Examples with InsertValuesStepN org.jooq.InsertValuesStepN used on opensource projects

Example 1 with InsertValuesStepN

use of org.jooq.InsertValuesStepN in project hmftools by hartwigmedical.

the class CopyNumberDAO method writeCopyNumberRegions.

void writeCopyNumberRegions(@NotNull final String sample, @NotNull List<FittedRegion> regions) {
    Timestamp timestamp = new Timestamp(new Date().getTime());
    context.delete(COPYNUMBERREGION).where(COPYNUMBERREGION.SAMPLEID.eq(sample)).execute();
    for (List<FittedRegion> splitRegions : Iterables.partition(regions, DB_BATCH_INSERT_SIZE)) {
        InsertValuesStepN inserter = context.insertInto(COPYNUMBERREGION, COPYNUMBERREGION.SAMPLEID, COPYNUMBERREGION.CHROMOSOME, COPYNUMBERREGION.START, COPYNUMBERREGION.END, COPYNUMBERREGION.GERMLINESTATUS, COPYNUMBERREGION.SVCLUSTER, COPYNUMBERREGION.RATIOSUPPORT, COPYNUMBERREGION.SEGMENTSTARTSUPPORT, COPYNUMBERREGION.BAFCOUNT, COPYNUMBERREGION.OBSERVEDBAF, COPYNUMBERREGION.OBSERVEDTUMORRATIO, COPYNUMBERREGION.OBSERVEDNORMALRATIO, COPYNUMBERREGION.OBSERVEDTUMORRATIOCOUNT, COPYNUMBERREGION.GCCONTENT, COPYNUMBERREGION.MODELPLOIDY, COPYNUMBERREGION.MODELBAF, COPYNUMBERREGION.MODELTUMORRATIO, COPYNUMBERREGION.ACTUALTUMORBAF, COPYNUMBERREGION.ACTUALTUMORCOPYNUMBER, COPYNUMBERREGION.REFNORMALISEDTUMORCOPYNUMBER, COPYNUMBERREGION.CNVDEVIATION, COPYNUMBERREGION.BAFDEVIATION, COPYNUMBERREGION.TOTALDEVIATION, COPYNUMBERREGION.PLOIDYPENALTY, COPYNUMBERREGION.FITTEDBAF, COPYNUMBERREGION.FITTEDCOPYNUMBER, COPYNUMBERREGION.MODIFIED);
        splitRegions.forEach(x -> addCopynumberRecord(timestamp, inserter, sample, x));
        inserter.execute();
    }
}

Example 2 with InsertValuesStepN

use of org.jooq.InsertValuesStepN in project hmftools by hartwigmedical.

the class SomaticVariantDAO method write.

void write(@NotNull final String sample, @NotNull List<EnrichedSomaticVariant> variants) {
    Timestamp timestamp = new Timestamp(new Date().getTime());
    context.delete(SOMATICVARIANT).where(SOMATICVARIANT.SAMPLEID.eq(sample)).execute();
    for (List<EnrichedSomaticVariant> splitRegions : Iterables.partition(variants, DB_BATCH_INSERT_SIZE)) {
        InsertValuesStepN inserter = context.insertInto(SOMATICVARIANT, SOMATICVARIANT.SAMPLEID, SOMATICVARIANT.CHROMOSOME, SOMATICVARIANT.POSITION, SOMATICVARIANT.FILTER, SOMATICVARIANT.TYPE, SOMATICVARIANT.REF, SOMATICVARIANT.ALT, SOMATICVARIANT.GENE, SOMATICVARIANT.GENESEFFECTED, SOMATICVARIANT.COSMICID, SOMATICVARIANT.DBSNPID, SOMATICVARIANT.WORSTEFFECT, SOMATICVARIANT.WORSTCODINGEFFECT, SOMATICVARIANT.WORSTEFFECTTRANSCRIPT, SOMATICVARIANT.CANONICALEFFECT, SOMATICVARIANT.CANONICALCODINGEFFECT, SOMATICVARIANT.ALLELEREADCOUNT, SOMATICVARIANT.TOTALREADCOUNT, SOMATICVARIANT.ADJUSTEDCOPYNUMBER, SOMATICVARIANT.ADJUSTEDVAF, SOMATICVARIANT.HIGHCONFIDENCE, SOMATICVARIANT.TRINUCLEOTIDECONTEXT, SOMATICVARIANT.MICROHOMOLOGY, SOMATICVARIANT.REPEATSEQUENCE, SOMATICVARIANT.REPEATCOUNT, SOMATICVARIANT.CLONALITY, SOMATICVARIANT.BIALLELIC, SOMATICVARIANT.HOTSPOT, SOMATICVARIANT.MAPPABILITY, SOMATICVARIANT.GERMLINESTATUS, SOMATICVARIANT.MINORALLELEPLOIDY, SOMATICVARIANT.MODIFIED);
        splitRegions.forEach(x -> addRecord(timestamp, inserter, sample, x));
        inserter.execute();
    }
}

Example 3 with InsertValuesStepN

use of org.jooq.InsertValuesStepN in project hmftools by hartwigmedical.

the class GeneCopyNumberDAO method writeCopyNumber.

void writeCopyNumber(@NotNull final String sample, @NotNull List<GeneCopyNumber> copyNumbers) {
    Timestamp timestamp = new Timestamp(new Date().getTime());
    context.delete(GENECOPYNUMBER).where(GENECOPYNUMBER.SAMPLEID.eq(sample)).execute();
    for (List<GeneCopyNumber> splitCopyNumbers : Iterables.partition(copyNumbers, DB_BATCH_INSERT_SIZE)) {
        InsertValuesStepN inserter = context.insertInto(GENECOPYNUMBER, GENECOPYNUMBER.SAMPLEID, GENECOPYNUMBER.CHROMOSOME, GENECOPYNUMBER.START, GENECOPYNUMBER.END, GENECOPYNUMBER.GENE, GENECOPYNUMBER.MINCOPYNUMBER, GENECOPYNUMBER.MAXCOPYNUMBER, GENECOPYNUMBER.SOMATICREGIONS, GENECOPYNUMBER.GERMLINEHOMREGIONS, GENECOPYNUMBER.GERMLINEHETREGIONS, GENECOPYNUMBER.TRANSCRIPTID, GENECOPYNUMBER.TRANSCRIPTVERSION, GENECOPYNUMBER.CHROMOSOMEBAND, GENECOPYNUMBER.MINREGIONS, GENECOPYNUMBER.MINREGIONSTART, GENECOPYNUMBER.MINREGIONEND, GENECOPYNUMBER.MINREGIONSTARTSUPPORT, GENECOPYNUMBER.MINREGIONENDSUPPORT, GENECOPYNUMBER.MINREGIONMETHOD, GENECOPYNUMBER.NONSENSEBIALLELICVARIANTS, GENECOPYNUMBER.NONSENSENONBIALLELICVARIANTS, GENECOPYNUMBER.NONSENSENONBIALLELICPLOIDY, GENECOPYNUMBER.SPLICEBIALLELICVARIANTS, GENECOPYNUMBER.SPLICENONBIALLELICVARIANTS, GENECOPYNUMBER.SPLICENONBIALLELICPLOIDY, GENECOPYNUMBER.MISSENSEBIALLELICVARIANTS, GENECOPYNUMBER.MISSENSENONBIALLELICVARIANTS, GENECOPYNUMBER.MISSENSENONBIALLELICPLOIDY, GENECOPYNUMBER.MINMINORALLELEPLOIDY, COPYNUMBER.MODIFIED);
        splitCopyNumbers.forEach(x -> addCopynumberRecord(timestamp, inserter, sample, x));
        inserter.execute();
    }
}

Example 4 with InsertValuesStepN

use of org.jooq.InsertValuesStepN in project jOOQ by jOOQ.

the class DefaultParseContext method parseInsert.

private final Query parseInsert(WithImpl with, boolean parseResultQuery) {
    scopeStart();
    parseKeyword("INSERT", "INS");
    parseKeywordIf("INTO");
    Table<?> table = parseTableNameIf();
    if (table == null)
        table = table(parseSelect());
    Name alias;
    if (parseKeywordIf("AS"))
        table = table.as(parseIdentifier());
    else if (!peekKeyword("DEFAULT VALUES", "SEL", "SELECT", "SET", "VALUES") && (alias = parseIdentifierIf()) != null)
        table = table.as(alias);
    scope(table);
    InsertSetStep<?> s1 = (with == null ? dsl.insertInto(table) : with.insertInto(table));
    Field<?>[] fields = null;
    if (!peekSelectOrWith(true) && parseIf('(') && !parseIf(')')) {
        fields = parseList(',', c -> parseField()).toArray(EMPTY_FIELD);
        parse(')');
    }
    InsertOnDuplicateStep<?> onDuplicate;
    InsertReturningStep<?> returning;
    try {
        // [#11821] The Teradata INSERT INTO t (1, 2) syntax can be recognised:
        // When there are non-references fields
        boolean hasExpressions = anyMatch(fields, f -> !(f instanceof TableField));
        if (hasExpressions || parseKeywordIf("VALUES")) {
            List<List<Field<?>>> allValues = new ArrayList<>();
            if (hasExpressions) {
                allValues.add(asList(fields));
                fields = null;
            }
            valuesLoop: do {
                if (hasExpressions && !parseIf(','))
                    break valuesLoop;
                parse('(');
                // [#6936] MySQL treats an empty VALUES() clause as the same thing as the standard DEFAULT VALUES
                if (fields == null && parseIf(')'))
                    break valuesLoop;
                List<Field<?>> values = parseList(',', c -> c.parseKeywordIf("DEFAULT") ? default_() : c.parseField());
                if (fields != null && fields.length != values.size())
                    throw exception("Insert field size (" + fields.length + ") must match values size (" + values.size() + ")");
                allValues.add(values);
                parse(')');
            } while (parseIf(','));
            InsertValuesStepN<?> step2 = (fields != null) ? s1.columns(fields) : (InsertValuesStepN<?>) s1;
            for (List<Field<?>> values : allValues) step2 = step2.values(values);
            returning = onDuplicate = step2;
        } else if (parseKeywordIf("SET")) {
            Map<Field<?>, Object> map = parseSetClauseList();
            returning = onDuplicate = s1.set(map);
        } else if (peekSelectOrWith(true)) {
            // [#10954] These are moved into the INSERT .. SELECT clause handling. They should not be necessary here
            // either, but it seems we currently don't correctly implement nesting scopes?
            scopeEnd(null);
            scopeStart();
            Select<?> select = parseWithOrSelect();
            returning = onDuplicate = (fields == null) ? s1.select(select) : s1.columns(fields).select(select);
        } else if (parseKeywordIf("DEFAULT VALUES")) {
            if (fields != null)
                throw notImplemented("DEFAULT VALUES without INSERT field list");
            else
                returning = onDuplicate = s1.defaultValues();
        } else
            throw expected("DEFAULT VALUES", "WITH", "SELECT", "SET", "VALUES");
        if (parseKeywordIf("ON")) {
            if (parseKeywordIf("DUPLICATE KEY UPDATE")) {
                parseKeywordIf("SET");
                InsertOnConflictWhereStep<?> where = onDuplicate.onDuplicateKeyUpdate().set(parseSetClauseList());
                if (parseKeywordIf("WHERE"))
                    returning = where.where(parseCondition());
                else
                    returning = where;
            } else if (parseKeywordIf("DUPLICATE KEY IGNORE")) {
                returning = onDuplicate.onDuplicateKeyIgnore();
            } else if (parseKeywordIf("CONFLICT")) {
                InsertOnConflictDoUpdateStep<?> doUpdate;
                if (parseKeywordIf("ON CONSTRAINT")) {
                    doUpdate = onDuplicate.onConflictOnConstraint(parseName());
                } else if (parseIf('(')) {
                    InsertOnConflictWhereIndexPredicateStep<?> where = onDuplicate.onConflict(parseList(',', c -> parseFieldName()));
                    parse(')');
                    doUpdate = parseKeywordIf("WHERE") ? where.where(parseCondition()) : where;
                } else {
                    doUpdate = onDuplicate.onConflict();
                }
                parseKeyword("DO");
                if (parseKeywordIf("NOTHING")) {
                    returning = doUpdate.doNothing();
                } else if (parseKeywordIf("UPDATE SET")) {
                    InsertOnConflictWhereStep<?> where = doUpdate.doUpdate().set(parseSetClauseList());
                    if (parseKeywordIf("WHERE"))
                        returning = where.where(parseCondition());
                    else
                        returning = where;
                } else
                    throw expected("NOTHING", "UPDATE");
            } else
                throw expected("CONFLICT", "DUPLICATE");
        }
        return (parseResultQuery ? parseKeyword("RETURNING") : parseKeywordIf("RETURNING")) ? returning.returning(parseSelectList()) : returning;
    } finally {
        scopeEnd(((InsertImpl) s1).getDelegate());
    }
}