Added method for creating reference genomes

Author: Markus Johansson

src/bonsai_libs/api_client/bonsai/client.py

@@ -13,6 +13,7 @@
 
 from .models import (
     CreateGroupInput,
+    CreateReferenceGenomeInput,
     CreateSampleResponse,
     CreateUserInput,
     GenomicResourceInput,
@@ -391,4 +392,25 @@ def get_igv_config(self, sample_id: str, *, analysis_id: str | None = None, vari
         except UnauthorizedError as exc:
             LOG.error("Failed authenticating user", exc_info=exc)
             raise
+        return resp.data
+
+    # ----------------------------
+    # References
+    # ----------------------------
+
+    def create_reference_genome(self, reference_genome: CreateReferenceGenomeInput,*, headers: OpHeaders = None) -> dict[str, Any]:
+        """Get a IGV configuration for a sample.
+        
+        Optional center the view on a variant by providing a analysis_id and variant_id
+        """
+        try:
+            resp = self.request_json(
+                "POST",
+                f"reference-genomes",
+                json=reference_genome.model_dump(mode="json"),
+                headers=headers,
+            )
+        except UnauthorizedError as exc:
+            LOG.error("Failed authenticating user", exc_info=exc)
+            raise
         return resp.data

src/bonsai_libs/api_client/bonsai/models.py

@@ -241,3 +241,32 @@ class GenomicResourceInput(Model):
     reference_genome_id: str
     pipeline_run_id: str
     resource_data: list[AnnotationTrack] = Field(default_factory=list, min_length=1)
+
+
+class GenomicResourceBase(Model):
+    """BED file track."""
+
+    # Classification
+    format: str = Field(..., description="File format, e.g. bed, gff, gtf")
+    type: str = Field(..., description="alignment | variant | annotation")
+
+    # Metadata
+    name: str = Field(..., description="Track name shown in IGV")
+
+    path: str = Field(..., description="Path to main resource file")
+    index_path: str | None = Field(
+        None, description="Optional path to index file."
+    )
+
+
+class CreateReferenceGenomeInput(Model):
+    """Input to create-reference-genome"""
+
+    name: str = Field(..., description="Human-readable name")
+    accession: str = Field(..., description="RefSeq accession")
+    organism: str = Field(..., description="Scientific name")
+
+    fasta_resource: str = Field(..., description="Path or URL to FASTA file")
+    fasta_index_resource: str = Field(..., description="Path or URL to FASTA index.")
+
+    reference_tracks: list[ResourceInput] = Field(default_factory=list, description="Optional list of reference tracks")