From 0e378db54754585efeff32adc98f2d3105a586c9 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 4 Nov 2025 09:43:45 +0100 Subject: [PATCH 1/3] improve packaging metadata; start versioning at 2.0.0 --- pom.xml | 26 ++++++++++++++++++++++---- 1 file changed, 22 insertions(+), 4 deletions(-) diff --git a/pom.xml b/pom.xml index 35ec2597..be9e884c 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,8 @@ jar Common Workflow Language SDK Schema Salad for parsing documents corresponding to the https://w3id.org/cwl/cwl# schema.]]> - 1.2.0-SNAPSHOT + 2.0.0 + https://www.commonwl.org/ 3.19.0 UTF-8 @@ -18,6 +19,18 @@ https://www.apache.org/licenses/LICENSE-2.0.txt + + + Michael R. Crusoe + mrc@commonwl.org + Common Workflow Language, a member project of Software Freedom Conservancy, Inc. + + + + scm:git:git://github.com/common-workflow-language/cwljava.git + scm:git:ssh://github.com/common-workflow-language/cwljava.git + https://github.com/common-workflow-language/cwljava/tree/cwl-1.2.0/ + @@ -51,9 +64,14 @@ org.apache.maven.plugins maven-javadoc-plugin - 3.12.0 - - + 3.12.0 + attach-javadocsjar + + + org.apache.maven.plugins + maven-source-plugin + 3.3.1 + attach-sourcesjar-no-fork org.apache.maven.plugins From 7c75d46b22c3a36cbbdbf3bcef1fc9598e6ebc48 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 4 Nov 2025 09:48:24 +0100 Subject: [PATCH 2/3] regen with escaped javadoc contents --- .../cwlsdk/cwl1_1/CommandInputParameter.java | 4 +-- .../cwl1_1/CommandInputParameterImpl.java | 4 +-- .../cwl1_1/CommandInputRecordField.java | 4 +-- .../cwl1_1/CommandInputRecordFieldImpl.java | 4 +-- .../cwlsdk/cwl1_1/CommandLineBinding.java | 6 ++-- .../cwlsdk/cwl1_1/CommandLineBindingImpl.java | 6 ++-- .../cwlsdk/cwl1_1/CommandLineTool.java | 6 ++-- .../cwlsdk/cwl1_1/CommandLineToolImpl.java | 6 ++-- .../cwlsdk/cwl1_1/CommandOutputBinding.java | 6 ++-- .../cwl1_1/CommandOutputBindingImpl.java | 6 ++-- .../cwlsdk/cwl1_1/CommandOutputParameter.java | 2 +- .../cwl1_1/CommandOutputParameterImpl.java | 2 +- .../cwl1_1/CommandOutputRecordField.java | 2 +- .../cwl1_1/CommandOutputRecordFieldImpl.java | 2 +- .../org/commonwl/cwlsdk/cwl1_1/Directory.java | 4 +-- .../commonwl/cwlsdk/cwl1_1/DirectoryImpl.java | 4 +-- .../cwlsdk/cwl1_1/DockerRequirement.java | 4 +-- .../cwlsdk/cwl1_1/DockerRequirementImpl.java | 4 +-- .../cwlsdk/cwl1_1/EnvVarRequirement.java | 2 +- .../cwlsdk/cwl1_1/EnvVarRequirementImpl.java | 2 +- .../cwl1_1/ExpressionToolOutputParameter.java | 2 +- .../ExpressionToolOutputParameterImpl.java | 2 +- .../org/commonwl/cwlsdk/cwl1_1/FieldBase.java | 2 +- .../java/org/commonwl/cwlsdk/cwl1_1/File.java | 20 +++++------ .../org/commonwl/cwlsdk/cwl1_1/FileImpl.java | 20 +++++------ .../cwl1_1/InitialWorkDirRequirement.java | 2 +- .../cwl1_1/InitialWorkDirRequirementImpl.java | 2 +- .../cwl1_1/InlineJavascriptRequirement.java | 2 +- .../InlineJavascriptRequirementImpl.java | 2 +- .../cwl1_1/InplaceUpdateRequirement.java | 2 +- .../cwl1_1/InplaceUpdateRequirementImpl.java | 2 +- .../commonwl/cwlsdk/cwl1_1/InputBinding.java | 2 +- .../cwlsdk/cwl1_1/InputBindingImpl.java | 2 +- .../cwlsdk/cwl1_1/InputParameter.java | 4 +-- .../cwlsdk/cwl1_1/InputRecordField.java | 4 +-- .../cwlsdk/cwl1_1/InputRecordFieldImpl.java | 4 +-- .../commonwl/cwlsdk/cwl1_1/LoadContents.java | 2 +- .../cwlsdk/cwl1_1/LoadListingRequirement.java | 2 +- .../cwl1_1/LoadListingRequirementImpl.java | 2 +- .../MultipleInputFeatureRequirement.java | 2 +- .../MultipleInputFeatureRequirementImpl.java | 2 +- .../commonwl/cwlsdk/cwl1_1/NetworkAccess.java | 2 +- .../cwlsdk/cwl1_1/NetworkAccessImpl.java | 2 +- .../cwlsdk/cwl1_1/OutputParameter.java | 2 +- .../cwlsdk/cwl1_1/OutputRecordField.java | 2 +- .../cwlsdk/cwl1_1/OutputRecordFieldImpl.java | 2 +- .../org/commonwl/cwlsdk/cwl1_1/Parameter.java | 2 +- .../cwlsdk/cwl1_1/ResourceRequirement.java | 20 +++++------ .../cwl1_1/ResourceRequirementImpl.java | 20 +++++------ .../cwl1_1/ScatterFeatureRequirement.java | 2 +- .../cwl1_1/ScatterFeatureRequirementImpl.java | 2 +- .../cwlsdk/cwl1_1/SchemaDefRequirement.java | 2 +- .../cwl1_1/SchemaDefRequirementImpl.java | 2 +- .../cwlsdk/cwl1_1/SecondaryFileSchema.java | 2 +- .../cwl1_1/SecondaryFileSchemaImpl.java | 2 +- .../cwl1_1/ShellCommandRequirement.java | 2 +- .../cwl1_1/ShellCommandRequirementImpl.java | 2 +- .../java/org/commonwl/cwlsdk/cwl1_1/Sink.java | 2 +- .../cwlsdk/cwl1_1/SoftwareRequirement.java | 2 +- .../cwl1_1/SoftwareRequirementImpl.java | 2 +- .../StepInputExpressionRequirement.java | 2 +- .../StepInputExpressionRequirementImpl.java | 2 +- .../cwl1_1/SubworkflowFeatureRequirement.java | 2 +- .../SubworkflowFeatureRequirementImpl.java | 2 +- .../commonwl/cwlsdk/cwl1_1/ToolTimeLimit.java | 2 +- .../cwlsdk/cwl1_1/ToolTimeLimitImpl.java | 2 +- .../org/commonwl/cwlsdk/cwl1_1/WorkReuse.java | 2 +- .../commonwl/cwlsdk/cwl1_1/WorkReuseImpl.java | 2 +- .../cwlsdk/cwl1_1/WorkflowInputParameter.java | 4 +-- .../cwl1_1/WorkflowInputParameterImpl.java | 4 +-- .../cwl1_1/WorkflowOutputParameter.java | 4 +-- .../cwl1_1/WorkflowOutputParameterImpl.java | 4 +-- .../commonwl/cwlsdk/cwl1_1/WorkflowStep.java | 2 +- .../cwlsdk/cwl1_1/WorkflowStepImpl.java | 2 +- .../cwlsdk/cwl1_1/WorkflowStepInput.java | 14 ++++---- .../cwlsdk/cwl1_1/WorkflowStepInputImpl.java | 14 ++++---- .../cwlsdk/cwl1_2/CommandInputParameter.java | 2 +- .../cwl1_2/CommandInputParameterImpl.java | 2 +- .../cwl1_2/CommandInputRecordField.java | 2 +- .../cwl1_2/CommandInputRecordFieldImpl.java | 2 +- .../cwlsdk/cwl1_2/CommandLineBinding.java | 4 +-- .../cwlsdk/cwl1_2/CommandLineBindingImpl.java | 4 +-- .../cwlsdk/cwl1_2/CommandLineTool.java | 10 +++--- .../cwlsdk/cwl1_2/CommandLineToolImpl.java | 10 +++--- .../cwlsdk/cwl1_2/CommandOutputBinding.java | 4 +-- .../cwl1_2/CommandOutputBindingImpl.java | 4 +-- .../cwlsdk/cwl1_2/CommandOutputParameter.java | 2 +- .../cwl1_2/CommandOutputParameterImpl.java | 2 +- .../cwl1_2/CommandOutputRecordField.java | 2 +- .../cwl1_2/CommandOutputRecordFieldImpl.java | 2 +- .../org/commonwl/cwlsdk/cwl1_2/Directory.java | 4 +-- .../commonwl/cwlsdk/cwl1_2/DirectoryImpl.java | 4 +-- .../org/commonwl/cwlsdk/cwl1_2/Dirent.java | 2 +- .../commonwl/cwlsdk/cwl1_2/DirentImpl.java | 2 +- .../cwlsdk/cwl1_2/DockerRequirement.java | 4 +-- .../cwlsdk/cwl1_2/DockerRequirementImpl.java | 4 +-- .../cwlsdk/cwl1_2/EnvVarRequirement.java | 2 +- .../cwlsdk/cwl1_2/EnvVarRequirementImpl.java | 2 +- .../cwlsdk/cwl1_2/ExpressionTool.java | 2 +- .../cwlsdk/cwl1_2/ExpressionToolImpl.java | 2 +- .../cwl1_2/ExpressionToolOutputParameter.java | 2 +- .../ExpressionToolOutputParameterImpl.java | 2 +- .../org/commonwl/cwlsdk/cwl1_2/FieldBase.java | 2 +- .../java/org/commonwl/cwlsdk/cwl1_2/File.java | 18 +++++----- .../org/commonwl/cwlsdk/cwl1_2/FileImpl.java | 18 +++++----- .../cwl1_2/InitialWorkDirRequirement.java | 2 +- .../cwl1_2/InitialWorkDirRequirementImpl.java | 2 +- .../cwl1_2/InlineJavascriptRequirement.java | 2 +- .../InlineJavascriptRequirementImpl.java | 2 +- .../cwl1_2/InplaceUpdateRequirement.java | 2 +- .../cwl1_2/InplaceUpdateRequirementImpl.java | 2 +- .../cwlsdk/cwl1_2/InputParameter.java | 2 +- .../cwlsdk/cwl1_2/InputRecordField.java | 2 +- .../cwlsdk/cwl1_2/InputRecordFieldImpl.java | 2 +- .../cwlsdk/cwl1_2/LoadListingRequirement.java | 2 +- .../cwl1_2/LoadListingRequirementImpl.java | 2 +- .../MultipleInputFeatureRequirement.java | 2 +- .../MultipleInputFeatureRequirementImpl.java | 2 +- .../commonwl/cwlsdk/cwl1_2/NetworkAccess.java | 2 +- .../cwlsdk/cwl1_2/NetworkAccessImpl.java | 2 +- .../org/commonwl/cwlsdk/cwl1_2/Operation.java | 2 +- .../commonwl/cwlsdk/cwl1_2/OperationImpl.java | 2 +- .../cwl1_2/OperationInputParameter.java | 2 +- .../cwl1_2/OperationInputParameterImpl.java | 2 +- .../cwl1_2/OperationOutputParameter.java | 2 +- .../cwl1_2/OperationOutputParameterImpl.java | 2 +- .../cwlsdk/cwl1_2/OutputParameter.java | 2 +- .../cwlsdk/cwl1_2/OutputRecordField.java | 2 +- .../cwlsdk/cwl1_2/OutputRecordFieldImpl.java | 2 +- .../org/commonwl/cwlsdk/cwl1_2/Parameter.java | 2 +- .../org/commonwl/cwlsdk/cwl1_2/Process.java | 2 +- .../cwlsdk/cwl1_2/ResourceRequirement.java | 22 ++++++------ .../cwl1_2/ResourceRequirementImpl.java | 22 ++++++------ .../cwl1_2/ScatterFeatureRequirement.java | 2 +- .../cwl1_2/ScatterFeatureRequirementImpl.java | 2 +- .../cwlsdk/cwl1_2/SchemaDefRequirement.java | 2 +- .../cwl1_2/SchemaDefRequirementImpl.java | 2 +- .../cwlsdk/cwl1_2/SecondaryFileSchema.java | 2 +- .../cwl1_2/SecondaryFileSchemaImpl.java | 2 +- .../cwl1_2/ShellCommandRequirement.java | 2 +- .../cwl1_2/ShellCommandRequirementImpl.java | 2 +- .../java/org/commonwl/cwlsdk/cwl1_2/Sink.java | 2 +- .../cwlsdk/cwl1_2/SoftwareRequirement.java | 2 +- .../cwl1_2/SoftwareRequirementImpl.java | 2 +- .../StepInputExpressionRequirement.java | 2 +- .../StepInputExpressionRequirementImpl.java | 2 +- .../cwl1_2/SubworkflowFeatureRequirement.java | 2 +- .../SubworkflowFeatureRequirementImpl.java | 2 +- .../commonwl/cwlsdk/cwl1_2/ToolTimeLimit.java | 2 +- .../cwlsdk/cwl1_2/ToolTimeLimitImpl.java | 2 +- .../org/commonwl/cwlsdk/cwl1_2/WorkReuse.java | 2 +- .../commonwl/cwlsdk/cwl1_2/WorkReuseImpl.java | 2 +- .../org/commonwl/cwlsdk/cwl1_2/Workflow.java | 6 ++-- .../commonwl/cwlsdk/cwl1_2/WorkflowImpl.java | 6 ++-- .../cwlsdk/cwl1_2/WorkflowInputParameter.java | 2 +- .../cwl1_2/WorkflowInputParameterImpl.java | 2 +- .../cwl1_2/WorkflowOutputParameter.java | 4 +-- .../cwl1_2/WorkflowOutputParameterImpl.java | 4 +-- .../commonwl/cwlsdk/cwl1_2/WorkflowStep.java | 4 +-- .../cwlsdk/cwl1_2/WorkflowStepImpl.java | 4 +-- .../cwlsdk/cwl1_2/WorkflowStepInput.java | 34 +++++++++---------- .../cwlsdk/cwl1_2/WorkflowStepInputImpl.java | 34 +++++++++---------- 162 files changed, 329 insertions(+), 329 deletions(-) diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputParameter.java index 950f71bd..410b3a48 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputParameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputParameter.java @@ -65,7 +65,7 @@ public interface CommandInputParameter extends InputParameter, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool @@ -127,7 +127,7 @@ public interface CommandInputParameter extends InputParameter, Saveable { * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * * */ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputParameterImpl.java index 6d30b778..ed59f1f2 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputParameterImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputParameterImpl.java @@ -86,7 +86,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool @@ -168,7 +168,7 @@ public Object getFormat() { * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * * */ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordField.java index 7b51b9d0..0d8ff342 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordField.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordField.java @@ -80,7 +80,7 @@ public interface CommandInputRecordField extends InputRecordField, CommandLineBi * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool @@ -135,7 +135,7 @@ public interface CommandInputRecordField extends InputRecordField, CommandLineBi * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * * */ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordFieldImpl.java index bdc8c333..4521f10e 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordFieldImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordFieldImpl.java @@ -111,7 +111,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool @@ -181,7 +181,7 @@ public Object getFormat() { * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * * */ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBinding.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBinding.java index b1c37c5f..f73e19ac 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBinding.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBinding.java @@ -21,8 +21,8 @@ * Auto-generated interface for https://w3id.org/cwl/cwl#CommandLineBinding
This interface is implemented by {@link CommandLineBindingImpl}
When listed under `inputBinding` in the input schema, the term - "value" refers to the the corresponding value in the input object. For - binding objects listed in `CommandLineTool.arguments`, the term "value" + "value" refers to the the corresponding value in the input object. For + binding objects listed in `CommandLineTool.arguments`, the term "value" refers to the effective value after evaluating `valueFrom`. The binding behavior when building the command line depends on the data @@ -71,7 +71,7 @@ public interface CommandLineBinding extends InputBinding, Saveable { * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * *
*/ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBindingImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBindingImpl.java index 6e7a6deb..023e4788 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBindingImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBindingImpl.java @@ -24,8 +24,8 @@ * Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandLineBinding
When listed under `inputBinding` in the input schema, the term - "value" refers to the the corresponding value in the input object. For - binding objects listed in `CommandLineTool.arguments`, the term "value" + "value" refers to the the corresponding value in the input object. For + binding objects listed in `CommandLineTool.arguments`, the term "value" refers to the effective value after evaluating `valueFrom`. The binding behavior when building the command line depends on the data @@ -82,7 +82,7 @@ public java.util.Map getExtensionFields() { * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * *
*/ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineTool.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineTool.java index 56602b42..387e1bd0 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineTool.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineTool.java @@ -150,7 +150,7 @@ public interface CommandLineTool extends Process, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stdin
*
- * A path to a file whose contents must be piped into the command's + * A path to a file whose contents must be piped into the command's * standard input stream. * *
*/ @@ -159,7 +159,7 @@ public interface CommandLineTool extends Process, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stderr
*
- * Capture the command's standard error stream to a file written to + * Capture the command's standard error stream to a file written to * the designated output directory. * * If `stderr` is a string, it specifies the file name to use. @@ -175,7 +175,7 @@ public interface CommandLineTool extends Process, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stdout
*
- * Capture the command's standard output stream to a file written to + * Capture the command's standard output stream to a file written to * the designated output directory. * * If `stdout` is a string, it specifies the file name to use. diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineToolImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineToolImpl.java index 09b01b2b..e7c3ac24 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineToolImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineToolImpl.java @@ -216,7 +216,7 @@ public java.util.Optional> getArguments() { /** * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stdin
*
- * A path to a file whose contents must be piped into the command's + * A path to a file whose contents must be piped into the command's * standard input stream. * *
*/ @@ -230,7 +230,7 @@ public Object getStdin() { /** * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stderr
*
- * Capture the command's standard error stream to a file written to + * Capture the command's standard error stream to a file written to * the designated output directory. * * If `stderr` is a string, it specifies the file name to use. @@ -251,7 +251,7 @@ public Object getStderr() { /** * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stdout
*
- * Capture the command's standard output stream to a file written to + * Capture the command's standard output stream to a file written to * the designated output directory. * * If `stdout` is a string, it specifies the file name to use. diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputBinding.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputBinding.java index 0eaf3c1a..019a06db 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputBinding.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputBinding.java @@ -42,7 +42,7 @@ public interface CommandOutputBinding extends LoadContents, Saveable { * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * *
*/ @@ -75,9 +75,9 @@ public interface CommandOutputBinding extends LoadContents, Saveable { * match and return files/directories which actually exist. * * If the value of glob is a relative path pattern (does not - * begin with a slash '/') then it is resolved relative to the + * begin with a slash '/') then it is resolved relative to the * output directory. If the value of the glob is an absolute - * path pattern (it does begin with a slash '/') then it must + * path pattern (it does begin with a slash '/') then it must * refer to a path within the output directory. It is an error * if any glob resolves to a path outside the output directory. * Specifically this means globs that resolve to paths outside the output diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputBindingImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputBindingImpl.java index cadccac1..597ac2e8 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputBindingImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputBindingImpl.java @@ -53,7 +53,7 @@ public java.util.Map getExtensionFields() { * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * *
*/ @@ -96,9 +96,9 @@ public java.util.Optional getLoadListing() { * match and return files/directories which actually exist. * * If the value of glob is a relative path pattern (does not - * begin with a slash '/') then it is resolved relative to the + * begin with a slash '/') then it is resolved relative to the * output directory. If the value of the glob is an absolute - * path pattern (it does begin with a slash '/') then it must + * path pattern (it does begin with a slash '/') then it must * refer to a path within the output directory. It is an error * if any glob resolves to a path outside the output directory. * Specifically this means globs that resolve to paths outside the output diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputParameter.java index 86153645..72ae65c2 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputParameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputParameter.java @@ -65,7 +65,7 @@ public interface CommandOutputParameter extends OutputParameter, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputParameterImpl.java index e39a9a03..b0b445e8 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputParameterImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputParameterImpl.java @@ -86,7 +86,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordField.java index 538ee909..e26042b5 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordField.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordField.java @@ -80,7 +80,7 @@ public interface CommandOutputRecordField extends OutputRecordField, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordFieldImpl.java index bf765d25..39b9f786 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordFieldImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordFieldImpl.java @@ -111,7 +111,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Directory.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Directory.java index 5742e263..44fb4f24 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Directory.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Directory.java @@ -109,8 +109,8 @@ public interface Directory extends Saveable { * `opendir(2)` syscall. * * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) - * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, - * ``, ``, and ``) or characters + * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, + * `<space>`, `<tab>`, and `<newline>`) or characters * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) * then implementations may terminate the process with a diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/DirectoryImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/DirectoryImpl.java index 0bcc3dd2..ebfc1eba 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/DirectoryImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/DirectoryImpl.java @@ -130,8 +130,8 @@ public java.util.Optional getLocation() { * `opendir(2)` syscall. * * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) - * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, - * ``, ``, and ``) or characters + * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, + * `<space>`, `<tab>`, and `<newline>`) or characters * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) * then implementations may terminate the process with a diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirement.java index 1424e698..d9d065a5 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirement.java @@ -68,7 +68,7 @@ concerns of the implicit hidden execution point (For further discussion, see If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a DockerRequirement, the environment variables must be provided to Docker - using `--env` or `--env-file` and interact with the container's preexisting + using `--env` or `--env-file` and interact with the container's preexisting environment as defined by Docker.
*/ @@ -80,7 +80,7 @@ public interface DockerRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/class
*
- * Always 'DockerRequirement' *
+ * Always 'DockerRequirement' *
*/ DockerRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirementImpl.java index 17290703..3f132d70 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirementImpl.java @@ -71,7 +71,7 @@ concerns of the implicit hidden execution point (For further discussion, see If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a DockerRequirement, the environment variables must be provided to Docker - using `--env` or `--env-file` and interact with the container's preexisting + using `--env` or `--env-file` and interact with the container's preexisting environment as defined by Docker. */ @@ -91,7 +91,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/class
*
- * Always 'DockerRequirement' *
+ * Always 'DockerRequirement' * */ public DockerRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirement.java index e06f7d2b..adbc73a3 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirement.java @@ -31,7 +31,7 @@ public interface EnvVarRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#EnvVarRequirement/class
*
- * Always 'EnvVarRequirement' *
+ * Always 'EnvVarRequirement' * */ EnvVarRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirementImpl.java index 31996783..feeb54f3 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirementImpl.java @@ -42,7 +42,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#EnvVarRequirement/class
*
- * Always 'EnvVarRequirement' *
+ * Always 'EnvVarRequirement' * */ public EnvVarRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolOutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolOutputParameter.java index f0028d09..614d46ab 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolOutputParameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolOutputParameter.java @@ -64,7 +64,7 @@ public interface ExpressionToolOutputParameter extends OutputParameter, Saveable * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolOutputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolOutputParameterImpl.java index c2dc1a63..5bca916e 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolOutputParameterImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolOutputParameterImpl.java @@ -85,7 +85,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/FieldBase.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/FieldBase.java index 392c67ed..ee318343 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/FieldBase.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/FieldBase.java @@ -57,7 +57,7 @@ public interface FieldBase extends Labeled, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/File.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/File.java index 2127913a..2bf6414a 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/File.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/File.java @@ -37,8 +37,8 @@ runtime environment of a command line tool execution (for command line tool outputs). If no `location` or `path` is specified, a file object must specify - `contents` with the UTF-8 text content of the file. This is a "file - literal". File literals do not correspond to external resources, but are + `contents` with the UTF-8 text content of the file. This is a "file + literal". File literals do not correspond to external resources, but are created on disk with `contents` with when needed for a executing a tool. Where appropriate, expressions can return file literals to define new files on a runtime. The maximum size of `contents` is 64 kilobytes. @@ -136,8 +136,8 @@ public interface File extends Saveable { * field to `location`, and remove the `path` field. * * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) - * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, - * ``, ``, and ``) or characters + * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, + * `<space>`, `<tab>`, and `<newline>`) or characters * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) * then implementations may terminate the process with a @@ -168,7 +168,7 @@ public interface File extends Saveable { * Getter for property https://w3id.org/cwl/cwl#File/dirname
*
* The name of the directory containing file, that is, the path leading up - * to the final slash in the path such that `dirname + '/' + basename == + * to the final slash in the path such that `dirname + '/' + basename == * path`. * * The implementation must set this field based on the value of `path` @@ -212,7 +212,7 @@ public interface File extends Saveable { * Getter for property https://w3id.org/cwl/cwl#File/checksum
*
* Optional hash code for validating file integrity. Currently must be in the form - * "sha1$ + hexadecimal string" using the SHA-1 algorithm. + * "sha1$ + hexadecimal string" using the SHA-1 algorithm. * *
*/ @@ -248,10 +248,10 @@ public interface File extends Saveable { * input file format is the same, `owl:equivalentClass` or * `rdfs:subClassOf` the format required by the input parameter. * `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if - * ` owl:equivalentClass ` and ` owl:subclassOf ` then infer - * ` owl:subclassOf `. + * `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer + * `<C> owl:subclassOf <A>`. * - * File format ontologies may be provided in the "$schemas" metadata at the + * File format ontologies may be provided in the "$schemas" metadata at the * root of the document. If no ontologies are specified in `$schemas`, the * runtime may perform exact file format matches. * *
@@ -270,7 +270,7 @@ public interface File extends Saveable { * * If `loadContents` of `inputBinding` or `outputBinding` is true and * `location` is valid, the implementation must read up to the first 64 - * KiB of text from the file and place it in the "contents" field. + * KiB of text from the file and place it in the "contents" field. * * */ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/FileImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/FileImpl.java index 1d9098d1..9f53483f 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/FileImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/FileImpl.java @@ -40,8 +40,8 @@ runtime environment of a command line tool execution (for command line tool outputs). If no `location` or `path` is specified, a file object must specify - `contents` with the UTF-8 text content of the file. This is a "file - literal". File literals do not correspond to external resources, but are + `contents` with the UTF-8 text content of the file. This is a "file + literal". File literals do not correspond to external resources, but are created on disk with `contents` with when needed for a executing a tool. Where appropriate, expressions can return file literals to define new files on a runtime. The maximum size of `contents` is 64 kilobytes. @@ -157,8 +157,8 @@ public java.util.Optional getLocation() { * field to `location`, and remove the `path` field. * * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) - * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, - * ``, ``, and ``) or characters + * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, + * `<space>`, `<tab>`, and `<newline>`) or characters * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) * then implementations may terminate the process with a @@ -199,7 +199,7 @@ public java.util.Optional getBasename() { * Getter for property https://w3id.org/cwl/cwl#File/dirname
*
* The name of the directory containing file, that is, the path leading up - * to the final slash in the path such that `dirname + '/' + basename == + * to the final slash in the path such that `dirname + '/' + basename == * path`. * * The implementation must set this field based on the value of `path` @@ -258,7 +258,7 @@ public java.util.Optional getNameext() { * Getter for property https://w3id.org/cwl/cwl#File/checksum
*
* Optional hash code for validating file integrity. Currently must be in the form - * "sha1$ + hexadecimal string" using the SHA-1 algorithm. + * "sha1$ + hexadecimal string" using the SHA-1 algorithm. * *
*/ @@ -309,10 +309,10 @@ public java.util.Optional> getSecondaryFiles() { * input file format is the same, `owl:equivalentClass` or * `rdfs:subClassOf` the format required by the input parameter. * `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if - * ` owl:equivalentClass ` and ` owl:subclassOf ` then infer - * ` owl:subclassOf `. + * `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer + * `<C> owl:subclassOf <A>`. * - * File format ontologies may be provided in the "$schemas" metadata at the + * File format ontologies may be provided in the "$schemas" metadata at the * root of the document. If no ontologies are specified in `$schemas`, the * runtime may perform exact file format matches. * *
@@ -336,7 +336,7 @@ public java.util.Optional getFormat() { * * If `loadContents` of `inputBinding` or `outputBinding` is true and * `location` is valid, the implementation must read up to the first 64 - * KiB of text from the file and place it in the "contents" field. + * KiB of text from the file and place it in the "contents" field. * * */ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirement.java index 52ce795e..993b1cdd 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirement.java @@ -40,7 +40,7 @@ public interface InitialWorkDirRequirement extends ProcessRequirement, Saveable * designated output directory prior to executing the command line tool. * * May be an expression. If so, the expression return value must validate as - * `{type: array, items: ["null", File, File[], Directory, Directory[], Dirent]}`. + * `{type: array, items: ["null", File, File[], Directory, Directory[], Dirent]}`. * * Files or Directories which are listed in the input parameters and * appear in the `InitialWorkDirRequirement` listing must have their diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirementImpl.java index 905e7ba9..585a6681 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirementImpl.java @@ -56,7 +56,7 @@ public InitialWorkDirRequirement_class getClass_() { * designated output directory prior to executing the command line tool. * * May be an expression. If so, the expression return value must validate as - * `{type: array, items: ["null", File, File[], Directory, Directory[], Dirent]}`. + * `{type: array, items: ["null", File, File[], Directory, Directory[], Dirent]}`. * * Files or Directories which are listed in the input parameters and * appear in the `InitialWorkDirRequirement` listing must have their diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirement.java index 20cb3830..ce361717 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirement.java @@ -32,7 +32,7 @@ public interface InlineJavascriptRequirement extends ProcessRequirement, Saveabl /** * Getter for property https://w3id.org/cwl/cwl#InlineJavascriptRequirement/class
*
- * Always 'InlineJavascriptRequirement' *
+ * Always 'InlineJavascriptRequirement' * */ InlineJavascriptRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirementImpl.java index 7074770c..d3fecbc1 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirementImpl.java @@ -43,7 +43,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#InlineJavascriptRequirement/class
*
- * Always 'InlineJavascriptRequirement' *
+ * Always 'InlineJavascriptRequirement' * */ public InlineJavascriptRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirement.java index 5a5322d3..9e47cb5c 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirement.java @@ -59,7 +59,7 @@ public interface InplaceUpdateRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#InplaceUpdateRequirement/class
*
- * Always 'InplaceUpdateRequirement' *
+ * Always 'InplaceUpdateRequirement' * */ InplaceUpdateRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirementImpl.java index e792af7d..539cfafd 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirementImpl.java @@ -70,7 +70,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#InplaceUpdateRequirement/class
*
- * Always 'InplaceUpdateRequirement' *
+ * Always 'InplaceUpdateRequirement' * */ public InplaceUpdateRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputBinding.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputBinding.java index 2c2d4e94..7fceba16 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputBinding.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputBinding.java @@ -35,7 +35,7 @@ public interface InputBinding extends Saveable { * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * * */ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputBindingImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputBindingImpl.java index 6623cc74..79bd3638 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputBindingImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputBindingImpl.java @@ -46,7 +46,7 @@ public java.util.Map getExtensionFields() { * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * * */ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputParameter.java index 82310a9c..e3d87d6b 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputParameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputParameter.java @@ -57,7 +57,7 @@ public interface InputParameter extends Parameter, InputFormat, LoadContents, Sa * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool @@ -119,7 +119,7 @@ public interface InputParameter extends Parameter, InputFormat, LoadContents, Sa * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * * */ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordField.java index 9e26261e..4da330ac 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordField.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordField.java @@ -80,7 +80,7 @@ public interface InputRecordField extends CWLRecordField, FieldBase, InputFormat * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool @@ -135,7 +135,7 @@ public interface InputRecordField extends CWLRecordField, FieldBase, InputFormat * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * * */ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordFieldImpl.java index 3898945e..9dfadc92 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordFieldImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordFieldImpl.java @@ -111,7 +111,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool @@ -181,7 +181,7 @@ public Object getFormat() { * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * * */ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadContents.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadContents.java index 07930367..c3433e39 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadContents.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadContents.java @@ -31,7 +31,7 @@ public interface LoadContents extends Saveable { * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * * */ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirement.java index c9f88690..056180cb 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirement.java @@ -31,7 +31,7 @@ public interface LoadListingRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#LoadListingRequirement/class
*
- * Always 'LoadListingRequirement' *
+ * Always 'LoadListingRequirement' * */ LoadListingRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirementImpl.java index 6b46c160..8923f1eb 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirementImpl.java @@ -42,7 +42,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#LoadListingRequirement/class
*
- * Always 'LoadListingRequirement' *
+ * Always 'LoadListingRequirement' * */ public LoadListingRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirement.java index 0a1ebb9d..905d851c 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirement.java @@ -31,7 +31,7 @@ public interface MultipleInputFeatureRequirement extends ProcessRequirement, Sav /** * Getter for property https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement/class
*
- * Always 'MultipleInputFeatureRequirement' *
+ * Always 'MultipleInputFeatureRequirement' * */ MultipleInputFeatureRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirementImpl.java index 18dad168..8343a743 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirementImpl.java @@ -42,7 +42,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement/class
*
- * Always 'MultipleInputFeatureRequirement' *
+ * Always 'MultipleInputFeatureRequirement' * */ public MultipleInputFeatureRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccess.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccess.java index 8317a2d2..137c4304 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccess.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccess.java @@ -44,7 +44,7 @@ public interface NetworkAccess extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#NetworkAccess/class
*
- * Always 'NetworkAccess' *
+ * Always 'NetworkAccess' * */ NetworkAccess_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccessImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccessImpl.java index f65e93c7..7468c94f 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccessImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccessImpl.java @@ -55,7 +55,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#NetworkAccess/class
*
- * Always 'NetworkAccess' *
+ * Always 'NetworkAccess' * */ public NetworkAccess_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputParameter.java index 7ff65a02..eddf67a2 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputParameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputParameter.java @@ -57,7 +57,7 @@ public interface OutputParameter extends Parameter, OutputFormat, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordField.java index 57cc62a4..7fa04694 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordField.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordField.java @@ -80,7 +80,7 @@ public interface OutputRecordField extends CWLRecordField, FieldBase, OutputForm * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordFieldImpl.java index 4d98b3c5..f43a03e9 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordFieldImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordFieldImpl.java @@ -111,7 +111,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Parameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Parameter.java index 70944268..0c69293a 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Parameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Parameter.java @@ -59,7 +59,7 @@ public interface Parameter extends FieldBase, Documented, Identified, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirement.java index 469c950e..5d7e16a9 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirement.java @@ -21,24 +21,24 @@ * Auto-generated interface for https://w3id.org/cwl/cwl#ResourceRequirement
This interface is implemented by {@link ResourceRequirementImpl}
Specify basic hardware resource requirements. - "min" is the minimum amount of a resource that must be reserved to schedule - a job. If "min" cannot be satisfied, the job should not be run. + "min" is the minimum amount of a resource that must be reserved to schedule + a job. If "min" cannot be satisfied, the job should not be run. - "max" is the maximum amount of a resource that the job shall be permitted + "max" is the maximum amount of a resource that the job shall be permitted to use. If a node has sufficient resources, multiple jobs may be scheduled - on a single node provided each job's "max" resource requirements are - met. If a job attempts to exceed its "max" resource allocation, an + on a single node provided each job's "max" resource requirements are + met. If a job attempts to exceed its "max" resource allocation, an implementation may deny additional resources, which may result in job failure. - If "min" is specified but "max" is not, then "max" == "min" - If "max" is specified by "min" is not, then "min" == "max". + If "min" is specified but "max" is not, then "max" == "min" + If "max" is specified by "min" is not, then "min" == "max". - It is an error if max < min. + It is an error if max < min. It is an error if the value of any of these fields is negative. - If neither "min" nor "max" is specified for a resource, use the default values below. + If neither "min" nor "max" is specified for a resource, use the default values below.
*/ public interface ResourceRequirement extends ProcessRequirement, Saveable { @@ -49,7 +49,7 @@ public interface ResourceRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/class
*
- * Always 'ResourceRequirement' *
+ * Always 'ResourceRequirement' * */ ResourceRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirementImpl.java index 8b9de21d..0deae6e7 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirementImpl.java @@ -24,24 +24,24 @@ * Auto-generated class implementation for https://w3id.org/cwl/cwl#ResourceRequirement
Specify basic hardware resource requirements. - "min" is the minimum amount of a resource that must be reserved to schedule - a job. If "min" cannot be satisfied, the job should not be run. + "min" is the minimum amount of a resource that must be reserved to schedule + a job. If "min" cannot be satisfied, the job should not be run. - "max" is the maximum amount of a resource that the job shall be permitted + "max" is the maximum amount of a resource that the job shall be permitted to use. If a node has sufficient resources, multiple jobs may be scheduled - on a single node provided each job's "max" resource requirements are - met. If a job attempts to exceed its "max" resource allocation, an + on a single node provided each job's "max" resource requirements are + met. If a job attempts to exceed its "max" resource allocation, an implementation may deny additional resources, which may result in job failure. - If "min" is specified but "max" is not, then "max" == "min" - If "max" is specified by "min" is not, then "min" == "max". + If "min" is specified but "max" is not, then "max" == "min" + If "max" is specified by "min" is not, then "min" == "max". - It is an error if max < min. + It is an error if max < min. It is an error if the value of any of these fields is negative. - If neither "min" nor "max" is specified for a resource, use the default values below. + If neither "min" nor "max" is specified for a resource, use the default values below.
*/ public class ResourceRequirementImpl extends SaveableImpl implements ResourceRequirement { @@ -60,7 +60,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/class
*
- * Always 'ResourceRequirement' *
+ * Always 'ResourceRequirement' * */ public ResourceRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirement.java index 4387e905..350e1c52 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirement.java @@ -31,7 +31,7 @@ public interface ScatterFeatureRequirement extends ProcessRequirement, Saveable /** * Getter for property https://w3id.org/cwl/cwl#ScatterFeatureRequirement/class
*
- * Always 'ScatterFeatureRequirement' *
+ * Always 'ScatterFeatureRequirement' * */ ScatterFeatureRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirementImpl.java index ab826911..b722b7d7 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirementImpl.java @@ -42,7 +42,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#ScatterFeatureRequirement/class
*
- * Always 'ScatterFeatureRequirement' *
+ * Always 'ScatterFeatureRequirement' * */ public ScatterFeatureRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirement.java index 9fc51cb2..824b7f33 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirement.java @@ -36,7 +36,7 @@ public interface SchemaDefRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#SchemaDefRequirement/class
*
- * Always 'SchemaDefRequirement' *
+ * Always 'SchemaDefRequirement' * */ SchemaDefRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirementImpl.java index 6ad1720f..c8a65893 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirementImpl.java @@ -47,7 +47,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#SchemaDefRequirement/class
*
- * Always 'SchemaDefRequirement' *
+ * Always 'SchemaDefRequirement' * */ public SchemaDefRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SecondaryFileSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SecondaryFileSchema.java index 805ed37d..245f5eec 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SecondaryFileSchema.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SecondaryFileSchema.java @@ -40,7 +40,7 @@ public interface SecondaryFileSchema extends Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SecondaryFileSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SecondaryFileSchemaImpl.java index 38f071e3..b22c20fd 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SecondaryFileSchemaImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SecondaryFileSchemaImpl.java @@ -51,7 +51,7 @@ public java.util.Map getExtensionFields() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirement.java index 1ed7d619..11f719a0 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirement.java @@ -36,7 +36,7 @@ public interface ShellCommandRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#ShellCommandRequirement/class
*
- * Always 'ShellCommandRequirement' *
+ * Always 'ShellCommandRequirement' * */ ShellCommandRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirementImpl.java index 2c8a635c..53ebc7d3 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirementImpl.java @@ -47,7 +47,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#ShellCommandRequirement/class
*
- * Always 'ShellCommandRequirement' *
+ * Always 'ShellCommandRequirement' * */ public ShellCommandRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Sink.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Sink.java index ea563d9d..af30b22a 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Sink.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Sink.java @@ -38,7 +38,7 @@ public interface Sink extends Saveable { * Getter for property https://w3id.org/cwl/cwl#Sink/linkMerge
*
* The method to use to merge multiple inbound links into a single array. - * If not specified, the default method is "merge_nested". + * If not specified, the default method is "merge_nested". * *
*/ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirement.java index 88a6940e..b2de49f1 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirement.java @@ -31,7 +31,7 @@ public interface SoftwareRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#SoftwareRequirement/class
*
- * Always 'SoftwareRequirement' *
+ * Always 'SoftwareRequirement' * */ SoftwareRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirementImpl.java index 9f623c3f..ffb0a220 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirementImpl.java @@ -42,7 +42,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#SoftwareRequirement/class
*
- * Always 'SoftwareRequirement' *
+ * Always 'SoftwareRequirement' * */ public SoftwareRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirement.java index e6363436..073dd11b 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirement.java @@ -31,7 +31,7 @@ public interface StepInputExpressionRequirement extends ProcessRequirement, Save /** * Getter for property https://w3id.org/cwl/cwl#StepInputExpressionRequirement/class
*
- * Always 'StepInputExpressionRequirement' *
+ * Always 'StepInputExpressionRequirement' * */ StepInputExpressionRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirementImpl.java index 2bf4d2ce..55ec06d0 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirementImpl.java @@ -42,7 +42,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#StepInputExpressionRequirement/class
*
- * Always 'StepInputExpressionRequirement' *
+ * Always 'StepInputExpressionRequirement' * */ public StepInputExpressionRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirement.java index ce5d6ae1..56bd4437 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirement.java @@ -31,7 +31,7 @@ public interface SubworkflowFeatureRequirement extends ProcessRequirement, Savea /** * Getter for property https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement/class
*
- * Always 'SubworkflowFeatureRequirement' *
+ * Always 'SubworkflowFeatureRequirement' * */ SubworkflowFeatureRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirementImpl.java index 230383db..afbddd9d 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirementImpl.java @@ -42,7 +42,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement/class
*
- * Always 'SubworkflowFeatureRequirement' *
+ * Always 'SubworkflowFeatureRequirement' * */ public SubworkflowFeatureRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimit.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimit.java index 0c738c6e..51bda027 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimit.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimit.java @@ -36,7 +36,7 @@ public interface ToolTimeLimit extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#ToolTimeLimit/class
*
- * Always 'ToolTimeLimit' *
+ * Always 'ToolTimeLimit' * */ ToolTimeLimit_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimitImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimitImpl.java index 2b4954d9..648c52d4 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimitImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimitImpl.java @@ -47,7 +47,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#ToolTimeLimit/class
*
- * Always 'ToolTimeLimit' *
+ * Always 'ToolTimeLimit' * */ public ToolTimeLimit_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuse.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuse.java index e3de98d8..1f40837f 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuse.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuse.java @@ -38,7 +38,7 @@ public interface WorkReuse extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#WorkReuse/class
*
- * Always 'WorkReuse' *
+ * Always 'WorkReuse' * */ WorkReuse_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuseImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuseImpl.java index 5e1f2448..0c70d853 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuseImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuseImpl.java @@ -49,7 +49,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#WorkReuse/class
*
- * Always 'WorkReuse' *
+ * Always 'WorkReuse' * */ public WorkReuse_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowInputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowInputParameter.java index 2e890650..90069300 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowInputParameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowInputParameter.java @@ -64,7 +64,7 @@ public interface WorkflowInputParameter extends InputParameter, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool @@ -126,7 +126,7 @@ public interface WorkflowInputParameter extends InputParameter, Saveable { * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * * */ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowInputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowInputParameterImpl.java index 986b788a..d6dba623 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowInputParameterImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowInputParameterImpl.java @@ -85,7 +85,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool @@ -167,7 +167,7 @@ public Object getFormat() { * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * * */ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowOutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowOutputParameter.java index 12967443..d42f0571 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowOutputParameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowOutputParameter.java @@ -69,7 +69,7 @@ public interface WorkflowOutputParameter extends OutputParameter, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool @@ -136,7 +136,7 @@ public interface WorkflowOutputParameter extends OutputParameter, Saveable { * Getter for property https://w3id.org/cwl/cwl#WorkflowOutputParameter/linkMerge
*
* The method to use to merge multiple sources into a single array. - * If not specified, the default method is "merge_nested". + * If not specified, the default method is "merge_nested". * *
*/ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowOutputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowOutputParameterImpl.java index 3e196dd7..c4acce74 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowOutputParameterImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowOutputParameterImpl.java @@ -90,7 +90,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool @@ -182,7 +182,7 @@ public Object getOutputSource() { * Getter for property https://w3id.org/cwl/cwl#WorkflowOutputParameter/linkMerge
*
* The method to use to merge multiple sources into a single array. - * If not specified, the default method is "merge_nested". + * If not specified, the default method is "merge_nested". * *
*/ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStep.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStep.java index 1ace23c2..47bde358 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStep.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStep.java @@ -30,7 +30,7 @@ underlying process implementation (such as `CommandLineTool` or another [ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified in the workflow or workflow step requirements. - A "scatter" operation specifies that the associated workflow step or + A "scatter" operation specifies that the associated workflow step or subworkflow should execute separately over a list of input elements. Each job making up a scatter operation is independent and may be executed concurrently. diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepImpl.java index 90b6ce04..5f30f569 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepImpl.java @@ -33,7 +33,7 @@ underlying process implementation (such as `CommandLineTool` or another [ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified in the workflow or workflow step requirements. - A "scatter" operation specifies that the associated workflow step or + A "scatter" operation specifies that the associated workflow step or subworkflow should execute separately over a list of input elements. Each job making up a scatter operation is independent and may be executed concurrently. diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepInput.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepInput.java index a28e88ae..3f2bfd3b 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepInput.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepInput.java @@ -46,18 +46,18 @@ though additonal parameters may be specified (for use within `valueFrom` scatter](#WorkflowStep) operation, there may be multiple inbound data links listed in the `source` field. The values from the input links are merged depending on the method specified in the `linkMerge` field. If not - specified, the default method is "merge_nested". + specified, the default method is "merge_nested". * **merge_nested** The input must be an array consisting of exactly one entry for each - input link. If "merge_nested" is specified with a single link, the value + input link. If "merge_nested" is specified with a single link, the value from the link must be wrapped in a single-item list. * **merge_flattened** 1. The source and sink parameters must be compatible types, or the source - type must be compatible with single element from the "items" type of + type must be compatible with single element from the "items" type of the destination array parameter. 2. Source parameters which are arrays are concatenated. Source parameters which are single element types are appended as @@ -89,7 +89,7 @@ public interface WorkflowStepInput extends Identified, Sink, LoadContents, Label * Getter for property https://w3id.org/cwl/cwl#Sink/linkMerge
*
* The method to use to merge multiple inbound links into a single array. - * If not specified, the default method is "merge_nested". + * If not specified, the default method is "merge_nested". * *
*/ @@ -100,7 +100,7 @@ public interface WorkflowStepInput extends Identified, Sink, LoadContents, Label * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * * */ @@ -154,9 +154,9 @@ public interface WorkflowStepInput extends Identified, Sink, LoadContents, Label * The `self` value in the parameter reference or expression must be * 1. `null` if there is no `source` field * 2. the value of the parameter(s) specified in the `source` field when this - * workflow input parameter **is not** specified in this workflow step's `scatter` field. + * workflow input parameter **is not** specified in this workflow step's `scatter` field. * 3. an element of the parameter specified in the `source` field when this workflow input - * parameter **is** specified in this workflow step's `scatter` field. + * parameter **is** specified in this workflow step's `scatter` field. * * The value of `inputs` in the parameter reference or expression must be * the input object to the workflow step after assigning the `source` diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepInputImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepInputImpl.java index b5911fb9..882958b4 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepInputImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepInputImpl.java @@ -49,18 +49,18 @@ though additonal parameters may be specified (for use within `valueFrom` scatter](#WorkflowStep) operation, there may be multiple inbound data links listed in the `source` field. The values from the input links are merged depending on the method specified in the `linkMerge` field. If not - specified, the default method is "merge_nested". + specified, the default method is "merge_nested". * **merge_nested** The input must be an array consisting of exactly one entry for each - input link. If "merge_nested" is specified with a single link, the value + input link. If "merge_nested" is specified with a single link, the value from the link must be wrapped in a single-item list. * **merge_flattened** 1. The source and sink parameters must be compatible types, or the source - type must be compatible with single element from the "items" type of + type must be compatible with single element from the "items" type of the destination array parameter. 2. Source parameters which are arrays are concatenated. Source parameters which are single element types are appended as @@ -110,7 +110,7 @@ public Object getSource() { * Getter for property https://w3id.org/cwl/cwl#Sink/linkMerge
*
* The method to use to merge multiple inbound links into a single array. - * If not specified, the default method is "merge_nested". + * If not specified, the default method is "merge_nested". * *
*/ @@ -126,7 +126,7 @@ public java.util.Optional getLinkMerge() { * Only valid when `type: File` or is an array of `items: File`. * * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. + * "contents" field of the file object for use by expressions. * * */ @@ -200,9 +200,9 @@ public java.util.Optional getDefault() { * The `self` value in the parameter reference or expression must be * 1. `null` if there is no `source` field * 2. the value of the parameter(s) specified in the `source` field when this - * workflow input parameter **is not** specified in this workflow step's `scatter` field. + * workflow input parameter **is not** specified in this workflow step's `scatter` field. * 3. an element of the parameter specified in the `source` field when this workflow input - * parameter **is** specified in this workflow step's `scatter` field. + * parameter **is** specified in this workflow step's `scatter` field. * * The value of `inputs` in the parameter reference or expression must be * the input object to the workflow step after assigning the `source` diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputParameter.java index 81bf8926..7811fc0c 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputParameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputParameter.java @@ -65,7 +65,7 @@ public interface CommandInputParameter extends InputParameter, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputParameterImpl.java index fd7d5091..2f421b51 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputParameterImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputParameterImpl.java @@ -86,7 +86,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordField.java index 6fa2c2be..8c8c37b7 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordField.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordField.java @@ -80,7 +80,7 @@ public interface CommandInputRecordField extends InputRecordField, CommandLineBi * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordFieldImpl.java index 029c772f..77d7cdb1 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordFieldImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordFieldImpl.java @@ -111,7 +111,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBinding.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBinding.java index 957526ae..9e96b3fd 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBinding.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBinding.java @@ -21,8 +21,8 @@ * Auto-generated interface for https://w3id.org/cwl/cwl#CommandLineBinding
This interface is implemented by {@link CommandLineBindingImpl}
When listed under `inputBinding` in the input schema, the term - "value" refers to the corresponding value in the input object. For - binding objects listed in `CommandLineTool.arguments`, the term "value" + "value" refers to the corresponding value in the input object. For + binding objects listed in `CommandLineTool.arguments`, the term "value" refers to the effective value after evaluating `valueFrom`. The binding behavior when building the command line depends on the data diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBindingImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBindingImpl.java index d3cfee9e..12f98f9c 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBindingImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBindingImpl.java @@ -24,8 +24,8 @@ * Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandLineBinding
When listed under `inputBinding` in the input schema, the term - "value" refers to the corresponding value in the input object. For - binding objects listed in `CommandLineTool.arguments`, the term "value" + "value" refers to the corresponding value in the input object. For + binding objects listed in `CommandLineTool.arguments`, the term "value" refers to the effective value after evaluating `valueFrom`. The binding behavior when building the command line depends on the data diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineTool.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineTool.java index 0678a9d9..d94c1ac0 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineTool.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineTool.java @@ -130,7 +130,7 @@ public interface CommandLineTool extends Process, Saveable { * represents the type of operation, preferably defined within an ontology. * * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), + * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), * like [Alignment](http://edamontology.org/operation_2928), * or [Clustering](http://edamontology.org/operation_3432); or a more * specific Operation concept like @@ -175,7 +175,7 @@ public interface CommandLineTool extends Process, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stdin
*
- * A path to a file whose contents must be piped into the command's + * A path to a file whose contents must be piped into the command's * standard input stream. * *
*/ @@ -184,7 +184,7 @@ public interface CommandLineTool extends Process, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stderr
*
- * Capture the command's standard error stream to a file written to + * Capture the command's standard error stream to a file written to * the designated output directory. * * If `stderr` is a string, it specifies the file name to use. @@ -200,11 +200,11 @@ public interface CommandLineTool extends Process, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stdout
*
- * Capture the command's standard output stream to a file written to + * 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 + * (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. diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineToolImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineToolImpl.java index 8a8803a8..82abf905 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineToolImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineToolImpl.java @@ -186,7 +186,7 @@ public java.util.Optional getCwlVersion() { * represents the type of operation, preferably defined within an ontology. * * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), + * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), * like [Alignment](http://edamontology.org/operation_2928), * or [Clustering](http://edamontology.org/operation_3432); or a more * specific Operation concept like @@ -246,7 +246,7 @@ public java.util.Optional> getArguments() { /** * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stdin
*
- * A path to a file whose contents must be piped into the command's + * A path to a file whose contents must be piped into the command's * standard input stream. * *
*/ @@ -260,7 +260,7 @@ public Object getStdin() { /** * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stderr
*
- * Capture the command's standard error stream to a file written to + * Capture the command's standard error stream to a file written to * the designated output directory. * * If `stderr` is a string, it specifies the file name to use. @@ -281,11 +281,11 @@ public Object getStderr() { /** * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stdout
*
- * Capture the command's standard output stream to a file written to + * 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 + * (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. diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputBinding.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputBinding.java index e91c9bd3..be7e7d0f 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputBinding.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputBinding.java @@ -79,9 +79,9 @@ public interface CommandOutputBinding extends LoadContents, Saveable { * match and return files/directories which actually exist. * * If the value of glob is a relative path pattern (does not - * begin with a slash '/') then it is resolved relative to the + * begin with a slash '/') then it is resolved relative to the * output directory. If the value of the glob is an absolute - * path pattern (it does begin with a slash '/') then it must + * path pattern (it does begin with a slash '/') then it must * refer to a path within the output directory. It is an error * if any glob resolves to a path outside the output directory. * Specifically this means globs that resolve to paths outside the output diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputBindingImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputBindingImpl.java index 8bf84292..14eda29e 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputBindingImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputBindingImpl.java @@ -100,9 +100,9 @@ public java.util.Optional getLoadListing() { * match and return files/directories which actually exist. * * If the value of glob is a relative path pattern (does not - * begin with a slash '/') then it is resolved relative to the + * begin with a slash '/') then it is resolved relative to the * output directory. If the value of the glob is an absolute - * path pattern (it does begin with a slash '/') then it must + * path pattern (it does begin with a slash '/') then it must * refer to a path within the output directory. It is an error * if any glob resolves to a path outside the output directory. * Specifically this means globs that resolve to paths outside the output diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputParameter.java index 4fa8649c..4dbff8dc 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputParameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputParameter.java @@ -65,7 +65,7 @@ public interface CommandOutputParameter extends OutputParameter, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputParameterImpl.java index 31ddcf41..c9408c81 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputParameterImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputParameterImpl.java @@ -86,7 +86,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordField.java index 6b2a31a3..835ec36e 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordField.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordField.java @@ -80,7 +80,7 @@ public interface CommandOutputRecordField extends OutputRecordField, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordFieldImpl.java index 488f122b..38f5477c 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordFieldImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordFieldImpl.java @@ -111,7 +111,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Directory.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Directory.java index 25817bf5..45ebf075 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Directory.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Directory.java @@ -109,8 +109,8 @@ public interface Directory extends Saveable { * `opendir(2)` syscall. * * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) - * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, - * ``, ``, and ``) or characters + * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, + * `<space>`, `<tab>`, and `<newline>`) or characters * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) * then implementations may terminate the process with a diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DirectoryImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/DirectoryImpl.java index ca110334..c3fe5326 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DirectoryImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/DirectoryImpl.java @@ -130,8 +130,8 @@ public java.util.Optional getLocation() { * `opendir(2)` syscall. * * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) - * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, - * ``, ``, and ``) or characters + * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, + * `<space>`, `<tab>`, and `<newline>`) or characters * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) * then implementations may terminate the process with a diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Dirent.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Dirent.java index a788e932..1db78fe6 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Dirent.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Dirent.java @@ -37,7 +37,7 @@ public interface Dirent extends Saveable { /** * Getter for property https://w3id.org/cwl/cwl#entryname
*
- * The "target" name of the file or subdirectory. If `entry` is + * The "target" name of the file or subdirectory. If `entry` is * a File or Directory, the `entryname` field overrides the value * of `basename` of the File or Directory object. * diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DirentImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/DirentImpl.java index cd56eb48..9c547a2d 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DirentImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/DirentImpl.java @@ -48,7 +48,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#entryname
*
- * The "target" name of the file or subdirectory. If `entry` is + * The "target" name of the file or subdirectory. If `entry` is * a File or Directory, the `entryname` field overrides the value * of `basename` of the File or Directory object. * diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirement.java index de173dd5..81d46d9d 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirement.java @@ -68,7 +68,7 @@ concerns of the implicit hidden execution point (For further discussion, see If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a DockerRequirement, the environment variables must be provided to Docker - using `--env` or `--env-file` and interact with the container's preexisting + using `--env` or `--env-file` and interact with the container's preexisting environment as defined by Docker.
*/ @@ -80,7 +80,7 @@ public interface DockerRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/class
*
- * Always 'DockerRequirement' *
+ * Always 'DockerRequirement' *
*/ DockerRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirementImpl.java index 6ad9754b..4db71713 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirementImpl.java @@ -71,7 +71,7 @@ concerns of the implicit hidden execution point (For further discussion, see If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a DockerRequirement, the environment variables must be provided to Docker - using `--env` or `--env-file` and interact with the container's preexisting + using `--env` or `--env-file` and interact with the container's preexisting environment as defined by Docker.
*/ @@ -91,7 +91,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/class
*
- * Always 'DockerRequirement' *
+ * Always 'DockerRequirement' *
*/ public DockerRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirement.java index 8e1e917f..073635a3 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirement.java @@ -31,7 +31,7 @@ public interface EnvVarRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#EnvVarRequirement/class
*
- * Always 'EnvVarRequirement' *
+ * Always 'EnvVarRequirement' *
*/ EnvVarRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirementImpl.java index 086f4cd8..9e34d369 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirementImpl.java @@ -42,7 +42,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#EnvVarRequirement/class
*
- * Always 'EnvVarRequirement' *
+ * Always 'EnvVarRequirement' *
*/ public EnvVarRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionTool.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionTool.java index c0c52555..1b8cd65e 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionTool.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionTool.java @@ -136,7 +136,7 @@ public interface ExpressionTool extends Process, Saveable { * represents the type of operation, preferably defined within an ontology. * * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), + * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), * like [Alignment](http://edamontology.org/operation_2928), * or [Clustering](http://edamontology.org/operation_3432); or a more * specific Operation concept like diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolImpl.java index 595f1119..78fdced9 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolImpl.java @@ -192,7 +192,7 @@ public java.util.Optional getCwlVersion() { * represents the type of operation, preferably defined within an ontology. * * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), + * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), * like [Alignment](http://edamontology.org/operation_2928), * or [Clustering](http://edamontology.org/operation_3432); or a more * specific Operation concept like diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolOutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolOutputParameter.java index 306985d9..a4182e3f 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolOutputParameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolOutputParameter.java @@ -64,7 +64,7 @@ public interface ExpressionToolOutputParameter extends OutputParameter, Saveable * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolOutputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolOutputParameterImpl.java index 1e3b20cb..f4e71be9 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolOutputParameterImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolOutputParameterImpl.java @@ -85,7 +85,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/FieldBase.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/FieldBase.java index 76852b5e..9a9bea2a 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/FieldBase.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/FieldBase.java @@ -57,7 +57,7 @@ public interface FieldBase extends Labeled, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/File.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/File.java index d7ba075e..e49370ac 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/File.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/File.java @@ -37,8 +37,8 @@ runtime environment of a command line tool execution (for command line tool outputs). If no `location` or `path` is specified, a file object must specify - `contents` with the UTF-8 text content of the file. This is a "file - literal". File literals do not correspond to external resources, but are + `contents` with the UTF-8 text content of the file. This is a "file + literal". File literals do not correspond to external resources, but are created on disk with `contents` with when needed for executing a tool. Where appropriate, expressions can return file literals to define new files on a runtime. The maximum size of `contents` is 64 kilobytes. @@ -136,8 +136,8 @@ public interface File extends Saveable { * field to `location`, and remove the `path` field. * * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) - * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, - * ``, ``, and ``) or characters + * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, + * `<space>`, `<tab>`, and `<newline>`) or characters * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) * then implementations may terminate the process with a @@ -168,7 +168,7 @@ public interface File extends Saveable { * Getter for property https://w3id.org/cwl/cwl#File/dirname
*
* The name of the directory containing file, that is, the path leading up - * to the final slash in the path such that `dirname + '/' + basename == + * to the final slash in the path such that `dirname + '/' + basename == * path`. * * The implementation must set this field based on the value of `path` @@ -212,7 +212,7 @@ public interface File extends Saveable { * Getter for property https://w3id.org/cwl/cwl#File/checksum
*
* Optional hash code for validating file integrity. Currently, must be in the form - * "sha1$ + hexadecimal string" using the SHA-1 algorithm. + * "sha1$ + hexadecimal string" using the SHA-1 algorithm. * *
*/ @@ -248,10 +248,10 @@ public interface File extends Saveable { * input file format is the same, `owl:equivalentClass` or * `rdfs:subClassOf` the format required by the input parameter. * `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if - * ` owl:equivalentClass ` and ` owl:subclassOf ` then infer - * ` owl:subclassOf `. + * `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer + * `<C> owl:subclassOf <A>`. * - * File format ontologies may be provided in the "$schemas" metadata at the + * File format ontologies may be provided in the "$schemas" metadata at the * root of the document. If no ontologies are specified in `$schemas`, the * runtime may perform exact file format matches. * *
diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/FileImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/FileImpl.java index 8deb6089..b375a23e 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/FileImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/FileImpl.java @@ -40,8 +40,8 @@ runtime environment of a command line tool execution (for command line tool outputs). If no `location` or `path` is specified, a file object must specify - `contents` with the UTF-8 text content of the file. This is a "file - literal". File literals do not correspond to external resources, but are + `contents` with the UTF-8 text content of the file. This is a "file + literal". File literals do not correspond to external resources, but are created on disk with `contents` with when needed for executing a tool. Where appropriate, expressions can return file literals to define new files on a runtime. The maximum size of `contents` is 64 kilobytes. @@ -157,8 +157,8 @@ public java.util.Optional getLocation() { * field to `location`, and remove the `path` field. * * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) - * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, - * ``, ``, and ``) or characters + * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, + * `<space>`, `<tab>`, and `<newline>`) or characters * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) * then implementations may terminate the process with a @@ -199,7 +199,7 @@ public java.util.Optional getBasename() { * Getter for property https://w3id.org/cwl/cwl#File/dirname
*
* The name of the directory containing file, that is, the path leading up - * to the final slash in the path such that `dirname + '/' + basename == + * to the final slash in the path such that `dirname + '/' + basename == * path`. * * The implementation must set this field based on the value of `path` @@ -258,7 +258,7 @@ public java.util.Optional getNameext() { * Getter for property https://w3id.org/cwl/cwl#File/checksum
*
* Optional hash code for validating file integrity. Currently, must be in the form - * "sha1$ + hexadecimal string" using the SHA-1 algorithm. + * "sha1$ + hexadecimal string" using the SHA-1 algorithm. * *
*/ @@ -309,10 +309,10 @@ public java.util.Optional> getSecondaryFiles() { * input file format is the same, `owl:equivalentClass` or * `rdfs:subClassOf` the format required by the input parameter. * `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if - * ` owl:equivalentClass ` and ` owl:subclassOf ` then infer - * ` owl:subclassOf `. + * `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer + * `<C> owl:subclassOf <A>`. * - * File format ontologies may be provided in the "$schemas" metadata at the + * File format ontologies may be provided in the "$schemas" metadata at the * root of the document. If no ontologies are specified in `$schemas`, the * runtime may perform exact file format matches. * *
diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirement.java index 73d54aac..922060ff 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirement.java @@ -40,7 +40,7 @@ public interface InitialWorkDirRequirement extends ProcessRequirement, Saveable * The list of files or subdirectories that must be staged prior * to executing the command line tool. * - * Return type of each expression must validate as `["null", + * Return type of each expression must validate as `["null", * File, Directory, Dirent, {type: array, items: [File, * Directory]}]`. * diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirementImpl.java index 3e488f33..5f0dd804 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirementImpl.java @@ -56,7 +56,7 @@ public InitialWorkDirRequirement_class getClass_() { * The list of files or subdirectories that must be staged prior * to executing the command line tool. * - * Return type of each expression must validate as `["null", + * Return type of each expression must validate as `["null", * File, Directory, Dirent, {type: array, items: [File, * Directory]}]`. * diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirement.java index 1d03d48a..45e00df9 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirement.java @@ -32,7 +32,7 @@ public interface InlineJavascriptRequirement extends ProcessRequirement, Saveabl /** * Getter for property https://w3id.org/cwl/cwl#InlineJavascriptRequirement/class
*
- * Always 'InlineJavascriptRequirement' *
+ * Always 'InlineJavascriptRequirement' *
*/ InlineJavascriptRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirementImpl.java index 56b349f9..3d573758 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirementImpl.java @@ -43,7 +43,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#InlineJavascriptRequirement/class
*
- * Always 'InlineJavascriptRequirement' *
+ * Always 'InlineJavascriptRequirement' *
*/ public InlineJavascriptRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirement.java index 452bc892..671dc574 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirement.java @@ -59,7 +59,7 @@ public interface InplaceUpdateRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#InplaceUpdateRequirement/class
*
- * Always 'InplaceUpdateRequirement' *
+ * Always 'InplaceUpdateRequirement' * */ InplaceUpdateRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirementImpl.java index 37c27405..07f5a598 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirementImpl.java @@ -70,7 +70,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#InplaceUpdateRequirement/class
*
- * Always 'InplaceUpdateRequirement' *
+ * Always 'InplaceUpdateRequirement' * */ public InplaceUpdateRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputParameter.java index b5911163..01155244 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputParameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputParameter.java @@ -57,7 +57,7 @@ public interface InputParameter extends Parameter, InputFormat, LoadContents, Sa * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordField.java index 1f8063af..644b9999 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordField.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordField.java @@ -80,7 +80,7 @@ public interface InputRecordField extends CWLRecordField, FieldBase, InputFormat * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordFieldImpl.java index 045e19e7..dec00e08 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordFieldImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordFieldImpl.java @@ -111,7 +111,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirement.java index d1c7f0d0..f0ceaaeb 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirement.java @@ -31,7 +31,7 @@ public interface LoadListingRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#LoadListingRequirement/class
*
- * Always 'LoadListingRequirement' *
+ * Always 'LoadListingRequirement' * */ LoadListingRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirementImpl.java index bc64e221..5467fadd 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirementImpl.java @@ -42,7 +42,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#LoadListingRequirement/class
*
- * Always 'LoadListingRequirement' *
+ * Always 'LoadListingRequirement' * */ public LoadListingRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirement.java index b075fbad..674885a1 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirement.java @@ -31,7 +31,7 @@ public interface MultipleInputFeatureRequirement extends ProcessRequirement, Sav /** * Getter for property https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement/class
*
- * Always 'MultipleInputFeatureRequirement' *
+ * Always 'MultipleInputFeatureRequirement' * */ MultipleInputFeatureRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirementImpl.java index e3e28d33..d0cec697 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirementImpl.java @@ -42,7 +42,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement/class
*
- * Always 'MultipleInputFeatureRequirement' *
+ * Always 'MultipleInputFeatureRequirement' * */ public MultipleInputFeatureRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccess.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccess.java index 2d02328a..3255648c 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccess.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccess.java @@ -44,7 +44,7 @@ public interface NetworkAccess extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#NetworkAccess/class
*
- * Always 'NetworkAccess' *
+ * Always 'NetworkAccess' * */ NetworkAccess_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccessImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccessImpl.java index fc982627..79c1dcf6 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccessImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccessImpl.java @@ -55,7 +55,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#NetworkAccess/class
*
- * Always 'NetworkAccess' *
+ * Always 'NetworkAccess' * */ public NetworkAccess_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Operation.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Operation.java index fe026b94..609a08b9 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Operation.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Operation.java @@ -136,7 +136,7 @@ public interface Operation extends Process, Saveable { * represents the type of operation, preferably defined within an ontology. * * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), + * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), * like [Alignment](http://edamontology.org/operation_2928), * or [Clustering](http://edamontology.org/operation_3432); or a more * specific Operation concept like diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationImpl.java index b88a7c0d..a8eee4cd 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationImpl.java @@ -192,7 +192,7 @@ public java.util.Optional getCwlVersion() { * represents the type of operation, preferably defined within an ontology. * * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), + * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), * like [Alignment](http://edamontology.org/operation_2928), * or [Clustering](http://edamontology.org/operation_3432); or a more * specific Operation concept like diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationInputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationInputParameter.java index 0acb947a..1d2ca926 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationInputParameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationInputParameter.java @@ -66,7 +66,7 @@ public interface OperationInputParameter extends InputParameter, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationInputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationInputParameterImpl.java index 88a6c97e..a0458165 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationInputParameterImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationInputParameterImpl.java @@ -87,7 +87,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationOutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationOutputParameter.java index aec2a6e5..12532bd6 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationOutputParameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationOutputParameter.java @@ -66,7 +66,7 @@ public interface OperationOutputParameter extends OutputParameter, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationOutputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationOutputParameterImpl.java index 2cb07a23..84ff46b2 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationOutputParameterImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationOutputParameterImpl.java @@ -87,7 +87,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputParameter.java index c6d47671..d541ae9a 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputParameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputParameter.java @@ -57,7 +57,7 @@ public interface OutputParameter extends Parameter, OutputFormat, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordField.java index 6913c54b..d34876c7 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordField.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordField.java @@ -80,7 +80,7 @@ public interface OutputRecordField extends CWLRecordField, FieldBase, OutputForm * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordFieldImpl.java index 6292695c..f5ded71f 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordFieldImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordFieldImpl.java @@ -111,7 +111,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Parameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Parameter.java index a416c3ba..da4df6f6 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Parameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Parameter.java @@ -59,7 +59,7 @@ public interface Parameter extends FieldBase, Documented, Identified, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Process.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Process.java index f8caeed8..52590e40 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Process.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Process.java @@ -116,7 +116,7 @@ public interface Process extends Identified, Labeled, Documented, Saveable { * represents the type of operation, preferably defined within an ontology. * * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), + * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), * like [Alignment](http://edamontology.org/operation_2928), * or [Clustering](http://edamontology.org/operation_3432); or a more * specific Operation concept like diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirement.java index f1dda9ef..cd82cafe 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirement.java @@ -21,29 +21,29 @@ * Auto-generated interface for https://w3id.org/cwl/cwl#ResourceRequirement
This interface is implemented by {@link ResourceRequirementImpl}
Specify basic hardware resource requirements. - "min" is the minimum amount of a resource that must be reserved to - schedule a job. If "min" cannot be satisfied, the job should not + "min" is the minimum amount of a resource that must be reserved to + schedule a job. If "min" cannot be satisfied, the job should not be run. - "max" is the maximum amount of a resource that the job shall be + "max" is the maximum amount of a resource that the job shall be allocated. If a node has sufficient resources, multiple jobs may - be scheduled on a single node provided each job's "max" resource + be scheduled on a single node provided each job's "max" resource requirements are met. If a job attempts to exceed its resource allocation, an implementation may deny additional resources, which may result in job failure. - If both "min" and "max" are specified, an implementation may - choose to allocate any amount between "min" and "max", with the + If both "min" and "max" are specified, an implementation may + choose to allocate any amount between "min" and "max", with the actual allocation provided in the `runtime` object. - If "min" is specified but "max" is not, then "max" == "min" - If "max" is specified by "min" is not, then "min" == "max". + If "min" is specified but "max" is not, then "max" == "min" + If "max" is specified by "min" is not, then "min" == "max". - It is an error if max < min. + It is an error if max < min. It is an error if the value of any of these fields is negative. - If neither "min" nor "max" is specified for a resource, use the default values below. + If neither "min" nor "max" is specified for a resource, use the default values below.
*/ public interface ResourceRequirement extends ProcessRequirement, Saveable { @@ -54,7 +54,7 @@ public interface ResourceRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/class
*
- * Always 'ResourceRequirement' *
+ * Always 'ResourceRequirement' * */ ResourceRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirementImpl.java index f0f503f5..f1dda845 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirementImpl.java @@ -24,29 +24,29 @@ * Auto-generated class implementation for https://w3id.org/cwl/cwl#ResourceRequirement
Specify basic hardware resource requirements. - "min" is the minimum amount of a resource that must be reserved to - schedule a job. If "min" cannot be satisfied, the job should not + "min" is the minimum amount of a resource that must be reserved to + schedule a job. If "min" cannot be satisfied, the job should not be run. - "max" is the maximum amount of a resource that the job shall be + "max" is the maximum amount of a resource that the job shall be allocated. If a node has sufficient resources, multiple jobs may - be scheduled on a single node provided each job's "max" resource + be scheduled on a single node provided each job's "max" resource requirements are met. If a job attempts to exceed its resource allocation, an implementation may deny additional resources, which may result in job failure. - If both "min" and "max" are specified, an implementation may - choose to allocate any amount between "min" and "max", with the + If both "min" and "max" are specified, an implementation may + choose to allocate any amount between "min" and "max", with the actual allocation provided in the `runtime` object. - If "min" is specified but "max" is not, then "max" == "min" - If "max" is specified by "min" is not, then "min" == "max". + If "min" is specified but "max" is not, then "max" == "min" + If "max" is specified by "min" is not, then "min" == "max". - It is an error if max < min. + It is an error if max < min. It is an error if the value of any of these fields is negative. - If neither "min" nor "max" is specified for a resource, use the default values below. + If neither "min" nor "max" is specified for a resource, use the default values below.
*/ public class ResourceRequirementImpl extends SaveableImpl implements ResourceRequirement { @@ -65,7 +65,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/class
*
- * Always 'ResourceRequirement' *
+ * Always 'ResourceRequirement' * */ public ResourceRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirement.java index 4068fe07..284fee1b 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirement.java @@ -31,7 +31,7 @@ public interface ScatterFeatureRequirement extends ProcessRequirement, Saveable /** * Getter for property https://w3id.org/cwl/cwl#ScatterFeatureRequirement/class
*
- * Always 'ScatterFeatureRequirement' *
+ * Always 'ScatterFeatureRequirement' * */ ScatterFeatureRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirementImpl.java index 0718a6b2..e6ab50eb 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirementImpl.java @@ -42,7 +42,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#ScatterFeatureRequirement/class
*
- * Always 'ScatterFeatureRequirement' *
+ * Always 'ScatterFeatureRequirement' * */ public ScatterFeatureRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirement.java index 6473059a..4ffa1ad0 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirement.java @@ -41,7 +41,7 @@ public interface SchemaDefRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#SchemaDefRequirement/class
*
- * Always 'SchemaDefRequirement' *
+ * Always 'SchemaDefRequirement' * */ SchemaDefRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirementImpl.java index 765d9032..253ed7d4 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirementImpl.java @@ -52,7 +52,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#SchemaDefRequirement/class
*
- * Always 'SchemaDefRequirement' *
+ * Always 'SchemaDefRequirement' * */ public SchemaDefRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecondaryFileSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecondaryFileSchema.java index 1150e8c1..cbdec02e 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecondaryFileSchema.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecondaryFileSchema.java @@ -71,7 +71,7 @@ public interface SecondaryFileSchema extends Saveable { * `path` where the secondary file will be staged to in the * CommandLineTool. * - * The expression may return "null" in which case there is no + * The expression may return "null" in which case there is no * secondary file from that expression. * * To work on non-filename-preserving storage systems, portable diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecondaryFileSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecondaryFileSchemaImpl.java index a677c1fd..97b1de5c 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecondaryFileSchemaImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecondaryFileSchemaImpl.java @@ -82,7 +82,7 @@ public java.util.Map getExtensionFields() { * `path` where the secondary file will be staged to in the * CommandLineTool. * - * The expression may return "null" in which case there is no + * The expression may return "null" in which case there is no * secondary file from that expression. * * To work on non-filename-preserving storage systems, portable diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirement.java index f56d6bc8..900ff621 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirement.java @@ -36,7 +36,7 @@ public interface ShellCommandRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#ShellCommandRequirement/class
*
- * Always 'ShellCommandRequirement' *
+ * Always 'ShellCommandRequirement' * */ ShellCommandRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirementImpl.java index 65352c3d..90f80081 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirementImpl.java @@ -47,7 +47,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#ShellCommandRequirement/class
*
- * Always 'ShellCommandRequirement' *
+ * Always 'ShellCommandRequirement' * */ public ShellCommandRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Sink.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Sink.java index 9156ecd9..67882f37 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Sink.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Sink.java @@ -38,7 +38,7 @@ public interface Sink extends Saveable { * Getter for property https://w3id.org/cwl/cwl#Sink/linkMerge
*
* The method to use to merge multiple inbound links into a single array. - * If not specified, the default method is "merge_nested". + * If not specified, the default method is "merge_nested". * *
*/ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirement.java index 5840063a..96d4ef94 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirement.java @@ -31,7 +31,7 @@ public interface SoftwareRequirement extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#SoftwareRequirement/class
*
- * Always 'SoftwareRequirement' *
+ * Always 'SoftwareRequirement' * */ SoftwareRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirementImpl.java index 0b07c1f9..91ac0ff0 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirementImpl.java @@ -42,7 +42,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#SoftwareRequirement/class
*
- * Always 'SoftwareRequirement' *
+ * Always 'SoftwareRequirement' * */ public SoftwareRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirement.java index 9b5f60d0..4a69d1f3 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirement.java @@ -31,7 +31,7 @@ public interface StepInputExpressionRequirement extends ProcessRequirement, Save /** * Getter for property https://w3id.org/cwl/cwl#StepInputExpressionRequirement/class
*
- * Always 'StepInputExpressionRequirement' *
+ * Always 'StepInputExpressionRequirement' * */ StepInputExpressionRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirementImpl.java index 86c3abd2..358c5472 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirementImpl.java @@ -42,7 +42,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#StepInputExpressionRequirement/class
*
- * Always 'StepInputExpressionRequirement' *
+ * Always 'StepInputExpressionRequirement' * */ public StepInputExpressionRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirement.java index 03156cb9..cc63a242 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirement.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirement.java @@ -31,7 +31,7 @@ public interface SubworkflowFeatureRequirement extends ProcessRequirement, Savea /** * Getter for property https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement/class
*
- * Always 'SubworkflowFeatureRequirement' *
+ * Always 'SubworkflowFeatureRequirement' * */ SubworkflowFeatureRequirement_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirementImpl.java index d347673f..281e8a07 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirementImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirementImpl.java @@ -42,7 +42,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement/class
*
- * Always 'SubworkflowFeatureRequirement' *
+ * Always 'SubworkflowFeatureRequirement' * */ public SubworkflowFeatureRequirement_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimit.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimit.java index 8d3d2731..70baa0ff 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimit.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimit.java @@ -36,7 +36,7 @@ public interface ToolTimeLimit extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#ToolTimeLimit/class
*
- * Always 'ToolTimeLimit' *
+ * Always 'ToolTimeLimit' * */ ToolTimeLimit_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimitImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimitImpl.java index 16bab350..e6666877 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimitImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimitImpl.java @@ -47,7 +47,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#ToolTimeLimit/class
*
- * Always 'ToolTimeLimit' *
+ * Always 'ToolTimeLimit' * */ public ToolTimeLimit_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuse.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuse.java index 4e459bd4..da56a4d9 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuse.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuse.java @@ -38,7 +38,7 @@ public interface WorkReuse extends ProcessRequirement, Saveable { /** * Getter for property https://w3id.org/cwl/cwl#WorkReuse/class
*
- * Always 'WorkReuse' *
+ * Always 'WorkReuse' * */ WorkReuse_class getClass_(); diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuseImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuseImpl.java index 7a909268..1013ffac 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuseImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuseImpl.java @@ -49,7 +49,7 @@ public java.util.Map getExtensionFields() { /** * Getter for property https://w3id.org/cwl/cwl#WorkReuse/class
*
- * Always 'WorkReuse' *
+ * Always 'WorkReuse' * */ public WorkReuse_class getClass_() { diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Workflow.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Workflow.java index 1c554b6e..89cc57ba 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Workflow.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Workflow.java @@ -37,12 +37,12 @@ The `source` field on each workflow step input parameter expresses the data links that contribute to the value of the step input - parameter (the "sink"). A workflow step can only begin execution + parameter (the "sink"). A workflow step can only begin execution when every data link connected to a step has been fulfilled. The `outputSource` field on each workflow step input parameter expresses the data links that contribute to the value of the - workflow output parameter (the "sink"). Workflow execution cannot + workflow output parameter (the "sink"). Workflow execution cannot complete successfully until every data link connected to an output parameter has been fulfilled. @@ -180,7 +180,7 @@ public interface Workflow extends Process, Saveable { * represents the type of operation, preferably defined within an ontology. * * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), + * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), * like [Alignment](http://edamontology.org/operation_2928), * or [Clustering](http://edamontology.org/operation_3432); or a more * specific Operation concept like diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowImpl.java index 1630c219..93b225d6 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowImpl.java @@ -40,12 +40,12 @@ The `source` field on each workflow step input parameter expresses the data links that contribute to the value of the step input - parameter (the "sink"). A workflow step can only begin execution + parameter (the "sink"). A workflow step can only begin execution when every data link connected to a step has been fulfilled. The `outputSource` field on each workflow step input parameter expresses the data links that contribute to the value of the - workflow output parameter (the "sink"). Workflow execution cannot + workflow output parameter (the "sink"). Workflow execution cannot complete successfully until every data link connected to an output parameter has been fulfilled. @@ -236,7 +236,7 @@ public java.util.Optional getCwlVersion() { * represents the type of operation, preferably defined within an ontology. * * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), + * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), * like [Alignment](http://edamontology.org/operation_2928), * or [Clustering](http://edamontology.org/operation_3432); or a more * specific Operation concept like diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowInputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowInputParameter.java index ac48d9e1..0683cc21 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowInputParameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowInputParameter.java @@ -64,7 +64,7 @@ public interface WorkflowInputParameter extends InputParameter, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowInputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowInputParameterImpl.java index 4adaf13e..38d24ce4 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowInputParameterImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowInputParameterImpl.java @@ -85,7 +85,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowOutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowOutputParameter.java index ab45069c..20ec6de9 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowOutputParameter.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowOutputParameter.java @@ -72,7 +72,7 @@ public interface WorkflowOutputParameter extends OutputParameter, Saveable { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool @@ -142,7 +142,7 @@ public interface WorkflowOutputParameter extends OutputParameter, Saveable { * Getter for property https://w3id.org/cwl/cwl#WorkflowOutputParameter/linkMerge
*
* The method to use to merge multiple sources into a single array. - * If not specified, the default method is "merge_nested". + * If not specified, the default method is "merge_nested". * *
*/ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowOutputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowOutputParameterImpl.java index 1b045a40..0b0f625e 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowOutputParameterImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowOutputParameterImpl.java @@ -93,7 +93,7 @@ public java.util.Optional getLabel() { * `path` or `location` and `basename` fields set, or an array consisting * of strings or File or Directory objects. It is legal to reference an * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile + * The expression may return "null" in which case there is no secondaryFile * from that expression. * * To work on non-filename-preserving storage systems, portable tool @@ -188,7 +188,7 @@ public Object getOutputSource() { * Getter for property https://w3id.org/cwl/cwl#WorkflowOutputParameter/linkMerge
*
* The method to use to merge multiple sources into a single array. - * If not specified, the default method is "merge_nested". + * If not specified, the default method is "merge_nested". * *
*/ diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStep.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStep.java index 16cf0891..2e95bd90 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStep.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStep.java @@ -30,7 +30,7 @@ underlying process implementation (such as `CommandLineTool` or another [ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified in the workflow or workflow step requirements. - A "scatter" operation specifies that the associated workflow step or + A "scatter" operation specifies that the associated workflow step or subworkflow should execute separately over a list of input elements. Each job making up a scatter operation is independent and may be executed concurrently. @@ -69,7 +69,7 @@ underlying process implementation (such as `CommandLineTool` or another # Conditional execution (Optional) Conditional execution makes execution of a step conditional on an - expression. A step that is not executed is "skipped". A skipped + expression. A step that is not executed is "skipped". A skipped step produces `null` for all output parameters. The condition is evaluated after `scatter`, using the input object diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepImpl.java index 67d97be7..5b230f8c 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepImpl.java @@ -33,7 +33,7 @@ underlying process implementation (such as `CommandLineTool` or another [ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified in the workflow or workflow step requirements. - A "scatter" operation specifies that the associated workflow step or + A "scatter" operation specifies that the associated workflow step or subworkflow should execute separately over a list of input elements. Each job making up a scatter operation is independent and may be executed concurrently. @@ -72,7 +72,7 @@ underlying process implementation (such as `CommandLineTool` or another # Conditional execution (Optional) Conditional execution makes execution of a step conditional on an - expression. A step that is not executed is "skipped". A skipped + expression. A step that is not executed is "skipped". A skipped step produces `null` for all output parameters. The condition is evaluated after `scatter`, using the input object diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepInput.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepInput.java index 57403473..0b1368ac 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepInput.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepInput.java @@ -48,7 +48,7 @@ though additional parameters may be specified (for use within `valueFrom` input links are merged depending on the method specified in the `linkMerge` field. If both `linkMerge` and `pickValue` are null or not specified, and there is more than one element in the - `source` array, the default method is "merge_nested". + `source` array, the default method is "merge_nested". If both `linkMerge` and `pickValue` are null or not specified, and there is only a single element in the `source`, then the input @@ -58,13 +58,13 @@ parameter takes the scalar value from the single input link (it is * **merge_nested** The input must be an array consisting of exactly one entry for each - input link. If "merge_nested" is specified with a single link, the value + input link. If "merge_nested" is specified with a single link, the value from the link must be wrapped in a single-item list. * **merge_flattened** 1. The source and sink parameters must be compatible types, or the source - type must be compatible with single element from the "items" type of + type must be compatible with single element from the "items" type of the destination array parameter. 2. Source parameters which are arrays are concatenated. Source parameters which are single element types are appended as @@ -91,9 +91,9 @@ steps may be connected to a single input (`source` is a list), and For the first level of a list input, pick the first non-null element. The result is a scalar. It is an error if there is no non-null element. Examples: - * `[null, x, null, y] -> x` - * `[null, [null], null, y] -> [null]` - * `[null, null, null] -> Runtime Error` + * `[null, x, null, y] -> x` + * `[null, [null], null, y] -> [null]` + * `[null, null, null] -> Runtime Error` *Intended use case*: If-else pattern where the value comes either from a conditional step or from a default or @@ -105,10 +105,10 @@ fallback value. The conditional step(s) should be placed first in For the first level of a list input, pick the single non-null element. The result is a scalar. It is an error if there is more than one non-null element. Examples: - * `[null, x, null] -> x` - * `[null, x, null, y] -> Runtime Error` - * `[null, [null], null] -> [null]` - * `[null, null, null] -> Runtime Error` + * `[null, x, null] -> x` + * `[null, x, null, y] -> Runtime Error` + * `[null, [null], null] -> [null]` + * `[null, null, null] -> Runtime Error` *Intended use case*: Switch type patterns where developer considers more than one active code path as a workflow error @@ -119,10 +119,10 @@ fallback value. The conditional step(s) should be placed first in For the first level of a list input, pick all non-null values. The result is a list, which may be empty. Examples: - * `[null, x, null] -> [x]` - * `[x, null, y] -> [x, y]` - * `[null, [x], [null]] -> [[x], [null]]` - * `[null, null, null] -> []` + * `[null, x, null] -> [x]` + * `[x, null, y] -> [x, y]` + * `[null, [x], [null]] -> [[x], [null]]` + * `[null, null, null] -> []` *Intended use case*: It is valid to have more than one source, but sources are conditional, so null sources (from skipped steps) @@ -154,7 +154,7 @@ public interface WorkflowStepInput extends Identified, Sink, LoadContents, Label * Getter for property https://w3id.org/cwl/cwl#Sink/linkMerge
*
* The method to use to merge multiple inbound links into a single array. - * If not specified, the default method is "merge_nested". + * If not specified, the default method is "merge_nested". * *
*/ @@ -231,9 +231,9 @@ public interface WorkflowStepInput extends Identified, Sink, LoadContents, Label * The `self` value in the parameter reference or expression must be * 1. `null` if there is no `source` field * 2. the value of the parameter(s) specified in the `source` field when this - * workflow input parameter **is not** specified in this workflow step's `scatter` field. + * workflow input parameter **is not** specified in this workflow step's `scatter` field. * 3. an element of the parameter specified in the `source` field when this workflow input - * parameter **is** specified in this workflow step's `scatter` field. + * parameter **is** specified in this workflow step's `scatter` field. * * The value of `inputs` in the parameter reference or expression must be * the input object to the workflow step after assigning the `source` diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepInputImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepInputImpl.java index 58745d72..57e8e93a 100644 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepInputImpl.java +++ b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepInputImpl.java @@ -51,7 +51,7 @@ though additional parameters may be specified (for use within `valueFrom` input links are merged depending on the method specified in the `linkMerge` field. If both `linkMerge` and `pickValue` are null or not specified, and there is more than one element in the - `source` array, the default method is "merge_nested". + `source` array, the default method is "merge_nested". If both `linkMerge` and `pickValue` are null or not specified, and there is only a single element in the `source`, then the input @@ -61,13 +61,13 @@ parameter takes the scalar value from the single input link (it is * **merge_nested** The input must be an array consisting of exactly one entry for each - input link. If "merge_nested" is specified with a single link, the value + input link. If "merge_nested" is specified with a single link, the value from the link must be wrapped in a single-item list. * **merge_flattened** 1. The source and sink parameters must be compatible types, or the source - type must be compatible with single element from the "items" type of + type must be compatible with single element from the "items" type of the destination array parameter. 2. Source parameters which are arrays are concatenated. Source parameters which are single element types are appended as @@ -94,9 +94,9 @@ steps may be connected to a single input (`source` is a list), and For the first level of a list input, pick the first non-null element. The result is a scalar. It is an error if there is no non-null element. Examples: - * `[null, x, null, y] -> x` - * `[null, [null], null, y] -> [null]` - * `[null, null, null] -> Runtime Error` + * `[null, x, null, y] -> x` + * `[null, [null], null, y] -> [null]` + * `[null, null, null] -> Runtime Error` *Intended use case*: If-else pattern where the value comes either from a conditional step or from a default or @@ -108,10 +108,10 @@ fallback value. The conditional step(s) should be placed first in For the first level of a list input, pick the single non-null element. The result is a scalar. It is an error if there is more than one non-null element. Examples: - * `[null, x, null] -> x` - * `[null, x, null, y] -> Runtime Error` - * `[null, [null], null] -> [null]` - * `[null, null, null] -> Runtime Error` + * `[null, x, null] -> x` + * `[null, x, null, y] -> Runtime Error` + * `[null, [null], null] -> [null]` + * `[null, null, null] -> Runtime Error` *Intended use case*: Switch type patterns where developer considers more than one active code path as a workflow error @@ -122,10 +122,10 @@ fallback value. The conditional step(s) should be placed first in For the first level of a list input, pick all non-null values. The result is a list, which may be empty. Examples: - * `[null, x, null] -> [x]` - * `[x, null, y] -> [x, y]` - * `[null, [x], [null]] -> [[x], [null]]` - * `[null, null, null] -> []` + * `[null, x, null] -> [x]` + * `[x, null, y] -> [x, y]` + * `[null, [x], [null]] -> [[x], [null]]` + * `[null, null, null] -> []` *Intended use case*: It is valid to have more than one source, but sources are conditional, so null sources (from skipped steps) @@ -175,7 +175,7 @@ public Object getSource() { * Getter for property https://w3id.org/cwl/cwl#Sink/linkMerge
*
* The method to use to merge multiple inbound links into a single array. - * If not specified, the default method is "merge_nested". + * If not specified, the default method is "merge_nested". * *
*/ @@ -282,9 +282,9 @@ public java.util.Optional getDefault() { * The `self` value in the parameter reference or expression must be * 1. `null` if there is no `source` field * 2. the value of the parameter(s) specified in the `source` field when this - * workflow input parameter **is not** specified in this workflow step's `scatter` field. + * workflow input parameter **is not** specified in this workflow step's `scatter` field. * 3. an element of the parameter specified in the `source` field when this workflow input - * parameter **is** specified in this workflow step's `scatter` field. + * parameter **is** specified in this workflow step's `scatter` field. * * The value of `inputs` in the parameter reference or expression must be * the input object to the workflow step after assigning the `source` From 81909d58429b9e079e6dc9c9be1066d561c4301f Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 4 Nov 2025 10:07:41 +0100 Subject: [PATCH 3/3] mvn deploy, sign with gpg, generate javadocs, upload --- pom.xml | 67 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 67 insertions(+) diff --git a/pom.xml b/pom.xml index be9e884c..ff9719dd 100644 --- a/pom.xml +++ b/pom.xml @@ -125,6 +125,73 @@ + + deployment + + + + org.apache.maven.plugins + maven-javadoc-plugin + 3.10.1 + + + attach-javadocs + + jar + + + + + + org.apache.maven.plugins + maven-source-plugin + 3.3.1 + + + attach-sources + + jar-no-fork + + + + + + org.apache.maven.plugins + maven-gpg-plugin + 3.2.8 + + + ${gpg.keyname} + + + --pinentry-mode + loopback + + + + + sign-artifacts + verify + + sign + + + + + + org.sonatype.central + central-publishing-maven-plugin + 0.9.0 + true + + central + true + uploaded + + + + + github