Merge pull request #40 from RIMS-Code/error_catching_json_calibration…

…_read Add a more reasonable error on json cal loading error
RIMS-Code · Aug 10, 2022 · 0aa2e79 · 0aa2e79
2 parents 8b89463 + 7cf0910
commit 0aa2e79
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Showing 4 changed files with 177 additions and 2 deletions.
diff --git a/rimseval/interfacer.py b/rimseval/interfacer.py
@@ -70,6 +70,7 @@ def load_cal_file(crd: CRDFileProcessor, fname: Path = None) -> None:
         `.json` suffix.
 
     :raises OSError: Calibration file does not exist.
+    :raises OSError: JSON file cannot be decoded. JSON error message is returned too.
     """
     if fname is None:
         fname = crd.fname.with_suffix(".json")
@@ -78,7 +79,12 @@ def load_cal_file(crd: CRDFileProcessor, fname: Path = None) -> None:
         raise OSError(f"The requested calibration file {fname} does not exist.")
 
     with fname.open("r", encoding="utf-8") as fin:
-        json_object = json.load(fin)
+        try:
+            json_object = json.load(fin)
+        except json.decoder.JSONDecodeError as orig_err:
+            raise OSError(
+                f"Cannot open the calibration file {fname.name}. JSON decode error."
+            ) from orig_err
 
     def entry_loader(key: str, json_obj: Any) -> Any:
         """Return the value of a json_object dictionary if existent, otherwise None."""

diff --git a/tests/func/conftest.py b/tests/func/conftest.py
@@ -47,3 +47,13 @@ def crd_int_delta(crd_file) -> CRDFileProcessor:
     )
     crd.integrals_pkg = np.array([crd.integrals, crd.integrals])
     return crd
+
+
+@pytest.fixture
+def data_files_path(request) -> Path:
+    """Provides the path to the `data_files` folder.
+
+    :return: Path to the folder
+    """
+    curr = Path(request.fspath).parents[0]
+    return Path(curr).joinpath("data_files").absolute()
diff --git a/tests/func/data_files/faulty_cal_file.json b/tests/func/data_files/faulty_cal_file.json
@@ -0,0 +1,147 @@
+{
+    "mcal": [
+        [
+            5.302762235136544,
+            89.9046977
+        ],
+        [
+            5.552698550914553,
+            90.9056396
+        ],
+        [
+            5.8006809603321,
+            91.9050347
+        ],
+        [
+            6.293683219315044,
+            93.9063108
+        ],
+        [
+            6.781419663024983,
+            95.9082714
+        ]
+    ],
+    "integral_names": [
+        "Zr-90",
+        "Zr-91",
+        "Zr-92",
+        "Zr-94",
+        "Zr-96",
+    ],
+    "integrals": [
+        [
+            89.7446977,
+            90.0646977
+        ],
+        [
+            90.7456396,
+            91.0656396
+        ],
+        [
+            91.7450347,
+            92.0650347
+        ],
+        [
+            93.7463108,
+            94.0663108
+        ],
+        [
+            95.74827140000001,
+            96.0682714
+        ]
+    ],
+   "background_names": [
+        "Zr-96",
+        "Zr-96",
+        "Zr-94",
+        "Zr-94",
+        "Zr-92",
+        "Zr-92",
+        "Zr-91",
+        "Zr-91",
+        "Zr-90",
+        "Zr-90"
+    ],
+    "backgrounds": [
+        [
+            95.55629192191135,
+            95.7582714
+        ],
+        [
+            96.05827140000001,
+            96.20540570285735
+        ],
+        [
+            93.51206792520081,
+            93.7563108
+        ],
+        [
+            94.0563108,
+            94.23868782924484
+        ],
+        [
+            91.49690872465203,
+            91.7550347
+        ],
+        [
+            92.05503470000001,
+            92.20415209792155
+        ],
+        [
+            90.57652351286292,
+            90.7556396
+        ],
+        [
+            91.0556396,
+            91.22563729380892
+        ],
+        [
+            89.59800870875029,
+            89.7546977
+        ],
+        [
+            90.0546977,
+            90.23743422430904
+        ]
+    ],
+    "applied_filters": {
+        "spectrum_part": [
+            true,
+            [
+                [
+                    0,
+                    125000
+                ]
+            ]
+        ],
+        "max_ions_per_shot": [
+            false,
+            15
+        ],
+        "max_ions_per_time": [
+            false,
+            1,
+            0.01
+        ],
+        "max_ions_per_tof_window": [
+            false,
+            1,
+            [
+                2.07,
+                2.2
+            ]
+        ],
+        "packages": [
+            false,
+            1000
+        ],
+        "max_ions_per_pkg": [
+            false,
+            1000
+        ],
+        "dead_time_corr": [
+            true,
+            15
+        ]
+    }
+}
diff --git a/tests/func/test_interfacer.py b/tests/func/test_interfacer.py
@@ -6,7 +6,6 @@
 import numpy as np
 
 from rimseval import interfacer
-from rimseval.processor import CRDFileProcessor
 
 
 def test_read_lion_eval_calfile(mocker, crd_proc_mock):
@@ -39,3 +38,16 @@ def test_read_lion_eval_calfile(mocker, crd_proc_mock):
     np.testing.assert_almost_equal(integrals_rec[1], integrals_exp[1])
     assert backgrounds_rec[0] == backgrounds_exp[0]
     np.testing.assert_almost_equal(backgrounds_rec[1], backgrounds_exp[1])
+
+
+def test_read_lion_eval_calfile_read_error(data_files_path, crd_proc_mock):
+    """Raise IOError if the calibration file cannot be read successfully."""
+    cal_file = data_files_path.joinpath("faulty_cal_file.json")
+
+    err_exp = f"Cannot open the calibration file {cal_file.name}. JSON decode error."
+
+    with pytest.raises(IOError) as err:
+        interfacer.load_cal_file(crd_proc_mock, cal_file)
+
+    msg = err.value.args[0]
+    assert msg == err_exp