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

Class GeoBrowser

java.lang.Object

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

public class GeoBrowser
extends Object

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

Constructor Summary

Constructors

Constructor	Description
GeoBrowser()

Method Summary

Modifier and Type	Method	Description
Collection<GeoRecord>	getAllGEOPlatforms()	A bit hacky, can be improved.
Collection<GeoRecord>	getGeoRecords(Collection<String> accessions)	Retrieve records for experiments
List<GeoRecord>	getGeoRecordsBySearchTerm(String searchTerms, int start, int pageSize, boolean detailed, Collection<String> allowedTaxa, Collection<String> limitPlatforms)	Provides more details than getRecentGeoRecords.
List<GeoRecord>	getRecentGeoRecords(int startPage, int pageSize)	Retrieves and parses tab delimited file from GEO.

Methods inherited from class java.lang.Object

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

Constructor Detail

GeoBrowser

public GeoBrowser()

Method Detail

getGeoRecords

public Collection<GeoRecord> getGeoRecords(Collection<String> accessions)
                                    throws IOException

Retrieve records for experiments

Parameters:

accessions - of experiments

Returns:

collection of records

Throws:

IOException

getAllGEOPlatforms

public Collection<GeoRecord> getAllGEOPlatforms()
                                         throws IOException

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)

Returns:

all relevant platforms up to single-query limit of NCBI

Throws:

IOException

getGeoRecordsBySearchTerm

public List<GeoRecord> getGeoRecordsBySearchTerm(String searchTerms,
                                                 int start,
                                                 int pageSize,
                                                 boolean detailed,
                                                 Collection<String> allowedTaxa,
                                                 Collection<String> limitPlatforms)
                                          throws IOException

Provides more details than getRecentGeoRecords. Performs an E-utilities query of the GEO database with the given searchTerms (search terms can be omitted). Returns at most pageSize records. Does some screening of results for expression studies, and (optionally) taxa. This is used for identifying data sets for loading.

Parameters:

start - start an offset to retrieve batches

pageSize - page size how many to retrive

searchTerms - search terms in NCBI Entrez query format

detailed - if true, additional information is fetched (slower)

allowedTaxa - if not null, data sets not containing any of these taxa will be skipped

limitPlatforms - not null or empty, platforms to limit the query to (combining with searchTerms not supported yet)

Returns:

list of GeoRecords

Throws:

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

getRecentGeoRecords

public List<GeoRecord> getRecentGeoRecords(int startPage,
                                           int pageSize)
                                    throws IOException

Retrieves and parses tab delimited file from GEO. File contains pageSize GEO records starting from startPage. The retrieved information is pretty minimal.

Parameters:

startPage - start page

pageSize - page size

Returns:

list of GeoRecords

Throws:

IOException - if there is a problem while manipulating the file