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

Interface CellXGeneDataLoaderService

All Known Implementing Classes:

CellXGeneDataLoaderServiceImpl

public interface CellXGeneDataLoaderService

High-level service for fetching and loading CELLxGENE datasets.

Author:

poirigui

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.

Method Details

fetchAndLoad

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

Fetch a CELLxGENE dataset and load it into the database.

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:

IllegalArgumentException - if a dataset with the given short name already exists in the database, or if the platform taxon does not match that of the CELLxGENE dataset

IOException

setProgressReporterFactory

void setProgressReporterFactory(ProgressReporterFactory progressReporterFactory)

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