Merge branch 'master' into pre-commit-ci-update-config

.github/workflows/ci_tests.yml

@@ -34,11 +34,14 @@ jobs:
       #  https://pyup.io/vulnerabilities/CVE-2021-41495/44715/
       #  https://pyup.io/vulnerabilities/CVE-2021-41496/44716/
       #  https://pyup.io/vulnerabilities/CVE-2021-34141/44717/
+      # 70612: Jinja2 vulnerability. Only used as subdependency for mkdocs++ in tripper.
+      #  https://data.safetycli.com/v/70612/97c/
       safety_options: |
         --ignore=48547
         --ignore=44715
         --ignore=44716
         --ignore=44717
+        --ignore=70612
 
       ## Build package
       run_build_package: true

tests/convert/test_convert.py

@@ -5,6 +5,7 @@
 import pytest
 
 
+# if True:
 def test_convertions():
     """Test convertions. Uses rdflib as triplestore backend"""
 
@@ -33,30 +34,77 @@ def test_convertions():
             "key5": True,
             "key6": False,
             "key7": ["a", 1, 2.2, True, None],
+            "key8": [{"a": 1, "b": 2}, {"a": 2.2, "b": 3.3}],
+            "key9": [["a11", "a12", "a13"], ["a21", "a22", "a23"]],
+        },
+    }
+
+    config3 = {
+        "Simulation": {
+            "command": "run_sim",
+            "files": [
+                {"target_file": "run_sim.sh", "source_iri": "http://..."},
+                {"target_file": "other.txt", "source_iri": "http://..."},
+            ],
+            "input": {
+                "onto:DataSet": [
+                    {
+                        "function": {
+                            "functionType": "application/vnd.dlite-generate",
+                            "configuration": {
+                                "driver": "myplugin",
+                                "location": "myfile.inp",
+                                "datamodel": "http:...",
+                            },
+                        },
+                    },
+                ],
+            },
         },
     }
 
     # Store dictionaries to triplestore
     save_container(ts, config1, EX.config1)
     save_container(ts, config2, EX.config2)
+    save_container(ts, config3, EX.config3)
 
     # Print content of triplestore
     # print(ts.serialize())
 
     # Load dictionaries from triplestore
     d1 = load_container(ts, EX.config1)
     d2 = load_container(ts, EX.config2)
+    d3 = load_container(ts, EX.config3)
 
     # Check that we got back what we stored
     assert d1 == config1
     assert d2 == config2
+    assert d3 == config3
 
     # Now, test serialising using recognised_keys
     save_container(ts, config1, EX.config1b, recognised_keys="basic")
     save_container(ts, config2, EX.config2b, recognised_keys="basic")
+    save_container(ts, config3, EX.config3b, recognised_keys="basic")
 
     d1b = load_container(ts, EX.config1b, recognised_keys="basic")
     d2b = load_container(ts, EX.config2b, recognised_keys="basic")
+    d3b = load_container(ts, EX.config3b, recognised_keys="basic")
 
     assert d1b == config1
     assert d2b == config2
+    assert d3b == config3
+
+    # Check custom recognised keys
+    from tripper.convert import BASIC_RECOGNISED_KEYS
+
+    reg_keys = BASIC_RECOGNISED_KEYS.copy()
+    reg_keys.update(
+        Simulation=EX.Simulation,
+        files=EX.files,
+        command=EX.command,
+        input=EX.input,
+        output=EX.output,
+    )
+    save_container(ts, config3, EX.config3c, recognised_keys=reg_keys)
+    d3c = load_container(ts, EX.config3c, recognised_keys=reg_keys)
+    assert d3c == config3

tripper/convert/__init__.py

@@ -1,6 +1,7 @@
 """Tripper sub-package for converting between RDF and other repetations."""
 
 from .convert import (
+    BASIC_RECOGNISED_KEYS,
     from_container,
     from_dict,
     load_container,
@@ -10,6 +11,7 @@
 )
 
 __all__ = [
+    "BASIC_RECOGNISED_KEYS",
     "from_container",
     "save_container",
     "load_container",

tripper/convert/convert.py

@@ -222,13 +222,19 @@ def load_container(
     Returns:
         A Python container object corresponding to `iri`.
     """
+    # pylint: disable=too-many-branches
     if iri == RDF.nil:
         return []
 
     if recognised_keys == "basic":
         recognised_keys = BASIC_RECOGNISED_KEYS
 
-    parents = set(o for s, p, o in ts.triples(subject=iri, predicate=RDF.type))
+    recognised_iris = (
+        {v: k for k, v in recognised_keys.items()}  # type: ignore
+        if recognised_keys
+        else {}
+    )
+    parents = set(ts.objects(iri, RDF.type))
 
     def get_obj(value):
         """Return Python object for `value`."""
@@ -243,14 +249,19 @@ def get_obj(value):
 
     if OTEIO.Dictionary in parents:
         container = {}
-        for _, _, pair in ts.triples(
-            subject=iri, predicate=OTEIO.hasKeyValuePair
-        ):
-            key_iri = ts.value(pair, OTEIO.hasDictionaryKey)
-            key = ts.value(key_iri, EMMO.hasStringValue)
-            value_iri = ts.value(pair, OTEIO.hasDictionaryValue)
-            value = ts.value(value_iri, EMMO.hasValue)
-            container[str(key)] = get_obj(value)
+        for pred, obj in ts.predicate_objects(iri):
+            if pred == OTEIO.hasKeyValuePair:
+                key_iri = ts.value(obj, OTEIO.hasDictionaryKey)
+                key = ts.value(key_iri, EMMO.hasStringValue)
+                value_iri = ts.value(obj, OTEIO.hasDictionaryValue)
+                value = ts.value(value_iri, EMMO.hasValue)
+                container[str(key)] = get_obj(value)
+            elif pred in recognised_iris:
+                container[recognised_iris[pred]] = get_obj(obj)
+            elif pred not in (RDF.type,):
+                raise ValueError(
+                    f"Unrecognised predicate '{pred}' in dict: {iri}"
+                )
 
         # Recognised IRIs
         if recognised_keys:

tripper/utils.py

@@ -74,12 +74,16 @@ def infer_iri(obj):
             properties = schema["properties"]
             if "uri" in properties and isinstance(properties["uri"], str):
                 iri = properties["uri"]
-            if "identity" in properties and isinstance(
+            elif "identity" in properties and isinstance(
                 properties["identity"], str
             ):
                 iri = properties["identity"]
-            if "uuid" in properties and properties["uuid"]:
+            elif "uuid" in properties and properties["uuid"]:
                 iri = str(properties["uuid"])
+            else:
+                raise TypeError(
+                    f"cannot infer IRI from pydantic object: {obj!r}"
+                )
     else:
         raise TypeError(f"cannot infer IRI from object: {obj!r}")
     return str(iri)