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An API that exposes Pathling functionality to language libraries.

There is a newer version: 7.0.1

/*
 * Copyright 2023 Commonwealth Scientific and Industrial Research
 * Organisation (CSIRO) ABN 41 687 119 230.
 *
 * 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 au.csiro.pathling.library.io.source;

import static java.util.stream.Collectors.toSet;

import au.csiro.pathling.library.FhirMimeTypes;
import au.csiro.pathling.library.PathlingContext;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
import java.util.function.Function;
import javax.annotation.Nonnull;
import org.hl7.fhir.r4.model.Enumerations.ResourceType;

/**
 * A class for making data within a set of FHIR Bundles available for query.
 *
 * @author John Grimes
 */
public class BundlesSource extends FileSource {

  private static final Map MIME_TYPE_TO_EXTENSION;

  static {
    MIME_TYPE_TO_EXTENSION = new HashMap<>();
    MIME_TYPE_TO_EXTENSION.put(FhirMimeTypes.FHIR_JSON, "json");
    MIME_TYPE_TO_EXTENSION.put(FhirMimeTypes.FHIR_XML, "xml");
  }

  public BundlesSource(@Nonnull final PathlingContext context, @Nonnull final String path,
      @Nonnull final String mimeType, @Nonnull final Set resourceTypes) {
    super(context, path,
        // Map to the fixed set of resource types for all files.
        fixedResourceSetMapper(resourceTypes),
        // Use the file extension that matches the FHIR MIME type.
        MIME_TYPE_TO_EXTENSION.get(mimeType),
        // Treat the whole file as a record, rather than individual lines.
        context.getSpark().read().option("wholetext", true).format("text"),
        // Extract the nominated resource types from each file and encode using the specified MIME
        // type.
        (sourceData, resourceType) ->
            context.encodeBundle(sourceData, resourceType.toCode(), mimeType));
  }

  /**
   * Creates a mapper that maps a file path to a fixed set of resource types.
   *
   * @param resourceTypes the set of resource types to map to
   * @return a mapper that maps a file path to a fixed set of resource types
   */
  @Nonnull
  private static Function> fixedResourceSetMapper(
      @Nonnull final Set resourceTypes) {
    return path -> resourceTypes.stream().map(ResourceType::toCode).collect(toSet());
  }

}