io.github.musharna/plant-genomics-mcp

What we checked

Six static checks, weighted by risk. Every result reflects only what could be observed in the published package and repository — never intent.

• Injection surface

  unscannable25% of grade

  Tool descriptions/manifest scanned for instruction-injection patterns (imperatives at the model, hidden text, 'ignore previous', data-exfil URLs).

  No tool descriptions, server instructions, prompts, or resources were fetched; nothing to scan for injection.

• Supply chain

  fail25% of grade

  Package provenance: namespace verification, repo linkage, maintainer count, account age, postinstall scripts, typosquat distance.

  Python build script executes at build time: network call in build script

• Credential hygiene

  pass15% of grade

  How the server takes secrets (env vs plaintext config vs hardcoded); secrets appearing in tool schemas.

  Reads secrets from the environment (e.g. scripts/verify_organisms.py) — the recommended intake shape. PASS = no static red flag; static analysis cannot prove the code honors env-based secret handling at runtime.

• Permission scope

  pass15% of grade

  Declared tools vs. breadth (filesystem, network, exec); flags shell-exec and unbounded filesystem access.

  Network egress present (examples/_run_chain.py: outbound HTTP/socket call) — expected for most servers and not a finding on its own. No shell-exec, unbounded/sensitive filesystem, or download-and-run primitives found in scanned source. PASS = no static red flag. Static scanning is blind to code fetched or executed at runtime.

• Version behavior

  fail10% of grade

  Diff of tool definitions between versions; new permissions or changed descriptions in a patch release (the postmark-mcp class).

  vs prior 1.20.0 (minor bump): new capability primitive(s) in source: http-client, net; new hardcoded outbound host/BCC destination(s): 127.0.0.1, atted, atted.jp, bar.utoronto.ca, blast.ncbi.nlm.nih.gov, data, data.gramene.org, europepmc.org, evil.example, example.test, github.com, phytozome-next.jgi.doe.gov, pmn.plantcyc.org, rest, rest.ensembl.org, rest.ensembl.org., rest.kegg.jp, rest.uniprot.org, string-db, string-db.org, websvc.biocyc.org, www, www.arabidopsis.org, www.ebi.ac.uk, www.ncbi.nlm.nih.gov, www.uniprot.org, x.

• Transport config

  unscannable10% of grade

  Remote servers: TLS and auth mode (none/token/OAuth). Local servers: whether the manifest indicates it phones home.

  local stdio server: no remote transport or auth surface, and no phone-home/telemetry signal found in source. Absence of transport findings is NOT a safety guarantee — phone-home hosts can be constructed at runtime and defeat static analysis.