Warn and remove if empty entries in config.stratigraphy (#386)

src/fmu/dataio/dataio.py

@@ -89,6 +89,10 @@ def _check_global_config(
 
     Currently far from a full validation. For now, just check that some required
     keys are present in the config and warn/raise if not.
+
+    PS! Seems like a good job for jsonschema, but the produced error message are not
+    informative enough to provide meaningful information to user when something is
+    wrong.
     """
 
     if not globalconfig and not strict:
@@ -97,20 +101,73 @@ def _check_global_config(
         )
         return False
 
-    # strict is True:
-    config_required_keys = ["access", "masterdata", "model"]
+    msg = ""
     missing_keys = []
+
+    # check required key presence
+    config_required_keys = ["access", "masterdata", "model"]
     for required_key in config_required_keys:
         if required_key not in globalconfig:
             missing_keys.append(required_key)
 
     if missing_keys:
-        msg = (
+        msg += (
             "One or more keys required for valid metadata are not found: "
             f"{missing_keys} (perhaps the config is empty?) "
         )
+
+    # check "stratigraphy"
+    if "stratigraphy" in globalconfig:
+        # we currently allow (why?) stratigraphy key missing from config.
+        strat = globalconfig["stratigraphy"]
+        if not isinstance(strat, dict):
+            msg += "The 'stratigraphy' must be a dictionary.\n"
+
+        # Loop the entries in 'stratigraphy'
+        # These keys are custom, but we want error messages to point to the key when
+        # issues are discovered. This makes it tricky to use jsonschema. Pydantic might
+        # be an option. But for now, just go through all items and do defined checks.
+
+        for key, item in strat.items():
+            if "name" not in item:
+                msg += f"stratigraphy.{key}: 'name' is missing. \n"
+            elif not isinstance(item["name"], str):
+                msg += f"stratigraphy.{key}: 'name' must be a string.\n"
+
+            if "stratigraphic" not in item:
+                msg += f"stratigraphy.{key}: 'stratigraphic' is missing.\n"
+            elif not isinstance(item["stratigraphic"], bool):
+                msg += f"stratigraphy.{key}: 'stratigraphic' must be a boolean.\n"
+
+            if "alias" in item:
+                if not isinstance(item["alias"], list):
+                    msg += f"stratigraphy.{key}: 'alias' must be a list.\n"
+                else:
+                    for alias in item["alias"]:
+                        if not isinstance(alias, str):
+                            msg += (
+                                f"stratigraphy.{key}: 'alias' items must be strings\n"
+                            )
+
+                    # After checking and warning, remove empty entries
+                    item["alias"] = list(filter(lambda i: i is not None, item["alias"]))
+
+            if "stratigraphic_alias" in item:
+                if not isinstance(item["stratigraphic_alias"], list):
+                    msg += f"stratigraphy.{key}: 'stratigraphic_alias' must be list.\n"
+                else:
+                    for alias in item["stratigraphic_alias"]:
+                        if not isinstance(alias, str):
+                            msg += f"stratigraphy.{key}: 'stratigraphic_alias' items "
+                            msg += "must be strings.\n"
+
+                    # After checking and warning, remove empty entries
+                    item["stratigraphic_alias"] = list(
+                        filter(lambda i: i is not None, item["stratigraphic_alias"])
+                    )
+
+    if msg:
         if "err" in action:
-            msg = msg + " STOP!"
             raise ValueError(msg)
         else:
             msg += (

tests/test_units/test_dataio.py

@@ -4,6 +4,8 @@
 import pathlib
 import sys
 
+from copy import deepcopy
+
 import pytest
 import yaml
 
@@ -77,6 +79,62 @@ def test_config_miss_required_fields(globalconfig1, regsurf):
         read_metadata(out)
 
 
+def test_config_stratigraphy_empty_entries_alias(globalconfig2, regsurf):
+    """Test that empty entries in 'alias' is detected and warned and removed."""
+    cfg = deepcopy(globalconfig2)
+    cfg["stratigraphy"]["TopVolantis"]["alias"] += [None]
+
+    with pytest.warns(PendingDeprecationWarning, match="'alias' items must be strings"):
+        exp = ExportData(config=cfg, content="depth", name="TopVolantis")
+        metadata = exp.generate_metadata(regsurf)
+
+    assert None not in metadata["data"]["alias"]
+
+
+def test_config_stratigraphy_empty_entries_stratigraphic_alias(globalconfig2, regsurf):
+    """Test that empty entries in 'stratigraphic_alias' detected and warned."""
+
+    # Note! stratigraphic_alias is not implemented, but we still check consistency
+
+    cfg = deepcopy(globalconfig2)
+    cfg["stratigraphy"]["TopVolantis"]["stratigraphic_alias"] += [None]
+
+    with pytest.warns(
+        PendingDeprecationWarning, match="'stratigraphic_alias' items must be strings"
+    ):
+        ExportData(config=cfg, content="depth")
+
+
+def test_config_stratigraphy_empty_name(globalconfig2):
+    """Test that empty 'name' is detected and warned."""
+    cfg = deepcopy(globalconfig2)
+    cfg["stratigraphy"]["TopVolantis"]["name"] = None
+
+    with pytest.warns(
+        PendingDeprecationWarning,
+        match="stratigraphy.TopVolantis: 'name' must be a string",
+    ):
+        ExportData(config=cfg, content="depth")
+
+
+def test_config_stratigraphy_stratigraphic_not_bool(globalconfig2):
+    """Test that non-boolean 'stratigraphic' is detected and warned."""
+    cfg = deepcopy(globalconfig2)
+    cfg["stratigraphy"]["TopVolantis"]["stratigraphic"] = None
+
+    with pytest.warns(
+        PendingDeprecationWarning, match="'stratigraphic' must be a bool"
+    ):
+        ExportData(config=cfg, content="depth")
+
+    cfg["stratigraphy"]["TopVolantis"]["stratigraphic"] = "a string"
+
+    with pytest.warns(
+        PendingDeprecationWarning, match="'stratigraphic' must be a bool"
+    ):
+        ExportData(config=cfg, content="depth")
+
+
 def test_update_check_settings_shall_fail(globalconfig1):
     # pylint: disable=unexpected-keyword-arg
     with pytest.raises(TypeError):