Modifier and Type | Method and Description |
---|---|
abstract void |
CommandExecutor.execute() |
Modifier and Type | Method and Description |
---|---|
void |
InstallCommandExecutor.execute() |
Modifier and Type | Method and Description |
---|---|
static SpeciesConfiguration.Assembly |
SpeciesUtils.getDefaultAssembly(SpeciesConfiguration speciesConfiguration)
Get the default assembly for species.
|
static Species |
SpeciesUtils.getSpecies(CellBaseConfiguration configuration,
String userProvidedSpecies,
String userProvidedAssembly)
Return species object based on species name and assembly.
|
Constructor and Description |
---|
DownloadManager(CellBaseConfiguration configuration,
Path targetDirectory,
SpeciesConfiguration speciesConfiguration,
SpeciesConfiguration.Assembly assembly) |
Modifier and Type | Method and Description |
---|---|
void |
IndexManager.createMongoDBIndexes(String collectionName,
String databaseName,
boolean dropIndexesFirst)
Create indexes for specified collection.
|
void |
IndexManager.createMongoDBIndexes(String data,
String speciesName,
String assemblyName,
boolean dropIndexesFirst)
Create indexes.
|
Modifier and Type | Method and Description |
---|---|
void |
InstallManager.install(String speciesName,
String assemblyName)
Add shard indexes and ranges in Mongo based on config file entries.
|
static void |
MongoDBShardUtils.shard(org.opencb.commons.datastore.mongodb.MongoDataStore mongoDataStore,
CellBaseConfiguration cellBaseConfiguration,
Species species)
Add shards.
|
Constructor and Description |
---|
GenericRestWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
GenericRestWSServer(String version,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
MetaWSServer(String version,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
SpeciesWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
Constructor and Description |
---|
ClinicalWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
Constructor and Description |
---|
ClinicalLegacyWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr)
Deprecated.
|
GeneWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
IdWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
ProteinWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
TranscriptWSServer(String version,
String species,
String exclude,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
VariationWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
Constructor and Description |
---|
ChromosomeWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
RegionWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
VariantWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
Constructor and Description |
---|
PathwayWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
PathwayWSServerMongo(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
ProteinProteinInteractionWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
Constructor and Description |
---|
PhenotypeWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
Constructor and Description |
---|
MiRnaGeneWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
MiRnaMatureWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
RegulatoryWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
TfWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
Constructor and Description |
---|
UtilsWSServer(String version,
String species,
javax.ws.rs.core.UriInfo uriInfo,
javax.servlet.http.HttpServletRequest hsr) |
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