ome.services.graphs

Class BaseGraphSpec

java.lang.Object

ome.services.graphs.BaseGraphSpec

All Implemented Interfaces:

GraphSpec, org.springframework.beans.factory.BeanNameAware

Direct Known Subclasses:

AbstractHierarchyGraphSpec, RenderingDefGraphSpec

Deprecated.

will be removed in OMERO 5.2, so use the new graphs implementation

@Deprecated
public class BaseGraphSpec
extends Object
implements GraphSpec, org.springframework.beans.factory.BeanNameAware

GraphSpec which takes the id of some id as the root of action.

Since:

Beta4.2.1

Author:

Josh Moore, josh at glencoesoftware.com

See Also:

IGraph

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BaseGraphSpec.SubSpecIterator Deprecated. Iterator which walks returns all GraphSpecs which are reachable from the given spec, depth first including the spec itself.

Field Summary

Fields

Modifier and Type	Field and Description
protected ExtendedMetadata	em Deprecated.
protected List<GraphEntry>	entries Deprecated. The paths which make up this graph specification.
protected long	id Deprecated. The id of the root type which will be processed.
protected Map<String,String>	options Deprecated. Options passed to the #initialize(long, Map) method, which may be used during GraphState.execute(int) to alter behavior.
protected String	superspec Deprecated. Path of the superspec.

Constructor Summary

Constructors

Constructor and Description
BaseGraphSpec(List<String> entries) Deprecated.
BaseGraphSpec(String name, String... entries) Deprecated. Simplified constructor, primarily used for testing.

Method Summary

Methods

Modifier and Type	Method and Description
protected org.hibernate.Query	buildQuery(String[] sub, GraphEntry subpath, QueryBuilder qb, QueryBuilder and, org.hibernate.Session session) Deprecated.
QueryBuilder	chgrpQuery(EventContext ec, String table, GraphOpts opts) Deprecated. Return a QueryBuilder which has been properly initialized to take the parameters "id" and "grp" and then have QueryBuilder.query(Session) called.
QueryBuilder	chmodQuery(EventContext ec, String table, GraphOpts opts) Deprecated.
protected QueryBuilder	createQueryBuilder(String[] sub, GraphEntry subpath) Deprecated.
QueryBuilder	deleteQuery(EventContext ec, String table, GraphOpts opts) Deprecated.
List<GraphEntry>	entries() Deprecated. Returns a copy of the list of GraphEntry instances contained in this GraphSpec
Class<ome.model.IObject>	getHibernateClass(String table) Deprecated. Return the Hibernate type (ome.model.*) for the given table.
String	getName() Deprecated. The name of this specification.
String	getSuperSpec() Deprecated. Specification of where this GraphSpec is attached under another .
ome.model.meta.ExperimenterGroup	groupInfo(ome.util.SqlAction sql) Deprecated. Like GraphSpec.load(Session) uses the current table and id information to look up information on the given target.
int	initialize(long id, String superspec, Map<String,String> options) Deprecated. Called as each action is started.
protected void	join(QueryBuilder qb, String from, String fromAlias, String to, String toAlias) Deprecated. Used to generate a join statement on the QueryBuilder making use of {@link ExtendedMetadata#getRelationship(String, String).
protected void	joinDataset(QueryBuilder qb, String dataset, String fileset) Deprecated.
protected void	joinPlate(QueryBuilder qb, String plate, String fileset) Deprecated.
ome.model.IObject	load(org.hibernate.Session session) Deprecated. Loads the object that this spec points to.
boolean	overrideKeep() Deprecated. Always returns false.
protected long[][]	parseResults(String[] sub, GraphEntry subpath, List<List<Long>> results) Deprecated.
void	permissionsClause(EventContext ec, QueryBuilder qb, boolean sqlQuery) Deprecated. Appends a clause to the QueryBuilder based on the current user.
void	postProcess(org.springframework.beans.factory.ListableBeanFactory factory) Deprecated. Gives all specs a chance to reference subspecs.
long[][]	queryBackupIds(org.hibernate.Session session, int step, GraphEntry subpath, QueryBuilder and) Deprecated. If a given path is processed before its sub-path, this points to a one-to-one relationship.
protected List<List<Long>>	runQuery(String[] sub, GraphEntry subpath, org.hibernate.Query q, org.hibernate.Session session) Deprecated.
void	setBeanName(String beanName) Deprecated. Set the name of the bean in the bean factory that created this bean.
void	setExtendedMetadata(ExtendedMetadata em) Deprecated.
String	toString() Deprecated.
Iterator<GraphSpec>	walk() Deprecated. Returns an iterator over all subspecs and their subspecs, depth-first.
protected void	walk(String[] sub, GraphEntry entry, QueryBuilder qb) Deprecated. Walks the parts given adding a new relationship between each.

Methods inherited from class java.lang.Object

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

Field Detail

entries

protected final List<GraphEntry> entries

Deprecated.

The paths which make up this graph specification. These count as the steps which will be performed by multiple calls to GraphState.execute(int)

em

protected ExtendedMetadata em

Deprecated.

id

protected long id

Deprecated.

The id of the root type which will be processed. Note: if this action comes from a subspec, then the id points to the type of the supertype not the type for this entry itself. For example, if this is "/Dataset" but it is being processed as a part of "/Project" then the id refers to the project and not the dataset.

superspec

protected String superspec

Deprecated.

Path of the superspec.

options

protected Map<String,String> options

Deprecated.

Options passed to the #initialize(long, Map) method, which may be used during GraphState.execute(int) to alter behavior.

Constructor Detail

BaseGraphSpec

public BaseGraphSpec(String name,
             String... entries)

Deprecated.

Simplified constructor, primarily used for testing.

BaseGraphSpec

public BaseGraphSpec(List<String> entries)

Deprecated.

Method Detail

setBeanName

public void setBeanName(String beanName)

Deprecated.

Description copied from interface: org.springframework.beans.factory.BeanNameAware

Set the name of the bean in the bean factory that created this bean.

Invoked after population of normal bean properties but before an init callback such as InitializingBean.afterPropertiesSet() or a custom init-method.

Specified by:

setBeanName in interface org.springframework.beans.factory.BeanNameAware

Parameters:

beanName - the name of the bean in the factory. Note that this name is the actual bean name used in the factory, which may differ from the originally specified name: in particular for inner bean names, the actual bean name might have been made unique through appending "#..." suffixes. Use the BeanFactoryUtils.originalBeanName(String) method to extract the original bean name (without suffix), if desired.

setExtendedMetadata

public void setExtendedMetadata(ExtendedMetadata em)

Deprecated.

getName

public String getName()

Deprecated.

Description copied from interface: GraphSpec

The name of this specification. Usually the first component of the entries in spec.xml

Specified by:

getName in interface GraphSpec

getSuperSpec

public String getSuperSpec()

Deprecated.

Description copied from interface: GraphSpec

Specification of where this GraphSpec is attached under another . The reverse of GraphEntry.getSubSpec().

Specified by:

getSuperSpec in interface GraphSpec

getHibernateClass

public Class<ome.model.IObject> getHibernateClass(String table)

Deprecated.

Description copied from interface: GraphSpec

Return the Hibernate type (ome.model.*) for the given table.

Specified by:

getHibernateClass in interface GraphSpec

postProcess

public void postProcess(org.springframework.beans.factory.ListableBeanFactory factory)

Deprecated.

Description copied from interface: GraphSpec

Gives all specs a chance to reference subspecs.

Specified by:

postProcess in interface GraphSpec

initialize

public int initialize(long id,
             String superspec,
             Map<String,String> options)
               throws GraphException

Deprecated.

Description copied from interface: GraphSpec

Called as each action is started. This instance will only be used serially (i.e. by one thread) and so this is safe. When the last step is reached, GraphState.execute(int) can take clean up actions.

Specified by:

initialize in interface GraphSpec

Parameters:

id - identifier of the root object which defines the graph to be processed.

superspec - points to the relationship between the root object and the current graph. In many cases, this value will be null so that the current object is taken to be the root, but if this is a subspec, or a non-standard naming is being used, then the superspec will be used.

options - possibly null or empty map of options which can override the operations provided in the definition of the specification. For example, if the spec "/Image" defines "/Image/Annotation" as "HARD" (the default), then the options map could contain

 {"/Image/Annotation":"ORPHAN"}
 

to modify that setting.

Returns:

number of steps which are to be processed.

Throws:

GraphException

walk

public Iterator<GraphSpec> walk()

Deprecated.

Description copied from interface: GraphSpec

Returns an iterator over all subspecs and their subspecs, depth-first.

Specified by:

walk in interface GraphSpec

entries

public List<GraphEntry> entries()

Deprecated.

Description copied from interface: GraphSpec

Returns a copy of the list of GraphEntry instances contained in this GraphSpec

Specified by:

entries in interface GraphSpec

overrideKeep

public boolean overrideKeep()

Deprecated.

Always returns false. See interface for documentation.

Specified by:

overrideKeep in interface GraphSpec

load

public ome.model.IObject load(org.hibernate.Session session)
                       throws GraphException

Deprecated.

Description copied from interface: GraphSpec

Loads the object that this spec points to. Performs similar logic to the GraphSpec.queryBackupIds(Session, int, GraphEntry, QueryBuilder) but only returns the last element.

Specified by:

load in interface GraphSpec

Returns:

possibly null.

Throws:

GraphException

groupInfo

public ome.model.meta.ExperimenterGroup groupInfo(ome.util.SqlAction sql)

Deprecated.

Description copied from interface: GraphSpec

Like GraphSpec.load(Session) uses the current table and id information to look up information on the given target.

Specified by:

groupInfo in interface GraphSpec

createQueryBuilder

protected QueryBuilder createQueryBuilder(String[] sub,
                              GraphEntry subpath)

Deprecated.

buildQuery

protected org.hibernate.Query buildQuery(String[] sub,
                             GraphEntry subpath,
                             QueryBuilder qb,
                             QueryBuilder and,
                             org.hibernate.Session session)
                                  throws GraphException

Deprecated.

Throws:

GraphException

runQuery

protected List<List<Long>> runQuery(String[] sub,
                        GraphEntry subpath,
                        org.hibernate.Query q,
                        org.hibernate.Session session)

Deprecated.

parseResults

protected long[][] parseResults(String[] sub,
                    GraphEntry subpath,
                    List<List<Long>> results)

Deprecated.

queryBackupIds

public long[][] queryBackupIds(org.hibernate.Session session,
                      int step,
                      GraphEntry subpath,
                      QueryBuilder and)
                        throws GraphException

Deprecated.

Description copied from interface: GraphSpec

If a given path is processed before its sub-path, this points to a one-to-one relationship. If the first object is processed without having loaded the later one, then there will be no way to find the dangling object. Therefore, we load those objects first. In the case of superspecs, we also store the root ids for the sub-spec to handle cases such as links, etc. Returns a list of all root ids per step which should be processed. These are precalculated on #initialize(long, Map) so that foreign key constraints which require a higher level object to be processed first, can be processed. For example,

 /Channel
 /Channel/StatsInfo
 

requires the Channel to be processed first, but without the Channel, there's no way to detect which StatsInfo should be removed. Therefore, #backupIds in this case would contain:

 [
  null,      # Nothing for Channel.
  [1,2,3],   # The ids of all StatsInfo object which should be removed.
 ]
 

Specified by:

queryBackupIds in interface GraphSpec

Throws:

GraphException

chgrpQuery

public QueryBuilder chgrpQuery(EventContext ec,
                      String table,
                      GraphOpts opts)

Deprecated.

Description copied from interface: GraphSpec

Return a QueryBuilder which has been properly initialized to take the parameters "id" and "grp" and then have QueryBuilder.query(Session) called.

Specified by:

chgrpQuery in interface GraphSpec

chmodQuery

public QueryBuilder chmodQuery(EventContext ec,
                      String table,
                      GraphOpts opts)

Deprecated.

Specified by:

chmodQuery in interface GraphSpec

deleteQuery

public QueryBuilder deleteQuery(EventContext ec,
                       String table,
                       GraphOpts opts)

Deprecated.

Specified by:

deleteQuery in interface GraphSpec

permissionsClause

public void permissionsClause(EventContext ec,
                     QueryBuilder qb,
                     boolean sqlQuery)

Deprecated.

Appends a clause to the QueryBuilder based on the current user. If the user is an admin like root, then nothing is appended, and any action is permissible. If the user is a leader of the current group, then the object must be in the current group. Otherwise, the object must belong to the current user.

walk

protected void walk(String[] sub,
        GraphEntry entry,
        QueryBuilder qb)
             throws GraphException

Deprecated.

Walks the parts given adding a new relationship between each. If this is a synthetic "Fileset" relationship, use the workaround methods joinDataset(QueryBuilder, String, String) and joinPlate(QueryBuilder, String, String).

Throws:

GraphException

joinDataset

protected void joinDataset(QueryBuilder qb,
               String dataset,
               String fileset)

Deprecated.

joinPlate

protected void joinPlate(QueryBuilder qb,
             String plate,
             String fileset)

Deprecated.

join

protected void join(QueryBuilder qb,
        String from,
        String fromAlias,
        String to,
        String toAlias)
             throws GraphException

Deprecated.

Used to generate a join statement on the QueryBuilder making use of ExtendedMetadata#getRelationship(String, String). If the value returned by that value is null, a {@link GraphException} will be thrown. Otherwise something of the form:

 join FROM.rel as TO
 

will be added to the {@link QueryBuilder}

Throws:

GraphException

toString

public String toString()

Deprecated.

Overrides:

toString in class Object