Fails to parse requirements correctly

[jdidion]

When I parse this workflow, the resulting CommandLineToolImpl contains two copies of the InlineJavascriptRequirement.

cwlVersion: v1.2

class: CommandLineTool

requirements:
  - class: InlineJavascriptRequirement
  - class: InitialWorkDirRequirement
    listing:
      - entryname: emptyWritableDir
        entry: "$({class: 'Directory', listing: []})"
        writable: true

hints:
  - class: DockerRequirement
    dockerPull: alpine

inputs: []
outputs:
  out:
    type: Directory
    outputBinding:
      glob: emptyWritableDir
arguments: [touch, emptyWritableDir/blurg]

[mr-c]

Interesting! The Python parser does not have this bug..

[mr-c]

Okay, I can confirm the bug on the Java side

package org.w3id.cwl.cwl1_2.utils;

import java.nio.file.FileSystems;
import org.junit.Assert;
import org.junit.Test;
import org.w3id.cwl.cwl1_2.CWLVersion;
import org.w3id.cwl.cwl1_2.InlineJavascriptRequirement;
import org.w3id.cwl.cwl1_2.Process;

public class ExamplesTest {
  Process doc =
      (Process)
          RootLoader.loadDocument(
              FileSystems.getDefault().getPath("/home/michael/cwljava/java-31.cwl"));

  @Test
  public void className() {
    Assert.assertEquals(doc.getClass().getSimpleName(), "CommandLineToolImpl");
  }

  @Test
  public void version() {
    java.util.Optional<CWLVersion> version = doc.getCwlVersion();
    Assert.assertTrue(version.isPresent());
    Assert.assertEquals(CWLVersion.V1_2, version.get());
  }

  @Test
  public void hints() {
    java.util.Optional<java.util.List<Object>> hints = doc.getHints();
    Assert.assertTrue(hints.isPresent());
    java.util.List<Object> hintList = hints.get();
    Assert.assertEquals(hintList.size(), 1);
  }

  @Test
  public void reqs() {
    java.util.Optional<java.util.List<Object>> reqs = doc.getRequirements();
    Assert.assertTrue(reqs.isPresent());
    java.util.List<Object> reqList = reqs.get();
    Assert.assertEquals(reqList.size(), 2);
    InlineJavascriptRequirement reqOne = (InlineJavascriptRequirement) reqList.get(0);
    Assert.assertEquals(reqOne.getClass().getSimpleName(), "InlineJavascriptRequirementImpl");
    Assert.assertNotEquals(
        reqList.get(1).getClass().getSimpleName(), "InlineJavascriptRequirementImpl");
  }
}

[mr-c]

The reason is that

1. the Java loaders do not verify the value of the class field, and since InlineJavascriptRequirement has no mandatory fields, it erroneously accepts the InitialWorkDirRequirement map

Compare https://github.com/common-workflow-lab/cwljava/blob/952d107fb26d77a94d043f4668a1eeee83952ce0/src/main/java/org/w3id/cwl/cwl1_2/InlineJavascriptRequirementImpl.java#L83 to https://github.com/common-workflow-language/cwl-utils/blob/61df4b08a368098951864e2cc2adaf682a8e12f8/cwl_utils/parser_v1_2.py#L3592

Python implementation is at https://github.com/common-workflow-language/schema_salad/blob/5e8fe097babff522cf30cd2c2f49f371a6162fa8/schema_salad/python_codegen.py#L196

2. The Java loaders do not reject extra fields; here the extra listing field should have failed parsing as an InlineJavascriptRequirement

Example:
https://github.com/common-workflow-language/cwl-utils/blob/61df4b08a368098951864e2cc2adaf682a8e12f8/cwl_utils/parser_v1_2.py#L3623

[mr-c]

Fixes are inbound:
#32
common-workflow-language/cwl-v1.2#62
common-workflow-language/schema_salad#362

[mr-c]

Fixed in #32 and test added in #34