Merge pull request #328 from lbl-anp/fix-compendium-json-errors

Enable the latest Compendium materials JSON format to be read

becquerel/tools/materials_compendium.py

@@ -18,7 +18,7 @@
 import warnings
 import numpy as np
 import pandas as pd
-from .materials_error import MaterialsWarning
+from .materials_error import MaterialsWarning, MaterialsError
 
 FNAME = os.path.join(os.path.split(__file__)[0], "MaterialsCompendium.json")
 
@@ -60,6 +60,23 @@ def fetch_compendium_data():
             data = json.load(f)
 
     # extract relevant data
+    if isinstance(data, list):
+        print("Pre-March 2022 JSON detected")
+    elif isinstance(data, dict):
+        print("Post-March 2022 JSON detected")
+        if "siteVersion" not in data.keys() or "data" not in data.keys():
+            raise MaterialsError(
+                "Attempt to read Compendium JSON failed; "
+                "dictionary must have keys 'siteVersion' "
+                "and 'data' but have keys " + str(list(data.keys()))
+            )
+        print(f"Compendium data - site version: {data['siteVersion']}")
+        data = data["data"]
+    else:
+        raise MaterialsError(
+            "Attempt to read Compendium JSON failed; "
+            "object must be a list or dict but is a " + str(type(data))
+        )
     names = [datum["Name"] for datum in data]
     formulae = [datum["Formula"] if "Formula" in datum else "-" for datum in data]
     densities = [datum["Density"] for datum in data]

tests/materials_test.py

@@ -87,8 +87,11 @@ def test_materials_dummy_csv():
 
 
 @pytest.mark.webtest
-def test_materials_dummy_compendium():
-    """Test fetch_materials with a dummy Compendium JSON file."""
+def test_materials_dummy_compendium_pre2022():
+    """Test fetch_materials with a dummy Compendium JSON file.
+
+    The dummy JSON file uses the format seen prior to March 2022.
+    """
     # point to an generate a dummy JSON file
     fname_orig = materials_compendium.FNAME
     materials_compendium.FNAME = fname_orig[:-5] + "_dummy.json"
@@ -128,6 +131,79 @@ def test_materials_dummy_compendium():
     materials_compendium.FNAME = fname_orig
 
 
+@pytest.mark.webtest
+def test_materials_dummy_compendium_2022():
+    """Test fetch_materials with a dummy Compendium JSON file.
+
+    The dummy JSON file uses the format first seen in March 2022.
+    """
+    # point to an generate a dummy JSON file
+    fname_orig = materials_compendium.FNAME
+    materials_compendium.FNAME = fname_orig[:-5] + "_dummy.json"
+    data = {
+        "siteVersion": "0.0.0",
+        "data": [
+            {
+                "Density": 8.4e-5,
+                "Elements": [
+                    {
+                        "AtomFraction_whole": 1.0,
+                        "Element": "H",
+                        "WeightFraction_whole": 1.0,
+                    }
+                ],
+                "Formula": "H2",
+                "Name": "Hydrogen",
+            },
+            {
+                "Density": 1.16e-3,
+                "Elements": [
+                    {
+                        "AtomFraction_whole": 1.0,
+                        "Element": "N",
+                        "WeightFraction_whole": 1.0,
+                    }
+                ],
+                "Formula": "N2",
+                "Name": "Nitrogen",
+            },
+        ],
+    }
+    with open(materials_compendium.FNAME, "w") as f:
+        json.dump(data, f, indent=4)
+    with pytest.warns(None) as record:
+        materials._load_and_compile_materials()
+    assert len(record) == 0, "Expected no MaterialsWarnings to be raised"
+    # remove siteVersion and make sure there is an error raised
+    del data["siteVersion"]
+    with open(materials_compendium.FNAME, "w") as f:
+        json.dump(data, f, indent=4)
+    with pytest.raises(MaterialsError):
+        materials._load_and_compile_materials()
+    # remove the dummy file and point back to original
+    os.remove(materials_compendium.FNAME)
+    materials_compendium.FNAME = fname_orig
+
+
+@pytest.mark.webtest
+def test_materials_dummy_compendium_error():
+    """Test fetch_materials with a dummy Compendium JSON file.
+
+    The dummy JSON file returns something that is not a list or dict.
+    """
+    # point to an generate a dummy JSON file
+    fname_orig = materials_compendium.FNAME
+    materials_compendium.FNAME = fname_orig[:-5] + "_dummy.json"
+    data = None
+    with open(materials_compendium.FNAME, "w") as f:
+        json.dump(data, f, indent=4)
+    with pytest.raises(MaterialsError):
+        materials._load_and_compile_materials()
+    # remove the dummy file and point back to original
+    os.remove(materials_compendium.FNAME)
+    materials_compendium.FNAME = fname_orig
+
+
 @pytest.mark.webtest
 def test_materials_no_compendium():
     """Test fetch_materials with no Compendium JSON file."""