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, DatabaseEntryService databaseEntryService, TaxonReadService taxonReadService, 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.
DatabaseEntry	replaceVersionAccession(ExpressionExperiment ee, String datasetId)	Replace a CELLxGENE accession that holds a dataset version ID by one that holds the permanent dataset ID.
void	setProgressReporterFactory(ProgressReporterFactory progressReporterFactory)	Set the progress reporter factory to use for reporting progress during data downloading.

Methods inherited from class 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,
 DatabaseEntryService databaseEntryService,
 TaxonReadService taxonReadService,
 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 permanent dataset ID, dataset version ID or dataset title, or null if the collection holds a single dataset. The resulting accession records the permanent ID, with the version ID as its accession version.

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

replaceVersionAccession

@Transactional
@Audited(value=CommentedEvent.class,
         messageSpel="'Replaced the CELLxGENE accession ' + #result.accessionVersion + ' (a dataset version ID) by the permanent dataset ID ' + #datasetId + ', keeping ' + #result.accessionVersion + ' as its accession version.'")
public DatabaseEntry replaceVersionAccession(ExpressionExperiment ee,
 String datasetId)

Description copied from interface: CellXGeneDataLoaderService

Replace a CELLxGENE accession that holds a dataset version ID by one that holds the permanent dataset ID.

Datasets loaded before permanent IDs were recorded store the version ID as their accession. The new accession keeps that version ID as its accession version, since it designates the data that was actually loaded, and keeps the same URI. The previous DatabaseEntry is removed.

Specified by:

replaceVersionAccession in interface CellXGeneDataLoaderService

Parameters:

datasetId - the permanent CELLxGENE dataset ID that the current accession is a version of

Returns:

the new accession

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