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

Interface GeoBrowser

All Known Implementing Classes:

GeoBrowserImpl

public interface GeoBrowser

Gets records from GEO and compares them to Gemma. This is used to identify data sets that are new in GEO and not in Gemma.

See Programmatic access to GEO for some information.

Author:

pavlidis, poirigui

Method Summary

Modifier and Type	Method	Description
Collection<GeoRecord>	getAllGeoRecords(GeoRecordType recordType, Collection<String> allowedTaxa, int maxRecords)	Retrieve all GEO records of a given type.
default GeoRecord	getGeoRecord(GeoRecordType recordType, String accession)	Retrieve a single GEO series using the default preset.
GeoRecord	getGeoRecord(GeoRecordType recordType, String accession, GeoRetrieveConfig config)	Retrieve a single GEO record.
default Collection<GeoRecord>	getGeoRecords(GeoRecordType recordType, Collection<String> accessions)
Collection<GeoRecord>	getGeoRecords(GeoRecordType recordType, Collection<String> accessions, GeoRetrieveConfig config)	Retrieve a collection of GEO series.
Slice<GeoRecord>	getRecentGeoRecords(GeoRecordType recordType, int start, int pageSize)	Retrieve recent GEO records from GEO browser.
Collection<GeoRecord>	retrieveAllGeoRecords(GeoQuery query, GeoRetrieveConfig config)
default Slice<GeoRecord>	retrieveGeoRecords(GeoQuery query, int start, int pageSize)
Slice<GeoRecord>	retrieveGeoRecords(GeoQuery query, int start, int pageSize, GeoRetrieveConfig config)	Retrieve records from a GEO query.
default Slice<GeoRecord>	searchAndRetrieveGeoRecords(GeoRecordType recordType, String searchTerms, GeoSearchField field, Collection<String> allowedTaxa, Collection<String> limitPlatforms, Collection<String> seriesTypes, int start, int pageSize, boolean detailed)	Search and retrieve GEO records.
GeoQuery	searchGeoRecords(GeoRecordType recordType, String term)	Search GEO records.
GeoQuery	searchGeoRecords(GeoRecordType recordType, String searchTerms, GeoSearchField field, Collection<String> allowedTaxa, Collection<String> limitPlatforms, Collection<String> seriesTypes)	Search GEO records.

Method Detail

getGeoRecord

@Nullable
default GeoRecord getGeoRecord(GeoRecordType recordType,
                               String accession)
                        throws IOException

Retrieve a single GEO series using the default preset.

Throws:

IOException

getGeoRecord

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

Retrieve a single GEO record.

Throws:

IOException

getGeoRecords

default Collection<GeoRecord> getGeoRecords(GeoRecordType recordType,
                                            Collection<String> accessions)
                                     throws IOException

Throws:

IOException

getGeoRecords

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

Retrieve a collection of GEO series.

Throws:

IOException

getAllGeoRecords

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

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)

Parameters:

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

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

Retrieve recent GEO records from GEO browser.

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

Parameters:

start - start page

pageSize - page size

Returns:

a slice of GEO records

Throws:

IOException

searchAndRetrieveGeoRecords

default Slice<GeoRecord> searchAndRetrieveGeoRecords(GeoRecordType recordType,
                                                     @Nullable
                                                     String searchTerms,
                                                     @Nullable
                                                     GeoSearchField field,
                                                     @Nullable
                                                     Collection<String> allowedTaxa,
                                                     @Nullable
                                                     Collection<String> limitPlatforms,
                                                     @Nullable
                                                     Collection<String> seriesTypes,
                                                     int start,
                                                     int pageSize,
                                                     boolean detailed)
                                              throws IOException

Search and retrieve GEO records.

Throws:

IOException

See Also:

searchGeoRecords(GeoRecordType, String, GeoSearchField, Collection, Collection, Collection), retrieveGeoRecords(GeoQuery, int, int, GeoRetrieveConfig)

searchGeoRecords

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

Search GEO records.

Provides more details than 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.

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 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

GeoQuery searchGeoRecords(GeoRecordType recordType,
                          String term)
                   throws IOException

Search GEO records.

Throws:

IOException

retrieveGeoRecords

default Slice<GeoRecord> retrieveGeoRecords(GeoQuery query,
                                            int start,
                                            int pageSize)
                                     throws IOException

Throws:

IOException

retrieveGeoRecords

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

Retrieve records from a GEO query.

Parameters:

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

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

Throws:

IOException