Forge Tools sra_run

sra_run read

scidex.forge.sra_run

Search NCBI Sequence Read Archive (SRA) for sequencing run metadata. Accepts free-text queries (gene names, diseases, organisms, experimental terms) or direct SRR/SRP/ERP/DRP accession lookups. Returns run_accession, study_accession, organism, platform, library_strategy, library_layout, spots, bases, published date, and title. Optional filters: organism, platform, library_strategy. SRA hosts >50M runs across Illumina, PacBio, Oxford Nanopore and other platforms. Set NCBI_API_KEY for 10 rps (default 3 rps anonymous).

HTTP: POST /api/scidex/forge/sra_run

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.sra_run``.",
  "properties": {
    "query": {
      "description": "Free-text search term (e.g. ``'TP53 RNA-Seq'``, ``'pancreatic cancer'``) or an SRA accession (SRR*, SRP*, ERP*, DRP*).",
      "maxLength": 512,
      "minLength": 1,
      "title": "Query",
      "type": "string"
    },
    "organism": {
      "anyOf": [
        {
          "maxLength": 128,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Organism filter — scientific name passed as ``[Organism]`` qualifier (e.g. ``'Homo sapiens'``, ``'Mus musculus'``). ``None`` = no filter.",
      "title": "Organism"
    },
    "platform": {
      "anyOf": [
        {
          "maxLength": 64,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Sequencing platform filter (e.g. ``'ILLUMINA'``, ``'OXFORD_NANOPORE'``, ``'PACBIO_SMRT'``). Case-insensitive. ``None`` = no filter.",
      "title": "Platform"
    },
    "library_strategy": {
      "anyOf": [
        {
          "maxLength": 64,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Library strategy filter (e.g. ``'RNA-Seq'``, ``'WGS'``, ``'ChIP-Seq'``). ``None`` = no filter.",
      "title": "Library Strategy"
    },
    "limit": {
      "default": 10,
      "description": "Maximum number of SRA run records to return.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeSRARunIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "SRARunEntry": {
      "description": "One SRA run record.",
      "properties": {
        "run_accession": {
          "description": "SRR accession (the primary SRA run ID).",
          "title": "Run Accession",
          "type": "string"
        },
        "study_accession": {
          "default": "",
          "description": "SRP/ERP/DRP study accession.",
          "title": "Study Accession",
          "type": "string"
        },
        "organism": {
          "default": "",
          "description": "Scientific name of the sequenced organism.",
          "title": "Organism",
          "type": "string"
        },
        "platform": {
          "default": "",
          "description": "Sequencing platform (e.g. ILLUMINA, PACBIO_SMRT, OXFORD_NANOPORE).",
          "title": "Platform",
          "type": "string"
        },
        "library_strategy": {
          "default": "",
          "description": "Library strategy (e.g. RNA-Seq, WGS, ChIP-Seq, AMPLICON).",
          "title": "Library Strategy",
          "type": "string"
        },
        "library_layout": {
          "default": "",
          "description": "Library layout: SINGLE or PAIRED.",
          "title": "Library Layout",
          "type": "string"
        },
        "spots": {
          "default": 0,
          "description": "Total number of spots (reads) in the run.",
          "title": "Spots",
          "type": "integer"
        },
        "bases": {
          "default": 0,
          "description": "Total base count for the run.",
          "title": "Bases",
          "type": "integer"
        },
        "published": {
          "default": "",
          "description": "Public release date in YYYY-MM-DD format (empty if unavailable).",
          "title": "Published",
          "type": "string"
        },
        "title": {
          "default": "",
          "description": "Run title or library name.",
          "title": "Title",
          "type": "string"
        }
      },
      "required": [
        "run_accession"
      ],
      "title": "SRARunEntry",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.sra_run``.",
  "properties": {
    "results": {
      "description": "SRA run records matching the query.",
      "items": {
        "$ref": "#/$defs/SRARunEntry"
      },
      "title": "Results",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total SRA UIDs returned by esearch before the limit was applied.",
      "title": "Total Found",
      "type": "integer"
    },
    "not_found": {
      "default": false,
      "description": "True when the query returned no matching runs.",
      "title": "Not Found",
      "type": "boolean"
    },
    "query": {
      "default": "",
      "description": "The original query string.",
      "title": "Query",
      "type": "string"
    },
    "took_ms": {
      "description": "Wall-clock time for all upstream calls in ms.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "took_ms"
  ],
  "title": "ForgeSRARunOut",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/sra_run' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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