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

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package org.molgenis.genomebrowser;

import com.google.auto.value.AutoValue;
import java.util.stream.Collectors;
import javax.annotation.Nullable;
import org.json.JSONArray;
import org.json.JSONObject;
import org.molgenis.data.meta.model.EntityType;
import org.molgenis.data.rest.v2.RestControllerV2;
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 {
  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) {
    return new AutoValue_GenomeBrowserTrack(
        id,
        label,
        labelAttr,
        entity,
        trackType,
        molgenisReferenceTracks,
        molgenisReferenceMode,
        genomeBrowserAttrs,
        actions,
        attrs,
        scoreAttr,
        exonKey);
  }

  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());
  }

  public abstract String getId();

  public abstract String getLabel();

  public abstract String getLabelAttr();

  public abstract EntityType getEntity();

  public abstract GenomeBrowserSettings.TrackType getTrackType();

  @Nullable
  public abstract Iterable getMolgenisReferenceTracks();

  public abstract GenomeBrowserSettings.MolgenisReferenceMode getMolgenisReferenceMode();

  public abstract GenomeBrowserAttributes getGenomeBrowserAttrs();

  @Nullable
  public abstract String getActions();

  @Nullable
  public abstract String getAttrs();

  @Nullable
  public abstract String getScoreAttr();

  @Nullable
  public abstract String getExonKey();

  public JSONObject toTrackJson() {
    JSONObject json = new JSONObject();
    json.put("name", getLabel());
    json.put("entity", getEntity().getId());
    json.put("tier_type", "molgenis");
    json.put(
        "uri",
        UriComponentsBuilder.fromPath(RestControllerV2.BASE_URI)
            .pathSegment(getEntity().getId())
            .toUriString());
    json.put("genome_attrs", getGenomeBrowserAttrsJSON(getGenomeBrowserAttrs()));
    if (getLabelAttr() != null) json.put("label_attr", getLabelAttr());
    if (getAttrs() != null) json.put("attrs", getAttrsJSON(getAttrs()));
    if (getActions() != null) json.put("actions", getActions());
    if (getTrackType() != null) json.put("track_type", getTrackType());
    if (getScoreAttr() != null) json.put("score_attr", getScoreAttr());
    if (getExonKey() != null) json.put("exon_key", getExonKey());
    return json;
  }

  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;
  }
}