added model of output metadata

bedboss/bedmaker/bedmaker.py

@@ -195,6 +195,7 @@ def make(self) -> dict:
         return {
             "bed_type": bed_type,
             "file_type": file_type,
+            "genome": self.genome,
         }
 
     def make_bed(self) -> None:

bedboss/bedstat/bedstat.py

@@ -24,6 +24,7 @@
 )
 from bedboss.utils import download_file, convert_unit
 from bedboss.exceptions import OpenSignalMatrixException
+from bedboss.models import BedMetadata
 
 
 _LOGGER = logging.getLogger("bedboss")
@@ -56,6 +57,8 @@ def load_to_pephub(
         sample_data = {}
         sample_data.update({"sample_name": bed_digest, "genome": genome})
 
+        metadata = BedMetadata(**metadata).model_dump()
+
         for key, value in metadata.items():
             # TODO: Confirm this key is in the schema
             # Then update sample_data

bedboss/models.py

@@ -0,0 +1,29 @@
+from pydantic import BaseModel, ConfigDict, Field
+
+from enum import Enum
+
+
+class BED_TYPE(str, Enum):
+    BED = "bed"
+    NARROWPEAK = "narrowpeak"
+    BROADPEAK = "broadpeak"
+
+
+class BedMetadata(BaseModel):
+    sample_name: str
+    genome: str
+    file_type: BED_TYPE = BED_TYPE.BED
+    bed_type: str = Field(
+        default="bed3", pattern="^bed(?:[3-9]|1[0-2])(?:\+|$)[0-9]?+$"
+    )
+    description: str = None
+    organism: str = None
+    cell_type: str = None
+    tissue: str = None
+    antibody: str = None
+    sample_library_strategy: str = None
+
+    model_config = ConfigDict(
+        populate_by_name=True,
+        extra="allow",
+    )