LinkML-Map Compliance Suite

LinkML-Map Compliance Suite

This is the output from running the full compliance test suite.

It is organized into Feature Sets that test a particular feature or group of features, and combinations of different schemas, input objects, and transformation specifications. This is intended to exhaustively test all combinations of features, and provide informative output.

Each test is designed to demonstrate:

data mapping (transformation)
derived schemas
inversion (reverse transformation) (in some cases)
compilation to other frameworks (coming soon)

Feature Set: test_map_types

Test mapping between basic data types.

This test uses an ultra-minimal schema with a single class and a single attribute, the transformation specification maps that attribute onto itself, with a different type, demonstrating type coercion.

Some cases will be trivially isomorphic (where source_datatype == target_datatype), but these are executed anyway.

source_datatype: linkml datatype of source object
target_datatype: linkml datatype of target object
source_value: value of source object
target_value: expected value of slot in target object
invertible: True if the transformation is invertible

Combo: test_map_types[string-string-foo-foo-True]

Mapping string => string

Isomorphic mapping: input should equal output

Source Schema:

name: types
description: Minimal single-attribute schema for testing datatype mapping
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: string

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        range: string

Object Transformation:

Source Object:

s1: foo

Target Object:

s1: foo

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: string

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        range: string

Combo: test_map_types[integer-integer-5-5-True]

Mapping integer => integer

Isomorphic mapping: input should equal output

Source Schema:

name: types
description: Minimal single-attribute schema for testing datatype mapping
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: integer

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        range: integer

Object Transformation:

Source Object:

s1: 5

Target Object:

s1: 5

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: integer

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        range: integer

Combo: test_map_types[string-integer-5-5-True]

Mapping string => integer

Should coerce datatype

Source Schema:

name: types
description: Minimal single-attribute schema for testing datatype mapping
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: string

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        range: integer

Object Transformation:

Source Object:

s1: '5'

Target Object:

s1: 5

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: integer

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        range: string

Combo: test_map_types[integer-float-5-5.0-True] {#combo-test_map_typesinteger-float-5-50-true}

Mapping integer => float

Should coerce datatype

Source Schema:

name: types
description: Minimal single-attribute schema for testing datatype mapping
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: integer

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        range: float

Object Transformation:

Source Object:

s1: 5

Target Object:

s1: 5.0

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: float

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        range: integer

Combo: test_map_types[float-integer-5.0-5-True] {#combo-test_map_typesfloat-integer-50-5-true}

Mapping float => integer

Should coerce datatype

Source Schema:

name: types
description: Minimal single-attribute schema for testing datatype mapping
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: float

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        range: integer

Object Transformation:

Source Object:

s1: 5.0

Target Object:

s1: 5

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: integer

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        range: float

Combo: test_map_types[float-integer-5.2-5-False] {#combo-test_map_typesfloat-integer-52-5-false}

Mapping float => integer

Should coerce datatype

Source Schema:

name: types
description: Minimal single-attribute schema for testing datatype mapping
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: float

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        range: integer

Object Transformation:

Source Object:

s1: 5.2

Target Object:

s1: 5

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: integer

Combo: test_map_types[integer-boolean-5-True-False]

Mapping integer => boolean

Should coerce datatype

Source Schema:

name: types
description: Minimal single-attribute schema for testing datatype mapping
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: integer

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        range: boolean

Object Transformation:

Source Object:

s1: 5

Target Object:

s1: true

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: boolean

Combo: test_map_types[integer-boolean-0-False-False]

Mapping integer => boolean

Should coerce datatype

Source Schema:

name: types
description: Minimal single-attribute schema for testing datatype mapping
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: integer

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        range: boolean

Object Transformation:

Source Object:

s1: 0

Target Object:

s1: false

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: boolean

Feature Set: test_map_collections

Test mapping between collection data types (lists and dicts).

This makes use of the cast_collection_as construct

source_datatype:
target_datatype:
source_value:
target_value:
invertible:

Combo: test_map_collections[string-string-source_value0-target_value0-True]

Mapping string => string

Isomorphic mapping: input should equal output

Source Schema:

name: types
description: Mapping between collection types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      ds:
        name: ds
        multivalued: true
        range: D
        inlined: true
        inlined_as_list: true
    tree_root: true
  D:
    name: D
    attributes:
      id:
        name: id
        identifier: true
      s1:
        name: s1
        range: string

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      ds:
        name: ds
        populated_from: ds
        cast_collection_as: MultiValuedDict
        dictionary_key: id
  D:
    name: D
    slot_derivations:
      id:
        name: id
        populated_from: id
      s1:
        name: s1
        populated_from: s1
        range: string

Object Transformation:

Source Object:

ds:
- id: X
  s1: foo
- id: Y
  s1: bar

Target Object:

ds:
  X:
    s1: foo
  Y:
    s1: bar

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      ds:
        name: ds
        multivalued: true
        domain_of:
        - C
        range: D
        inlined: true
        inlined_as_list: false
    tree_root: true
  D:
    name: D
    attributes:
      id:
        name: id
        identifier: true
        domain_of:
        - D
        required: true
      s1:
        name: s1
        domain_of:
        - D
        range: string

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      ds:
        name: ds
        populated_from: ds
        cast_collection_as: MultiValuedList
  D:
    name: D
    populated_from: D
    slot_derivations:
      id:
        name: id
        populated_from: id
      s1:
        name: s1
        populated_from: s1
        range: string

Combo: test_map_collections[string-string-source_value1-target_value1-True]

Mapping string => string

Isomorphic mapping: input should equal output

Source Schema:

name: types
description: Mapping between collection types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      ds:
        name: ds
        multivalued: true
        range: D
        inlined: true
        inlined_as_list: false
    tree_root: true
  D:
    name: D
    attributes:
      id:
        name: id
        identifier: true
      s1:
        name: s1
        range: string

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      ds:
        name: ds
        populated_from: ds
        cast_collection_as: MultiValuedList
  D:
    name: D
    slot_derivations:
      id:
        name: id
        populated_from: id
      s1:
        name: s1
        populated_from: s1
        range: string

Object Transformation:

Source Object:

ds:
  X:
    s1: foo
  Y:
    s1: bar

Target Object:

ds:
- id: X
  s1: foo
- id: Y
  s1: bar

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      ds:
        name: ds
        multivalued: true
        domain_of:
        - C
        range: D
        inlined: true
        inlined_as_list: true
    tree_root: true
  D:
    name: D
    attributes:
      id:
        name: id
        identifier: true
        domain_of:
        - D
        required: true
      s1:
        name: s1
        domain_of:
        - D
        range: string

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      ds:
        name: ds
        populated_from: ds
        cast_collection_as: MultiValuedDict
        dictionary_key: id
  D:
    name: D
    populated_from: D
    slot_derivations:
      id:
        name: id
        populated_from: id
      s1:
        name: s1
        populated_from: s1
        range: string

Feature Set: test_expr

Test transformation using pythonic expressions.

This test uses a simple source schema with two slots (s1 and s2). These are combined using a pythonic expression, to populate the only slot in the target schema (called derived).

The values of s1 and s2 can be numbers or strings.

If the expression wraps a slot in {...} then the presence of a None forces the entire expression to be None

Limitations: At this time, the framework cannot generate a complete derived schema or inversion for expressions. This will be fixed in future.

expr: pythonic expression
source_object: source object
target_value: expected value of slot in target object

Combo: test_expr[s1 + s2-source_object0-11] {#combo-test_exprs1--s2-source_object0-11}

Source Schema:

name: expr
id: expr
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: integer
      s2:
        name: s2
        range: integer
    tree_root: true

Transformer Specification:

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      derived:
        name: derived
        expr: s1 + s2

Object Transformation:

Source Object:

s1: 5
s2: 6

Target Object:

derived: 11

Target Schema (Derived):

name: expr-derived
id: expr-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: expr-derived/
classes:
  C:
    name: C
    attributes:
      derived:
        name: derived
    tree_root: true

Combo: test_expr[{s1} + {s2}-source_object1-11] {#combo-test_exprs1--s2-source_object1-11}

Source Schema:

name: expr
id: expr
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: integer
      s2:
        name: s2
        range: integer
    tree_root: true

Transformer Specification:

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      derived:
        name: derived
        expr: '{s1} + {s2}'

Object Transformation:

Source Object:

s1: 5
s2: 6

Target Object:

derived: 11

Target Schema (Derived):

name: expr-derived
id: expr-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: expr-derived/
classes:
  C:
    name: C
    attributes:
      derived:
        name: derived
    tree_root: true

Combo: test_expr[{s1} + {s2}-source_object2-None] {#combo-test_exprs1--s2-source_object2-none}

Source Schema:

name: expr
id: expr
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: integer
    tree_root: true

Transformer Specification:

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      derived:
        name: derived
        expr: '{s1} + {s2}'

Object Transformation:

Source Object:

s1: 5

Target Object:

{}

Target Schema (Derived):

name: expr-derived
id: expr-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: expr-derived/
classes:
  C:
    name: C
    attributes:
      derived:
        name: derived
    tree_root: true

Combo: test_expr[s1 + s2.s3-source_object3-11] {#combo-test_exprs1--s2s3-source_object3-11}

Source Schema:

name: expr
id: expr
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: integer
      s2:
        name: s2
        range: D
    tree_root: true
  D:
    name: D
    attributes:
      s3:
        name: s3
        range: integer

Transformer Specification:

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      derived:
        name: derived
        expr: s1 + s2.s3

Object Transformation:

Source Object:

s1: 5
s2:
  s3: 6

Target Object:

derived: 11

Target Schema (Derived):

name: expr-derived
id: expr-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: expr-derived/
classes:
  C:
    name: C
    attributes:
      derived:
        name: derived
    tree_root: true

Combo: test_expr[s1 + s2.s3.s4-source_object4-11] {#combo-test_exprs1--s2s3s4-source_object4-11}

Source Schema:

name: expr
id: expr
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: integer
      s2:
        name: s2
        range: D
    tree_root: true
  D:
    name: D
    attributes:
      s4:
        name: s4
        range: integer
      s3:
        name: s3
        range: D

Transformer Specification:

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      derived:
        name: derived
        expr: s1 + s2.s3.s4

Object Transformation:

Source Object:

s1: 5
s2:
  s3:
    s4: 6

Target Object:

derived: 11

Target Schema (Derived):

name: expr-derived
id: expr-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: expr-derived/
classes:
  C:
    name: C
    attributes:
      derived:
        name: derived
    tree_root: true

Combo: test_expr[s1 + s2-source_object5-ab] {#combo-test_exprs1--s2-source_object5-ab}

Source Schema:

name: expr
id: expr
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: string
      s2:
        name: s2
        range: string
    tree_root: true

Transformer Specification:

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      derived:
        name: derived
        expr: s1 + s2

Object Transformation:

Source Object:

s1: a
s2: b

Target Object:

derived: ab

Target Schema (Derived):

name: expr-derived
id: expr-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: expr-derived/
classes:
  C:
    name: C
    attributes:
      derived:
        name: derived
    tree_root: true

Combo: test_expr[s1 + s2-source_object6-target_value6] {#combo-test_exprs1--s2-source_object6-target_value6}

Source Schema:

name: expr
id: expr
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        multivalued: true
        range: string
      s2:
        name: s2
        multivalued: true
        range: string
    tree_root: true

Transformer Specification:

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      derived:
        name: derived
        expr: s1 + s2

Object Transformation:

Source Object:

s1:
- a
s2:
- b

Target Object:

derived:
- a
- b

Target Schema (Derived):

name: expr-derived
id: expr-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: expr-derived/
classes:
  C:
    name: C
    attributes:
      derived:
        name: derived
    tree_root: true

Combo: test_expr[len(s1)-source_object7-1]

Source Schema:

name: expr
id: expr
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        multivalued: true
        range: string
    tree_root: true

Transformer Specification:

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      derived:
        name: derived
        expr: len(s1)

Object Transformation:

Source Object:

s1:
- a

Target Object:

derived: 1

Target Schema (Derived):

name: expr-derived
id: expr-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: expr-derived/
classes:
  C:
    name: C
    attributes:
      derived:
        name: derived
    tree_root: true

Combo: test_expr[s1 \< s2-source_object8-True] {#combo-test_exprs1--s2-source_object8-true}

Source Schema:

name: expr
id: expr
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: integer
      s2:
        name: s2
        range: integer
    tree_root: true

Transformer Specification:

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      derived:
        name: derived
        expr: s1 < s2

Object Transformation:

Source Object:

s1: 5
s2: 6

Target Object:

derived: true

Target Schema (Derived):

name: expr-derived
id: expr-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: expr-derived/
classes:
  C:
    name: C
    attributes:
      derived:
        name: derived
    tree_root: true

Feature Set: test_simple_unit_conversion

Test unit conversion.

This test uses a simple source schema with a single class and a single attribute, where the attribute is described using the units metaslot.

The recommended way to describe unit slots in LinkML is with UCUM, but a number of other schemes can be used. We explicitly test for some known cases where UCUM uses non-standard units (e.g. Cel, mo), as well as UCUM-specific syntax (e.g. m.s-1) and extensions (e.g. using annotations like {Cre}).

Developers note: to run this test, the units extension should be installed:

poetry install -E units

This installs the pint framework.

source_slot: name of slot in source schema
target_slot: name of slot in target schema
source_unit: unit of source slot
target_unit: unit of target slot
source_value: magnitude of source slot (to be converted)
target_value: expected magnitude of target slot (output of conversion)
err:

Combo: test_simple_unit_conversion[s1-s1-m-cm-ucum_code-1.0-100.0-None-None] {#combo-test_simple_unit_conversions1-s1-m-cm-ucum_code-10-1000-none-none}

Unit Conversion: 1.0 m => 100.0 cm [with s1]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: float
        unit:
          ucum_code: m

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: cm

Object Transformation:

Source Object:

s1: 1.0

Target Object:

s1: 100.0

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: float
        unit:
          ucum_code: cm

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: m
          target_unit_scheme: ucum_code
          source_unit: cm

Combo: test_simple_unit_conversion[s1-s1-m-cm-symbol-1.0-100.0-None-None] {#combo-test_simple_unit_conversions1-s1-m-cm-symbol-10-1000-none-none}

Unit Conversion: 1.0 m => 100.0 cm [with s1]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: float
        unit:
          symbol: m

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: cm

Object Transformation:

Source Object:

s1: 1.0

Target Object:

s1: 100.0

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: float
        unit:
          ucum_code: cm

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: m
          target_unit_scheme: symbol
          source_unit: cm

Combo: test_simple_unit_conversion[s1-s1-m-m-ucum_code-1.0-1.0-None-None] {#combo-test_simple_unit_conversions1-s1-m-m-ucum_code-10-10-none-none}

Unit Conversion: 1.0 m => 1.0 m [with s1]

Isomorphic mapping: input should equal output Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: float
        unit:
          ucum_code: m

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: m

Object Transformation:

Source Object:

s1: 1.0

Target Object:

s1: 1.0

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: float
        unit:
          ucum_code: m

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: m
          target_unit_scheme: ucum_code
          source_unit: m

Combo: test_simple_unit_conversion[s1-s1-a-mo-ucum_code-10.0-120.0-None-None] {#combo-test_simple_unit_conversions1-s1-a-mo-ucum_code-100-1200-none-none}

Unit Conversion: 10.0 a => 120.0 mo [with s1]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: float
        unit:
          ucum_code: a

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: mo

Object Transformation:

Source Object:

s1: 10.0

Target Object:

s1: 120.0

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: float
        unit:
          ucum_code: mo

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: a
          target_unit_scheme: ucum_code
          source_unit: mo

Combo: test_simple_unit_conversion[s1-s1-a-mo-symbol-10.0-None-UndefinedUnitError-None] {#combo-test_simple_unit_conversions1-s1-a-mo-symbol-100-none-undefineduniterror-none}

Unit Conversion: 10.0 a => None mo [with s1]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: float
        unit:
          symbol: a

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: mo

Object Transformation:

Expected Error: UndefinedUnitError

Source Object:

s1: 10.0

Target Object:

null
...

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: float
        unit:
          ucum_code: mo

Combo: test_simple_unit_conversion[s1-s1-m-ml-ucum_code-1.0-None-DimensionalityError-None] {#combo-test_simple_unit_conversions1-s1-m-ml-ucum_code-10-none-dimensionalityerror-none}

Unit Conversion: 1.0 m => None ml [with s1]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: float
        unit:
          ucum_code: m

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: ml

Object Transformation:

Expected Error: DimensionalityError

Source Object:

s1: 1.0

Target Object:

null
...

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: float
        unit:
          ucum_code: ml

Combo: test_simple_unit_conversion[s1-s1-m-pinknoodles-ucum_code-1.0-None-UndefinedUnitError-None] {#combo-test_simple_unit_conversions1-s1-m-pinknoodles-ucum_code-10-none-undefineduniterror-none}

Unit Conversion: 1.0 m => None pinknoodles [with s1]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: float
        unit:
          ucum_code: m

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: pinknoodles

Object Transformation:

Expected Error: UndefinedUnitError

Source Object:

s1: 1.0

Target Object:

null
...

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: float
        unit:
          ucum_code: pinknoodles

Combo: test_simple_unit_conversion[s1-s1-ml-m-ucum_code-1.0-None-DimensionalityError-None] {#combo-test_simple_unit_conversions1-s1-ml-m-ucum_code-10-none-dimensionalityerror-none}

Unit Conversion: 1.0 ml => None m [with s1]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: float
        unit:
          ucum_code: ml

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: m

Object Transformation:

Expected Error: DimensionalityError

Source Object:

s1: 1.0

Target Object:

null
...

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: float
        unit:
          ucum_code: m

Combo: test_simple_unit_conversion[s1-s1-pinknoodles-m-ucum_code-1.0-None-UndefinedUnitError-None] {#combo-test_simple_unit_conversions1-s1-pinknoodles-m-ucum_code-10-none-undefineduniterror-none}

Unit Conversion: 1.0 pinknoodles => None m [with s1]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: float
        unit:
          ucum_code: pinknoodles

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: m

Object Transformation:

Expected Error: UndefinedUnitError

Source Object:

s1: 1.0

Target Object:

null
...

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: float
        unit:
          ucum_code: m

Combo: test_simple_unit_conversion[s1-s1-m/s-cm/s-ucum_code-1.0-100.0-None-None] {#combo-test_simple_unit_conversions1-s1-ms-cms-ucum_code-10-1000-none-none}

Unit Conversion: 1.0 m/s => 100.0 cm/s [with s1]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: float
        unit:
          ucum_code: m/s

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: cm/s

Object Transformation:

Source Object:

s1: 1.0

Target Object:

s1: 100.0

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: float
        unit:
          ucum_code: cm/s

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: m/s
          target_unit_scheme: ucum_code
          source_unit: cm/s

Combo: test_simple_unit_conversion[s1-s1-m.s-1-cm.s-1-ucum_code-1.0-100.0-None-None] {#combo-test_simple_unit_conversions1-s1-ms-1-cms-1-ucum_code-10-1000-none-none}

Unit Conversion: 1.0 m.s-1 => 100.0 cm.s-1 [with s1]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: float
        unit:
          ucum_code: m.s-1

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: cm.s-1

Object Transformation:

Source Object:

s1: 1.0

Target Object:

s1: 100.0

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: float
        unit:
          ucum_code: cm.s-1

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: m.s-1
          target_unit_scheme: ucum_code
          source_unit: cm.s-1

Combo: test_simple_unit_conversion[s1-s1-g.m2-1-kg.m2-1-ucum_code-1.0-0.001-None-https://github.com/dalito/ucumvert/issues/8] {#combo-test_simple_unit_conversions1-s1-gm2-1-kgm2-1-ucum_code-10-0001-none-httpsgithubcomdalitoucumvertissues8}

s### Combo: test_simple_unit_conversion[height_in_m-height_in_cm-m-cm-ucum_code-1.0-100.0-None-None]

Unit Conversion: 1.0 m => 100.0 cm [with height_in_m]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      height_in_m:
        name: height_in_m
        range: float
        unit:
          ucum_code: m

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      height_in_cm:
        name: height_in_cm
        populated_from: height_in_m
        unit_conversion:
          target_unit: cm

Object Transformation:

Source Object:

height_in_m: 1.0

Target Object:

height_in_cm: 100.0

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      height_in_cm:
        name: height_in_cm
        domain_of:
        - C
        range: float
        unit:
          ucum_code: cm

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      height_in_m:
        name: height_in_m
        populated_from: height_in_cm
        unit_conversion:
          target_unit: m
          target_unit_scheme: ucum_code
          source_unit: cm

Combo: test_simple_unit_conversion[s1-s1-m[H2O]{35Cel}-m[H2O]{35Cel}-ucum_code-1.0-1.0-None-None] {#combo-test_simple_unit_conversions1-s1-mh2o35cel-mh2o35cel-ucum_code-10-10-none-none}

Unit Conversion: 1.0 m[H2O]{35Cel} => 1.0 m[H2O]{35Cel} [with s1]

Isomorphic mapping: input should equal output Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: float
        unit:
          ucum_code: m[H2O]{35Cel}

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: m[H2O]{35Cel}

Object Transformation:

Source Object:

s1: 1.0

Target Object:

s1: 1.0

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: float
        unit:
          ucum_code: m[H2O]{35Cel}

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
        unit_conversion:
          target_unit: m[H2O]{35Cel}
          target_unit_scheme: ucum_code
          source_unit: m[H2O]{35Cel}

Feature Set: test_complex_unit_conversion

Test unit conversion, from complex object to simple scalar.

source_unit:
target_unit:
source_value:
target_value:
roundtrip_object:
err:

Combo: test_complex_unit_conversion[m-cm-1.0-100.0-roundtrip_object0-None] {#combo-test_complex_unit_conversionm-cm-10-1000-roundtrip_object0-none}

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  Q:
    name: Q
    attributes:
      magnitude:
        name: magnitude
        range: float
      unit:
        name: unit
        range: string
  C:
    name: C
    attributes:
      q:
        name: q
        range: Q
    tree_root: true

Transformer Specification:

class_derivations:
  D:
    name: D
    populated_from: C
    slot_derivations:
      q_in_cm:
        name: q_in_cm
        populated_from: q
        unit_conversion:
          target_unit: cm
          source_unit_slot: unit
          source_magnitude_slot: magnitude

Object Transformation:

Source Object:

q:
  magnitude: 1.0
  unit: m

Target Object:

q_in_cm: 100.0

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  D:
    name: D
    attributes:
      q_in_cm:
        name: q_in_cm
        domain_of:
        - C
        range: Q
        unit:
          ucum_code: cm
    tree_root: true

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: D
    slot_derivations:
      q:
        name: q
        populated_from: q_in_cm
        unit_conversion:
          source_unit: cm
          target_unit_slot: unit
          target_magnitude_slot: magnitude

Combo: test_complex_unit_conversion[cm-cm-100.0-100.0-roundtrip_object1-None] {#combo-test_complex_unit_conversioncm-cm-1000-1000-roundtrip_object1-none}

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  Q:
    name: Q
    attributes:
      magnitude:
        name: magnitude
        range: float
      unit:
        name: unit
        range: string
  C:
    name: C
    attributes:
      q:
        name: q
        range: Q
    tree_root: true

Transformer Specification:

class_derivations:
  D:
    name: D
    populated_from: C
    slot_derivations:
      q_in_cm:
        name: q_in_cm
        populated_from: q
        unit_conversion:
          target_unit: cm
          source_unit_slot: unit
          source_magnitude_slot: magnitude

Object Transformation:

Source Object:

q:
  magnitude: 100.0
  unit: cm

Target Object:

q_in_cm: 100.0

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  D:
    name: D
    attributes:
      q_in_cm:
        name: q_in_cm
        domain_of:
        - C
        range: Q
        unit:
          ucum_code: cm
    tree_root: true

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: D
    slot_derivations:
      q:
        name: q
        populated_from: q_in_cm
        unit_conversion:
          source_unit: cm
          target_unit_slot: unit
          target_magnitude_slot: magnitude

Combo: test_complex_unit_conversion[cm-ml-100.0-None-None-DimensionalityError] {#combo-test_complex_unit_conversioncm-ml-1000-none-none-dimensionalityerror}

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  Q:
    name: Q
    attributes:
      magnitude:
        name: magnitude
        range: float
      unit:
        name: unit
        range: string
  C:
    name: C
    attributes:
      q:
        name: q
        range: Q
    tree_root: true

Transformer Specification:

class_derivations:
  D:
    name: D
    populated_from: C
    slot_derivations:
      q_in_ml:
        name: q_in_ml
        populated_from: q
        unit_conversion:
          target_unit: ml
          source_unit_slot: unit
          source_magnitude_slot: magnitude

Object Transformation:

Expected Error: DimensionalityError

Source Object:

q:
  magnitude: 100.0
  unit: cm

Target Object:

null
...

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  D:
    name: D
    attributes:
      q_in_ml:
        name: q_in_ml
        domain_of:
        - C
        range: Q
        unit:
          ucum_code: ml
    tree_root: true

Combo: test_complex_unit_conversion[cm-pinknoodles-100.0-None-None-UndefinedUnitError] {#combo-test_complex_unit_conversioncm-pinknoodles-1000-none-none-undefineduniterror}

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  Q:
    name: Q
    attributes:
      magnitude:
        name: magnitude
        range: float
      unit:
        name: unit
        range: string
  C:
    name: C
    attributes:
      q:
        name: q
        range: Q
    tree_root: true

Transformer Specification:

class_derivations:
  D:
    name: D
    populated_from: C
    slot_derivations:
      q_in_pinknoodles:
        name: q_in_pinknoodles
        populated_from: q
        unit_conversion:
          target_unit: pinknoodles
          source_unit_slot: unit
          source_magnitude_slot: magnitude

Object Transformation:

Expected Error: UndefinedUnitError

Source Object:

q:
  magnitude: 100.0
  unit: cm

Target Object:

null
...

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  D:
    name: D
    attributes:
      q_in_pinknoodles:
        name: q_in_pinknoodles
        domain_of:
        - C
        range: Q
        unit:
          ucum_code: pinknoodles
    tree_root: true

Feature Set: test_stringify

Test compaction of multivalued slots into a string.

Stringification is primarily intended for mapping from complex nested formats to simple tabular TSV formats, where some of the following methodologies can be used:

flattening lists using an (internal) delimiter
flattening lists or more complex objects using JSON or YAML

syntax: SerializationSyntaxType
delimiter: delimiter to use in stringification
source_value: source value (a list)
target_value: expected value of slot in target object (a string)

Combo: test_stringify[None-,-source_value0-a,b]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        multivalued: true
        range: string

Transformer Specification:

class_derivations:
  D:
    name: D
    populated_from: C
    slot_derivations:
      s1_verbatim:
        name: s1_verbatim
        populated_from: s1
        stringification:
          delimiter: ','

Object Transformation:

Source Object:

s1:
- a
- b

Target Object:

s1_verbatim: a,b

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  D:
    name: D
    attributes:
      s1_verbatim:
        name: s1_verbatim
        multivalued: false
        domain_of:
        - C
        range: string

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: D
    slot_derivations:
      s1:
        name: s1
        populated_from: s1_verbatim
        stringification:
          delimiter: ','
          reversed: true

Compiled Specification (SQLCompiler):

INSERT INTO D SELECT s1_verbatim AS STRING_AGG(s1, \',\') FROM D;

Combo: test_stringify[None-|-source_value1-a|b]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        multivalued: true
        range: string

Transformer Specification:

class_derivations:
  D:
    name: D
    populated_from: C
    slot_derivations:
      s1_verbatim:
        name: s1_verbatim
        populated_from: s1
        stringification:
          delimiter: '|'

Object Transformation:

Source Object:

s1:
- a
- b

Target Object:

s1_verbatim: a|b

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  D:
    name: D
    attributes:
      s1_verbatim:
        name: s1_verbatim
        multivalued: false
        domain_of:
        - C
        range: string

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: D
    slot_derivations:
      s1:
        name: s1
        populated_from: s1_verbatim
        stringification:
          delimiter: '|'
          reversed: true

Compiled Specification (SQLCompiler):

INSERT INTO D SELECT s1_verbatim AS STRING_AGG(s1, \'|\') FROM D;

Combo: test_stringify[None-|-source_value2-a]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        multivalued: true
        range: string

Transformer Specification:

class_derivations:
  D:
    name: D
    populated_from: C
    slot_derivations:
      s1_verbatim:
        name: s1_verbatim
        populated_from: s1
        stringification:
          delimiter: '|'

Object Transformation:

Source Object:

s1:
- a

Target Object:

s1_verbatim: a

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  D:
    name: D
    attributes:
      s1_verbatim:
        name: s1_verbatim
        multivalued: false
        domain_of:
        - C
        range: string

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: D
    slot_derivations:
      s1:
        name: s1
        populated_from: s1_verbatim
        stringification:
          delimiter: '|'
          reversed: true

Compiled Specification (SQLCompiler):

INSERT INTO D SELECT s1_verbatim AS STRING_AGG(s1, \'|\') FROM D;

Combo: test_stringify[None-|-source_value3-]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        multivalued: true
        range: string

Transformer Specification:

class_derivations:
  D:
    name: D
    populated_from: C
    slot_derivations:
      s1_verbatim:
        name: s1_verbatim
        populated_from: s1
        stringification:
          delimiter: '|'

Object Transformation:

Source Object:

{}

Target Object:

s1_verbatim: ''

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  D:
    name: D
    attributes:
      s1_verbatim:
        name: s1_verbatim
        multivalued: false
        domain_of:
        - C
        range: string

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: D
    slot_derivations:
      s1:
        name: s1
        populated_from: s1_verbatim
        stringification:
          delimiter: '|'
          reversed: true

Compiled Specification (SQLCompiler):

INSERT INTO D SELECT s1_verbatim AS STRING_AGG(s1, \'|\') FROM D;

Combo: test_stringify[JSON-None-source_value4-[\"a\", \"b\"]]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        multivalued: true
        range: string

Transformer Specification:

class_derivations:
  D:
    name: D
    populated_from: C
    slot_derivations:
      s1_verbatim:
        name: s1_verbatim
        populated_from: s1
        stringification:
          syntax: JSON

Object Transformation:

Source Object:

s1:
- a
- b

Target Object:

s1_verbatim: '["a", "b"]'

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  D:
    name: D
    attributes:
      s1_verbatim:
        name: s1_verbatim
        multivalued: false
        domain_of:
        - C
        range: string

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: D
    slot_derivations:
      s1:
        name: s1
        populated_from: s1_verbatim
        stringification:
          reversed: true
          syntax: JSON

Compiled Specification (SQLCompiler):

INSERT INTO D SELECT s1_verbatim AS CAST(s1 AS TEXT) FROM D;

Combo: test_stringify[JSON-None-source_value5-[]]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        multivalued: true
        range: string

Transformer Specification:

class_derivations:
  D:
    name: D
    populated_from: C
    slot_derivations:
      s1_verbatim:
        name: s1_verbatim
        populated_from: s1
        stringification:
          syntax: JSON

Object Transformation:

Source Object:

{}

Target Object:

s1_verbatim: '[]'

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  D:
    name: D
    attributes:
      s1_verbatim:
        name: s1_verbatim
        multivalued: false
        domain_of:
        - C
        range: string

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: D
    slot_derivations:
      s1:
        name: s1
        populated_from: s1_verbatim
        stringification:
          reversed: true
          syntax: JSON

Compiled Specification (SQLCompiler):

INSERT INTO D SELECT s1_verbatim AS CAST(s1 AS TEXT) FROM D;

Combo: test_stringify[YAML-None-source_value6-[a, b]]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        multivalued: true
        range: string

Transformer Specification:

class_derivations:
  D:
    name: D
    populated_from: C
    slot_derivations:
      s1_verbatim:
        name: s1_verbatim
        populated_from: s1
        stringification:
          syntax: YAML

Object Transformation:

Source Object:

s1:
- a
- b

Target Object:

s1_verbatim: '[a, b]'

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  D:
    name: D
    attributes:
      s1_verbatim:
        name: s1_verbatim
        multivalued: false
        domain_of:
        - C
        range: string

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: D
    slot_derivations:
      s1:
        name: s1
        populated_from: s1_verbatim
        stringification:
          reversed: true
          syntax: YAML

Compiled Specification (SQLCompiler):

INSERT INTO D SELECT s1_verbatim AS s1 FROM D;

Feature Set: test_isomorphic

Test mapping a schema to an identical schema (i.e copy).

This also tests for the ability to recursively descend a nested structure.

source_object:
use_expr:
supply_source_schema: TODO: always True for now

Combo: test_isomorphic[True-True-source_object0]

Source Schema:

name: isomorphic
id: isomorphic
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  Container:
    name: Container
    attributes:
      c_list:
        name: c_list
        multivalued: true
        range: C
      d:
        name: d
        range: D
    tree_root: true
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: string
      s2:
        name: s2
        range: string
  D:
    name: D
    attributes:
      s3:
        name: s3
        range: string

Transformer Specification:

class_derivations:
  Container:
    name: Container
    populated_from: Container
    slot_derivations:
      c_list:
        name: c_list
        populated_from: c_list
        range: C
      d:
        name: d
        populated_from: d
        range: D
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
      s2:
        name: s2
        populated_from: s2
  D:
    name: D
    populated_from: D
    slot_derivations:
      s3:
        name: s3
        expr: s3

Object Transformation:

Source Object:

c_list:
- s1: a
  s2: b
- s1: c
  s2: d
d:
  s3: e

Target Object:

c_list:
- s1: a
  s2: b
- s1: c
  s2: d
d:
  s3: e

Target Schema (Derived):

name: isomorphic-derived
id: isomorphic-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: isomorphic-derived/
classes:
  Container:
    name: Container
    attributes:
      c_list:
        name: c_list
        multivalued: true
        domain_of:
        - Container
        range: C
      d:
        name: d
        domain_of:
        - Container
        range: D
    tree_root: true
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: string
      s2:
        name: s2
        domain_of:
        - C
        range: string
  D:
    name: D
    attributes:
      s3:
        name: s3
        domain_of:
        - D
        range: string

Inverted Transformation Specification (Derived):

class_derivations:
  Container:
    name: Container
    populated_from: Container
    slot_derivations:
      c_list:
        name: c_list
        populated_from: c_list
        range: C
      d:
        name: d
        populated_from: d
        range: D
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
      s2:
        name: s2
        populated_from: s2
  D:
    name: D
    populated_from: D
    slot_derivations:
      s3:
        name: s3
        populated_from: s3

Combo: test_isomorphic[True-False-source_object0]

Source Schema:

name: isomorphic
id: isomorphic
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  Container:
    name: Container
    attributes:
      c_list:
        name: c_list
        multivalued: true
        range: C
      d:
        name: d
        range: D
    tree_root: true
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: string
      s2:
        name: s2
        range: string
  D:
    name: D
    attributes:
      s3:
        name: s3
        range: string

Transformer Specification:

class_derivations:
  Container:
    name: Container
    populated_from: Container
    slot_derivations:
      c_list:
        name: c_list
        populated_from: c_list
        range: C
      d:
        name: d
        populated_from: d
        range: D
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
      s2:
        name: s2
        populated_from: s2
  D:
    name: D
    populated_from: D
    slot_derivations:
      s3:
        name: s3
        populated_from: s3

Object Transformation:

Source Object:

c_list:
- s1: a
  s2: b
- s1: c
  s2: d
d:
  s3: e

Target Object:

c_list:
- s1: a
  s2: b
- s1: c
  s2: d
d:
  s3: e

Target Schema (Derived):

name: isomorphic-derived
id: isomorphic-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: isomorphic-derived/
classes:
  Container:
    name: Container
    attributes:
      c_list:
        name: c_list
        multivalued: true
        domain_of:
        - Container
        range: C
      d:
        name: d
        domain_of:
        - Container
        range: D
    tree_root: true
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: string
      s2:
        name: s2
        domain_of:
        - C
        range: string
  D:
    name: D
    attributes:
      s3:
        name: s3
        domain_of:
        - D
        range: string

Inverted Transformation Specification (Derived):

class_derivations:
  Container:
    name: Container
    populated_from: Container
    slot_derivations:
      c_list:
        name: c_list
        populated_from: c_list
        range: C
      d:
        name: d
        populated_from: d
        range: D
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
      s2:
        name: s2
        populated_from: s2
  D:
    name: D
    populated_from: D
    slot_derivations:
      s3:
        name: s3
        populated_from: s3

Feature Set: test_join

Test joining two objects into a single object, aka denormalization.

source_object: normalized source object
target_object: denormalized target object
inlined: True if the source objects are inlined

Combo: test_join[source_object0-target_object0-True]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  R:
    name: R
    attributes:
      s1:
        name: s1
        range: E
        inlined: true
      s2:
        name: s2
        range: E
        inlined: true
    tree_root: true
  E:
    name: E
    attributes:
      id:
        name: id
        identifier: true
        range: string
      name:
        name: name
        range: string

Transformer Specification:

class_derivations:
  R:
    name: R
    populated_from: R
    slot_derivations:
      s1_id:
        name: s1_id
        expr: s1.id
      s1_name:
        name: s1_name
        expr: s1.name
      s2_id:
        name: s2_id
        expr: s2.id
      s2_name:
        name: s2_name
        expr: s2.name

Object Transformation:

Source Object:

s1:
  id: x1
  name: foo
s2:
  id: x2
  name: bar

Target Object:

s1_id: x1
s1_name: foo
s2_id: x2
s2_name: bar

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  R:
    name: R
    attributes:
      s1_id:
        name: s1_id
      s1_name:
        name: s1_name
      s2_id:
        name: s2_id
      s2_name:
        name: s2_name
    tree_root: true

Combo: test_join[source_object0-target_object0-False]

Source Schema:

name: types
id: types
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  R:
    name: R
    attributes:
      s1:
        name: s1
        range: E
        inlined: false
      s2:
        name: s2
        range: E
        inlined: false
    tree_root: false
  E:
    name: E
    attributes:
      id:
        name: id
        identifier: true
        range: string
      name:
        name: name
        range: string
  Container:
    name: Container
    attributes:
      r_list:
        name: r_list
        multivalued: true
        range: R
      e_list:
        name: e_list
        multivalued: true
        range: E
        inlined_as_list: true
    tree_root: true

Transformer Specification:

class_derivations:
  R:
    name: R
    populated_from: R
    slot_derivations:
      s1_id:
        name: s1_id
        expr: s1.id
      s1_name:
        name: s1_name
        expr: s1.name
      s2_id:
        name: s2_id
        expr: s2.id
      s2_name:
        name: s2_name
        expr: s2.name
  Container:
    name: Container
    populated_from: Container
    slot_derivations:
      r_list:
        name: r_list
        populated_from: r_list

Object Transformation:

Source Object:

r_list:
- s1: x1
  s2: x2
e_list:
- id: x1
  name: foo
- id: x2
  name: bar

Target Object:

r_list:
- s1_id: x1
  s1_name: foo
  s2_id: x2
  s2_name: bar

Target Schema (Derived):

name: types-derived
id: types-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: types-derived/
classes:
  R:
    name: R
    attributes:
      s1_id:
        name: s1_id
      s1_name:
        name: s1_name
      s2_id:
        name: s2_id
      s2_name:
        name: s2_name
    tree_root: false
  Container:
    name: Container
    attributes:
      r_list:
        name: r_list
        multivalued: true
        domain_of:
        - Container
        range: R
    tree_root: true

Feature Set: test_map_enum

Test mapping between enum values.

Currently this only supports simple dictionary-style mapping between permissible values, akin to SSSOM, but in future additional expressivity will be supported, including:

mapping ranges to categorical values
boolean/branching logic

source_value:
mapping:
target_value:

Combo: test_map_enum[A-mapping0-B-False]

Source Schema:

name: enums
id: enums
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
enums:
  E:
    name: E
    permissible_values:
      A:
        text: A
      B:
        text: B
      C:
        text: C
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: E

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
enum_derivations:
  E:
    name: E
    mirror_source: false
    populated_from: E
    permissible_value_derivations:
      B:
        name: B
        populated_from: A

Object Transformation:

Source Object:

s1: A

Target Object:

s1: B

Target Schema (Derived):

name: enums-derived
id: enums-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: enums-derived/
enums:
  E:
    name: E
    permissible_values:
      A:
        text: A
      B:
        text: B
      C:
        text: C
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: E

Inverted Transformation Specification (Derived):

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
enum_derivations:
  E:
    name: E
    populated_from: E
    permissible_value_derivations:
      A:
        name: A
        populated_from: B

Combo: test_map_enum[Z-mapping1-None-False]

Source Schema:

name: enums
id: enums
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
enums:
  E:
    name: E
    permissible_values:
      A:
        text: A
      B:
        text: B
      C:
        text: C
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: E

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
enum_derivations:
  E:
    name: E
    mirror_source: false
    populated_from: E
    permissible_value_derivations:
      B:
        name: B
        populated_from: A

Object Transformation:

Source Object:

s1: Z

Target Object:

{}

Target Schema (Derived):

name: enums-derived
id: enums-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: enums-derived/
enums:
  E:
    name: E
    permissible_values:
      A:
        text: A
      B:
        text: B
      C:
        text: C
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: E

Combo: test_map_enum[C-mapping2-C-True]

Source Schema:

name: enums
id: enums
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
enums:
  E:
    name: E
    permissible_values:
      A:
        text: A
      B:
        text: B
      C:
        text: C
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: E

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
enum_derivations:
  E:
    name: E
    mirror_source: true
    populated_from: E
    permissible_value_derivations:
      B:
        name: B
        populated_from: A

s### Combo: test_map_enum[A-mapping3-B-False]

Source Schema:

name: enums
id: enums
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
enums:
  E:
    name: E
    permissible_values:
      A:
        text: A
      B:
        text: B
      C:
        text: C
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: E

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
enum_derivations:
  E:
    name: E
    mirror_source: false
    populated_from: E
    permissible_value_derivations:
      B:
        name: B
        sources:
        - A
        - C

Object Transformation:

Source Object:

s1: A

Target Object:

s1: B

Target Schema (Derived):

name: enums-derived
id: enums-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: enums-derived/
enums:
  E:
    name: E
    permissible_values:
      A:
        text: A
      B:
        text: B
      C:
        text: C
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: E

Combo: test_map_enum[C-mapping4-B-False]

Source Schema:

name: enums
id: enums
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
enums:
  E:
    name: E
    permissible_values:
      A:
        text: A
      B:
        text: B
      C:
        text: C
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        range: E

Transformer Specification:

class_derivations:
  C:
    name: C
    slot_derivations:
      s1:
        name: s1
        populated_from: s1
enum_derivations:
  E:
    name: E
    mirror_source: false
    populated_from: E
    permissible_value_derivations:
      B:
        name: B
        sources:
        - A
        - C

Object Transformation:

Source Object:

s1: C

Target Object:

s1: B

Target Schema (Derived):

name: enums-derived
id: enums-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: enums-derived/
enums:
  E:
    name: E
    permissible_values:
      A:
        text: A
      B:
        text: B
      C:
        text: C
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: E

Feature Set: test_inheritance

Test inheritance.

Transformation specifications can utilize inheritance, in the same way that LinkML schemas can.

is_a: use is_as instead of mixins in test schema
flatten: roll down inherited slots

Combo: test_inheritance[False-True]

Source Schema:

name: expr
id: expr
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    is_a: D
    attributes:
      s1:
        name: s1
        range: integer
    tree_root: true
  D:
    name: D
    attributes:
      s2:
        name: s2
        range: integer

Transformer Specification:

class_derivations:
  C:
    name: C
    is_a: D
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        expr: s1 + 1
  D:
    name: D
    populated_from: D
    slot_derivations:
      s2:
        name: s2
        expr: s2 + 1

Object Transformation:

Source Object:

s1: 1
s2: 2

Target Object:

s1: 2
s2: 3

Target Schema (Derived):

name: expr-derived
id: expr-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: expr-derived/
classes:
  C:
    name: C
    is_a: D
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: integer
    tree_root: true
  D:
    name: D
    attributes:
      s2:
        name: s2
        domain_of:
        - D
        range: integer

Combo: test_inheritance[False-False]

Source Schema:

name: expr
id: expr
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    mixins:
    - D
    attributes:
      s1:
        name: s1
        range: integer
    tree_root: true
  D:
    name: D
    attributes:
      s2:
        name: s2
        range: integer

Transformer Specification:

class_derivations:
  C:
    name: C
    mixins:
    - D
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        expr: s1 + 1
  D:
    name: D
    populated_from: D
    slot_derivations:
      s2:
        name: s2
        expr: s2 + 1

Object Transformation:

Source Object:

s1: 1
s2: 2

Target Object:

s1: 2
s2: 3

Target Schema (Derived):

name: expr-derived
id: expr-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: expr-derived/
classes:
  C:
    name: C
    mixins:
    - D
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: integer
    tree_root: true
  D:
    name: D
    attributes:
      s2:
        name: s2
        domain_of:
        - D
        range: integer

Combo: test_inheritance[True-True]

Source Schema:

name: expr
id: expr
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    is_a: D
    attributes:
      s1:
        name: s1
        range: integer
    tree_root: true
  D:
    name: D
    attributes:
      s2:
        name: s2
        range: integer

Transformer Specification:

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        expr: s1 + 1
      s2:
        name: s2
        expr: s2 + 1

Object Transformation:

Source Object:

s1: 1
s2: 2

Target Object:

s1: 2
s2: 3

Target Schema (Derived):

name: expr-derived
id: expr-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: expr-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: integer
      s2:
        name: s2
        domain_of:
        - D
        range: integer
    tree_root: true

Combo: test_inheritance[True-False]

Source Schema:

name: expr
id: expr
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: test
classes:
  C:
    name: C
    mixins:
    - D
    attributes:
      s1:
        name: s1
        range: integer
    tree_root: true
  D:
    name: D
    attributes:
      s2:
        name: s2
        range: integer

Transformer Specification:

class_derivations:
  C:
    name: C
    populated_from: C
    slot_derivations:
      s1:
        name: s1
        expr: s1 + 1
      s2:
        name: s2
        expr: s2 + 1

Object Transformation:

Source Object:

s1: 1
s2: 2

Target Object:

s1: 2
s2: 3

Target Schema (Derived):

name: expr-derived
id: expr-derived
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  test:
    prefix_prefix: test
    prefix_reference: http://example.org/test/
default_prefix: expr-derived/
classes:
  C:
    name: C
    attributes:
      s1:
        name: s1
        domain_of:
        - C
        range: integer
      s2:
        name: s2
        domain_of:
        - D
        range: integer
    tree_root: true

. 55 passed, 2 skipped, 83 warnings in 3.98s