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 List<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 DatasetMetadata	getDatasetMetadata(CollectionMetadata cm, DatasetVersion datasetVersion)	Select the metadata of a resolved dataset from a collection.
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.
static DatasetVersion	resolveDataset(String collectionId, List<DatasetVersion> datasets, String identifier)	Resolve a dataset in a collection from a user-supplied identifier.

Methods inherited from class Object

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

Field Details

GENE_EXPRESSION_ASSAYS

public static final List<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).

resolveDataset

public static DatasetVersion resolveDataset(String collectionId,
 List<DatasetVersion> datasets,
 String identifier)

Resolve a dataset in a collection from a user-supplied identifier.

The identifier is matched, in order, against the permanent dataset ID, the dataset version ID and the dataset title. Titles are compared exactly first, then ignoring case and surrounding whitespace. Titles are not unique across CELLxGENE, which is why resolution is always scoped to a collection.

Parameters:

collectionId - used in error messages only

datasets - the datasets of the collection, as reported by the curation API

identifier - a permanent dataset ID, a dataset version ID or a dataset title

Throws:

IllegalArgumentException - if no dataset or more than one dataset matches

getDatasetMetadata

public static DatasetMetadata getDatasetMetadata(CollectionMetadata cm,
 DatasetVersion datasetVersion)

Select the metadata of a resolved dataset from a collection.

Throws:

IllegalStateException - if the collection metadata does not list the dataset's current version, which happens if the dataset was revised between the two requests

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.