@cyanheads/brapi-mcp-server 0.3.5
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 +391 -0
- package/Dockerfile +99 -0
- package/LICENSE +201 -0
- package/README.md +590 -0
- package/changelog/0.1.x/0.1.0.md +19 -0
- package/changelog/0.1.x/0.1.1.md +27 -0
- package/changelog/0.1.x/0.1.2.md +22 -0
- package/changelog/0.2.x/0.2.0.md +35 -0
- package/changelog/0.2.x/0.2.1.md +36 -0
- package/changelog/0.3.x/0.3.0.md +38 -0
- package/changelog/0.3.x/0.3.1.md +40 -0
- package/changelog/0.3.x/0.3.2.md +29 -0
- package/changelog/0.3.x/0.3.3.md +19 -0
- package/changelog/0.3.x/0.3.4.md +33 -0
- package/changelog/0.3.x/0.3.5.md +24 -0
- package/changelog/template.md +51 -0
- package/dist/config/alias-credentials.d.ts +82 -0
- package/dist/config/alias-credentials.d.ts.map +1 -0
- package/dist/config/alias-credentials.js +159 -0
- package/dist/config/alias-credentials.js.map +1 -0
- package/dist/config/server-config.d.ts +39 -0
- package/dist/config/server-config.d.ts.map +1 -0
- package/dist/config/server-config.js +128 -0
- package/dist/config/server-config.js.map +1 -0
- package/dist/index.d.ts +10 -0
- package/dist/index.d.ts.map +1 -0
- package/dist/index.js +85 -0
- package/dist/index.js.map +1 -0
- package/dist/mcp-server/prompts/definitions/brapi-eda-study.prompt.d.ts +14 -0
- package/dist/mcp-server/prompts/definitions/brapi-eda-study.prompt.d.ts.map +1 -0
- package/dist/mcp-server/prompts/definitions/brapi-eda-study.prompt.js +75 -0
- package/dist/mcp-server/prompts/definitions/brapi-eda-study.prompt.js.map +1 -0
- package/dist/mcp-server/prompts/definitions/brapi-meta-analysis.prompt.d.ts +16 -0
- package/dist/mcp-server/prompts/definitions/brapi-meta-analysis.prompt.d.ts.map +1 -0
- package/dist/mcp-server/prompts/definitions/brapi-meta-analysis.prompt.js +109 -0
- package/dist/mcp-server/prompts/definitions/brapi-meta-analysis.prompt.js.map +1 -0
- package/dist/mcp-server/resources/definitions/brapi-calls.resource.d.ts +11 -0
- package/dist/mcp-server/resources/definitions/brapi-calls.resource.d.ts.map +1 -0
- package/dist/mcp-server/resources/definitions/brapi-calls.resource.js +46 -0
- package/dist/mcp-server/resources/definitions/brapi-calls.resource.js.map +1 -0
- package/dist/mcp-server/resources/definitions/brapi-dataset.resource.d.ts +13 -0
- package/dist/mcp-server/resources/definitions/brapi-dataset.resource.d.ts.map +1 -0
- package/dist/mcp-server/resources/definitions/brapi-dataset.resource.js +26 -0
- package/dist/mcp-server/resources/definitions/brapi-dataset.resource.js.map +1 -0
- package/dist/mcp-server/resources/definitions/brapi-filters.resource.d.ts +19 -0
- package/dist/mcp-server/resources/definitions/brapi-filters.resource.d.ts.map +1 -0
- package/dist/mcp-server/resources/definitions/brapi-filters.resource.js +45 -0
- package/dist/mcp-server/resources/definitions/brapi-filters.resource.js.map +1 -0
- package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.d.ts +18 -0
- package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.d.ts.map +1 -0
- package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.js +34 -0
- package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.js.map +1 -0
- package/dist/mcp-server/resources/definitions/brapi-server-info.resource.d.ts +11 -0
- package/dist/mcp-server/resources/definitions/brapi-server-info.resource.d.ts.map +1 -0
- package/dist/mcp-server/resources/definitions/brapi-server-info.resource.js +28 -0
- package/dist/mcp-server/resources/definitions/brapi-server-info.resource.js.map +1 -0
- package/dist/mcp-server/resources/definitions/brapi-study.resource.d.ts +18 -0
- package/dist/mcp-server/resources/definitions/brapi-study.resource.d.ts.map +1 -0
- package/dist/mcp-server/resources/definitions/brapi-study.resource.js +34 -0
- package/dist/mcp-server/resources/definitions/brapi-study.resource.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts +82 -0
- package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-connect.tool.js +106 -0
- package/dist/mcp-server/tools/definitions/brapi-connect.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-describe-filters.tool.d.ts +41 -0
- package/dist/mcp-server/tools/definitions/brapi-describe-filters.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-describe-filters.tool.js +88 -0
- package/dist/mcp-server/tools/definitions/brapi-describe-filters.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts +74 -0
- package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.js +386 -0
- package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.d.ts +72 -0
- package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.js +290 -0
- package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-images.tool.d.ts +65 -0
- package/dist/mcp-server/tools/definitions/brapi-find-images.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-images.tool.js +243 -0
- package/dist/mcp-server/tools/definitions/brapi-find-images.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.d.ts +63 -0
- package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.js +278 -0
- package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts +74 -0
- package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.js +288 -0
- package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.d.ts +69 -0
- package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.js +243 -0
- package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.d.ts +86 -0
- package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.js +337 -0
- package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.d.ts +59 -0
- package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.js +248 -0
- package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.d.ts +59 -0
- package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.js +306 -0
- package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-get-image.tool.d.ts +57 -0
- package/dist/mcp-server/tools/definitions/brapi-get-image.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-get-image.tool.js +291 -0
- package/dist/mcp-server/tools/definitions/brapi-get-image.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-get-study.tool.d.ts +75 -0
- package/dist/mcp-server/tools/definitions/brapi-get-study.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-get-study.tool.js +323 -0
- package/dist/mcp-server/tools/definitions/brapi-get-study.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-manage-dataset.tool.d.ts +87 -0
- package/dist/mcp-server/tools/definitions/brapi-manage-dataset.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-manage-dataset.tool.js +296 -0
- package/dist/mcp-server/tools/definitions/brapi-manage-dataset.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.d.ts +35 -0
- package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.js +148 -0
- package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.d.ts +33 -0
- package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.js +126 -0
- package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-server-info.tool.d.ts +51 -0
- package/dist/mcp-server/tools/definitions/brapi-server-info.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-server-info.tool.js +41 -0
- package/dist/mcp-server/tools/definitions/brapi-server-info.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.d.ts +117 -0
- package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.js +574 -0
- package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.d.ts +52 -0
- package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.js +420 -0
- package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.js.map +1 -0
- package/dist/mcp-server/tools/shared/connect-auth-schema.d.ts +29 -0
- package/dist/mcp-server/tools/shared/connect-auth-schema.d.ts.map +1 -0
- package/dist/mcp-server/tools/shared/connect-auth-schema.js +55 -0
- package/dist/mcp-server/tools/shared/connect-auth-schema.js.map +1 -0
- package/dist/mcp-server/tools/shared/find-helpers.d.ts +143 -0
- package/dist/mcp-server/tools/shared/find-helpers.d.ts.map +1 -0
- package/dist/mcp-server/tools/shared/find-helpers.js +319 -0
- package/dist/mcp-server/tools/shared/find-helpers.js.map +1 -0
- package/dist/mcp-server/tools/shared/orientation-envelope.d.ts +97 -0
- package/dist/mcp-server/tools/shared/orientation-envelope.d.ts.map +1 -0
- package/dist/mcp-server/tools/shared/orientation-envelope.js +254 -0
- package/dist/mcp-server/tools/shared/orientation-envelope.js.map +1 -0
- package/dist/mcp-server/tools/shared/raw-routing-hints.d.ts +10 -0
- package/dist/mcp-server/tools/shared/raw-routing-hints.d.ts.map +1 -0
- package/dist/mcp-server/tools/shared/raw-routing-hints.js +46 -0
- package/dist/mcp-server/tools/shared/raw-routing-hints.js.map +1 -0
- package/dist/services/brapi-client/brapi-client.d.ts +76 -0
- package/dist/services/brapi-client/brapi-client.d.ts.map +1 -0
- package/dist/services/brapi-client/brapi-client.js +320 -0
- package/dist/services/brapi-client/brapi-client.js.map +1 -0
- package/dist/services/brapi-client/index.d.ts +9 -0
- package/dist/services/brapi-client/index.d.ts.map +1 -0
- package/dist/services/brapi-client/index.js +7 -0
- package/dist/services/brapi-client/index.js.map +1 -0
- package/dist/services/brapi-client/types.d.ts +82 -0
- package/dist/services/brapi-client/types.d.ts.map +1 -0
- package/dist/services/brapi-client/types.js +8 -0
- package/dist/services/brapi-client/types.js.map +1 -0
- package/dist/services/brapi-filters/catalog.d.ts +14 -0
- package/dist/services/brapi-filters/catalog.d.ts.map +1 -0
- package/dist/services/brapi-filters/catalog.js +490 -0
- package/dist/services/brapi-filters/catalog.js.map +1 -0
- package/dist/services/brapi-filters/index.d.ts +8 -0
- package/dist/services/brapi-filters/index.d.ts.map +1 -0
- package/dist/services/brapi-filters/index.js +7 -0
- package/dist/services/brapi-filters/index.js.map +1 -0
- package/dist/services/brapi-filters/types.d.ts +23 -0
- package/dist/services/brapi-filters/types.d.ts.map +1 -0
- package/dist/services/brapi-filters/types.js +9 -0
- package/dist/services/brapi-filters/types.js.map +1 -0
- package/dist/services/capability-registry/capability-registry.d.ts +51 -0
- package/dist/services/capability-registry/capability-registry.d.ts.map +1 -0
- package/dist/services/capability-registry/capability-registry.js +234 -0
- package/dist/services/capability-registry/capability-registry.js.map +1 -0
- package/dist/services/capability-registry/index.d.ts +9 -0
- package/dist/services/capability-registry/index.d.ts.map +1 -0
- package/dist/services/capability-registry/index.js +7 -0
- package/dist/services/capability-registry/index.js.map +1 -0
- package/dist/services/capability-registry/types.d.ts +67 -0
- package/dist/services/capability-registry/types.d.ts.map +1 -0
- package/dist/services/capability-registry/types.js +9 -0
- package/dist/services/capability-registry/types.js.map +1 -0
- package/dist/services/dataset-store/dataset-store.d.ts +35 -0
- package/dist/services/dataset-store/dataset-store.d.ts.map +1 -0
- package/dist/services/dataset-store/dataset-store.js +190 -0
- package/dist/services/dataset-store/dataset-store.js.map +1 -0
- package/dist/services/dataset-store/index.d.ts +8 -0
- package/dist/services/dataset-store/index.d.ts.map +1 -0
- package/dist/services/dataset-store/index.js +7 -0
- package/dist/services/dataset-store/index.js.map +1 -0
- package/dist/services/dataset-store/types.d.ts +65 -0
- package/dist/services/dataset-store/types.d.ts.map +1 -0
- package/dist/services/dataset-store/types.js +8 -0
- package/dist/services/dataset-store/types.js.map +1 -0
- package/dist/services/ontology-resolver/index.d.ts +8 -0
- package/dist/services/ontology-resolver/index.d.ts.map +1 -0
- package/dist/services/ontology-resolver/index.js +7 -0
- package/dist/services/ontology-resolver/index.js.map +1 -0
- package/dist/services/ontology-resolver/ontology-resolver.d.ts +49 -0
- package/dist/services/ontology-resolver/ontology-resolver.d.ts.map +1 -0
- package/dist/services/ontology-resolver/ontology-resolver.js +99 -0
- package/dist/services/ontology-resolver/ontology-resolver.js.map +1 -0
- package/dist/services/ontology-resolver/types.d.ts +38 -0
- package/dist/services/ontology-resolver/types.d.ts.map +1 -0
- package/dist/services/ontology-resolver/types.js +8 -0
- package/dist/services/ontology-resolver/types.js.map +1 -0
- package/dist/services/reference-data-cache/index.d.ts +9 -0
- package/dist/services/reference-data-cache/index.d.ts.map +1 -0
- package/dist/services/reference-data-cache/index.js +7 -0
- package/dist/services/reference-data-cache/index.js.map +1 -0
- package/dist/services/reference-data-cache/reference-data-cache.d.ts +31 -0
- package/dist/services/reference-data-cache/reference-data-cache.d.ts.map +1 -0
- package/dist/services/reference-data-cache/reference-data-cache.js +131 -0
- package/dist/services/reference-data-cache/reference-data-cache.js.map +1 -0
- package/dist/services/reference-data-cache/types.d.ts +42 -0
- package/dist/services/reference-data-cache/types.d.ts.map +1 -0
- package/dist/services/reference-data-cache/types.js +9 -0
- package/dist/services/reference-data-cache/types.js.map +1 -0
- package/dist/services/server-registry/index.d.ts +9 -0
- package/dist/services/server-registry/index.d.ts.map +1 -0
- package/dist/services/server-registry/index.js +7 -0
- package/dist/services/server-registry/index.js.map +1 -0
- package/dist/services/server-registry/server-registry.d.ts +57 -0
- package/dist/services/server-registry/server-registry.d.ts.map +1 -0
- package/dist/services/server-registry/server-registry.js +210 -0
- package/dist/services/server-registry/server-registry.js.map +1 -0
- package/dist/services/server-registry/types.d.ts +43 -0
- package/dist/services/server-registry/types.d.ts.map +1 -0
- package/dist/services/server-registry/types.js +10 -0
- package/dist/services/server-registry/types.js.map +1 -0
- package/package.json +86 -0
- package/server.json +99 -0
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/**
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* @fileoverview `brapi_find_germplasm` — search germplasm by name, synonym,
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* accession, attribute, or free text. Matches BrAPI's registered-synonym
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* semantics. Returns distributions for crop / genus / species / collection
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* and spills to DatasetStore when the upstream total exceeds loadLimit.
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*
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* @module mcp-server/tools/definitions/brapi-find-germplasm.tool
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*/
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import { tool, z } from '@cyanheads/mcp-ts-core';
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import { getServerConfig } from '../../../config/server-config.js';
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import { getBrapiClient } from '../../../services/brapi-client/index.js';
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import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
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import { getDatasetStore } from '../../../services/dataset-store/index.js';
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import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
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import { AliasInput, asString, buildRefinementHint, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderDatasetHandle, renderDistributions, } from '../shared/find-helpers.js';
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const GermplasmRowSchema = z
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.object({
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germplasmDbId: z.string().describe('Server-side identifier for the germplasm.'),
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germplasmName: z.string().nullish().describe('Display name.'),
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germplasmPUI: z.string().nullish().describe('Persistent unique identifier (URI).'),
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commonCropName: z.string().nullish().describe('Common crop name (e.g. "Maize", "Wheat").'),
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accessionNumber: z.string().nullish().describe('Gene-bank catalog number.'),
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genus: z.string().nullish().describe('Botanical genus.'),
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species: z.string().nullish().describe('Botanical species.'),
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subtaxa: z.string().nullish().describe('Botanical subtaxa (subspecies, variety, etc.).'),
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defaultDisplayName: z.string().nullish().describe('Preferred display label.'),
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pedigree: z.string().nullish().describe('Pedigree as a free-text string (e.g. "A/B//C").'),
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biologicalStatusOfAccessionDescription: z
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.string()
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.nullish()
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.describe('MCPD biological-status label (wild / landrace / breeding / cultivar, etc.).'),
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germplasmOrigin: z
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.array(z
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.object({})
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.passthrough()
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.describe('One origin record (collection coordinates and uncertainty per BrAPI v2).'))
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.nullish()
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.describe('Origin records — array of collection-site objects per BrAPI v2.'),
|
|
39
|
+
countryOfOriginCode: z.string().nullish().describe('ISO 3166-1 alpha-3 country code.'),
|
|
40
|
+
collection: z.string().nullish().describe('Collection name this accession belongs to.'),
|
|
41
|
+
instituteCode: z
|
|
42
|
+
.string()
|
|
43
|
+
.nullish()
|
|
44
|
+
.describe('FAO WIEWS institute code of the holding institute.'),
|
|
45
|
+
instituteName: z.string().nullish().describe('Display name of the holding institute.'),
|
|
46
|
+
synonyms: z
|
|
47
|
+
.array(z
|
|
48
|
+
.object({
|
|
49
|
+
synonym: z.string().nullish().describe('Synonym value.'),
|
|
50
|
+
type: z.string().nullish().describe('Synonym type (e.g. "COMMON", "SYNONYM").'),
|
|
51
|
+
})
|
|
52
|
+
.passthrough()
|
|
53
|
+
.describe('Registered synonym for this germplasm.'))
|
|
54
|
+
.nullish()
|
|
55
|
+
.describe('All registered synonyms (alternative names).'),
|
|
56
|
+
})
|
|
57
|
+
.passthrough()
|
|
58
|
+
.describe('One BrAPI germplasm record.');
|
|
59
|
+
const OutputSchema = z.object({
|
|
60
|
+
alias: z.string().describe('Alias of the registered BrAPI connection the call used.'),
|
|
61
|
+
results: z
|
|
62
|
+
.array(GermplasmRowSchema)
|
|
63
|
+
.describe('Germplasm rows returned in-context (up to loadLimit).'),
|
|
64
|
+
returnedCount: z.number().int().nonnegative().describe('Length of `results[]`.'),
|
|
65
|
+
totalCount: z.number().int().nonnegative().describe('Total rows reported by the server.'),
|
|
66
|
+
hasMore: z.boolean().describe('True when more rows exist beyond the returned set.'),
|
|
67
|
+
distributions: z
|
|
68
|
+
.object({
|
|
69
|
+
commonCropName: z
|
|
70
|
+
.record(z.string(), z.number())
|
|
71
|
+
.describe('Common crop name → count of rows for that crop.'),
|
|
72
|
+
genus: z.record(z.string(), z.number()).describe('Genus → count of rows with that genus.'),
|
|
73
|
+
species: z
|
|
74
|
+
.record(z.string(), z.number())
|
|
75
|
+
.describe('Species → count of rows with that species.'),
|
|
76
|
+
collection: z
|
|
77
|
+
.record(z.string(), z.number())
|
|
78
|
+
.describe('Collection name → count of rows in that collection.'),
|
|
79
|
+
countryOfOriginCode: z
|
|
80
|
+
.record(z.string(), z.number())
|
|
81
|
+
.describe('ISO country code → count of rows from that country.'),
|
|
82
|
+
})
|
|
83
|
+
.describe('Value frequency per field across the full result set.'),
|
|
84
|
+
refinementHint: z
|
|
85
|
+
.string()
|
|
86
|
+
.optional()
|
|
87
|
+
.describe('Suggested next-step query refinement when the result set is large.'),
|
|
88
|
+
dataset: DatasetHandleSchema.optional().describe('Dataset handle when the full result set was persisted to DatasetStore.'),
|
|
89
|
+
warnings: z
|
|
90
|
+
.array(z.string())
|
|
91
|
+
.describe('Advisory messages (filter overrides, partial data, capability gaps, etc.).'),
|
|
92
|
+
appliedFilters: z
|
|
93
|
+
.record(z.string(), z.unknown())
|
|
94
|
+
.describe('The final filter map sent to the server (named + extraFilters).'),
|
|
95
|
+
});
|
|
96
|
+
export const brapiFindGermplasm = tool('brapi_find_germplasm', {
|
|
97
|
+
description: 'Find germplasm by name, synonym, accession number, PUI, crop, or free-text query. Matches across registered synonyms. Returns a dataset handle when the upstream total exceeds loadLimit.',
|
|
98
|
+
annotations: { readOnlyHint: true, openWorldHint: true },
|
|
99
|
+
input: z.object({
|
|
100
|
+
alias: AliasInput,
|
|
101
|
+
names: z.array(z.string()).optional().describe('Filter by germplasm display names.'),
|
|
102
|
+
germplasmDbIds: z.array(z.string()).optional().describe('Filter by DbIds.'),
|
|
103
|
+
germplasmPUIs: z.array(z.string()).optional().describe('Persistent unique identifiers.'),
|
|
104
|
+
accessionNumbers: z
|
|
105
|
+
.array(z.string())
|
|
106
|
+
.optional()
|
|
107
|
+
.describe('Filter by accession numbers (gene-bank catalog codes).'),
|
|
108
|
+
crops: z.array(z.string()).optional().describe('Filter by common crop names.'),
|
|
109
|
+
synonyms: z.array(z.string()).optional().describe('Match registered synonyms.'),
|
|
110
|
+
collections: z.array(z.string()).optional().describe('Filter by germplasm collection names.'),
|
|
111
|
+
genus: z.string().optional().describe('Botanical genus.'),
|
|
112
|
+
species: z.string().optional().describe('Botanical species.'),
|
|
113
|
+
text: z.string().optional().describe('Free-text query. Server-supported subset.'),
|
|
114
|
+
loadLimit: LoadLimitInput,
|
|
115
|
+
extraFilters: ExtraFiltersInput,
|
|
116
|
+
}),
|
|
117
|
+
output: OutputSchema,
|
|
118
|
+
async handler(input, ctx) {
|
|
119
|
+
const registry = getServerRegistry();
|
|
120
|
+
const capabilities = getCapabilityRegistry();
|
|
121
|
+
const client = getBrapiClient();
|
|
122
|
+
const datasetStore = getDatasetStore();
|
|
123
|
+
const config = getServerConfig();
|
|
124
|
+
const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
|
|
125
|
+
const capabilityLookup = {};
|
|
126
|
+
if (connection.resolvedAuth)
|
|
127
|
+
capabilityLookup.auth = connection.resolvedAuth;
|
|
128
|
+
await capabilities.ensure(connection.baseUrl, { service: 'germplasm', method: 'GET' }, ctx, capabilityLookup);
|
|
129
|
+
const warnings = [];
|
|
130
|
+
const filters = mergeFilters({
|
|
131
|
+
germplasmNames: input.names,
|
|
132
|
+
germplasmDbIds: input.germplasmDbIds,
|
|
133
|
+
germplasmPUIs: input.germplasmPUIs,
|
|
134
|
+
accessionNumbers: input.accessionNumbers,
|
|
135
|
+
commonCropNames: input.crops,
|
|
136
|
+
synonyms: input.synonyms,
|
|
137
|
+
collections: input.collections,
|
|
138
|
+
genus: input.genus,
|
|
139
|
+
species: input.species,
|
|
140
|
+
searchText: input.text,
|
|
141
|
+
}, input.extraFilters, warnings);
|
|
142
|
+
const loadLimit = input.loadLimit ?? config.loadLimit;
|
|
143
|
+
const firstPage = await loadInitialPage(client, connection, '/germplasm', filters, loadLimit, ctx);
|
|
144
|
+
const { fullRows, dataset: datasetMeta } = await maybeSpill({
|
|
145
|
+
firstPage,
|
|
146
|
+
client,
|
|
147
|
+
connection,
|
|
148
|
+
path: '/germplasm',
|
|
149
|
+
filters,
|
|
150
|
+
source: 'find_germplasm',
|
|
151
|
+
loadLimit,
|
|
152
|
+
ctx,
|
|
153
|
+
store: datasetStore,
|
|
154
|
+
});
|
|
155
|
+
const distributions = {
|
|
156
|
+
commonCropName: computeDistribution(fullRows, (r) => asString(r.commonCropName)),
|
|
157
|
+
genus: computeDistribution(fullRows, (r) => asString(r.genus)),
|
|
158
|
+
species: computeDistribution(fullRows, (r) => asString(r.species)),
|
|
159
|
+
collection: computeDistribution(fullRows, (r) => asString(r.collection)),
|
|
160
|
+
countryOfOriginCode: computeDistribution(fullRows, (r) => asString(r.countryOfOriginCode)),
|
|
161
|
+
};
|
|
162
|
+
const totalCount = firstPage.totalCount ?? firstPage.rows.length;
|
|
163
|
+
const refinementHint = buildRefinementHint(totalCount, loadLimit, distributions);
|
|
164
|
+
// Heuristic: if the user asked for a text filter and the upstream returned
|
|
165
|
+
// every row that matches all the *other* filters (i.e. the text didn't
|
|
166
|
+
// narrow anything), the server probably doesn't honor the filter.
|
|
167
|
+
if (input.text &&
|
|
168
|
+
totalCount > 0 &&
|
|
169
|
+
firstPage.totalCount !== undefined &&
|
|
170
|
+
firstPage.rows.length === firstPage.totalCount &&
|
|
171
|
+
!hasRowsMatchingText(firstPage.rows, input.text)) {
|
|
172
|
+
warnings.push(`Free-text filter '${input.text}' may not be honored by this server — none of the returned rows obviously match the query string.`);
|
|
173
|
+
}
|
|
174
|
+
const result = {
|
|
175
|
+
alias: connection.alias,
|
|
176
|
+
results: firstPage.rows,
|
|
177
|
+
returnedCount: firstPage.rows.length,
|
|
178
|
+
totalCount,
|
|
179
|
+
hasMore: firstPage.hasMore,
|
|
180
|
+
distributions,
|
|
181
|
+
warnings,
|
|
182
|
+
appliedFilters: filters,
|
|
183
|
+
};
|
|
184
|
+
if (refinementHint)
|
|
185
|
+
result.refinementHint = refinementHint;
|
|
186
|
+
if (datasetMeta)
|
|
187
|
+
result.dataset = datasetMeta;
|
|
188
|
+
return result;
|
|
189
|
+
},
|
|
190
|
+
format: (result) => {
|
|
191
|
+
const lines = [];
|
|
192
|
+
lines.push(`# ${result.returnedCount} of ${result.totalCount} germplasm — \`${result.alias}\``);
|
|
193
|
+
lines.push('');
|
|
194
|
+
if (result.hasMore) {
|
|
195
|
+
lines.push(`⚠ More rows exist beyond the returned set. ${result.dataset ? `Full set persisted as dataset \`${result.dataset.datasetId}\`.` : 'Narrow filters or raise loadLimit.'}`);
|
|
196
|
+
lines.push('');
|
|
197
|
+
}
|
|
198
|
+
if (result.refinementHint) {
|
|
199
|
+
lines.push(`**Refinement hint:** ${result.refinementHint}`);
|
|
200
|
+
lines.push('');
|
|
201
|
+
}
|
|
202
|
+
lines.push(`Applied filters: \`${JSON.stringify(result.appliedFilters)}\``);
|
|
203
|
+
lines.push('');
|
|
204
|
+
lines.push('## Distributions');
|
|
205
|
+
lines.push(renderDistributions(result.distributions) || '_No values to summarize._');
|
|
206
|
+
lines.push('');
|
|
207
|
+
lines.push('## Germplasm');
|
|
208
|
+
if (result.results.length === 0) {
|
|
209
|
+
lines.push('_No rows returned._');
|
|
210
|
+
}
|
|
211
|
+
else {
|
|
212
|
+
for (const g of result.results) {
|
|
213
|
+
const parts = [
|
|
214
|
+
`**${g.germplasmName ?? g.defaultDisplayName ?? g.germplasmDbId}**`,
|
|
215
|
+
];
|
|
216
|
+
parts.push(`id=\`${g.germplasmDbId}\``);
|
|
217
|
+
if (g.germplasmPUI)
|
|
218
|
+
parts.push(`pui=${g.germplasmPUI}`);
|
|
219
|
+
if (g.accessionNumber)
|
|
220
|
+
parts.push(`accession=${g.accessionNumber}`);
|
|
221
|
+
if (g.commonCropName)
|
|
222
|
+
parts.push(`crop=${g.commonCropName}`);
|
|
223
|
+
if (g.genus)
|
|
224
|
+
parts.push(`genus=${g.genus}`);
|
|
225
|
+
if (g.species)
|
|
226
|
+
parts.push(`species=${g.species}`);
|
|
227
|
+
if (g.subtaxa)
|
|
228
|
+
parts.push(`subtaxa=${g.subtaxa}`);
|
|
229
|
+
if (g.countryOfOriginCode)
|
|
230
|
+
parts.push(`country=${g.countryOfOriginCode}`);
|
|
231
|
+
if (g.collection)
|
|
232
|
+
parts.push(`collection=${g.collection}`);
|
|
233
|
+
if (g.instituteCode)
|
|
234
|
+
parts.push(`institute=${g.instituteCode}`);
|
|
235
|
+
if (g.instituteName)
|
|
236
|
+
parts.push(`instituteName=${g.instituteName}`);
|
|
237
|
+
if (g.germplasmOrigin?.length)
|
|
238
|
+
parts.push(`germplasmOrigin=${g.germplasmOrigin.length} record(s)`);
|
|
239
|
+
if (g.biologicalStatusOfAccessionDescription)
|
|
240
|
+
parts.push(`status=${g.biologicalStatusOfAccessionDescription}`);
|
|
241
|
+
if (g.pedigree)
|
|
242
|
+
parts.push(`pedigree=${g.pedigree}`);
|
|
243
|
+
if (g.defaultDisplayName)
|
|
244
|
+
parts.push(`displayName=${g.defaultDisplayName}`);
|
|
245
|
+
if (g.synonyms?.length) {
|
|
246
|
+
const synStr = g.synonyms
|
|
247
|
+
.map((s) => `${s.synonym ?? '?'}${s.type ? ` (${s.type})` : ''}`)
|
|
248
|
+
.join(',');
|
|
249
|
+
parts.push(`synonyms=${synStr}`);
|
|
250
|
+
}
|
|
251
|
+
lines.push(`- ${parts.join(' · ')}`);
|
|
252
|
+
}
|
|
253
|
+
}
|
|
254
|
+
if (result.dataset) {
|
|
255
|
+
lines.push('');
|
|
256
|
+
lines.push('## Dataset handle');
|
|
257
|
+
lines.push(...renderDatasetHandle(result.dataset));
|
|
258
|
+
}
|
|
259
|
+
if (result.warnings.length > 0) {
|
|
260
|
+
lines.push('');
|
|
261
|
+
lines.push('## Warnings');
|
|
262
|
+
for (const w of result.warnings)
|
|
263
|
+
lines.push(`- ${w}`);
|
|
264
|
+
}
|
|
265
|
+
return [{ type: 'text', text: lines.join('\n') }];
|
|
266
|
+
},
|
|
267
|
+
});
|
|
268
|
+
function hasRowsMatchingText(rows, text) {
|
|
269
|
+
const needle = text.toLowerCase();
|
|
270
|
+
const containsNeedle = (value) => typeof value === 'string' && value.toLowerCase().includes(needle);
|
|
271
|
+
for (const row of rows) {
|
|
272
|
+
if (containsNeedle(row.germplasmName) ||
|
|
273
|
+
containsNeedle(row.germplasmPUI) ||
|
|
274
|
+
containsNeedle(row.accessionNumber) ||
|
|
275
|
+
containsNeedle(row.defaultDisplayName)) {
|
|
276
|
+
return true;
|
|
277
|
+
}
|
|
278
|
+
if (Array.isArray(row.synonyms)) {
|
|
279
|
+
for (const entry of row.synonyms) {
|
|
280
|
+
if (entry &&
|
|
281
|
+
typeof entry === 'object' &&
|
|
282
|
+
containsNeedle(entry.synonym)) {
|
|
283
|
+
return true;
|
|
284
|
+
}
|
|
285
|
+
}
|
|
286
|
+
}
|
|
287
|
+
}
|
|
288
|
+
return false;
|
|
289
|
+
}
|
|
290
|
+
//# sourceMappingURL=brapi-find-germplasm.tool.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
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/**
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* @fileoverview `brapi_find_images` — filter images by observation unit,
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* study, observation, descriptive ontology, file name, or MIME type. Returns
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* metadata only; pull bytes via `brapi_get_image`. Spills the full set to
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* DatasetStore when the upstream total exceeds loadLimit.
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*
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* @module mcp-server/tools/definitions/brapi-find-images.tool
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*/
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import { z } from '@cyanheads/mcp-ts-core';
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export declare const brapiFindImages: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
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alias: z.ZodOptional<z.ZodString>;
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images: z.ZodOptional<z.ZodArray<z.ZodString>>;
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observationUnits: z.ZodOptional<z.ZodArray<z.ZodString>>;
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observations: z.ZodOptional<z.ZodArray<z.ZodString>>;
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studies: z.ZodOptional<z.ZodArray<z.ZodString>>;
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imageFileNames: z.ZodOptional<z.ZodArray<z.ZodString>>;
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mimeTypes: z.ZodOptional<z.ZodArray<z.ZodString>>;
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descriptiveOntologyTerms: z.ZodOptional<z.ZodArray<z.ZodString>>;
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loadLimit: z.ZodOptional<z.ZodNumber>;
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extraFilters: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
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}, z.core.$strip>, z.ZodObject<{
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alias: z.ZodString;
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results: z.ZodArray<z.ZodObject<{
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imageDbId: z.ZodString;
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imageName: z.ZodOptional<z.ZodString>;
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imageFileName: z.ZodOptional<z.ZodString>;
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imageFileSize: z.ZodOptional<z.ZodNumber>;
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imageHeight: z.ZodOptional<z.ZodNumber>;
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imageWidth: z.ZodOptional<z.ZodNumber>;
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mimeType: z.ZodOptional<z.ZodString>;
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imageTimeStamp: z.ZodOptional<z.ZodString>;
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imageURL: z.ZodOptional<z.ZodString>;
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observationUnitDbId: z.ZodOptional<z.ZodString>;
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observationUnitName: z.ZodOptional<z.ZodString>;
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observationDbIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
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studyDbId: z.ZodOptional<z.ZodString>;
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studyName: z.ZodOptional<z.ZodString>;
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descriptiveOntologyTerms: z.ZodOptional<z.ZodArray<z.ZodString>>;
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copyright: z.ZodOptional<z.ZodString>;
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description: z.ZodOptional<z.ZodString>;
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}, z.core.$loose>>;
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returnedCount: z.ZodNumber;
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totalCount: z.ZodNumber;
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hasMore: z.ZodBoolean;
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distributions: z.ZodObject<{
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mimeType: z.ZodRecord<z.ZodString, z.ZodNumber>;
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studyName: z.ZodRecord<z.ZodString, z.ZodNumber>;
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+
observationUnitName: z.ZodRecord<z.ZodString, z.ZodNumber>;
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descriptiveOntologyTerms: z.ZodRecord<z.ZodString, z.ZodNumber>;
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+
}, z.core.$strip>;
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+
refinementHint: z.ZodOptional<z.ZodString>;
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+
dataset: z.ZodOptional<z.ZodObject<{
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+
datasetId: z.ZodString;
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+
rowCount: z.ZodNumber;
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+
sizeBytes: z.ZodNumber;
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columns: z.ZodArray<z.ZodString>;
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createdAt: z.ZodString;
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expiresAt: z.ZodString;
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truncated: z.ZodOptional<z.ZodBoolean>;
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maxRows: z.ZodOptional<z.ZodNumber>;
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}, z.core.$strip>>;
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+
warnings: z.ZodArray<z.ZodString>;
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appliedFilters: z.ZodRecord<z.ZodString, z.ZodUnknown>;
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}, z.core.$strip>, undefined>;
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65
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//# sourceMappingURL=brapi-find-images.tool.d.ts.map
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1
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{"version":3,"file":"brapi-find-images.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-images.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAiGjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAuK1B,CAAC"}
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@@ -0,0 +1,243 @@
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1
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/**
|
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2
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+
* @fileoverview `brapi_find_images` — filter images by observation unit,
|
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3
|
+
* study, observation, descriptive ontology, file name, or MIME type. Returns
|
|
4
|
+
* metadata only; pull bytes via `brapi_get_image`. Spills the full set to
|
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5
|
+
* DatasetStore when the upstream total exceeds loadLimit.
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6
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+
*
|
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7
|
+
* @module mcp-server/tools/definitions/brapi-find-images.tool
|
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8
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+
*/
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9
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+
import { tool, z } from '@cyanheads/mcp-ts-core';
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10
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+
import { getServerConfig } from '../../../config/server-config.js';
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11
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+
import { getBrapiClient } from '../../../services/brapi-client/index.js';
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12
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+
import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
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13
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+
import { getDatasetStore } from '../../../services/dataset-store/index.js';
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14
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+
import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
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15
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+
import { AliasInput, asString, buildRefinementHint, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderDatasetHandle, renderDistributions, } from '../shared/find-helpers.js';
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16
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const ImageRowSchema = z
|
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17
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.object({
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18
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imageDbId: z.string().describe('Server-side identifier for the image.'),
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imageName: z.string().optional().describe('Display name.'),
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imageFileName: z.string().optional().describe('Original uploaded filename.'),
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imageFileSize: z.number().optional().describe('File size in bytes.'),
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imageHeight: z.number().optional().describe('Pixel height.'),
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imageWidth: z.number().optional().describe('Pixel width.'),
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+
mimeType: z.string().optional().describe('MIME type (e.g. "image/jpeg").'),
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25
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+
imageTimeStamp: z.string().optional().describe('ISO 8601 capture timestamp.'),
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+
imageURL: z
|
|
27
|
+
.string()
|
|
28
|
+
.optional()
|
|
29
|
+
.describe('URL where the bytes live (may be relative to baseUrl or absolute).'),
|
|
30
|
+
observationUnitDbId: z
|
|
31
|
+
.string()
|
|
32
|
+
.optional()
|
|
33
|
+
.describe('FK to the observation unit this image depicts.'),
|
|
34
|
+
observationUnitName: z.string().optional().describe('Display name of the observation unit.'),
|
|
35
|
+
observationDbIds: z
|
|
36
|
+
.array(z.string().describe('Observation identifier.'))
|
|
37
|
+
.optional()
|
|
38
|
+
.describe('FKs to observations this image is evidence for.'),
|
|
39
|
+
studyDbId: z.string().optional().describe('FK to the study the image belongs to.'),
|
|
40
|
+
studyName: z.string().optional().describe('Display name of the study.'),
|
|
41
|
+
descriptiveOntologyTerms: z
|
|
42
|
+
.array(z.string().describe('Ontology term ID or label.'))
|
|
43
|
+
.optional()
|
|
44
|
+
.describe('Descriptive ontology tags (e.g. "CO_334:plot").'),
|
|
45
|
+
copyright: z.string().optional().describe('Copyright or rights notice.'),
|
|
46
|
+
description: z.string().optional().describe('Free-text description.'),
|
|
47
|
+
})
|
|
48
|
+
.passthrough()
|
|
49
|
+
.describe('One BrAPI image metadata record.');
|
|
50
|
+
const OutputSchema = z.object({
|
|
51
|
+
alias: z.string().describe('Alias of the registered BrAPI connection the call used.'),
|
|
52
|
+
results: z
|
|
53
|
+
.array(ImageRowSchema)
|
|
54
|
+
.describe('Image metadata rows returned in-context (up to loadLimit).'),
|
|
55
|
+
returnedCount: z.number().int().nonnegative().describe('Length of `results[]`.'),
|
|
56
|
+
totalCount: z.number().int().nonnegative().describe('Total rows reported by the server.'),
|
|
57
|
+
hasMore: z.boolean().describe('True when more rows exist beyond the returned set.'),
|
|
58
|
+
distributions: z
|
|
59
|
+
.object({
|
|
60
|
+
mimeType: z
|
|
61
|
+
.record(z.string(), z.number())
|
|
62
|
+
.describe('MIME type → count of images with that type.'),
|
|
63
|
+
studyName: z
|
|
64
|
+
.record(z.string(), z.number())
|
|
65
|
+
.describe('Study name → count of images in that study.'),
|
|
66
|
+
observationUnitName: z
|
|
67
|
+
.record(z.string(), z.number())
|
|
68
|
+
.describe('Observation unit name → count of images tied to that unit.'),
|
|
69
|
+
descriptiveOntologyTerms: z
|
|
70
|
+
.record(z.string(), z.number())
|
|
71
|
+
.describe('Ontology term → count of images tagged with that term.'),
|
|
72
|
+
})
|
|
73
|
+
.describe('Value frequency per field across the full result set.'),
|
|
74
|
+
refinementHint: z
|
|
75
|
+
.string()
|
|
76
|
+
.optional()
|
|
77
|
+
.describe('Suggested next-step query refinement when the result set is large.'),
|
|
78
|
+
dataset: DatasetHandleSchema.optional().describe('Dataset handle when the full result set was persisted to DatasetStore.'),
|
|
79
|
+
warnings: z
|
|
80
|
+
.array(z.string())
|
|
81
|
+
.describe('Advisory messages (filter overrides, partial data, capability gaps, etc.).'),
|
|
82
|
+
appliedFilters: z
|
|
83
|
+
.record(z.string(), z.unknown())
|
|
84
|
+
.describe('The final filter map sent to the server (named + extraFilters).'),
|
|
85
|
+
});
|
|
86
|
+
export const brapiFindImages = tool('brapi_find_images', {
|
|
87
|
+
description: 'Filter images by observation unit, observation, study, descriptive ontology term, file name, or MIME type. Returns metadata only — use brapi_get_image to fetch bytes inline. Returns a dataset handle when the upstream total exceeds loadLimit.',
|
|
88
|
+
annotations: { readOnlyHint: true, openWorldHint: true },
|
|
89
|
+
input: z.object({
|
|
90
|
+
alias: AliasInput,
|
|
91
|
+
images: z.array(z.string()).optional().describe('Filter by imageDbIds.'),
|
|
92
|
+
observationUnits: z.array(z.string()).optional().describe('Filter by observationUnitDbIds.'),
|
|
93
|
+
observations: z.array(z.string()).optional().describe('Filter by observationDbIds.'),
|
|
94
|
+
studies: z.array(z.string()).optional().describe('Filter by studyDbIds.'),
|
|
95
|
+
imageFileNames: z.array(z.string()).optional().describe('Filter by uploaded file name.'),
|
|
96
|
+
mimeTypes: z
|
|
97
|
+
.array(z.string())
|
|
98
|
+
.optional()
|
|
99
|
+
.describe('Filter by MIME type — e.g. "image/jpeg", "image/png".'),
|
|
100
|
+
descriptiveOntologyTerms: z
|
|
101
|
+
.array(z.string())
|
|
102
|
+
.optional()
|
|
103
|
+
.describe('Filter by ontology tags (e.g. "CO_334:plot").'),
|
|
104
|
+
loadLimit: LoadLimitInput,
|
|
105
|
+
extraFilters: ExtraFiltersInput,
|
|
106
|
+
}),
|
|
107
|
+
output: OutputSchema,
|
|
108
|
+
async handler(input, ctx) {
|
|
109
|
+
const registry = getServerRegistry();
|
|
110
|
+
const capabilities = getCapabilityRegistry();
|
|
111
|
+
const client = getBrapiClient();
|
|
112
|
+
const datasetStore = getDatasetStore();
|
|
113
|
+
const config = getServerConfig();
|
|
114
|
+
const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
|
|
115
|
+
const capabilityLookup = {};
|
|
116
|
+
if (connection.resolvedAuth)
|
|
117
|
+
capabilityLookup.auth = connection.resolvedAuth;
|
|
118
|
+
await capabilities.ensure(connection.baseUrl, { service: 'images', method: 'GET' }, ctx, capabilityLookup);
|
|
119
|
+
const warnings = [];
|
|
120
|
+
const filters = mergeFilters({
|
|
121
|
+
imageDbIds: input.images,
|
|
122
|
+
observationUnitDbIds: input.observationUnits,
|
|
123
|
+
observationDbIds: input.observations,
|
|
124
|
+
studyDbIds: input.studies,
|
|
125
|
+
imageFileNames: input.imageFileNames,
|
|
126
|
+
mimeTypes: input.mimeTypes,
|
|
127
|
+
descriptiveOntologyTerms: input.descriptiveOntologyTerms,
|
|
128
|
+
}, input.extraFilters, warnings);
|
|
129
|
+
const loadLimit = input.loadLimit ?? config.loadLimit;
|
|
130
|
+
const firstPage = await loadInitialPage(client, connection, '/images', filters, loadLimit, ctx);
|
|
131
|
+
const { fullRows, dataset: datasetMeta } = await maybeSpill({
|
|
132
|
+
firstPage,
|
|
133
|
+
client,
|
|
134
|
+
connection,
|
|
135
|
+
path: '/images',
|
|
136
|
+
filters,
|
|
137
|
+
source: 'find_images',
|
|
138
|
+
loadLimit,
|
|
139
|
+
ctx,
|
|
140
|
+
store: datasetStore,
|
|
141
|
+
});
|
|
142
|
+
const distributions = {
|
|
143
|
+
mimeType: computeDistribution(fullRows, (r) => asString(r.mimeType)),
|
|
144
|
+
studyName: computeDistribution(fullRows, (r) => asString(r.studyName)),
|
|
145
|
+
observationUnitName: computeDistribution(fullRows, (r) => asString(r.observationUnitName)),
|
|
146
|
+
descriptiveOntologyTerms: computeDistribution(fullRows, (r) => {
|
|
147
|
+
const terms = r.descriptiveOntologyTerms;
|
|
148
|
+
if (!Array.isArray(terms))
|
|
149
|
+
return;
|
|
150
|
+
return terms.filter((t) => typeof t === 'string' && t.length > 0);
|
|
151
|
+
}),
|
|
152
|
+
};
|
|
153
|
+
const totalCount = firstPage.totalCount ?? firstPage.rows.length;
|
|
154
|
+
const refinementHint = buildRefinementHint(totalCount, loadLimit, distributions);
|
|
155
|
+
const result = {
|
|
156
|
+
alias: connection.alias,
|
|
157
|
+
results: firstPage.rows,
|
|
158
|
+
returnedCount: firstPage.rows.length,
|
|
159
|
+
totalCount,
|
|
160
|
+
hasMore: firstPage.hasMore,
|
|
161
|
+
distributions,
|
|
162
|
+
warnings,
|
|
163
|
+
appliedFilters: filters,
|
|
164
|
+
};
|
|
165
|
+
if (refinementHint)
|
|
166
|
+
result.refinementHint = refinementHint;
|
|
167
|
+
if (datasetMeta)
|
|
168
|
+
result.dataset = datasetMeta;
|
|
169
|
+
return result;
|
|
170
|
+
},
|
|
171
|
+
format: (result) => {
|
|
172
|
+
const lines = [];
|
|
173
|
+
lines.push(`# ${result.returnedCount} of ${result.totalCount} images — \`${result.alias}\``);
|
|
174
|
+
lines.push('');
|
|
175
|
+
if (result.hasMore) {
|
|
176
|
+
lines.push(`⚠ More rows exist beyond the returned set. ${result.dataset ? `Full set persisted as dataset \`${result.dataset.datasetId}\`.` : 'Narrow filters or raise loadLimit.'}`);
|
|
177
|
+
lines.push('');
|
|
178
|
+
}
|
|
179
|
+
if (result.refinementHint) {
|
|
180
|
+
lines.push(`**Refinement hint:** ${result.refinementHint}`);
|
|
181
|
+
lines.push('');
|
|
182
|
+
}
|
|
183
|
+
lines.push(`Applied filters: \`${JSON.stringify(result.appliedFilters)}\``);
|
|
184
|
+
lines.push('');
|
|
185
|
+
lines.push('## Distributions');
|
|
186
|
+
lines.push(renderDistributions(result.distributions) || '_No values to summarize._');
|
|
187
|
+
lines.push('');
|
|
188
|
+
lines.push('## Images');
|
|
189
|
+
if (result.results.length === 0) {
|
|
190
|
+
lines.push('_No rows returned._');
|
|
191
|
+
}
|
|
192
|
+
else {
|
|
193
|
+
for (const img of result.results) {
|
|
194
|
+
const parts = [`**${img.imageName ?? img.imageFileName ?? img.imageDbId}**`];
|
|
195
|
+
parts.push(`id=\`${img.imageDbId}\``);
|
|
196
|
+
if (img.imageFileName)
|
|
197
|
+
parts.push(`file=${img.imageFileName}`);
|
|
198
|
+
if (img.mimeType)
|
|
199
|
+
parts.push(`mime=${img.mimeType}`);
|
|
200
|
+
if (img.imageWidth && img.imageHeight) {
|
|
201
|
+
parts.push(`${img.imageWidth}×${img.imageHeight}`);
|
|
202
|
+
}
|
|
203
|
+
if (img.imageFileSize)
|
|
204
|
+
parts.push(`size=${img.imageFileSize}B`);
|
|
205
|
+
if (img.observationUnitName)
|
|
206
|
+
parts.push(`unit=${img.observationUnitName}`);
|
|
207
|
+
if (img.observationUnitDbId)
|
|
208
|
+
parts.push(`unitDbId=${img.observationUnitDbId}`);
|
|
209
|
+
if (img.observationDbIds?.length)
|
|
210
|
+
parts.push(`obs=${img.observationDbIds.join(',')}`);
|
|
211
|
+
if (img.studyName)
|
|
212
|
+
parts.push(`study=${img.studyName}`);
|
|
213
|
+
if (img.studyDbId)
|
|
214
|
+
parts.push(`studyDbId=${img.studyDbId}`);
|
|
215
|
+
if (img.descriptiveOntologyTerms?.length) {
|
|
216
|
+
parts.push(`terms=${img.descriptiveOntologyTerms.join(',')}`);
|
|
217
|
+
}
|
|
218
|
+
if (img.imageTimeStamp)
|
|
219
|
+
parts.push(`time=${img.imageTimeStamp}`);
|
|
220
|
+
if (img.imageURL)
|
|
221
|
+
parts.push(`url=${img.imageURL}`);
|
|
222
|
+
if (img.copyright)
|
|
223
|
+
parts.push(`©${img.copyright}`);
|
|
224
|
+
if (img.description)
|
|
225
|
+
parts.push(`desc=${img.description}`);
|
|
226
|
+
lines.push(`- ${parts.join(' · ')}`);
|
|
227
|
+
}
|
|
228
|
+
}
|
|
229
|
+
if (result.dataset) {
|
|
230
|
+
lines.push('');
|
|
231
|
+
lines.push('## Dataset handle');
|
|
232
|
+
lines.push(...renderDatasetHandle(result.dataset));
|
|
233
|
+
}
|
|
234
|
+
if (result.warnings.length > 0) {
|
|
235
|
+
lines.push('');
|
|
236
|
+
lines.push('## Warnings');
|
|
237
|
+
for (const w of result.warnings)
|
|
238
|
+
lines.push(`- ${w}`);
|
|
239
|
+
}
|
|
240
|
+
return [{ type: 'text', text: lines.join('\n') }];
|
|
241
|
+
},
|
|
242
|
+
});
|
|
243
|
+
//# sourceMappingURL=brapi-find-images.tool.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
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