@cyanheads/brapi-mcp-server 0.4.11 → 0.4.13
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.
- package/CLAUDE.md +1 -1
- package/README.md +152 -503
- package/changelog/0.4.x/0.4.12.md +29 -0
- package/changelog/0.4.x/0.4.13.md +42 -0
- package/dist/config/alias-credentials.d.ts +27 -15
- package/dist/config/alias-credentials.d.ts.map +1 -1
- package/dist/config/alias-credentials.js +79 -30
- package/dist/config/alias-credentials.js.map +1 -1
- package/dist/config/builtin-aliases.d.ts +51 -0
- package/dist/config/builtin-aliases.d.ts.map +1 -0
- package/dist/config/builtin-aliases.js +126 -0
- package/dist/config/builtin-aliases.js.map +1 -0
- package/dist/mcp-server/prompts/definitions/brapi-meta-analysis.prompt.js +4 -4
- package/dist/mcp-server/prompts/definitions/brapi-meta-analysis.prompt.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts +6 -0
- package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-connect.tool.js +3 -3
- package/dist/mcp-server/tools/definitions/brapi-connect.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.d.ts +2 -2
- package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.js +2 -2
- package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-dataframe-drop.tool.d.ts +2 -2
- package/dist/mcp-server/tools/definitions/brapi-dataframe-drop.tool.js +2 -2
- package/dist/mcp-server/tools/definitions/brapi-dataframe-drop.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.d.ts +2 -2
- package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.js +7 -5
- package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.js +2 -2
- package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.js +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.js +8 -4
- package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-get-image.tool.js +1 -1
- package/dist/mcp-server/tools/definitions/brapi-get-image.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-get-study.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-get-study.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-get-study.tool.js +8 -4
- package/dist/mcp-server/tools/definitions/brapi-get-study.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-manage-dataset.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-manage-dataset.tool.js +3 -3
- package/dist/mcp-server/tools/definitions/brapi-manage-dataset.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.js +1 -1
- package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-server-info.tool.d.ts +6 -0
- package/dist/mcp-server/tools/definitions/brapi-server-info.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.js +1 -1
- package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/index.d.ts +22 -10
- package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
- package/dist/mcp-server/tools/shared/connect-auth-schema.d.ts.map +1 -1
- package/dist/mcp-server/tools/shared/connect-auth-schema.js +15 -6
- package/dist/mcp-server/tools/shared/connect-auth-schema.js.map +1 -1
- package/dist/mcp-server/tools/shared/find-helpers.js +1 -1
- package/dist/mcp-server/tools/shared/find-helpers.js.map +1 -1
- package/dist/mcp-server/tools/shared/orientation-envelope.d.ts +12 -0
- package/dist/mcp-server/tools/shared/orientation-envelope.d.ts.map +1 -1
- package/dist/mcp-server/tools/shared/orientation-envelope.js +45 -4
- package/dist/mcp-server/tools/shared/orientation-envelope.js.map +1 -1
- package/dist/mcp-server/tools/shared/raw-routing-hints.js +2 -2
- package/dist/mcp-server/tools/shared/raw-routing-hints.js.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
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1
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+
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AG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,SAAS,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC;gBACzF,QAAQ,CAAC,IAAI,CACX,WAAW,KAAK,CAAC,SAAS,eAAe,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,eAAe,CAAC,QAAQ,eAAe,0CAA0C,MAAM,GAAG,QAAQ,2CAA2C,CAC5M,CAAC;YACJ,CAAC;YACD,SAAS;QACX,CAAC;QACD,IAAI,OAAO;YAAE,SAAS;QAEtB,MAAM,MAAM,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QAC/C,MAAM,QAAQ,GAAG,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,QAAQ,CAAC,MAAM,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC;QAC9E,QAAQ,CAAC,IAAI,CACX,WAAW,KAAK,CAAC,SAAS,eAAe,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,eAAe,CAAC,yFAAyF,MAAM,GAAG,QAAQ,GAAG,CAC5L,CAAC;IACJ,CAAC;AACH,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,YAAY,CAC1B,SAAiB,EACjB,eAAmE,EACnE,IAAwC,EACxC,SAAiB,EACjB,UAA8C,EAAE;IAEhD,OAAO;QACL,SAAS;QACT,eAAe;QACf,YAAY,EAAE,mBAAmB,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC;QACtE,GAAG,OAAO;KACX,CAAC;AACJ,CAAC;AAWD;;;;;;GAMG;AACH,MAAM,UAAU,mBAAmB,CACjC,UAAkB,EAClB,SAAiB,EACjB,aAAqD,EACrD,UAAiC,EAAE;IAEnC,IAAI,UAAU,IAAI,SAAS;QAAE,OAAO;IACpC,IAAI,IAAyF,CAAC;IAC9F,KAAK,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,CAAC;QAC5D,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC;QACvC,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC;YAAE,SAAS;QACjC,MAAM,GAAG,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;QACvB,IAAI,CAAC,GAAG;YAAE,SAAS;QACnB,MAAM,CAAC,QAAQ,EAAE,KAAK,CAAC,GAAG,GAAG,CAAC;QAC9B,IAAI,CAAC,IAAI,IAAI,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC;YAC/C,IAAI,GAAG,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,EAAE,WAAW,EAAE,OAAO,CAAC,MAAM,EAAE,CAAC;QACjE,CAAC;IACH,CAAC;IACD,IAAI,IAAI,EAAE,CAAC;QACT,OAAO,GAAG,UAAU,0BAA0B,SAAS,SAAS,IAAI,CAAC,KAAK,uBAAuB,IAAI,CAAC,WAAW,4BAA4B,IAAI,CAAC,QAAQ,oBAAoB,IAAI,CAAC,KAAK,QAAQ,CAAC;IACnM,CAAC;IACD,IAAI,OAAO,CAAC,gBAAgB,IAAI,OAAO,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACpE,MAAM,WAAW,GAAG,OAAO,CAAC,gBAAgB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QAC/E,OAAO,GAAG,UAAU,0BAA0B,SAAS,oFAAoF,WAAW,uBAAuB,CAAC;IAChL,CAAC;IACD,OAAO,GAAG,UAAU,0BAA0B,SAAS,iDAAiD,CAAC;AAC3G,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,uBAAuB,CACrC,GAA4B,EAC5B,YAAiC;IAEjC,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;QAC/C,IAAI,YAAY,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,KAAK,KAAK,SAAS,IAAI,KAAK,KAAK,IAAI;YAAE,SAAS;QAC7E,MAAM,QAAQ,GAAG,OAAO,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;QACnF,KAAK,CAAC,IAAI,CAAC,GAAG,GAAG,IAAI,QAAQ,EAAE,CAAC,CAAC;IACnC,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,sBAAsB,CACpC,KAAe,EACf,MAA+B,EAC/B,YAAiC;IAEjC,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC;QAClD,IAAI,YAAY,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,KAAK,KAAK,SAAS,IAAI,KAAK,KAAK,IAAI;YAAE,SAAS;QAC7E,MAAM,QAAQ,GAAG,OAAO,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;QACnF,KAAK,CAAC,IAAI,CAAC,OAAO,GAAG,OAAO,QAAQ,EAAE,CAAC,CAAC;IAC1C,CAAC;AACH,CAAC"}
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@@ -57,6 +57,12 @@ export declare const OrientationContentSchema: z.ZodObject<{
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57
57
|
programCount: z.ZodOptional<z.ZodNumber>;
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58
58
|
locationCount: z.ZodOptional<z.ZodNumber>;
|
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59
59
|
}, z.core.$strip>;
|
|
60
|
+
export declare const OrientationAttributionSchema: z.ZodObject<{
|
|
61
|
+
homepage: z.ZodString;
|
|
62
|
+
license: z.ZodString;
|
|
63
|
+
citation: z.ZodString;
|
|
64
|
+
isDemo: z.ZodOptional<z.ZodBoolean>;
|
|
65
|
+
}, z.core.$strip>;
|
|
60
66
|
export declare const OrientationEnvelopeSchema: z.ZodObject<{
|
|
61
67
|
alias: z.ZodString;
|
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62
68
|
baseUrl: z.ZodString;
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@@ -105,6 +111,12 @@ export declare const OrientationEnvelopeSchema: z.ZodObject<{
|
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|
105
111
|
programCount: z.ZodOptional<z.ZodNumber>;
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106
112
|
locationCount: z.ZodOptional<z.ZodNumber>;
|
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107
113
|
}, z.core.$strip>;
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114
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+
attribution: z.ZodOptional<z.ZodObject<{
|
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115
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+
homepage: z.ZodString;
|
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116
|
+
license: z.ZodString;
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117
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+
citation: z.ZodString;
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118
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+
isDemo: z.ZodOptional<z.ZodBoolean>;
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119
|
+
}, z.core.$strip>>;
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108
120
|
notes: z.ZodArray<z.ZodString>;
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109
121
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fetchedAt: z.ZodString;
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110
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}, z.core.$strip>;
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"orientation-envelope.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/orientation-envelope.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EAAE,KAAK,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;
|
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1
|
+
{"version":3,"file":"orientation-envelope.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/orientation-envelope.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EAAE,KAAK,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAEzD,OAAO,KAAK,EAAE,WAAW,EAAuB,MAAM,kCAAkC,CAAC;AAEzF,OAAO,KAAK,EAEV,kBAAkB,EACnB,MAAM,yCAAyC,CAAC;AAEjD,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,qCAAqC,CAAC;AAsB5E,eAAO,MAAM,oBAAoB;;;;;;;;iBAUmD,CAAC;AAErF,eAAO,MAAM,qBAAqB;;;;;;;;;;iBAQ0C,CAAC;AAE7E,eAAO,MAAM,6BAA6B;;;;iBAciD,CAAC;AAE5F,eAAO,MAAM,wBAAwB;;;;;;;;;;;;iBA0BgD,CAAC;AAEtF,eAAO,MAAM,wBAAwB;;;;;;iBA8B2D,CAAC;AAEjG,eAAO,MAAM,4BAA4B;;;;;iBAgBtC,CAAC;AAEJ,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAmBpC,CAAC;AAEH,MAAM,MAAM,mBAAmB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,yBAAyB,CAAC,CAAC;AAE5E,MAAM,WAAW,iBAAiB;IAChC,MAAM,EAAE,WAAW,CAAC;IACpB,QAAQ,EAAE,kBAAkB,CAAC;CAC9B;AAED;;;;;;;GAOG;AACH,wBAAsB,wBAAwB,CAC5C,GAAG,EAAE,OAAO,EACZ,UAAU,EAAE,gBAAgB,EAC5B,IAAI,EAAE,iBAAiB,GACtB,OAAO,CAAC,mBAAmB,CAAC,CA8E9B;AAsED,wBAAgB,yBAAyB,CAAC,QAAQ,EAAE,mBAAmB,GAAG,MAAM,CAoF/E"}
|
|
@@ -9,6 +9,7 @@
|
|
|
9
9
|
* @module mcp-server/tools/shared/orientation-envelope
|
|
10
10
|
*/
|
|
11
11
|
import { z } from '@cyanheads/mcp-ts-core';
|
|
12
|
+
import { findBuiltinAlias } from '../../../config/builtin-aliases.js';
|
|
12
13
|
import { detectDialectId, dialectEnvVar, getDialectById } from '../../../services/brapi-dialect/index.js';
|
|
13
14
|
/**
|
|
14
15
|
* BrAPI endpoints we treat as the "common floor" — their absence is worth
|
|
@@ -71,10 +72,10 @@ export const OrientationDialectSchema = z
|
|
|
71
72
|
.describe('Active dialect id (e.g. "spec", "cassavabase"). Names a registered adapter that translates outbound filters and declares known-dead routes.'),
|
|
72
73
|
source: z
|
|
73
74
|
.enum(['env-override', 'url-pattern', 'server-name', 'organization-name', 'fallback'])
|
|
74
|
-
.describe('Where the dialect id came from:
|
|
75
|
+
.describe('Where the dialect id came from: env-var override, URL host match, /serverinfo serverName, organizationName, or the spec passthrough fallback.'),
|
|
75
76
|
envVar: z
|
|
76
77
|
.string()
|
|
77
|
-
.describe('
|
|
78
|
+
.describe('Env var that pins the dialect for this alias (e.g. BRAPI_DEFAULT_DIALECT) when detection misfires.'),
|
|
78
79
|
disabledSearchEndpoints: z
|
|
79
80
|
.array(z.string().describe('A POST /search/{noun} route the dialect routes around.'))
|
|
80
81
|
.describe('POST /search nouns the active dialect treats as known-dead. Tools using these routes will refuse with a recovery hint.'),
|
|
@@ -82,7 +83,7 @@ export const OrientationDialectSchema = z
|
|
|
82
83
|
.array(z.string().describe('Verified compatibility note exposed by the active dialect.'))
|
|
83
84
|
.describe('Dialect-level compatibility notes for this server family.'),
|
|
84
85
|
})
|
|
85
|
-
.describe('Active dialect summary —
|
|
86
|
+
.describe('Active dialect summary — declares known quirks for this server family.');
|
|
86
87
|
export const OrientationContentSchema = z
|
|
87
88
|
.object({
|
|
88
89
|
crops: z
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@@ -114,6 +115,21 @@ export const OrientationContentSchema = z
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114
115
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.describe('Total locations hosted, when the server exposes a cheap count.'),
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115
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})
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116
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.describe('Content summary. Counts are populated only when the server supports cheap totals.');
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118
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+
export const OrientationAttributionSchema = z
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119
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+
.object({
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120
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+
homepage: z.string().describe('Public homepage of the upstream dataset.'),
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121
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+
license: z
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122
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+
.string()
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123
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+
.describe('License under which the upstream dataset is published (e.g. "CC-BY").'),
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124
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+
citation: z
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125
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+
.string()
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126
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+
.describe('Citation requested by the upstream when data is reused in publications.'),
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127
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+
isDemo: z
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128
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+
.boolean()
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129
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+
.optional()
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130
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+
.describe('True when this server hosts demo / sample data, not production records.'),
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131
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+
})
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132
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+
.describe('Attribution metadata for connections served from the built-in known-server registry. Surfaces license + citation alongside the data so reuse terms (e.g. CC-BY attribution) can be satisfied. Absent when the connection uses a custom baseUrl — those carry no curated attribution.');
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117
133
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export const OrientationEnvelopeSchema = z.object({
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118
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alias: z.string().describe('Connection alias.'),
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119
135
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baseUrl: z.string().describe('BrAPI v2 base URL for this connection.'),
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@@ -122,6 +138,7 @@ export const OrientationEnvelopeSchema = z.object({
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122
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capabilities: OrientationCapabilitiesSchema.describe('Capability profile derived from /serverinfo.'),
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123
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dialect: OrientationDialectSchema.describe('Active dialect adapter — translates outbound filters and declares known-dead routes for this server.'),
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124
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content: OrientationContentSchema.describe('Content summary (crops + optional totals).'),
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141
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+
attribution: OrientationAttributionSchema.optional().describe('Attribution metadata for built-in known-server connections. Absent for custom (env-only) connections.'),
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125
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|
notes: z
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126
143
|
.array(z.string().describe('Server-specific quirk or degradation note.'))
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127
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.describe('Server-specific quirks or degradation notes.'),
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@@ -172,7 +189,11 @@ export async function buildOrientationEnvelope(ctx, connection, deps) {
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172
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|
if (connection.resolvedAuth?.expiresAt)
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|
173
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|
auth.expiresAt = connection.resolvedAuth.expiresAt;
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|
174
191
|
const dialect = buildDialectSummary(connection, profile);
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|
175
|
-
|
|
192
|
+
const builtin = findBuiltinAlias(connection.alias);
|
|
193
|
+
if (builtin?.isDemo) {
|
|
194
|
+
notes.push(`Alias '${connection.alias}' points at a demo Breedbase instance (${builtin.homepage}) — sample data only, not production records.`);
|
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195
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+
}
|
|
196
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+
const envelope = {
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176
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alias: connection.alias,
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|
177
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|
baseUrl: connection.baseUrl,
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|
178
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server: { ...profile.server },
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@@ -187,6 +208,17 @@ export async function buildOrientationEnvelope(ctx, connection, deps) {
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|
187
208
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notes,
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|
188
209
|
fetchedAt: new Date().toISOString(),
|
|
189
210
|
};
|
|
211
|
+
if (builtin) {
|
|
212
|
+
const attribution = {
|
|
213
|
+
homepage: builtin.homepage,
|
|
214
|
+
license: builtin.license,
|
|
215
|
+
citation: builtin.citation,
|
|
216
|
+
};
|
|
217
|
+
if (builtin.isDemo)
|
|
218
|
+
attribution.isDemo = true;
|
|
219
|
+
envelope.attribution = attribution;
|
|
220
|
+
}
|
|
221
|
+
return envelope;
|
|
190
222
|
}
|
|
191
223
|
function buildDialectSummary(connection, profile) {
|
|
192
224
|
const detection = detectDialectId(connection.alias, profile);
|
|
@@ -294,6 +326,15 @@ export function formatOrientationEnvelope(envelope) {
|
|
|
294
326
|
lines.push(`- Programs: ${envelope.content.programCount}`);
|
|
295
327
|
if (envelope.content.locationCount !== undefined)
|
|
296
328
|
lines.push(`- Locations: ${envelope.content.locationCount}`);
|
|
329
|
+
if (envelope.attribution) {
|
|
330
|
+
lines.push('');
|
|
331
|
+
lines.push('## Attribution');
|
|
332
|
+
lines.push(`- **License:** ${envelope.attribution.license}`);
|
|
333
|
+
lines.push(`- **Homepage:** ${envelope.attribution.homepage}`);
|
|
334
|
+
lines.push(`- **Citation:** ${envelope.attribution.citation}`);
|
|
335
|
+
if (envelope.attribution.isDemo)
|
|
336
|
+
lines.push('- **Demo dataset** — sample data, not production.');
|
|
337
|
+
}
|
|
297
338
|
if (envelope.notes.length > 0) {
|
|
298
339
|
lines.push('');
|
|
299
340
|
lines.push('## Notes');
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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G,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,cAAc,QAAQ,CAAC,IAAI,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC,EAAE,EAAE,CACtL,CAAC;IAEF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACf,KAAK,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC;IAC9B,KAAK,CAAC,IAAI,CAAC,KAAK,QAAQ,CAAC,YAAY,CAAC,cAAc,wBAAwB,CAAC,CAAC;IAC9E,IAAI,QAAQ,CAAC,YAAY,CAAC,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC/C,KAAK,CAAC,IAAI,CAAC,gBAAgB,QAAQ,CAAC,YAAY,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAC3E,CAAC;IACD,IAAI,QAAQ,CAAC,YAAY,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACjD,KAAK,CAAC,IAAI,CACR,mDAAmD,QAAQ,CAAC,YAAY,CAAC,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAClG,CAAC;IACJ,CAAC;IAED,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACf,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;IACzB,KAAK,CAAC,IAAI,CAAC,mBAAmB,QAAQ,CAAC,OAAO,CAAC,EAAE,qBAAqB,QAAQ,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC;IAClG,KAAK,CAAC,IAAI,CAAC,yBAAyB,QAAQ,CAAC,OAAO,CAAC,MAAM,IAAI,CAAC,CAAC;IACjE,IAAI,QAAQ,CAAC,OAAO,CAAC,uBAAuB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxD,KAAK,CAAC,IAAI,CACR,4CAA4C,QAAQ,CAAC,OAAO,CAAC,uBAAuB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAClG,CAAC;IACJ,CAAC;IACD,IAAI,QAAQ,CAAC,OAAO,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACtC,KAAK,MAAM,IAAI,IAAI,QAAQ,CAAC,OAAO,CAAC,KAAK;YAAE,KAAK,CAAC,IAAI,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC;IACrE,CAAC;IAED,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACf,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;IACzB,IAAI,QAAQ,CAAC,OAAO,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACtC,KAAK,CAAC,IAAI,CACR,cAAc,QAAQ,CAAC,OAAO,CAAC,KAAK,CAAC,MAAM,QAAQ,QAAQ,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CACvF,CAAC;IACJ,CAAC;SAAM,CAAC;QACN,KAAK,CAAC,IAAI,CAAC,qDAAqD,CAAC,CAAC;IACpE,CAAC;IACD,IAAI,QAAQ,CAAC,OAAO,CAAC,UAAU,KAAK,SAAS;QAC3C,KAAK,CAAC,IAAI,CAAC,cAAc,QAAQ,CAAC,OAAO,CAAC,UAAU,EAAE,CAAC,CAAC;IAC1D,IAAI,QAAQ,CAAC,OAAO,CAAC,cAAc,KAAK,SAAS;QAC/C,KAAK,CAAC,IAAI,CAAC,gBAAgB,QAAQ,CAAC,OAAO,CAAC,cAAc,EAAE,CAAC,CAAC;IAChE,IAAI,QAAQ,CAAC,OAAO,CAAC,YAAY,KAAK,SAAS;QAC7C,KAAK,CAAC,IAAI,CAAC,eAAe,QAAQ,CAAC,OAAO,CAAC,YAAY,EAAE,CAAC,CAAC;IAC7D,IAAI,QAAQ,CAAC,OAAO,CAAC,aAAa,KAAK,SAAS;QAC9C,KAAK,CAAC,IAAI,CAAC,gBAAgB,QAAQ,CAAC,OAAO,CAAC,aAAa,EAAE,CAAC,CAAC;IAE/D,IAAI,QAAQ,CAAC,WAAW,EAAE,CAAC;QACzB,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACf,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC;QAC7B,KAAK,CAAC,IAAI,CAAC,kBAAkB,QAAQ,CAAC,WAAW,CAAC,OAAO,EAAE,CAAC,CAAC;QAC7D,KAAK,CAAC,IAAI,CAAC,mBAAmB,QAAQ,CAAC,WAAW,CAAC,QAAQ,EAAE,CAAC,CAAC;QAC/D,KAAK,CAAC,IAAI,CAAC,mBAAmB,QAAQ,CAAC,WAAW,CAAC,QAAQ,EAAE,CAAC,CAAC;QAC/D,IAAI,QAAQ,CAAC,WAAW,CAAC,MAAM;YAC7B,KAAK,CAAC,IAAI,CAAC,mDAAmD,CAAC,CAAC;IACpE,CAAC;IAED,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC9B,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACf,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;QACvB,KAAK,MAAM,IAAI,IAAI,QAAQ,CAAC,KAAK;YAAE,KAAK,CAAC,IAAI,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC;IAC7D,CAAC;IAED,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACf,KAAK,CAAC,IAAI,CAAC,eAAe,QAAQ,CAAC,SAAS,IAAI,CAAC,CAAC;IAClD,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AAC1B,CAAC"}
|
|
@@ -14,7 +14,7 @@ const GET_NUDGES = {
|
|
|
14
14
|
studies: 'This endpoint is also served by `brapi_find_studies` which enriches with program/trial/location FKs and returns distributions in one call.',
|
|
15
15
|
germplasm: 'This endpoint is also served by `brapi_find_germplasm` which adds distributions and dataset spillover.',
|
|
16
16
|
observations: 'This endpoint is also served by `brapi_find_observations` which adds distributions and dataset spillover.',
|
|
17
|
-
variables: 'This endpoint is also served by `brapi_find_variables` which adds free-text ranking
|
|
17
|
+
variables: 'This endpoint is also served by `brapi_find_variables` which adds free-text ranking against ontology terms.',
|
|
18
18
|
images: 'This endpoint is also served by `brapi_find_images`; use `brapi_get_image` to pull bytes inline.',
|
|
19
19
|
variants: 'This endpoint is also served by `brapi_find_variants` which handles distributions and dataset spillover.',
|
|
20
20
|
locations: 'This endpoint is also served by `brapi_find_locations` which adds distributions and optional bounding-box filtering.',
|
|
@@ -26,7 +26,7 @@ const SEARCH_NUDGES = {
|
|
|
26
26
|
studies: 'Consider `brapi_find_studies` — handles async polling + FK resolution automatically.',
|
|
27
27
|
germplasm: 'Consider `brapi_find_germplasm` — handles distributions + spillover.',
|
|
28
28
|
observations: 'Consider `brapi_find_observations` — handles spillover and distributions.',
|
|
29
|
-
variables: 'Consider `brapi_find_variables` —
|
|
29
|
+
variables: 'Consider `brapi_find_variables` — ranks results client-side against ontology terms when text is provided.',
|
|
30
30
|
calls: 'Consider `brapi_find_genotype_calls` — handles async-search polling, deployment-side pull limit, and dataset spillover automatically.',
|
|
31
31
|
images: 'Consider `brapi_find_images`.',
|
|
32
32
|
variants: 'Consider `brapi_find_variants`.',
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"raw-routing-hints.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/raw-routing-hints.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH;;;;GAIG;AACH,MAAM,UAAU,GAA2B;IACzC,OAAO,EACL,4IAA4I;IAC9I,SAAS,EACP,wGAAwG;IAC1G,YAAY,EACV,2GAA2G;IAC7G,SAAS,EACP,
|
|
1
|
+
{"version":3,"file":"raw-routing-hints.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/raw-routing-hints.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH;;;;GAIG;AACH,MAAM,UAAU,GAA2B;IACzC,OAAO,EACL,4IAA4I;IAC9I,SAAS,EACP,wGAAwG;IAC1G,YAAY,EACV,2GAA2G;IAC7G,SAAS,EACP,6GAA6G;IAC/G,MAAM,EACJ,kGAAkG;IACpG,QAAQ,EACN,0GAA0G;IAC5G,SAAS,EACP,sHAAsH;IACxH,UAAU,EACR,uGAAuG;IACzG,KAAK,EAAE,2EAA2E;IAClF,eAAe,EAAE,+DAA+D;CACjF,CAAC;AAEF,MAAM,aAAa,GAA2B;IAC5C,OAAO,EAAE,sFAAsF;IAC/F,SAAS,EAAE,sEAAsE;IACjF,YAAY,EAAE,2EAA2E;IACzF,SAAS,EACP,2GAA2G;IAC7G,KAAK,EACH,uIAAuI;IACzI,MAAM,EAAE,+BAA+B;IACvC,QAAQ,EAAE,iCAAiC;IAC3C,SAAS,EAAE,kCAAkC;CAC9C,CAAC;AAEF,uDAAuD;AACvD,SAAS,WAAW,CAAC,IAAY;IAC/B,OAAO,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;AACtD,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,IAAY;IACxC,MAAM,GAAG,GAAG,WAAW,CAAC,IAAI,CAAC,CAAC;IAC9B,OAAO,UAAU,CAAC,GAAG,CAAC,CAAC;AACzB,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,IAAY;IAC3C,OAAO,aAAa,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,CAAC;AACjD,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/brapi-mcp-server",
|
|
3
3
|
"mcpName": "io.github.cyanheads/brapi-mcp-server",
|
|
4
|
-
"version": "0.4.
|
|
4
|
+
"version": "0.4.13",
|
|
5
5
|
"description": "BrAPI v2.1 MCP server — studies, germplasm, observations, genotypes, images, and pedigrees.",
|
|
6
6
|
"author": "Casey Hand @cyanheads (https://github.com/cyanheads/brapi-mcp-server#readme)",
|
|
7
7
|
"type": "module",
|
package/server.json
CHANGED
|
@@ -6,14 +6,14 @@
|
|
|
6
6
|
"url": "https://github.com/cyanheads/brapi-mcp-server",
|
|
7
7
|
"source": "github"
|
|
8
8
|
},
|
|
9
|
-
"version": "0.4.
|
|
9
|
+
"version": "0.4.13",
|
|
10
10
|
"packages": [
|
|
11
11
|
{
|
|
12
12
|
"registryType": "npm",
|
|
13
13
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
14
14
|
"identifier": "@cyanheads/brapi-mcp-server",
|
|
15
15
|
"runtimeHint": "bun",
|
|
16
|
-
"version": "0.4.
|
|
16
|
+
"version": "0.4.13",
|
|
17
17
|
"packageArguments": [
|
|
18
18
|
{ "type": "positional", "value": "run" },
|
|
19
19
|
{ "type": "positional", "value": "start:stdio" }
|
|
@@ -49,7 +49,7 @@
|
|
|
49
49
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
50
50
|
"identifier": "@cyanheads/brapi-mcp-server",
|
|
51
51
|
"runtimeHint": "bun",
|
|
52
|
-
"version": "0.4.
|
|
52
|
+
"version": "0.4.13",
|
|
53
53
|
"packageArguments": [
|
|
54
54
|
{ "type": "positional", "value": "run" },
|
|
55
55
|
{ "type": "positional", "value": "start:http" }
|