bump schema-salad version, document narrowing types

Author: mr-c

Makefile

@@ -34,7 +34,7 @@ COVBASE=coverage run --append
 
 # Updating the Major & Minor version below?
 # Don't forget to update setup.py as well
-VERSION=8.2.$(shell date +%Y%m%d%H%M%S --utc --date=`git log --first-parent \
+VERSION=8.3.$(shell date +%Y%m%d%H%M%S --utc --date=`git log --first-parent \
 	--max-count=1 --format=format:%cI`)
 
 ## all         : default task

schema_salad/avro/schema.py

@@ -303,7 +303,7 @@ def __init__(
                 type_schema = make_avsc_object(atype, names)
             except Exception as e:
                 raise SchemaParseException(
-                    f'Type property "{atype}" not a valid Avro schema.'
+                    f'Type property "{atype}" not a valid Avro schema: {e}'
                 ) from e
         self.set_prop("type", type_schema)
         self.set_prop("name", name)
@@ -409,8 +409,8 @@ def __init__(
                 items_schema = make_avsc_object(items, names)
             except Exception as err:
                 raise SchemaParseException(
-                    f"Items schema ({items}) not a valid Avro schema: (known "
-                    f"names: {list(names.names.keys())})."
+                    f"Items schema ({items}) not a valid Avro schema: {err}. "
+                    f"Known names: {list(names.names.keys())})."
                 ) from err
 
         self.set_prop("items", items_schema)
@@ -451,7 +451,7 @@ def __init__(
                     new_schema = make_avsc_object(schema, names)
                 except Exception as err:
                     raise SchemaParseException(
-                        f"Union item must be a valid Avro schema: {schema}"
+                        f"Union item must be a valid Avro schema: {err}; {schema},"
                     ) from err
             # check the new schema
             if (
@@ -506,10 +506,6 @@ def make_field_objects(field_data: List[PropsType], names: Names) -> List[Field]
                 # make sure field name has not been used yet
                 if new_field.name in parsed_fields:
                     old_field = parsed_fields[new_field.name]
-                    if "inherited_from" not in old_field:
-                        raise SchemaParseException(
-                            f"Field name {new_field.name} already in use."
-                        )
                     if not is_subtype(old_field["type"], field["type"]):
                         raise SchemaParseException(
                             f"Field name {new_field.name} already in use with "

schema_salad/metaschema.py

@@ -22,7 +22,7 @@
     Type,
     Union,
 )
-from urllib.parse import quote, urlsplit, urlunsplit, urlparse
+from urllib.parse import quote, urlparse, urlsplit, urlunsplit
 from urllib.request import pathname2url
 
 from ruamel.yaml.comments import CommentedMap

schema_salad/metaschema/metaschema.yml

@@ -309,7 +309,8 @@ $graph:
       type: boolean?
       doc: |
         If true, this record is abstract and may be used as a base for other
-        records, but is not valid on its own.
+        records, but is not valid on its own. Inherited fields may be
+        re-specified to narrow their type.
 
     - name: extends
       type:
@@ -321,7 +322,7 @@ $graph:
         refScope: 1
       doc: |
         Indicates that this record inherits fields from one or more base records.
-
+        Inherited fields may be re-specified to narrow their type.
     - name: specialize
       type:
         - SpecializeDef[]?

schema_salad/metaschema/salad.md

@@ -9,6 +9,7 @@ Contributors:
 * The developers of Apache Avro
 * The developers of JSON-LD
 * Nebojša Tijanić <[email protected]>, Seven Bridges Genomics
+* Michael R. Crusoe, ELIXIR-DE
 
 # Abstract
 
@@ -86,6 +87,13 @@ specification, the following changes have been made:
   is poorly documented, not included in conformance testing,
   and not widely supported.
 
+## Introduction to v1.2
+
+This is the fourth version of the Schema Salad specification. It was created to
+ease the development of extensions to CWL v1.2. The only change is that
+inherited records can narrow the types of fields if those fields are re-specified
+with a matching jsonldPredicate.
+
 ## References to Other Specifications
 
 **Javascript Object Notation (JSON)**: http://json.org

schema_salad/python_codegen_support.py

@@ -19,7 +19,7 @@
     Type,
     Union,
 )
-from urllib.parse import quote, urlsplit, urlunsplit, urlparse
+from urllib.parse import quote, urlparse, urlsplit, urlunsplit
 from urllib.request import pathname2url
 
 from ruamel.yaml.comments import CommentedMap

schema_salad/tests/metaschema-pre.yml

@@ -20,3 +20,7 @@ $graph:
   doc: |
     This is an arbitrary abstract thing from a base schema that might
     be extended.
+  fields:
+    override_me:
+      type: [ string, int ]
+      jsonldPredicate: "bs:override_me"

schema_salad/tests/test_schema/avro_naming_base.yml

@@ -0,0 +1,25 @@
+$base: "https://example.com/derived_schema#"
+
+$namespaces:
+  bs: "https://example.com/base_schema#"
+
+$graph:
+
+- $import: avro_naming_base.yml
+
+- name: ExtendedThing
+  type: record
+  doc: |
+    A refinement of the base schema's arbitrary abstract thing,
+    that allows one of the base schema's types as a field.
+  inVocab: false
+  extends: bs:AbstractThing
+  fields:
+    field_one:
+      type:
+        type: array
+        items: [string, bs:RealThing]
+    override_me:
+      type: string
+      jsonldPredicate: "bs:override_me"
+

schema_salad/tests/test_schema/avro_subtype.yml

@@ -0,0 +1,25 @@
+$base: "https://example.com/derived_schema#"
+
+$namespaces:
+  bs: "https://example.com/base_schema#"
+
+$graph:
+
+- $import: avro_naming_base.yml
+
+- name: ExtendedThing
+  type: record
+  doc: |
+    A refinement of the base schema's arbitrary abstract thing,
+    that allows one of the base schema's types as a field.
+  inVocab: false
+  extends: bs:AbstractThing
+  fields:
+    field_one:
+      type:
+        type: array
+        items: [string, bs:RealThing]
+    override_me:
+      type: Any
+      jsonldPredicate: bs:override_me
+