auto-triage: validate genome_fasta content at schema level

src/modelseed_api/schemas/jobs.py

@@ -7,7 +7,7 @@
 
 from typing import Literal, Optional
 
-from pydantic import BaseModel, Field, model_validator
+from pydantic import BaseModel, Field, field_validator, model_validator
 
 
 # Valid template_type values. Mirrors TEMPLATE_FILES in jobs/tasks.py
@@ -87,6 +87,29 @@ class ReconstructionRequest(BaseModel):
     media: Optional[str] = None
     output_path: Optional[str] = None
 
+    @field_validator("genome_fasta")
+    @classmethod
+    def _validate_genome_fasta_content(cls, v):
+        if v is None:
+            return v
+        has_seq = False
+        in_record = False
+        for line in v.splitlines():
+            stripped = line.strip()
+            if stripped.startswith(">"):
+                in_record = True
+            elif stripped and in_record:
+                has_seq = True
+                break
+        if not has_seq:
+            raise ValueError(
+                "genome_fasta must contain at least one FASTA record "
+                "(a >header line followed by sequence data); got no valid "
+                "records. Pass actual FASTA content, not a file path or "
+                "workspace reference."
+            )
+        return v
+
     @model_validator(mode="after")
     def _validate_input_modes(self) -> "ReconstructionRequest":
         """At most ONE of (genome_fasta, rast_job_id) may be set.

tests/routes/test_job_routes.py

@@ -57,6 +57,36 @@ def test_with_dna_fasta(self, local_client, auth_headers):
         assert resp.status_code == 200
 
 
+    def test_invalid_genome_fasta_no_sequence_returns_422(self, local_client, auth_headers):
+        # Headers-only FASTA (no sequence data) must be rejected at request
+        # time with a 422, not bubble up as a Celery task failure.
+        resp = local_client.post(
+            "/api/jobs/reconstruct",
+            json={"genome": "custom", "genome_fasta": ">contig1\n>contig2\n"},
+            headers=auth_headers,
+        )
+        assert resp.status_code == 422
+        assert "FASTA" in resp.text
+
+    def test_genome_fasta_as_path_returns_422(self, local_client, auth_headers):
+        # A workspace path passed as genome_fasta content should be rejected.
+        resp = local_client.post(
+            "/api/jobs/reconstruct",
+            json={"genome": "custom", "genome_fasta": "/username/data/genome.fasta"},
+            headers=auth_headers,
+        )
+        assert resp.status_code == 422
+        assert "FASTA" in resp.text
+
+    def test_whitespace_only_genome_fasta_returns_422(self, local_client, auth_headers):
+        resp = local_client.post(
+            "/api/jobs/reconstruct",
+            json={"genome": "custom", "genome_fasta": "   \n   \n"},
+            headers=auth_headers,
+        )
+        assert resp.status_code == 422
+
+
 class TestGapfillJob:
     def test_dispatch(self, local_client, auth_headers):
         resp = local_client.post(

tests/unit/test_reconstruction_schema.py

@@ -0,0 +1,30 @@
+"""Unit tests for ReconstructionRequest schema validation."""
+import pytest
+from pydantic import ValidationError
+from modelseed_api.schemas.jobs import ReconstructionRequest
+
+
+class TestGenomeFastaValidation:
+    def test_none_is_valid(self):
+        req = ReconstructionRequest(genome="83333.1", genome_fasta=None)
+        assert req.genome_fasta is None
+
+    def test_valid_protein_fasta(self):
+        req = ReconstructionRequest(genome="custom", genome_fasta=">p1\nMKKLVAV")
+        assert req.genome_fasta is not None
+
+    def test_valid_dna_fasta(self):
+        req = ReconstructionRequest(genome="custom", genome_fasta=">contig1\nACGTACGT")
+        assert req.genome_fasta is not None
+
+    def test_headers_only_rejected(self):
+        with pytest.raises(ValidationError, match="FASTA"):
+            ReconstructionRequest(genome="custom", genome_fasta=">c1\n>c2\n")
+
+    def test_path_string_rejected(self):
+        with pytest.raises(ValidationError, match="FASTA"):
+            ReconstructionRequest(genome="custom", genome_fasta="/user/data/genome.fasta")
+
+    def test_whitespace_only_rejected(self):
+        with pytest.raises(ValidationError, match="FASTA"):
+            ReconstructionRequest(genome="custom", genome_fasta="   \n   ")