Merge pull request #49 from common-workflow-lab/packed_tests

add tests for packed versions of the conformance tests

Author: mr-c

pom.xml

@@ -107,6 +107,16 @@
             <artifactId>snakeyaml-engine</artifactId>
             <version>2.3</version>
         </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+            <version>2.10.0.pr1</version>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.dataformat</groupId>
+            <artifactId>jackson-dataformat-yaml</artifactId>
+            <version>2.9.8</version>
+        </dependency>
     </dependencies>
 
     <profiles>

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

@@ -86,7 +86,7 @@ public ArraySchemaImpl(
     try {
       items =
           LoaderInstances
-              .uri_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_StringInstance_False_True_2
+              .typedsl_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_StringInstance_2
               .loadField(__doc.get("items"), __baseUri, __loadingOptions);
     } catch (ValidationException e) {
       items = null; // won't be used but prevents compiler from complaining.

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

@@ -165,7 +165,7 @@ public CommandInputArraySchemaImpl(
     try {
       items =
           LoaderInstances
-              .uri_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_False_True_2
+              .typedsl_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_2
               .loadField(__doc.get("items"), __baseUri, __loadingOptions);
     } catch (ValidationException e) {
       items = null; // won't be used but prevents compiler from complaining.

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

@@ -69,9 +69,10 @@ public interface CommandLineBinding extends InputBinding, Savable {
   /**
    * Getter for property <I>https://w3id.org/cwl/cwl#CommandLineBinding/position</I><BR>
    * <BLOCKQUOTE>
-   * The sorting key.  Default position is 0. If the inputBinding is
-   * associated with an input parameter, then the value of `self` in the
-   * expression will be the value of the input parameter.  Input parameter
+   * The sorting key.  Default position is 0. If a [CWL Parameter Reference](#Parameter_references)
+   * or [CWL Expression](#Expressions_(Optional)) is used and if the
+   * inputBinding is associated with an input parameter, then the value of
+   * `self` will be the value of the input parameter.  Input parameter
    * defaults (as specified by the `InputParameter.default` field) must be
    * applied before evaluating the expression. Expressions must return a
    * single value of type int or a null.

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

@@ -84,9 +84,10 @@ public java.util.Optional<Boolean> getLoadContents() {
   /**
    * Getter for property <I>https://w3id.org/cwl/cwl#CommandLineBinding/position</I><BR>
    * <BLOCKQUOTE>
-   * The sorting key.  Default position is 0. If the inputBinding is
-   * associated with an input parameter, then the value of `self` in the
-   * expression will be the value of the input parameter.  Input parameter
+   * The sorting key.  Default position is 0. If a [CWL Parameter Reference](#Parameter_references)
+   * or [CWL Expression](#Expressions_(Optional)) is used and if the
+   * inputBinding is associated with an input parameter, then the value of
+   * `self` will be the value of the input parameter.  Input parameter
    * defaults (as specified by the `InputParameter.default` field) must be
    * applied before evaluating the expression. Expressions must return a
    * single value of type int or a null.

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

@@ -153,7 +153,7 @@ public CommandOutputArraySchemaImpl(
     try {
       items =
           LoaderInstances
-              .uri_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_False_True_2
+              .typedsl_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_2
               .loadField(__doc.get("items"), __baseUri, __loadingOptions);
     } catch (ValidationException e) {
       items = null; // won't be used but prevents compiler from complaining.

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

@@ -26,8 +26,8 @@ Represents a file (or group of files when `secondaryFiles` is provided) that
  a number of properties that provide metadata about the file.
  
  The `location` property of a File is a URI that uniquely identifies the
- file.  Implementations must support the file:// URI scheme and may support
- other schemes such as http://.  The value of `location` may also be a
+ file.  Implementations must support the `file://` URI scheme and may support
+ other schemes such as `http://` and `https://`.  The value of `location` may also be a
  relative reference, in which case it must be resolved relative to the URI
  of the document it appears in.  Alternately to `location`, implementations
  must also accept the `path` property on File, which must be a filesystem
@@ -215,7 +215,7 @@ public interface File extends Savable {
   /**
    * Getter for property <I>https://w3id.org/cwl/cwl#File/size</I><BR>
    * <BLOCKQUOTE>
-   * Optional file size   * </BLOCKQUOTE>
+   * Optional file size (in bytes)   * </BLOCKQUOTE>
    */
 
   Object getSize();
@@ -246,8 +246,8 @@ public interface File extends Savable {
    * `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer
    * `<C> owl:subclassOf <A>`.
    * 
-   * File format ontologies may be provided in the "$schema" metadata at the
-   * root of the document.  If no ontologies are specified in `$schema`, the
+   * File format ontologies may be provided in the "$schemas" metadata at the
+   * root of the document.  If no ontologies are specified in `$schemas`, the
    * runtime may perform exact file format matches.
    *    * </BLOCKQUOTE>
    */

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

@@ -30,8 +30,8 @@ Represents a file (or group of files when `secondaryFiles` is provided) that
  a number of properties that provide metadata about the file.
  
  The `location` property of a File is a URI that uniquely identifies the
- file.  Implementations must support the file:// URI scheme and may support
- other schemes such as http://.  The value of `location` may also be a
+ file.  Implementations must support the `file://` URI scheme and may support
+ other schemes such as `http://` and `https://`.  The value of `location` may also be a
  relative reference, in which case it must be resolved relative to the URI
  of the document it appears in.  Alternately to `location`, implementations
  must also accept the `path` property on File, which must be a filesystem
@@ -265,7 +265,7 @@ public java.util.Optional<String> getChecksum() {
   /**
    * Getter for property <I>https://w3id.org/cwl/cwl#File/size</I><BR>
    * <BLOCKQUOTE>
-   * Optional file size   * </BLOCKQUOTE>
+   * Optional file size (in bytes)   * </BLOCKQUOTE>
    */
 
   public Object getSize() {
@@ -306,8 +306,8 @@ public java.util.Optional<java.util.List<Object>> getSecondaryFiles() {
    * `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer
    * `<C> owl:subclassOf <A>`.
    * 
-   * File format ontologies may be provided in the "$schema" metadata at the
-   * root of the document.  If no ontologies are specified in `$schema`, the
+   * File format ontologies may be provided in the "$schemas" metadata at the
+   * root of the document.  If no ontologies are specified in `$schemas`, the
    * runtime may perform exact file format matches.
    *    * </BLOCKQUOTE>
    */

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

@@ -153,7 +153,7 @@ public InputArraySchemaImpl(
     try {
       items =
           LoaderInstances
-              .uri_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_False_True_2
+              .typedsl_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_2
               .loadField(__doc.get("items"), __baseUri, __loadingOptions);
     } catch (ValidationException e) {
       items = null; // won't be used but prevents compiler from complaining.

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

@@ -153,7 +153,7 @@ public OutputArraySchemaImpl(
     try {
       items =
           LoaderInstances
-              .uri_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_False_True_2
+              .typedsl_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_2
               .loadField(__doc.get("items"), __baseUri, __loadingOptions);
     } catch (ValidationException e) {
       items = null; // won't be used but prevents compiler from complaining.