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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -8,6 +8,7 @@ | |
| * @author Jacobo Coll <[email protected]> | ||
| */ | ||
| public class CohortMetadata extends StudyResourceMetadata<CohortMetadata> { | ||
| public static final String INVALID_STATS_NUM_SAMPLES = "invalidStatsNumSamples"; | ||
|
|
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| // private int studyId; | ||
| // private int id; | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -23,12 +23,12 @@ | |
| import org.opencb.commons.datastore.core.DataResult; | ||
| import org.opencb.commons.datastore.core.Query; | ||
| import org.opencb.commons.datastore.core.QueryOptions; | ||
| import org.opencb.opencga.core.response.VariantQueryResult; | ||
| import org.opencb.opencga.storage.core.metadata.VariantStorageMetadataManager; | ||
| import org.opencb.opencga.storage.core.metadata.models.StudyMetadata; | ||
| import org.opencb.opencga.storage.core.variant.adaptors.iterators.VariantDBIterator; | ||
| import org.opencb.opencga.storage.core.variant.query.ParsedVariantQuery; | ||
| import org.opencb.opencga.storage.core.variant.query.VariantQueryParser; | ||
| import org.opencb.opencga.storage.core.variant.query.VariantQueryResult; | ||
| import org.opencb.opencga.storage.core.variant.query.projection.VariantQueryProjectionParser; | ||
| import org.opencb.opencga.storage.core.variant.stats.VariantStatsWrapper; | ||
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@@ -37,30 +37,13 @@ | |
| import java.util.List; | ||
| import java.util.Map; | ||
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| import static org.opencb.opencga.storage.core.variant.query.VariantQueryUtils.addSamplesMetadataIfRequested; | ||
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| /** | ||
| * @author Ignacio Medina <[email protected]> | ||
| * @author Jacobo Coll <[email protected]> | ||
| * @author Cristina Yenyxe Gonzalez Garcia <[email protected]> | ||
| */ | ||
| public interface VariantDBAdaptor extends VariantIterable, AutoCloseable { | ||
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|
||
| /** | ||
| * This method inserts Variants into the given Study. If the Study already exists then it just adds the new Sample | ||
| * genotypes, also new variants are inserted. If it is a new Study then Sample genotypes are added to the new Study. | ||
| * | ||
| * @param variants List of variants in OpenCB data model to be inserted | ||
| * @param studyName Name or alias of the study | ||
| * @param options Query modifiers, accepted values are: include, exclude, limit, skip, sort and count | ||
| * @return A DataResult with the number of inserted variants | ||
| */ | ||
| @Deprecated | ||
| default DataResult insert(List<Variant> variants, String studyName, QueryOptions options) { | ||
| throw new UnsupportedOperationException(); | ||
| } | ||
|
|
||
| /** | ||
| /** | ||
| * Fetch all variants resulting of executing the query in the database. Returned fields are taken from | ||
| * the 'include' and 'exclude' fields at options. | ||
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@@ -71,26 +54,29 @@ default DataResult insert(List<Variant> variants, String studyName, QueryOptions | |
| * @return A DataResult with the result of the query | ||
| */ | ||
| default VariantQueryResult<Variant> get(Iterator<?> variants, Query query, QueryOptions options) { | ||
| DataResult<Variant> queryResult = iterator(variants, query, options).toDataResult(); | ||
| return addSamplesMetadataIfRequested(queryResult, query, options, getMetadataManager()); | ||
| ParsedVariantQuery variantQuery = new VariantQueryParser(null, getMetadataManager()).parseQuery(query, options, true); | ||
| try (VariantDBIterator iterator = iterator(variants, query, options)) { | ||
| return iterator.toDataResult(variantQuery); | ||
| } catch (Exception e) { | ||
| throw VariantQueryException.internalException(e); | ||
| } | ||
| } | ||
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| @Deprecated | ||
| default VariantDBIterator iterator(Query query, QueryOptions options) { | ||
| return iterator(new VariantQueryParser(null, getMetadataManager()).parseQuery(query, options, true), options); | ||
| return iterator(new VariantQueryParser(null, getMetadataManager()).parseQuery(query, options, true)); | ||
| } | ||
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| VariantDBIterator iterator(ParsedVariantQuery query, QueryOptions options); | ||
| VariantDBIterator iterator(ParsedVariantQuery query); | ||
|
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| /** | ||
| * Fetch all variants resulting of executing the query in the database. Returned fields are taken from | ||
| * the 'include' and 'exclude' fields at options. | ||
| * | ||
| * @param query Query to be executed in the database to filter variants | ||
| * @param options Query modifiers, accepted values are: include, exclude, limit, skip, sort and count | ||
| * @return A DataResult with the result of the query | ||
| */ | ||
| VariantQueryResult<Variant> get(ParsedVariantQuery query, QueryOptions options); | ||
| VariantQueryResult<Variant> get(ParsedVariantQuery query); | ||
|
|
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| /** | ||
| * Fetch all variants resulting of executing the query in the database. Returned fields are taken from | ||
|
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@@ -102,7 +88,7 @@ default VariantDBIterator iterator(Query query, QueryOptions options) { | |
| */ | ||
| @Deprecated | ||
| default VariantQueryResult<Variant> get(Query query, QueryOptions options) { | ||
| return get(new VariantQueryParser(null, getMetadataManager()).parseQuery(query, options, true), options); | ||
| return get(new VariantQueryParser(null, getMetadataManager()).parseQuery(query, options, true)); | ||
| } | ||
|
|
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| /** | ||
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18 changes: 17 additions & 1 deletion
18
...va/org/opencb/opencga/storage/core/variant/adaptors/iterators/LimitVariantDBIterator.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,16 +1,32 @@ | ||
| package org.opencb.opencga.storage.core.variant.adaptors.iterators; | ||
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| import org.opencb.biodata.models.variant.Variant; | ||
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| import java.util.NoSuchElementException; | ||
|
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| public class LimitVariantDBIterator extends DelegatedVariantDBIterator { | ||
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| private final int limit; | ||
| private int count; | ||
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| LimitVariantDBIterator(VariantDBIterator delegated, int limit) { | ||
| super(delegated); | ||
| this.limit = limit; | ||
| this.count = 0; | ||
| } | ||
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| @Override | ||
| public boolean hasNext() { | ||
| return getCount() < limit && super.hasNext(); | ||
| return count < limit && super.hasNext(); | ||
| } | ||
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| @Override | ||
| public Variant next() { | ||
| if (!this.hasNext()) { | ||
| throw new NoSuchElementException(); | ||
| } else { | ||
| ++this.count; | ||
| return super.next(); | ||
| } | ||
| } | ||
| } |
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