
+ const p = resolveUserPath(options.queryFile);
39
+ try {
40
+ return (await readFile(p, "utf8")).trim();
41
+ }
42
+ catch {
43
+ throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, `无法读取 --query-file: ${options.queryFile}`);
44
+ }
45
+ }
46
+ return options.query?.trim() ?? "";
47
+ }
48
+ async function runWorkflow(params) {
49
+ const body = buildNsfcExecuteBody({
50
+ query: params.query,
51
+ inputs: params.inputs,
52
+ appId: params.appId,
53
+ appName: params.appName,
54
+ orderId: params.orderId,
55
+ end: false,
56
+ });
57
+ return streamNsfcWorkflow({
58
+ path: NSFC_EXECUTE_API_PATH,
59
+ body,
60
+ format: params.format,
61
+ startLabel: params.labels.start,
62
+ progressLabel: params.labels.progress,
63
+ finishLabel: params.labels.finish,
64
+ failureMessage: params.labels.fail,
65
+ emptyMessage: params.labels.empty,
66
+ allowEmptyText: params.allowEmptyText,
67
+ });
68
+ }
69
+ export async function runAnalyzeNsfcHypothesis(options) {
70
+ const format = options.format ?? "markdown";
71
+ const log = createFormatLogger(format);
72
+ if (!options.hasHypothesis || !options.nextSubStep) {
73
+ throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "hypothesis analyze 必须提供 --has-hypothesis 与 --next-sub-step(来自 Step1 _handoff)");
74
+ }
75
+ if (!options.inputsFile?.trim()) {
76
+ throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "hypothesis analyze 必须提供 --inputs-file(Step1 data.inputs JSON)");
77
+ }
78
+ const hasHypothesis = parseNsfcHasHypothesis(options.hasHypothesis);
79
+ const nextSubStep = parseNsfcNextSubStep(options.nextSubStep);
80
+ const inputs = await readJsonFile(options.inputsFile);
81
+ let query = await resolveQuery(options);
82
+ if (!query) {
83
+ query = String((hasHypothesis === "existing" ? inputs.text : inputs.input) ?? "").trim();
84
+ }
85
+ if (!query && nextSubStep !== "research_path") {
86
+ throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "缺少主文本 query(--query / --query-file 或 inputs.input/text)");
87
+ }
88
+ const projectLevel = String(inputs.projectLevel ?? "");
89
+ const outlineAppSuffix = resolveOutlineAppSuffix(hasHypothesis);
90
+ log("接口正在处理中,请耐心等待...");
91
+ const order = await createNsfcOrder({
92
+ index: 0,
93
+ count: 1,
94
+ query,
95
+ inputs,
96
+ parent_order_id: null,
97
+ });
98
+ const orderId = extractNsfcOrderId(order);
99
+ const baseCache = {
100
+ orderId,
101
+ query,
102
+ inputs,
103
+ hasHypothesis,
104
+ nextSubStep,
105
+ outlineAppSuffix,
106
+ };
107
+ // —— Path: background_genes ——
108
+ if (nextSubStep === "background_genes") {
109
+ const fileContent = extractFileContent(inputs, "file");
110
+ if (!fileContent) {
111
+ throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "background_genes 路径需要 inputs.file[0].content(Step1 上传解析结果)");
112
+ }
113
+ const stream = await runWorkflow({
114
+ orderId,
115
+ query,
116
+ inputs: {
117
+ List_Disease: query,
118
+ text: articleContentToJsonArrayString(fileContent),
119
+ },
120
+ appId: NSFC_HYPOTHESIS_APP_IDS.articleAnalysis,
121
+ appName: NSFC_APP_NAMES.generateHypothesis,
122
+ format,
123
+ allowEmptyText: true,
124
+ labels: {
125
+ start: "研究背景分析中…",
126
+ progress: "背景分析进行中",
127
+ finish: "背景分析完成",
128
+ fail: "研究背景分析失败,请稍后重试",
129
+ empty: "研究背景分析未返回有效结果",
130
+ },
131
+ });
132
+ const parsed = parseNsfcV2ArticleWorkflowResult(stream.outputs?.result);
133
+ if (!parsed) {
134
+ throw new helixlifeError(helixlifeErrorCode.INVALID_RESPONSE, "研究背景分析未返回有效候选基因结果");
135
+ }
136
+ await saveNsfcSessionCache({
137
+ ...baseCache,
138
+ backgroundReport: parsed.backgroundReport,
139
+ genes: parsed.genes,
140
+ workflowRunId: stream.workflowRunId,
141
+ });
142
+ const result = {
143
+ path: "background_genes",
144
+ backgroundReport: parsed.backgroundReport,
145
+ genes: parsed.genes.map((g) => ({
146
+ id: g.id,
147
+ gene: g.gene,
148
+ directions: g.directions,
149
+ mechanism: g.mechanism,
150
+ results: g.results,
151
+ })),
152
+ selectionOptions: buildGeneSelectionOptions(parsed.genes),
153
+ ready: true,
154
+ };
155
+ if (format === "json") {
156
+ printOutput(wrapWorkbenchResult(result, { step: "hypothesis-analyze", subType: "nsfc" }, {
157
+ orderId,
158
+ workflowRunId: stream.workflowRunId,
159
+ hasHypothesis,
160
+ nextSubStep,
161
+ outlineAppSuffix,
162
+ }), "json");
163
+ return;
164
+ }
165
+ console.log(`\n## 研究背景分析完成${formatElapsedHint(stream.elapsedTime)}\n`);
166
+ if (parsed.backgroundReport) {
167
+ console.log("### 研究背景\n");
168
+ console.log(parsed.backgroundReport.slice(0, 500) +
169
+ (parsed.backgroundReport.length > 500 ? "…\n" : "\n"));
170
+ }
171
+ console.log(`候选基因 ${parsed.genes.length} 个。请用选择器 N 选 1,再执行 hypothesis genes select。`);
172
+ console.log(`(内部 order 请用 --format=json 的 _handoff 串联,勿展示给用户)`);
173
+ return;
174
+ }
175
+ // —— Path: hypothesis_pick(无前期) ——
176
+ if (nextSubStep === "hypothesis_pick") {
177
+ const isProvince = projectLevel === "省部级";
178
+ const stream = await runWorkflow({
179
+ orderId,
180
+ query: "",
181
+ inputs: {
182
+ project: isProvince
183
+ ? NSFC_PROVINCE_PROGRAM
184
+ : String(inputs.project ?? ""),
185
+ theme: String(inputs.input ?? query),
186
+ value: String(inputs.value ?? ""),
187
+ },
188
+ appId: resolvePickNoPriorAppId(projectLevel),
189
+ appName: NSFC_APP_NAMES.generateHypothesis,
190
+ format,
191
+ allowEmptyText: true,
192
+ labels: {
193
+ start: "科学假说生成中…",
194
+ progress: "假说生成进行中",
195
+ finish: "假说生成完成",
196
+ fail: "科学假说生成失败,请稍后重试",
197
+ empty: "科学假说生成结果为空",
198
+ },
199
+ });
200
+ const hypotheses = tryParseHypothesisList(stream.outputs);
201
+ if (!hypotheses.length) {
202
+ throw new helixlifeError(helixlifeErrorCode.INVALID_RESPONSE, "科学假说生成结果为空,请稍后重试");
203
+ }
204
+ await saveNsfcSessionCache({
205
+ ...baseCache,
206
+ hypotheses,
207
+ workflowRunId: stream.workflowRunId,
208
+ });
209
+ const result = {
210
+ path: "hypothesis_pick",
211
+ hypotheses: hypotheses.map((h) => ({
212
+ id: h.id,
213
+ text: h.new_text || h.original_text,
214
+ })),
215
+ selectionOptions: buildHypothesisSelectionOptions(hypotheses),
216
+ ready: true,
217
+ };
218
+ if (format === "json") {
219
+ printOutput(wrapWorkbenchResult(result, { step: "hypothesis-analyze", subType: "nsfc" }, {
220
+ orderId,
221
+ workflowRunId: stream.workflowRunId,
222
+ hasHypothesis,
223
+ nextSubStep,
224
+ outlineAppSuffix,
225
+ }), "json");
226
+ return;
227
+ }
228
+ console.log(`\n## 科学假说候选${formatElapsedHint(stream.elapsedTime)}\n`);
229
+ hypotheses.forEach((h, i) => {
230
+ console.log(`### ${i + 1}\n${h.new_text || h.original_text}\n`);
231
+ });
232
+ console.log("请选择或自定义假说,再执行 hypothesis pick。");
233
+ return;
234
+ }
235
+ // —— Path: research_path ——
236
+ if (nextSubStep === "research_path") {
237
+ const disease = String(inputs.value ?? "").trim();
238
+ const hypothesisText = String(inputs.text ?? query).trim();
239
+ if (!disease || !hypothesisText) {
240
+ throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "research_path 需要 inputs.value(疾病)与 inputs.text(假说)");
241
+ }
242
+ let genePreResultsText = String(inputs.gene_pre_results_text ?? "").trim();
243
+ const file1Content = extractFileContent(inputs, "file1");
244
+ if (file1Content && !genePreResultsText) {
245
+ const attachStream = await runWorkflow({
246
+ orderId,
247
+ query: disease,
248
+ inputs: {
249
+ List_Disease: disease,
250
+ text: articleContentToJsonArrayString(file1Content),
251
+ },
252
+ appId: NSFC_HYPOTHESIS_APP_IDS.articleAnalysis,
253
+ appName: NSFC_APP_NAMES.generateHypothesis,
254
+ format,
255
+ allowEmptyText: true,
256
+ labels: {
257
+ start: "附件分析中…",
258
+ progress: "附件分析进行中",
259
+ finish: "附件分析完成",
260
+ fail: "附件分析失败,请稍后重试",
261
+ empty: "附件分析未返回有效结果",
262
+ },
263
+ });
264
+ const attachParsed = parseNsfcV2ArticleWorkflowResult(attachStream.outputs?.result);
265
+ genePreResultsText = buildNsfcV2GenePreResultsText(attachParsed?.genes ?? []);
266
+ }
267
+ const isProvince = projectLevel === "省部级";
268
+ const program = isProvince
269
+ ? NSFC_PROVINCE_PROGRAM
270
+ : String(inputs.program ?? inputs.project ?? "");
271
+ const stream = await runWorkflow({
272
+ orderId,
273
+ query: "",
274
+ inputs: {
275
+ List_Disease: disease,
276
+ text: articleContentToJsonArrayString(file1Content || ""),
277
+ program,
278
+ hypothesis: hypothesisText,
279
+ },
280
+ appId: resolveResearchPathAppId(projectLevel),
281
+ appName: NSFC_APP_NAMES.generateHypothesis,
282
+ format,
283
+ allowEmptyText: true,
284
+ labels: {
285
+ start: "研究思路分析中…",
286
+ progress: "研究路径分析进行中",
287
+ finish: "研究路径分析完成",
288
+ fail: "研究思路分析失败,请稍后重试",
289
+ empty: "研究思路分析未返回有效结果",
290
+ },
291
+ });
292
+ const analysisResult = stream.outputs?.result;
293
+ if (analysisResult === undefined || analysisResult === null) {
294
+ throw new helixlifeError(helixlifeErrorCode.INVALID_RESPONSE, "研究思路分析未返回有效结果");
295
+ }
296
+ const researchPathText = getResearchPathReportText(analysisResult);
297
+ const missingInfo = parseMissingInfoFromAnalysisResult(analysisResult);
298
+ const missingInfoEmpty = missingInfo.length === 0;
299
+ await saveNsfcSessionCache({
300
+ ...baseCache,
301
+ query: hypothesisText,
302
+ inputs: {
303
+ ...inputs,
304
+ gene_pre_results_text: genePreResultsText,
305
+ },
306
+ researchPathText,
307
+ researchPathResult: analysisResult,
308
+ missingInfo,
309
+ genePreResultsText,
310
+ workflowRunId: stream.workflowRunId,
311
+ });
312
+ const result = {
313
+ path: "research_path",
314
+ researchPath: researchPathText,
315
+ missingInfo: missingInfo.map((b) => ({
316
+ title: b.title,
317
+ options: b.select,
318
+ selectionOptions: buildMissingInfoBlockSelectionOptions(b),
319
+ })),
320
+ missingInfoEmpty,
321
+ ready: true,
322
+ };
323
+ if (format === "json") {
324
+ printOutput(wrapWorkbenchResult(result, { step: "hypothesis-analyze", subType: "nsfc" }, {
325
+ orderId,
326
+ workflowRunId: stream.workflowRunId,
327
+ hasHypothesis,
328
+ nextSubStep,
329
+ outlineAppSuffix,
330
+ missingInfoEmpty,
331
+ }), "json");
332
+ return;
333
+ }
334
+ console.log(`\n## 研究路径${formatElapsedHint(stream.elapsedTime)}\n`);
335
+ console.log(researchPathText || "(暂无相关数据)");
336
+ console.log("\n## 缺失信息\n");
337
+ if (missingInfoEmpty) {
338
+ console.log("暂无缺失信息。请立即执行 research-path confirm 生成提纲。");
339
+ }
340
+ else {
341
+ missingInfo.forEach((b, i) => {
342
+ console.log(`### ${i + 1}. ${b.title}`);
343
+ b.select.forEach((o, j) => console.log(` ${j + 1}) ${o}`));
344
+ });
345
+ console.log("\n请从当前缺失信息选项中至少选一项,再执行 research-path confirm(禁止自定义假说/忽略并继续)。");
346
+ }
347
+ return;
348
+ }
349
+ throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, `未支持的 nextSubStep: ${String(nextSubStep)}`);
350
+ }
351
+ //# sourceMappingURL=hypothesis-analyze.js.map
@@ -0,0 +1 @@
1
+ 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@@ -0,0 +1,21 @@
1
+ import { type OutputFormat } from "../../../../core/index.js";
2
+ export interface CreateNsfcHypothesisOptions {
3
+ hasHypothesis?: string;
4
+ projectLevel?: string;
5
+ project?: string;
6
+ priorResult?: string;
7
+ query?: string;
8
+ queryFile?: string;
9
+ disease?: string;
10
+ diseaseFile?: string;
11
+ attach?: string;
12
+ yes?: boolean;
13
+ format?: OutputFormat;
14
+ }
15
+ export interface NsfcHypothesisCreateResult {
16
+ query: string;
17
+ inputs: Record<string, unknown>;
18
+ ready: true;
19
+ }
20
+ export declare function runCreateNsfcHypothesis(options: CreateNsfcHypothesisOptions): Promise<void>;
21
+ //# sourceMappingURL=hypothesis-create.d.ts.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"hypothesis-create.d.ts","sourceRoot":"","sources":["../../../../../src/modules/fund/nsfc/commands/hypothesis-create.ts"],"names":[],"mappings":"AAEA,OAAO,EAML,KAAK,YAAY,EAClB,MAAM,2BAA2B,CAAC;AAqBnC,MAAM,WAAW,2BAA2B;IAC1C,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,MAAM,CAAC,EAAE,YAAY,CAAC;CACvB;AAED,MAAM,WAAW,0BAA0B;IACzC,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAChC,KAAK,EAAE,IAAI,CAAC;CACb;AAmFD,wBAAsB,uBAAuB,CAC3C,OAAO,EAAE,2BAA2B,GACnC,OAAO,CAAC,IAAI,CAAC,CAoKf"}
@@ -0,0 +1,197 @@
1
+ // Step1:生成假说 — 采集 + 校验 + 可选上传,不调假说工作流
2
+ import { readFile } from "node:fs/promises";
3
+ import { helixlifeError, helixlifeErrorCode, printOutput, createFormatLogger, resolveUserPath, } from "../../../../core/index.js";
4
+ import { wrapWorkbenchResult } from "../../../shared/result-wrapper.js";
5
+ import { parseNsfcHasHypothesis, parseNsfcPriorResult, parseNsfcProjectLevel, parseNsfcProjectType, } from "../constants.js";
6
+ import { promptNsfcHypothesisCreate } from "../prompt-hypothesis.js";
7
+ import { buildNsfcHandoff, buildNsfcHypothesisBody, } from "../request-body.js";
8
+ import { uploadNsfcAttach } from "../upload.js";
9
+ import { validateNsfcHypothesisCreate } from "../validate.js";
10
+ async function resolveTextOrFile(options) {
11
+ if (options.text?.trim() && options.file?.trim()) {
12
+ throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, `${options.label} 不能同时使用内联参数与 *-file,请二选一`);
13
+ }
14
+ if (options.file?.trim()) {
15
+ const filePath = resolveUserPath(options.file);
16
+ try {
17
+ return (await readFile(filePath, "utf8")).trim();
18
+ }
19
+ catch {
20
+ throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, `无法读取文件: ${options.file}`);
21
+ }
22
+ }
23
+ if (options.text?.trim()) {
24
+ return options.text.trim();
25
+ }
26
+ return undefined;
27
+ }
28
+ function parseOptionalFlags(options) {
29
+ return {
30
+ hasHypothesis: options.hasHypothesis
31
+ ? parseNsfcHasHypothesis(options.hasHypothesis)
32
+ : undefined,
33
+ projectLevel: options.projectLevel
34
+ ? parseNsfcProjectLevel(options.projectLevel)
35
+ : undefined,
36
+ project: options.project
37
+ ? parseNsfcProjectType(options.project)
38
+ : undefined,
39
+ priorResult: options.priorResult
40
+ ? parseNsfcPriorResult(options.priorResult)
41
+ : undefined,
42
+ };
43
+ }
44
+ function isIncomplete(params) {
45
+ if (!params.hasHypothesis || !params.projectLevel || !params.query?.trim()) {
46
+ return true;
47
+ }
48
+ if (params.projectLevel === "国家级" && !params.project) {
49
+ return true;
50
+ }
51
+ if (params.hasHypothesis === "blank" && !params.priorResult) {
52
+ return true;
53
+ }
54
+ if (params.hasHypothesis === "existing" && !params.disease?.trim()) {
55
+ return true;
56
+ }
57
+ if (params.hasHypothesis === "blank" &&
58
+ params.priorResult === "yes" &&
59
+ !params.attachPath?.trim()) {
60
+ return true;
61
+ }
62
+ return false;
63
+ }
64
+ export async function runCreateNsfcHypothesis(options) {
65
+ const format = options.format ?? "markdown";
66
+ const log = createFormatLogger(format);
67
+ const queryFromArgs = await resolveTextOrFile({
68
+ text: options.query,
69
+ file: options.queryFile,
70
+ label: "主文本(--query / --query-file)",
71
+ });
72
+ const diseaseFromArgs = await resolveTextOrFile({
73
+ text: options.disease,
74
+ file: options.diseaseFile,
75
+ label: "疾病名称(--disease / --disease-file)",
76
+ });
77
+ const parsed = parseOptionalFlags(options);
78
+ let hasHypothesis = parsed.hasHypothesis;
79
+ let projectLevel = parsed.projectLevel;
80
+ let project = parsed.project;
81
+ let priorResult = parsed.priorResult;
82
+ let query = queryFromArgs;
83
+ let disease = diseaseFromArgs;
84
+ let attachPath = options.attach?.trim() || undefined;
85
+ if (options.yes) {
86
+ if (isIncomplete({
87
+ hasHypothesis,
88
+ projectLevel,
89
+ project,
90
+ priorResult,
91
+ query,
92
+ disease,
93
+ attachPath,
94
+ })) {
95
+ // 用校验器给出明确缺项错误(缺枚举时先补齐最小报错)
96
+ if (!hasHypothesis || !projectLevel) {
97
+ throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "使用 -y/--yes 时必须提供 --has-hypothesis 与 --project-level,以及当前路径全部必填项");
98
+ }
99
+ validateNsfcHypothesisCreate({
100
+ hasHypothesis,
101
+ projectLevel,
102
+ project,
103
+ priorResult,
104
+ query,
105
+ disease,
106
+ attachPath,
107
+ });
108
+ }
109
+ }
110
+ else if (isIncomplete({
111
+ hasHypothesis,
112
+ projectLevel,
113
+ project,
114
+ priorResult,
115
+ query,
116
+ disease,
117
+ attachPath,
118
+ })) {
119
+ const prompted = await promptNsfcHypothesisCreate({
120
+ hasHypothesis,
121
+ projectLevel,
122
+ project,
123
+ priorResult,
124
+ query,
125
+ disease,
126
+ attachPath,
127
+ });
128
+ hasHypothesis = prompted.hasHypothesis;
129
+ projectLevel = prompted.projectLevel;
130
+ project = prompted.project;
131
+ priorResult = prompted.priorResult;
132
+ query = prompted.query;
133
+ disease = prompted.disease;
134
+ attachPath = prompted.attachPath;
135
+ }
136
+ if (!hasHypothesis || !projectLevel || !query) {
137
+ throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "缺少必填项:是否有科学假说 / 项目级别 / 主文本");
138
+ }
139
+ const validated = validateNsfcHypothesisCreate({
140
+ hasHypothesis,
141
+ projectLevel,
142
+ project,
143
+ priorResult,
144
+ query,
145
+ disease,
146
+ attachPath,
147
+ });
148
+ let attachFiles;
149
+ if (validated.attachPath) {
150
+ log("接口正在处理中,请耐心等待...");
151
+ const uploaded = await uploadNsfcAttach(validated.attachPath);
152
+ attachFiles = [uploaded];
153
+ }
154
+ const body = buildNsfcHypothesisBody({
155
+ hasHypothesis: validated.hasHypothesis,
156
+ projectLevel: validated.projectLevel,
157
+ project: validated.project,
158
+ priorResult: validated.priorResult,
159
+ query: validated.query,
160
+ disease: validated.disease,
161
+ attachFiles,
162
+ });
163
+ const handoff = buildNsfcHandoff({
164
+ hasHypothesis: validated.hasHypothesis,
165
+ priorResult: validated.priorResult,
166
+ });
167
+ const result = {
168
+ query: body.query,
169
+ inputs: body.inputs,
170
+ ready: true,
171
+ };
172
+ if (format === "json") {
173
+ printOutput(wrapWorkbenchResult(result, { step: "hypothesis", subType: "nsfc" }, handoff), "json");
174
+ return;
175
+ }
176
+ const pathLabel = validated.hasHypothesis === "blank"
177
+ ? validated.priorResult === "yes"
178
+ ? "无假说 · 有前期研究结果"
179
+ : "无假说 · 无前期研究结果"
180
+ : "已有科学假说";
181
+ console.log("## 基金申请 · 第 1 步已就绪\n");
182
+ console.log(`- 路径:${pathLabel}`);
183
+ console.log(`- 项目级别:${validated.projectLevel}`);
184
+ if (validated.project) {
185
+ console.log(`- 项目类型:${validated.project}`);
186
+ }
187
+ console.log(`- 主文本:${validated.query.slice(0, 80)}${validated.query.length > 80 ? "…" : ""}`);
188
+ if (validated.disease) {
189
+ console.log(`- 疾病名称:${validated.disease}`);
190
+ }
191
+ if (attachFiles?.length) {
192
+ console.log(`- 补充材料:已上传 ${attachFiles[0].file_name}`);
193
+ }
194
+ console.log("\n参数已校验通过,可进入第 2 步「确认假说」。");
195
+ console.log("(使用 `--format=json` 可获取 Agent 串联用完整 payload)");
196
+ }
197
+ //# sourceMappingURL=hypothesis-create.js.map
@@ -0,0 +1 @@
1
+ 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@@ -0,0 +1,9 @@
1
+ import { type OutputFormat } from "../../../../core/index.js";
2
+ export interface HypothesisFigureOptions {
3
+ orderId?: string;
4
+ output?: string;
5
+ yes?: boolean;
6
+ format?: OutputFormat;
7
+ }
8
+ export declare function runNsfcHypothesisFigure(options: HypothesisFigureOptions): Promise<void>;
9
+ //# sourceMappingURL=hypothesis-figure.d.ts.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"hypothesis-figure.d.ts","sourceRoot":"","sources":["../../../../../src/modules/fund/nsfc/commands/hypothesis-figure.ts"],"names":[],"mappings":"AAGA,OAAO,EAOL,KAAK,YAAY,EAClB,MAAM,2BAA2B,CAAC;AAiBnC,MAAM,WAAW,uBAAuB;IACtC,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,MAAM,CAAC,EAAE,YAAY,CAAC;CACvB;AAiBD,wBAAsB,uBAAuB,CAC3C,OAAO,EAAE,uBAAuB,GAC/B,OAAO,CAAC,IAAI,CAAC,CAgIf"}