#161 modified the crate reader to consider entities as data entities if linked not just directly from the root data entity's hasPart, but also recursively from the hasPart of another data entity. This leads to problems when hasPart is used on a File to refer to sections of it. For instance, in ml-predict-pipeline-cwltool-runcrate :

{
    "@id": "packed.cwl",
    "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow", "HowTo"],
    "hasPart": [
        {"@id": "packed.cwl#classify_tumor.cwl"},
        {"@id": "packed.cwl#extract_tissue.cwl"}
    ]
},
{
    "@id": "packed.cwl#classify_tumor.cwl",
    "@type": "SoftwareApplication"
}

"packed.cwl#classify_tumor.cwl" is read in as a data entity. This PR changes ROCrate.__add_parts to consider only hasPart from Dataset entities.