{
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  "Slug": "brapi-mcp-server",
  "Name": "brapi-mcp-server",
  "CanonicalUrl": "https://askpod.ai/mcp/brapi-mcp-server/issues",
  "ServerUrl": "https://askpod.ai/mcp/brapi-mcp-server",
  "IssueTotal": 46,
  "Held": 24,
  "Issues": [
    {
      "Title": "feat(loadLimit): decouple in-context cap from upstream pageSize",
      "Excerpt": "`loadLimit` does three jobs and the entanglement leaks into agent behavior:\n\n1. In-context row cap returned to the LLM\n2. Spillover trigger threshold (`maybeSpill` returns first-page only when `totalCount ≤ loadLimit`)\n3. Upstream `pageSize` for both first call and every spillover page (`spillToCanvas` in `src/mcp-server/tools/shared/find-helpers.ts`)\n\n## Footgun\n\nAn agent that lowers `loadLimit` to \"see fewer rows inline\" silently shrinks dataframe spillover capacity proportionally — `loadLimit",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/26",
      "PublishedAt": "2026-05-05T11:09:16.000Z",
      "State": "closed",
      "Comments": 5,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "Add brapi_germplasm_performance tool — aggregate observations across studies",
      "Excerpt": "### Use case\n\n\"How does line X-401 perform across the germplasm pool's history?\" is the breeder's primary question. Today this requires N `find_observations` calls + manual aggregation, and is easy to get wrong on dialects that drop the germplasm filter (returning the global aggregate instead of the per-germplasm one).\n\n### Dependency\n\n**Blocked by #8.** This issue depends on what `brapi_build_phenotype_matrix` outputs. The implementation path and final shape are confirmed after #8 lands.\n\n### T",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/9",
      "PublishedAt": "2026-05-01T23:55:01.000Z",
      "State": "closed",
      "Comments": 5,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "Dialect detection: URL pattern matching + verified-flag per mapping",
      "Excerpt": "## Motivation\n\nToday `detectDialectFromName` only matches on `serverInfo.serverName` (and `organizationName`). Two real-world failure modes:\n\n1. **Generic server names.** Some SGN-family deployments report `serverName: 'BrAPI'` or omit it entirely. We catch \"Boyce Thompson Institute\" via `organizationName` but miss anything else hosted on `*.cassavabase.org`, `*.sweetpotatobase.org`, `*.yambase.org`, etc.\n2. **Mapping confidence is invisible.** `PLURAL_TO_SINGULAR` in `cassavabase-dialect.ts` mi",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/5",
      "PublishedAt": "2026-05-01T03:06:14.000Z",
      "State": "closed",
      "Comments": 5,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(find_observations): Sweetpotatobase study spillover can run past client timeout",
      "Excerpt": "### Server version\n\n0.7.2\n\n### mcp-ts-core version\n\n^0.9.21\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun ≥ 1.3.0\n\n### Transport\n\nstdio / direct handler validation\n\n### Description\n\n`brapi_find_observations({ studies: [\"1131\"] })` against Sweetpotatobase is not an `all_filters_dropped` dialect failure on the current tree. The Breedbase dialect rewrites `studyDbIds` to `studyDbId`, and the upstream GET route returns the expected 1,221 observations.\n\nThe rough edge is spillover latency: at the forme",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/21",
      "PublishedAt": "2026-05-02T03:31:32.000Z",
      "State": "closed",
      "Comments": 4,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "feat(walk_pedigree): spill large pedigree results to canvas dataframe(s)",
      "Excerpt": "`brapi_walk_pedigree` is the only walking tool in this server that does not follow the `find_*` spillover pattern. When a pedigree walk returns thousands of nodes (cassavabase descendant walks easily hit this), the full `nodes[]` and `edges[]` arrays are returned inline regardless of size. Two related problems:\n\n1. **The `MAX_NODES = 1000` cap is loose.** The check (`src/mcp-server/tools/definitions/brapi-walk-pedigree.tool.ts:198`) runs at the start of each depth iteration, but a single depth c",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/17",
      "PublishedAt": "2026-05-02T02:31:44.000Z",
      "State": "closed",
      "Comments": 4,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(get_*): upstream 5xx on missing DbId surfaces as transport error + 4-retry storm; not_found contract never fires",
      "Excerpt": "### Server version\n\n0.5.3\n\n### mcp-ts-core version\n\n0.8.17\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.3.11\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### OS\n\nmacOS 25.1.0\n\n### Description\n\nSingleton GET tools — `brapi_get_study`, `brapi_get_germplasm`, plus the `brapi://study/{id}` and `brapi://germplasm/{id}` resources — surface upstream-server bugs as opaque transport errors when the upstream returns 5xx for a missing DbId. On Breedbase (one of the built-in aliases), `/studies/{nonexistent}` r",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/30",
      "PublishedAt": "2026-05-06T05:53:07.000Z",
      "State": "closed",
      "Comments": 3,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(error-contracts): data.recovery.hint missing on the wire for several declared-contract throws",
      "Excerpt": "### Server version\n\n0.5.3\n\n### mcp-ts-core version\n\n0.8.17\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.3.11\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### OS\n\nmacOS 25.1.0\n\n### Description\n\nSeveral tools declare typed error contracts with a `recovery` field but throw via `ctx.fail(reason, ...)` **without** spreading `ctx.recoveryFor(reason)` into the data payload. The framework requires the spread to opt the contract recovery onto the wire (see `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` \"Err",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/29",
      "PublishedAt": "2026-05-06T05:52:49.000Z",
      "State": "closed",
      "Comments": 3,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "Dialect: add normalizeRow hook for null-vs-omitted shape coercion",
      "Excerpt": "## Motivation\n\nCassavaBase returns `null` for many optional fields where the BrAPI v2.1 spec says the field should be omitted entirely. Today every BrAPI tool's row schema absorbs this with `.nullish()` — repeated across dozens of fields and growing every time we discover a new sparse upstream shape.\n\nThat's a structural smell:\n- The same defensive change has to be applied in every schema.\n- Renderer code has to repeat `if (g.value)` guards row-by-row to avoid `'lat=null'` style output.\n- Future",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/6",
      "PublishedAt": "2026-05-01T03:06:45.000Z",
      "State": "closed",
      "Comments": 3,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(builtin-aliases): t3-wheat / t3-oat / t3-barley now answer 401 on /serverinfo",
      "Excerpt": "### Server version\n\n0.7.10 (reproduces on the 0.7.11 tree)\n\n### mcp-ts-core version\n\n0.12.3\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0\n\n### Transport\n\nstdio\n\n### Description\n\nThe three built-in T3 aliases in `src/config/builtin-aliases.ts` (`t3-wheat`, `t3-oat`, `t3-barley`) are documented as no-auth public endpoints in `.env.example` and the README. All three hosts now answer HTTP 401 on `GET /brapi/v2/serverinfo` anonymously:\n\n```\ncurl -s -o /dev/null -w '%{http_code}' https://wheat.tri",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/52",
      "PublishedAt": "2026-08-22T21:32:46.000Z",
      "State": "open",
      "Comments": 0,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(brapi-client): singleton HTTP 500 bypasses the Breedbase not-found reclassification",
      "Excerpt": "### Server version\n\n0.7.10 (reproduces on the 0.7.11 tree)\n\n### mcp-ts-core version\n\n0.12.3\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0\n\n### Transport\n\nhttp\n\n### Description\n\n`reclassifyHttpError` in `src/services/brapi-client/brapi-client.ts` documents that a 5xx on a singleton `/{noun}/{id}` fetch is treated as `NotFound`, because Breedbase answers HTTP 500 for an unknown DbId. The guard at the top of the function returns early unless `err.code === JsonRpcErrorCode.ServiceUnavailable`, b",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/51",
      "PublishedAt": "2026-08-22T21:32:44.000Z",
      "State": "open",
      "Comments": 0,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "feat(dataframe): name the dataframe tools in responses that stage a dataframe",
      "Excerpt": "Thirteen tools stage rows as a canvas dataframe and hand back a `df_XXXXX_XXXXX` handle, but nothing in the response payload tells the agent to reach that data with `brapi_dataframe_describe` and `brapi_dataframe_query`. The handle is an opaque generated name; an agent that receives one without a pointer either reports the truncation and stops, or re-runs the producing tool with narrower filters — re-fetching rows that are already staged one SQL query away.\n\nThe gap is in the **runtime response*",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/50",
      "PublishedAt": "2026-08-13T01:08:13.000Z",
      "State": "open",
      "Comments": 0,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "feat(isolation): fail closed on credentialed connection state when no session key exists",
      "Excerpt": "Under `BRAPI_SESSION_ISOLATION=true` (the default), both the connection registry and the canvas bridge key their state on `ctx.sessionId`, and when it is absent both fall back silently to the shared per-tenant namespace (`scopePrefix()` in `src/services/server-registry/server-registry.ts`, `DEFAULT_CANVAS_KEY` in `src/services/canvas-bridge/canvas-bridge.ts`). For the connection registry that shared namespace holds `RegisteredServer` entries whose `resolvedAuth` is the live upstream credential h",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/49",
      "PublishedAt": "2026-07-27T08:00:50.000Z",
      "State": "open",
      "Comments": 0,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "feat(observations): parallelize per-study pulls in germplasm_performance and build_phenotype_matrix",
      "Excerpt": "`brapi_germplasm_performance` and `brapi_build_phenotype_matrix` both collect observations study-by-study through a sequential `for` loop around the shared `pullStudyObservations` helper — one full HTTP round trip (plus the `/observationunits` fallback) per study, awaited before starting the next. Neither tool bounds concurrency. `BRAPI_MAX_CONCURRENT_REQUESTS` (default 4, documented in README/.env.example as a \"per-connection concurrency cap\") is declared in `server-config.ts` but isn't read by",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/48",
      "PublishedAt": "2026-07-16T10:22:22.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(dataframe_describe): renders every column name uncapped",
      "Excerpt": "### Server version\n\n0.7.6\n\n### mcp-ts-core version\n\n^0.10.14\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.3.14\n\n### Transport\n\nHTTP JSON-RPC\n\n### Description\n\n`brapi_dataframe_describe` renders one line per column with no size bound. For a dataframe with a normal shape (a `find_*` spillover, ~18 columns) that is correct and cheap. For a genotype matrix, one column is registered per variant, so a wide matrix makes the tool emit a column name per variant into `content[]`.\n\nRelated: #46\n\n### Steps",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/47",
      "PublishedAt": "2026-07-16T05:46:47.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "feat(export_genotype_matrix): bound columnCount, not just total calls",
      "Excerpt": "`brapi_export_genotype_matrix` bounds the total genotype calls it pulls (`maxCalls`, clamped to `BRAPI_GENOTYPE_CALLS_MAX_PULL`), but nothing bounds how those calls distribute across the germplasm × variant grid. A schema-legal skew — one germplasm × `maxCalls` variants — makes `columnCount` equal the entire call budget, and every per-variant output scales with it.\n\nRelated: #42, #45\n\n## Proposal\n\nBound `columnCount` directly, mirroring the `maxCalls` clamp #45 established: a deployment-level ce",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/46",
      "PublishedAt": "2026-07-16T05:45:57.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(export_genotype_matrix): maxCalls is unbounded and bypasses the deployment call ceiling",
      "Excerpt": "### Server version\n\n0.7.6\n\n### mcp-ts-core version\n\n^0.10.9\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.3.14\n\n### Transport\n\nHTTP\n\n### Description\n\n`brapi_export_genotype_matrix`'s `maxCalls` input carries no `.max()` bound and is never clamped against the deployment's `genotypeCallsMaxPull` config ceiling. A caller can pass an arbitrarily large `maxCalls` and the tool honors it, so the documented \"hard ceiling\" is advisory only.\n\n`brapi_find_genotype_calls` does not have this gap — it uses th",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/45",
      "PublishedAt": "2026-07-16T05:07:26.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(docker): HEALTHCHECK uses curl, which the bun slim base image does not ship",
      "Excerpt": "### Server version\n\n0.7.6\n\n### mcp-ts-core version\n\n^0.10.9\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.3.14\n\n### Transport\n\nHTTP\n\n### Description\n\nThe `Dockerfile` `HEALTHCHECK` probes `/healthz` with `curl -f`, but the `oven/bun:*-slim` production base ships neither `curl` nor `wget`. The probe can never succeed, so a container run from the published image reports `unhealthy` for its entire lifetime even while the server is serving correctly.\n\nAny orchestrator that gates on container health ",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/44",
      "PublishedAt": "2026-07-16T05:07:08.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "feat(germplasm_performance): add a retrieval path when study discovery hits the cap",
      "Excerpt": "### Server version\n\n0.7.6\n\n### mcp-ts-core version\n\n^0.10.14\n\n### Runtime\n\nBun\n\n### Description\n\n`brapi_germplasm_performance` caps automatic study discovery at `STUDY_DISCOVERY_CAP = 200`. When that cap is hit, the response warns that aggregates may be incomplete and suggests narrowing with a study-specific phenotype matrix, but the tool does not expose a continuation cursor, an offset, or a dataframe/list handle that lets an agent retrieve the omitted study slice.\n\nThat leaves a truncation pat",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/43",
      "PublishedAt": "2026-07-05T18:58:57.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(export_genotype_matrix): content[] previews VCF/PLINK text and column legend",
      "Excerpt": "### Server version\n\n0.7.6\n\n### mcp-ts-core version\n\n^0.10.9\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.3.14\n\n### Transport\n\nHTTP JSON-RPC / direct formatter check\n\n### Description\n\n`brapi_export_genotype_matrix` puts generated VCF/PLINK serializations in `structuredContent`, but `format()` emits only a preview and tells clients to read `structuredContent.<field>`. Content-only clients lose generated rows.\n\nThe same formatter caps the variant column legend at 20 remappings.\n\n### Steps to repro",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/42",
      "PublishedAt": "2026-07-05T18:58:43.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(format): shared renderers omit full distributions and large passthrough fields from content[]",
      "Excerpt": "### Server version\n\n0.7.6\n\n### mcp-ts-core version\n\n^0.10.9\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.3.14\n\n### Transport\n\nHTTP JSON-RPC\n\n### Description\n\nSeveral shared format helpers render summaries in `content[]` for fields that are complete in `structuredContent`. Content-only clients cannot recover those values because the text points to `structuredContent`, which those clients do not read.\n\nThis breaks parity between the two result surfaces. Both surfaces are used by different AI clie",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/41",
      "PublishedAt": "2026-07-05T18:58:29.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(get_study): variableCount/observationCount report server-wide totals, not study-scoped",
      "Excerpt": "### Server version\n\n0.7.4\n\n### mcp-ts-core version\n\n0.10.6 (`^0.10.6`)\n\n### Runtime\n\nBun\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\n`brapi_get_study` returns companion counts (`variableCount`, `observationCount`) that are **server-wide totals, not scoped to the study**. The enrichment scopes them with a `studyDbIds` filter, which the `brapi-test` dialect drops upstream (the response even carries the `dropped filter 'studyDbIds'` warning), so the counts silently collapse to the glob",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/40",
      "PublishedAt": "2026-06-18T11:26:15.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(dataframe_query): every query fails on internal probe — \"Ambiguous reference to column name table_name\"",
      "Excerpt": "### Server version\n\n0.7.4\n\n### mcp-ts-core version\n\n0.10.6 (`^0.10.6`)\n\n### Runtime\n\nBun\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\nEvery `brapi_dataframe_query` call fails *before* the user SQL runs — including `SELECT 1`. The handler issues an internal pre-flight probe against the DuckDB catalog whose `WHERE` clause references an unqualified `table_name`, which DuckDB rejects as ambiguous. Named `brapi_dataframe_describe` hits the same wall (the no-arg list mode returns the inten",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/39",
      "PublishedAt": "2026-06-18T11:26:13.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(submit_observations): apply mode hard-blocked — ctx.elicit never defined at runtime (upstream mcp-ts-core#211)",
      "Excerpt": "`brapi_submit_observations` apply mode requires an elicitation confirm and correctly fails closed when the client lacks it: `elicit_unavailable` (Forbidden) unless `force=true`. Upstream cyanheads/mcp-ts-core#211 means `ctx.elicit` is `undefined` on every production request regardless of client capability — the framework's capability detection sniffs methods the SDK never attaches.\n\nNet effect today: apply mode returns `elicit_unavailable` on **all** clients, including elicit-capable ones. The r",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/38",
      "PublishedAt": "2026-06-10T20:43:58.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(find_variants): dataframe spillover throws on reserved-word column \"end\"",
      "Excerpt": "`brapi_find_variants` throws `Canvas column name \"end\" is a reserved SQL keyword. Choose another name.` whenever its result spills to a canvas dataframe. BrAPI `/variants` records carry an `end` field (variant end position), and the generic `find_*` spillover path registers rows under their raw upstream keys as DuckDB column names — `end` is a reserved word, so `assertValidIdentifier` rejects it at `registerTable` and the whole call fails (no dataframe is produced).\n\n### Reproduce\n\nAgainst the B",
      "SourceUrl": "https://github.com/cyanheads/brapi-mcp-server/issues/37",
      "PublishedAt": "2026-06-02T05:04:31.000Z",
      "State": "closed",
      "Comments": 2,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    }
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