Merge pull request #205 from joshmoore/csv-test

csv testing and bug fixes

Author: amc-corey-cox

linkml_runtime/loaders/rdflib_loader.py

@@ -164,6 +164,8 @@ def from_rdf_graph(
                             v = namespaces.curie_for(o)
                             for enum_name in enum_names:
                                 e = schemaview.get_enum(enum_name)
+                                if e is None:
+                                    raise ValueError(f"no enum found for {slot.range}: {o} (ns={v})")
                                 for pv in e.permissible_values.values():
                                     if v == pv.meaning or str(o) == pv.meaning:
                                         v = pv.text
@@ -206,9 +208,16 @@ def from_rdf_graph(
         # Step 2: replace inline pointers with object dicts
         def repl(v):
             if isinstance(v, Pointer):
-                v2 = obj_map[v.obj]
+                v2 = obj_map.get(v.obj)
                 if v2 is None:
-                    raise Exception(f"No mapping for pointer {v}")
+                    msg = f"No mapping for pointer {v}. Triples:"
+                    for s, p, o in graph.triples((None, None, v.obj)):
+                        for s2, p2, o2 in graph.triples((None, None, s)):
+                            msg += f"\n{s2} {p2} {o2}."
+                        msg += f"\n{s} {p} {o}."
+                    for s, p, o in graph.triples((v.obj, None, None)):
+                        msg += f"\n{s} {p} {o}."
+                    raise Exception(msg)
                 return v2
             else:
                 return v
@@ -236,6 +245,8 @@ def repl(v):
     def _get_id_dict(self, node: VALID_SUBJECT, schemaview: SchemaView, cn: ClassDefinitionName) -> ANYDICT:
         id_slot = schemaview.get_identifier_slot(cn)
         if not isinstance(node, BNode):
+            if id_slot is None:
+                raise Exception(f"no slot found for {cn}: bnode={node}")
             id_val = self._uri_to_id(node, id_slot, schemaview)
             # id_val = schemaview.namespaces().curie_for(node)
             if id_val is None:

linkml_runtime/utils/yamlutils.py

@@ -45,7 +45,9 @@ def __post_init__(self, *args: list[str], **kwargs):
             for k in kwargs.keys():
                 v = repr(kwargs[k])[:40].replace("\n", "\\n")
                 messages.append(f"{TypedNode.yaml_loc(k)} Unknown argument: {k} = {v}")
-            raise ValueError("\n".join(messages))
+            msg = f"Unknown arguments for: {self}\n"
+            msg += "\n".join(messages)
+            raise ValueError(msg)
 
     def _default(self, obj, filtr: Callable[[dict], dict] = None):
         """JSON serializer callback.

pyproject.toml

@@ -56,6 +56,8 @@ dependencies = [
 dev = [
     "coverage >=6.2",
     "requests-cache >=1.2.0",
+    "tox>=4",
+    "ruff==0.11.13",
 ]
 
 [project.scripts]

tests/test_loaders_dumpers/input/table-inlined.tsv

@@ -0,0 +1,2 @@
+columnA	columnB	columnB	columnC
+table:row1	first value	second value	something else

tests/test_loaders_dumpers/input/table-json.tsv

@@ -0,0 +1,2 @@
+columnA	objectB	columnC
+table:row1	{\"name\": \"foo\", \"value\": \"bar\"}	something else

tests/test_loaders_dumpers/models/table.py

@@ -0,0 +1,172 @@
+# Auto generated from table.yaml by pythongen.py version: 0.9.0
+# Generation date: 2022-10-10T16:55:54
+# Schema: table
+#
+# id: https://w3id.org/linkml/examples/table
+# description: Represent a table in linkml
+# license: https://creativecommons.org/publicdomain/zero/1.0/
+
+import dataclasses
+import sys
+import re
+from jsonasobj2 import JsonObj, as_dict
+from typing import Optional, List, Union, Dict, ClassVar, Any
+from dataclasses import dataclass
+from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions
+
+from linkml_runtime.utils.slot import Slot
+from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode
+from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
+from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
+from linkml_runtime.utils.formatutils import camelcase, underscore, sfx
+from linkml_runtime.utils.enumerations import EnumDefinitionImpl
+from rdflib import Namespace, URIRef
+from linkml_runtime.utils.curienamespace import CurieNamespace
+from linkml_runtime.linkml_model.types import String, Uriorcurie
+from linkml_runtime.utils.metamodelcore import URIorCURIE
+
+metamodel_version = "1.7.0"
+version = None
+
+# Overwrite dataclasses _init_fn to add **kwargs in __init__
+dataclasses._init_fn = dataclasses_init_fn_with_kwargs
+
+# Namespaces
+LINKML = CurieNamespace("linkml", "https://w3id.org/linkml/")
+TABLE = CurieNamespace("table", "https://w3id.org/linkml/examples/table/")
+DEFAULT_ = TABLE
+
+
+# Types
+
+
+# Class references
+class RowColumnA(URIorCURIE):
+    pass
+
+
+@dataclass
+class Object(YAMLRoot):
+    """
+    An object (bnode) which needs embedding in a single row
+    """
+
+    _inherited_slots: ClassVar[List[str]] = []
+
+    class_class_uri: ClassVar[URIRef] = TABLE.Object
+    class_class_curie: ClassVar[str] = "table:Object"
+    class_name: ClassVar[str] = "Object"
+    class_model_uri: ClassVar[URIRef] = TABLE.Object
+
+    name: Optional[str] = None
+    value: Optional[str] = None
+
+    def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
+        if self.name is not None and not isinstance(self.name, str):
+            self.name = str(self.name)
+
+        if self.value is not None and not isinstance(self.value, str):
+            self.value = str(self.value)
+
+        super().__post_init__(**kwargs)
+
+
+@dataclass
+class Row(YAMLRoot):
+    """
+    A single data point made up of columns.
+    """
+
+    _inherited_slots: ClassVar[List[str]] = []
+
+    class_class_uri: ClassVar[URIRef] = TABLE.Row
+    class_class_curie: ClassVar[str] = "table:Row"
+    class_name: ClassVar[str] = "Row"
+    class_model_uri: ClassVar[URIRef] = TABLE.Row
+
+    columnA: Union[str, RowColumnA] = None
+    objectB: Optional[Union[dict, Object]] = None
+    columnC: Optional[str] = None
+
+    def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
+        if self._is_empty(self.columnA):
+            self.MissingRequiredField("columnA")
+        if not isinstance(self.columnA, RowColumnA):
+            self.columnA = RowColumnA(self.columnA)
+
+        if self.objectB is not None and not isinstance(self.objectB, Object):
+            self.objectB = Object(**as_dict(self.objectB))
+
+        if self.columnC is not None and not isinstance(self.columnC, str):
+            self.columnC = str(self.columnC)
+
+        super().__post_init__(**kwargs)
+
+
+@dataclass
+class Table(YAMLRoot):
+    """
+    Container of rows.
+    """
+
+    _inherited_slots: ClassVar[List[str]] = []
+
+    class_class_uri: ClassVar[URIRef] = TABLE.Table
+    class_class_curie: ClassVar[str] = "table:Table"
+    class_name: ClassVar[str] = "Table"
+    class_model_uri: ClassVar[URIRef] = TABLE.Table
+
+    rows: Optional[Union[Dict[Union[str, RowColumnA], Union[dict, Row]], List[Union[dict, Row]]]] = empty_dict()
+
+    def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
+        self._normalize_inlined_as_list(slot_name="rows", slot_type=Row, key_name="columnA", keyed=True)
+
+        super().__post_init__(**kwargs)
+
+
+# Enumerations
+
+
+# Slots
+class slots:
+    pass
+
+
+slots.rows = Slot(
+    uri=TABLE.rows,
+    name="rows",
+    curie=TABLE.curie("rows"),
+    model_uri=TABLE.rows,
+    domain=None,
+    range=Optional[Union[Dict[Union[str, RowColumnA], Union[dict, Row]], List[Union[dict, Row]]]],
+)
+
+slots.columnA = Slot(
+    uri=TABLE.columnA, name="columnA", curie=TABLE.curie("columnA"), model_uri=TABLE.columnA, domain=None, range=URIRef
+)
+
+slots.objectB = Slot(
+    uri=TABLE.objectB,
+    name="objectB",
+    curie=TABLE.curie("objectB"),
+    model_uri=TABLE.objectB,
+    domain=None,
+    range=Optional[Union[dict, Object]],
+)
+
+slots.columnC = Slot(
+    uri=TABLE.columnC,
+    name="columnC",
+    curie=TABLE.curie("columnC"),
+    model_uri=TABLE.columnC,
+    domain=None,
+    range=Optional[str],
+)
+
+slots.name = Slot(
+    uri=TABLE.name, name="name", curie=TABLE.curie("name"), model_uri=TABLE.name, domain=None, range=Optional[str]
+)
+
+slots.value = Slot(
+    uri=TABLE.value, name="value", curie=TABLE.curie("value"), model_uri=TABLE.value, domain=None, range=Optional[str]
+)

tests/test_loaders_dumpers/models/table.yaml

@@ -0,0 +1,56 @@
+id: https://w3id.org/linkml/examples/table
+name: table
+description: |-
+  Represent a table in linkml
+license: https://creativecommons.org/publicdomain/zero/1.0/
+imports:
+  - linkml:types
+prefixes:
+  table: https://w3id.org/linkml/examples/table/
+  linkml: https://w3id.org/linkml/
+default_prefix: table
+default_range: string
+
+classes:
+
+  Object:
+    description: |-
+      An object (bnode) which needs embedding in a single row
+    slots:
+      - name
+      - value
+
+  Row:
+    description: |-
+      A single data point made up of columns.
+    slots:
+      - columnA
+      - objectB
+      - columnC
+
+  Table:
+    description: |-
+      Container of rows.
+    tree_root: true
+    slots:
+      - rows
+
+slots:
+  rows:
+    range: Row
+    inlined: true
+    inlined_as_list: true
+    multivalued: true
+  columnA:
+    range: uriorcurie
+    identifier: true
+  objectB:
+    range: Object
+    inlined: true
+  columnC:
+    range: string
+    multivalued: false
+  name:
+    range: string
+  value:
+    range: string