Merge pull request #20 from TheJacksonLaboratory/G3-227-geneset-add-e…

…ndpoint-via-json

G3-227: Update Geneset upload schema to better match batch upload schema

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-core"
-version = "0.9.1"
+version = "0.10.0a0"
 description = "The core of the Jax-Geneweaver Python library"
 authors = ["Jax Computational Sciences <cssc@jax.org>"]
 readme = "README.md"

src/geneweaver/core/schema/geneset.py

@@ -1,16 +1,17 @@
 """Schemas for geneset."""
 
 import datetime
-from typing import List, Optional
+from typing import List, Optional, Union
 
 from geneweaver.core.enum import (
     GeneIdentifier,
-    GenesetAccess,
     GenesetTier,
+    Microarray,
     ScoreType,
     Species,
 )
 from geneweaver.core.schema.gene import GeneValue
+from geneweaver.core.schema.score import GenesetScoreType
 from pydantic import BaseModel, Field
 
 
@@ -48,16 +49,15 @@ class GenesetGenes(BaseModel):
 class GenesetUpload(BaseModel):
     """Geneset upload schema."""
 
+    score: GenesetScoreType
+    species: Species
+    gene_id_type: Union[GeneIdentifier, Microarray]
+    pubmed_id: Optional[str] = None
+    private: bool = True
+    abbreviation: str
     name: str
-    label: str
-    score_type: ScoreType
-    description: str
-    pubmed_id: Optional[str]
-    access: GenesetAccess
-    groups: List[str] = []
-    species: str
-    gene_identifier: str
-    gene_list: List[GeneValue]
+    description: str = ""
+    values: List[GeneValue]
 
 
 class BatchUpload(BaseModel):

tests/unit/schema/conftest.py

@@ -57,15 +57,14 @@ def geneset_upload_data() -> dict:
     """Provide example geneset upload data."""
     return {
         "name": "name",
-        "label": "label",
-        "score_type": "p-value",
+        "abbreviation": "label",
+        "score": {"score_type": "p-value", "threshold": 0.05},
         "description": "description",
         "pubmed_id": "1",
-        "access": "private",
-        "groups": ["group"],
-        "species": "species",
-        "gene_identifier": "gene_identifier",
-        "gene_list": [{"symbol": "1", "value": "1"}],
+        "private": True,
+        "species": "Mus Musculus",
+        "gene_id_type": "Entrez",
+        "values": [{"symbol": "1", "value": 1.0}],
     }
 
 

tests/unit/schema/test_schema_create.py

@@ -54,15 +54,17 @@ def test_geneset_upload_schema(geneset_upload_data: dict) -> None:
     """Test creating a geneset upload from a dict."""
     geneset_upload = GenesetUpload(**geneset_upload_data)
     assert geneset_upload.name == geneset_upload_data["name"]
-    assert geneset_upload.label == geneset_upload_data["label"]
-    assert str(geneset_upload.score_type) == geneset_upload_data["score_type"]
+    assert geneset_upload.abbreviation == geneset_upload_data["abbreviation"]
+    assert (
+        str(geneset_upload.score.score_type)
+        == geneset_upload_data["score"]["score_type"]
+    )
     assert geneset_upload.description == geneset_upload_data["description"]
     assert geneset_upload.pubmed_id == geneset_upload_data["pubmed_id"]
-    assert geneset_upload.access == geneset_upload_data["access"]
-    assert geneset_upload.groups == geneset_upload_data["groups"]
-    assert geneset_upload.species == geneset_upload_data["species"]
-    assert geneset_upload.gene_identifier == geneset_upload_data["gene_identifier"]
-    assert len(geneset_upload.gene_list) == len(geneset_upload_data["gene_list"])
+    assert geneset_upload.private == geneset_upload_data["private"]
+    assert str(geneset_upload.species) == geneset_upload_data["species"]
+    assert str(geneset_upload.gene_id_type) == geneset_upload_data["gene_id_type"]
+    assert len(geneset_upload.values) == len(geneset_upload_data["values"])
 
 
 def test_batch_upload_schema(batch_upload_data: dict) -> None: