edits

Author: mr-c

draft-4/Workflow.yml

@@ -22,11 +22,12 @@ $graph:
     - |
       # Abstract
 
-      A Workflow is an analysis task represented by a directed graph describing
-      a sequence of operations that transform an input data set to output.
-      This specification defines the Common Workflow Language (CWL) Workflow
-      description, a vendor-neutral standard for representing workflows
-      intended to be portable across a variety of computing platforms.
+      One way to define a workflow is: an analysis task represented by a
+      directed graph describing a sequence of operations that transform an
+      input data set to output. This specification defines the Common Workflow
+      Language (CWL) Workflow description, a vendor-neutral standard for
+      representing workflows intended to be portable across a variety of
+      computing platforms.
 
     - {$include: intro.md}
 
@@ -85,7 +86,7 @@ $graph:
       specializeTo: "#ExpressionToolOutputParameter"
   documentRoot: true
   doc: |
-    Execute an expression as a process step.
+    Execute an expression as a Workflow step.
   fields:
     - name: "class"
       jsonldPredicate:
@@ -164,7 +165,7 @@ $graph:
     - name: source
       doc: |
         Specifies one or more workflow parameters that will provide input to
-        the underlying process parameter.
+        the underlying step parameter.
       jsonldPredicate:
         "_id": "cwl:source"
         "_type": "@id"
@@ -187,7 +188,7 @@ $graph:
   doc: |
     The input of a workflow step connects an upstream parameter (from the
     workflow inputs, or the outputs of other workflows steps) with the input
-    parameters of the underlying process.
+    parameters of the underlying step.
 
     ## Input object
 
@@ -296,9 +297,9 @@ $graph:
   docParent: "#Workflow"
   doc: |
     A workflow step is an executable element of a workflow.  It specifies the
-    underlying process implementation (such as `CommandLineTool`) in the `run`
-    field and connects the input and output parameters of the underlying
-    process to workflow parameters.
+    underlying process implementation (such as `CommandLineTool` or another
+    `Workflow`) in the `run` field and connects the input and output parameters
+    of the underlying process to workflow parameters.
 
     # Scatter/gather
 
@@ -436,15 +437,15 @@ $graph:
     specializeTo: "#WorkflowOutputParameter"
   doc: |
     A workflow describes a set of **steps** and the **dependencies** between
-    those processes.  When a process produces output that will be consumed by a
-    second process, the first process is a dependency of the second process.
+    those steps.  When a step produces output that will be consumed by a
+    second step, the first step is a dependency of the second step.
 
     When there is a dependency, the workflow engine must execute the preceeding
-    process and wait for it to successfully produce output before executing the
-    dependent process.  If two processes are defined in the workflow graph that
-    are not directly or indirectly dependent, these processes are
-    **independent**, and may execute in any order or execute concurrently.  A
-    workflow is complete when all steps have been executed.
+    step and wait for it to successfully produce output before executing the
+    dependent step.  If two steps are defined in the workflow graph that
+    are not directly or indirectly dependent, these steps are **independent**,
+    and may execute in any order or execute concurrently.  A workflow is
+    complete when all steps have been executed.
 
     Dependencies between parameters are expressed using the `source` field on
     [workflow step input parameters](#WorkflowStepInput) and [workflow output
@@ -458,21 +459,21 @@ $graph:
 
     ## Workflow success and failure
 
-    A completed process must result in one of `success`, `temporaryFailure` or
-    `permanentFailure` states.  An implementation may choose to retry a process
+    A completed step must result in one of `success`, `temporaryFailure` or
+    `permanentFailure` states.  An implementation may choose to retry a step
     execution which resulted in `temporaryFailure`.  An implementation may
     choose to either continue running other steps of a workflow, or terminate
     immediately upon `permanentFailure`.
 
-    * If any step of a workflow execution results in `permanentFailure`, then the
-    workflow status is `permanentFailure`.
+    * If any step of a workflow execution results in `permanentFailure`, then
+    the workflow status is `permanentFailure`.
 
     * If one or more steps result in `temporaryFailure` and all other steps
     complete `success` or are not executed, then the workflow status is
     `temporaryFailure`.
 
-    * If all workflow steps are executed and complete with `success`, then the workflow
-    status is `success`.
+    * If all workflow steps are executed and complete with `success`, then the
+    workflow status is `success`.
 
     # Extensions
 

draft-4/concepts.md

@@ -62,19 +62,21 @@ boolean, array, or object.
 A **document** is a file containing a serialized object, or an array of objects.
 
 A **process** is a basic unit of computation which accepts input data,
-performs some computation, and produces output data.
+performs some computation, and produces output data. Examples include
+CommandLineTools, Workflows, and ExpressionTools.
 
-An **input object** is an object describing the inputs to a invocation of process.
+An **input object** is an object describing the inputs to a invocation of
+process.
 
-An **output object** is an object describing the output of an invocation of a process.
+An **output object** is an object describing the output of an invocation of a
+process.
 
 An **input schema** describes the valid format (required fields, data types)
 for an input object.
 
 An **output schema** describes the valid format for a output object.
 
-**Metadata** is information about workflows, tools, or input items that is
-not used directly in the computation.
+**Metadata** is information about workflows, tools, or input items.
 
 ## Syntax
 
@@ -140,8 +142,9 @@ form a directed graph, and independent steps may run concurrently.
 A **runtime environment** is the actual hardware and software environment when
 executing a command line tool.  It includes, but is not limited to, the
 hardware architecture, hardware resources, operating system, software runtime
-(if applicable, such as the Python interpreter or the JVM), libraries, modules,
-packages, utilities, and data files required to run the tool.
+(if applicable, such as the specific Python interpreter or the specific Java
+virtual machine), libraries, modules, packages, utilities, and data files
+required to run the tool.
 
 A **workflow platform** is a specific hardware and software implementation
 capable of interpreting CWL documents and executing the processes specified by
@@ -201,7 +204,7 @@ warning if a hint cannot be satisfied.
 
 Requirements are inherited.  A requirement specified in a Workflow applies
 to all workflow steps; a requirement specified on a workflow step will
-apply to the process implementation.
+apply to the process implementation of that step and any of its substeps.
 
 If the same process requirement appears at different levels of the
 workflow, the most specific instance of the requirement is used, that is,
@@ -223,7 +226,7 @@ field permitting the pseudo-type `Expression`, as specified by this document.
 Conforming implementations must support parameter references.  Parameter
 references use the following subset of
 [Javascript/ECMAScript 5.1](http://www.ecma-international.org/ecma-262/5.1/)
-syntax.
+syntax but they are designed to not require a Javascript engine for evaluation.
 
 In the following BNF grammar, character classes and grammar rules are denoted
 in '{}', '-' denotes exclusion from a character class, '(())' denotes grouping,
@@ -232,12 +235,12 @@ one or more repeats, all other characters are literal values.
 
 <p>
 <table class="table">
-<tr><td>symbol::   </td><td>{Unicode alphanumeric}+</td></tr>
-<tr><td>singleq::  </td><td>[' (( {character - '} | \' ))* ']</td></tr>
-<tr><td>doubleq::  </td><td>[" (( {character - "} | \" ))* "]</td></tr>
-<tr><td>index::    </td><td>[ {decimal digit}+ ]</td></tr>
-<tr><td>segment::  </td><td>. {symbol} | {singleq} | {doubleq} | {index}</td></tr>
-<tr><td>parameter::</td><td>$( {symbol} {segment}*)</td></tr>
+<tr><td>symbol::             </td><td>{Unicode alphanumeric}+</td></tr>
+<tr><td>singleq::            </td><td>[' (( {character - '} | \' ))* ']</td></tr>
+<tr><td>doubleq::            </td><td>[" (( {character - "} | \" ))* "]</td></tr>
+<tr><td>index::              </td><td>[ {decimal digit}+ ]</td></tr>
+<tr><td>segment::            </td><td>. {symbol} | {singleq} | {doubleq} | {index}</td></tr>
+<tr><td>parameter reference::</td><td>$( {symbol} {segment}*)</td></tr>
 </table>
 </p>
 

site/cwlsite-draft4-job.json

@@ -43,7 +43,7 @@
                 "https://w3id.org/cwl/cwl#CreateFileRequirement=CommandLineTool.html#CreateFileRequirement",
                 "https://w3id.org/cwl/cwl#EnvVarRequirement=CommandLineTool.html#EnvVarRequirement",
                 "https://w3id.org/cwl/cwl#ShellCommandRequirement=CommandLineTool.html#ShellCommandRequirement",
-                "https://w3id.org/cwl/cwl#ResourceRequirement=CommandLineTool.html#ResourceRequirement",
+                "https://w3id.org/cwl/cwl#ResourceRequirement=CommandLineTool.html#ResourceRequirement"
             ],
             "brandlink": "index.html",
             "brandimg": "<img src='../CWL-Logo-Header.png' style='height: 61px; margin-top: -20px; margin-left: -20px'></img>",
@@ -62,5 +62,15 @@
             "brandlink": "index.html",
             "brandimg": "<img src='../CWL-Logo-Header.png' style='height: 61px; margin-top: -20px; margin-left: -20px'></img>",
             "primtype": null
+        },
+        {
+            "source": {"$import": "userguide-draft4-input.json"},
+            "target": "draft-4/UserGuide.html",
+            "renderlist": [],
+            "redirect": [],
+            "brandlink": "index.html",
+            "brandimg": "<img src='../CWL-Logo-Header.png' style='height: 61px; margin-top: -20px; margin-left: -20px'></img>",
+            "primtype": null
         }
+
     ]