refresh with latest schema-salad, proposed CWL v1.2.1 changes

Author: mr-c

src/main/java/org/w3id/cwl/cwl1_2/CWLType.java

@@ -17,10 +17,17 @@
 import org.w3id.cwl.cwl1_2.utils.ValidationException;
 
 public enum CWLType {
+  NULL("null"),
+  BOOLEAN("boolean"),
+  INT("int"),
+  LONG("long"),
+  FLOAT("float"),
+  DOUBLE("double"),
+  STRING("string"),
   FILE("File"),
   DIRECTORY("Directory");
 
-  private static String[] symbols = new String[] {"File", "Directory"};
+  private static String[] symbols = new String[] {"null", "boolean", "int", "long", "float", "double", "string", "File", "Directory"};
   private String docVal;
 
   private CWLType(final String docVal) {

src/main/java/org/w3id/cwl/cwl1_2/CommandLineTool.java

@@ -193,6 +193,10 @@ public interface CommandLineTool extends Process, Savable {
    * Capture the command's standard output stream to a file written to
    * the designated output directory.
    * 
+   * If the `CommandLineTool` contains logically chained commands
+   * (e.g. `echo a && echo b`) `stdout` must include the output of
+   * every command.
+   * 
    * If `stdout` is a string, it specifies the file name to use.
    * 
    * If `stdout` is an expression, the expression is evaluated and must

src/main/java/org/w3id/cwl/cwl1_2/CommandLineToolImpl.java

@@ -273,6 +273,10 @@ public Object getStderr() {
    * Capture the command's standard output stream to a file written to
    * the designated output directory.
    * 
+   * If the `CommandLineTool` contains logically chained commands
+   * (e.g. `echo a && echo b`) `stdout` must include the output of
+   * every command.
+   * 
    * If `stdout` is a string, it specifies the file name to use.
    * 
    * If `stdout` is an expression, the expression is evaluated and must

src/main/java/org/w3id/cwl/cwl1_2/InitialWorkDirRequirement.java

@@ -19,7 +19,7 @@
 /**
 * Auto-generated interface for <I>https://w3id.org/cwl/cwl#InitialWorkDirRequirement</I><BR>This interface is implemented by {@link InitialWorkDirRequirementImpl}<BR> <BLOCKQUOTE>
  Define a list of files and subdirectories that must be staged by the workflow platform prior to executing the command line tool.
- 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`. Together with `DockerRequirement.dockerOutputDirectory` this it possible to control the locations of both input and output files when running in containers. </BLOCKQUOTE>
+ 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. </BLOCKQUOTE>
  */
 public interface InitialWorkDirRequirement extends ProcessRequirement, Savable {
   /**

src/main/java/org/w3id/cwl/cwl1_2/InitialWorkDirRequirementImpl.java

@@ -23,7 +23,7 @@
 /**
 * Auto-generated class implementation for <I>https://w3id.org/cwl/cwl#InitialWorkDirRequirement</I><BR> <BLOCKQUOTE>
  Define a list of files and subdirectories that must be staged by the workflow platform prior to executing the command line tool.
- 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`. Together with `DockerRequirement.dockerOutputDirectory` this it possible to control the locations of both input and output files when running in containers. </BLOCKQUOTE>
+ 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. </BLOCKQUOTE>
  */
 public class InitialWorkDirRequirementImpl extends SavableImpl implements InitialWorkDirRequirement {
   private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build();

src/main/java/org/w3id/cwl/cwl1_2/SecondaryFileSchema.java

@@ -70,10 +70,11 @@ public interface SecondaryFileSchema extends Savable {
    * secondary file from that expression.
    * 
    * To work on non-filename-preserving storage systems, portable
-   * tool descriptions should treat `location` as an opaque
-   * identifier and avoid constructing new values from `location`,
-   * but should construct relative references using `basename` or
-   * `nameroot` instead, or propagate `location` from defined inputs.
+   * tool descriptions should treat `location` as an
+   * [opaque identifier](#opaque-strings) and avoid constructing new
+   * values from `location`, but should construct relative references
+   * using `basename` or `nameroot` instead, or propagate `location`
+   * from defined inputs.
    * 
    * If a value in `secondaryFiles` is a string that is not an expression,
    * it specifies that the following pattern should be applied to the path

src/main/java/org/w3id/cwl/cwl1_2/SecondaryFileSchemaImpl.java

@@ -80,10 +80,11 @@ public class SecondaryFileSchemaImpl extends SavableImpl implements SecondaryFil
    * secondary file from that expression.
    * 
    * To work on non-filename-preserving storage systems, portable
-   * tool descriptions should treat `location` as an opaque
-   * identifier and avoid constructing new values from `location`,
-   * but should construct relative references using `basename` or
-   * `nameroot` instead, or propagate `location` from defined inputs.
+   * tool descriptions should treat `location` as an
+   * [opaque identifier](#opaque-strings) and avoid constructing new
+   * values from `location`, but should construct relative references
+   * using `basename` or `nameroot` instead, or propagate `location`
+   * from defined inputs.
    * 
    * If a value in `secondaryFiles` is a string that is not an expression,
    * it specifies that the following pattern should be applied to the path

src/main/java/org/w3id/cwl/cwl1_2/ShellCommandRequirement.java

@@ -19,8 +19,8 @@
 /**
 * Auto-generated interface for <I>https://w3id.org/cwl/cwl#ShellCommandRequirement</I><BR>This interface is implemented by {@link ShellCommandRequirementImpl}<BR> <BLOCKQUOTE>
  Modify the behavior of CommandLineTool to generate a single string
- containing a shell command line.  Each item in the argument list must be
- joined into a string separated by single spaces and quoted to prevent
+ containing a shell command line.  Each item in the `arguments` list must
+ be joined into a string separated by single spaces and quoted to prevent
  intepretation by the shell, unless `CommandLineBinding` for that argument
  contains `shellQuote: false`.  If `shellQuote: false` is specified, the
  argument is joined into the command string without quoting, which allows

src/main/java/org/w3id/cwl/cwl1_2/ShellCommandRequirementImpl.java

@@ -23,8 +23,8 @@
 /**
 * Auto-generated class implementation for <I>https://w3id.org/cwl/cwl#ShellCommandRequirement</I><BR> <BLOCKQUOTE>
  Modify the behavior of CommandLineTool to generate a single string
- containing a shell command line.  Each item in the argument list must be
- joined into a string separated by single spaces and quoted to prevent
+ containing a shell command line.  Each item in the `arguments` list must
+ be joined into a string separated by single spaces and quoted to prevent
  intepretation by the shell, unless `CommandLineBinding` for that argument
  contains `shellQuote: false`.  If `shellQuote: false` is specified, the
  argument is joined into the command string without quoting, which allows

src/main/java/org/w3id/cwl/cwl1_2/WorkflowOutputParameter.java

@@ -124,8 +124,11 @@ public interface WorkflowOutputParameter extends OutputParameter, Savable {
   /**
    * Getter for property <I>https://w3id.org/cwl/cwl#outputSource</I><BR>
    * <BLOCKQUOTE>
-   * Specifies one or more workflow parameters that supply the value of to
-   * the output parameter.
+   * Specifies one or more names of an output from a workflow step (in the form 
+   * `step_name/output_name` with a `/` separator`), or a workflow input name,
+   * that supply their value(s) to the output parameter.
+   * the output parameter.  It is valid to reference workflow level inputs
+   * here.
    *    * </BLOCKQUOTE>
    */