org.molgenis.bootstrap.populate.GenomeBrowserAttributesPopulator Maven / Gradle / Ivy

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package org.molgenis.bootstrap.populate;

import static java.util.Objects.requireNonNull;

import org.molgenis.data.DataService;
import org.molgenis.genomebrowser.meta.GenomeBrowserAttributesFactory;
import org.molgenis.genomebrowser.meta.GenomeBrowserAttributesMetadata;
import org.springframework.stereotype.Component;

@Component
public class GenomeBrowserAttributesPopulator {
  private final DataService dataService;
  private final GenomeBrowserAttributesFactory gbaFactory;

  public GenomeBrowserAttributesPopulator(
      DataService dataService, GenomeBrowserAttributesFactory gbaFactory) {
    this.gbaFactory = requireNonNull(gbaFactory);
    this.dataService = requireNonNull(dataService);
  }

  public void populate() {
    // Only apply default settings if table does not contain the genomebrowser setting
    if (dataService.findOneById(GenomeBrowserAttributesMetadata.GENOMEBROWSERATTRIBUTES, "simple1")
        == null) {
      dataService.add(
          GenomeBrowserAttributesMetadata.GENOMEBROWSERATTRIBUTES,
          gbaFactory.create("simple1", true, 0, "start", "chr", null, null, null));
    }
    if (dataService.findOneById(GenomeBrowserAttributesMetadata.GENOMEBROWSERATTRIBUTES, "VCF")
        == null) {
      dataService.add(
          GenomeBrowserAttributesMetadata.GENOMEBROWSERATTRIBUTES,
          gbaFactory.create("VCF", true, 1, "POS", "#CHROM", "REF", "ALT", null));
    }
    if (dataService.findOneById(GenomeBrowserAttributesMetadata.GENOMEBROWSERATTRIBUTES, "full")
        == null) {
      dataService.add(
          GenomeBrowserAttributesMetadata.GENOMEBROWSERATTRIBUTES,
          gbaFactory.create("full", true, 2, "start", "chr", "ref", "alt", "stop"));
    }
    if (dataService.findOneById(GenomeBrowserAttributesMetadata.GENOMEBROWSERATTRIBUTES, "simple2")
        == null) {
      dataService.add(
          GenomeBrowserAttributesMetadata.GENOMEBROWSERATTRIBUTES,
          gbaFactory.create("simple2", true, 3, "POS", "#CHROM", null, null, null));
    }
  }
}