Language cleanup

.github/config/wordlist.txt

@@ -1,3 +1,4 @@
+abstractworkflowstep
 acyclic
 amstutz
 arrayschema
@@ -160,6 +161,9 @@ loadlistingrequirement
 localhost
 lookahead
 loopback
+loopinput
+loopoutputmethod
+loopworkflowstep
 maccallum
 macos
 mappredicate
@@ -194,6 +198,7 @@ outputbinding
 outputenumschema
 outputeval
 outputformat
+outputmethod
 outputschema
 outputsink
 outputsource
@@ -231,6 +236,7 @@ saladversion
 sbgenomics
 scatterfeaturerequirement
 scattermethod
+scatterworkflowstep
 schemadefrequirement
 schemaorg
 schemas

.github/workflows/cwltool.yml

@@ -33,4 +33,4 @@ jobs:
         run: cp conformance_tests.yaml conformance_tests.cwltest.yaml
 
       - name: Run tests against the reference runner
-        run: python -m pytest conformance_tests.cwltest.yaml -n auto -rs
+        run: python -m pytest conformance_tests.cwltest.yaml -n auto -rsfE

CONFORMANCE_TESTS.md

@@ -144,7 +144,7 @@ We will use this single entry to explain the format
      Must include one or more of the following tags: `command_line_tool`, `expression_tool` or `workflow`.
      If the test does not test any optional features, the tag `required` is required.
 
-Because `conformance_tests.yaml` is a `schema-salad` processed document, [`$import`](https://www.commonwl.org/v1.2/SchemaSalad.html#Import)
+Because `conformance_tests.yaml` is a `schema-salad` processed document, [`$import`](https://www.commonwl.org/v1.3/SchemaSalad.html#Import)
 can be used to organize the tests into separate files.
 
 Currently, the main file is too big (over 3400 lines); we are slowly re-organizing it.
@@ -166,7 +166,7 @@ At any level, if there is an extra field, then that will be considered an error.
 An exception to this is `class: File` and `class: Directory` objects, the `cwl-runner` under test can add additional fields here without causing a test to fail.
 Likewise, if you don't want to test some aspect of a `class: File` or `class: Directory` object (like `nameext`) you can just omit it.
 
-[According to the CWL standards](https://www.commonwl.org/v1.2/CommandLineTool.html#File), the format of the `location` field in 
+[According to the CWL standards](https://www.commonwl.org/v1.3/CommandLineTool.html#File), the format of the `location` field in 
 `class: File` and `class: Directory` is implementation specific and we should not be testing them.
 Please remember to use `location: Any` for them.
 

CommandLineTool.yml

@@ -52,6 +52,20 @@ $graph:
       ## Changelog for v1.3.0-dev1
 
       See also the [CWL Workflow Description, v1.3.0-dev1 changelog](Workflow.html#Changelog).
+
+      * New field `networkAccess` on
+        [CommandLineTool](#CommandLineTool).  This supersedes the
+        [NetworkAccess](#NetworkAccess) requirement, which is now
+        deprecated.
+      * New field `envDef` on [CommandLineTool](#CommandLineTool).
+        This supersedes the [EnvVarRequirement](#EnvVarRequirement)
+        requirement, which is now deprecated.
+      * New field `initialWorkDir` on
+        [CommandLineTool](#CommandLineTool).  This supersedes the
+        [InitialWorkDirRequirement](#InitialWorkDirRequirement)
+        requirement, which is now deprecated.
+
+
       For other changes since CWL v1.0, see the
       [CWL Command Line Tool Description, v1.1 changelog](https://www.commonwl.org/v1.1/CommandLineTool.html#Changelog)
       and
@@ -711,6 +725,94 @@ $graph:
 
         If not specified, all exit codes except 0 are considered permanent failure.
 
+    - name: networkAccess
+      type: ['null', boolean, Expression]
+      jsonldPredicate: "cwl:NetworkAccess/networkAccess"
+      doc: |
+        Indicate whether a process requires outgoing IPv4/IPv6 network
+        access.  Choice of IPv4 or IPv6 is implementation and site
+        specific, correct tools must support both.
+
+        If `networkAccess` is false or not specified, tools must not
+        assume network access, except for localhost (the loopback device).
+
+        If `networkAccess` is true, the tool must be able to make outgoing
+        connections to network resources.  Resources may be on a private
+        subnet or the public Internet.  However, implementations and sites
+        may apply their own security policies to restrict what is
+        accessible by the tool.
+
+        Enabling network access does not imply a publicly routable IP
+        address or the ability to accept inbound connections.
+
+    - name: initialWorkDir
+      type:
+        - 'null'
+        - Expression
+        - type: array
+          items:
+            - "null"
+            - Dirent
+            - Expression
+            - File
+            - Directory
+            - type: array
+              items:
+                - File
+                - Directory
+      doc: |
+        Define a list of files and subdirectories that must be staged
+        by the workflow platform prior to executing the command line
+        tool.  Normally this is the designated output directory, but
+        when containers are used, it is possible to stage to other
+        locations, see discussion below.
+
+        Return type of each expression must validate as `["null",
+        File, Directory, Dirent, {type: array, items: [File,
+        Directory]}]`.
+
+        Each `File` or `Directory` that is returned by an Expression
+        must be added to the designated output directory prior to
+        executing the tool.
+
+        Each `Dirent` record that is listed or returned by an
+        expression specifies a file to be created or staged in the
+        designated output directory prior to executing the tool.
+
+        Expressions may return null, in which case they have no effect.
+
+        Files or Directories which are listed in the input parameters
+        and appear in `initialWorkDir` must have their `path` set to
+        their staged location.  If the same File or Directory appears
+        more than once in the `initialWorkDir`, the implementation
+        must choose exactly one value for `path`; how this value is
+        chosen is undefined.
+
+        Normally files are staged within the designated output
+        directory.  However, when running inside containers, files may
+        be staged at arbitrary locations, see discussion for
+        [`Dirent.entryname`](#Dirent).  Together with
+        `DockerRequirement.dockerOutputDirectory` it is possible to
+        control the locations of both input and output files when
+        running in containers.
+
+        Files listed in `inputs` that are not listed in
+        `initialWorkDir` shall be staged to an arbitrary location on
+        the file system.  This location must be outside the designated
+        output directory.
+
+    - name: envDef
+      type: EnvironmentDef[]?
+      doc: |
+        Define a list of environment variables which will be set in
+        the execution environment of the tool.  See
+        [EnvironmentDef](#EnvironmentDef) for details.
+      jsonldPredicate:
+        "_id": "cwl:EnvVarRequirement/envDef"
+        mapSubject: envName
+        mapPredicate: envValue
+
+
 
 - type: record
   name: DockerRequirement
@@ -991,7 +1093,9 @@ $graph:
 - name: InitialWorkDirRequirement
   type: record
   extends: ProcessRequirement
-  doc:
+  doc: |
+    **Deprecated as of v1.3**  Prefer [CommandLineTool.initialWorkDir](#CommandLineTool)
+
     Define a list of files and subdirectories that must be staged by
     the workflow platform prior to executing the command line tool.
 
@@ -1059,6 +1163,8 @@ $graph:
   type: record
   extends: ProcessRequirement
   doc: |
+    **Deprecated as of v1.3**  Prefer [CommandLineTool.envDef](#CommandLineTool)
+
     Define a list of environment variables which will be set in the
     execution environment of the tool.  See `EnvironmentDef` for details.
   fields:
@@ -1076,6 +1182,7 @@ $graph:
       type: EnvironmentDef[]
       doc: The list of environment variables.
       jsonldPredicate:
+        "_id": "cwl:EnvVarRequirement/envDef"
         mapSubject: envName
         mapPredicate: envValue
 
@@ -1291,6 +1398,8 @@ $graph:
   name: NetworkAccess
   extends: ProcessRequirement
   doc: |
+    **Deprecated as of v1.3**  Prefer [CommandLineTool.networkAccess](#CommandLineTool)
+
     Indicate whether a process requires outgoing IPv4/IPv6 network
     access.  Choice of IPv4 or IPv6 is implementation and site
     specific, correct tools must support both.
@@ -1320,6 +1429,7 @@ $graph:
         "_type": "@vocab"
     - name: networkAccess
       type: [boolean, Expression]
+      jsonldPredicate: "cwl:NetworkAccess/networkAccess"
 
 - name: InplaceUpdateRequirement
   type: record