diff --git a/src/main/java/org/w3id/cwl/cwl1_2/ArraySchema.java b/src/main/java/org/w3id/cwl/cwl1_2/ArraySchema.java index 216cd57..2c0aee6 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/ArraySchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/ArraySchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/salad#ArraySchema
This interface is implemented by {@link ArraySchemaImpl}
*/ -public interface ArraySchema extends Savable { +public interface ArraySchema extends Saveable { /** * Getter for property https://w3id.org/cwl/salad#items
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/ArraySchemaImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/ArraySchemaImpl.java index d0dac46..05a1f2c 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/ArraySchemaImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/ArraySchemaImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/salad#ArraySchema
*/ -public class ArraySchemaImpl extends SavableImpl implements ArraySchema { +public class ArraySchemaImpl extends SaveableImpl implements ArraySchema { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CWLType.java b/src/main/java/org/w3id/cwl/cwl1_2/CWLType.java index 75bdf6b..b294328 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CWLType.java +++ b/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) { diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputArraySchema.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputArraySchema.java index f9a791b..a1fe961 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputArraySchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputArraySchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputArraySchema
This interface is implemented by {@link CommandInputArraySchemaImpl}
*/ -public interface CommandInputArraySchema extends InputArraySchema, CommandInputSchema, CommandLineBindable, Savable { +public interface CommandInputArraySchema extends InputArraySchema, CommandInputSchema, CommandLineBindable, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputArraySchemaImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputArraySchemaImpl.java index ff15ad9..3b6fbd1 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputArraySchemaImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputArraySchemaImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputArraySchema
*/ -public class CommandInputArraySchemaImpl extends SavableImpl implements CommandInputArraySchema { +public class CommandInputArraySchemaImpl extends SaveableImpl implements CommandInputArraySchema { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputEnumSchema.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputEnumSchema.java index abf1fcd..f112b93 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputEnumSchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputEnumSchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputEnumSchema
This interface is implemented by {@link CommandInputEnumSchemaImpl}
*/ -public interface CommandInputEnumSchema extends InputEnumSchema, CommandInputSchema, CommandLineBindable, Savable { +public interface CommandInputEnumSchema extends InputEnumSchema, CommandInputSchema, CommandLineBindable, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputEnumSchemaImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputEnumSchemaImpl.java index 3f3d49d..68c769d 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputEnumSchemaImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputEnumSchemaImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputEnumSchema
*/ -public class CommandInputEnumSchemaImpl extends SavableImpl implements CommandInputEnumSchema { +public class CommandInputEnumSchemaImpl extends SaveableImpl implements CommandInputEnumSchema { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputParameter.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputParameter.java index ebc0b18..89d4c7d 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputParameter.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputParameter.java @@ -14,13 +14,13 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputParameter
This interface is implemented by {@link CommandInputParameterImpl}
An input parameter for a CommandLineTool.
*/ -public interface CommandInputParameter extends InputParameter, Savable { +public interface CommandInputParameter extends InputParameter, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Identified/id
*
@@ -158,7 +158,7 @@ public interface CommandInputParameter extends InputParameter, Savable { * *
*/ - java.util.Optional getDefault(); + Object getDefault(); /** * Getter for property https://w3id.org/cwl/salad#type
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputParameterImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputParameterImpl.java index 382a021..39d32a9 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputParameterImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputParameterImpl.java @@ -17,14 +17,14 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputParameter
An input parameter for a CommandLineTool.
*/ -public class CommandInputParameterImpl extends SavableImpl implements CommandInputParameter { +public class CommandInputParameterImpl extends SaveableImpl implements CommandInputParameter { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); @@ -196,7 +196,7 @@ public java.util.Optional getLoadListing() { return this.loadListing; } - private java.util.Optional default_; + private Object default_; /** * Getter for property https://w3id.org/cwl/salad#default
@@ -208,7 +208,7 @@ public java.util.Optional getLoadListing() { * * */ - public java.util.Optional getDefault() { + public Object getDefault() { return this.default_; } @@ -419,13 +419,13 @@ public CommandInputParameterImpl( } else { loadListing = null; } - java.util.Optional default_; + Object default_; if (__doc.containsKey("default")) { try { default_ = LoaderInstances - .optional_AnyInstance + .union_of_NullInstance_or_File_or_Directory_or_AnyInstance .loadField(__doc.get("default"), __baseUri, __loadingOptions); } catch (ValidationException e) { default_ = null; // won't be used but prevents compiler from complaining. @@ -475,7 +475,7 @@ public CommandInputParameterImpl( this.format = (Object) format; this.loadContents = (java.util.Optional) loadContents; this.loadListing = (java.util.Optional) loadListing; - this.default_ = (java.util.Optional) default_; + this.default_ = (Object) default_; this.type = (Object) type; this.inputBinding = (java.util.Optional) inputBinding; } diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputRecordField.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputRecordField.java index c098ec1..e32b33d 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputRecordField.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputRecordField.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputRecordField
This interface is implemented by {@link CommandInputRecordFieldImpl}
*/ -public interface CommandInputRecordField extends InputRecordField, CommandLineBindable, Savable { +public interface CommandInputRecordField extends InputRecordField, CommandLineBindable, Saveable { /** * Getter for property https://w3id.org/cwl/salad#RecordField/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputRecordFieldImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputRecordFieldImpl.java index 71ca02e..adc3abf 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputRecordFieldImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputRecordFieldImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputRecordField
*/ -public class CommandInputRecordFieldImpl extends SavableImpl implements CommandInputRecordField { +public class CommandInputRecordFieldImpl extends SaveableImpl implements CommandInputRecordField { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputRecordSchema.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputRecordSchema.java index e7fe6fc..8837214 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputRecordSchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputRecordSchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputRecordSchema
This interface is implemented by {@link CommandInputRecordSchemaImpl}
*/ -public interface CommandInputRecordSchema extends InputRecordSchema, CommandInputSchema, CommandLineBindable, Savable { +public interface CommandInputRecordSchema extends InputRecordSchema, CommandInputSchema, CommandLineBindable, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputRecordSchemaImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputRecordSchemaImpl.java index 5332c67..cd92752 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputRecordSchemaImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputRecordSchemaImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputRecordSchema
*/ -public class CommandInputRecordSchemaImpl extends SavableImpl implements CommandInputRecordSchema { +public class CommandInputRecordSchemaImpl extends SaveableImpl implements CommandInputRecordSchema { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputSchema.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputSchema.java index d5f5f70..4dd291d 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandInputSchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandInputSchema.java @@ -14,10 +14,10 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputSchema
*/ -public interface CommandInputSchema extends Savable { +public interface CommandInputSchema extends Saveable { } diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandLineBindable.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandLineBindable.java index dfba862..7b64da1 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandLineBindable.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandLineBindable.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#CommandLineBindable
This interface is implemented by {@link CommandLineBindableImpl}
*/ -public interface CommandLineBindable extends Savable { +public interface CommandLineBindable extends Saveable { /** * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandLineBindableImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandLineBindableImpl.java index 2a40415..ef87609 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandLineBindableImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandLineBindableImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandLineBindable
*/ -public class CommandLineBindableImpl extends SavableImpl implements CommandLineBindable { +public class CommandLineBindableImpl extends SaveableImpl implements CommandLineBindable { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandLineBinding.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandLineBinding.java index ea1fdb4..53f8461 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandLineBinding.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandLineBinding.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#CommandLineBinding
This interface is implemented by {@link CommandLineBindingImpl}
@@ -55,7 +55,7 @@ - **null**: Add nothing.
*/ -public interface CommandLineBinding extends InputBinding, Savable { +public interface CommandLineBinding extends InputBinding, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#InputBinding/loadContents
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandLineBindingImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandLineBindingImpl.java index 10a57bc..a77dcc2 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandLineBindingImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandLineBindingImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -59,7 +59,7 @@ - **null**: Add nothing.
*/ -public class CommandLineBindingImpl extends SavableImpl implements CommandLineBinding { +public class CommandLineBindingImpl extends SaveableImpl implements CommandLineBinding { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandLineTool.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandLineTool.java index 02393ef..ce81d03 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandLineTool.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandLineTool.java @@ -14,18 +14,22 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#CommandLineTool
This interface is implemented by {@link CommandLineToolImpl}
This defines the schema of the CWL Command Line Tool Description document.
*/ -public interface CommandLineTool extends Process, Savable { +public interface CommandLineTool extends Process, Saveable { /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * Getter for property https://w3id.org/cwl/cwl#Process/id
*
- * The unique identifier for this object. *
+ * The unique identifier for this object. + * + * Only useful for `$graph` at `Process` level. Should not be exposed + * to users in graphical or terminal user interfaces. + * *
*/ java.util.Optional getId(); @@ -193,6 +197,10 @@ 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 diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandLineToolImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandLineToolImpl.java index c8d3693..531ca25 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandLineToolImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandLineToolImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -25,7 +25,7 @@ This defines the schema of the CWL Command Line Tool Description document.
*/ -public class CommandLineToolImpl extends SavableImpl implements CommandLineTool { +public class CommandLineToolImpl extends SaveableImpl implements CommandLineTool { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); @@ -33,9 +33,13 @@ public class CommandLineToolImpl extends SavableImpl implements CommandLineTool private java.util.Optional id; /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * Getter for property https://w3id.org/cwl/cwl#Process/id
*
- * The unique identifier for this object. *
+ * The unique identifier for this object. + * + * Only useful for `$graph` at `Process` level. Should not be exposed + * to users in graphical or terminal user interfaces. + * *
*/ public java.util.Optional getId() { @@ -273,6 +277,10 @@ 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 @@ -482,7 +490,7 @@ public CommandLineToolImpl( try { hints = LoaderInstances - .idmap_hints_optional_array_of_AnyInstance + .idmap_hints_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance .loadField(__doc.get("hints"), __baseUri, __loadingOptions); } catch (ValidationException e) { hints = null; // won't be used but prevents compiler from complaining. diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputArraySchema.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputArraySchema.java index 9ee96d7..4f6aee7 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputArraySchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputArraySchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputArraySchema
This interface is implemented by {@link CommandOutputArraySchemaImpl}
*/ -public interface CommandOutputArraySchema extends OutputArraySchema, Savable { +public interface CommandOutputArraySchema extends OutputArraySchema, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputArraySchemaImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputArraySchemaImpl.java index bb246cd..55b53e4 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputArraySchemaImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputArraySchemaImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputArraySchema
*/ -public class CommandOutputArraySchemaImpl extends SavableImpl implements CommandOutputArraySchema { +public class CommandOutputArraySchemaImpl extends SaveableImpl implements CommandOutputArraySchema { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputBinding.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputBinding.java index 5757b57..d8b70fe 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputBinding.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputBinding.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputBinding
This interface is implemented by {@link CommandOutputBindingImpl}
@@ -30,7 +30,7 @@ - secondaryFiles
*/ -public interface CommandOutputBinding extends LoadContents, Savable { +public interface CommandOutputBinding extends LoadContents, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputBindingImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputBindingImpl.java index e95d757..204bacf 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputBindingImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputBindingImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -34,7 +34,7 @@ - secondaryFiles
*/ -public class CommandOutputBindingImpl extends SavableImpl implements CommandOutputBinding { +public class CommandOutputBindingImpl extends SaveableImpl implements CommandOutputBinding { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputEnumSchema.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputEnumSchema.java index a89f5c1..519bb8e 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputEnumSchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputEnumSchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputEnumSchema
This interface is implemented by {@link CommandOutputEnumSchemaImpl}
*/ -public interface CommandOutputEnumSchema extends OutputEnumSchema, Savable { +public interface CommandOutputEnumSchema extends OutputEnumSchema, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputEnumSchemaImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputEnumSchemaImpl.java index cd25b17..11e1a73 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputEnumSchemaImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputEnumSchemaImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputEnumSchema
*/ -public class CommandOutputEnumSchemaImpl extends SavableImpl implements CommandOutputEnumSchema { +public class CommandOutputEnumSchemaImpl extends SaveableImpl implements CommandOutputEnumSchema { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputParameter.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputParameter.java index dc2ec90..ec07146 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputParameter.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputParameter.java @@ -14,13 +14,13 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputParameter
This interface is implemented by {@link CommandOutputParameterImpl}
An output parameter for a CommandLineTool.
*/ -public interface CommandOutputParameter extends OutputParameter, Savable { +public interface CommandOutputParameter extends OutputParameter, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Identified/id
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputParameterImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputParameterImpl.java index 6ed0c3e..c5c9b42 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputParameterImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputParameterImpl.java @@ -17,14 +17,14 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputParameter
An output parameter for a CommandLineTool.
*/ -public class CommandOutputParameterImpl extends SavableImpl implements CommandOutputParameter { +public class CommandOutputParameterImpl extends SaveableImpl implements CommandOutputParameter { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputRecordField.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputRecordField.java index f1ce721..b16606a 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputRecordField.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputRecordField.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputRecordField
This interface is implemented by {@link CommandOutputRecordFieldImpl}
*/ -public interface CommandOutputRecordField extends OutputRecordField, Savable { +public interface CommandOutputRecordField extends OutputRecordField, Saveable { /** * Getter for property https://w3id.org/cwl/salad#RecordField/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputRecordFieldImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputRecordFieldImpl.java index 0400180..1bf6bc1 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputRecordFieldImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputRecordFieldImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordField
*/ -public class CommandOutputRecordFieldImpl extends SavableImpl implements CommandOutputRecordField { +public class CommandOutputRecordFieldImpl extends SaveableImpl implements CommandOutputRecordField { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputRecordSchema.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputRecordSchema.java index 8ed384d..d495451 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputRecordSchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputRecordSchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputRecordSchema
This interface is implemented by {@link CommandOutputRecordSchemaImpl}
*/ -public interface CommandOutputRecordSchema extends OutputRecordSchema, Savable { +public interface CommandOutputRecordSchema extends OutputRecordSchema, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputRecordSchemaImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputRecordSchemaImpl.java index 5a6437d..d616e3b 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputRecordSchemaImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputRecordSchemaImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordSchema
*/ -public class CommandOutputRecordSchemaImpl extends SavableImpl implements CommandOutputRecordSchema { +public class CommandOutputRecordSchemaImpl extends SaveableImpl implements CommandOutputRecordSchema { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/Directory.java b/src/main/java/org/w3id/cwl/cwl1_2/Directory.java index 3f033c8..34f3a5b 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/Directory.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/Directory.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#Directory
This interface is implemented by {@link DirectoryImpl}
@@ -50,7 +50,7 @@ must be a filesystem path available on the same host as the CWL runner (for the same Directory. When executing a CommandLineTool, Directories must be recursively staged - first and have local values of `path` assigend. + first and have local values of `path` assigned. Directory objects in CommandLineTool output must provide either a `location` URI or a `path` property in the context of the tool execution @@ -63,7 +63,7 @@ Name conflicts (the same `basename` appearing multiple times in `listing` or in any entry in `secondaryFiles` in the listing) is a fatal error.
*/ -public interface Directory extends Savable { +public interface Directory extends Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Directory/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/DirectoryImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/DirectoryImpl.java index 813377a..d905c36 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/DirectoryImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/DirectoryImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -54,7 +54,7 @@ must be a filesystem path available on the same host as the CWL runner (for the same Directory. When executing a CommandLineTool, Directories must be recursively staged - first and have local values of `path` assigend. + first and have local values of `path` assigned. Directory objects in CommandLineTool output must provide either a `location` URI or a `path` property in the context of the tool execution @@ -67,7 +67,7 @@ Name conflicts (the same `basename` appearing multiple times in `listing` or in any entry in `secondaryFiles` in the listing) is a fatal error.
*/ -public class DirectoryImpl extends SavableImpl implements Directory { +public class DirectoryImpl extends SaveableImpl implements Directory { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/Dirent.java b/src/main/java/org/w3id/cwl/cwl1_2/Dirent.java index a06d7a9..4d991a8 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/Dirent.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/Dirent.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#Dirent
This interface is implemented by {@link DirentImpl}
@@ -28,7 +28,7 @@ arbitrary locations, see discussion for `entryname`.
*/ -public interface Dirent extends Savable { +public interface Dirent extends Saveable { /** * Getter for property https://w3id.org/cwl/cwl#entryname
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/DirentImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/DirentImpl.java index 4fc8aa1..cb34c30 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/DirentImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/DirentImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -32,7 +32,7 @@ arbitrary locations, see discussion for `entryname`.
*/ -public class DirentImpl extends SavableImpl implements Dirent { +public class DirentImpl extends SaveableImpl implements Dirent { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/DockerRequirement.java b/src/main/java/org/w3id/cwl/cwl1_2/DockerRequirement.java index 8b1cc60..d18aad0 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/DockerRequirement.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/DockerRequirement.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#DockerRequirement
This interface is implemented by {@link DockerRequirementImpl}
@@ -71,7 +71,7 @@ concerns of the implicit hidden execution point (For further discussion, see environment as defined by Docker.
*/ -public interface DockerRequirement extends ProcessRequirement, Savable { +public interface DockerRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/DockerRequirementImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/DockerRequirementImpl.java index d8922fc..0fabdbe 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/DockerRequirementImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/DockerRequirementImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -75,7 +75,7 @@ concerns of the implicit hidden execution point (For further discussion, see environment as defined by Docker.
*/ -public class DockerRequirementImpl extends SavableImpl implements DockerRequirement { +public class DockerRequirementImpl extends SaveableImpl implements DockerRequirement { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/Documented.java b/src/main/java/org/w3id/cwl/cwl1_2/Documented.java index 6b58911..62460ab 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/Documented.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/Documented.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/salad#Documented
*/ -public interface Documented extends Savable { +public interface Documented extends Saveable { /** * Getter for property https://w3id.org/cwl/salad#Documented/doc
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/EnumSchema.java b/src/main/java/org/w3id/cwl/cwl1_2/EnumSchema.java index bc0a28d..d13db5a 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/EnumSchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/EnumSchema.java @@ -14,14 +14,14 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/salad#EnumSchema
This interface is implemented by {@link EnumSchemaImpl}
Define an enumerated type.
*/ -public interface EnumSchema extends Savable { +public interface EnumSchema extends Saveable { /** * Getter for property https://w3id.org/cwl/salad#symbols
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/EnumSchemaImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/EnumSchemaImpl.java index c58edd5..f822cf2 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/EnumSchemaImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/EnumSchemaImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -25,7 +25,7 @@ Define an enumerated type.
*/ -public class EnumSchemaImpl extends SavableImpl implements EnumSchema { +public class EnumSchemaImpl extends SaveableImpl implements EnumSchema { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/EnvVarRequirement.java b/src/main/java/org/w3id/cwl/cwl1_2/EnvVarRequirement.java index f4b3533..197df67 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/EnvVarRequirement.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/EnvVarRequirement.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#EnvVarRequirement
This interface is implemented by {@link EnvVarRequirementImpl}
@@ -22,7 +22,7 @@ execution environment of the tool. See `EnvironmentDef` for details.
*/ -public interface EnvVarRequirement extends ProcessRequirement, Savable { +public interface EnvVarRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#EnvVarRequirement/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/EnvVarRequirementImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/EnvVarRequirementImpl.java index 353c254..ff36568 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/EnvVarRequirementImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/EnvVarRequirementImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -26,7 +26,7 @@ execution environment of the tool. See `EnvironmentDef` for details.
*/ -public class EnvVarRequirementImpl extends SavableImpl implements EnvVarRequirement { +public class EnvVarRequirementImpl extends SaveableImpl implements EnvVarRequirement { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/EnvironmentDef.java b/src/main/java/org/w3id/cwl/cwl1_2/EnvironmentDef.java index 7e5f9c9..d3e92f0 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/EnvironmentDef.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/EnvironmentDef.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#EnvironmentDef
This interface is implemented by {@link EnvironmentDefImpl}
@@ -23,7 +23,7 @@ result of executing an expression, such as getting a parameter from input.
*/ -public interface EnvironmentDef extends Savable { +public interface EnvironmentDef extends Saveable { /** * Getter for property https://w3id.org/cwl/cwl#EnvironmentDef/envName
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/EnvironmentDefImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/EnvironmentDefImpl.java index ccf1e99..2e1d835 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/EnvironmentDefImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/EnvironmentDefImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -27,7 +27,7 @@ result of executing an expression, such as getting a parameter from input.
*/ -public class EnvironmentDefImpl extends SavableImpl implements EnvironmentDef { +public class EnvironmentDefImpl extends SaveableImpl implements EnvironmentDef { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/ExpressionTool.java b/src/main/java/org/w3id/cwl/cwl1_2/ExpressionTool.java index 503f8cb..d7a9b7b 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/ExpressionTool.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/ExpressionTool.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#ExpressionTool
This interface is implemented by {@link ExpressionToolImpl}
@@ -27,11 +27,15 @@ or allowed.
*/ -public interface ExpressionTool extends Process, Savable { +public interface ExpressionTool extends Process, Saveable { /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * Getter for property https://w3id.org/cwl/cwl#Process/id
*
- * The unique identifier for this object. *
+ * The unique identifier for this object. + * + * Only useful for `$graph` at `Process` level. Should not be exposed + * to users in graphical or terminal user interfaces. + * *
*/ java.util.Optional getId(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/ExpressionToolImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/ExpressionToolImpl.java index d1a2103..89e5675 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/ExpressionToolImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/ExpressionToolImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -31,7 +31,7 @@ or allowed.
*/ -public class ExpressionToolImpl extends SavableImpl implements ExpressionTool { +public class ExpressionToolImpl extends SaveableImpl implements ExpressionTool { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); @@ -39,9 +39,13 @@ public class ExpressionToolImpl extends SavableImpl implements ExpressionTool { private java.util.Optional id; /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * Getter for property https://w3id.org/cwl/cwl#Process/id
*
- * The unique identifier for this object. *
+ * The unique identifier for this object. + * + * Only useful for `$graph` at `Process` level. Should not be exposed + * to users in graphical or terminal user interfaces. + * *
*/ public java.util.Optional getId() { @@ -359,7 +363,7 @@ public ExpressionToolImpl( try { hints = LoaderInstances - .idmap_hints_optional_array_of_AnyInstance + .idmap_hints_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance .loadField(__doc.get("hints"), __baseUri, __loadingOptions); } catch (ValidationException e) { hints = null; // won't be used but prevents compiler from complaining. diff --git a/src/main/java/org/w3id/cwl/cwl1_2/ExpressionToolOutputParameter.java b/src/main/java/org/w3id/cwl/cwl1_2/ExpressionToolOutputParameter.java index 6978ecf..94c9717 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/ExpressionToolOutputParameter.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/ExpressionToolOutputParameter.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#ExpressionToolOutputParameter
This interface is implemented by {@link ExpressionToolOutputParameterImpl}
*/ -public interface ExpressionToolOutputParameter extends OutputParameter, Savable { +public interface ExpressionToolOutputParameter extends OutputParameter, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Identified/id
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/ExpressionToolOutputParameterImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/ExpressionToolOutputParameterImpl.java index 0106464..7c7ddce 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/ExpressionToolOutputParameterImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/ExpressionToolOutputParameterImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#ExpressionToolOutputParameter
*/ -public class ExpressionToolOutputParameterImpl extends SavableImpl implements ExpressionToolOutputParameter { +public class ExpressionToolOutputParameterImpl extends SaveableImpl implements ExpressionToolOutputParameter { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/FieldBase.java b/src/main/java/org/w3id/cwl/cwl1_2/FieldBase.java index eeb27ff..3482912 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/FieldBase.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/FieldBase.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#FieldBase
*/ -public interface FieldBase extends Labeled, Savable { +public interface FieldBase extends Labeled, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Labeled/label
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/File.java b/src/main/java/org/w3id/cwl/cwl1_2/File.java index bb75220..b31e423 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/File.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/File.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#File
This interface is implemented by {@link FileImpl}
@@ -86,7 +86,7 @@ property in the context of the tool execution runtime (local to the compute the same value for `location`.
*/ -public interface File extends Savable { +public interface File extends Saveable { /** * Getter for property https://w3id.org/cwl/cwl#File/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/FileImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/FileImpl.java index 3da9b69..f011977 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/FileImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/FileImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -90,7 +90,7 @@ property in the context of the tool execution runtime (local to the compute the same value for `location`.
*/ -public class FileImpl extends SavableImpl implements File { +public class FileImpl extends SaveableImpl implements File { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/IOSchema.java b/src/main/java/org/w3id/cwl/cwl1_2/IOSchema.java index ac95cb1..c6324d8 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/IOSchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/IOSchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#IOSchema
*/ -public interface IOSchema extends Labeled, Documented, Savable { +public interface IOSchema extends Labeled, Documented, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Labeled/label
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/Identified.java b/src/main/java/org/w3id/cwl/cwl1_2/Identified.java index 2b78989..1f28ce9 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/Identified.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/Identified.java @@ -14,10 +14,10 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#Identified
*/ -public interface Identified extends Savable { +public interface Identified extends Saveable { } diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InitialWorkDirRequirement.java b/src/main/java/org/w3id/cwl/cwl1_2/InitialWorkDirRequirement.java index b129d9f..8d23446 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InitialWorkDirRequirement.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InitialWorkDirRequirement.java @@ -14,14 +14,14 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#InitialWorkDirRequirement
This interface is implemented by {@link InitialWorkDirRequirementImpl}
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.
+ 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.
*/ -public interface InitialWorkDirRequirement extends ProcessRequirement, Savable { +public interface InitialWorkDirRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#InitialWorkDirRequirement/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InitialWorkDirRequirementImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/InitialWorkDirRequirementImpl.java index 079b765..4c137c9 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InitialWorkDirRequirementImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InitialWorkDirRequirementImpl.java @@ -17,15 +17,15 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#InitialWorkDirRequirement
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.
+ 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.
*/ -public class InitialWorkDirRequirementImpl extends SavableImpl implements InitialWorkDirRequirement { +public class InitialWorkDirRequirementImpl extends SaveableImpl implements InitialWorkDirRequirement { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InlineJavascriptRequirement.java b/src/main/java/org/w3id/cwl/cwl1_2/InlineJavascriptRequirement.java index 8f95e99..a33fbd4 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InlineJavascriptRequirement.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InlineJavascriptRequirement.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#InlineJavascriptRequirement
This interface is implemented by {@link InlineJavascriptRequirementImpl}
@@ -23,7 +23,7 @@ interpolatation.
*/ -public interface InlineJavascriptRequirement extends ProcessRequirement, Savable { +public interface InlineJavascriptRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#InlineJavascriptRequirement/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InlineJavascriptRequirementImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/InlineJavascriptRequirementImpl.java index 3325e0b..7076901 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InlineJavascriptRequirementImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InlineJavascriptRequirementImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -27,7 +27,7 @@ interpolatation.
*/ -public class InlineJavascriptRequirementImpl extends SavableImpl implements InlineJavascriptRequirement { +public class InlineJavascriptRequirementImpl extends SaveableImpl implements InlineJavascriptRequirement { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InplaceUpdateRequirement.java b/src/main/java/org/w3id/cwl/cwl1_2/InplaceUpdateRequirement.java index ee5824e..b20f2e8 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InplaceUpdateRequirement.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InplaceUpdateRequirement.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#InplaceUpdateRequirement
This interface is implemented by {@link InplaceUpdateRequirementImpl}
@@ -50,7 +50,7 @@ is writable by one workflow step file is accessed (for reading or not be enabled.
*/ -public interface InplaceUpdateRequirement extends ProcessRequirement, Savable { +public interface InplaceUpdateRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#InplaceUpdateRequirement/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InplaceUpdateRequirementImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/InplaceUpdateRequirementImpl.java index cbab692..2f82d01 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InplaceUpdateRequirementImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InplaceUpdateRequirementImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -54,7 +54,7 @@ is writable by one workflow step file is accessed (for reading or not be enabled.
*/ -public class InplaceUpdateRequirementImpl extends SavableImpl implements InplaceUpdateRequirement { +public class InplaceUpdateRequirementImpl extends SaveableImpl implements InplaceUpdateRequirement { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InputArraySchema.java b/src/main/java/org/w3id/cwl/cwl1_2/InputArraySchema.java index ac055e5..4fa0a1b 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InputArraySchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InputArraySchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#InputArraySchema
This interface is implemented by {@link InputArraySchemaImpl}
*/ -public interface InputArraySchema extends ArraySchema, InputSchema, Savable { +public interface InputArraySchema extends ArraySchema, InputSchema, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InputArraySchemaImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/InputArraySchemaImpl.java index 9b28cff..f9106c0 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InputArraySchemaImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InputArraySchemaImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#InputArraySchema
*/ -public class InputArraySchemaImpl extends SavableImpl implements InputArraySchema { +public class InputArraySchemaImpl extends SaveableImpl implements InputArraySchema { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InputBinding.java b/src/main/java/org/w3id/cwl/cwl1_2/InputBinding.java index c5a56fb..7124d07 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InputBinding.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InputBinding.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#InputBinding
This interface is implemented by {@link InputBindingImpl}
*/ -public interface InputBinding extends Savable { +public interface InputBinding extends Saveable { /** * Getter for property https://w3id.org/cwl/cwl#InputBinding/loadContents
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InputBindingImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/InputBindingImpl.java index 89ee1d7..132e8f3 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InputBindingImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InputBindingImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#InputBinding
*/ -public class InputBindingImpl extends SavableImpl implements InputBinding { +public class InputBindingImpl extends SaveableImpl implements InputBinding { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InputEnumSchema.java b/src/main/java/org/w3id/cwl/cwl1_2/InputEnumSchema.java index 8bfa24a..7a12a90 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InputEnumSchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InputEnumSchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#InputEnumSchema
This interface is implemented by {@link InputEnumSchemaImpl}
*/ -public interface InputEnumSchema extends EnumSchema, InputSchema, Savable { +public interface InputEnumSchema extends EnumSchema, InputSchema, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InputEnumSchemaImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/InputEnumSchemaImpl.java index 98e4c38..14f157a 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InputEnumSchemaImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InputEnumSchemaImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#InputEnumSchema
*/ -public class InputEnumSchemaImpl extends SavableImpl implements InputEnumSchema { +public class InputEnumSchemaImpl extends SaveableImpl implements InputEnumSchema { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InputFormat.java b/src/main/java/org/w3id/cwl/cwl1_2/InputFormat.java index 7bdf165..350f66b 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InputFormat.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InputFormat.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#InputFormat
*/ -public interface InputFormat extends Savable { +public interface InputFormat extends Saveable { /** * Getter for property https://w3id.org/cwl/cwl#format
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InputParameter.java b/src/main/java/org/w3id/cwl/cwl1_2/InputParameter.java index d9a9928..3433233 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InputParameter.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InputParameter.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#InputParameter
*/ -public interface InputParameter extends Parameter, InputFormat, LoadContents, Savable { +public interface InputParameter extends Parameter, InputFormat, LoadContents, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Labeled/label
*
@@ -150,5 +150,5 @@ public interface InputParameter extends Parameter, InputFormat, LoadContents, Sa * *
*/ - java.util.Optional getDefault(); + Object getDefault(); } diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InputRecordField.java b/src/main/java/org/w3id/cwl/cwl1_2/InputRecordField.java index d26075f..c988108 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InputRecordField.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InputRecordField.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#InputRecordField
This interface is implemented by {@link InputRecordFieldImpl}
*/ -public interface InputRecordField extends RecordField, FieldBase, InputFormat, LoadContents, Savable { +public interface InputRecordField extends RecordField, FieldBase, InputFormat, LoadContents, Saveable { /** * Getter for property https://w3id.org/cwl/salad#RecordField/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InputRecordFieldImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/InputRecordFieldImpl.java index 64e2423..2ce418c 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InputRecordFieldImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InputRecordFieldImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordField
*/ -public class InputRecordFieldImpl extends SavableImpl implements InputRecordField { +public class InputRecordFieldImpl extends SaveableImpl implements InputRecordField { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InputRecordSchema.java b/src/main/java/org/w3id/cwl/cwl1_2/InputRecordSchema.java index d09c771..0b87d9b 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InputRecordSchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InputRecordSchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#InputRecordSchema
This interface is implemented by {@link InputRecordSchemaImpl}
*/ -public interface InputRecordSchema extends RecordSchema, InputSchema, Savable { +public interface InputRecordSchema extends RecordSchema, InputSchema, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InputRecordSchemaImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/InputRecordSchemaImpl.java index 443ab43..ecde015 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InputRecordSchemaImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InputRecordSchemaImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordSchema
*/ -public class InputRecordSchemaImpl extends SavableImpl implements InputRecordSchema { +public class InputRecordSchemaImpl extends SaveableImpl implements InputRecordSchema { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/InputSchema.java b/src/main/java/org/w3id/cwl/cwl1_2/InputSchema.java index d496e0b..f06ff5b 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/InputSchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/InputSchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#InputSchema
*/ -public interface InputSchema extends IOSchema, Savable { +public interface InputSchema extends IOSchema, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Labeled/label
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/Labeled.java b/src/main/java/org/w3id/cwl/cwl1_2/Labeled.java index c985180..c0dd625 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/Labeled.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/Labeled.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#Labeled
*/ -public interface Labeled extends Savable { +public interface Labeled extends Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Labeled/label
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/LoadContents.java b/src/main/java/org/w3id/cwl/cwl1_2/LoadContents.java index 68f6847..cb97973 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/LoadContents.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/LoadContents.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#LoadContents
*/ -public interface LoadContents extends Savable { +public interface LoadContents extends Saveable { /** * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/LoadListingRequirement.java b/src/main/java/org/w3id/cwl/cwl1_2/LoadListingRequirement.java index c870a76..2a73589 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/LoadListingRequirement.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/LoadListingRequirement.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#LoadListingRequirement
This interface is implemented by {@link LoadListingRequirementImpl}
@@ -22,7 +22,7 @@ a Directory object for use by expressions.
*/ -public interface LoadListingRequirement extends ProcessRequirement, Savable { +public interface LoadListingRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#LoadListingRequirement/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/LoadListingRequirementImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/LoadListingRequirementImpl.java index 296b4ec..18bddc8 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/LoadListingRequirementImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/LoadListingRequirementImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -26,7 +26,7 @@ a Directory object for use by expressions.
*/ -public class LoadListingRequirementImpl extends SavableImpl implements LoadListingRequirement { +public class LoadListingRequirementImpl extends SaveableImpl implements LoadListingRequirement { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/MultipleInputFeatureRequirement.java b/src/main/java/org/w3id/cwl/cwl1_2/MultipleInputFeatureRequirement.java index 4ba73ae..28d19fe 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/MultipleInputFeatureRequirement.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/MultipleInputFeatureRequirement.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement
This interface is implemented by {@link MultipleInputFeatureRequirementImpl}
@@ -22,7 +22,7 @@ listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput).
*/ -public interface MultipleInputFeatureRequirement extends ProcessRequirement, Savable { +public interface MultipleInputFeatureRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/MultipleInputFeatureRequirementImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/MultipleInputFeatureRequirementImpl.java index 1b362bf..0700dbd 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/MultipleInputFeatureRequirementImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/MultipleInputFeatureRequirementImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -26,7 +26,7 @@ listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput).
*/ -public class MultipleInputFeatureRequirementImpl extends SavableImpl implements MultipleInputFeatureRequirement { +public class MultipleInputFeatureRequirementImpl extends SaveableImpl implements MultipleInputFeatureRequirement { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/NetworkAccess.java b/src/main/java/org/w3id/cwl/cwl1_2/NetworkAccess.java index f7f5cce..bade28f 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/NetworkAccess.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/NetworkAccess.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#NetworkAccess
This interface is implemented by {@link NetworkAccessImpl}
@@ -35,7 +35,7 @@ assume network access, except for localhost (the loopback device). address or the ability to accept inbound connections.
*/ -public interface NetworkAccess extends ProcessRequirement, Savable { +public interface NetworkAccess extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#NetworkAccess/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/NetworkAccessImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/NetworkAccessImpl.java index 4a59d3c..a8df9ed 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/NetworkAccessImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/NetworkAccessImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -39,7 +39,7 @@ assume network access, except for localhost (the loopback device). address or the ability to accept inbound connections.
*/ -public class NetworkAccessImpl extends SavableImpl implements NetworkAccess { +public class NetworkAccessImpl extends SaveableImpl implements NetworkAccess { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/Operation.java b/src/main/java/org/w3id/cwl/cwl1_2/Operation.java index 4a17dd4..296c1c7 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/Operation.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/Operation.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#Operation
This interface is implemented by {@link OperationImpl}
@@ -27,11 +27,15 @@ an Operation to a concrete process (such as Workflow, CommandLineTool, or ExpressionTool) with a compatible signature.
*/ -public interface Operation extends Process, Savable { +public interface Operation extends Process, Saveable { /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * Getter for property https://w3id.org/cwl/cwl#Process/id
*
- * The unique identifier for this object. *
+ * The unique identifier for this object. + * + * Only useful for `$graph` at `Process` level. Should not be exposed + * to users in graphical or terminal user interfaces. + * *
*/ java.util.Optional getId(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/OperationImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/OperationImpl.java index 2f89a9e..6bd8f7e 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/OperationImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/OperationImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -31,7 +31,7 @@ an Operation to a concrete process (such as Workflow, CommandLineTool, or ExpressionTool) with a compatible signature.
*/ -public class OperationImpl extends SavableImpl implements Operation { +public class OperationImpl extends SaveableImpl implements Operation { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); @@ -39,9 +39,13 @@ public class OperationImpl extends SavableImpl implements Operation { private java.util.Optional id; /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * Getter for property https://w3id.org/cwl/cwl#Process/id
*
- * The unique identifier for this object. *
+ * The unique identifier for this object. + * + * Only useful for `$graph` at `Process` level. Should not be exposed + * to users in graphical or terminal user interfaces. + * *
*/ public java.util.Optional getId() { @@ -344,7 +348,7 @@ public OperationImpl( try { hints = LoaderInstances - .idmap_hints_optional_array_of_AnyInstance + .idmap_hints_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance .loadField(__doc.get("hints"), __baseUri, __loadingOptions); } catch (ValidationException e) { hints = null; // won't be used but prevents compiler from complaining. diff --git a/src/main/java/org/w3id/cwl/cwl1_2/OperationInputParameter.java b/src/main/java/org/w3id/cwl/cwl1_2/OperationInputParameter.java index 4029369..49c0cc6 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/OperationInputParameter.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/OperationInputParameter.java @@ -14,14 +14,14 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#OperationInputParameter
This interface is implemented by {@link OperationInputParameterImpl}
Describe an input parameter of an operation.
*/ -public interface OperationInputParameter extends InputParameter, Savable { +public interface OperationInputParameter extends InputParameter, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Identified/id
*
@@ -159,7 +159,7 @@ public interface OperationInputParameter extends InputParameter, Savable { * *
*/ - java.util.Optional getDefault(); + Object getDefault(); /** * Getter for property https://w3id.org/cwl/salad#type
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/OperationInputParameterImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/OperationInputParameterImpl.java index fffe6a7..907e362 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/OperationInputParameterImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/OperationInputParameterImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -25,7 +25,7 @@ Describe an input parameter of an operation.
*/ -public class OperationInputParameterImpl extends SavableImpl implements OperationInputParameter { +public class OperationInputParameterImpl extends SaveableImpl implements OperationInputParameter { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); @@ -197,7 +197,7 @@ public java.util.Optional getLoadListing() { return this.loadListing; } - private java.util.Optional default_; + private Object default_; /** * Getter for property https://w3id.org/cwl/salad#default
@@ -209,7 +209,7 @@ public java.util.Optional getLoadListing() { * * */ - public java.util.Optional getDefault() { + public Object getDefault() { return this.default_; } @@ -406,13 +406,13 @@ public OperationInputParameterImpl( } else { loadListing = null; } - java.util.Optional default_; + Object default_; if (__doc.containsKey("default")) { try { default_ = LoaderInstances - .optional_AnyInstance + .union_of_NullInstance_or_File_or_Directory_or_AnyInstance .loadField(__doc.get("default"), __baseUri, __loadingOptions); } catch (ValidationException e) { default_ = null; // won't be used but prevents compiler from complaining. @@ -445,7 +445,7 @@ public OperationInputParameterImpl( this.format = (Object) format; this.loadContents = (java.util.Optional) loadContents; this.loadListing = (java.util.Optional) loadListing; - this.default_ = (java.util.Optional) default_; + this.default_ = (Object) default_; this.type = (Object) type; } } diff --git a/src/main/java/org/w3id/cwl/cwl1_2/OperationOutputParameter.java b/src/main/java/org/w3id/cwl/cwl1_2/OperationOutputParameter.java index aedf502..2939f1d 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/OperationOutputParameter.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/OperationOutputParameter.java @@ -14,14 +14,14 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#OperationOutputParameter
This interface is implemented by {@link OperationOutputParameterImpl}
Describe an output parameter of an operation.
*/ -public interface OperationOutputParameter extends OutputParameter, Savable { +public interface OperationOutputParameter extends OutputParameter, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Identified/id
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/OperationOutputParameterImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/OperationOutputParameterImpl.java index 4aaf237..cd8e795 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/OperationOutputParameterImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/OperationOutputParameterImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -25,7 +25,7 @@ Describe an output parameter of an operation.
*/ -public class OperationOutputParameterImpl extends SavableImpl implements OperationOutputParameter { +public class OperationOutputParameterImpl extends SaveableImpl implements OperationOutputParameter { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/OutputArraySchema.java b/src/main/java/org/w3id/cwl/cwl1_2/OutputArraySchema.java index be6745c..3424bec 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/OutputArraySchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/OutputArraySchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#OutputArraySchema
This interface is implemented by {@link OutputArraySchemaImpl}
*/ -public interface OutputArraySchema extends ArraySchema, OutputSchema, Savable { +public interface OutputArraySchema extends ArraySchema, OutputSchema, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/OutputArraySchemaImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/OutputArraySchemaImpl.java index cfcba47..b047e47 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/OutputArraySchemaImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/OutputArraySchemaImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputArraySchema
*/ -public class OutputArraySchemaImpl extends SavableImpl implements OutputArraySchema { +public class OutputArraySchemaImpl extends SaveableImpl implements OutputArraySchema { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/OutputEnumSchema.java b/src/main/java/org/w3id/cwl/cwl1_2/OutputEnumSchema.java index b12106a..72a0daa 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/OutputEnumSchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/OutputEnumSchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#OutputEnumSchema
This interface is implemented by {@link OutputEnumSchemaImpl}
*/ -public interface OutputEnumSchema extends EnumSchema, OutputSchema, Savable { +public interface OutputEnumSchema extends EnumSchema, OutputSchema, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/OutputEnumSchemaImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/OutputEnumSchemaImpl.java index aee0b4d..de919af 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/OutputEnumSchemaImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/OutputEnumSchemaImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputEnumSchema
*/ -public class OutputEnumSchemaImpl extends SavableImpl implements OutputEnumSchema { +public class OutputEnumSchemaImpl extends SaveableImpl implements OutputEnumSchema { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/OutputFormat.java b/src/main/java/org/w3id/cwl/cwl1_2/OutputFormat.java index 36e6d4e..327ba84 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/OutputFormat.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/OutputFormat.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#OutputFormat
*/ -public interface OutputFormat extends Savable { +public interface OutputFormat extends Saveable { /** * Getter for property https://w3id.org/cwl/cwl#format
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/OutputParameter.java b/src/main/java/org/w3id/cwl/cwl1_2/OutputParameter.java index 02a6537..269ca01 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/OutputParameter.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/OutputParameter.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#OutputParameter
*/ -public interface OutputParameter extends Parameter, OutputFormat, Savable { +public interface OutputParameter extends Parameter, OutputFormat, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Labeled/label
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/OutputRecordField.java b/src/main/java/org/w3id/cwl/cwl1_2/OutputRecordField.java index 6b3acb2..32f825d 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/OutputRecordField.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/OutputRecordField.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#OutputRecordField
This interface is implemented by {@link OutputRecordFieldImpl}
*/ -public interface OutputRecordField extends RecordField, FieldBase, OutputFormat, Savable { +public interface OutputRecordField extends RecordField, FieldBase, OutputFormat, Saveable { /** * Getter for property https://w3id.org/cwl/salad#RecordField/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/OutputRecordFieldImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/OutputRecordFieldImpl.java index 7d9a9e4..1e3bcb0 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/OutputRecordFieldImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/OutputRecordFieldImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordField
*/ -public class OutputRecordFieldImpl extends SavableImpl implements OutputRecordField { +public class OutputRecordFieldImpl extends SaveableImpl implements OutputRecordField { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/OutputRecordSchema.java b/src/main/java/org/w3id/cwl/cwl1_2/OutputRecordSchema.java index 5fbb36e..30af418 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/OutputRecordSchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/OutputRecordSchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#OutputRecordSchema
This interface is implemented by {@link OutputRecordSchemaImpl}
*/ -public interface OutputRecordSchema extends RecordSchema, OutputSchema, Savable { +public interface OutputRecordSchema extends RecordSchema, OutputSchema, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/OutputRecordSchemaImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/OutputRecordSchemaImpl.java index 828a7f3..8aa7496 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/OutputRecordSchemaImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/OutputRecordSchemaImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordSchema
*/ -public class OutputRecordSchemaImpl extends SavableImpl implements OutputRecordSchema { +public class OutputRecordSchemaImpl extends SaveableImpl implements OutputRecordSchema { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/OutputSchema.java b/src/main/java/org/w3id/cwl/cwl1_2/OutputSchema.java index f09ce68..c13b40f 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/OutputSchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/OutputSchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#OutputSchema
*/ -public interface OutputSchema extends IOSchema, Savable { +public interface OutputSchema extends IOSchema, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Labeled/label
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/Parameter.java b/src/main/java/org/w3id/cwl/cwl1_2/Parameter.java index e24435a..b8f4fb4 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/Parameter.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/Parameter.java @@ -14,14 +14,14 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#Parameter
Define an input or output parameter to a process.
*/ -public interface Parameter extends FieldBase, Documented, Identified, Savable { +public interface Parameter extends FieldBase, Documented, Identified, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Labeled/label
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/Process.java b/src/main/java/org/w3id/cwl/cwl1_2/Process.java index dfe00c1..23b842a 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/Process.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/Process.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#Process
@@ -24,7 +24,7 @@ directly executed.
*/ -public interface Process extends Identified, Labeled, Documented, Savable { +public interface Process extends Identified, Labeled, Documented, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Labeled/label
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/ProcessRequirement.java b/src/main/java/org/w3id/cwl/cwl1_2/ProcessRequirement.java index 1398329..b49aa64 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/ProcessRequirement.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/ProcessRequirement.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#ProcessRequirement
@@ -26,5 +26,5 @@ the CWL core specification.
*/ -public interface ProcessRequirement extends Savable { +public interface ProcessRequirement extends Saveable { } diff --git a/src/main/java/org/w3id/cwl/cwl1_2/RecordField.java b/src/main/java/org/w3id/cwl/cwl1_2/RecordField.java index 5b26a47..4b23b65 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/RecordField.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/RecordField.java @@ -14,13 +14,13 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/salad#RecordField
This interface is implemented by {@link RecordFieldImpl}
A field of a record.
*/ -public interface RecordField extends Documented, Savable { +public interface RecordField extends Documented, Saveable { /** * Getter for property https://w3id.org/cwl/salad#RecordField/name
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/RecordFieldImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/RecordFieldImpl.java index c280795..9727cb2 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/RecordFieldImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/RecordFieldImpl.java @@ -17,14 +17,14 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/salad#RecordField
A field of a record.
*/ -public class RecordFieldImpl extends SavableImpl implements RecordField { +public class RecordFieldImpl extends SaveableImpl implements RecordField { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/RecordSchema.java b/src/main/java/org/w3id/cwl/cwl1_2/RecordSchema.java index 5481186..a50eb9a 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/RecordSchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/RecordSchema.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/salad#RecordSchema
This interface is implemented by {@link RecordSchemaImpl}
*/ -public interface RecordSchema extends Savable { +public interface RecordSchema extends Saveable { /** * Getter for property https://w3id.org/cwl/salad#fields
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/RecordSchemaImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/RecordSchemaImpl.java index 125bc0a..096fc04 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/RecordSchemaImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/RecordSchemaImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/salad#RecordSchema
*/ -public class RecordSchemaImpl extends SavableImpl implements RecordSchema { +public class RecordSchemaImpl extends SaveableImpl implements RecordSchema { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/ResourceRequirement.java b/src/main/java/org/w3id/cwl/cwl1_2/ResourceRequirement.java index a76a552..481ab17 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/ResourceRequirement.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/ResourceRequirement.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#ResourceRequirement
This interface is implemented by {@link ResourceRequirementImpl}
@@ -45,7 +45,7 @@ If neither "min" nor "max" is specified for a resource, use the default values below.
*/ -public interface ResourceRequirement extends ProcessRequirement, Savable { +public interface ResourceRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/ResourceRequirementImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/ResourceRequirementImpl.java index d601eb1..a0c3aa7 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/ResourceRequirementImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/ResourceRequirementImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -49,7 +49,7 @@ If neither "min" nor "max" is specified for a resource, use the default values below.
*/ -public class ResourceRequirementImpl extends SavableImpl implements ResourceRequirement { +public class ResourceRequirementImpl extends SaveableImpl implements ResourceRequirement { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/ScatterFeatureRequirement.java b/src/main/java/org/w3id/cwl/cwl1_2/ScatterFeatureRequirement.java index eae4ffb..d323e05 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/ScatterFeatureRequirement.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/ScatterFeatureRequirement.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#ScatterFeatureRequirement
This interface is implemented by {@link ScatterFeatureRequirementImpl}
@@ -22,7 +22,7 @@ `scatterMethod` fields of [WorkflowStep](#WorkflowStep).
*/ -public interface ScatterFeatureRequirement extends ProcessRequirement, Savable { +public interface ScatterFeatureRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#ScatterFeatureRequirement/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/ScatterFeatureRequirementImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/ScatterFeatureRequirementImpl.java index 8cba26e..fe107c8 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/ScatterFeatureRequirementImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/ScatterFeatureRequirementImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -26,7 +26,7 @@ `scatterMethod` fields of [WorkflowStep](#WorkflowStep).
*/ -public class ScatterFeatureRequirementImpl extends SavableImpl implements ScatterFeatureRequirement { +public class ScatterFeatureRequirementImpl extends SaveableImpl implements ScatterFeatureRequirement { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/SchemaDefRequirement.java b/src/main/java/org/w3id/cwl/cwl1_2/SchemaDefRequirement.java index e92ce47..43868fa 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/SchemaDefRequirement.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/SchemaDefRequirement.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#SchemaDefRequirement
This interface is implemented by {@link SchemaDefRequirementImpl}
@@ -32,7 +32,7 @@ - A file can contain a list of type definitions
*/ -public interface SchemaDefRequirement extends ProcessRequirement, Savable { +public interface SchemaDefRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#SchemaDefRequirement/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/SchemaDefRequirementImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/SchemaDefRequirementImpl.java index 80c98bb..9c35413 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/SchemaDefRequirementImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/SchemaDefRequirementImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -36,7 +36,7 @@ - A file can contain a list of type definitions
*/ -public class SchemaDefRequirementImpl extends SavableImpl implements SchemaDefRequirement { +public class SchemaDefRequirementImpl extends SaveableImpl implements SchemaDefRequirement { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/SecondaryFileSchema.java b/src/main/java/org/w3id/cwl/cwl1_2/SecondaryFileSchema.java index f7be6e8..c08ed21 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/SecondaryFileSchema.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/SecondaryFileSchema.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#SecondaryFileSchema
This interface is implemented by {@link SecondaryFileSchemaImpl}
@@ -33,7 +33,7 @@ in the Schema Salad specification.
*/ -public interface SecondaryFileSchema extends Savable { +public interface SecondaryFileSchema extends Saveable { /** * Getter for property https://w3id.org/cwl/cwl#SecondaryFileSchema/pattern
*
@@ -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 diff --git a/src/main/java/org/w3id/cwl/cwl1_2/SecondaryFileSchemaImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/SecondaryFileSchemaImpl.java index 20bc739..d37cc37 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/SecondaryFileSchemaImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/SecondaryFileSchemaImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -37,7 +37,7 @@ in the Schema Salad specification.
*/ -public class SecondaryFileSchemaImpl extends SavableImpl implements SecondaryFileSchema { +public class SecondaryFileSchemaImpl extends SaveableImpl implements SecondaryFileSchema { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); @@ -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 diff --git a/src/main/java/org/w3id/cwl/cwl1_2/ShellCommandRequirement.java b/src/main/java/org/w3id/cwl/cwl1_2/ShellCommandRequirement.java index 8a92f51..f0329ad 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/ShellCommandRequirement.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/ShellCommandRequirement.java @@ -14,20 +14,20 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#ShellCommandRequirement
This interface is implemented by {@link ShellCommandRequirementImpl}
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 the use of shell metacharacters such as `|` for pipes.
*/ -public interface ShellCommandRequirement extends ProcessRequirement, Savable { +public interface ShellCommandRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#ShellCommandRequirement/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/ShellCommandRequirementImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/ShellCommandRequirementImpl.java index f1f6c08..3bab156 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/ShellCommandRequirementImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/ShellCommandRequirementImpl.java @@ -17,21 +17,21 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#ShellCommandRequirement
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 the use of shell metacharacters such as `|` for pipes.
*/ -public class ShellCommandRequirementImpl extends SavableImpl implements ShellCommandRequirement { +public class ShellCommandRequirementImpl extends SaveableImpl implements ShellCommandRequirement { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/Sink.java b/src/main/java/org/w3id/cwl/cwl1_2/Sink.java index 3b2f8f5..26e1c05 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/Sink.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/Sink.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#Sink
*/ -public interface Sink extends Savable { +public interface Sink extends Saveable { /** * Getter for property https://w3id.org/cwl/cwl#source
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/SoftwarePackage.java b/src/main/java/org/w3id/cwl/cwl1_2/SoftwarePackage.java index 555c25d..e110a18 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/SoftwarePackage.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/SoftwarePackage.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#SoftwarePackage
This interface is implemented by {@link SoftwarePackageImpl}
*/ -public interface SoftwarePackage extends Savable { +public interface SoftwarePackage extends Saveable { /** * Getter for property https://w3id.org/cwl/cwl#SoftwarePackage/package
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/SoftwarePackageImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/SoftwarePackageImpl.java index ad578da..cbe87ac 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/SoftwarePackageImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/SoftwarePackageImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#SoftwarePackage
*/ -public class SoftwarePackageImpl extends SavableImpl implements SoftwarePackage { +public class SoftwarePackageImpl extends SaveableImpl implements SoftwarePackage { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/SoftwareRequirement.java b/src/main/java/org/w3id/cwl/cwl1_2/SoftwareRequirement.java index b1489ee..baac338 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/SoftwareRequirement.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/SoftwareRequirement.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#SoftwareRequirement
This interface is implemented by {@link SoftwareRequirementImpl}
@@ -22,7 +22,7 @@ the defined process.
*/ -public interface SoftwareRequirement extends ProcessRequirement, Savable { +public interface SoftwareRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#SoftwareRequirement/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/SoftwareRequirementImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/SoftwareRequirementImpl.java index 241e5f4..51e7ef4 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/SoftwareRequirementImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/SoftwareRequirementImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -26,7 +26,7 @@ the defined process.
*/ -public class SoftwareRequirementImpl extends SavableImpl implements SoftwareRequirement { +public class SoftwareRequirementImpl extends SaveableImpl implements SoftwareRequirement { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/StepInputExpressionRequirement.java b/src/main/java/org/w3id/cwl/cwl1_2/StepInputExpressionRequirement.java index 8330b84..f5ed04d 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/StepInputExpressionRequirement.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/StepInputExpressionRequirement.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#StepInputExpressionRequirement
This interface is implemented by {@link StepInputExpressionRequirementImpl}
@@ -22,7 +22,7 @@ of [WorkflowStepInput](#WorkflowStepInput).
*/ -public interface StepInputExpressionRequirement extends ProcessRequirement, Savable { +public interface StepInputExpressionRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#StepInputExpressionRequirement/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/StepInputExpressionRequirementImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/StepInputExpressionRequirementImpl.java index e706d7e..f755812 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/StepInputExpressionRequirementImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/StepInputExpressionRequirementImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -26,7 +26,7 @@ of [WorkflowStepInput](#WorkflowStepInput).
*/ -public class StepInputExpressionRequirementImpl extends SavableImpl implements StepInputExpressionRequirement { +public class StepInputExpressionRequirementImpl extends SaveableImpl implements StepInputExpressionRequirement { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/SubworkflowFeatureRequirement.java b/src/main/java/org/w3id/cwl/cwl1_2/SubworkflowFeatureRequirement.java index 4be94bc..9cdbb84 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/SubworkflowFeatureRequirement.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/SubworkflowFeatureRequirement.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement
This interface is implemented by {@link SubworkflowFeatureRequirementImpl}
@@ -22,7 +22,7 @@ the `run` field of [WorkflowStep](#WorkflowStep).
*/ -public interface SubworkflowFeatureRequirement extends ProcessRequirement, Savable { +public interface SubworkflowFeatureRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/SubworkflowFeatureRequirementImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/SubworkflowFeatureRequirementImpl.java index 8e9a490..2faeef7 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/SubworkflowFeatureRequirementImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/SubworkflowFeatureRequirementImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -26,7 +26,7 @@ the `run` field of [WorkflowStep](#WorkflowStep).
*/ -public class SubworkflowFeatureRequirementImpl extends SavableImpl implements SubworkflowFeatureRequirement { +public class SubworkflowFeatureRequirementImpl extends SaveableImpl implements SubworkflowFeatureRequirement { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/ToolTimeLimit.java b/src/main/java/org/w3id/cwl/cwl1_2/ToolTimeLimit.java index 0a8f91e..b47df0b 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/ToolTimeLimit.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/ToolTimeLimit.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#ToolTimeLimit
This interface is implemented by {@link ToolTimeLimitImpl}
@@ -27,7 +27,7 @@ wall-time for the execution of the command line itself.
*/ -public interface ToolTimeLimit extends ProcessRequirement, Savable { +public interface ToolTimeLimit extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#ToolTimeLimit/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/ToolTimeLimitImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/ToolTimeLimitImpl.java index 51aa8a8..37fa68f 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/ToolTimeLimitImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/ToolTimeLimitImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -31,7 +31,7 @@ wall-time for the execution of the command line itself.
*/ -public class ToolTimeLimitImpl extends SavableImpl implements ToolTimeLimit { +public class ToolTimeLimitImpl extends SaveableImpl implements ToolTimeLimit { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/WorkReuse.java b/src/main/java/org/w3id/cwl/cwl1_2/WorkReuse.java index 89e0df2..a1510d8 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/WorkReuse.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/WorkReuse.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#WorkReuse
This interface is implemented by {@link WorkReuseImpl}
@@ -29,7 +29,7 @@ For implementations that support reusing output from past work (on is enabled by default.
*/ -public interface WorkReuse extends ProcessRequirement, Savable { +public interface WorkReuse extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#WorkReuse/class
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/WorkReuseImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/WorkReuseImpl.java index 793683c..7bd4bd9 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/WorkReuseImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/WorkReuseImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -33,7 +33,7 @@ For implementations that support reusing output from past work (on is enabled by default.
*/ -public class WorkReuseImpl extends SavableImpl implements WorkReuse { +public class WorkReuseImpl extends SaveableImpl implements WorkReuse { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/Workflow.java b/src/main/java/org/w3id/cwl/cwl1_2/Workflow.java index 16a5506..575b58b 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/Workflow.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/Workflow.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#Workflow
This interface is implemented by {@link WorkflowImpl}
@@ -71,11 +71,15 @@ workflow output parameter (the "sink"). Workflow execution cannot workflow semantics.
*/ -public interface Workflow extends Process, Savable { +public interface Workflow extends Process, Saveable { /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * Getter for property https://w3id.org/cwl/cwl#Process/id
*
- * The unique identifier for this object. *
+ * The unique identifier for this object. + * + * Only useful for `$graph` at `Process` level. Should not be exposed + * to users in graphical or terminal user interfaces. + * *
*/ java.util.Optional getId(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowImpl.java index f6ea512..7c5a96e 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -75,7 +75,7 @@ workflow output parameter (the "sink"). Workflow execution cannot workflow semantics.
*/ -public class WorkflowImpl extends SavableImpl implements Workflow { +public class WorkflowImpl extends SaveableImpl implements Workflow { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); @@ -83,9 +83,13 @@ public class WorkflowImpl extends SavableImpl implements Workflow { private java.util.Optional id; /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
+ * Getter for property https://w3id.org/cwl/cwl#Process/id
*
- * The unique identifier for this object. *
+ * The unique identifier for this object. + * + * Only useful for `$graph` at `Process` level. Should not be exposed + * to users in graphical or terminal user interfaces. + * *
*/ public java.util.Optional getId() { @@ -404,7 +408,7 @@ public WorkflowImpl( try { hints = LoaderInstances - .idmap_hints_optional_array_of_AnyInstance + .idmap_hints_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance .loadField(__doc.get("hints"), __baseUri, __loadingOptions); } catch (ValidationException e) { hints = null; // won't be used but prevents compiler from complaining. diff --git a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowInputParameter.java b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowInputParameter.java index eb9bebe..3e38704 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowInputParameter.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowInputParameter.java @@ -14,12 +14,12 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowInputParameter
This interface is implemented by {@link WorkflowInputParameterImpl}
*/ -public interface WorkflowInputParameter extends InputParameter, Savable { +public interface WorkflowInputParameter extends InputParameter, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Identified/id
*
@@ -157,7 +157,7 @@ public interface WorkflowInputParameter extends InputParameter, Savable { * *
*/ - java.util.Optional getDefault(); + Object getDefault(); /** * Getter for property https://w3id.org/cwl/salad#type
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowInputParameterImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowInputParameterImpl.java index e41b8fd..38f45ca 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowInputParameterImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowInputParameterImpl.java @@ -17,13 +17,13 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** * Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowInputParameter
*/ -public class WorkflowInputParameterImpl extends SavableImpl implements WorkflowInputParameter { +public class WorkflowInputParameterImpl extends SaveableImpl implements WorkflowInputParameter { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); @@ -195,7 +195,7 @@ public java.util.Optional getLoadListing() { return this.loadListing; } - private java.util.Optional default_; + private Object default_; /** * Getter for property https://w3id.org/cwl/salad#default
@@ -207,7 +207,7 @@ public java.util.Optional getLoadListing() { * * */ - public java.util.Optional getDefault() { + public Object getDefault() { return this.default_; } @@ -418,13 +418,13 @@ public WorkflowInputParameterImpl( } else { loadListing = null; } - java.util.Optional default_; + Object default_; if (__doc.containsKey("default")) { try { default_ = LoaderInstances - .optional_AnyInstance + .union_of_NullInstance_or_File_or_Directory_or_AnyInstance .loadField(__doc.get("default"), __baseUri, __loadingOptions); } catch (ValidationException e) { default_ = null; // won't be used but prevents compiler from complaining. @@ -474,7 +474,7 @@ public WorkflowInputParameterImpl( this.format = (Object) format; this.loadContents = (java.util.Optional) loadContents; this.loadListing = (java.util.Optional) loadListing; - this.default_ = (java.util.Optional) default_; + this.default_ = (Object) default_; this.type = (Object) type; this.inputBinding = (java.util.Optional) inputBinding; } diff --git a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowOutputParameter.java b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowOutputParameter.java index 5ca836d..000cff3 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowOutputParameter.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowOutputParameter.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowOutputParameter
This interface is implemented by {@link WorkflowOutputParameterImpl}
@@ -27,7 +27,7 @@ `linkMerge` and `pickValue`.
*/ -public interface WorkflowOutputParameter extends OutputParameter, Savable { +public interface WorkflowOutputParameter extends OutputParameter, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Identified/id
*
@@ -124,8 +124,11 @@ public interface WorkflowOutputParameter extends OutputParameter, Savable { /** * Getter for property https://w3id.org/cwl/cwl#outputSource
*
- * 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. * *
*/ diff --git a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowOutputParameterImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowOutputParameterImpl.java index 3f39c8a..2370af6 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowOutputParameterImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowOutputParameterImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -31,7 +31,7 @@ `linkMerge` and `pickValue`.
*/ -public class WorkflowOutputParameterImpl extends SavableImpl implements WorkflowOutputParameter { +public class WorkflowOutputParameterImpl extends SaveableImpl implements WorkflowOutputParameter { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); @@ -164,8 +164,11 @@ public Object getFormat() { /** * Getter for property https://w3id.org/cwl/cwl#outputSource
*
- * 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. * *
*/ @@ -365,7 +368,7 @@ public WorkflowOutputParameterImpl( try { outputSource = LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_0 + .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_1 .loadField(__doc.get("outputSource"), __baseUri, __loadingOptions); } catch (ValidationException e) { outputSource = null; // won't be used but prevents compiler from complaining. diff --git a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStep.java b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStep.java index f17b767..49c2fc8 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStep.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStep.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowStep
This interface is implemented by {@link WorkflowStepImpl}
@@ -99,7 +99,7 @@ input object (or individual scatter job), and returns a boolean a subworkflow (recursive workflows are not allowed).
*/ -public interface WorkflowStep extends Identified, Labeled, Documented, Savable { +public interface WorkflowStep extends Identified, Labeled, Documented, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Identified/id
*
@@ -169,7 +169,8 @@ public interface WorkflowStep extends Identified, Labeled, Documented, Savable { /** * Getter for property https://w3id.org/cwl/cwl#run
*
- * Specifies the process to run. + * Specifies the process to run. If `run` is a string, it must be an absolute IRI + * or a relative path from the primary document. * *
*/ diff --git a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepImpl.java index 17ba31b..f794921 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -103,7 +103,7 @@ input object (or individual scatter job), and returns a boolean a subworkflow (recursive workflows are not allowed).
*/ -public class WorkflowStepImpl extends SavableImpl implements WorkflowStep { +public class WorkflowStepImpl extends SaveableImpl implements WorkflowStep { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); @@ -214,7 +214,8 @@ public java.util.Optional> getHints() { /** * Getter for property https://w3id.org/cwl/cwl#run
*
- * Specifies the process to run. + * Specifies the process to run. If `run` is a string, it must be an absolute IRI + * or a relative path from the primary document. * *
*/ diff --git a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepInput.java b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepInput.java index 4e88e81..4b1c44a 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepInput.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepInput.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowStepInput
This interface is implemented by {@link WorkflowStepInputImpl}
@@ -128,7 +128,7 @@ sources are conditional, so null sources (from skipped steps) should be filtered out.
*/ -public interface WorkflowStepInput extends Identified, Sink, LoadContents, Labeled, Savable { +public interface WorkflowStepInput extends Identified, Sink, LoadContents, Labeled, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Identified/id
*
@@ -221,7 +221,7 @@ public interface WorkflowStepInput extends Identified, Sink, LoadContents, Label * this input parameter. * * If `valueFrom` is a parameter reference or expression, it must be - * evaluated to yield the actual value to be assiged to the input field. + * evaluated to yield the actual value to be assigned to the input field. * * The `self` value in the parameter reference or expression must be * 1. `null` if there is no `source` field diff --git a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepInputImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepInputImpl.java index 05eb089..d8be25f 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepInputImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepInputImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -132,7 +132,7 @@ sources are conditional, so null sources (from skipped steps) should be filtered out.
*/ -public class WorkflowStepInputImpl extends SavableImpl implements WorkflowStepInput { +public class WorkflowStepInputImpl extends SaveableImpl implements WorkflowStepInput { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); @@ -271,7 +271,7 @@ public java.util.Optional getDefault() { * this input parameter. * * If `valueFrom` is a parameter reference or expression, it must be - * evaluated to yield the actual value to be assiged to the input field. + * evaluated to yield the actual value to be assigned to the input field. * * The `self` value in the parameter reference or expression must be * 1. `null` if there is no `source` field diff --git a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepOutput.java b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepOutput.java index 0067162..71e3704 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepOutput.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepOutput.java @@ -14,7 +14,7 @@ package org.w3id.cwl.cwl1_2; -import org.w3id.cwl.cwl1_2.utils.Savable; +import org.w3id.cwl.cwl1_2.utils.Saveable; /** * Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowStepOutput
This interface is implemented by {@link WorkflowStepOutputImpl}
@@ -28,7 +28,7 @@ parameter. The workflow parameter (given in the `id` field) be may be used to connect the output value to downstream parameters.
*/ -public interface WorkflowStepOutput extends Identified, Savable { +public interface WorkflowStepOutput extends Identified, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#Identified/id
*
diff --git a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepOutputImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepOutputImpl.java index aeb5400..9f17496 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepOutputImpl.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/WorkflowStepOutputImpl.java @@ -17,7 +17,7 @@ import org.w3id.cwl.cwl1_2.utils.LoaderInstances; import org.w3id.cwl.cwl1_2.utils.LoadingOptions; import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder; -import org.w3id.cwl.cwl1_2.utils.SavableImpl; +import org.w3id.cwl.cwl1_2.utils.SaveableImpl; import org.w3id.cwl.cwl1_2.utils.ValidationException; /** @@ -32,7 +32,7 @@ parameter. The workflow parameter (given in the `id` field) be may be used to connect the output value to downstream parameters.
*/ -public class WorkflowStepOutputImpl extends SavableImpl implements WorkflowStepOutput { +public class WorkflowStepOutputImpl extends SaveableImpl implements WorkflowStepOutput { private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); private java.util.Map extensionFields_ = new java.util.HashMap(); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/utils/LoaderInstances.java b/src/main/java/org/w3id/cwl/cwl1_2/utils/LoaderInstances.java index 3ba793c..a8816ec 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/utils/LoaderInstances.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/utils/LoaderInstances.java @@ -154,7 +154,7 @@ public class LoaderInstances { public static Loader> array_of_OutputRecordField = new ArrayLoader(OutputRecordField); public static Loader>> optional_array_of_OutputRecordField = new OptionalLoader(array_of_OutputRecordField); public static Loader>> idmap_fields_optional_array_of_OutputRecordField = new IdMapLoader(optional_array_of_OutputRecordField, "name", "type"); - public static Loader> optional_AnyInstance = new OptionalLoader(AnyInstance); + public static Loader union_of_NullInstance_or_File_or_Directory_or_AnyInstance = new UnionLoader(new Loader[] { NullInstance, File, Directory, AnyInstance }); public static Loader union_of_CommandInputParameter_or_WorkflowInputParameter_or_OperationInputParameter = new UnionLoader(new Loader[] { CommandInputParameter, WorkflowInputParameter, OperationInputParameter }); public static Loader> array_of_union_of_CommandInputParameter_or_WorkflowInputParameter_or_OperationInputParameter = new ArrayLoader(union_of_CommandInputParameter_or_WorkflowInputParameter_or_OperationInputParameter); public static Loader> idmap_inputs_array_of_union_of_CommandInputParameter_or_WorkflowInputParameter_or_OperationInputParameter = new IdMapLoader(array_of_union_of_CommandInputParameter_or_WorkflowInputParameter_or_OperationInputParameter, "id", "type"); @@ -165,9 +165,10 @@ public class LoaderInstances { public static Loader> array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement = new ArrayLoader(union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement); public static Loader>> optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement = new OptionalLoader(array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement); public static Loader>> idmap_requirements_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement = new IdMapLoader(optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement, "class", "None"); - public static Loader> array_of_AnyInstance = new ArrayLoader(AnyInstance); - public static Loader>> optional_array_of_AnyInstance = new OptionalLoader(array_of_AnyInstance); - public static Loader>> idmap_hints_optional_array_of_AnyInstance = new IdMapLoader(optional_array_of_AnyInstance, "class", "None"); + public static Loader union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance = new UnionLoader(new Loader[] { InlineJavascriptRequirement, SchemaDefRequirement, LoadListingRequirement, DockerRequirement, SoftwareRequirement, InitialWorkDirRequirement, EnvVarRequirement, ShellCommandRequirement, ResourceRequirement, WorkReuse, NetworkAccess, InplaceUpdateRequirement, ToolTimeLimit, SubworkflowFeatureRequirement, ScatterFeatureRequirement, MultipleInputFeatureRequirement, StepInputExpressionRequirement, AnyInstance }); + public static Loader> array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance = new ArrayLoader(union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance); + public static Loader>> optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance = new OptionalLoader(array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance); + public static Loader>> idmap_hints_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance = new IdMapLoader(optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance, "class", "None"); public static Loader> optional_CWLVersion = new OptionalLoader(CWLVersion); public static Loader> uri_optional_CWLVersion_False_True_None = new UriLoader(optional_CWLVersion, false, true, null); public static Loader>> optional_array_of_StringInstance = new OptionalLoader(array_of_StringInstance); @@ -254,16 +255,21 @@ public class LoaderInstances { public static Loader> idmap_inputs_array_of_WorkflowInputParameter = new IdMapLoader(array_of_WorkflowInputParameter, "id", "type"); public static Loader> array_of_ExpressionToolOutputParameter = new ArrayLoader(ExpressionToolOutputParameter); public static Loader> idmap_outputs_array_of_ExpressionToolOutputParameter = new IdMapLoader(array_of_ExpressionToolOutputParameter, "id", "type"); - public static Loader uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_0 = new UriLoader(union_of_NullInstance_or_StringInstance_or_array_of_StringInstance, false, false, 0); + public static Loader uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_1 = new UriLoader(union_of_NullInstance_or_StringInstance_or_array_of_StringInstance, false, false, 1); public static Loader> optional_LinkMergeMethod = new OptionalLoader(LinkMergeMethod); public static Loader> optional_PickValueMethod = new OptionalLoader(PickValueMethod); public static Loader uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_2 = new UriLoader(union_of_NullInstance_or_StringInstance_or_array_of_StringInstance, false, false, 2); + public static Loader> optional_AnyInstance = new OptionalLoader(AnyInstance); public static Loader> array_of_WorkflowStepInput = new ArrayLoader(WorkflowStepInput); public static Loader> idmap_in_array_of_WorkflowStepInput = new IdMapLoader(array_of_WorkflowStepInput, "id", "source"); public static Loader union_of_StringInstance_or_WorkflowStepOutput = new UnionLoader(new Loader[] { StringInstance, WorkflowStepOutput }); public static Loader> array_of_union_of_StringInstance_or_WorkflowStepOutput = new ArrayLoader(union_of_StringInstance_or_WorkflowStepOutput); public static Loader> uri_array_of_union_of_StringInstance_or_WorkflowStepOutput_True_False_None = new UriLoader(array_of_union_of_StringInstance_or_WorkflowStepOutput, true, false, null); + public static Loader> array_of_AnyInstance = new ArrayLoader(AnyInstance); + public static Loader>> optional_array_of_AnyInstance = new OptionalLoader(array_of_AnyInstance); + public static Loader>> idmap_hints_optional_array_of_AnyInstance = new IdMapLoader(optional_array_of_AnyInstance, "class", "None"); public static Loader union_of_StringInstance_or_CommandLineTool_or_ExpressionTool_or_Workflow_or_Operation = new UnionLoader(new Loader[] { StringInstance, CommandLineTool, ExpressionTool, Workflow, Operation }); + public static Loader uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_0 = new UriLoader(union_of_NullInstance_or_StringInstance_or_array_of_StringInstance, false, false, 0); public static Loader> optional_ScatterMethod = new OptionalLoader(ScatterMethod); public static Loader> uri_optional_ScatterMethod_False_True_None = new UriLoader(optional_ScatterMethod, false, true, null); public static Loader Workflow_class = new EnumLoader(Workflow_class.class); diff --git a/src/main/java/org/w3id/cwl/cwl1_2/utils/RecordLoader.java b/src/main/java/org/w3id/cwl/cwl1_2/utils/RecordLoader.java index 7e45402..4d04c40 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/utils/RecordLoader.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/utils/RecordLoader.java @@ -3,11 +3,11 @@ import java.lang.reflect.Constructor; import java.lang.reflect.InvocationTargetException; -public class RecordLoader implements Loader { - private final Class savableClass; +public class RecordLoader implements Loader { + private final Class saveableClass; - public RecordLoader(final Class savableClass) { - this.savableClass = savableClass; + public RecordLoader(final Class saveableClass) { + this.saveableClass = saveableClass; } public T load( @@ -18,7 +18,7 @@ public T load( Loader.validateOfJavaType(java.util.Map.class, doc); try { final Constructor constructor = - this.savableClass.getConstructor( + this.saveableClass.getConstructor( new Class[] {Object.class, String.class, LoadingOptions.class, String.class}); final T ret = constructor.newInstance(doc, baseUri, loadingOptions, docRoot); return ret; diff --git a/src/main/java/org/w3id/cwl/cwl1_2/utils/SavableImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/utils/SavableImpl.java deleted file mode 100644 index b581ec8..0000000 --- a/src/main/java/org/w3id/cwl/cwl1_2/utils/SavableImpl.java +++ /dev/null @@ -1,5 +0,0 @@ -package org.w3id.cwl.cwl1_2.utils; - -public class SavableImpl implements Savable { - public SavableImpl(Object doc, String baseUri, LoadingOptions loadingOptions, String docRoot) {} -} diff --git a/src/main/java/org/w3id/cwl/cwl1_2/utils/Savable.java b/src/main/java/org/w3id/cwl/cwl1_2/utils/Saveable.java similarity index 85% rename from src/main/java/org/w3id/cwl/cwl1_2/utils/Savable.java rename to src/main/java/org/w3id/cwl/cwl1_2/utils/Saveable.java index 022b9bc..9f250c1 100644 --- a/src/main/java/org/w3id/cwl/cwl1_2/utils/Savable.java +++ b/src/main/java/org/w3id/cwl/cwl1_2/utils/Saveable.java @@ -1,6 +1,6 @@ package org.w3id.cwl.cwl1_2.utils; -public interface Savable { +public interface Saveable { // TODO: implement writable interface // public abstract void save(boolean top, String baseUrl, boolean relativeUris); } diff --git a/src/main/java/org/w3id/cwl/cwl1_2/utils/SaveableImpl.java b/src/main/java/org/w3id/cwl/cwl1_2/utils/SaveableImpl.java new file mode 100644 index 0000000..0bcd9f4 --- /dev/null +++ b/src/main/java/org/w3id/cwl/cwl1_2/utils/SaveableImpl.java @@ -0,0 +1,5 @@ +package org.w3id.cwl.cwl1_2.utils; + +public class SaveableImpl implements Saveable { + public SaveableImpl(Object doc, String baseUri, LoadingOptions loadingOptions, String docRoot) {} +} diff --git a/src/test/java/org/w3id/cwl/cwl1_2/utils/ExamplesTest.java b/src/test/java/org/w3id/cwl/cwl1_2/utils/ExamplesTest.java index 585f472..f2fadc7 100644 --- a/src/test/java/org/w3id/cwl/cwl1_2/utils/ExamplesTest.java +++ b/src/test/java/org/w3id/cwl/cwl1_2/utils/ExamplesTest.java @@ -171,6 +171,30 @@ public void testvalid_wc_tool_shortcutByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_record_outputevalByString() throws Exception { + java.net.URL url = getClass().getResource("valid_record_outputeval.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_record_outputevalByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_record_outputeval.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_record_outputevalByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_record_outputeval.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_packed_timelimit3_wfByString() throws Exception { java.net.URL url = getClass().getResource("valid_packed_timelimit3-wf.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -1227,6 +1251,30 @@ public void testvalid_wc2_toolByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_packed_synth_fileByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_synth-file.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_synth_fileByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_synth-file.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_synth_fileByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_synth-file.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_iwd_passthrough1ByString() throws Exception { java.net.URL url = getClass().getResource("valid_iwd-passthrough1.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -2067,6 +2115,30 @@ public void testvalid_packed_dirByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_wf_renByString() throws Exception { + java.net.URL url = getClass().getResource("valid_wf_ren.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_wf_renByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_wf_ren.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_wf_renByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_wf_ren.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_count_lines14_wfByString() throws Exception { java.net.URL url = getClass().getResource("valid_count-lines14-wf.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -2379,6 +2451,30 @@ public void testvalid_packed_js_quoteByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_packed_js_input_recordByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_js-input-record.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_js_input_recordByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_js-input-record.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_js_input_recordByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_js-input-record.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_scatter_valuefrom_wf5ByString() throws Exception { java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf5.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -2643,6 +2739,30 @@ public void testvalid_packed_cond_wf_002_nojsByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_synth_fileByString() throws Exception { + java.net.URL url = getClass().getResource("valid_synth-file.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_synth_fileByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_synth-file.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_synth_fileByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_synth-file.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_packed_env_tool1ByString() throws Exception { java.net.URL url = getClass().getResource("valid_packed_env-tool1.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -3051,6 +3171,30 @@ public void testvalid_writable_dirByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_colon_testByString() throws Exception { + java.net.URL url = getClass().getResource("valid_colon:test.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_colon_testByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_colon:test.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_colon_testByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_colon:test.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_null_expression2_toolByString() throws Exception { java.net.URL url = getClass().getResource("valid_null-expression2-tool.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -3507,6 +3651,30 @@ public void testvalid_packed_tmap_toolByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_packed_cat4_from_dirByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_cat4-from-dir.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_cat4_from_dirByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_cat4-from-dir.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_cat4_from_dirByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_cat4-from-dir.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_packed_envvarByString() throws Exception { java.net.URL url = getClass().getResource("valid_packed_envvar.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -3675,6 +3843,30 @@ public void testvalid_packed_count_lines1_wfByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_packed_schemadef_types_with_import_wfByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_schemadef_types_with_import-wf.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_schemadef_types_with_import_wfByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_schemadef_types_with_import-wf.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_schemadef_types_with_import_wfByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_schemadef_types_with_import-wf.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_wc_toolByString() throws Exception { java.net.URL url = getClass().getResource("valid_wc-tool.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -4347,6 +4539,30 @@ public void testvalid_count_lines9_wfByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_packed_multiple_input_feature_requirementByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_multiple_input_feature_requirement.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_multiple_input_feature_requirementByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_multiple_input_feature_requirement.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_multiple_input_feature_requirementByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_multiple_input_feature_requirement.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_packed_iwd_passthrough3ByString() throws Exception { java.net.URL url = getClass().getResource("valid_packed_iwd-passthrough3.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -4779,6 +4995,30 @@ public void testvalid_packed_record_in_secondaryFilesByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_packed_record_orderByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_record-order.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_record_orderByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_record-order.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_record_orderByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_record-order.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_packed_count_lines8_wf_noETByString() throws Exception { java.net.URL url = getClass().getResource("valid_packed_count-lines8-wf-noET.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -4803,6 +5043,30 @@ public void testvalid_packed_count_lines8_wf_noETByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_output_reference_workflow_inputByString() throws Exception { + java.net.URL url = getClass().getResource("valid_output_reference_workflow_input.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_output_reference_workflow_inputByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_output_reference_workflow_input.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_output_reference_workflow_inputByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_output_reference_workflow_input.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_count_lines5_wfByString() throws Exception { java.net.URL url = getClass().getResource("valid_count-lines5-wf.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -4947,6 +5211,30 @@ public void testvalid_packed_empty_array_inputByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_packed_colon_test_outputByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_colon_test_output.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_colon_test_outputByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_colon_test_output.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_colon_test_outputByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_colon_test_output.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_cat3_tool_dockerByString() throws Exception { java.net.URL url = getClass().getResource("valid_cat3-tool-docker.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -5523,6 +5811,30 @@ public void testvalid_packed_count_lines10_wfByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_packed_valid_schemadef_types_with_import_wfByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_valid_schemadef_types_with_import-wf.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_valid_schemadef_types_with_import_wfByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_valid_schemadef_types_with_import-wf.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_valid_schemadef_types_with_import_wfByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_valid_schemadef_types_with_import-wf.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_packed_cond_wf_004ByString() throws Exception { java.net.URL url = getClass().getResource("valid_packed_cond-wf-004.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -5715,6 +6027,30 @@ public void testvalid_packed_iwd_container_entryname2ByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_colon_test_outputByString() throws Exception { + java.net.URL url = getClass().getResource("valid_colon_test_output.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_colon_test_outputByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_colon_test_output.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_colon_test_outputByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_colon_test_output.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_packed_dir4ByString() throws Exception { java.net.URL url = getClass().getResource("valid_packed_dir4.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -6315,16 +6651,40 @@ public void testvalid_stage_file_arrayByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test - public void testvalid_packed_wf_loadContents3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf-loadContents3.cwl"); + public void testvalid_packed_checkByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_check.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); RootLoader.loadDocument(yaml, url.toString()); } @org.junit.Test - public void testvalid_packed_wf_loadContents3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf-loadContents3.cwl"); + public void testvalid_packed_checkByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_check.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_checkByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_check.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test + public void testvalid_packed_wf_loadContents3ByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_wf-loadContents3.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_wf_loadContents3ByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_wf-loadContents3.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); RootLoader.loadDocument(resPath); } @@ -6723,6 +7083,30 @@ public void testvalid_cond_wf_013ByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_runtime_outdirByString() throws Exception { + java.net.URL url = getClass().getResource("valid_runtime-outdir.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_runtime_outdirByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_runtime-outdir.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_runtime_outdirByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_runtime-outdir.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_packed_cond_wf_003ByString() throws Exception { java.net.URL url = getClass().getResource("valid_packed_cond-wf-003.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -7107,6 +7491,30 @@ public void testvalid_docker_run_cmdByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_schemadef_types_with_import_wfByString() throws Exception { + java.net.URL url = getClass().getResource("valid_schemadef_types_with_import-wf.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_schemadef_types_with_import_wfByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_schemadef_types_with_import-wf.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_schemadef_types_with_import_wfByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_schemadef_types_with_import-wf.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_packed_no_outputs_wfByString() throws Exception { java.net.URL url = getClass().getResource("valid_packed_no-outputs-wf.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -7275,6 +7683,30 @@ public void testvalid_packed_stage_file_array_basename_and_entrynameByMap() thro RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_packed_runtime_outdirByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_runtime-outdir.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_runtime_outdirByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_runtime-outdir.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_runtime_outdirByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_runtime-outdir.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_packed_operationByString() throws Exception { java.net.URL url = getClass().getResource("valid_packed_operation.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -7587,6 +8019,30 @@ public void testvalid_searchByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_packed_params_input_length_non_arrayByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_params_input_length_non_array.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_params_input_length_non_arrayByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_params_input_length_non_array.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_params_input_length_non_arrayByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_params_input_length_non_array.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_echo_tool_packedByString() throws Exception { java.net.URL url = getClass().getResource("valid_echo-tool-packed.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -7755,6 +8211,30 @@ public void testvalid_packed_cat1_testcliByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_params_input_length_non_arrayByString() throws Exception { + java.net.URL url = getClass().getResource("valid_params_input_length_non_array.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_params_input_length_non_arrayByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_params_input_length_non_array.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_params_input_length_non_arrayByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_params_input_length_non_array.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_packed_step_valuefrom_wfByString() throws Exception { java.net.URL url = getClass().getResource("valid_packed_step-valuefrom-wf.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -7995,6 +8475,30 @@ public void testvalid_packed_count_lines13_wfByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_packed_record_outputeval_nojsByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_record_outputeval_nojs.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_record_outputeval_nojsByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_record_outputeval_nojs.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_record_outputeval_nojsByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_record_outputeval_nojs.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_barByString() throws Exception { java.net.URL url = getClass().getResource("valid_bar.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -8307,6 +8811,30 @@ public void testvalid_listing_shallow1ByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_packed_colon_testByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_colon:test.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_colon_testByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_colon:test.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_colon_testByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_colon:test.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_scatter_valuefrom_wf6ByString() throws Exception { java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf6.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -9291,6 +9819,30 @@ public void testvalid_packed_stage_arrayByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_packed_output_reference_workflow_inputByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_output_reference_workflow_input.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_output_reference_workflow_inputByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_output_reference_workflow_input.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_output_reference_workflow_inputByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_output_reference_workflow_input.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_env_tool3ByString() throws Exception { java.net.URL url = getClass().getResource("valid_env-tool3.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -9459,6 +10011,30 @@ public void testvalid_packed_cat3_toolByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_packed_wf_renByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_wf_ren.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_wf_renByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_wf_ren.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_wf_renByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_wf_ren.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_packed_exitcodeByString() throws Exception { java.net.URL url = getClass().getResource("valid_packed_exitcode.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -9771,6 +10347,30 @@ public void testvalid_tmap_toolByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_packed_record_outputevalByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_record_outputeval.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_record_outputevalByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_record_outputeval.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_record_outputevalByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_record_outputeval.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_cond_wf_012ByString() throws Exception { java.net.URL url = getClass().getResource("valid_cond-wf-012.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -10203,6 +10803,30 @@ public void testvalid_size_expression_toolByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_cat4_from_dirByString() throws Exception { + java.net.URL url = getClass().getResource("valid_cat4-from-dir.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_cat4_from_dirByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_cat4-from-dir.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_cat4_from_dirByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_cat4-from-dir.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_record_out_formatByString() throws Exception { java.net.URL url = getClass().getResource("valid_record-out-format.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -11691,6 +12315,30 @@ public void testvalid_packed_template_toolByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_stdout_chained_commandsByString() throws Exception { + java.net.URL url = getClass().getResource("valid_stdout_chained_commands.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_stdout_chained_commandsByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_stdout_chained_commands.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_stdout_chained_commandsByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_stdout_chained_commands.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_packed_formattest3ByString() throws Exception { java.net.URL url = getClass().getResource("valid_packed_formattest3.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -11715,6 +12363,30 @@ public void testvalid_packed_formattest3ByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_js_input_recordByString() throws Exception { + java.net.URL url = getClass().getResource("valid_js-input-record.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_js_input_recordByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_js-input-record.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_js_input_recordByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_js-input-record.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_dynresreq_workflow_tooldefaultByString() throws Exception { java.net.URL url = getClass().getResource("valid_dynresreq-workflow-tooldefault.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -11763,6 +12435,30 @@ public void testvalid_test_cwl_outByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_multiple_input_feature_requirementByString() throws Exception { + java.net.URL url = getClass().getResource("valid_multiple_input_feature_requirement.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_multiple_input_feature_requirementByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_multiple_input_feature_requirement.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_multiple_input_feature_requirementByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_multiple_input_feature_requirement.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_dynresreq_defaultByString() throws Exception { java.net.URL url = getClass().getResource("valid_dynresreq-default.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -12027,6 +12723,30 @@ public void testvalid_count_lines4_wfByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_checkByString() throws Exception { + java.net.URL url = getClass().getResource("valid_check.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_checkByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_check.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_checkByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_check.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_packed_updateval_inplaceByString() throws Exception { java.net.URL url = getClass().getResource("valid_packed_updateval_inplace.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -12267,6 +12987,30 @@ public void testvalid_packed_count_lines5_wfByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_record_outputeval_nojsByString() throws Exception { + java.net.URL url = getClass().getResource("valid_record_outputeval_nojs.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_record_outputeval_nojsByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_record_outputeval_nojs.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_record_outputeval_nojsByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_record_outputeval_nojs.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_packed_scatter_valueFrom_toolByString() throws Exception { java.net.URL url = getClass().getResource("valid_packed_scatter-valueFrom-tool.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -12795,6 +13539,30 @@ public void testvalid_count_lines8_wfByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_record_orderByString() throws Exception { + java.net.URL url = getClass().getResource("valid_record-order.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_record_orderByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_record-order.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_record_orderByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_record-order.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_catByString() throws Exception { java.net.URL url = getClass().getResource("valid_cat.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); @@ -13467,6 +14235,30 @@ public void testvalid_optional_numerical_output_0ByMap() throws Exception { RootLoader.loadDocument(doc, url.toString()); } @org.junit.Test + public void testvalid_packed_stdout_chained_commandsByString() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_stdout_chained_commands.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + RootLoader.loadDocument(yaml, url.toString()); + } + + @org.junit.Test + public void testvalid_packed_stdout_chained_commandsByPath() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_stdout_chained_commands.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + RootLoader.loadDocument(resPath); + } + + @org.junit.Test + public void testvalid_packed_stdout_chained_commandsByMap() throws Exception { + java.net.URL url = getClass().getResource("valid_packed_stdout_chained_commands.cwl"); + java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); + String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); + java.util.Map doc; + doc = (java.util.Map) YamlUtils.mapFromString(yaml); + RootLoader.loadDocument(doc, url.toString()); + } + @org.junit.Test public void testvalid_updateval_inplaceByString() throws Exception { java.net.URL url = getClass().getResource("valid_updateval_inplace.cwl"); java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/check.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/check.cwl new file mode 100644 index 0000000..da8b5c9 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/check.cwl @@ -0,0 +1,18 @@ +class: CommandLineTool +cwlVersion: v1.2 +inputs: + p: File + checkname: string +outputs: [] +arguments: + - sh + - "-c" + - | + name=`basename $(inputs.p.path)` + ls -l $(inputs.p.path) + if test $name = $(inputs.checkname) ; then + echo success + else + echo expected basename to be $(inputs.checkname) but was $name + exit 1 + fi diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/rename.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/rename.cwl new file mode 100644 index 0000000..7bc0025 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/rename.cwl @@ -0,0 +1,16 @@ +class: CommandLineTool +cwlVersion: v1.2 +baseCommand: "true" +requirements: + InitialWorkDirRequirement: + listing: + - entryname: $(inputs.newname) + entry: $(inputs.srcfile) +inputs: + srcfile: File + newname: string +outputs: + outfile: + type: File + outputBinding: + glob: $(inputs.newname) diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/schemadef_types_with_import-tool.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/schemadef_types_with_import-tool.cwl new file mode 100644 index 0000000..1197249 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/schemadef_types_with_import-tool.cwl @@ -0,0 +1,26 @@ +#!/usr/bin/env cwl-runner +class: CommandLineTool +cwlVersion: v1.2 + +requirements: + - class: InlineJavascriptRequirement + - class: SchemaDefRequirement + types: + - $import: schemadef_types_with_import_readgroup.yml + +inputs: + - id: message + type: "schemadef_types_with_import_readgroup.yml#readgroups_bam_file" + inputBinding: + valueFrom: $(self.readgroup_meta_list[0]['DT']) + +outputs: + - id: out + type: string + outputBinding: + glob: output.txt + loadContents: true + outputEval: $(self[0].contents) + +stdout: output.txt +baseCommand: echo diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/schemadef_types_with_import_readgroup.yml b/src/test/resources/org/w3id/cwl/cwl1_2/utils/schemadef_types_with_import_readgroup.yml new file mode 100644 index 0000000..c7ffe8e --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/schemadef_types_with_import_readgroup.yml @@ -0,0 +1,27 @@ +- name: readgroup_meta + type: record + fields: + - name: CN + type: string + - name: DT + type: string + - name: ID + type: string + - name: LB + type: string + - name: PI + type: string + - name: PL + type: string + - name: SM + type: string + +- name: readgroups_bam_file + type: record + fields: + - name: bam + type: File + - name: readgroup_meta_list + type: + type: array + items: readgroup_meta diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_cat4-from-dir.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_cat4-from-dir.cwl new file mode 100755 index 0000000..077310c --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_cat4-from-dir.cwl @@ -0,0 +1,14 @@ +#!/usr/bin/env cwl-runner +class: CommandLineTool +cwlVersion: v1.2 +inputs: + dir1: + type: Directory + inputBinding: + valueFrom: $(self.listing[0].listing[0].path) +outputs: + output_file: + type: File + outputBinding: {glob: output.txt} +baseCommand: cat +stdout: output.txt diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_check.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_check.cwl new file mode 100644 index 0000000..da8b5c9 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_check.cwl @@ -0,0 +1,18 @@ +class: CommandLineTool +cwlVersion: v1.2 +inputs: + p: File + checkname: string +outputs: [] +arguments: + - sh + - "-c" + - | + name=`basename $(inputs.p.path)` + ls -l $(inputs.p.path) + if test $name = $(inputs.checkname) ; then + echo success + else + echo expected basename to be $(inputs.checkname) but was $name + exit 1 + fi diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_colon:test.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_colon:test.cwl new file mode 100755 index 0000000..7b675b0 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_colon:test.cwl @@ -0,0 +1,23 @@ +#!/usr/bin/env cwl-runner +class: CommandLineTool +cwlVersion: v1.2 +hints: + DockerRequirement: + dockerPull: docker.io/bash:4.4 +inputs: + input_file: File + outdir_name: string + +baseCommand: [ bash, -c ] +stdout: re:sult +arguments: + - | + mkdir $(inputs.outdir_name); + cp $(inputs.input_file.path) $(inputs.outdir_name)/; + echo Status: done! +outputs: + log: stdout + result: + type: Directory + outputBinding: + glob: $(inputs.outdir_name) diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_colon_test_output.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_colon_test_output.cwl new file mode 100755 index 0000000..5e84b81 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_colon_test_output.cwl @@ -0,0 +1,20 @@ +#!/usr/bin/env cwl-runner +class: CommandLineTool +cwlVersion: v1.2 +hints: + DockerRequirement: + dockerPull: docker.io/bash:4.4 +inputs: + input_file: File + outdir_name: string + +baseCommand: [ bash, -c ] +arguments: + - | + mkdir $(inputs.outdir_name); + cp $(inputs.input_file.path) $(inputs.outdir_name)/; +outputs: + result: + type: Directory + outputBinding: + glob: $(inputs.outdir_name) diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_js-input-record.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_js-input-record.cwl new file mode 100644 index 0000000..80e1317 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_js-input-record.cwl @@ -0,0 +1,33 @@ +cwlVersion: v1.0 + +class: CommandLineTool + +requirements: + - class: InlineJavascriptRequirement + +baseCommand: ['echo'] + +inputs: + message: + type: + type: record + name: message_object + fields: + text: + type: string + inputBinding: + position: 1 + newlines: + type: boolean? + inputBinding: + position: 0 + prefix: -n + +outputs: + out: + type: string + outputBinding: + glob: output.txt + loadContents: true + outputEval: $(self[0].contents) +stdout: output.txt diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_multiple_input_feature_requirement.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_multiple_input_feature_requirement.cwl new file mode 100644 index 0000000..57b8c68 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_multiple_input_feature_requirement.cwl @@ -0,0 +1,29 @@ +cwlVersion: v1.2 +class: Workflow + +requirements: + - class: MultipleInputFeatureRequirement + +inputs: [] + +steps: + step1: + run: echo-tool.cwl + in: + in: + default: hello + out: [out] + step2: + run: echo-tool.cwl + in: + in: + default: world + out: [out] + +outputs: + hello_world_in_two_lines: + type: + type: array + items: string + # Only allowed with MultipleInputFeatureRequirement + outputSource: [step1/out, step2/out] diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_output_reference_workflow_input.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_output_reference_workflow_input.cwl new file mode 100644 index 0000000..808132a --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_output_reference_workflow_input.cwl @@ -0,0 +1,14 @@ +cwlVersion: v1.2 +class: Workflow + +inputs: + first: + type: string + default: me + +steps: [] + +outputs: + last: + type: string + outputSource: first diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_cat4-from-dir.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_cat4-from-dir.cwl new file mode 100644 index 0000000..7a884e4 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_cat4-from-dir.cwl @@ -0,0 +1,13 @@ +baseCommand: cat +class: CommandLineTool +cwlVersion: v1.2 +inputs: +- id: dir1 + inputBinding: {valueFrom: '$(self.listing[0].listing[0].path)'} + type: Directory +outputs: +- id: output_file + outputBinding: {glob: output.txt} + type: File +requirements: [] +stdout: output.txt diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_check.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_check.cwl new file mode 100644 index 0000000..eaa45cf --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_check.cwl @@ -0,0 +1,10 @@ +arguments: [sh, -c, "name=`basename $(inputs.p.path)`\nls -l $(inputs.p.path)\nif + test $name = $(inputs.checkname) ; then\n echo success\nelse\n echo expected + basename to be $(inputs.checkname) but was $name\n exit 1\nfi\n"] +class: CommandLineTool +cwlVersion: v1.2 +inputs: +- {id: p, type: File} +- {id: checkname, type: string} +outputs: [] +requirements: [] diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_colon:test.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_colon:test.cwl new file mode 100644 index 0000000..9f51d60 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_colon:test.cwl @@ -0,0 +1,22 @@ +arguments: ['mkdir $(inputs.outdir_name); + + cp $(inputs.input_file.path) $(inputs.outdir_name)/; + + echo Status: done! + + '] +baseCommand: [bash, -c] +class: CommandLineTool +cwlVersion: v1.2 +hints: + DockerRequirement: {dockerPull: 'docker.io/bash:4.4'} +inputs: +- {id: input_file, type: File} +- {id: outdir_name, type: string} +outputs: +- {id: log, type: stdout} +- id: result + outputBinding: {glob: $(inputs.outdir_name)} + type: Directory +requirements: [] +stdout: re:sult diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_colon_test_output.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_colon_test_output.cwl new file mode 100644 index 0000000..22e1a38 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_colon_test_output.cwl @@ -0,0 +1,18 @@ +arguments: ['mkdir $(inputs.outdir_name); + + cp $(inputs.input_file.path) $(inputs.outdir_name)/; + + '] +baseCommand: [bash, -c] +class: CommandLineTool +cwlVersion: v1.2 +hints: + DockerRequirement: {dockerPull: 'docker.io/bash:4.4'} +inputs: +- {id: input_file, type: File} +- {id: outdir_name, type: string} +outputs: +- id: result + outputBinding: {glob: $(inputs.outdir_name)} + type: Directory +requirements: [] diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_js-input-record.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_js-input-record.cwl new file mode 100644 index 0000000..673eb84 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_js-input-record.cwl @@ -0,0 +1,22 @@ +baseCommand: [echo] +class: CommandLineTool +cwlVersion: v1.0 +inputs: +- id: message + type: + fields: + - inputBinding: {position: 1} + name: text + type: string + - inputBinding: {position: 0, prefix: -n} + name: newlines + type: ['null', boolean] + name: message_object + type: record +outputs: +- id: out + outputBinding: {glob: output.txt, loadContents: true, outputEval: '$(self[0].contents)'} + type: string +requirements: +- {class: InlineJavascriptRequirement} +stdout: output.txt diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_multiple_input_feature_requirement.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_multiple_input_feature_requirement.cwl new file mode 100644 index 0000000..5f8fca0 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_multiple_input_feature_requirement.cwl @@ -0,0 +1,46 @@ +class: Workflow +cwlVersion: v1.2 +inputs: [] +outputs: +- id: hello_world_in_two_lines + outputSource: [step1/out, step2/out] + type: {items: string, type: array} +requirements: +- {class: MultipleInputFeatureRequirement} +steps: +- id: step1 + in: + - {default: hello, id: in} + out: [out] + run: + baseCommand: echo + class: CommandLineTool + cwlVersion: v1.2 + inputs: + - id: in + inputBinding: {} + type: Any + outputs: + - id: out + outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} + type: string + requirements: [] + stdout: out.txt +- id: step2 + in: + - {default: world, id: in} + out: [out] + run: + baseCommand: echo + class: CommandLineTool + cwlVersion: v1.2 + inputs: + - id: in + inputBinding: {} + type: Any + outputs: + - id: out + outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} + type: string + requirements: [] + stdout: out.txt diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_output_reference_workflow_input.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_output_reference_workflow_input.cwl new file mode 100644 index 0000000..61ca2e2 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_output_reference_workflow_input.cwl @@ -0,0 +1,8 @@ +class: Workflow +cwlVersion: v1.2 +inputs: +- {default: me, id: first, type: string} +outputs: +- {id: last, outputSource: first, type: string} +requirements: [] +steps: [] diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_params_input_length_non_array.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_params_input_length_non_array.cwl new file mode 100644 index 0000000..4859141 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_params_input_length_non_array.cwl @@ -0,0 +1,33 @@ +baseCommand: 'true' +class: CommandLineTool +cwlVersion: v1.2 +inputs: +- {default: 1, id: length, type: int} +- id: bar + type: + fields: + - {name: length, type: int} + name: bar_record + type: record +- id: baz + type: + fields: + - name: length + type: + fields: + - {name: bap, type: int} + name: length_record + type: record + name: baz_record + type: record +outputs: +- id: output1 + outputBinding: {outputEval: $(inputs.length)} + type: int +- id: output2 + outputBinding: {outputEval: $(inputs.bar.length)} + type: int +- id: output3 + outputBinding: {outputEval: $(inputs.baz.length.bap)} + type: int +requirements: [] diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_record-order.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_record-order.cwl new file mode 100644 index 0000000..fd8a758 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_record-order.cwl @@ -0,0 +1,36 @@ +baseCommand: python +class: CommandLineTool +cwlVersion: v1.2 +hints: +- {class: DockerRequirement, dockerPull: 'docker.io/python:3-slim'} +inputs: +- default: {class: File, location: args.py} + id: args.py + inputBinding: {position: -1} + type: File +- id: a + inputBinding: {position: 5, prefix: -a} + type: + fields: + - inputBinding: {position: 1, prefix: -b} + name: b + type: int + - inputBinding: {position: 3, prefix: -c} + name: c + type: int + type: record +- id: d + inputBinding: {position: 6, prefix: -d} + type: + fields: + - inputBinding: {position: 2, prefix: -e} + name: e + type: int + - inputBinding: {position: 4, prefix: -f} + name: f + type: int + type: record +outputs: +- id: args + type: {items: string, type: array} +requirements: [] diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_record_outputeval.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_record_outputeval.cwl new file mode 100644 index 0000000..48f3694 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_record_outputeval.cwl @@ -0,0 +1,22 @@ +arguments: [touch GRC$(inputs.organism_prefix)38.primary_assembly.genome.fa ; touch gencode.v$(inputs.gtf_version).primary_assembly.annotation.gtf] +baseCommand: [bash, -c] +class: CommandLineTool +cwlVersion: v1.2 +inputs: +- {default: M21, id: gtf_version, type: string} +- {default: mouse, id: organism, type: string} +- {default: m, id: organism_prefix, type: string} +outputs: +- id: references + outputBinding: {outputEval: '$({ "genome_fa": { "class": "File", "path": runtime.outdir+"/"+"GRC" + + inputs.organism_prefix + "38.primary_assembly.genome.fa" }, "annotation_gtf": + { "class": "File", "path": runtime.outdir+"/"+"gencode.v" + inputs.gtf_version + + ".primary_assembly.annotation.gtf" } })'} + type: + fields: + - {name: genome_fa, type: File} + - {name: annotation_gtf, type: File} + name: References + type: record +requirements: +- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_record_outputeval_nojs.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_record_outputeval_nojs.cwl new file mode 100644 index 0000000..248c517 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_record_outputeval_nojs.cwl @@ -0,0 +1,22 @@ +arguments: [$(inputs.ref.genome_fa) $(inputs.ref.annotation_gtf)] +baseCommand: echo +class: CommandLineTool +cwlVersion: v1.2 +inputs: +- default: {annotation_gtf: gencode.vM21.primary_assembly.annotation.gtf, genome_fa: GRCm38.primary_assembly.genome.fa} + id: ref + type: + fields: + - {name: genome_fa, type: string} + - {name: annotation_gtf, type: string} + type: record +outputs: +- id: references + outputBinding: {outputEval: $(inputs.ref)} + type: + fields: + - {name: genome_fa, type: string} + - {name: annotation_gtf, type: string} + type: record +- {id: summary, type: stdout} +requirements: [] diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_runtime-outdir.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_runtime-outdir.cwl new file mode 100644 index 0000000..a26a8fb --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_runtime-outdir.cwl @@ -0,0 +1,16 @@ +arguments: ['mkdir -p foo + + touch baz.txt + + touch foo/bar.txt + + '] +baseCommand: [bash, -c] +class: CommandLineTool +cwlVersion: v1.2 +inputs: [] +outputs: +- id: stuff + outputBinding: {glob: $(runtime.outdir)} + type: Directory +requirements: [] diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_schemadef_types_with_import-wf.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_schemadef_types_with_import-wf.cwl new file mode 100644 index 0000000..44ea1ce --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_schemadef_types_with_import-wf.cwl @@ -0,0 +1,64 @@ +class: Workflow +cwlVersion: v1.2 +inputs: +- id: readgroups_bam + type: + fields: + - {name: bam, type: File} + - name: readgroup_meta_list + type: + items: + fields: + - {name: CN, type: string} + - {name: DT, type: string} + - {name: ID, type: string} + - {name: LB, type: string} + - {name: PI, type: string} + - {name: PL, type: string} + - {name: SM, type: string} + name: readgroup_meta + type: record + type: array + name: readgroups_bam_file + type: record +outputs: +- {id: out, outputSource: step1/out, type: string} +requirements: [] +steps: +- id: step1 + in: + - {id: message, source: readgroups_bam} + out: [out] + run: + baseCommand: echo + class: CommandLineTool + cwlVersion: v1.2 + inputs: + - id: message + inputBinding: {valueFrom: '$(self.readgroup_meta_list[0][''DT''])'} + type: + fields: + - {name: bam, type: File} + - name: readgroup_meta_list + type: + items: + fields: + - {name: CN, type: string} + - {name: DT, type: string} + - {name: ID, type: string} + - {name: LB, type: string} + - {name: PI, type: string} + - {name: PL, type: string} + - {name: SM, type: string} + name: readgroup_meta_23 + type: record + type: array + name: readgroups_bam_file_18 + type: record + outputs: + - id: out + outputBinding: {glob: output.txt, loadContents: true, outputEval: '$(self[0].contents)'} + type: string + requirements: + - {class: InlineJavascriptRequirement} + stdout: output.txt diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_stdout_chained_commands.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_stdout_chained_commands.cwl new file mode 100644 index 0000000..2051744 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_stdout_chained_commands.cwl @@ -0,0 +1,16 @@ +arguments: +- echo +- a +- {shellQuote: false, valueFrom: '&&'} +- echo +- b +class: CommandLineTool +cwlVersion: v1.2 +inputs: [] +outputs: +- id: out + outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} + type: string +requirements: +- {class: ShellCommandRequirement} +stdout: out.txt diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_synth-file.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_synth-file.cwl new file mode 100644 index 0000000..4aa8468 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_synth-file.cwl @@ -0,0 +1,10 @@ +baseCommand: [cat] +class: CommandLineTool +cwlVersion: v1.2 +inputs: +- id: names + inputBinding: {position: 1} + type: File +outputs: +- {id: sequence, type: stdout} +requirements: [] diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_valid_schemadef_types_with_import-wf.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_valid_schemadef_types_with_import-wf.cwl new file mode 100644 index 0000000..44ea1ce --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_valid_schemadef_types_with_import-wf.cwl @@ -0,0 +1,64 @@ +class: Workflow +cwlVersion: v1.2 +inputs: +- id: readgroups_bam + type: + fields: + - {name: bam, type: File} + - name: readgroup_meta_list + type: + items: + fields: + - {name: CN, type: string} + - {name: DT, type: string} + - {name: ID, type: string} + - {name: LB, type: string} + - {name: PI, type: string} + - {name: PL, type: string} + - {name: SM, type: string} + name: readgroup_meta + type: record + type: array + name: readgroups_bam_file + type: record +outputs: +- {id: out, outputSource: step1/out, type: string} +requirements: [] +steps: +- id: step1 + in: + - {id: message, source: readgroups_bam} + out: [out] + run: + baseCommand: echo + class: CommandLineTool + cwlVersion: v1.2 + inputs: + - id: message + inputBinding: {valueFrom: '$(self.readgroup_meta_list[0][''DT''])'} + type: + fields: + - {name: bam, type: File} + - name: readgroup_meta_list + type: + items: + fields: + - {name: CN, type: string} + - {name: DT, type: string} + - {name: ID, type: string} + - {name: LB, type: string} + - {name: PI, type: string} + - {name: PL, type: string} + - {name: SM, type: string} + name: readgroup_meta_23 + type: record + type: array + name: readgroups_bam_file_18 + type: record + outputs: + - id: out + outputBinding: {glob: output.txt, loadContents: true, outputEval: '$(self[0].contents)'} + type: string + requirements: + - {class: InlineJavascriptRequirement} + stdout: output.txt diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_wf_ren.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_wf_ren.cwl new file mode 100644 index 0000000..5de38b2 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_packed_wf_ren.cwl @@ -0,0 +1,48 @@ +class: Workflow +cwlVersion: v1.2 +inputs: +- default: {class: File, location: whale.txt} + id: f1 + type: File +- {default: badger.txt, id: newname, type: string} +outputs: [] +requirements: +- {class: StepInputExpressionRequirement} +- {class: InlineJavascriptRequirement} +steps: +- id: rename + in: + - {id: f1, source: f1} + - {id: newname, source: newname} + out: [out] + run: + baseCommand: 'true' + class: CommandLineTool + cwlVersion: v1.2 + inputs: + - {id: srcfile, type: File} + - {id: newname, type: string} + outputs: + - id: outfile + outputBinding: {glob: $(inputs.newname)} + type: File + requirements: + - class: InitialWorkDirRequirement + listing: + - {entry: $(inputs.srcfile), entryname: $(inputs.newname)} +- id: echo + in: + - {id: p, source: rename/out} + - {id: checkname, source: newname} + out: [] + run: + arguments: [sh, -c, "name=`basename $(inputs.p.path)`\nls -l $(inputs.p.path)\nif + test $name = $(inputs.checkname) ; then\n echo success\nelse\n echo expected + basename to be $(inputs.checkname) but was $name\n exit 1\nfi\n"] + class: CommandLineTool + cwlVersion: v1.2 + inputs: + - {id: p, type: File} + - {id: checkname, type: string} + outputs: [] + requirements: [] diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_params_input_length_non_array.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_params_input_length_non_array.cwl new file mode 100644 index 0000000..bbe5084 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_params_input_length_non_array.cwl @@ -0,0 +1,40 @@ +class: CommandLineTool +cwlVersion: v1.2 +inputs: + length: + type: int + default: 1 + bar: + type: + type: record + name: bar_record + fields: + length: + type: int + baz: + type: + type: record + name: baz_record + fields: + length: + type: + type: record + name: length_record + fields: + bap: + type: int + +outputs: + output1: + type: int + outputBinding: + outputEval: $(inputs.length) + output2: + type: int + outputBinding: + outputEval: $(inputs.bar.length) + output3: + type: int + outputBinding: + outputEval: $(inputs.baz.length.bap) +baseCommand: "true" \ No newline at end of file diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_record-order.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_record-order.cwl new file mode 100644 index 0000000..19762da --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_record-order.cwl @@ -0,0 +1,55 @@ +class: CommandLineTool +cwlVersion: v1.2 + +baseCommand: python +inputs: + - id: args.py + type: File + default: + class: File + location: args.py + inputBinding: + position: -1 + - id: a + type: + type: record + fields: + - name: b + type: int + inputBinding: + position: 1 + prefix: -b + - name: c + type: int + inputBinding: + position: 3 + prefix: -c + inputBinding: + position: 5 + prefix: -a + - id: d + type: + type: record + fields: + - name: e + type: int + inputBinding: + position: 2 + prefix: -e + - name: f + type: int + inputBinding: + position: 4 + prefix: -f + inputBinding: + position: 6 + prefix: -d +outputs: + - id: args + type: + type: array + items: string + +hints: + - class: DockerRequirement + dockerPull: docker.io/python:3-slim diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_record_outputeval.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_record_outputeval.cwl new file mode 100644 index 0000000..6540c1e --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_record_outputeval.cwl @@ -0,0 +1,36 @@ +cwlVersion: v1.2 +class: CommandLineTool +requirements: + InlineJavascriptRequirement: {} + +inputs: + gtf_version: + type: string + default: M21 + organism: + type: string + default: mouse + organism_prefix: + type: string + default: m + +baseCommand: + - bash + - -c +arguments: + - touch GRC$(inputs.organism_prefix)38.primary_assembly.genome.fa ; touch gencode.v$(inputs.gtf_version).primary_assembly.annotation.gtf +outputs: + - id: references + type: + name: References + fields: + - name: genome_fa + type: File + - name: annotation_gtf + type: File + type: record + outputBinding: + outputEval: '$({ "genome_fa": { "class": "File", "path": runtime.outdir+"/"+"GRC" + + inputs.organism_prefix + "38.primary_assembly.genome.fa" }, "annotation_gtf": + { "class": "File", "path": runtime.outdir+"/"+"gencode.v" + inputs.gtf_version + + ".primary_assembly.annotation.gtf" } })' diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_record_outputeval_nojs.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_record_outputeval_nojs.cwl new file mode 100644 index 0000000..b29c662 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_record_outputeval_nojs.cwl @@ -0,0 +1,26 @@ +cwlVersion: v1.2 +class: CommandLineTool +inputs: + ref: + type: + type: record + fields: + genome_fa: string + annotation_gtf: string + default: { genome_fa: GRCm38.primary_assembly.genome.fa, + annotation_gtf: gencode.vM21.primary_assembly.annotation.gtf } + +baseCommand: echo +arguments: + - $(inputs.ref.genome_fa) $(inputs.ref.annotation_gtf) +outputs: + references: + type: + type: record + fields: + genome_fa: string + annotation_gtf: string + outputBinding: + outputEval: $(inputs.ref) + summary: + type: stdout diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_runtime-outdir.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_runtime-outdir.cwl new file mode 100644 index 0000000..41bb7b0 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_runtime-outdir.cwl @@ -0,0 +1,14 @@ +cwlVersion: v1.2 +class: CommandLineTool +baseCommand: [bash, -c] +arguments: + - | + mkdir -p foo + touch baz.txt + touch foo/bar.txt +inputs: [] +outputs: + stuff: + type: Directory + outputBinding: + glob: $(runtime.outdir) diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_schemadef_types_with_import-wf.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_schemadef_types_with_import-wf.cwl new file mode 100644 index 0000000..6af93dd --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_schemadef_types_with_import-wf.cwl @@ -0,0 +1,25 @@ +#!/usr/bin/env cwl-runner +# See https://github.com/jeremiahsavage/cwl_schemadef/, thanks to Jeremiah H. Savage. +cwlVersion: v1.2 +class: Workflow + +requirements: + - class: SchemaDefRequirement + types: + - $import: schemadef_types_with_import_readgroup.yml + +inputs: + readgroups_bam: + type: "schemadef_types_with_import_readgroup.yml#readgroups_bam_file" + +steps: + step1: + run: schemadef_types_with_import-tool.cwl + in: + message: readgroups_bam + out: [out] + +outputs: + out: + type: string + outputSource: step1/out diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_stdout_chained_commands.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_stdout_chained_commands.cwl new file mode 100644 index 0000000..b0cf25d --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_stdout_chained_commands.cwl @@ -0,0 +1,19 @@ +cwlVersion: v1.2 +class: CommandLineTool +requirements: + - class: ShellCommandRequirement +inputs: [] +outputs: + out: + type: string + outputBinding: + glob: out.txt + loadContents: true + outputEval: $(self[0].contents) +stdout: out.txt +arguments: + - echo + - a + - {valueFrom: '&&', shellQuote: false} + - echo + - b diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_synth-file.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_synth-file.cwl new file mode 100644 index 0000000..10b59c2 --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_synth-file.cwl @@ -0,0 +1,14 @@ +cwlVersion: v1.2 +class: CommandLineTool + +inputs: + names: + type: File + inputBinding: + position: 1 + +baseCommand: [ cat ] + +outputs: + sequence: + type: stdout diff --git a/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_wf_ren.cwl b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_wf_ren.cwl new file mode 100644 index 0000000..d2affce --- /dev/null +++ b/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_wf_ren.cwl @@ -0,0 +1,29 @@ +class: Workflow +cwlVersion: v1.2 +inputs: + f1: + type: File + default: + class: File + location: whale.txt + newname: + type: string + default: "badger.txt" +outputs: [] +requirements: + StepInputExpressionRequirement: {} + InlineJavascriptRequirement: {} +steps: + rename: + in: + f1: f1 + newname: newname + run: rename.cwl + out: [out] + + echo: + in: + p: rename/out + checkname: newname + out: [] + run: check.cwl