Package ubic.gemma.core.loader.expression.cellxgene

Class CellXGeneDataLoaderServiceImpl

java.lang.Object

ubic.gemma.core.loader.expression.cellxgene.CellXGeneDataLoaderServiceImpl

All Implemented Interfaces:

CellXGeneDataLoaderService

@Service
@Transactional(propagation=NEVER)
public class CellXGeneDataLoaderServiceImpl
extends Object
implements CellXGeneDataLoaderService

Author:

poirigui

Constructor Summary

Constructors

Constructor

Description

CellXGeneDataLoaderServiceImpl(Persister persister, ArrayDesignService arrayDesignService, ExpressionExperimentService expressionExperimentService, SingleCellExpressionExperimentService singleCellExpressionExperimentService, ExternalDatabaseService externalDatabaseService, TaxonService taxonService, SingleCellDataTransformationFactory singleCellDataTransformationFactory, org.springframework.transaction.PlatformTransactionManager transactionManager, Path cellXGeneDownloadPath, Path cellXGeneTransposedPath, String ncbiApiKey)

Method Summary

Modifier and Type	Method	Description
ExpressionExperiment	fetchAndLoad(String collectionId, String datasetId, String assetId, ArrayDesign platform, String datasetShortName, boolean loadSingleCellData, boolean keepPooledSample, boolean keepUnknownSample, boolean dryRun)	Fetch a CELLxGENE dataset and load it into the database.
void	setProgressReporterFactory(ProgressReporterFactory progressReporterFactory)	Set the progress reporter factory to use for reporting progress during data downloading.

Methods inherited from class java.lang.Object

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

Constructor Details

CellXGeneDataLoaderServiceImpl

@Autowired
public CellXGeneDataLoaderServiceImpl(Persister persister,
 ArrayDesignService arrayDesignService,
 ExpressionExperimentService expressionExperimentService,
 SingleCellExpressionExperimentService singleCellExpressionExperimentService,
 ExternalDatabaseService externalDatabaseService,
 TaxonService taxonService,
 SingleCellDataTransformationFactory singleCellDataTransformationFactory,
 org.springframework.transaction.PlatformTransactionManager transactionManager,
 @Value("${cellxgene.local.singleCellData.basepath}")
 Path cellXGeneDownloadPath,
 @Value("${gemma.download.path}/singleCellData/CELLxGENE_Transposed")
 Path cellXGeneTransposedPath,
 @Value("${entrez.efetch.apikey}")
 String ncbiApiKey)

Method Details

fetchAndLoad

public ExpressionExperiment fetchAndLoad(String collectionId,
 @Nullable
 String datasetId,
 @Nullable
 String assetId,
 ArrayDesign platform,
 String datasetShortName,
 boolean loadSingleCellData,
 boolean keepPooledSample,
 boolean keepUnknownSample,
 boolean dryRun)
                                  throws IOException

Description copied from interface: CellXGeneDataLoaderService

Fetch a CELLxGENE dataset and load it into the database.

Specified by:

fetchAndLoad in interface CellXGeneDataLoaderService

Parameters:

datasetId - CELLxGENE dataset identifier

assetId - CELLxGENE dataset asset identifier

platform - platform to use for mapping design elements from the data, the primary taxon must correspond to that of the dataset.

datasetShortName - short name to use for the resulting dataset

loadSingleCellData - whether to load the single-cell data vectors, this can be done later if needed

keepPooledSample - whether to keep the "pooled" sample

keepUnknownSample - whether to keep the "unknown" sample

Returns:

a persistent ExpressionExperiment pre-populated with CELLxGENE metadata and single-cell data (if requested)

Throws:

IOException

setProgressReporterFactory

public void setProgressReporterFactory(ProgressReporterFactory progressReporterFactory)

Description copied from interface: CellXGeneDataLoaderService

Set the progress reporter factory to use for reporting progress during data downloading.

Specified by:

setProgressReporterFactory in interface CellXGeneDataLoaderService