bug(fcsfile): fix recursion when file has no spill string

Author: gegnew

cellengine/resources/fcs_file.py

@@ -35,7 +35,8 @@ class FcsFile(DataClassMixin):
     sample_name: Optional[str] = field(default=ReadOnly(optional=True))  # type: ignore
     size: int = field(default=ReadOnly())  # type: ignore
     _spill_string: Optional[str] = field(
-        metadata=config(field_name="spillString"), default=None
+        metadata=config(field_name="spillString"),
+        default=None,
     )
 
     def __repr__(self):
@@ -197,6 +198,10 @@ def plot(
 
     def get_file_internal_compensation(self) -> Compensation:
         """Get the file-internal Compensation."""
+        if not self.has_file_internal_comp or self._spill_string == "":
+            raise ValueError(
+                f"FCS File '{self._id}' does not have an internal compensation."
+            )
         return Compensation.from_spill_string(self.spill_string)
 
     @property
@@ -225,10 +230,16 @@ def events(self, events):
     def spill_string(self):
         if self._spill_string:
             return self._spill_string
+        elif self.has_file_internal_comp:
+            self._spill_string = (
+                ce.APIClient().get_fcs_file(self.experiment_id, self._id, as_dict=True)[
+                    "spillString"
+                ]
+                or ""
+            )  # type: ignore
         else:
-            ss = ce.APIClient().get_fcs_file(self.experiment_id, self._id).spill_string
-            self._spill_string = ss
-            return ss
+            self._spill_string = ""
+        return self._spill_string
 
     def get_events(
         self, inplace: bool = False, destination=None, **kwargs

tests/unit/resources/test_fcsfile.py

@@ -1,12 +1,14 @@
-import os
+from io import BufferedReader, BytesIO
 import json
+import os
+
 from fcsparser.api import FCSParser
 from pandas.core.frame import DataFrame
+import pytest
 import responses
-from io import BufferedReader, BytesIO
 
-from cellengine.resources.fcs_file import FcsFile
 from cellengine.resources.compensation import Compensation
+from cellengine.resources.fcs_file import FcsFile
 
 
 EXP_ID = "5d38a6f79fae87499999a74b"
@@ -79,6 +81,31 @@ def test_gets_file_internal_compensation(ENDPOINT_BASE, client, fcs_files, spill
     assert type(comp) == Compensation
 
 
+@responses.activate
+def test_throws_correct_error_when_no_file_internal_compensation(
+    ENDPOINT_BASE, client, fcs_files
+):
+    # Given: An FcsFile with no spill string
+    file_data = fcs_files[0]
+    file_data["spillString"] = ""
+    file = FcsFile.from_dict(file_data)
+    expected_response = fcs_files[0].copy()
+    responses.add(
+        responses.GET,
+        f"{ENDPOINT_BASE}/experiments/{EXP_ID}/fcsfiles/{file._id}",
+        json=expected_response,
+    )
+
+    # When:
+    with pytest.raises(ValueError) as err:
+        comp = file.get_file_internal_compensation()
+        # Then:
+    assert (
+        err.value.args[0]
+        == f"FCS File '{file._id}' does not have an internal compensation."
+    )
+
+
 def test_parse_fcs_file():
     events_body = open("tests/data/Acea - Novocyte.fcs", "rb")
     parser = FCSParser.from_data(events_body.read())