Clarify visualize error handling

bionetgen/core/tools/visualize.py

@@ -1,6 +1,8 @@
 import os, bionetgen, glob
 from tempfile import TemporaryDirectory
+from typing import NoReturn, Optional
 
+from bionetgen.core.exc import BNGError, BNGFileError
 from bionetgen.core.utils.logging import BNGLogger
 
 
@@ -135,7 +137,7 @@ def run(self) -> VisResult:
         self.logger.debug("Running", loc=f"{__file__} : BNGVisualize.run()")
         return self._normal_mode()
 
-    def _normal_mode(self):
+    def _normal_mode(self) -> VisResult:
         self.logger.debug(
             f"Running on normal mode, loading model {self.input}",
             loc=f"{__file__} : BNGVisualize._normal_mode()",
@@ -182,42 +184,51 @@ def _normal_mode(self):
             with TemporaryDirectory() as out:
                 # instantiate a CLI object with the info
                 cli = BNGCLI(model, out, self.bngpath, suppress=self.suppress)
-                try:
-                    cli.run()
-                    # load vis
-                    vis_res = VisResult(
-                        os.path.abspath(os.getcwd()),
-                        name=model.model_name,
-                        vtype=self.vtype,
-                    )
-                    # go back
-                    os.chdir(cur_dir)
-                    # dump files
-                    vis_res._dump_files(cur_dir)
-                    return vis_res
-                except Exception as e:
-                    os.chdir(cur_dir)
-                    print("Couldn't run the simulation, see error.")
-                    raise e
-        else:
-            # instantiate a CLI object with the info
-            cli = BNGCLI(model, self.output, self.bngpath, suppress=self.suppress)
-            try:
-                cli.run()
-                # load vis
-                vis_res = VisResult(
-                    os.path.abspath(os.getcwd()),
-                    name=model.model_name,
-                    vtype=self.vtype,
-                )
-                # go back
-                os.chdir(cur_dir)
-                return vis_res
-            except Exception as e:
-                self.logger.error(
-                    "Failed to run file",
-                    loc=f"{__file__} : BNGVisualize._normal_mode()",
+                return self._run_and_collect_vis(
+                    cli,
+                    model_name=model.model_name,
+                    cur_dir=cur_dir,
+                    dump_dir=cur_dir,
                 )
-                os.chdir(cur_dir)
-                print("Couldn't run the simulation, see error.")
-                raise e
+
+        # instantiate a CLI object with the info
+        cli = BNGCLI(model, self.output, self.bngpath, suppress=self.suppress)
+        return self._run_and_collect_vis(
+            cli,
+            model_name=model.model_name,
+            cur_dir=cur_dir,
+        )
+
+    def _run_and_collect_vis(
+        self, cli, *, model_name: str, cur_dir: str, dump_dir: Optional[str] = None
+    ) -> VisResult:
+        try:
+            cli.run()
+            vis_res = VisResult(
+                os.path.abspath(os.getcwd()),
+                name=model_name,
+                vtype=self.vtype,
+            )
+            if dump_dir is not None:
+                vis_res._dump_files(dump_dir)
+            return vis_res
+        except BNGError as exc:
+            self._log_visualization_failure(exc)
+            raise
+        except OSError as exc:
+            self._raise_visualization_file_error(exc)
+        finally:
+            os.chdir(cur_dir)
+
+    def _log_visualization_failure(self, exc: BaseException) -> None:
+        self.logger.error(
+            f"Failed to generate visualization files: {exc}",
+            loc=f"{__file__} : BNGVisualize._normal_mode()",
+        )
+
+    def _raise_visualization_file_error(self, exc: OSError) -> NoReturn:
+        self._log_visualization_failure(exc)
+        raise BNGFileError(
+            self.input,
+            message=f"Failed to generate visualization files: {exc}",
+        ) from exc

tests/test_visualize_errors.py

@@ -0,0 +1,66 @@
+from unittest import mock
+
+import pytest
+
+from bionetgen.core.exc import BNGFileError, BNGRunError
+
+
+@pytest.mark.parametrize("use_output", [False, True])
+def test_normal_mode_logs_and_reraises_cli_failures(tmp_path, capsys, use_output):
+    from bionetgen.core.tools.visualize import BNGVisualize
+
+    fake_model = mock.MagicMock()
+    fake_model.model_name = "test_model"
+    output = str(tmp_path / "viz") if use_output else None
+    visualize = BNGVisualize("test.bngl", output=output)
+    visualize.logger = mock.MagicMock()
+
+    with mock.patch(
+        "bionetgen.core.tools.visualize.bionetgen.modelapi.bngmodel",
+        return_value=fake_model,
+    ), mock.patch("bionetgen.core.main.BNGCLI") as mock_cli_cls:
+        mock_cli_cls.return_value.run.side_effect = BNGRunError(
+            ["perl", "BNG2.pl", "test.bngl"],
+            message="boom",
+        )
+
+        with pytest.raises(BNGRunError, match="boom"):
+            visualize._normal_mode()
+
+    captured = capsys.readouterr()
+    assert captured.out == ""
+    visualize.logger.error.assert_called_once()
+    error_args, error_kwargs = visualize.logger.error.call_args
+    assert error_args[0].startswith("Failed to generate visualization files:")
+    assert "boom" in error_args[0]
+    assert "BNGVisualize._normal_mode()" in error_kwargs["loc"]
+
+
+def test_normal_mode_wraps_dump_failures(capsys):
+    from bionetgen.core.tools.visualize import BNGVisualize
+
+    fake_model = mock.MagicMock()
+    fake_model.model_name = "test_model"
+    fake_vis_result = mock.MagicMock()
+    fake_vis_result._dump_files.side_effect = OSError("disk full")
+    visualize = BNGVisualize("test.bngl")
+    visualize.logger = mock.MagicMock()
+
+    with mock.patch(
+        "bionetgen.core.tools.visualize.bionetgen.modelapi.bngmodel",
+        return_value=fake_model,
+    ), mock.patch("bionetgen.core.main.BNGCLI"), mock.patch(
+        "bionetgen.core.tools.visualize.VisResult",
+        return_value=fake_vis_result,
+    ):
+        with pytest.raises(
+            BNGFileError, match="Failed to generate visualization files: disk full"
+        ):
+            visualize._normal_mode()
+
+    captured = capsys.readouterr()
+    assert captured.out == ""
+    visualize.logger.error.assert_called_once()
+    error_args, error_kwargs = visualize.logger.error.call_args
+    assert "Failed to generate visualization files: disk full" in error_args[0]
+    assert "BNGVisualize._normal_mode()" in error_kwargs["loc"]