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

Class CellXGeneUtils

java.lang.Object

ubic.gemma.core.loader.expression.cellxgene.CellXGeneUtils

public class CellXGeneUtils
extends Object

Author:

poirigui

Field Summary

Fields

Modifier and Type	Field	Description
static final OntologyTerm[]	GENE_EXPRESSION_ASSAYS	List of all known gene expression assays from CELLxGENE.

Constructor Summary

Constructors

Constructor	Description
CellXGeneUtils()

Method Summary

Modifier and Type	Method	Description
static String	getCollectionUri(String collectionId)
static String	getDatasetUri(String datasetId)	FIXME: CELLxGENE does not have a landing page for datasets.
static Set<String>	getGeoAccessions(CollectionMetadata cm)	Extract GEO accessions from the given collection metadata.
static String	getTermUri(String termId)	Convert a CELLxGENE ontology term ID into a URI.
static String	getTermUri(OntologyTerm term)	Convert a CELLxGENE ontology term into a URI.
static boolean	isAnnData(DatasetAsset a)	Check if the given dataset asset is in AnnData format.
static boolean	isGeneExpressionAssay(OntologyTerm a)	Determine if the given assay corresponds to a single cell assay producing gene expression data.

Methods inherited from class java.lang.Object

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

Field Details

GENE_EXPRESSION_ASSAYS

public static final OntologyTerm[] GENE_EXPRESSION_ASSAYS

List of all known gene expression assays from CELLxGENE.

TODO: we should keep a list of supported assays in a shared location

Constructor Details

CellXGeneUtils

public CellXGeneUtils()

Method Details

getCollectionUri

public static String getCollectionUri(String collectionId)

getDatasetUri

@Nullable
public static String getDatasetUri(String datasetId)

FIXME: CELLxGENE does not have a landing page for datasets. The workaround is to fill in the DatabaseEntry.getUri() with a link to the collection obtained by getCollectionUri(String).

getGeoAccessions

public static Set<String> getGeoAccessions(CollectionMetadata cm)

Extract GEO accessions from the given collection metadata.

isGeneExpressionAssay

public static boolean isGeneExpressionAssay(OntologyTerm a)

Determine if the given assay corresponds to a single cell assay producing gene expression data.

isAnnData

public static boolean isAnnData(DatasetAsset a)

Check if the given dataset asset is in AnnData format.

TODO: handle FileType.RAW_H5AD

getTermUri

public static String getTermUri(OntologyTerm term)

Convert a CELLxGENE ontology term into a URI.

getTermUri

public static String getTermUri(String termId)

Convert a CELLxGENE ontology term ID into a URI.