ome.util

Class SqlAction.Impl

java.lang.Object

ome.util.SqlAction.Impl

All Implemented Interfaces:

SqlAction

Direct Known Subclasses:

PostgresSqlAction

Enclosing interface:

SqlAction

public abstract static class SqlAction.Impl
extends Object
implements SqlAction

Base implementation which can be used

Nested Class Summary

Nested classes/interfaces inherited from interface ome.util.SqlAction

SqlAction.DeleteLog, SqlAction.IdRowMapper, SqlAction.Impl, SqlAction.LoggingSqlAction, SqlAction.StringRowMapper

Field Summary

Fields

Modifier and Type	Field and Description
protected org.slf4j.Logger	log
protected static int	MAX_IN_SIZE

Constructor Summary

Constructors

Constructor and Description
Impl()

Method Summary

Modifier and Type	Method and Description
protected abstract SimpleJdbcOperations	_jdbc()
protected abstract String	_lookup(String key)
void	addMessageWithinDbPatchEnd(String version, int patch, String message) Add a unique message to the DB patch table within the current patch.
void	addMessageWithinDbPatchStart(String version, int patch, String message) Add a unique message to the DB patch table within the current patch.
protected String	addMimetypes(Collection<String> mimetypes, Map<String,Object> params) Returns the "and_mimetype" clause which must be appended to a given query.
int	changeGroupPermissions(Long id, Long internal)
int	changeTablePermissionsForGroup(String table, Long id, Long internal)
boolean	clearPermissionsBit(String table, long id, int bit) Sets the given permissions bit to 0.
int	closeNode(String uuid)
int	closeNodeSessions(String uuid)
String	configValue(String key)
String	createIdsTempTable(Collection<Long> ids) Creates a temporary table filled with the given ids and returns its name.
void	createInsertTrigger(String name, String table, String procedure) Creates an insert trigger of the given name, for the given table, with the given procedure.
int	delConfigValue(String key)
void	delCurrentEventLog(String key)
int	deleteRepoDeleteLogs(SqlAction.DeleteLog template) Delete all SqlAction.DeleteLog entries which match all of the non-null fields provided in the template.
List<Long>	fileIdsInDb(String uuid, Set<String> mimetypes) Return all IDs matching the given mimetypes, or all IDs if mimetypes is null.
String	fileRepo(long fileId)
List<Long>	filterFileIdsByRepo(String uuid, List<Long> fileIds) Find the original file IDs among those given that are in the given repository.
List<SqlAction.DeleteLog>	findRepoDeleteLogs(SqlAction.DeleteLog template) Find all SqlAction.DeleteLog entries which match all of the non-null fields provided in the template.
Long	findRepoFile(String uuid, String dirname, String basename) Calls SqlAction.findRepoFile(String, String, String, Set) passing null.
Long	findRepoFile(String uuid, String dirname, String basename, Set<String> mimetypes) Lookup the id of an OriginalFile in a given repository or return null if none is found.
Long	findRepoFile(String uuid, String dirname, String basename, String mimetype) Calls SqlAction.findRepoFile(String, String, String, Set)
String	findRepoFilePath(String uuid, long id)
List<Long>	findRepoFiles(String uuid, String dirname) Return a list of original file ids that all have a path value matching the passed dirname in the given repository.
Map<String,Long>	findRepoFiles(String uuid, String dirname, List<String> basenames, Set<String> mimetypes) Like SqlAction.findRepoFile(String, String, String, Set), but queries in bulk and returns a map for the found IDs.
String	findRepoRootPath(String uuid) Find the path of the repository root.
List<Object[]>	getEventLogPartitions(Collection<String> types, Collection<String> actions, long offset, long limit) Loads up to "limit" event logs using partioning so that only the last event log of a particular (type, id) pair is returned.
float	getEventLogPercent(String key) Returns the percent (e.g. 0-100%) as calculated by the number of rows represented as completed by the configuration table row of this key divided by the total number of rows in the event log.
Map<String,Long>	getGroupIds(Collection<String> names)
long	getGroupPermissions(long groupId) Returns the permissions for the given group id.
List<Long>	getLdapExperimenters() Gets the experimenters who have the ldap attribute enabled.
String	getPasswordHash(Long experimenterID)
Map<Long,byte[]>	getShareData(List<Long> ids) Returns a map of Share ID to Share data blob.
Collection<String>	getUserEmailsByGroup(long groupId) Load all the non-empty email addresses for users in a given group.
List<String>	getUserGroups(String userName)
Long	getUserId(String userName) Get the user's ID
String	getUsername(long userId) Get the user's name
ExperimenterGroup	groupInfoFor(String table, long id) Return a mostly unloaded ExperimenterGroup object containing only the id, name, and permissions.
boolean	hasUnicodeUnits()
int	isFileInRepo(String uuid, long id, Set<String> mimetypes)
boolean	isLdapExperimenter(Long id) Checks whether the specified experimenter ID has the ldap flag set.
List<long[]>	nextPixelsDataLogForRepo(String repo, long lastEventId, int rows) Returns arrays of longs for the following SQL return values: experimenter, eventlog, entityid as pixels, rownumber The oldest N eventlogs with action = "PIXELDATA" and entitytype = "ome.model.core.Pixels" is found per user and returned.
protected String	printThrowable(Throwable t)
void	refreshEventLogFromUpdatedAnnotations() Convert the _updated_annotations table to REINDEX entries in the event log.
int	repoScriptCount(String uuid, Set<String> mimetypes)
String	rewriteHql(String query, String key, Object value) Allows the specific database implementations a chance to modify queries.
String	scriptRepo(long fileId, Set<String> mimetypes) Similar to SqlAction.fileRepo(long), but only returns values for files which are also scripts.
long	selectCurrentEventLog(String key)
void	setCurrentEventLog(long id, String key)
boolean	setPermissionsBit(String table, long id, int bit) Sets the given permissions bit to 1.
long	setStatsInfo(Channel ch, StatsInfo si)
boolean	setUserPassword(Long experimenterID, String password)
int	updateOrInsertConfigValue(String name, String value)

Methods inherited from class java.lang.Object

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

Methods inherited from interface ome.util.SqlAction

activeSession, closeSessions, countFormat, createSavepoint, currentUserNames, currValue, dbUuid, dbVersion, deferConstraints, findRepoImageFromPixels, findRepoPixels, getDeletedIds, getPixelsNamePathRepo, getShapeIds, insertFormat, insertLogs, insertSession, nextSessionId, nextValue, nodeId, now, prepareSession, releaseSavepoint, removePassword, repoFile, roiByImageAndNs, rollbackSavepoint, sessionId, setFileRepo, setPixelsNamePathRepo, synchronizeJobs, updateConfiguration

Field Detail

MAX_IN_SIZE

protected static final int MAX_IN_SIZE

See Also:

Constant Field Values

log

protected final org.slf4j.Logger log

Constructor Detail

Impl

public Impl()

Method Detail

_jdbc

protected abstract SimpleJdbcOperations _jdbc()

_lookup

protected abstract String _lookup(String key)

printThrowable

protected String printThrowable(Throwable t)

createInsertTrigger

public void createInsertTrigger(String name,
                                String table,
                                String procedure)

Description copied from interface: SqlAction

Creates an insert trigger of the given name, for the given table, with the given procedure. No error handling is performed.

Specified by:

createInsertTrigger in interface SqlAction

rewriteHql

public String rewriteHql(String query,
                         String key,
                         Object value)

Description copied from interface: SqlAction

Allows the specific database implementations a chance to modify queries.

Specified by:

rewriteHql in interface SqlAction

Parameters:

query - String query (non-null) which is in effect.

key - Key of the argument e.g. (:ids)

value - value which has been passed in for that parameter.

Returns:

Returns a query replacement.

See Also:

ticket 3697

createIdsTempTable

public String createIdsTempTable(Collection<Long> ids)

Description copied from interface: SqlAction

Creates a temporary table filled with the given ids and returns its name. The table is only available for the period if the transaction.

Specified by:

createIdsTempTable in interface SqlAction

closeNodeSessions

public int closeNodeSessions(String uuid)

Specified by:

closeNodeSessions in interface SqlAction

closeNode

public int closeNode(String uuid)

Specified by:

closeNode in interface SqlAction

setUserPassword

public boolean setUserPassword(Long experimenterID,
                               String password)

Specified by:

setUserPassword in interface SqlAction

changeGroupPermissions

public int changeGroupPermissions(Long id,
                                  Long internal)

Specified by:

changeGroupPermissions in interface SqlAction

changeTablePermissionsForGroup

public int changeTablePermissionsForGroup(String table,
                                          Long id,
                                          Long internal)

Specified by:

changeTablePermissionsForGroup in interface SqlAction

setPermissionsBit

public boolean setPermissionsBit(String table,
                                 long id,
                                 int bit)

Description copied from interface: SqlAction

Sets the given permissions bit to 1. Note: Actually sets the bit to 1 in the value stored in the database, does not adopt the inverse convention associated with permissions flags.

Specified by:

setPermissionsBit in interface SqlAction

Parameters:

table - the table in which to find the row

id - the value of the table's id column that identifies the row to update

bit - the bit number to set to 1, counting from 0 as the least significant bit

Returns:

if the row was found in the table, regardless of the given bit's previous value

clearPermissionsBit

public boolean clearPermissionsBit(String table,
                                   long id,
                                   int bit)

Description copied from interface: SqlAction

Sets the given permissions bit to 0. Note: Actually sets the bit to 0 in the value stored in the database, does not adopt the inverse convention associated with permissions flags.

Specified by:

clearPermissionsBit in interface SqlAction

Parameters:

table - the table in which to find the row

id - the value of the table's id column that identifies the row to update

bit - the bit number to set to 0, counting from 0 as the least significant bit

Returns:

if the row was found in the table, regardless of the given bit's previous value

addMimetypes

protected String addMimetypes(Collection<String> mimetypes,
                              Map<String,Object> params)

Returns the "and_mimetype" clause which must be appended to a given query. Note: the rest of the SQL statement to which this clause is appended must use named SQL parameters otherwise "Can't infer the SQL type to use" will be raised.

Parameters:

mimetypes - If null, then "" will be returned.

params - sql parameter source to be passed to JDBC methods.

Returns:

Possibly empty String, but never null.

findRepoFile

public Long findRepoFile(String uuid,
                         String dirname,
                         String basename)

Description copied from interface: SqlAction

Calls SqlAction.findRepoFile(String, String, String, Set) passing null.

Specified by:

findRepoFile in interface SqlAction

findRepoFile

public Long findRepoFile(String uuid,
                         String dirname,
                         String basename,
                         String mimetype)

Description copied from interface: SqlAction

Calls SqlAction.findRepoFile(String, String, String, Set)

Specified by:

findRepoFile in interface SqlAction

findRepoFile

public Long findRepoFile(String uuid,
                         String dirname,
                         String basename,
                         Set<String> mimetypes)

Description copied from interface: SqlAction

Lookup the id of an OriginalFile in a given repository or return null if none is found.

Specified by:

findRepoFile in interface SqlAction

Parameters:

uuid - The UUID of the repository (originalfile.sha1)

dirname - the full directory path minus the file name.

basename - i.e. the filename without any directory path

mimetypes - if null, then no mimetype query fragement will be added.

Returns:

null if no OriginalFile is found, otherwise the id.

findRepoFiles

public Map<String,Long> findRepoFiles(String uuid,
                                      String dirname,
                                      List<String> basenames,
                                      Set<String> mimetypes)

Description copied from interface: SqlAction

Like SqlAction.findRepoFile(String, String, String, Set), but queries in bulk and returns a map for the found IDs.

Specified by:

findRepoFiles in interface SqlAction

repoScriptCount

public int repoScriptCount(String uuid,
                           Set<String> mimetypes)

Specified by:

repoScriptCount in interface SqlAction

Parameters:

uuid - repository identifier

mimetypes - file mimetypes to check; if null, all files;

isFileInRepo

public int isFileInRepo(String uuid,
                        long id,
                        Set<String> mimetypes)

Specified by:

isFileInRepo in interface SqlAction

Parameters:

uuid - Repository identifier

id - file identifier

mimetypes - Set of mimetypes to check; if null, all files.

fileIdsInDb

public List<Long> fileIdsInDb(String uuid,
                              Set<String> mimetypes)

Description copied from interface: SqlAction

Return all IDs matching the given mimetypes, or all IDs if mimetypes is null.

Specified by:

fileIdsInDb in interface SqlAction

filterFileIdsByRepo

public List<Long> filterFileIdsByRepo(String uuid,
                                      List<Long> fileIds)

Description copied from interface: SqlAction

Find the original file IDs among those given that are in the given repository.

Specified by:

filterFileIdsByRepo in interface SqlAction

Parameters:

uuid - a repository UUID

fileIds - IDs of original files

Returns:

those IDs among those given whose original files are in the given repository

findRepoFiles

public List<Long> findRepoFiles(String uuid,
                                String dirname)

Description copied from interface: SqlAction

Return a list of original file ids that all have a path value matching the passed dirname in the given repository.

Specified by:

findRepoFiles in interface SqlAction

Returns:

possibly empty list of ids.

findRepoDeleteLogs

public List<SqlAction.DeleteLog> findRepoDeleteLogs(SqlAction.DeleteLog template)

Description copied from interface: SqlAction

Find all SqlAction.DeleteLog entries which match all of the non-null fields provided in the template.

Specified by:

findRepoDeleteLogs in interface SqlAction

Parameters:

template - non-null.

Returns:

a list of SqlAction.DeleteLog entries

deleteRepoDeleteLogs

public int deleteRepoDeleteLogs(SqlAction.DeleteLog template)

Description copied from interface: SqlAction

Delete all SqlAction.DeleteLog entries which match all of the non-null fields provided in the template.

Specified by:

deleteRepoDeleteLogs in interface SqlAction

Parameters:

template - not-null

Returns:

the number of rows deleted.

findRepoRootPath

public String findRepoRootPath(String uuid)

Description copied from interface: SqlAction

Find the path of the repository root.

Specified by:

findRepoRootPath in interface SqlAction

Parameters:

uuid - a repository UUID

Returns:

the repository root

findRepoFilePath

public String findRepoFilePath(String uuid,
                               long id)

Specified by:

findRepoFilePath in interface SqlAction

nextPixelsDataLogForRepo

public List<long[]> nextPixelsDataLogForRepo(String repo,
                                             long lastEventId,
                                             int rows)

Description copied from interface: SqlAction

Returns arrays of longs for the following SQL return values: experimenter, eventlog, entityid as pixels, rownumber The oldest N eventlogs with action = "PIXELDATA" and entitytype = "ome.model.core.Pixels" is found per user and returned. Multiple eventlogs are returned per user in order to support multi-threading. Duplicate pixel ids are stripped.

Specified by:

nextPixelsDataLogForRepo in interface SqlAction

getGroupPermissions

public long getGroupPermissions(long groupId)

Description copied from interface: SqlAction

Returns the permissions for the given group id.

Specified by:

getGroupPermissions in interface SqlAction

getGroupIds

public Map<String,Long> getGroupIds(Collection<String> names)

Specified by:

getGroupIds in interface SqlAction

getPasswordHash

public String getPasswordHash(Long experimenterID)

Specified by:

getPasswordHash in interface SqlAction

getUserId

public Long getUserId(String userName)

Description copied from interface: SqlAction

Get the user's ID

Specified by:

getUserId in interface SqlAction

Parameters:

userName - the user's name

Returns:

their ID, or null if they cannot be found

getUserEmailsByGroup

public Collection<String> getUserEmailsByGroup(long groupId)

Description copied from interface: SqlAction

Load all the non-empty email addresses for users in a given group.

Specified by:

getUserEmailsByGroup in interface SqlAction

Returns:

a non-null Collection of non-empty user email addresses.

getUsername

public String getUsername(long userId)

Description copied from interface: SqlAction

Get the user's name

Specified by:

getUsername in interface SqlAction

Parameters:

userId - the user's ID

Returns:

their name, or null if they cannot be found

getLdapExperimenters

public List<Long> getLdapExperimenters()

Description copied from interface: SqlAction

Gets the experimenters who have the ldap attribute enabled.

Specified by:

getLdapExperimenters in interface SqlAction

Returns:

a list of user IDs.

isLdapExperimenter

public boolean isLdapExperimenter(Long id)

Description copied from interface: SqlAction

Checks whether the specified experimenter ID has the ldap flag set.

Specified by:

isLdapExperimenter in interface SqlAction

Parameters:

id - The experimenter ID.

Returns:

true if the experimenter is an LDAP user; false otherwise.

getUserGroups

public List<String> getUserGroups(String userName)

Specified by:

getUserGroups in interface SqlAction

groupInfoFor

public ExperimenterGroup groupInfoFor(String table,
                                      long id)

Description copied from interface: SqlAction

Return a mostly unloaded ExperimenterGroup object containing only the id, name, and permissions.

Specified by:

groupInfoFor in interface SqlAction

fileRepo

public String fileRepo(long fileId)

Specified by:

fileRepo in interface SqlAction

scriptRepo

public String scriptRepo(long fileId,
                         Set<String> mimetypes)

Description copied from interface: SqlAction

Similar to SqlAction.fileRepo(long), but only returns values for files which are also scripts. Null may be returned

Specified by:

scriptRepo in interface SqlAction

mimetypes - null implies all files are checked

setStatsInfo

public long setStatsInfo(Channel ch,
                         StatsInfo si)

Specified by:

setStatsInfo in interface SqlAction

configValue

public String configValue(String key)

Specified by:

configValue in interface SqlAction

delConfigValue

public int delConfigValue(String key)

Specified by:

delConfigValue in interface SqlAction

updateOrInsertConfigValue

public int updateOrInsertConfigValue(String name,
                                     String value)

Specified by:

updateOrInsertConfigValue in interface SqlAction

selectCurrentEventLog

public long selectCurrentEventLog(String key)

Specified by:

selectCurrentEventLog in interface SqlAction

getEventLogPercent

public float getEventLogPercent(String key)

Description copied from interface: SqlAction

Returns the percent (e.g. 0-100%) as calculated by the number of rows represented as completed by the configuration table row of this key divided by the total number of rows in the event log. Since this method executes 2 counts over the event log table, it can take a significant amount of time.

Specified by:

getEventLogPercent in interface SqlAction

Parameters:

key - PersistentEventLogLoader key for lookup in the configuration table

Returns:

float value between 0 and 100 of the percent completed

getEventLogPartitions

public List<Object[]> getEventLogPartitions(Collection<String> types,
                                            Collection<String> actions,
                                            long offset,
                                            long limit)

Description copied from interface: SqlAction

Loads up to "limit" event logs using partioning so that only the last event log of a particular (type, id) pair is returned. The contents of the object array are:

1. the id of the event log (Long)
2. the entity type of the event log (String)
3. the entity id of the event log (Long)
4. the action of the event log (String)
5. the number of skipped event logs (Integer)

Specified by:

getEventLogPartitions in interface SqlAction

Parameters:

types - Collection of entityType strings which should be queried

actions - Collection of ACTION strings which should be queried

offset - Offset to the row which should be queried first

limit - Maximum number of rows (after partionting) which should be returned.

setCurrentEventLog

public void setCurrentEventLog(long id,
                               String key)

Specified by:

setCurrentEventLog in interface SqlAction

delCurrentEventLog

public void delCurrentEventLog(String key)

Specified by:

delCurrentEventLog in interface SqlAction

refreshEventLogFromUpdatedAnnotations

public void refreshEventLogFromUpdatedAnnotations()

Description copied from interface: SqlAction

Convert the _updated_annotations table to REINDEX entries in the event log.

Specified by:

refreshEventLogFromUpdatedAnnotations in interface SqlAction

hasUnicodeUnits

public boolean hasUnicodeUnits()

Specified by:

hasUnicodeUnits in interface SqlAction

Returns:

if the database's type system contains correctly encoded units of measure

addMessageWithinDbPatchStart

public void addMessageWithinDbPatchStart(String version,
                                         int patch,
                                         String message)

Description copied from interface: SqlAction

Add a unique message to the DB patch table within the current patch. This method marks the start of the corresponding DB adjustment process.

Specified by:

addMessageWithinDbPatchStart in interface SqlAction

Parameters:

version - the version of the current DB

patch - the patch of the current DB

message - the new message to note

addMessageWithinDbPatchEnd

public void addMessageWithinDbPatchEnd(String version,
                                       int patch,
                                       String message)

Description copied from interface: SqlAction

Add a unique message to the DB patch table within the current patch. This method marks the end of the corresponding DB adjustment process.

Specified by:

addMessageWithinDbPatchEnd in interface SqlAction

Parameters:

version - the version of the current DB

patch - the patch of the current DB

message - the new message to note

getShareData

public Map<Long,byte[]> getShareData(List<Long> ids)

Description copied from interface: SqlAction

Returns a map of Share ID to Share data blob.

Specified by:

getShareData in interface SqlAction

Parameters:

ids - IDs of Shares for which data blobs are to be returned.

Returns:

map of ID to data blob.