public class SQLCache extends VolatilCache implements Cache
Modifier and Type | Field and Description |
---|---|
(package private) static int |
CONNECTION_ERROR |
private java.sql.PreparedStatement |
deleteAlignment |
private java.sql.PreparedStatement |
deleteAlignmentCells |
private java.sql.PreparedStatement |
deleteAlignmentUri |
private java.sql.PreparedStatement |
deleteDependencies |
private java.sql.PreparedStatement |
deleteExtensions |
private java.sql.PreparedStatement |
deleteNetwork |
private java.sql.PreparedStatement |
findAlignmentCells |
private java.sql.PreparedStatement |
findAlignmentDescription |
private java.sql.PreparedStatement |
findAlignments |
private java.sql.PreparedStatement |
findAlignmentUris |
private java.sql.PreparedStatement |
findExtensions |
private java.sql.PreparedStatement |
findNetworkAlignments |
private java.sql.PreparedStatement |
findNetworkOntologies |
private java.sql.PreparedStatement |
findNetworks |
private java.sql.PreparedStatement |
findOntology |
private java.sql.PreparedStatement |
findServers |
(package private) java.lang.String |
host |
(package private) static int |
INIT_ERROR |
private java.sql.PreparedStatement |
insertAlignmentCell |
private java.sql.PreparedStatement |
insertAlignmentDescription |
private java.sql.PreparedStatement |
insertAlignmentUri |
private java.sql.PreparedStatement |
insertExtension |
private java.sql.PreparedStatement |
insertNetwork |
private java.sql.PreparedStatement |
insertNetworkAlignment |
private java.sql.PreparedStatement |
insertNetworkOntology |
private java.sql.PreparedStatement |
insertOntology |
(package private) static org.slf4j.Logger |
logger |
static java.lang.String |
mySERIAL |
static java.lang.String |
pgSERIAL |
(package private) java.lang.String |
port |
private java.sql.PreparedStatement |
registerServer |
(package private) int |
rights |
(package private) DBService |
service |
(package private) static int |
SUCCESS |
private java.sql.PreparedStatement |
unregisterServer |
private java.sql.PreparedStatement |
updateOntology |
(package private) int |
VERSION |
ALID, alignmentURITable, CACHED, idprefix, ONID, OURI1, OURI2, STORED, SVCNS
Modifier and Type | Method and Description |
---|---|
void |
changeColumnType(java.sql.Statement st,
java.lang.String tableName,
java.lang.String columnName,
java.lang.String newType) |
void |
close() |
void |
compileQueries() |
java.sql.PreparedStatement |
createInsertStatement(java.lang.String updatePattern) |
java.sql.Statement |
createStatement() |
java.sql.PreparedStatement |
createStatement(java.lang.String query) |
protected Alignment |
fetchAlignment(java.lang.String uri,
Alignment result)
retrieve full alignment from id (and cache it)
|
void |
init(java.util.Properties p,
java.lang.String prefix)
loads the alignment descriptions from the database and put them in the
alignmentTable hashtable
|
void |
initDatabase() |
void |
initEDOALTables(java.sql.Statement st) |
private void |
load(boolean force)
loads the alignment descriptions and networks of ontologies from the
database and put them in the indexes
|
void |
recordOntology(java.sql.Statement st,
java.net.URI uri,
java.net.URI file,
Ontology<java.lang.Object> onto) |
private void |
registerServer(java.lang.String host,
java.lang.String port,
java.lang.Boolean writeable,
java.lang.String prefix) |
void |
renameColumn(java.sql.Statement st,
java.lang.String tableName,
java.lang.String oldName,
java.lang.String newName,
java.lang.String newType) |
void |
reset() |
void |
resetDatabase(boolean force) |
protected Alignment |
retrieveAlignment(java.lang.String uri,
Alignment alignment)
loads the full alignment from the database and put it in the
alignmentTable hastable
should be invoked when:
( result.getExtension(CACHED) == ""
AND result.getExtension(STORED) != "") {
|
protected Alignment |
retrieveDescription(java.lang.String id)
loads the description of alignments from the database and set them
in an alignment object
|
void |
retrieveOntology(java.lang.String uri,
Ontology<?> ob) |
protected OntologyNetwork |
retrieveOntologyNetwork(java.lang.String id) |
void |
storeAlignment(java.lang.String uri) |
void |
storeExtensions(java.lang.String id,
java.util.Collection<java.lang.String[]> extensions) |
void |
storeOntologyNetwork(java.lang.String uri) |
void |
unstoreAlignment(java.lang.String uri)
Non publicised class
|
void |
unstoreAlignment(java.lang.String uri,
Alignment alignment) |
void |
unstoreEDOALAlignment(java.lang.String id,
Alignment alignment) |
void |
unstoreOntologyNetwork(java.lang.String uri,
BasicOntologyNetwork network) |
void |
updateDatabase()
These queries are NOT compiled (through they could for most of them)
As this is obviously called before queries could be compiled
|
alignments, alignments, cleanUpCache, eraseAlignment, eraseOntologyNetwork, flushAlignment, flushCache, generateAlignmentUri, generateCellId, generateOntologyNetworkUri, getAlignment, getAlignmentByURI, getAlignments, getAlignments, getAlignmentsByDescription, getMetadata, getOntologyNetwork, isAlignmentStored, isNetworkStored, listAlignments, ontologies, ontologyNetworks, ontologyNetworkUris, recordAlignment, recordNetwork, recordNewAlignment, recordNewAlignment, recordNewNetwork, recordNewNetwork, recoverAlignmentUri, recoverNetworkUri, resetCacheStamp, resetCacheStamp, resetTables, stripAlignmentUri, stripNetworkUri, unRecordAlignment, unRecordNetwork, unstoreOntologyNetwork
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
alignments, alignments, eraseAlignment, eraseOntologyNetwork, flushCache, generateAlignmentUri, generateOntologyNetworkUri, getAlignment, getAlignmentByURI, getAlignments, getAlignments, getAlignmentsByDescription, getMetadata, getOntologyNetwork, isAlignmentStored, isNetworkStored, ontologies, ontologyNetworks, recordNewAlignment, recordNewAlignment, recordNewNetwork, recordNewNetwork
static final org.slf4j.Logger logger
java.lang.String host
java.lang.String port
int rights
final int VERSION
DBService service
static final int CONNECTION_ERROR
static final int SUCCESS
static final int INIT_ERROR
private java.sql.PreparedStatement findServers
private java.sql.PreparedStatement registerServer
private java.sql.PreparedStatement unregisterServer
private java.sql.PreparedStatement findAlignmentUris
private java.sql.PreparedStatement insertAlignmentUri
private java.sql.PreparedStatement deleteAlignmentUri
private java.sql.PreparedStatement findAlignments
private java.sql.PreparedStatement deleteAlignment
private java.sql.PreparedStatement findAlignmentCells
private java.sql.PreparedStatement insertAlignmentCell
private java.sql.PreparedStatement deleteAlignmentCells
private java.sql.PreparedStatement findAlignmentDescription
private java.sql.PreparedStatement insertAlignmentDescription
private java.sql.PreparedStatement findExtensions
private java.sql.PreparedStatement insertExtension
private java.sql.PreparedStatement deleteExtensions
private java.sql.PreparedStatement deleteDependencies
private java.sql.PreparedStatement findOntology
private java.sql.PreparedStatement insertOntology
private java.sql.PreparedStatement updateOntology
private java.sql.PreparedStatement findNetworks
private java.sql.PreparedStatement insertNetwork
private java.sql.PreparedStatement deleteNetwork
private java.sql.PreparedStatement findNetworkOntologies
private java.sql.PreparedStatement insertNetworkOntology
private java.sql.PreparedStatement findNetworkAlignments
private java.sql.PreparedStatement insertNetworkAlignment
public static final java.lang.String mySERIAL
public static final java.lang.String pgSERIAL
public SQLCache(DBService serv)
public java.sql.Statement createStatement() throws java.sql.SQLException
java.sql.SQLException
public java.sql.PreparedStatement createStatement(java.lang.String query) throws java.sql.SQLException
java.sql.SQLException
public java.sql.PreparedStatement createInsertStatement(java.lang.String updatePattern) throws java.sql.SQLException
java.sql.SQLException
public void compileQueries() throws java.sql.SQLException
java.sql.SQLException
public void reset() throws AlignmentException
reset
in interface Cache
reset
in class VolatilCache
AlignmentException
public void init(java.util.Properties p, java.lang.String prefix) throws AlignmentException
init
in interface Cache
init
in class VolatilCache
p:
- the initialisation parametersprefix:
- the URI prefix of the current serverAlignmentException
- when something goes wrong (cannot access database, but format)public void close() throws AlignmentException
close
in interface Cache
close
in class VolatilCache
AlignmentException
private void load(boolean force) throws java.sql.SQLException
force:
- true if data is downloaded from the databasejava.sql.SQLException
- when something goes wrong (e.g., no database access)protected Alignment retrieveDescription(java.lang.String id) throws java.sql.SQLException
id:
- the id of an alignmentjava.sql.SQLException
public void retrieveOntology(java.lang.String uri, Ontology<?> ob) throws java.sql.SQLException, AlignmentException, java.net.URISyntaxException
java.sql.SQLException
AlignmentException
java.net.URISyntaxException
protected Alignment retrieveAlignment(java.lang.String uri, Alignment alignment) throws java.sql.SQLException, AlignmentException, java.net.URISyntaxException
uri:
- the uri of an alignmentalignment:
- the alignment structure containing its metadatajava.sql.SQLException
- when the database is not accessiblejava.net.URISyntaxException
- when the URI is invalidAlignmentException
- when something else goes wrong (no corresponding alignment)protected OntologyNetwork retrieveOntologyNetwork(java.lang.String id)
protected Alignment fetchAlignment(java.lang.String uri, Alignment result) throws AlignmentException
fetchAlignment
in class VolatilCache
uri:
- the URI of an alignmentresult:
- its alignment structureAlignmentException
- when something goes wrongpublic void unstoreAlignment(java.lang.String uri) throws AlignmentException
uri:
- the URI of the alignment to suppress from the storeAlignmentException
- when something goes wrong (cannot resolve URI)public void unstoreAlignment(java.lang.String uri, Alignment alignment) throws AlignmentException
unstoreAlignment
in class VolatilCache
AlignmentException
public void unstoreEDOALAlignment(java.lang.String id, Alignment alignment) throws AlignmentException
AlignmentException
public void storeAlignment(java.lang.String uri) throws AlignmentException
storeAlignment
in interface Cache
storeAlignment
in class VolatilCache
AlignmentException
public void recordOntology(java.sql.Statement st, java.net.URI uri, java.net.URI file, Ontology<java.lang.Object> onto) throws java.sql.SQLException
java.sql.SQLException
public void storeOntologyNetwork(java.lang.String uri) throws AlignmentException
storeOntologyNetwork
in interface Cache
storeOntologyNetwork
in class VolatilCache
AlignmentException
public void storeExtensions(java.lang.String id, java.util.Collection<java.lang.String[]> extensions) throws java.sql.SQLException
java.sql.SQLException
public void unstoreOntologyNetwork(java.lang.String uri, BasicOntologyNetwork network) throws AlignmentException
AlignmentException
public void initDatabase() throws java.sql.SQLException
java.sql.SQLException
public void initEDOALTables(java.sql.Statement st) throws java.sql.SQLException
java.sql.SQLException
public void resetDatabase(boolean force) throws java.sql.SQLException, AlignmentException
java.sql.SQLException
AlignmentException
private void registerServer(java.lang.String host, java.lang.String port, java.lang.Boolean writeable, java.lang.String prefix) throws java.sql.SQLException
java.sql.SQLException
public void renameColumn(java.sql.Statement st, java.lang.String tableName, java.lang.String oldName, java.lang.String newName, java.lang.String newType) throws java.sql.SQLException
java.sql.SQLException
public void changeColumnType(java.sql.Statement st, java.lang.String tableName, java.lang.String columnName, java.lang.String newType) throws java.sql.SQLException
java.sql.SQLException
public void updateDatabase() throws java.sql.SQLException, AlignmentException
java.sql.SQLException
AlignmentException
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