at least 1 assay column required

constants.py

@@ -35,7 +35,7 @@ REQUIRED_COLUMNS: list[str] = [
     "antibody_name",
     "vh_protein_sequence",
     "vl_protein_sequence",
-] + ASSAY_LIST
+]
 ANTIBODY_NAMES = pd.read_csv("data/example-predictions.csv")["antibody_name"].tolist()
 
 # Huggingface API

test/conftest.py

@@ -1,27 +1,10 @@
 import pytest
 import pandas as pd
-from constants import MINIMAL_NUMBER_OF_ROWS, ASSAY_LIST, ANTIBODY_NAMES
 
 
 @pytest.fixture
-def valid_csv_data():
-    return {
-        "antibody_name": ANTIBODY_NAMES[:MINIMAL_NUMBER_OF_ROWS],
-        "vh_protein_sequence": [
-            "EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMHWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDYGDGYYFDYWGQGTLVTVSS"
-        ]
-        * MINIMAL_NUMBER_OF_ROWS,
-        "vl_protein_sequence": [
-            "DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASTLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPFTFGQGTKVEIK"
-        ]
-        * MINIMAL_NUMBER_OF_ROWS,
-        **{assay: [0.85] * MINIMAL_NUMBER_OF_ROWS for assay in ASSAY_LIST},
-    }
-
-
-@pytest.fixture
-def valid_input_dataframe(valid_csv_data):
-    return pd.DataFrame(valid_csv_data)
+def valid_input_dataframe():
+    return pd.read_csv("data/example-predictions.csv")
 
 
 @pytest.fixture

test/test_validation.py

@@ -2,7 +2,7 @@ import pytest
 import pandas as pd
 import gradio as gr
 from validation import validate_csv_file, validate_csv_can_be_read, validate_dataframe
-from constants import REQUIRED_COLUMNS, MINIMAL_NUMBER_OF_ROWS
+from constants import REQUIRED_COLUMNS, MINIMAL_NUMBER_OF_ROWS, ASSAY_LIST
 
 
 class TestValidateCsvCanBeRead:
@@ -11,8 +11,6 @@ class TestValidateCsvCanBeRead:
     def test_valid_csv_can_be_read(self, valid_csv_content):
         df = validate_csv_can_be_read(valid_csv_content)
         assert isinstance(df, pd.DataFrame)
-        assert len(df) == MINIMAL_NUMBER_OF_ROWS
-        assert list(df.columns) == list(REQUIRED_COLUMNS)
 
     def test_empty_csv_raises_error(self):
         empty_csv = ""
@@ -56,6 +54,15 @@ class TestValidateDataframe:
 
         assert f"Missing required columns: {missing_column}" in str(exc_info.value)
 
+    def test_at_least_one_assay_column_raises_error(self, valid_input_dataframe):
+        df = valid_input_dataframe.copy()
+        df.drop(columns=ASSAY_LIST, inplace=True, errors="ignore")
+        with pytest.raises(gr.Error) as exc_info:
+            validate_dataframe(df)
+        assert "CSV should include at least one of the following assay columns" in str(
+            exc_info.value
+        )
+
     def test_empty_dataframe_raises_error(self, valid_input_dataframe):
         empty_df = valid_input_dataframe.head(0)
 

validation.py

@@ -1,7 +1,12 @@
 import pandas as pd
 import io
 import gradio as gr
-from constants import REQUIRED_COLUMNS, MINIMAL_NUMBER_OF_ROWS, ANTIBODY_NAMES
+from constants import (
+    REQUIRED_COLUMNS,
+    MINIMAL_NUMBER_OF_ROWS,
+    ANTIBODY_NAMES,
+    ASSAY_LIST,
+)
 
 
 def validate_csv_can_be_read(file_content: str) -> pd.DataFrame:
@@ -57,12 +62,22 @@ def validate_dataframe(df: pd.DataFrame) -> None:
     if missing_columns:
         raise gr.Error(f"❌ Missing required columns: {', '.join(missing_columns)}")
 
+    # Should include at least 1 assay column
+    assay_columns = [col for col in df.columns if col in ASSAY_LIST]
+    if len(assay_columns) < 1:
+        raise gr.Error(
+            "❌ CSV should include at least one of the following assay columns: "
+            + ", ".join(ASSAY_LIST)
+        )
+    # Submission are name, sequence, and at least one assay column
+    submission_columns = REQUIRED_COLUMNS + assay_columns
+
     # Data should not be empty
     if df.empty:
         raise gr.Error("❌ CSV file is empty")
 
-    # No missing values in required columns
-    for col in REQUIRED_COLUMNS:
+    # No missing values in submission columns
+    for col in submission_columns:
         missing_count = df[col].isnull().sum()
         if missing_count > 0:
             raise gr.Error(f"❌ Column '{col}' contains {missing_count} missing values")