Java Code Examples for org.jooq.Record#get()

private int findCoordSystemId()
{
    final String version = mRefGenomeVersion == HG37 ? "GRCh37" : "GRCh38";

    final String queryStr = "select coord_system_id from coord_system"
            + " where version = '" + version + "'"
            + " order by rank  limit 1";

    LNX_LOGGER.debug("gene query: {}", queryStr);

    Result<?> results = mDbContext.fetch(queryStr);

    for(final Record record : results)
    {
        UInteger coordSystemId = (UInteger) record.get("coord_system_id");
        return coordSystemId.intValue();
    }

    return -1;
}
 

/**
 * [#2700] [#3582] If a POJO attribute is NULL, but the column is NOT NULL
 * then we should let the database apply DEFAULT values
 */
private static final void resetChangedOnNotNull(Record record) {
    int size = record.size();

    for (int i = 0; i < size; i++)
        if (record.get(i) == null)
            if (!record.field(i).getDataType().nullable())
                record.changed(i, false);
}
 

private void writeGeneData(final String outputFile)
{
    LNX_LOGGER.info("caching gene data to {}", outputFile);

    try
    {
        BufferedWriter writer = createBufferedWriter(outputFile, false);

        writer.write("GeneId,GeneName,Chromosome,Strand,GeneStart,GeneEnd,EntrezIds,KaryotypeBand,Synonyms");
        writer.newLine();

        Result<?> results = queryAllGeneData();

        for(final Record record : results)
        {
            UInteger geneStart = (UInteger) record.get("GeneStart");
            UInteger geneEnd = (UInteger) record.get("GeneEnd");
            Byte strand = (Byte) record.get("Strand");

            writer.write(String.format("%s,%s,%s,%d,%d,%d,%s,%s,%s",
                    record.get("GeneId"), record.get("GeneName"), record.get("Chromosome"),
                    strand.intValue(), geneStart.intValue(), geneEnd.intValue(),
                    record.get("EntrezIds"), record.get("KaryotypeBand"), record.get("Synonyms")));

            writer.newLine();
        }

        writer.close();
    }
    catch (final IOException e)
    {
        LNX_LOGGER.error("error writing Ensembl gene data file: {}", e.toString());
    }
}
 

private void writeTranscriptProteinData(final String outputFile)
{
    LNX_LOGGER.info("caching protein data to {}", outputFile);

    try
    {
        BufferedWriter writer = createBufferedWriter(outputFile, false);

        writer.write("TranscriptId,TranslationId,ProteinFeatureId,SeqStart,SeqEnd,HitDescription");
        writer.newLine();

        Result<?> results = queryAllProteinData();

        for(final Record record : results)
        {
            UInteger transcriptId = (UInteger) record.get("TranscriptId");
            UInteger translationId = (UInteger) record.get("TranslationId");
            UInteger proteinId = (UInteger) record.get("ProteinFeatureId");
            Integer seqStart = (Integer) record.get("SeqStart");
            Integer seqEnd = (Integer) record.get("SeqEnd");

            writer.write(String.format("%d,%d,%d,%d,%d,%s",
                    transcriptId.intValue(), translationId.intValue(), proteinId.intValue(),
                    seqStart.intValue(), seqEnd.intValue(), record.get("HitDescription")));

            writer.newLine();
        }

        writer.close();
    }
    catch (final IOException e)
    {
        LNX_LOGGER.error("error writing Ensembl trans-protein data file: {}", e.toString());
    }
}
 

/**
 * [#2700] [#3582] If a POJO attribute is NULL, but the column is NOT NULL
 * then we should let the database apply DEFAULT values
 */
private static final void resetChangedOnNotNull(Record record) {
    int size = record.size();

    for (int i = 0; i < size; i++)
        if (record.get(i) == null)
            if (!record.field(i).getDataType().nullable())
                record.changed(i, false);
}
 

public Map<String, Cloud> getCloudsDataForPlatform(Connection conn, long platformId) {
  DSLContext create = DSL.using(conn, SQLDialect.POSTGRES);

  Map<String, Cloud> platformCloudMap = new HashMap<String, Cloud>();

  // Fetching All Clouds for platform
  Result<Record> cloudsInPlatformRecords = create.select().from(CM_CI_RELATIONS)
      .join(MD_RELATIONS).on(MD_RELATIONS.RELATION_ID.eq(CM_CI_RELATIONS.RELATION_ID)).join(CM_CI)
      .on(CM_CI.CI_ID.eq(CM_CI_RELATIONS.TO_CI_ID))
      .where(MD_RELATIONS.RELATION_NAME.eq("base.Consumes"))
      .and(CM_CI_RELATIONS.FROM_CI_ID.eq(platformId)).fetch();

  for (Record cloudsInPlatformRecord : cloudsInPlatformRecords) {

    long relationID = cloudsInPlatformRecord.get(CM_CI_RELATIONS.CI_RELATION_ID);
    long cloudCid = cloudsInPlatformRecord.get(CM_CI_RELATIONS.TO_CI_ID);
    String cloudName = cloudsInPlatformRecord.get(CM_CI.CI_NAME);

    Result<Record> cloudsPlatformRelationshipAttributesRecords =
        create.select().from(CM_CI_RELATION_ATTRIBUTES).join(MD_RELATION_ATTRIBUTES)
            .on(CM_CI_RELATION_ATTRIBUTES.ATTRIBUTE_ID.eq(MD_RELATION_ATTRIBUTES.ATTRIBUTE_ID))
            .where(CM_CI_RELATION_ATTRIBUTES.CI_RELATION_ID.eq(relationID)).fetch();
    Cloud cloud = new Cloud();
    cloud.setId(cloudName);
    for (Record cloudsPlatformRelationshipAttributesRecord : cloudsPlatformRelationshipAttributesRecords) {

        String attributeValue = cloudsPlatformRelationshipAttributesRecord
              .get(CM_CI_ATTRIBUTES.DF_ATTRIBUTE_VALUE);

      switch (cloudsPlatformRelationshipAttributesRecord
          .get(MD_RELATION_ATTRIBUTES.ATTRIBUTE_NAME)) {
        case "priority":
            if (NumberUtils.isNumber(attributeValue)) {
                int priority = Integer.valueOf(attributeValue.trim());
                cloud.setPriority(priority);
            } else {
                log.warn("can not set priority attribute for cloudCid: " + cloudCid
                        + " , cloudName: " + cloudName + " attributeValue: " + attributeValue);
            }

          break;
        case "adminstatus":
          cloud.setAdminstatus(attributeValue);
          break;
        case "dpmt_order":
          if (NumberUtils.isNumber(attributeValue)) {
              cloud.setDeploymentorder(Integer.valueOf(attributeValue.trim()));
          } else {
              log.warn("can not set dpmt order attribute for cloudCid: " + cloudCid
                      + " , cloudName: " + cloudName + " attributeValue: " + attributeValue);
          }
          break;
        case "pct_scale":
            if (NumberUtils.isNumber(attributeValue)) {
                cloud.setScalepercentage(Integer.valueOf(attributeValue.trim()));
            } else {
                log.warn("can not set pct_scale attribute for cloudCid: " + cloudCid
                        + " , cloudName: " + " attributeValue: " + attributeValue);
            }
          break;
      }
    }
    platformCloudMap.put(cloudName, cloud);


  }

  return platformCloudMap;

}
 

private void writeTranscriptExonData(final String outputFile)
{
    LNX_LOGGER.info("caching transcript & exon data to {}", outputFile);

    try
    {
        BufferedWriter writer = createBufferedWriter(outputFile, false);

        writer.write("GeneId,CanonicalTranscriptId,Strand,TransId,TransName,BioType,TransStart,TransEnd");
        writer.write(",ExonRank,ExonStart,ExonEnd,ExonPhase,ExonEndPhase,CodingStart,CodingEnd");
        writer.newLine();

        Result<?> results = queryAllTranscriptExonData();

        for(final Record record : results)
        {
            UInteger canTransId = (UInteger) record.get("CanonicalTranscriptId");
            UInteger transId = (UInteger) record.get("TransId");
            Byte strand = (Byte) record.get("Strand");
            UInteger transStart = (UInteger) record.get("TransStart");
            UInteger transEnd = (UInteger) record.get("TransEnd");
            Integer exonRank = (Integer) record.get("ExonRank");
            UInteger exonStart = (UInteger) record.get("ExonStart");
            UInteger exonEnd = (UInteger) record.get("ExonEnd");
            Byte exonPhase = (Byte) record.get("ExonPhase");
            Byte exonPhaseEnd = (Byte) record.get("ExonEndPhase");
            ULong codingStart = (ULong) record.get("CodingStart");
            ULong codingEnd = (ULong) record.get("CodingEnd");

            writer.write(String.format("%s,%d,%d,%d,%s,%s,%d,%d",
                    record.get("GeneId"), canTransId.intValue(), strand, transId.intValue(),
                    record.get("Trans"), record.get("BioType"), transStart.intValue(), transEnd.intValue()));

            writer.write(String.format(",%d,%d,%d,%d,%d,%s,%s",
                    exonRank.intValue(), exonStart.intValue(), exonEnd.intValue(), exonPhase, exonPhaseEnd,
                    codingStart != null ? codingStart.intValue() : "NULL",
                    codingEnd != null ? codingEnd.intValue() : "NULL"));

            writer.newLine();
        }

        writer.close();
    }
    catch (final IOException e)
    {
        LNX_LOGGER.error("error writing Ensembl trans-exon data file: {}", e.toString());
    }
}
 

/**
 * Get the given Field from the record, or null if the record does not have
 * the Field.
 *
 * @param <T> The type of the requested Field.
 * @param record The record to fetch the field from.
 * @param field The field to fetch from the record.
 * @return The value of the field, or null if the record does not have the
 * Field.
 */
public static <T> T getFieldOrNull(Record record, Field<T> field) {
    if (record.field(field) != null) {
        return record.get(field);
    }
    return null;
}