Examples with Resource org.phenopackets.schema.v1.core.Resource used on opensource projects

Example 1 with Resource

use of org.phenopackets.schema.v1.core.Resource in project biosamples-v4 by EBIBioSamples.

the class PhenopacketConversionHelper method getResource.

public Optional<Resource> getResource(PhenopacketAttribute attribute) {
    Optional<Resource> optionalResource = Optional.empty();
    if (attribute.getOntologyId() != null) {
        String ontology = attribute.getOntologyId().split(":")[0];
        OLSDataRetriever retriever = new OLSDataRetriever();
        retriever.readResourceInfoFromUrl(ontology);
        optionalResource = Optional.of(Resource.newBuilder().setId(retriever.getResourceId()).setName(retriever.getResourceName()).setUrl(retriever.getResourceUrl()).setNamespacePrefix(retriever.getResourcePrefix()).setVersion(retriever.getResourceVersion()).build());
    }
    return optionalResource;
}

Example 2 with Resource

use of org.phenopackets.schema.v1.core.Resource in project automatiko-engine by automatiko-io.

the class ResourceHandler method start.

@SuppressWarnings("unchecked")
public Object start(final String uri, final String localName, final Attributes attrs, final ExtensibleXmlParser parser) throws SAXException {
    parser.startElementBuilder(localName, attrs);
    String id = attrs.getValue("id");
    String name = attrs.getValue("name");
    ProcessBuildData buildData = (ProcessBuildData) parser.getData();
    Map<String, Resource> resources = (Map<String, Resource>) buildData.getMetaData("Resources");
    if (resources == null) {
        resources = new HashMap<String, Resource>();
        buildData.setMetaData("Resources", resources);
    }
    Resource resource = new Resource(id, name);
    ;
    resources.put(id, resource);
    return resource;
}

Example 3 with Resource

use of org.phenopackets.schema.v1.core.Resource in project automatiko-engine by automatiko-io.

the class UserTaskHandler method handleNode.

protected void handleNode(final Node node, final Element element, final String uri, final String localName, final ExtensibleXmlParser parser) throws SAXException {
    super.handleNode(node, element, uri, localName, parser);
    HumanTaskNode humanTaskNode = (HumanTaskNode) node;
    Work work = humanTaskNode.getWork();
    work.setName("Human Task");
    ProcessBuildData buildData = (ProcessBuildData) parser.getData();
    Map<String, Resource> resources = (Map<String, Resource>) buildData.getMetaData("Resources");
    Map<String, String> dataInputs = new HashMap<String, String>();
    Map<String, String> dataOutputs = new HashMap<String, String>();
    List<String> owners = new ArrayList<String>();
    org.w3c.dom.Node xmlNode = element.getFirstChild();
    while (xmlNode != null) {
        String nodeName = xmlNode.getNodeName();
        // ioSpec and data{Input,Output}Spec handled in super.handleNode(...)
        if ("potentialOwner".equals(nodeName)) {
            String owner = readPotentialOwner(xmlNode, humanTaskNode);
            if (owner != null) {
                owners.add(owner);
            }
        } else if ("performer".equals(nodeName)) {
            org.w3c.dom.Node resourceNode = xmlNode.getFirstChild();
            if (resourceNode != null) {
                String resourceId = resourceNode.getTextContent();
                if (resources.containsKey(resourceId)) {
                    owners.add(resources.get(resourceId).getName());
                }
            }
        }
        xmlNode = xmlNode.getNextSibling();
    }
    if (owners.size() > 0) {
        String owner = owners.get(0);
        for (int i = 1; i < owners.size(); i++) {
            owner += "," + owners.get(i);
        }
        humanTaskNode.getWork().setParameter("ActorId", owner);
    }
    humanTaskNode.getWork().setParameter("NodeName", humanTaskNode.getName());
}