Fix empty abstract prevents file input

client/src/pages/ProjectPage.tsx

@@ -632,6 +632,9 @@ export const ProjectPage = () => {
         if (res.valid_filenames?.length) {
           toast.success(`${res.valid_filenames.length} file(s) uploaded`);
         }
+        if ((res.empty_abstract_count ?? 0) > 0) {
+          toast.warn(`${res.empty_abstract_count} abstracts are empty - results will not be optimal`, { autoClose: 8000 })
+        }
         if (res.errors?.length) {
           ExpandableToast(res.errors);
           console.error("File upload errors:", res.errors);

server/src/schemas/file_service.py

@@ -11,7 +11,7 @@ class FileError(BaseModel):
 class ProcessedFiles(BaseModel):
     valid_filenames: List[str]
     errors: List[FileError]
-
+    empty_abstract_count: int = 0
 
 class UploadedFilePaper(BaseModel):
     title: str

server/src/schemas/publication.py

@@ -4,10 +4,10 @@
 
 class PublicationRowData(BaseModel):
     title: str
-    abstract: str
+    abstract: Optional[str]
     doi: Optional[str]
 
-    @field_validator("title", "abstract")
+    @field_validator("title")
     @classmethod
     def check_not_empty(cls, v, field):
         if not isinstance(v, str) or not str(v).strip():

server/src/services/file_service.py

@@ -48,18 +48,25 @@ async def process_files(
         """
         errors: List[FileError] = []
         valid_filenames: List[str] = []
+        empty_abstract_count_total = 0
 
         for f in files:
-            validation_errors = validate_csv(f.file, f.filename or "NONE")
+            validation_errors, file_empty_abstracts = validate_csv(
+                f.file, f.filename or "NONE"
+            )
             if validation_errors:
                 errors.extend(validation_errors)
                 continue
+
             if f.filename is None:
                 continue
             if f.file is None:
                 continue
             if f.content_type is None:
                 continue
+
+            empty_abstract_count_total += file_empty_abstracts
+
             try:
                 file_data = FileCreate(
                     project_uuid=project_uuid,
@@ -91,6 +98,8 @@ async def process_files(
                     }
                     if pd.isna(normalized.get("doi")):
                         normalized["doi"] = None
+                    if pd.isna(normalized.get("abstract")):
+                        normalized["abstract"] = None
 
                     papers.append(
                         PaperCreate(
@@ -127,7 +136,11 @@ async def process_files(
             except Exception as e:
                 raise e
 
-        return ProcessedFiles(valid_filenames=valid_filenames, errors=errors)
+        return ProcessedFiles(
+            valid_filenames=valid_filenames,
+            errors=errors,
+            empty_abstract_count=empty_abstract_count_total,
+        )
 
 
 def create_file_service(db_ctx: DBContext) -> FileService:

server/src/tests/test_010_unit.py

@@ -1,5 +1,7 @@
 import io
+
 import pytest
+
 from src.schemas.file_service import FileError
 from src.tools.csv_file_validation import validate_csv
 
@@ -8,15 +10,15 @@
 def test_validate_csv_success():
     csv_content = "title,abstract,doi\nTest Title,Test Abstract,10.1234/test"
     file_obj = io.BytesIO(csv_content.encode("utf-8"))
-    errors = validate_csv(file_obj, "test.csv")
+    errors, _ = validate_csv(file_obj, "test.csv")
     assert errors == []
 
 
 @pytest.mark.unit
 def test_validate_csv_missing_title_field():
     csv_content = "abstract,doi\nTest Abstract,10.1234/test"
     file_obj = io.BytesIO(csv_content.encode("utf-8"))
-    errors = validate_csv(file_obj, "test.csv")
+    errors, _ = validate_csv(file_obj, "test.csv")
     assert errors == [
         FileError(
             file="test.csv",
@@ -30,7 +32,7 @@ def test_validate_csv_missing_title_field():
 def test_validate_csv_missing_abstract_field():
     csv_content = "title,doi\nTest Title,10.1234/test"
     file_obj = io.BytesIO(csv_content.encode("utf-8"))
-    errors = validate_csv(file_obj, "test.csv")
+    errors, _ = validate_csv(file_obj, "test.csv")
     assert errors == [
         FileError(
             file="test.csv",
@@ -44,7 +46,7 @@ def test_validate_csv_missing_abstract_field():
 def test_validate_csv_missing_doi_field():
     csv_content = "title,abstract\nTest Title,Test Abstract"
     file_obj = io.BytesIO(csv_content.encode("utf-8"))
-    errors = validate_csv(file_obj, "test.csv")
+    errors, _ = validate_csv(file_obj, "test.csv")
     assert errors == [
         FileError(
             file="test.csv",

server/src/tools/csv_file_validation.py

@@ -1,40 +1,52 @@
 import io
 from typing import BinaryIO, List
+
 import pandas as pd
 from pydantic import ValidationError
-from src.schemas.publication import PublicationRowData
+
 from src.schemas.file_service import FileError
+from src.schemas.publication import PublicationRowData
 
 REQUIRED_FIELDS = {"title", "abstract", "doi"}
 
 
-def validate_csv(file_obj: BinaryIO, filename: str) -> List[FileError]:
+def validate_csv(file_obj: BinaryIO, filename: str) -> tuple[List[FileError], int]:
     errors: List[FileError] = []
+    empty_abstract_count = 0
     try:
         raw = file_obj.read()
         df = pd.read_csv(io.BytesIO(raw), encoding="utf-8-sig")
         df.columns = [str(c).strip().lower() for c in df.columns]
         missing = REQUIRED_FIELDS - set(df.columns)
         if missing:
-            return [
-                FileError(
-                    **{
-                        "file": filename or "NO_FILENAME",
-                        "row": "header",
-                        "message": f"Missing required columns: {', '.join(missing)}",
-                    }
-                )
-            ]
+            return (
+                [
+                    FileError(
+                        **{
+                            "file": filename or "NO_FILENAME",
+                            "row": "header",
+                            "message": f"Missing required columns: {', '.join(missing)}",
+                        }
+                    )
+                ],
+                0,
+            )
+
         df["doi"] = df["doi"].astype(str)
         for idx, row in df.iterrows():
+            if pd.isna(row.get("abstract")):
+                empty_abstract_count += 1
+                row["abstract"] = None
+
             if pd.isna(row.get("doi")):
                 row["doi"] = None
+
             try:
                 PublicationRowData(**row.to_dict())
             except ValidationError as e:
                 for err in e.errors():
                     errors.append(
-                        FileError(file=filename, row=int(idx), message=err["msg"])
+                        FileError(file=filename, row=str(idx), message=err["msg"])
                     )  # type: ignore
     except pd.errors.ParserError as e:
         errors.append(
@@ -51,4 +63,4 @@ def validate_csv(file_obj: BinaryIO, filename: str) -> List[FileError]:
             file_obj.seek(0)
         except Exception:
             pass
-    return errors
+    return errors, empty_abstract_count