Package ubic.gemma.core.loader.expression.geo.service

Class GeoBrowserImpl

java.lang.Object

ubic.gemma.core.loader.expression.geo.service.GeoBrowserImpl

All Implemented Interfaces:

GeoBrowser

public class GeoBrowserImpl
extends Object
implements GeoBrowser

Constructor Summary

Constructors

Constructor	Description
GeoBrowserImpl(String ncbiApiKey)

Method Summary

Modifier and Type	Method	Description
Collection<GeoRecord>	getAllGeoRecords(GeoRecordType recordType, Collection<String> allowedTaxa, int limit)	Retrieve all GEO records of a given type.
GeoRecord	getGeoRecord(GeoRecordType recordType, String accession, GeoRetrieveConfig config)	Retrieve a single GEO record.
Collection<GeoRecord>	getGeoRecords(GeoRecordType recordType, Collection<String> accessions, GeoRetrieveConfig config)	Retrieve records for experiments
Slice<GeoRecord>	getRecentGeoRecords(GeoRecordType recordType, int start, int pageSize)	Retrieve recent GEO records from GEO browser.
Collection<GeoRecord>	retrieveAllGeoRecords(GeoQuery query, GeoRetrieveConfig config)
Slice<GeoRecord>	retrieveGeoRecords(GeoQuery query, int start, int pageSize, GeoRetrieveConfig config)	Retrieve records from a GEO query.
GeoQuery	searchGeoRecords(GeoRecordType recordType, String term)	Search GEO records.
GeoQuery	searchGeoRecords(GeoRecordType recordType, String searchTerms, GeoSearchField field, Collection<String> allowedTaxa, Collection<String> limitPlatforms, Collection<GeoSeriesType> seriesTypes)	Search GEO records.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ubic.gemma.core.loader.expression.geo.service.GeoBrowser

getGeoRecord, getGeoRecords, retrieveGeoRecords, searchAndRetrieveGeoRecords

Constructor Detail

GeoBrowserImpl

public GeoBrowserImpl(String ncbiApiKey)

Method Detail

getGeoRecord

@Nullable
public GeoRecord getGeoRecord(GeoRecordType recordType,
                              String accession,
                              GeoRetrieveConfig config)
                       throws IOException

Description copied from interface: GeoBrowser

Retrieve a single GEO record.

Specified by:

getGeoRecord in interface GeoBrowser

Throws:

IOException

getGeoRecords

public Collection<GeoRecord> getGeoRecords(GeoRecordType recordType,
                                           Collection<String> accessions,
                                           GeoRetrieveConfig config)
                                    throws IOException

Retrieve records for experiments

Specified by:

getGeoRecords in interface GeoBrowser

Parameters:

accessions - of experiments

Returns:

collection of records

Throws:

IOException

getAllGeoRecords

public Collection<GeoRecord> getAllGeoRecords(GeoRecordType recordType,
                                              @Nullable
                                              Collection<String> allowedTaxa,
                                              int limit)
                                       throws IOException

Description copied from interface: GeoBrowser

Retrieve all GEO records of a given type.

A bit hacky, can be improved. Limited to human, mouse, rat, is not guaranteed to get everything, though as of 7/2021, this is sufficient (~8000 platforms)

Specified by:

getAllGeoRecords in interface GeoBrowser

allowedTaxa - a collection of allowed taxa, ignored if null or empty

Returns:

all relevant platforms up to single-query limit of NCBI

Throws:

IOException

getRecentGeoRecords

public Slice<GeoRecord> getRecentGeoRecords(GeoRecordType recordType,
                                            int start,
                                            int pageSize)
                                     throws IOException

Description copied from interface: GeoBrowser

Retrieve recent GEO records from GEO browser.

The retrieved information is pretty minimal. Use GeoBrowser.searchGeoRecords(GeoRecordType, String, GeoSearchField, Collection, Collection, Collection) for detailed records.

Specified by:

getRecentGeoRecords in interface GeoBrowser

start - start page

pageSize - page size

Returns:

a slice of GEO records

Throws:

IOException

searchGeoRecords

public GeoQuery searchGeoRecords(GeoRecordType recordType,
                                 @Nullable
                                 String searchTerms,
                                 @Nullable
                                 GeoSearchField field,
                                 @Nullable
                                 Collection<String> allowedTaxa,
                                 @Nullable
                                 Collection<String> limitPlatforms,
                                 @Nullable
                                 Collection<GeoSeriesType> seriesTypes)
                          throws IOException

Description copied from interface: GeoBrowser

Search GEO records.

Provides more details than GeoBrowser.getRecentGeoRecords(GeoRecordType, int, int). Performs an E-utilities query of the GEO database with the given search terms (search terms can be omitted). Returns at most pageSize records.

Note that the search is reversed in time. You get the most recent records first.

Specified by:

searchGeoRecords in interface GeoBrowser

Parameters:

recordType - the type of record to search for

searchTerms - search term, ignored if null or blank

field - a field to search in or null to search everywhere

allowedTaxa - restrict search to the given taxa if not null

limitPlatforms - restrict search to the given platforms if not null

seriesTypes - restrict search to the given series types if not null (i.e. Expression profiling by array)

Returns:

a GEO query that can be retrieved with GeoBrowser.retrieveGeoRecords(GeoQuery, int, int, GeoRetrieveConfig)

Throws:

IOException - if there is a problem obtaining or manipulating the file (some exceptions are not thrown and just logged)

searchGeoRecords

public GeoQuery searchGeoRecords(GeoRecordType recordType,
                                 String term)
                          throws IOException

Description copied from interface: GeoBrowser

Search GEO records.

Specified by:

searchGeoRecords in interface GeoBrowser

Throws:

IOException

retrieveGeoRecords

public Slice<GeoRecord> retrieveGeoRecords(GeoQuery query,
                                           int start,
                                           int pageSize,
                                           GeoRetrieveConfig config)
                                    throws IOException

Description copied from interface: GeoBrowser

Retrieve records from a GEO query.

Specified by:

retrieveGeoRecords in interface GeoBrowser

start - start at an offset to retrieve batches

pageSize - number of results to retrieve in a batch

config - configuration for populating the records

Throws:

IOException

retrieveAllGeoRecords

public Collection<GeoRecord> retrieveAllGeoRecords(GeoQuery query,
                                                   GeoRetrieveConfig config)
                                            throws IOException

Specified by:

retrieveAllGeoRecords in interface GeoBrowser

Throws:

IOException