@cyanheads/interpro-mcp-server 0.1.2 → 0.1.3
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/AGENTS.md +4 -4
- package/CLAUDE.md +4 -4
- package/README.md +33 -7
- package/changelog/0.1.x/0.1.3.md +24 -0
- package/dist/index.js +1 -1
- package/dist/index.js.map +1 -1
- package/dist/mcp-server/tools/definitions/interpro-find-proteins-by-domain.tool.d.ts +44 -2
- package/dist/mcp-server/tools/definitions/interpro-find-proteins-by-domain.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/interpro-find-proteins-by-domain.tool.js +56 -4
- package/dist/mcp-server/tools/definitions/interpro-find-proteins-by-domain.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/interpro-get-entry.tool.d.ts +59 -0
- package/dist/mcp-server/tools/definitions/interpro-get-entry.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/interpro-get-entry.tool.js +139 -5
- package/dist/mcp-server/tools/definitions/interpro-get-entry.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/interpro-get-protein-domains.tool.d.ts +20 -2
- package/dist/mcp-server/tools/definitions/interpro-get-protein-domains.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/interpro-get-protein-domains.tool.js +98 -22
- package/dist/mcp-server/tools/definitions/interpro-get-protein-domains.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/interpro-search-entries.tool.d.ts +6 -0
- package/dist/mcp-server/tools/definitions/interpro-search-entries.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/interpro-search-entries.tool.js +11 -2
- package/dist/mcp-server/tools/definitions/interpro-search-entries.tool.js.map +1 -1
- package/dist/services/interpro/format.d.ts.map +1 -1
- package/dist/services/interpro/format.js +8 -17
- package/dist/services/interpro/format.js.map +1 -1
- package/dist/services/interpro/schemas.d.ts +15 -0
- package/dist/services/interpro/schemas.d.ts.map +1 -1
- package/dist/services/interpro/schemas.js +8 -0
- package/dist/services/interpro/schemas.js.map +1 -1
- package/package.json +3 -3
- package/server.json +3 -3
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1
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AAM,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;qBAC5C,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,WAAW,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;gBAC7C,MAAM,QAAQ,GAAG,KAAK,IAAI,UAAU,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAC;gBAClE,MAAM,IAAI,GAAG,QAAQ,EAAE,QAAQ,IAAI,CAAC,CAAC;gBACrC,IAAI,IAAI,GAAG,CAAC,IAAI,CAAC,IAAI,IAAI,QAAQ,CAAC,MAAM,IAAI,QAAQ,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,QAAQ,EAAE,KAAK,CAAC;oBACtF,MAAM,KAAK,EAAE,CAAC;gBAChB,uBAAuB,GAAG,QAAQ,CAAC,MAAM,CAAC;gBAC1C,KAAK,IAAI,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,QAAQ,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE,CAAC;oBACxD,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAyC,CAAC;oBAC5E,KAAK,CAAC,IAAI,CAAC;wBACT,IAAI,EAAE,SAAS;wBACf,GAAG;wBACH,IAAI;wBACJ,aAAa,EAAE,OAAO;wBACtB,EAAE,EAAE;4BACF,QAAQ,EAAE,KAAK;4BACf,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,KAAK,EAAG,QAAQ,CAAC,KAAK,GAAG,CAAC,CAAuB,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;4BAC1E,YAAY;yBACb;qBACF,CAAC,CAAC;gBACL,CAAC;YACH,CAAC;QACH,CAAC;QAED,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,SAAS,EAAE,GAAG,eAAe,CAAC,KAAK,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;QAC5E,MAAM,EAAE,QAAQ,EAAE,GAAG,MAAM,CAAC;QAC5B,MAAM,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC;QAC1B,MAAM,OAAO,GAAa,EAAE,CAAC;QAC7B,IAAI,SAAS,EAAE,CAAC;YACd,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAS,CAAC;YAC9B,MAAM,CAAC,KAAK,EAAE,OAAO,EAAE,EAAE,CAAC,GACxB,IAAI,CAAC,IAAI,KAAK,OAAO;gBACnB,CAAC,CAAC,IAAI,CAAC,IAAI,KAAK,SAAS;oBACvB,CAAC,CAAC,CAAC,eAAe,EAAE,oBAAoB,EAAE,IAAI,CAAC,GAAG,CAAC;oBACnD,CAAC,CAAC,CAAC,cAAc,EAAE,mBAAmB,EAAE,IAAI,CAAC,GAAG,CAAC;gBACnD,CAAC,CAAC,CAAC,OAAO,EAAE,YAAY,EAAE,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;YAC7D,OAAO,CAAC,IAAI,CACV,GAAG,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,oEAAoE,YAAY,GAAG,CACnI,CAAC;QACJ,CAAC;QACD,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAC;YACxB,MAAM,MAAM,GAAG,IAAI;gBACjB,CAAC,CAAC,uBAAuB,YAAY,0BAA0B,IAAI,CAAC,IAAI,KAAK,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,cAAc,EAAE;gBAC7J,CAAC,CAAC,SAAS;oBACT,CAAC,CAAC,EAAE;oBACJ,CAAC,CAAC,oBAAoB,SAAS,0BAA0B,QAAQ,CAAC,cAAc,gBAAgB,CAAC;YACrG,MAAM,QAAQ,GAAG;gBACf,SAAS;gBACT,GAAG,CAAC,OAAO,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,eAAe,EAAE,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;gBAC9D,GAAG,CAAC,KAAK,CAAC,oBAAoB,CAAC,CAAC,CAAC,EAAE,oBAAoB,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;gBACrE,GAAG,CAAC,KAAK,CAAC,yBAAyB,CAAC,CAAC,CAAC,EAAE,yBAAyB,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;gBAC/E,MAAM,EAAE,QAAQ,CAAC,UAAU;aAC5B,CAAC;YACF,OAAO,CAAC,IAAI,CACV,8CAA8C,MAAM,gDAAgD,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,sDAAsD,CACnL,CAAC;QACJ,CAAC;aAAM,IAAI,OAAO;YAChB,OAAO,CAAC,IAAI,CACV,2HAA2H;gBACzH,CAAC,QAAQ,CAAC,eAAe,IAAI,CAAC,CAAC,MAAM,IAAI,KAAK,CAAC;oBAC7C,CAAC,CAAC,EAAE;oBACJ,CAAC,CAAC,yCAAyC,CAAC,CACjD,CAAC;aACC,IAAI,CAAC,QAAQ,CAAC,eAAe;YAChC,OAAO,CAAC,IAAI,CACV,OAAO,KAAK,SAAS;gBACnB,CAAC,CAAC,6FAA6F;gBAC/F,CAAC,CAAC,+EAA+E,CACpF,CAAC;QACJ,IAAI,OAAO;YACT,OAAO,CAAC,IAAI,CAAC,6EAA6E,CAAC,CAAC;QAC9F,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC;QAC/B,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC;QACvC,IAAI,QAAQ,CAAC,UAAU;YACrB,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,QAAQ,CAAC,eAAe,EAAE,GAAG,EAAE,SAAS,GAAG,SAAS,EAAE,CAAC,CAAC;QACxF,IAAI,OAAO,CAAC,MAAM;YAAE,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC;QACzD,OAAO,MAAM,CAAC;IAChB,CAAC;IACD,MAAM,EAAE,cAAc;CACvB,CAAC,CAAC"}
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@@ -112,6 +112,12 @@ export declare const interproSearchEntries: import("@cyanheads/mcp-ts-core").Too
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112
112
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}, z.core.$strip>;
|
|
113
113
|
sourceUrl: z.ZodString;
|
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114
114
|
}, z.core.$strip>, readonly [{
|
|
115
|
+
readonly reason: "incompatible_go_filters";
|
|
116
|
+
readonly code: JsonRpcErrorCode.ValidationError;
|
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117
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+
readonly when: "Both goTerm and goCategory are supplied.";
|
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118
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+
readonly retryable: false;
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119
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+
readonly recovery: "Search with goTerm alone or goCategory alone; either supports query and entryType filters.";
|
|
120
|
+
}, {
|
|
115
121
|
readonly reason: "go_filters_require_interpro";
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|
116
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|
readonly code: JsonRpcErrorCode.ValidationError;
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|
117
123
|
readonly when: "goTerm or goCategory is supplied for a member sourceDatabase.";
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"interpro-search-entries.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/interpro-search-entries.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmCjE,wEAAwE;AACxE,eAAO,MAAM,qBAAqB
|
|
1
|
+
{"version":3,"file":"interpro-search-entries.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/interpro-search-entries.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmCjE,wEAAwE;AACxE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAuLhC,CAAC"}
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|
@@ -35,8 +35,8 @@ export const interproSearchEntries = tool('interpro_search_entries', {
|
|
|
35
35
|
goTerm: optionalString(z
|
|
36
36
|
.string()
|
|
37
37
|
.trim()
|
|
38
|
-
.regex(/^GO:\d{7}$/)).describe('GO annotation identifier such as GO:0003677; requires sourceDatabase interpro.'),
|
|
39
|
-
goCategory: optionalString(z.enum(['P', 'F', 'C'])).describe('GO category: P biological process, F molecular function, C cellular component; requires sourceDatabase interpro.'),
|
|
38
|
+
.regex(/^GO:\d{7}$/)).describe('GO annotation identifier such as GO:0003677; requires sourceDatabase interpro and cannot combine with goCategory.'),
|
|
39
|
+
goCategory: optionalString(z.enum(['P', 'F', 'C'])).describe('GO category: P biological process, F molecular function, C cellular component; requires sourceDatabase interpro and cannot combine with goTerm.'),
|
|
40
40
|
integratedInto: optionalString(z
|
|
41
41
|
.string()
|
|
42
42
|
.trim()
|
|
@@ -66,6 +66,13 @@ export const interproSearchEntries = tool('interpro_search_entries', {
|
|
|
66
66
|
effectiveQuery: z.string().optional().describe('Applied filters as JSON.'),
|
|
67
67
|
},
|
|
68
68
|
errors: [
|
|
69
|
+
{
|
|
70
|
+
reason: 'incompatible_go_filters',
|
|
71
|
+
code: JsonRpcErrorCode.ValidationError,
|
|
72
|
+
when: 'Both goTerm and goCategory are supplied.',
|
|
73
|
+
retryable: false,
|
|
74
|
+
recovery: 'Search with goTerm alone or goCategory alone; either supports query and entryType filters.',
|
|
75
|
+
},
|
|
69
76
|
{
|
|
70
77
|
reason: 'go_filters_require_interpro',
|
|
71
78
|
code: JsonRpcErrorCode.ValidationError,
|
|
@@ -109,6 +116,8 @@ export const interproSearchEntries = tool('interpro_search_entries', {
|
|
|
109
116
|
async handler(input, ctx) {
|
|
110
117
|
if (input.sourceDatabase !== 'interpro' && (input.goTerm || input.goCategory))
|
|
111
118
|
throw ctx.fail('go_filters_require_interpro', 'GO filters select InterPro annotations and require sourceDatabase interpro.');
|
|
119
|
+
if (input.goTerm && input.goCategory)
|
|
120
|
+
throw ctx.fail('incompatible_go_filters', 'goTerm and goCategory cannot be combined.');
|
|
112
121
|
const limit = Math.min(input.limit, MAX_LIMIT);
|
|
113
122
|
const notices = input.limit > limit ? [`Requested limit ${input.limit} was clamped to ${limit}.`] : [];
|
|
114
123
|
if (input.integratedInto && input.sourceDatabase === 'interpro')
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"interpro-search-entries.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/interpro-search-entries.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EACL,YAAY,EACZ,YAAY,EACZ,YAAY,EACZ,YAAY,GACb,MAAM,gCAAgC,CAAC;AACxC,OAAO,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,+BAA+B,CAAC;AAChF,OAAO,EAAE,kBAAkB,EAAE,MAAM,yCAAyC,CAAC;AAC7E,OAAO,EAAE,YAAY,EAAE,MAAM,gCAAgC,CAAC;AAC9D,OAAO,EACL,eAAe,EACf,kBAAkB,EAClB,eAAe,EACf,eAAe,EACf,UAAU,EACV,cAAc,EACd,UAAU,EACV,oBAAoB,GACrB,MAAM,gCAAgC,CAAC;AACxC,OAAO,EAAE,eAAe,EAAE,MAAM,wCAAwC,CAAC;AAEzE,MAAM,SAAS,GAAG,GAAG,CAAC;AACtB,MAAM,WAAW,GAAG,CAAC,CAAC,MAAM,CAAC;IAC3B,cAAc,EAAE,oBAAoB;IACpC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;IAC7D,SAAS,EAAE,eAAe,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qBAAqB,CAAC;IACrE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;IAChE,UAAU,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;IAC/E,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;CAC1F,CAAC,CAAC;AACH,MAAM,SAAS,GAAG,CAAC;KAChB,MAAM,CAAC,EAAE,QAAQ,EAAE,kBAAkB,CAAC,QAAQ,CAAC,gBAAgB,CAAC,EAAE,CAAC;KACnE,QAAQ,CAAC,eAAe,CAAC,CAAC;AAE7B,wEAAwE;AACxE,MAAM,CAAC,MAAM,qBAAqB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACnE,KAAK,EAAE,yBAAyB;IAChC,WAAW,EACT,yPAAyP;IAC3P,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAC9E,IAAI,EAAE,CAAC,mCAAmC,CAAC;IAC3C,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,cAAc,EAAE,eAAe,CAAC,oBAAoB,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,QAAQ,CAChF,2CAA2C,CAC5C;QACD,KAAK,EAAE,cAAc,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAC/D,0DAA0D,CAC3D;QACD,SAAS,EAAE,cAAc,CAAC,eAAe,CAAC,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QAC7E,MAAM,EAAE,cAAc,CACpB,CAAC;aACE,MAAM,EAAE;aACR,IAAI,EAAE;aACN,KAAK,CAAC,YAAY,CAAC,CACvB,CAAC,QAAQ,
|
|
1
|
+
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@@ -1 +1 @@
|
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|
1
|
-
{"version":3,"file":"format.d.ts","sourceRoot":"","sources":["../../../src/services/interpro/format.ts"],"names":[],"mappings":"AAyBA,2GAA2G;AAC3G,wBAAgB,eAAe,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,GAAG,CAAC,CAW9C;AAED;;;;GAIG;AACH,wBAAgB,0BAA0B,CAAC,CAAC,SAAS,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC1E,QAAQ,EAAE,CAAC,EACX,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,MAAM,GACf;IAAE,QAAQ,EAAE,CAAC,CAAC;IAAC,MAAM,CAAC,EAAE,MAAM,CAAA;CAAE,CAoBlC;AAED,qGAAqG;AACrG,wBAAgB,cAAc,CAAC,KAAK,EAAE,OAAO,GAAG;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,EAAE,
|
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1
|
+
{"version":3,"file":"format.d.ts","sourceRoot":"","sources":["../../../src/services/interpro/format.ts"],"names":[],"mappings":"AAyBA,2GAA2G;AAC3G,wBAAgB,eAAe,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,GAAG,CAAC,CAW9C;AAED;;;;GAIG;AACH,wBAAgB,0BAA0B,CAAC,CAAC,SAAS,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC1E,QAAQ,EAAE,CAAC,EACX,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,MAAM,GACf;IAAE,QAAQ,EAAE,CAAC,CAAC;IAAC,MAAM,CAAC,EAAE,MAAM,CAAA;CAAE,CAoBlC;AAED,qGAAqG;AACrG,wBAAgB,cAAc,CAAC,KAAK,EAAE,OAAO,GAAG;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,EAAE,CAiD/E"}
|
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@@ -2,7 +2,7 @@
|
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|
2
2
|
* @fileoverview Reversible JSON output with usable source URL and image indexes.
|
|
3
3
|
* @module services/interpro/format
|
|
4
4
|
*/
|
|
5
|
-
import { markdown } from '@cyanheads/mcp-ts-core/utils';
|
|
5
|
+
import { markdown, markdownImage, markdownLink } from '@cyanheads/mcp-ts-core/utils';
|
|
6
6
|
/** Base64 prefixes of the image formats Wikipedia thumbnails arrive in, with their media types. */
|
|
7
7
|
const THUMBNAIL_SIGNATURES = [
|
|
8
8
|
['iVBORw0KGgo', 'image/png'],
|
|
@@ -104,26 +104,17 @@ export function formatInterpro(value) {
|
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|
104
104
|
.replace(/\u2028/g, '\\u2028')
|
|
105
105
|
.replace(/\u2029/g, '\\u2029');
|
|
106
106
|
const output = markdown().codeBlock(json, 'json');
|
|
107
|
-
/**
|
|
108
|
-
* CommonMark angle destinations retain parentheses, and entities decode to the original URL.
|
|
109
|
-
* Whitespace and control characters, which no indexed URL holds, are percent-encoded as a
|
|
110
|
-
* backstop so no destination can span a line.
|
|
111
|
-
*/
|
|
112
|
-
const destination = (url) => url
|
|
113
|
-
.replace(/&/g, '&')
|
|
114
|
-
.replace(/</g, '<')
|
|
115
|
-
.replace(/>/g, '>')
|
|
116
|
-
.replace(/\\/g, '\')
|
|
117
|
-
.replace(/[\s\p{Cc}]/gu, encodeURIComponent);
|
|
118
107
|
if (urls.size)
|
|
119
108
|
output
|
|
120
109
|
.raw('\n\nSources and links:\n')
|
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|
-
.raw([...urls].map((url, index) => `
|
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|
+
.raw([...urls].map((url, index) => markdownLink(`Link ${index + 1}`, url)).join('\n\n'));
|
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|
if (images.size)
|
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|
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output
|
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|
-
.
|
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|
-
|
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|
-
|
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|
+
output.raw('\n\nImages:\n').raw([...images]
|
|
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|
+
.map((url, index) =>
|
|
114
|
+
/** Validated base64 thumbnails intentionally render as images; the framework accepts only HTTP(S). */
|
|
115
|
+
DATA_IMAGE.test(url)
|
|
116
|
+
? ``
|
|
117
|
+
: markdownImage(`Image ${index + 1}`, url))
|
|
127
118
|
.join('\n\n'));
|
|
128
119
|
return [{ type: 'text', text: output.build() }];
|
|
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|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"format.js","sourceRoot":"","sources":["../../../src/services/interpro/format.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,QAAQ,EAAE,MAAM,8BAA8B,CAAC;
|
|
1
|
+
{"version":3,"file":"format.js","sourceRoot":"","sources":["../../../src/services/interpro/format.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,QAAQ,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,8BAA8B,CAAC;AAErF,mGAAmG;AACnG,MAAM,oBAAoB,GAAG;IAC3B,CAAC,aAAa,EAAE,WAAW,CAAC;IAC5B,CAAC,MAAM,EAAE,YAAY,CAAC;IACtB,CAAC,QAAQ,EAAE,WAAW,CAAC;CACf,CAAC;AACX,mEAAmE;AACnE,MAAM,MAAM,GAAG,wBAAwB,CAAC;AACxC,sGAAsG;AACtG,MAAM,UAAU,GAAG,4DAA4D,CAAC;AAChF,wDAAwD;AACxD,MAAM,UAAU,GAAG,qCAAqC,CAAC;AAEzD,SAAS,gBAAgB,CAAC,IAAY;IACpC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC;QAAE,OAAO,SAAS,CAAC;IACzC,MAAM,SAAS,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;IACxF,OAAO,SAAS,IAAI,QAAQ,SAAS,WAAW,IAAI,EAAE,CAAC;AACzD,CAAC;AAED,2GAA2G;AAC3G,MAAM,UAAU,eAAe,CAAI,KAAQ;IACzC,IAAI,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC;QAAE,OAAO,KAAK,CAAC,GAAG,CAAC,eAAe,CAAM,CAAC;IACjE,IAAI,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ;QACpC,OAAO,MAAM,CAAC,WAAW,CACvB,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAoB,EAAE,EAAE,CAAC;YAC5D,GAAG;YACH,CAAC,GAAG,KAAK,WAAW,IAAI,OAAO,IAAI,KAAK,QAAQ,IAAI,gBAAgB,CAAC,IAAI,CAAC,CAAC;gBACzE,eAAe,CAAC,IAAI,CAAC;SACxB,CAAC,CACE,CAAC;IACT,OAAO,KAAK,CAAC;AACf,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,0BAA0B,CACxC,QAAW,EACX,OAAgB,EAChB,QAAgB;IAEhB,IAAI,OAAO;QAAE,OAAO,EAAE,QAAQ,EAAE,CAAC;IACjC,IAAI,KAAK,GAAG,CAAC,CAAC;IACd,IAAI,KAAK,GAAG,CAAC,CAAC;IACd,MAAM,KAAK,GAAG,CAAC,IAAa,EAAW,EAAE;QACvC,IAAI,CAAC,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC;YAAE,OAAO,IAAI,CAAC;QAC1E,MAAM,EAAE,SAAS,EAAE,GAAG,IAAI,EAAE,GAAG,IAA+B,CAAC;QAC/D,IAAI,OAAO,SAAS,KAAK,QAAQ,IAAI,SAAS,KAAK,EAAE;YAAE,OAAO,IAAI,CAAC;QACnE,KAAK,IAAI,CAAC,CAAC;QACX,KAAK,IAAI,SAAS,CAAC,MAAM,CAAC;QAC1B,OAAO,IAAI,CAAC;IACd,CAAC,CAAC;IACF,MAAM,EAAE,SAAS,EAAE,GAAG,QAAQ,CAAC;IAC/B,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC;IACjF,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,QAAQ,EAAE,CAAC;IAChC,MAAM,OAAO,GAAG,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,yBAAyB,CAAC,CAAC,CAAC,GAAG,KAAK,uBAAuB,CAAC;IAC1F,OAAO;QACL,QAAQ,EAAE,EAAE,GAAG,QAAQ,EAAE,SAAS,EAAE,KAAK,EAAE;QAC3C,MAAM,EAAE,WAAW,OAAO,KAAK,KAAK,CAAC,cAAc,CAAC,OAAO,CAAC,wCAAwC,QAAQ,2CAA2C,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,GAAG;KACtL,CAAC;AACJ,CAAC;AAED,qGAAqG;AACrG,MAAM,UAAU,cAAc,CAAC,KAAc;IAC3C,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAC;IAC/B,MAAM,MAAM,GAAG,IAAI,GAAG,EAAU,CAAC;IACjC;;;OAGG;IACH,MAAM,MAAM,GAAG,CAAC,SAAiB,EAAE,KAAc,EAAW,EAAE;QAC5D,IAAI,CAAC;YACH,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,CAAC;YACxC,IAAI,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC;YACpB,IAAI,KAAK,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC;gBAAE,MAAM,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC;YAC9D,OAAO,IAAI,CAAC;QACd,CAAC;QAAC,MAAM,CAAC;YACP,OAAO,KAAK,CAAC;QACf,CAAC;IACH,CAAC,CAAC;IACF,MAAM,OAAO,GAAG,CAAC,IAAa,EAAQ,EAAE;QACtC,IAAI,OAAO,IAAI,KAAK,QAAQ,EAAE,CAAC;YAC7B,IAAI,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;gBAC1B,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;gBACjB,OAAO;YACT,CAAC;YACD,IAAI,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC;gBAAE,OAAO;YACzF,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,QAAQ,CAAC,+BAA+B,CAAC;gBAAE,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC;QAC9F,CAAC;aAAM,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC;YAAE,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;aACjD,IAAI,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ;YAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;IAClF,CAAC,CAAC;IACF,OAAO,CAAC,KAAK,CAAC,CAAC;IACf,MAAM,IAAI,GAAG,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC;SAC/B,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC;SAC7B,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAC;IACjC,MAAM,MAAM,GAAG,QAAQ,EAAE,CAAC,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;IAClD,IAAI,IAAI,CAAC,IAAI;QACX,MAAM;aACH,GAAG,CAAC,0BAA0B,CAAC;aAC/B,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,YAAY,CAAC,QAAQ,KAAK,GAAG,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC;IAC7F,IAAI,MAAM,CAAC,IAAI;QACb,MAAM,CAAC,GAAG,CAAC,eAAe,CAAC,CAAC,GAAG,CAC7B,CAAC,GAAG,MAAM,CAAC;aACR,GAAG,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE;QAClB,sGAAsG;QACtG,UAAU,CAAC,IAAI,CAAC,GAAG,CAAC;YAClB,CAAC,CAAC,WAAW,KAAK,GAAG,CAAC,MAAM,GAAG,IAAI;YACnC,CAAC,CAAC,aAAa,CAAC,SAAS,KAAK,GAAG,CAAC,EAAE,EAAE,GAAG,CAAC,CAC7C;aACA,IAAI,CAAC,MAAM,CAAC,CAChB,CAAC;IACJ,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC;AAClD,CAAC"}
|
|
@@ -170,6 +170,21 @@ export declare const ExtraFeaturesSchema: z.ZodRecord<z.ZodString, z.ZodObject<{
|
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|
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170
|
score: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
|
|
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|
}, z.core.$catchall<z.ZodJSONSchema>>>;
|
|
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172
|
}, z.core.$catchall<z.ZodJSONSchema>>>;
|
|
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|
+
/** Separate residue-rule annotations retain complete provenance and location records. */
|
|
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|
+
export declare const ResidueAnnotationsSchema: z.ZodRecord<z.ZodString, z.ZodObject<{
|
|
175
|
+
accession: z.ZodString;
|
|
176
|
+
source_database: z.ZodString;
|
|
177
|
+
locations: z.ZodArray<z.ZodObject<{
|
|
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|
+
fragments: z.ZodArray<z.ZodObject<{
|
|
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|
+
start: z.ZodNumber;
|
|
180
|
+
end: z.ZodNumber;
|
|
181
|
+
'dc-status': z.ZodOptional<z.ZodString>;
|
|
182
|
+
}, z.core.$catchall<z.ZodJSONSchema>>>;
|
|
183
|
+
representative: z.ZodOptional<z.ZodNullable<z.ZodBoolean>>;
|
|
184
|
+
model: z.ZodOptional<z.ZodNullable<z.ZodString>>;
|
|
185
|
+
score: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
|
|
186
|
+
}, z.core.$catchall<z.ZodJSONSchema>>>;
|
|
187
|
+
}, z.core.$catchall<z.ZodJSONSchema>>>;
|
|
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188
|
/** Standard list envelope; callers select the operation-specific row schema. */
|
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189
|
export declare const listSchema: <T extends z.ZodType>(row: T) => z.ZodObject<{
|
|
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|
count: z.ZodNumber;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"schemas.d.ts","sourceRoot":"","sources":["../../../src/services/interpro/schemas.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,2DAA2D;AAC3D,eAAO,MAAM,eAAe,iBAAiD,CAAC;AAC9E,oEAAoE;AACpE,eAAO,MAAM,gBAAgB,2CAEgB,CAAC;AAC9C,yFAAyF;AACzF,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;EAkBe,CAAC;AACjD,mCAAmC;AACnC,eAAO,MAAM,eAAe;;;;;;;;;;;;EAcS,CAAC;AACtC,kCAAkC;AAClC,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAIlE,sDAAsD;AACtD,eAAO,MAAM,cAAc,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,UAAU,CAAC,+CACjB,CAAC;AAC7C,4FAA4F;AAC5F,eAAO,MAAM,eAAe,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,UAAU,CAAC,gCAAoC,CAAC;AACnG,8EAA8E;AAC9E,eAAO,MAAM,eAAe,aAOyC,CAAC;AACtE;;;GAGG;AACH,eAAO,MAAM,WAAW,UAAW,OAAO,KAAG,KAAK,IAAI,MACwB,CAAC;AAC/E,6DAA6D;AAC7D,eAAO,MAAM,sBAAsB,aAIyD,CAAC;AAC7F,0CAA0C;AAC1C,eAAO,MAAM,YAAY;;;;;;;qCAaI,CAAC;AAC9B,8DAA8D;AAC9D,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;qCAcH,CAAC;AAC7B,wEAAwE;AACxE,eAAO,MAAM,mBAAmB;;;;;;;qCAcJ,CAAC;AAC7B,0FAA0F;AAC1F,eAAO,MAAM,yBAAyB;;;;;;;;qCAOpC,CAAC;AACH,kFAAkF;AAClF,eAAO,MAAM,cAAc;;;;;;;;;qCAqBqB,CAAC;AACjD,mFAAmF;AACnF,eAAO,MAAM,qBAAqB;;;;;;;;;;;qCAsBN,CAAC;AAC7B,gEAAgE;AAChE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qCAmBI,CAAC;AAC7B,sEAAsE;AACtE,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;sCAS/B,CAAC;AACF,gFAAgF;AAChF,eAAO,MAAM,UAAU,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,OAAO,CAAC;;;;;qCAQxB,CAAC;AAC/B,gCAAgC;AAChC,eAAO,MAAM,YAAY,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,YAAY,CAAC;;qCACqC,CAAC;AACnG,kCAAkC;AAClC,eAAO,MAAM,UAAU;;;;;;iBAarB,CAAC"}
|
|
1
|
+
{"version":3,"file":"schemas.d.ts","sourceRoot":"","sources":["../../../src/services/interpro/schemas.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,2DAA2D;AAC3D,eAAO,MAAM,eAAe,iBAAiD,CAAC;AAC9E,oEAAoE;AACpE,eAAO,MAAM,gBAAgB,2CAEgB,CAAC;AAC9C,yFAAyF;AACzF,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;EAkBe,CAAC;AACjD,mCAAmC;AACnC,eAAO,MAAM,eAAe;;;;;;;;;;;;EAcS,CAAC;AACtC,kCAAkC;AAClC,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAIlE,sDAAsD;AACtD,eAAO,MAAM,cAAc,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,UAAU,CAAC,+CACjB,CAAC;AAC7C,4FAA4F;AAC5F,eAAO,MAAM,eAAe,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,UAAU,CAAC,gCAAoC,CAAC;AACnG,8EAA8E;AAC9E,eAAO,MAAM,eAAe,aAOyC,CAAC;AACtE;;;GAGG;AACH,eAAO,MAAM,WAAW,UAAW,OAAO,KAAG,KAAK,IAAI,MACwB,CAAC;AAC/E,6DAA6D;AAC7D,eAAO,MAAM,sBAAsB,aAIyD,CAAC;AAC7F,0CAA0C;AAC1C,eAAO,MAAM,YAAY;;;;;;;qCAaI,CAAC;AAC9B,8DAA8D;AAC9D,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;qCAcH,CAAC;AAC7B,wEAAwE;AACxE,eAAO,MAAM,mBAAmB;;;;;;;qCAcJ,CAAC;AAC7B,0FAA0F;AAC1F,eAAO,MAAM,yBAAyB;;;;;;;;qCAOpC,CAAC;AACH,kFAAkF;AAClF,eAAO,MAAM,cAAc;;;;;;;;;qCAqBqB,CAAC;AACjD,mFAAmF;AACnF,eAAO,MAAM,qBAAqB;;;;;;;;;;;qCAsBN,CAAC;AAC7B,gEAAgE;AAChE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qCAmBI,CAAC;AAC7B,sEAAsE;AACtE,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;sCAS/B,CAAC;AACF,yFAAyF;AACzF,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;sCASpC,CAAC;AACF,gFAAgF;AAChF,eAAO,MAAM,UAAU,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,OAAO,CAAC;;;;;qCAQxB,CAAC;AAC/B,gCAAgC;AAChC,eAAO,MAAM,YAAY,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,YAAY,CAAC;;qCACqC,CAAC;AACnG,kCAAkC;AAClC,eAAO,MAAM,UAAU;;;;;;iBAarB,CAAC"}
|
|
@@ -197,6 +197,14 @@ export const ExtraFeaturesSchema = z.record(z.string(), z
|
|
|
197
197
|
locations: z.array(LocationSchema).describe('Feature locations.'),
|
|
198
198
|
})
|
|
199
199
|
.catchall(JsonValueSchema));
|
|
200
|
+
/** Separate residue-rule annotations retain complete provenance and location records. */
|
|
201
|
+
export const ResidueAnnotationsSchema = z.record(z.string(), z
|
|
202
|
+
.object({
|
|
203
|
+
accession: z.string().describe('Residue rule accession.'),
|
|
204
|
+
source_database: z.string().describe('Rule source database.'),
|
|
205
|
+
locations: z.array(LocationSchema).describe('Complete rule locations and residue fragments.'),
|
|
206
|
+
})
|
|
207
|
+
.catchall(JsonValueSchema));
|
|
200
208
|
/** Standard list envelope; callers select the operation-specific row schema. */
|
|
201
209
|
export const listSchema = (row) => z
|
|
202
210
|
.object({
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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+
{"version":3,"file":"schemas.js","sourceRoot":"","sources":["../../../src/services/interpro/schemas.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,2DAA2D;AAC3D,MAAM,CAAC,MAAM,eAAe,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC,CAAC;AAC9E,oEAAoE;AACpE,MAAM,CAAC,MAAM,gBAAgB,GAAG,CAAC;KAC9B,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,eAAe,CAAC;KACnC,QAAQ,CAAC,gCAAgC,CAAC,CAAC;AAC9C,yFAAyF;AACzF,MAAM,CAAC,MAAM,oBAAoB,GAAG,CAAC;KAClC,IAAI,CAAC;IACJ,UAAU;IACV,MAAM;IACN,SAAS;IACT,SAAS;IACT,OAAO;IACP,KAAK;IACL,SAAS;IACT,YAAY;IACZ,KAAK;IACL,SAAS;IACT,OAAO;IACP,QAAQ;IACR,OAAO;IACP,MAAM;IACN,SAAS;CACV,CAAC;KACD,QAAQ,CAAC,mCAAmC,CAAC,CAAC;AACjD,mCAAmC;AACnC,MAAM,CAAC,MAAM,eAAe,GAAG,CAAC;KAC7B,IAAI,CAAC;IACJ,QAAQ;IACR,QAAQ;IACR,QAAQ;IACR,wBAAwB;IACxB,aAAa;IACb,cAAc;IACd,gBAAgB;IAChB,KAAK;IACL,QAAQ;IACR,aAAa;IACb,YAAY;CACb,CAAC;KACD,QAAQ,CAAC,wBAAwB,CAAC,CAAC;AAGtC,6EAA6E;AAC7E,MAAM,SAAS,GAAG,CAAC,KAAc,EAAE,EAAE,CACnC,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,CAAC,IAAI,EAAE,KAAK,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK,CAAC;AACvE,sDAAsD;AACtD,MAAM,CAAC,MAAM,cAAc,GAAG,CAAsB,MAAS,EAAE,EAAE,CAC/D,CAAC,CAAC,UAAU,CAAC,SAAS,EAAE,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC;AAC7C,4FAA4F;AAC5F,MAAM,CAAC,MAAM,eAAe,GAAG,CAAsB,MAAS,EAAE,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC,SAAS,EAAE,MAAM,CAAC,CAAC;AACnG,8EAA8E;AAC9E,MAAM,CAAC,MAAM,eAAe,GAAG,CAAC;KAC7B,MAAM,EAAE;KACR,IAAI,EAAE;KACN,GAAG,CAAC,CAAC,CAAC;KACN,GAAG,CAAC,GAAG,CAAC;KACR,KAAK,CAAC,oBAAoB,CAAC;KAC3B,MAAM,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,KAAK,GAAG,IAAI,KAAK,KAAK,IAAI,EAAE,kCAAkC,CAAC;KACtF,QAAQ,CAAC,wDAAwD,CAAC,CAAC;AACtE;;;GAGG;AACH,MAAM,CAAC,MAAM,WAAW,GAAG,CAAC,KAAc,EAAmB,EAAE,CAC7D,OAAO,KAAK,KAAK,QAAQ,IAAI,eAAe,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,IAAI,KAAK,KAAK,CAAC;AAC/E,6DAA6D;AAC7D,MAAM,CAAC,MAAM,sBAAsB,GAAG,CAAC;KACpC,MAAM,EAAE;KACR,IAAI,EAAE;KACN,KAAK,CAAC,+EAA+E,CAAC;KACtF,QAAQ,CAAC,+EAA+E,CAAC,CAAC;AAC7F,0CAA0C;AAC1C,MAAM,CAAC,MAAM,YAAY,GAAG,CAAC;KAC1B,MAAM,CAAC;IACN,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;IACjD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;IAC1C,QAAQ,EAAE,CAAC;SACR,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;QAC9C,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;KAC/C,CAAC;SACD,QAAQ,CAAC,eAAe,CAAC;SACzB,QAAQ,CAAC,cAAc,CAAC;CAC5B,CAAC;KACD,QAAQ,CAAC,eAAe,CAAC;KACzB,QAAQ,CAAC,gBAAgB,CAAC,CAAC;AAC9B,8DAA8D;AAC9D,MAAM,CAAC,MAAM,kBAAkB,GAAG,CAAC;KAChC,MAAM,CAAC;IACN,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;IAClD,eAAe,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;IACjE,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;IAC5E,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;IAC5E,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;IACvF,gBAAgB,EAAE,CAAC;SAChB,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;SACpD,QAAQ,EAAE;SACV,QAAQ,EAAE;SACV,QAAQ,CAAC,wCAAwC,CAAC;IACrD,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;CAChG,CAAC;KACD,QAAQ,CAAC,eAAe,CAAC,CAAC;AAC7B,wEAAwE;AACxE,MAAM,CAAC,MAAM,mBAAmB,GAAG,CAAC;KACjC,MAAM,CAAC;IACN,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;IAClD,eAAe,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;IAC1D,IAAI,EAAE,CAAC;SACJ,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC;QAC7D,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,aAAa,CAAC;KAChE,CAAC;SACD,QAAQ,CAAC,eAAe,CAAC;SACzB,QAAQ,EAAE;SACV,QAAQ,EAAE;SACV,QAAQ,CAAC,qBAAqB,CAAC;CACnC,CAAC;KACD,QAAQ,CAAC,eAAe,CAAC,CAAC;AAC7B,0FAA0F;AAC1F,MAAM,CAAC,MAAM,yBAAyB,GAAG,mBAAmB,CAAC,MAAM,CAAC;IAClE,eAAe,EAAE,CAAC;SACf,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,+FAA+F,CAChG;CACJ,CAAC,CAAC;AACH,kFAAkF;AAClF,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC;KAC5B,MAAM,CAAC;IACN,SAAS,EAAE,CAAC;SACT,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QAC/E,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;QAC3E,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;KACrE,CAAC;SACD,QAAQ,CAAC,eAAe,CAAC;SACzB,MAAM,CAAC,CAAC,QAAQ,EAAE,EAAE,CAAC,QAAQ,CAAC,KAAK,IAAI,QAAQ,CAAC,GAAG,EAAE,6BAA6B,CAAC;SACnF,QAAQ,CAAC,yDAAyD,CAAC,CACvE;SACA,GAAG,CAAC,CAAC,CAAC;SACN,QAAQ,CAAC,8BAA8B,CAAC;IAC3C,cAAc,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,4BAA4B,CAAC;IACxF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;IACjE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;CAC1E,CAAC;KACD,QAAQ,CAAC,eAAe,CAAC;KACzB,QAAQ,CAAC,mCAAmC,CAAC,CAAC;AACjD,mFAAmF;AACnF,MAAM,CAAC,MAAM,qBAAqB,GAAG,CAAC;KACnC,MAAM,CAAC;IACN,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;IACpD,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAA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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/interpro-mcp-server",
|
|
3
|
-
"version": "0.1.
|
|
3
|
+
"version": "0.1.3",
|
|
4
4
|
"mcpName": "io.github.cyanheads/interpro-mcp-server",
|
|
5
5
|
"description": "Search InterPro entries, map protein domains and functional sites, and find proteins by domain via MCP. STDIO or Streamable HTTP.",
|
|
6
6
|
"author": "Casey Hand <casey@caseyjhand.com> (https://caseyjhand.com)",
|
|
@@ -86,13 +86,13 @@
|
|
|
86
86
|
"access": "public"
|
|
87
87
|
},
|
|
88
88
|
"dependencies": {
|
|
89
|
-
"@cyanheads/mcp-ts-core": "^0.13.
|
|
89
|
+
"@cyanheads/mcp-ts-core": "^0.13.16",
|
|
90
90
|
"htmlparser2": "^12.0.0",
|
|
91
91
|
"pino-pretty": "^13.2.0",
|
|
92
92
|
"zod": "^4.6.7"
|
|
93
93
|
},
|
|
94
94
|
"devDependencies": {
|
|
95
|
-
"@biomejs/biome": "2.
|
|
95
|
+
"@biomejs/biome": "2.6.2",
|
|
96
96
|
"@socketsecurity/bun-security-scanner": "^1.1.3",
|
|
97
97
|
"@types/node": "26.6.5",
|
|
98
98
|
"@vitest/coverage-istanbul": "5.0.5",
|
package/server.json
CHANGED
|
@@ -6,7 +6,7 @@
|
|
|
6
6
|
"url": "https://github.com/cyanheads/interpro-mcp-server",
|
|
7
7
|
"source": "github"
|
|
8
8
|
},
|
|
9
|
-
"version": "0.1.
|
|
9
|
+
"version": "0.1.3",
|
|
10
10
|
"remotes": [
|
|
11
11
|
{
|
|
12
12
|
"type": "streamable-http",
|
|
@@ -19,7 +19,7 @@
|
|
|
19
19
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
20
20
|
"identifier": "@cyanheads/interpro-mcp-server",
|
|
21
21
|
"runtimeHint": "npx",
|
|
22
|
-
"version": "0.1.
|
|
22
|
+
"version": "0.1.3",
|
|
23
23
|
"environmentVariables": [
|
|
24
24
|
{
|
|
25
25
|
"name": "MCP_LOG_LEVEL",
|
|
@@ -38,7 +38,7 @@
|
|
|
38
38
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
39
39
|
"identifier": "@cyanheads/interpro-mcp-server",
|
|
40
40
|
"runtimeHint": "npx",
|
|
41
|
-
"version": "0.1.
|
|
41
|
+
"version": "0.1.3",
|
|
42
42
|
"environmentVariables": [
|
|
43
43
|
{
|
|
44
44
|
"name": "MCP_TRANSPORT_TYPE",
|