initial support for CWL v1.1

Author: mr-c

Diff for: adding_new_cwl_versions.txt

@@ -0,0 +1,12 @@
+# discover the valid CWL files from the conformance tests:
+
+cd ~/cwl-v1.1 # my local checkout of https://github.com/common-workflow-language/cwl-v1.1/
+git ls-files -- tests | grep cwl$ | xargs -I{} bash -c 'cwltool --relax-path-checks --validate {} >/dev/null 2>/dev/null && echo {}' > valid_examples.txt
+#git ls-files -- tests | grep cwl$ | xargs -I{} bash -c 'cwltool --relax-path-checks --validate {} >/dev/null 2>/dev/null || echo {}' > invalid_examples.txt
+mkdir valid-examples; for file in $(cat valid_examples.txt); do cp ${file} valid-examples/valid_$(basename ${file}) ; done
+
+# build the Java parser
+schema-salad-tool --codegen java --codegen-package org.w3id.cwl.cwl1_1 --codegen-examples ~/cwl-v1.1/valid-examples ~/cwl-v1.1/CommonWorkflowLanguage.yml
+
+mvn test
+# copy missing files into ./src/test/resources/org/w3id/cwl/cwl1_1/utils

Diff for: src/main/java/org/w3id/cwl/cwl1_1/Any.java

@@ -0,0 +1,37 @@
+// Copyright Common Workflow Language project contributors
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//      http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package org.w3id.cwl.cwl1_1;
+
+import org.w3id.cwl.cwl1_1.utils.ValidationException;
+
+public enum Any {
+  ANY("Any");
+
+  private static String[] symbols = new String[] {"Any"};
+  private String docVal;
+
+  private Any(final String docVal) {
+    this.docVal = docVal;
+  }
+
+  public static Any fromDocumentVal(final String docVal) {
+    for(final Any val : Any.values()) {
+      if(val.docVal.equals(docVal)) {
+        return val;
+      }
+    }
+    throw new ValidationException(String.format("Expected one of %s", Any.symbols, docVal));
+  }
+}

Diff for: src/main/java/org/w3id/cwl/cwl1_1/ArraySchema.java

@@ -0,0 +1,37 @@
+// Copyright Common Workflow Language project contributors
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//      http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package org.w3id.cwl.cwl1_1;
+
+import org.w3id.cwl.cwl1_1.utils.Saveable;
+
+/**
+* Auto-generated interface for <I>https://w3id.org/cwl/salad#ArraySchema</I><BR>This interface is implemented by {@link ArraySchemaImpl}<BR>
+ */
+public interface ArraySchema extends Saveable {
+  /**
+   * Getter for property <I>https://w3id.org/cwl/salad#items</I><BR>
+   * <BLOCKQUOTE>
+   * Defines the type of the array elements.   * </BLOCKQUOTE>
+   */
+
+  Object getItems();
+  /**
+   * Getter for property <I>https://w3id.org/cwl/salad#type</I><BR>
+   * <BLOCKQUOTE>
+   * Must be `array`   * </BLOCKQUOTE>
+   */
+
+  enum_d062602be0b4b8fd33e69e29a841317b6ab665bc getType();
+}

Diff for: src/main/java/org/w3id/cwl/cwl1_1/ArraySchemaImpl.java

@@ -0,0 +1,113 @@
+// Copyright Common Workflow Language project contributors
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//      http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package org.w3id.cwl.cwl1_1;
+
+import org.w3id.cwl.cwl1_1.utils.LoaderInstances;
+import org.w3id.cwl.cwl1_1.utils.LoadingOptions;
+import org.w3id.cwl.cwl1_1.utils.LoadingOptionsBuilder;
+import org.w3id.cwl.cwl1_1.utils.SaveableImpl;
+import org.w3id.cwl.cwl1_1.utils.ValidationException;
+
+/**
+* Auto-generated class implementation for <I>https://w3id.org/cwl/salad#ArraySchema</I><BR>
+ */
+public class ArraySchemaImpl extends SaveableImpl implements ArraySchema {
+  private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build();
+  private java.util.Map<String, Object> extensionFields_ =
+      new java.util.HashMap<String, Object>();
+
+  private Object items;
+
+  /**
+   * Getter for property <I>https://w3id.org/cwl/salad#items</I><BR>
+   * <BLOCKQUOTE>
+   * Defines the type of the array elements.   * </BLOCKQUOTE>
+   */
+
+  public Object getItems() {
+    return this.items;
+  }
+
+  private enum_d062602be0b4b8fd33e69e29a841317b6ab665bc type;
+
+  /**
+   * Getter for property <I>https://w3id.org/cwl/salad#type</I><BR>
+   * <BLOCKQUOTE>
+   * Must be `array`   * </BLOCKQUOTE>
+   */
+
+  public enum_d062602be0b4b8fd33e69e29a841317b6ab665bc getType() {
+    return this.type;
+  }
+
+  /**
+   * Used by {@link org.w3id.cwl.cwl1_1.utils.RootLoader} to construct instances of ArraySchemaImpl.
+   *
+   * @param __doc_            Document fragment to load this record object from (presumably a
+                              {@link java.util.Map}).
+   * @param __baseUri_        Base URI to generate child document IDs against.
+   * @param __loadingOptions  Context for loading URIs and populating objects.
+   * @param __docRoot_        ID at this position in the document (if available) (maybe?)
+   * @throws ValidationException If the document fragment is not a {@link java.util.Map}
+   *                             or validation of fields fails.
+   */
+  public ArraySchemaImpl(
+      final Object __doc_,
+      final String __baseUri_,
+      LoadingOptions __loadingOptions,
+      final String __docRoot_) {
+    super(__doc_, __baseUri_, __loadingOptions, __docRoot_);
+    // Prefix plumbing variables with '__' to reduce likelihood of collision with
+    // generated names.
+    String __baseUri = __baseUri_;
+    String __docRoot = __docRoot_;
+    if (!(__doc_ instanceof java.util.Map)) {
+      throw new ValidationException("ArraySchemaImpl called on non-map");
+    }
+    final java.util.Map<String, Object> __doc = (java.util.Map<String, Object>) __doc_;
+    final java.util.List<ValidationException> __errors =
+        new java.util.ArrayList<ValidationException>();
+    if (__loadingOptions != null) {
+      this.loadingOptions_ = __loadingOptions;
+    }
+    Object items;
+    try {
+      items =
+          LoaderInstances
+              .typedsl_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_StringInstance_2
+              .loadField(__doc.get("items"), __baseUri, __loadingOptions);
+    } catch (ValidationException e) {
+      items = null; // won't be used but prevents compiler from complaining.
+      final String __message = "the `items` field is not valid because:";
+      __errors.add(new ValidationException(__message, e));
+    }
+    enum_d062602be0b4b8fd33e69e29a841317b6ab665bc type;
+    try {
+      type =
+          LoaderInstances
+              .typedsl_enum_d062602be0b4b8fd33e69e29a841317b6ab665bc_2
+              .loadField(__doc.get("type"), __baseUri, __loadingOptions);
+    } catch (ValidationException e) {
+      type = null; // won't be used but prevents compiler from complaining.
+      final String __message = "the `type` field is not valid because:";
+      __errors.add(new ValidationException(__message, e));
+    }
+    if (!__errors.isEmpty()) {
+      throw new ValidationException("Trying 'RecordField'", __errors);
+    }
+    this.items = (Object) items;
+    this.type = (enum_d062602be0b4b8fd33e69e29a841317b6ab665bc) type;
+  }
+}

Diff for: src/main/java/org/w3id/cwl/cwl1_1/CWLType.java

@@ -0,0 +1,45 @@
+// Copyright Common Workflow Language project contributors
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//      http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package org.w3id.cwl.cwl1_1;
+
+import org.w3id.cwl.cwl1_1.utils.ValidationException;
+
+public enum CWLType {
+  NULL("null"),
+  BOOLEAN("boolean"),
+  INT("int"),
+  LONG("long"),
+  FLOAT("float"),
+  DOUBLE("double"),
+  STRING("string"),
+  FILE("File"),
+  DIRECTORY("Directory");
+
+  private static String[] symbols = new String[] {"null", "boolean", "int", "long", "float", "double", "string", "File", "Directory"};
+  private String docVal;
+
+  private CWLType(final String docVal) {
+    this.docVal = docVal;
+  }
+
+  public static CWLType fromDocumentVal(final String docVal) {
+    for(final CWLType val : CWLType.values()) {
+      if(val.docVal.equals(docVal)) {
+        return val;
+      }
+    }
+    throw new ValidationException(String.format("Expected one of %s", CWLType.symbols, docVal));
+  }
+}

Diff for: src/main/java/org/w3id/cwl/cwl1_1/CWLVersion.java

@@ -0,0 +1,50 @@
+// Copyright Common Workflow Language project contributors
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//      http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package org.w3id.cwl.cwl1_1;
+
+import org.w3id.cwl.cwl1_1.utils.ValidationException;
+
+public enum CWLVersion {
+  DRAFT_2("draft-2"),
+  DRAFT_3_DEV1("draft-3.dev1"),
+  DRAFT_3_DEV2("draft-3.dev2"),
+  DRAFT_3_DEV3("draft-3.dev3"),
+  DRAFT_3_DEV4("draft-3.dev4"),
+  DRAFT_3_DEV5("draft-3.dev5"),
+  DRAFT_3("draft-3"),
+  DRAFT_4_DEV1("draft-4.dev1"),
+  DRAFT_4_DEV2("draft-4.dev2"),
+  DRAFT_4_DEV3("draft-4.dev3"),
+  V1_0_DEV4("v1.0.dev4"),
+  V1_0("v1.0"),
+  V1_1_0_DEV1("v1.1.0-dev1"),
+  V1_1("v1.1");
+
+  private static String[] symbols = new String[] {"draft-2", "draft-3.dev1", "draft-3.dev2", "draft-3.dev3", "draft-3.dev4", "draft-3.dev5", "draft-3", "draft-4.dev1", "draft-4.dev2", "draft-4.dev3", "v1.0.dev4", "v1.0", "v1.1.0-dev1", "v1.1"};
+  private String docVal;
+
+  private CWLVersion(final String docVal) {
+    this.docVal = docVal;
+  }
+
+  public static CWLVersion fromDocumentVal(final String docVal) {
+    for(final CWLVersion val : CWLVersion.values()) {
+      if(val.docVal.equals(docVal)) {
+        return val;
+      }
+    }
+    throw new ValidationException(String.format("Expected one of %s", CWLVersion.symbols, docVal));
+  }
+}

Diff for: src/main/java/org/w3id/cwl/cwl1_1/CommandInputArraySchema.java

@@ -0,0 +1,65 @@
+// Copyright Common Workflow Language project contributors
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//      http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package org.w3id.cwl.cwl1_1;
+
+import org.w3id.cwl.cwl1_1.utils.Saveable;
+
+/**
+* Auto-generated interface for <I>https://w3id.org/cwl/cwl#CommandInputArraySchema</I><BR>This interface is implemented by {@link CommandInputArraySchemaImpl}<BR>
+ */
+public interface CommandInputArraySchema extends InputArraySchema, CommandInputSchema, CommandLineBindable, Saveable {
+  /**
+   * Getter for property <I>https://w3id.org/cwl/cwl#IOSchema/name</I><BR>
+   * <BLOCKQUOTE>
+   * The identifier for this type   * </BLOCKQUOTE>
+   */
+
+  java.util.Optional<String> getName();
+  /**
+   * Getter for property <I>https://w3id.org/cwl/salad#items</I><BR>
+   * <BLOCKQUOTE>
+   * Defines the type of the array elements.   * </BLOCKQUOTE>
+   */
+
+  Object getItems();
+  /**
+   * Getter for property <I>https://w3id.org/cwl/salad#type</I><BR>
+   * <BLOCKQUOTE>
+   * Must be `array`   * </BLOCKQUOTE>
+   */
+
+  enum_d062602be0b4b8fd33e69e29a841317b6ab665bc getType();
+  /**
+   * Getter for property <I>https://w3id.org/cwl/cwl#Labeled/label</I><BR>
+   * <BLOCKQUOTE>
+   * A short, human-readable label of this object.   * </BLOCKQUOTE>
+   */
+
+  java.util.Optional<String> getLabel();
+  /**
+   * Getter for property <I>https://w3id.org/cwl/salad#Documented/doc</I><BR>
+   * <BLOCKQUOTE>
+   * A documentation string for this object, or an array of strings which should be concatenated.   * </BLOCKQUOTE>
+   */
+
+  Object getDoc();
+  /**
+   * Getter for property <I>https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding</I><BR>
+   * <BLOCKQUOTE>
+   * Describes how to turn this object into command line arguments.   * </BLOCKQUOTE>
+   */
+
+  java.util.Optional<CommandLineBinding> getInputBinding();
+}