Merge pull request #314 from sneakers-the-rat/pretty-print

pretty print models

Author: cmungall

linkml_runtime/linkml_model/meta.py

@@ -148,7 +148,7 @@ class TypeMappingFramework(extended_str):
 
 Anything = Any
 
-@dataclass
+@dataclass(repr=False)
 class CommonMetadata(YAMLRoot):
     """
     Generic metadata shared across definitions
@@ -311,7 +311,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class Element(YAMLRoot):
     """
     A named element in the model
@@ -516,7 +516,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class SchemaDefinition(Element):
     """
     A collection of definitions that make up a schema or a data model.
@@ -628,7 +628,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class AnonymousTypeExpression(YAMLRoot):
     """
     A type expression that is not a top-level named type definition. Used for nesting.
@@ -696,7 +696,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class TypeDefinition(Element):
     """
     an element that whose instances are atomic scalar values that can be mapped to primitive types
@@ -791,7 +791,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class SubsetDefinition(Element):
     """
     an element that can be used to group other metamodel elements
@@ -814,7 +814,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class Definition(Element):
     """
     abstract base class for core metaclasses
@@ -863,7 +863,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class AnonymousEnumExpression(YAMLRoot):
     """
     An enum_expression that is not named
@@ -927,7 +927,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class EnumDefinition(Definition):
     """
     an element whose instances must be drawn from a specified set of permissible values
@@ -1001,7 +1001,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class EnumBinding(YAMLRoot):
     """
     A binding of a slot or a class to a permissible value from an enumeration.
@@ -1186,7 +1186,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class MatchQuery(YAMLRoot):
     """
     A query that is used on an enum expression to dynamically obtain a set of permissivle values via a query that
@@ -1212,7 +1212,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class ReachabilityQuery(YAMLRoot):
     """
     A query that is used on an enum expression to dynamically obtain a set of permissible values via walking from a
@@ -1256,7 +1256,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class StructuredAlias(YAMLRoot):
     """
     object that contains meta data about a synonym or alias including where it came from (source) and its scope
@@ -1453,7 +1453,7 @@ class Expression(YAMLRoot):
     class_model_uri: ClassVar[URIRef] = LINKML.Expression
 
 
-@dataclass
+@dataclass(repr=False)
 class TypeExpression(Expression):
     """
     An abstract class grouping named types and anonymous type expressions
@@ -1521,7 +1521,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class EnumExpression(Expression):
     """
     An expression that constrains the range of a slot
@@ -1585,7 +1585,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class AnonymousExpression(YAMLRoot):
     """
     An abstract parent class for any nested expression
@@ -1754,7 +1754,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class PathExpression(YAMLRoot):
     """
     An expression that describes an abstract path from an object to another through a sequence of slot lookups
@@ -1959,7 +1959,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class SlotExpression(Expression):
     """
     an expression that constrains the range of values a slot can take
@@ -2092,7 +2092,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class AnonymousSlotExpression(AnonymousExpression):
     _inherited_slots: ClassVar[List[str]] = ["range", "required", "recommended", "multivalued", "inlined", "inlined_as_list", "minimum_value", "maximum_value", "pattern", "structured_pattern", "value_presence", "equals_string", "equals_string_in", "equals_number", "equals_expression", "exact_cardinality", "minimum_cardinality", "maximum_cardinality"]
 
@@ -2222,7 +2222,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class SlotDefinition(Definition):
     """
     an element that describes how instances are related to other instances
@@ -2531,7 +2531,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class ClassExpression(YAMLRoot):
     """
     A boolean expression that can be used to dynamically determine membership of a class
@@ -2571,7 +2571,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class AnonymousClassExpression(AnonymousExpression):
     _inherited_slots: ClassVar[List[str]] = []
 
@@ -2612,7 +2612,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class ClassDefinition(Definition):
     """
     an element whose instances are complex objects that may have slot-value assignments
@@ -2747,7 +2747,7 @@ class ClassLevelRule(YAMLRoot):
     class_model_uri: ClassVar[URIRef] = LINKML.ClassLevelRule
 
 
-@dataclass
+@dataclass(repr=False)
 class ClassRule(ClassLevelRule):
     """
     A rule that applies to instances of a class
@@ -2940,7 +2940,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class ArrayExpression(YAMLRoot):
     """
     defines the dimensions of an array
@@ -3123,7 +3123,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class DimensionExpression(YAMLRoot):
     """
     defines one of the dimensions of an array
@@ -3308,7 +3308,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class PatternExpression(YAMLRoot):
     """
     a regular expression pattern used to evaluate conformance of a string
@@ -3489,7 +3489,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class ImportExpression(YAMLRoot):
     """
     an expression describing an import
@@ -3671,7 +3671,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class Setting(YAMLRoot):
     """
     assignment of a key to a value
@@ -3700,7 +3700,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class Prefix(YAMLRoot):
     """
     prefix URI tuple
@@ -3729,7 +3729,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class LocalName(YAMLRoot):
     """
     an attributed label
@@ -3758,7 +3758,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class Example(YAMLRoot):
     """
     usage example and description
@@ -3784,7 +3784,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class AltDescription(YAMLRoot):
     """
     an attributed description
@@ -3813,7 +3813,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class PermissibleValue(YAMLRoot):
     """
     a permissible value, accompanied by intended text and an optional mapping to a concept URI
@@ -4015,7 +4015,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class UniqueKey(YAMLRoot):
     """
     a collection of slots whose values uniquely identify an instance of a class

linkml_runtime/utils/enumerations.py

@@ -102,4 +102,4 @@ def __str__(self) -> str:
 
     def __repr__(self) -> str:
         rlist = [(f.name, getattr(self._code, f.name)) for f in fields(self._code)]
-        return '(' + ', '.join([f"{f[0]}={repr(f[1])}" for f in rlist if f[1]]) + ')'
+        return self.__class__.__name__ + '(' + ', '.join([f"{f[0]}={repr(f[1])}" for f in rlist if f[1]]) + ')'

linkml_runtime/utils/yamlutils.py

@@ -1,6 +1,9 @@
 from copy import copy
 from json import JSONDecoder
 from typing import Union, Any, List, Optional, Type, Callable, Dict
+from pprint import pformat
+import textwrap
+import re
 
 import yaml
 from deprecated.classic import deprecated
@@ -10,7 +13,7 @@
 from yaml.constructor import ConstructorError
 
 from linkml_runtime.utils.context_utils import CONTEXTS_PARAM_TYPE, merge_contexts
-from linkml_runtime.utils.formatutils import is_empty
+from linkml_runtime.utils.formatutils import is_empty, remove_empty_items, is_list, is_dict, items
 
 YAMLObjTypes = Union[JsonObjTypes, "YAMLRoot"]
 
@@ -277,6 +280,47 @@ def MissingRequiredField(self, field_name: str) -> None:
         """ Generic loader error handler """
         raise ValueError(f"{field_name} must be supplied")
 
+    def __repr__(self):
+        return _pformat(items(self), self.__class__.__name__)
+
+    def __str__(self):
+        return repr(self)
+
+def _pformat(fields:dict, cls_name:str, indent:str = '  ') -> str:
+    """
+    pretty format the fields of the items of a ``YAMLRoot`` object without the wonky indentation of pformat.
+    see ``YAMLRoot.__repr__``.
+
+    formatting is similar to black - items at similar levels of nesting have similar levels of indentation,
+    rather than getting placed at essentially random levels of indentation depending on what came before them.
+    """
+    res = []
+    total_len = 0
+    for key, val in fields:
+        if val == [] or val == {} or val is None:
+            continue
+        # pformat handles everything else that isn't a YAMLRoot object, but it sure does look ugly
+        # use it to split lines and as the thing of last resort, but otherwise indent = 0, we'll do that
+        val_str = pformat(val, indent=0, compact=True, sort_dicts=False)
+        # now we indent everything except the first line by indenting and then using regex to remove just the first indent
+        val_str = re.sub(rf'\A{re.escape(indent)}', '', textwrap.indent(val_str, indent))
+        # now recombine with the key in a format that can be re-eval'd into an object if indent is just whitespace
+        val_str = f"'{key}': " + val_str
+
+        # count the total length of this string so we know if we need to linebreak or not later
+        total_len += len(val_str)
+        res.append(val_str)
+
+    if total_len > 80:
+        inside = ',\n'.join(res)
+        # we indent twice - once for the inner contents of every inner object, and one to
+        # offset from the root element. that keeps us from needing to be recursive except for the
+        # single pformat call
+        inside = textwrap.indent(inside, indent)
+        return cls_name + '({\n' + inside + '\n})'
+    else:
+        return cls_name + '({' + ', '.join(res) + '})'
+
 
 def root_representer(dumper: yaml.Dumper, data: YAMLRoot):
     """ YAML callback -- used to filter out empty values (None, {}, [] and false)