public class MongoDBAdaptor extends Object
Modifier and Type | Field and Description |
---|---|
protected String |
assembly |
protected org.slf4j.Logger |
logger |
protected org.opencb.commons.datastore.mongodb.MongoDataStore |
mongoDataStore |
protected org.opencb.commons.datastore.mongodb.MongoDBCollection |
mongoDBCollection |
protected com.fasterxml.jackson.databind.ObjectMapper |
objectMapper |
protected String |
species |
Constructor and Description |
---|
MongoDBAdaptor(org.opencb.commons.datastore.mongodb.MongoDataStore mongoDataStore) |
MongoDBAdaptor(String species,
String assembly,
org.opencb.commons.datastore.mongodb.MongoDataStore mongoDataStore) |
Modifier and Type | Method and Description |
---|---|
protected org.opencb.commons.datastore.core.QueryOptions |
addExcludeReturnFields(String returnField,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
protected org.opencb.commons.datastore.core.QueryOptions |
addIncludeReturnFields(String returnField,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
protected org.opencb.commons.datastore.core.QueryOptions |
addPrivateExcludeOptions(org.opencb.commons.datastore.core.QueryOptions options) |
protected org.opencb.commons.datastore.core.QueryOptions |
addPrivateExcludeOptions(org.opencb.commons.datastore.core.QueryOptions options,
String csvFields) |
protected <T> void |
createOrQuery(List<T> queryValues,
String mongoDbField,
List<org.bson.conversions.Bson> andBsonList) |
protected void |
createOrQuery(org.opencb.commons.datastore.core.Query query,
String queryParam,
String mongoDbField,
List<org.bson.conversions.Bson> andBsonList) |
protected void |
createOrQuery(org.opencb.commons.datastore.core.Query query,
String queryParam,
String mongoDbField,
List<org.bson.conversions.Bson> andBsonList,
org.opencb.cellbase.lib.impl.MongoDBAdaptor.QueryValueType queryValueType) |
protected void |
createRegionQuery(org.opencb.commons.datastore.core.Query query,
String queryParam,
int chunkSize,
List<org.bson.conversions.Bson> andBsonList) |
protected void |
createRegionQuery(org.opencb.commons.datastore.core.Query query,
String queryParam,
List<org.bson.conversions.Bson> andBsonList) |
protected CellBaseDataResult |
executeAggregation2(Object id,
List<org.bson.conversions.Bson> pipeline,
org.opencb.commons.datastore.core.QueryOptions options) |
protected List<CellBaseDataResult> |
executeAggregationist2(List<? extends Object> ids,
List<List<org.bson.conversions.Bson>> pipelines,
org.opencb.commons.datastore.core.QueryOptions options,
org.opencb.commons.datastore.mongodb.MongoDBCollection mongoDBCollection2) |
protected List<CellBaseDataResult> |
executeAggregationList2(List<? extends Object> ids,
List<List<org.bson.conversions.Bson>> queries,
org.opencb.commons.datastore.core.QueryOptions options) |
protected CellBaseDataResult |
executeDistinct(Object id,
String fields,
org.bson.Document query) |
protected CellBaseDataResult |
executeQuery(Object id,
org.bson.Document query,
org.opencb.commons.datastore.core.QueryOptions options) |
protected CellBaseDataResult |
executeQuery(Object id,
org.bson.Document query,
org.opencb.commons.datastore.core.QueryOptions options,
org.opencb.commons.datastore.mongodb.MongoDBCollection mongoDBCollection2) |
protected List<CellBaseDataResult> |
executeQueryList2(List<? extends Object> ids,
List<org.bson.Document> queries,
org.opencb.commons.datastore.core.QueryOptions options) |
protected List<CellBaseDataResult> |
executeQueryList2(List<? extends Object> ids,
List<org.bson.Document> queries,
org.opencb.commons.datastore.core.QueryOptions options,
org.opencb.commons.datastore.mongodb.MongoDBCollection mongoDBCollection2) |
String |
getAssembly() |
protected int |
getChunkId(int position,
int chunkSize) |
protected String |
getChunkIdPrefix(String chromosome,
int position,
int chunkSize) |
protected List<IntervalFeatureFrequency> |
getIntervalFeatureFrequencies(org.opencb.biodata.models.core.Region region,
int interval,
List<Object[]> objectList) |
protected List<IntervalFeatureFrequency> |
getIntervalFeatureFrequencies(org.opencb.biodata.models.core.Region region,
int interval,
List<Object[]> objectList,
int numFeatures,
double maxSnpsInterval) |
CellBaseDataResult |
getIntervalFrequencies(org.bson.conversions.Bson query,
org.opencb.biodata.models.core.Region region,
int intervalSize,
org.opencb.commons.datastore.core.QueryOptions options) |
protected org.bson.Document |
getReturnFields(org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
String |
getSpecies() |
protected CellBaseDataResult |
groupBy(org.bson.conversions.Bson query,
List<String> groupByField,
String featureIdField,
org.opencb.commons.datastore.core.QueryOptions options) |
protected CellBaseDataResult |
groupBy(org.bson.conversions.Bson query,
String groupByField,
String featureIdField,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
next(String chromosome,
int position,
org.opencb.commons.datastore.core.QueryOptions options,
org.opencb.commons.datastore.mongodb.MongoDBCollection mongoDBCollection) |
void |
setAssembly(String assembly) |
void |
setSpecies(String species) |
protected String species
protected String assembly
protected org.opencb.commons.datastore.mongodb.MongoDataStore mongoDataStore
protected org.opencb.commons.datastore.mongodb.MongoDBCollection mongoDBCollection
protected org.slf4j.Logger logger
protected com.fasterxml.jackson.databind.ObjectMapper objectMapper
public MongoDBAdaptor(org.opencb.commons.datastore.mongodb.MongoDataStore mongoDataStore)
protected org.opencb.commons.datastore.core.QueryOptions addPrivateExcludeOptions(org.opencb.commons.datastore.core.QueryOptions options)
protected org.opencb.commons.datastore.core.QueryOptions addPrivateExcludeOptions(org.opencb.commons.datastore.core.QueryOptions options, String csvFields)
protected void createRegionQuery(org.opencb.commons.datastore.core.Query query, String queryParam, List<org.bson.conversions.Bson> andBsonList)
protected void createRegionQuery(org.opencb.commons.datastore.core.Query query, String queryParam, int chunkSize, List<org.bson.conversions.Bson> andBsonList)
protected void createOrQuery(org.opencb.commons.datastore.core.Query query, String queryParam, String mongoDbField, List<org.bson.conversions.Bson> andBsonList)
protected void createOrQuery(org.opencb.commons.datastore.core.Query query, String queryParam, String mongoDbField, List<org.bson.conversions.Bson> andBsonList, org.opencb.cellbase.lib.impl.MongoDBAdaptor.QueryValueType queryValueType)
protected <T> void createOrQuery(List<T> queryValues, String mongoDbField, List<org.bson.conversions.Bson> andBsonList)
protected CellBaseDataResult groupBy(org.bson.conversions.Bson query, String groupByField, String featureIdField, org.opencb.commons.datastore.core.QueryOptions options)
protected CellBaseDataResult groupBy(org.bson.conversions.Bson query, List<String> groupByField, String featureIdField, org.opencb.commons.datastore.core.QueryOptions options)
public CellBaseDataResult getIntervalFrequencies(org.bson.conversions.Bson query, org.opencb.biodata.models.core.Region region, int intervalSize, org.opencb.commons.datastore.core.QueryOptions options)
protected CellBaseDataResult executeDistinct(Object id, String fields, org.bson.Document query)
protected CellBaseDataResult executeQuery(Object id, org.bson.Document query, org.opencb.commons.datastore.core.QueryOptions options)
protected CellBaseDataResult executeQuery(Object id, org.bson.Document query, org.opencb.commons.datastore.core.QueryOptions options, org.opencb.commons.datastore.mongodb.MongoDBCollection mongoDBCollection2)
protected List<CellBaseDataResult> executeQueryList2(List<? extends Object> ids, List<org.bson.Document> queries, org.opencb.commons.datastore.core.QueryOptions options)
protected List<CellBaseDataResult> executeQueryList2(List<? extends Object> ids, List<org.bson.Document> queries, org.opencb.commons.datastore.core.QueryOptions options, org.opencb.commons.datastore.mongodb.MongoDBCollection mongoDBCollection2)
protected CellBaseDataResult executeAggregation2(Object id, List<org.bson.conversions.Bson> pipeline, org.opencb.commons.datastore.core.QueryOptions options)
protected List<CellBaseDataResult> executeAggregationList2(List<? extends Object> ids, List<List<org.bson.conversions.Bson>> queries, org.opencb.commons.datastore.core.QueryOptions options)
protected List<CellBaseDataResult> executeAggregationist2(List<? extends Object> ids, List<List<org.bson.conversions.Bson>> pipelines, org.opencb.commons.datastore.core.QueryOptions options, org.opencb.commons.datastore.mongodb.MongoDBCollection mongoDBCollection2)
protected int getChunkId(int position, int chunkSize)
public CellBaseDataResult next(String chromosome, int position, org.opencb.commons.datastore.core.QueryOptions options, org.opencb.commons.datastore.mongodb.MongoDBCollection mongoDBCollection)
@Deprecated protected org.opencb.commons.datastore.core.QueryOptions addIncludeReturnFields(String returnField, org.opencb.commons.datastore.core.QueryOptions options)
@Deprecated protected org.opencb.commons.datastore.core.QueryOptions addExcludeReturnFields(String returnField, org.opencb.commons.datastore.core.QueryOptions options)
@Deprecated protected org.bson.Document getReturnFields(org.opencb.commons.datastore.core.QueryOptions options)
protected List<IntervalFeatureFrequency> getIntervalFeatureFrequencies(org.opencb.biodata.models.core.Region region, int interval, List<Object[]> objectList, int numFeatures, double maxSnpsInterval)
protected List<IntervalFeatureFrequency> getIntervalFeatureFrequencies(org.opencb.biodata.models.core.Region region, int interval, List<Object[]> objectList)
public String getSpecies()
public void setSpecies(String species)
public String getAssembly()
public void setAssembly(String assembly)
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