# Reported issues for Plant Genomics Pod holds 13 of 13 GitHub reports that passed its relevance review. This can include external user reports, maintainer-confirmed bugs, and concrete feature gaps. Treat them as evidence to inspect, not a count of distinct defects. Back to [Plant Genomics](/mcp/plant-genomics). ## Most discussed ### Normalisation requests: six values this server passes through from upstream unchanged Written from the ARF family dossier in [`examples/arf_family/`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/), re-run at server commit `967bc36` (release `1.21.0`): 400 MCP calls over 48 genes x 16 tools, the family itself from a 742-call enumeration through the same tools. Each section below is one row of [`gaps.jsonl`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/gaps.jsonl), quoted as logged; `Check` names the captured response… [Read the thread](https://github.com/musharna/plant-genomics-mcp/issues/137) · 2026-09-22 · closed · 2 comments ### `locus_literature` promises a journal and returns null in all 160 hits Written from the ARF family dossier in [`examples/arf_family/`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/), re-run at server commit `967bc36` (release `1.21.0`): 400 MCP calls over 48 genes x 16 tools, the family itself from a 742-call enumeration through the same tools. Each section below is one row of [`gaps.jsonl`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/gaps.jsonl), quoted as logged; `Check` names the captured response… [Read the thread](https://github.com/musharna/plant-genomics-mcp/issues/134) · 2026-09-22 · closed · 1 comment ### Family, entry and gene-tree accessions come back from tools that nothing can take them into Written from the ARF family dossier in [`examples/arf_family/`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/), re-run at server commit `967bc36` (release `1.21.0`): 400 MCP calls over 48 genes x 16 tools, the family itself from a 742-call enumeration through the same tools. Each section below is one row of [`gaps.jsonl`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/gaps.jsonl), quoted as logged; `Check` names the captured response… [Read the thread](https://github.com/musharna/plant-genomics-mcp/issues/130) · 2026-09-22 · closed · 1 comment ### Both ortholog tools cap at 100 rows with no target-organism filter, so rice and wheat never come back Written from the ARF family dossier run in [`examples/arf_family/`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/), server version `1.21.0`, 2026-09-21 (29 genes x 16 tools, 248 MCP calls; the family itself from a 516-call enumeration through the same tools). Each section below is one row of [`gaps.jsonl`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/gaps.jsonl), quoted as logged; `Check` names the captured response to read it back… [Read the thread](https://github.com/musharna/plant-genomics-mcp/issues/125) · 2026-09-22 · closed · 1 comment ### `gene_report`: payloads carried twice, per-step timings always null, two names for one gene, GO bullets repeated Written from the ARF family dossier run in [`examples/arf_family/`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/), server version `1.21.0`, 2026-09-21 (29 genes x 16 tools, 248 MCP calls; the family itself from a 516-call enumeration through the same tools). Each section below is one row of [`gaps.jsonl`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/gaps.jsonl), quoted as logged; `Check` names the captured response to read it back… [Read the thread](https://github.com/musharna/plant-genomics-mcp/issues/122) · 2026-09-22 · closed · 1 comment ### Every wheat IWGSC locus is a 404 in STRING, though the same loci resolve to UniProt Written from the ARF family dossier in [`examples/arf_family/`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/), re-run at server commit `052e4ec` (release `1.21.0`): 64 MCP calls over 114 genes x 16 tools, the family itself from a 1163-call enumeration through the same tools. Each section below is one row of [`gaps.jsonl`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/gaps.jsonl), quoted as logged; `Check` names the captured… [Read the thread](https://github.com/musharna/plant-genomics-mcp/issues/155) · 2026-09-23 · closed · 0 comments ### `gene_report` answers ok with an empty result when its Ensembl step fails, where the description promises a degraded dossier Written from the ARF family dossier in [`examples/arf_family/`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/), re-run at server commit `052e4ec` (release `1.21.0`): 64 MCP calls over 114 genes x 16 tools, the family itself from a 1163-call enumeration through the same tools. Each section below is one row of [`gaps.jsonl`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/gaps.jsonl), quoted as logged; `Check` names the captured… [Read the thread](https://github.com/musharna/plant-genomics-mcp/issues/154) · 2026-09-23 · closed · 0 comments ### `batch_locus_call` fans out 8 wide, and OrthoDB refuses the excess as a rate limit Written from the ARF family dossier in [`examples/arf_family/`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/), re-run at server commit `052e4ec` (release `1.21.0`): 64 MCP calls over 114 genes x 16 tools, the family itself from a 1163-call enumeration through the same tools. Each section below is one row of [`gaps.jsonl`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/gaps.jsonl), quoted as logged; `Check` names the captured… [Read the thread](https://github.com/musharna/plant-genomics-mcp/issues/153) · 2026-09-23 · closed · 0 comments ## Most recent ### `string_interactions.accession` is a STRING id, not the UniProt accession the other tools mean by that name Written from the ARF family dossier in [`examples/arf_family/`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/), re-run at server commit `967bc36` (release `1.21.0`): 400 MCP calls over 48 genes x 16 tools, the family itself from a 742-call enumeration through the same tools. Each section below is one row of [`gaps.jsonl`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/gaps.jsonl), quoted as logged; `Check` names the captured response… [Read the thread](https://github.com/musharna/plant-genomics-mcp/issues/133) · 2026-09-22 · closed · 0 comments ### `locus_go_annotations` drops a row without a flag and ships a dedup the payload does not label Written from the ARF family dossier in [`examples/arf_family/`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/), re-run at server commit `967bc36` (release `1.21.0`): 400 MCP calls over 48 genes x 16 tools, the family itself from a 742-call enumeration through the same tools. Each section below is one row of [`gaps.jsonl`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/gaps.jsonl), quoted as logged; `Check` names the captured response… [Read the thread](https://github.com/musharna/plant-genomics-mcp/issues/132) · 2026-09-22 · closed · 0 comments ### 81% of responses report no upstream release, and three report one under a key nothing reads Written from the ARF family dossier run in [`examples/arf_family/`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/), server version `1.21.0`, 2026-09-21 (29 genes x 16 tools, 248 MCP calls; the family itself from a 516-call enumeration through the same tools). Each section below is one row of [`gaps.jsonl`](https://github.com/musharna/plant-genomics-mcp/blob/main/examples/arf_family/gaps.jsonl), quoted as logged; `Check` names the captured response to read it back… [Read the thread](https://github.com/musharna/plant-genomics-mcp/issues/121) · 2026-09-22 · closed · 0 comments ### fuzz: 1 crash(es) found 2026-09-20 Automated fuzzing (hypothesis) of pure entry-point helpers. Note: this session's sandbox denied all filesystem writes (Write tool, shell redirection, `mkdir`, even Python's `open()` were blocked), so tests ran as inline `uv run python -c` snippets rather than files under `fuzz_scratch/` as normally required — no files could be committed to that directory this run. ## Crash 1: `organisms.resolve()` — unhandled AttributeError/TypeError on non-str/int input `organisms.resolve()`… [Read the thread](https://github.com/musharna/plant-genomics-mcp/issues/118) · 2026-09-20 · closed · external user · 0 comments ### fuzz: 2 crash(es) found 2026-09-14 Hypothesis property-based fuzzing of pure, network-free entry points in `plant_genomics_mcp` (validators, organisms, batch, cache, synthesis reconciliation helpers). Ran with `--hypothesis-seed=0`, no fixed test files were persisted this run (sandbox write permissions were unavailable), tests were executed inline via `uv run python` with the same strategies described below. Both crashes are unhandled Python exceptions (`AttributeError` / `TypeError`) rather than a deliberate… [Read the thread](https://github.com/musharna/plant-genomics-mcp/issues/95) · 2026-09-14 · closed · external user · 0 comments The remaining reports are on [the project's issue tracker](https://github.com/musharna/plant-genomics-mcp/issues).