org.molgenis.genomebrowser.GenomeBrowserTrack Maven / Gradle / Ivy

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package org.molgenis.genomebrowser;

import static java.util.Collections.emptyList;

import com.google.auto.value.AutoValue;
import com.google.common.base.Strings;
import java.util.stream.Collectors;
import javax.annotation.CheckForNull;
import javax.annotation.Nullable;
import org.json.JSONArray;
import org.json.JSONObject;
import org.molgenis.data.meta.model.EntityType;
import org.molgenis.genomebrowser.meta.GenomeBrowserAttributes;
import org.molgenis.genomebrowser.meta.GenomeBrowserSettings;
import org.springframework.web.util.UriComponentsBuilder;

@AutoValue
@SuppressWarnings(
    "squid:S1610") // Abstract classes without fields should be converted to interfaces
public abstract class GenomeBrowserTrack {

  @SuppressWarnings("squid:S00107") // Methods should not have too many parameters
  public static GenomeBrowserTrack create(
      String id,
      String label,
      String labelAttr,
      EntityType entity,
      GenomeBrowserSettings.TrackType trackType,
      Iterable molgenisReferenceTracks,
      GenomeBrowserSettings.MolgenisReferenceMode molgenisReferenceMode,
      GenomeBrowserAttributes genomeBrowserAttrs,
      String actions,
      String attrs,
      String scoreAttr,
      String exonKey,
      String featureInfoPlugin) {
    return new AutoValue_GenomeBrowserTrack(
        id,
        label,
        labelAttr,
        entity,
        trackType,
        molgenisReferenceTracks != null ? molgenisReferenceTracks : emptyList(),
        molgenisReferenceMode,
        genomeBrowserAttrs,
        actions,
        attrs,
        scoreAttr,
        exonKey,
        featureInfoPlugin);
  }

  public static GenomeBrowserTrack create(GenomeBrowserSettings settings) {
    return new AutoValue_GenomeBrowserTrack(
        settings.getIdentifier(),
        settings.getLabel(),
        settings.getLabelAttr().getName(),
        settings.getEntity(),
        settings.getTrackType(),
        settings.getMolgenisReferenceTracks().collect(Collectors.toList()),
        settings.getMolgenisReferenceMode(),
        settings.getGenomeBrowserAttrs(),
        settings.getActions(),
        settings.getAttrs(),
        settings.getScoreAttr(),
        settings.getExonKey(),
        settings.getFeatureInfoPlugin());
  }

  public abstract String getId();

  public abstract String getLabel();

  public abstract String getLabelAttr();

  public abstract EntityType getEntity();

  public abstract GenomeBrowserSettings.TrackType getTrackType();

  public abstract Iterable getMolgenisReferenceTracks();

  public abstract GenomeBrowserSettings.MolgenisReferenceMode getMolgenisReferenceMode();

  public abstract GenomeBrowserAttributes getGenomeBrowserAttrs();

  @Nullable
  @CheckForNull
  public abstract String getActions();

  @Nullable
  @CheckForNull
  public abstract String getAttrs();

  @Nullable
  @CheckForNull
  public abstract String getScoreAttr();

  @Nullable
  @CheckForNull
  public abstract String getExonKey();

  @Nullable
  @CheckForNull
  public abstract String getFeatureInfoPlugin();

  public String toTrackString() {
    StringBuilder config = new StringBuilder("{");
    config.append(getConfigStringValue("name", getLabel()));
    config.append(",").append(getConfigStringValue("entity", getEntity().getId()));
    config.append(",").append(getConfigStringValue("tier_type", "molgenis"));
    config
        .append(",")
        .append(
            getConfigStringValue(
                "uri",
                UriComponentsBuilder.fromPath("/api/v2")
                    .pathSegment(getEntity().getId())
                    .toUriString()));
    config
        .append(",")
        .append(
            String.format(
                "\"%s\":%s",
                "genome_attrs", getGenomeBrowserAttrsJSON(getGenomeBrowserAttrs()).toString()));
    if (getLabelAttr() != null)
      config.append(",").append(getConfigStringValue("label_attr", getLabelAttr()));
    String attrs = getAttrs();
    if (attrs != null)
      config.append(",").append(getConfigObjectValue("attrs", getAttrsJSON(attrs).toString()));
    if (getActions() != null)
      config.append(",").append(getConfigObjectValue("actions", JSONObject.quote(getActions())));
    if (getTrackType() != null)
      config.append(",").append(getConfigStringValue("track_type", getTrackType().name()));
    if (getScoreAttr() != null)
      config.append(",").append(getConfigStringValue("score_attr", getScoreAttr()));
    if (getExonKey() != null)
      config.append(",").append(getConfigStringValue("exon_key", getExonKey()));
    if (!Strings.isNullOrEmpty(getFeatureInfoPlugin()))
      config
          .append(",")
          .append(
              getConfigObjectValue(
                  "featureInfoPlugin",
                  String.format("function(f, info) {%s}", getFeatureInfoPlugin())));
    config.append("}");
    return config.toString();
  }

  private String getConfigObjectValue(String key, String value) {
    return String.format("\"%s\":%s", key, value);
  }

  private String getConfigStringValue(String key, String value) {
    return String.format("\"%s\":\"%s\"", key, value);
  }

  private JSONObject getGenomeBrowserAttrsJSON(GenomeBrowserAttributes genomeBrowserAttrs) {
    JSONObject genomeAttrsJSON = new JSONObject();
    genomeAttrsJSON.put("chr", genomeBrowserAttrs.getChrom());
    genomeAttrsJSON.put("pos", genomeBrowserAttrs.getPos());
    if (genomeBrowserAttrs.getRef() != null) {
      genomeAttrsJSON.put("ref", genomeBrowserAttrs.getRef());
    }
    if (genomeBrowserAttrs.getAlt() != null) {
      genomeAttrsJSON.put("alt", genomeBrowserAttrs.getAlt());
    }
    if (genomeBrowserAttrs.getStop() != null) {
      genomeAttrsJSON.put("stop", genomeBrowserAttrs.getStop());
    }
    return genomeAttrsJSON;
  }

  private JSONArray getAttrsJSON(String attrsString) {
    JSONArray attrsArray = new JSONArray();
    String[] attrs = attrsString.split(",");
    for (String attr : attrs) {
      attrsArray.put(attr);
    }
    return attrsArray;
  }
}