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java.lang.Objectgov.nih.nci.caarray.services.util.db.ManagerDB
gov.nih.nci.caarray.services.vocab.VocabManagerDB
public class VocabManagerDB
Field Summary |
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Fields inherited from class gov.nih.nci.caarray.services.util.db.ManagerDB |
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CASCADE_LINK, CASCADE_NONE, CASCADE_OBJECT, ID_UNSET |
Constructor Summary | |
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VocabManagerDB()
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Method Summary | |
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long |
addOntology(OntologyEntry entry)
|
long |
addOntology(OntologyEntry entry,
long parentOntologyEntryId)
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void |
addOrSyncAnnotations(Describable describable)
Adds or synchronizes the vocabularies that represent the annotations of the specified Describable object. |
void |
addOrUpdateActionProtocolTypeMap(ActionProtocolTypeMap map)
Adds or updates the association object between an action represented by an OntologyEntry and one or more protocol types represented
by OntologyEntry 's. |
int |
countOntologies(VocabSearchCriteria searchCriteria)
|
boolean |
deleteOntology(long vocabId)
|
ActionProtocolTypeMap[] |
getActionProtocolTypeMaps()
Retrieves all available ActionProtocolTypeMap 's. |
Database[] |
getDatabases()
|
Database[] |
getDatabases(java.lang.String category,
java.lang.Boolean userDefined)
|
OntologyEntry[] |
getOntologies(long parentVocabId)
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OntologyEntry[] |
getOntologies(VocabSearchCriteria criteria)
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OntologyEntry |
getOntology(long id)
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OntologyEntry |
getOntology(java.lang.String category,
java.lang.String value)
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OntologyEntry |
getOntologyEntryOrNull(java.lang.String category,
java.lang.String value)
Returns the requested OntologyEntry or null if not found. |
OntologyEntry[] |
getProtocolTypes(long actionId)
Retrieves the list of protocol types that are mapped to the specified action. |
void |
syncExperimentDesignTypes(ExperimentDesign design)
Add or synchronize the vocabularies that represent the annotations of the specified Describable object. |
void |
updateOntology(OntologyEntry entry)
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Methods inherited from class gov.nih.nci.caarray.services.util.db.ManagerDB |
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clearCache, close, countObjects, countObjects, deleteByQuery, deleteMtoNRelation, deleteObject, deleteObject, deleteObject, deleteObjectByQuery, exists, getIdentifiable, getObject, getObject, getObject, getObject, getObject, getObject, getObjectIterator, getObjectIterator, getObjects, getObjects, getObjects, getPersistenceBroker, getSqlInLimit, insertMtoNRelation, insertMtoNRelation, insertObject, insertObject, link, link, removeFromCache, retrieveReference, retrieveReferences, setCascadeDelete, setCascadeRetrieve, setCascadeStore, storeObject, storeObject, unlink, unlink, updateObject, updateObject |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public VocabManagerDB()
Method Detail |
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public OntologyEntry getOntology(long id) throws java.lang.Exception
category
-
java.lang.Exception
public OntologyEntry[] getOntologies(VocabSearchCriteria criteria) throws java.lang.Exception
ojbCriteria
-
java.lang.Exception
public OntologyEntry getOntology(java.lang.String category, java.lang.String value) throws java.lang.Exception
java.lang.Exception
public OntologyEntry getOntologyEntryOrNull(java.lang.String category, java.lang.String value) throws java.lang.Exception
category
- category to findvalue
- value to find
java.lang.Exception
public OntologyEntry[] getOntologies(long parentVocabId) throws java.lang.Exception
java.lang.Exception
public long addOntology(OntologyEntry entry) throws java.lang.Exception
ontologyEntry
-
java.lang.Exception
public long addOntology(OntologyEntry entry, long parentOntologyEntryId) throws java.lang.Exception
ontologyEntry
-
java.lang.Exception
public boolean deleteOntology(long vocabId) throws java.lang.Exception
vocabId
-
java.lang.Exception
public void updateOntology(OntologyEntry entry) throws java.lang.Exception
entry
-
java.lang.Exception
public void addOrSyncAnnotations(Describable describable) throws java.lang.Exception
Describable
object. If a vocabulary already
exists, this method attempts to synchronize it with the one from the
persistence store. If it doesn't exist, it is inserted it contains
the necessary data.
describable
-
InsertObjectException
java.lang.Exception
public void syncExperimentDesignTypes(ExperimentDesign design) throws java.lang.Exception
Describable
object. If a vocabulary already
exists, this method attempts to synchronize it with the one from the
persistence store. If it doesn't exist, it is inserted it contains
the necessary data.
describable
-
InsertObjectException
java.lang.Exception
public int countOntologies(VocabSearchCriteria searchCriteria) throws java.lang.Exception
java.lang.Exception
public OntologyEntry[] getProtocolTypes(long actionId) throws java.lang.Exception
actionId
-
java.lang.Exception
public void addOrUpdateActionProtocolTypeMap(ActionProtocolTypeMap map) throws java.lang.Exception
OntologyEntry
and one or more protocol types represented
by OntologyEntry
's.
map
- - The association object describing which action maps to
which protocol types.
java.lang.Exception
public ActionProtocolTypeMap[] getActionProtocolTypeMaps() throws java.lang.Exception
ActionProtocolTypeMap
's.
java.lang.Exception
public Database[] getDatabases(java.lang.String category, java.lang.Boolean userDefined) throws java.lang.Exception
java.lang.Exception
public Database[] getDatabases() throws java.lang.Exception
java.lang.Exception
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