com.cerner.bunsen.r4.python.Functions Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of bunsen-r4 Show documentation
FHIR R4 Support for Bunsen
There is a newer version: 1.4.7
package com.cerner.bunsen.r4.python;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser;
import com.cerner.bunsen.FhirEncoders;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.util.List;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Resource;

/**
 * Common functions for working with FHIR resources.
 */
public class Functions {

  private static final FhirContext CONTEXT = FhirContext.forR4();

  /**
   * Converts a set of FHIR resources to JSON.
   *
   * @param dataset a dataset containing FHIR resources
   * @param resourceType the FHIR resource type
   * @return a dataset of JSON strings for the FHIR resources
   */
  public static Dataset toJson(Dataset dataset, String resourceType) {

    Dataset resourceDataset =
        dataset.as(FhirEncoders.forR4()
            .getOrCreate()
            .of(resourceType));

    return resourceDataset.map(new ToJson(), Encoders.STRING());
  }

  /**
   * Returns a bundle containing all resources in the dataset. This should be used
   * with caution for large datasets, since the returned bundle will include all data.
   *
   * @param dataset a dataset of FHIR resoruces
   * @return a bundle containing those resources.
   */
  public static Bundle toBundle(Dataset dataset) {

    List resources = (List) dataset.collectAsList();

    Bundle bundle = new Bundle();

    for (Resource resource : resources) {
      bundle.addEntry().setResource(resource);
    }

    return bundle;
  }

  /**
   * Returns a JSON string representing the resources as a bundle. This should be used
   * with caution for large datasets, since the returned string will include all data.
   *
   * @param dataset a dataset of FHIR resources.
   * @return A string containing the JSON representation of the bundle.
   */
  public static String toJsonBundle(Dataset dataset) {

    Bundle bundle = toBundle(dataset);

    return CONTEXT.newJsonParser().encodeResourceToString(bundle);
  }

  static class ToJson implements MapFunction {

    /**
     * Create a new parser instance for each object, since they are not
     * guaranteed to be thread safe.
     */
    private transient IParser parser = CONTEXT.newJsonParser();

    private void readObject(ObjectInputStream in) throws IOException,
        ClassNotFoundException {

      in.defaultReadObject();

      parser = CONTEXT.newJsonParser();
    }

    public String call(IBaseResource resource) throws Exception {

      return parser.encodeResourceToString(resource);
    }
  }

  /**
   * Converts a resource to its XML representation.
   *
   * @param resource the resource
   * @return a string containing XML for the resource.
   */
  public static String resourceToXml(Resource resource) {

    IParser parser = CONTEXT.newXmlParser();

    return parser.encodeResourceToString(resource);
  }

  /**
   * Converts a resource to its JSON representation.
   *
   * @param resource the resource
   * @return a string containing JSON for the resource.
   */
  public static String resourceToJson(Resource resource) {

    IParser parser = CONTEXT.newJsonParser();

    return parser.encodeResourceToString(resource);
  }
}