Added noLinkCheck to format field

CWL parsers should not follow `format` links.

.github/config/wordlist.txt

@@ -127,6 +127,7 @@ inplaceupdaterequirement
 inputarrayschema
 inputenumschema
 inputbinding
+inputfile
 inputformat
 inputrecordfield
 inputrecordschema

Base.yml

@@ -285,6 +285,7 @@ $graph:
         _id: cwl:format
         _type: "@id"
         identity: true
+        noLinkCheck: true
       doc: |
         The format of the file: this must be an IRI of a concept node that
         represents the file format, preferably defined within an ontology.
@@ -473,7 +474,6 @@ $graph:
       items:
         - "null"
         - CWLObjectType
-      flatten: false
     - type: map
       values:
         - "null"
@@ -491,4 +491,8 @@ $graph:
      items: ProcessRequirement
    - CWLObjectType
   doc: |
-    Type representing a valid CWL input file as a `map<string, union<array<ProcessRequirement>, CWLObjectType>>`.
+    Type representing a valid CWL input file as a `map<string, union<array<ProcessRequirement>, CWLObjectType>>`.
+  jsonldPredicate:
+    _id: "cwl:inputfile"
+    _container: "@list"
+    noLinkCheck: true

Process.yml

@@ -199,6 +199,7 @@ $graph:
         _id: cwl:format
         _type: "@id"
         identity: true
+        noLinkCheck: true
       doc: |
         Only valid when `type: File` or is an array of `items: File`.
 
@@ -221,6 +222,7 @@ $graph:
         _id: cwl:format
         _type: "@id"
         identity: true
+        noLinkCheck: true
       doc: |
         Only valid when `type: File` or is an array of `items: File`.
 
@@ -374,7 +376,8 @@ $graph:
     - name: default
       type: CWLObjectType?
       jsonldPredicate:
-        _id: sld:default
+        _id: "sld:default"
+        _container: "@list"
         noLinkCheck: true
       doc: |
         The default value to use for this parameter if the parameter is missing

Workflow.yml

@@ -593,6 +593,7 @@ $graph:
         default must be applied prior to scattering or evaluating `valueFrom`.
       jsonldPredicate:
         _id: "sld:default"
+        _container: "@list"
         noLinkCheck: true
     - name: valueFrom
       type:

concepts.md

@@ -331,7 +331,7 @@ prefix listed in the `$namespaces` section of the document as described in the
 [Schema Salad specification](SchemaSalad.html#Explicit_context).
 
 It is recommended that concepts from schema.org are used whenever possible.
-For the `$schemas` field we recommend their RDF encoding: http://schema.org/version/latest/schema.rdf
+For the `$schemas` field we recommend their RDF encoding: https://schema.org/version/latest/schemaorg-current-https.rdf
 
 Implementation extensions which modify execution semantics must be [listed in
 the `requirements` field](#Requirements_and_hints).

render.bash

@@ -1,14 +1,14 @@
 #!/usr/bin/env bash
 if [[ -z "$WORKSPACE" ]] ; then
-    WORKSPACE=$PWD
+    WORKSPACE=$PWD/temp/
 fi
 mkdir -p $WORKSPACE
 repo=https://github.com/common-workflow-language/cwl-website \
-bn=$(basename $repo)
+bn=$WORKSPACE/$(basename $repo)
 if [[ -d $bn ]] ; then
     (cd $bn && git fetch origin && git reset --hard origin/main)
 else
-    git clone $repo && pushd $bn; git checkout main ; git show --no-patch ; popd
+    git clone $repo $bn && pushd $bn; git checkout main ; git show --no-patch ; popd
 fi
 echo "- basename: Base.yml"  >> $WORKSPACE/cwl-website/site/v1.2-deps.yaml
 echo "  class: File"  >> $WORKSPACE/cwl-website/site/v1.2-deps.yaml

salad/schema_salad/metaschema/metaschema.yml

@@ -274,6 +274,7 @@ $graph:
       doc: |
         If true, indicates that the type is a valid at the document root.  At
         least one type in a schema must be tagged with `documentRoot: true`.
+      jsonldPredicate: sld:documentRoot
 
 
 - name: SaladRecordField
@@ -368,10 +369,17 @@ $graph:
 - name: SaladUnionSchema
   docParent: "#Schema"
   type: record
-  extends: [NamedType, UnionSchema, SchemaDefinedType]
+  extends: [NamedType, UnionSchema, DocType]
   documentRoot: true
   doc: |
     Define a union type.
+  fields:
+    - name: documentRoot
+      type: boolean?
+      doc: |
+        If true, indicates that the type is a valid at the document root.  At
+        least one type in a schema must be tagged with `documentRoot: true`.
+      jsonldPredicate: sld:documentRoot
 
 
 - name: Documentation

salad/schema_salad/metaschema/metaschema_base.yml

@@ -191,13 +191,6 @@ $graph:
         _type: "@vocab"
         refScope: 2
       doc: "Defines the type of the array elements."
-    flatten:
-      type: boolean?
-      jsonldPredicate:
-        _id: "sld:flatten"
-        _type: "@vocab"
-        refScope: 2
-      doc: "Flatten inner array objects into a single sequence (default: true)."
 
 
 - name: MapSchema

salad/schema_salad/metaschema/salad.md

@@ -10,6 +10,7 @@ Contributors:
 * The developers of JSON-LD
 * Nebojša Tijanić <[email protected]>, Seven Bridges Genomics
 * Michael R. Crusoe, ELIXIR-DE
+* Iacopo Colonnelli, University of Torino
 
 # Abstract
 
@@ -94,31 +95,15 @@ 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.
 
-### Changelog for v1.2.1
-
-There are no new features nor behavior changes in Schema Salad v1.2.1
-as compared to Schema-Salad v1.2. Schema Salad v1.2.1 only fixes typos and adds
-clarifications.
-
-* The `salad` directory's contents have been trimmed to the bare necessities.
-  The `salad/README.rst` has been refreshed from the [upstream repository](https://github.com/common-workflow-language/schema_salad/).
-* The [existing behaviour of `$import`](#Import) has been clarified.
-  If the `$import` node is in an array and the import operation yields an
-  array, it is flattened to the parent array. Otherwise the `$import`
-  node is replaced in the document structure by the object or array yielded
-  from the import operation. An [additional example](#import_example2)
-  has been added to illustrate this better.
-* A pair of missing brackets was added to the [Type DSL Example](#Type_DSL_example)'s
-  example input.
-* Missing newlines have been added to the [identifier map example](#Identifier_map_example)'s
-  example source and example result.
-* [Inherited fields in Salad types](#SaladRecordSchema) may be re-specified
-  to narrow their type and/or to override the `doc` field.
-* Clarify that fields with `jsonldPredicate: { _type: "@id" }` indicate that the
-  field is a [link fields](#SaladRecordSchema) and that if the `jsonldPredicate`
-  also has the field `identity` with the value `true`, then field is
-  resolved with [identifier resolution](#Identifier_resolution).
-  Otherwise the field is resolved with [link resolution](#Link_resolution).
+## Introduction to v1.3
+
+This is the fifth version of the Schema Salad specification. It was created to
+enhance code generation by representing CWL data types as specific Python objects
+(instead of  relying on the generic `Any` type). The following changes have been made:
+
+* Support for the Avro `map` schema
+* Add named versions of the `map` and `union` Avro types
+* Support for nested named `union` type definitions
 
 ## References to Other Specifications
 
@@ -173,7 +158,7 @@ enable or disable the behavior described.
 ## Data concepts
 
 An **object** is a data structure equivalent to the "object" type in JSON,
-consisting of an unordered set of name/value pairs (referred to here as
+consisting of a unordered set of name/value pairs (referred to here as
 **fields**) and where the name is a string and the value is a string, number,
 boolean, array, or object.