java.lang.Object
AbstractDataAdapter
org.bdgp.apps.dagedit.dataadapter.PostgresDataAdapter
- All Implemented Interfaces:
- DEDataAdapterI
- public class PostgresDataAdapter
- extends AbstractDataAdapter
- implements DEDataAdapterI
|
Method Summary |
protected void |
addDbxref(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term target,
org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.DbxrefEdit edit,
int operation_id,
int synonym_edit_id,
int synonym_id,
int definition_edit_id,
int definition_id)
|
private void |
buildCatList(java.sql.Statement stmt)
|
private java.util.Hashtable |
buildIDHash(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term root)
|
private void |
buildImpliedDeletes(org.bdgp.apps.dagedit.datamodel.Term term,
java.util.Vector deleted,
java.util.Vector impliedDeletes)
|
private void |
buildRelTypeList(java.sql.Statement stmt)
|
void |
changePassword(java.lang.String newPassword)
|
protected void |
checkConflicts(org.bdgp.apps.dagedit.datamodel.DEEditHistory history,
org.bdgp.apps.dagedit.datamodel.Term currentRoot)
Checks to see if two GO trees are in conflict |
protected void |
clearDatabase(java.sql.Statement stmt)
|
protected static java.lang.String |
convertType(int type)
|
protected static int |
convertType(java.lang.String type)
|
void |
delegateToIDAdapter(DEDataAdapterI idAdapter)
|
protected void |
deleteDbxref(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term target,
org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.DbxrefEdit edit,
int operation_id,
int synonym_edit_id,
int synonym_id,
int definition_edit_id,
int definition_id)
|
protected void |
doCleanup(java.sql.Connection con)
|
protected static java.util.Date |
extractDate(java.lang.String date)
|
protected java.lang.String |
formatString(java.lang.String in)
|
java.util.Vector |
getAllTerms()
|
protected java.util.Hashtable |
getCategoryIndex(java.sql.Statement stmt)
|
protected java.util.Vector |
getChildConflicts(org.bdgp.apps.dagedit.datamodel.Term oldTerm,
org.bdgp.apps.dagedit.datamodel.Term newTerm)
|
java.sql.Connection |
getConnection()
|
protected int |
getDatabaseIDForTerm(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term term)
|
java.util.Vector |
getHistories()
|
private static org.bdgp.apps.dagedit.datamodel.HistoryItem |
getHistoryItem(PostgresDataAdapter.OperationWrapper ow,
java.sql.Statement stmt,
java.util.Hashtable allterms_hash,
int session_id,
int ordernum,
int parent_operation_id)
|
static org.bdgp.apps.dagedit.datamodel.HistoryItem |
getHistoryItemForID(java.sql.Statement stmt,
java.util.Hashtable allterms_hash,
int session_id,
int ordernum,
int parent_operation_id)
|
java.lang.String[] |
getIDs(org.bdgp.apps.dagedit.datamodel.Term root,
org.bdgp.apps.dagedit.datamodel.Term term,
java.lang.String prefix,
int length,
int count)
|
java.lang.String[] |
getIDs(org.bdgp.apps.dagedit.datamodel.Term root,
org.bdgp.apps.dagedit.datamodel.Term term,
java.lang.String prefix,
int min,
int max,
int length,
int count)
|
protected static java.lang.Integer |
getInteger(java.sql.ResultSet rs,
java.lang.String fieldName)
|
protected static int |
getIntForType(org.bdgp.apps.dagedit.datamodel.TermRelationshipType type)
|
java.lang.String |
getName()
|
protected java.util.Vector |
getParentConflicts(org.bdgp.apps.dagedit.datamodel.Term oldTerm,
org.bdgp.apps.dagedit.datamodel.Term newTerm)
|
private java.lang.String |
getPrettyTermName(org.bdgp.apps.dagedit.datamodel.Term term)
|
protected static int |
getRefEditType(java.lang.String keyTypeString)
|
static org.bdgp.apps.dagedit.datamodel.TermRelationshipType |
getRelationshipTypeForID(java.sql.Statement stmt,
int id)
|
java.util.Vector |
getRelationshipTypes()
|
protected java.util.Hashtable |
getRelTypeIndex(java.sql.Statement stmt)
|
org.bdgp.apps.dagedit.datamodel.DEEditHistory |
getRoot()
|
org.bdgp.apps.dagedit.datamodel.DEEditHistory |
getRoot(boolean showProgress)
|
org.bdgp.apps.dagedit.datamodel.DEEditHistory |
getRoot(java.sql.Connection con,
boolean showProgress)
|
java.util.Properties |
getStateInformation()
|
IOOperation[] |
getSupportedOperations()
|
java.util.Vector |
getTermCategories()
|
static org.bdgp.apps.dagedit.datamodel.Term |
getTermForID(java.sql.Statement stmt,
int id)
|
java.lang.String |
getType()
|
protected static org.bdgp.apps.dagedit.datamodel.TermRelationshipType |
getTypeForInt(int type_id)
|
DataAdapterUI |
getUI(IOOperation op)
|
void |
init()
|
void |
init(java.lang.String driver,
java.lang.String url)
|
void |
init(java.lang.String driver,
java.lang.String url,
java.lang.String username,
java.lang.String password)
|
protected int |
loadDbxref(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Dbxref ref)
|
void |
readTerms(java.sql.Connection con)
|
void |
readTerms(java.sql.Connection con,
boolean showProgress)
|
protected void |
setDefaultType(org.bdgp.apps.dagedit.datamodel.TermRelationshipType defaultType)
|
void |
setForceHistory(boolean forceHistory)
|
void |
setRepopulate(boolean repopulate)
|
void |
setSaveComment(java.lang.String saveComment)
|
void |
setStateInformation(java.util.Properties props)
|
org.bdgp.apps.dagedit.datamodel.DEEditHistory |
write(org.bdgp.apps.dagedit.datamodel.DEEditHistory history)
|
void |
write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.HistoryItem item,
int index,
int parent_operation_id)
|
void |
write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermAddHistoryItem item,
int index,
int parent_operation_id)
|
void |
write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermCommitAndObsoleteHistoryItem item,
int index,
int parent_operation_id)
|
void |
write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermCopyHistoryItem item,
int index,
int parent_operation_id)
|
void |
write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermDeleteHistoryItem item,
int index,
int parent_operation_id)
|
void |
write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermMacroHistoryItem item,
int index,
int parent_operation_id)
|
void |
write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermMergeHistoryItem item,
int index,
int parent_operation_id)
|
void |
write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermMoveHistoryItem item,
int index,
int parent_operation_id)
|
void |
write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermRelationshipHistoryItem item,
int index,
int parent_operation_id)
|
void |
write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermSplitHistoryItem item,
int index,
int parent_operation_id)
|
void |
write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem item,
int index,
int parent_operation_id)
|
protected void |
writeCategories(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term target,
org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.CategoryEdit edit,
int operation_id,
int session_id,
java.util.Hashtable catIndex)
|
protected void |
writeComment(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term target)
|
protected void |
writeDbxrefs(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term target,
org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.DbxrefEdit edit,
int operation_id,
int session_id,
int synonym_edit_id,
int synonym_id,
int definition_edit_id,
int definition_id)
|
protected int |
writeDefinition(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term target)
|
protected void |
writeRelationships(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term term)
|
protected int |
writeSubtree(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term term,
boolean fireProgressEvents)
|
protected void |
writeSynonyms(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term target,
org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.SynonymEdit edit,
int operation_id,
int session_id)
|
protected int |
writeTerm(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term term)
|
protected int |
writeTermAndRelationships(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term term)
|
protected void |
writeTermText(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term target)
|
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
PERCENT_INC
private static int PERCENT_INC
dateFormat
private static final java.text.DateFormat dateFormat
driver
private java.lang.String driver
url
private java.lang.String url
username
private java.lang.String username
password
private java.lang.String password
driverLoaded
private boolean driverLoaded
saveComment
private java.lang.String saveComment
root_term
private org.bdgp.apps.dagedit.datamodel.Term root_term
allterms_hash
private java.util.Hashtable allterms_hash
databaseIDHash
private java.util.Hashtable databaseIDHash
idAdapter
private DEDataAdapterI idAdapter
repopulate
boolean repopulate
forceHistory
boolean forceHistory
defaultType
protected org.bdgp.apps.dagedit.datamodel.TermRelationshipType defaultType
catHash
private java.util.Hashtable catHash
catList
private java.util.Vector catList
relTypeHash
private static java.util.Hashtable relTypeHash
relTypeList
private java.util.Vector relTypeList
lastModified
java.util.Date lastModified
lastUser
java.lang.String lastUser
lastComment
java.lang.String lastComment
lastVersion
java.lang.String lastVersion
PostgresDataAdapter
public PostgresDataAdapter()
setForceHistory
public void setForceHistory(boolean forceHistory)
setDefaultType
protected void setDefaultType(org.bdgp.apps.dagedit.datamodel.TermRelationshipType defaultType)
doCleanup
protected void doCleanup(java.sql.Connection con)
throws java.sql.SQLException
extractDate
protected static java.util.Date extractDate(java.lang.String date)
getRelationshipTypes
public java.util.Vector getRelationshipTypes()
throws DataAdapterException
- Specified by:
getRelationshipTypes in interface DEDataAdapterI
convertType
protected static java.lang.String convertType(int type)
convertType
protected static int convertType(java.lang.String type)
setRepopulate
public void setRepopulate(boolean repopulate)
getName
public java.lang.String getName()
getType
public java.lang.String getType()
getIDs
public java.lang.String[] getIDs(org.bdgp.apps.dagedit.datamodel.Term root,
org.bdgp.apps.dagedit.datamodel.Term term,
java.lang.String prefix,
int length,
int count)
throws DataAdapterException
- Specified by:
getIDs in interface DEDataAdapterI
getIDs
public java.lang.String[] getIDs(org.bdgp.apps.dagedit.datamodel.Term root,
org.bdgp.apps.dagedit.datamodel.Term term,
java.lang.String prefix,
int min,
int max,
int length,
int count)
throws DataAdapterException
- Specified by:
getIDs in interface DEDataAdapterI
buildIDHash
private java.util.Hashtable buildIDHash(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term root)
throws java.sql.SQLException
clearDatabase
protected void clearDatabase(java.sql.Statement stmt)
throws java.sql.SQLException
checkConflicts
protected void checkConflicts(org.bdgp.apps.dagedit.datamodel.DEEditHistory history,
org.bdgp.apps.dagedit.datamodel.Term currentRoot)
throws PostgresDataAdapter.ConflictException
- Checks to see if two GO trees are in conflict
getPrettyTermName
private java.lang.String getPrettyTermName(org.bdgp.apps.dagedit.datamodel.Term term)
getParentConflicts
protected java.util.Vector getParentConflicts(org.bdgp.apps.dagedit.datamodel.Term oldTerm,
org.bdgp.apps.dagedit.datamodel.Term newTerm)
getChildConflicts
protected java.util.Vector getChildConflicts(org.bdgp.apps.dagedit.datamodel.Term oldTerm,
org.bdgp.apps.dagedit.datamodel.Term newTerm)
getHistoryItem
private static org.bdgp.apps.dagedit.datamodel.HistoryItem getHistoryItem(PostgresDataAdapter.OperationWrapper ow,
java.sql.Statement stmt,
java.util.Hashtable allterms_hash,
int session_id,
int ordernum,
int parent_operation_id)
getTypeForInt
protected static org.bdgp.apps.dagedit.datamodel.TermRelationshipType getTypeForInt(int type_id)
getIntForType
protected static int getIntForType(org.bdgp.apps.dagedit.datamodel.TermRelationshipType type)
getRefEditType
protected static int getRefEditType(java.lang.String keyTypeString)
getTermForID
public static org.bdgp.apps.dagedit.datamodel.Term getTermForID(java.sql.Statement stmt,
int id)
throws java.sql.SQLException
getRelationshipTypeForID
public static org.bdgp.apps.dagedit.datamodel.TermRelationshipType getRelationshipTypeForID(java.sql.Statement stmt,
int id)
throws java.sql.SQLException
getHistoryItemForID
public static org.bdgp.apps.dagedit.datamodel.HistoryItem getHistoryItemForID(java.sql.Statement stmt,
java.util.Hashtable allterms_hash,
int session_id,
int ordernum,
int parent_operation_id)
throws java.sql.SQLException
getInteger
protected static java.lang.Integer getInteger(java.sql.ResultSet rs,
java.lang.String fieldName)
throws java.sql.SQLException
getHistories
public java.util.Vector getHistories()
throws DataAdapterException
- Specified by:
getHistories in interface DEDataAdapterI
write
public org.bdgp.apps.dagedit.datamodel.DEEditHistory write(org.bdgp.apps.dagedit.datamodel.DEEditHistory history)
throws DataAdapterException
- Specified by:
write in interface DEDataAdapterI
delegateToIDAdapter
public void delegateToIDAdapter(DEDataAdapterI idAdapter)
- Specified by:
delegateToIDAdapter in interface DEDataAdapterI
write
public void write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermMergeHistoryItem item,
int index,
int parent_operation_id)
throws java.sql.SQLException
write
public void write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermMacroHistoryItem item,
int index,
int parent_operation_id)
throws java.sql.SQLException,
DataAdapterException
write
public void write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermCommitAndObsoleteHistoryItem item,
int index,
int parent_operation_id)
throws java.sql.SQLException
writeRelationships
protected void writeRelationships(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term term)
throws java.sql.SQLException
writeSubtree
protected int writeSubtree(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term term,
boolean fireProgressEvents)
throws java.sql.SQLException
writeTermAndRelationships
protected int writeTermAndRelationships(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term term)
throws java.sql.SQLException
loadDbxref
protected int loadDbxref(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Dbxref ref)
throws java.sql.SQLException
writeTerm
protected int writeTerm(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term term)
throws java.sql.SQLException
write
public void write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermSplitHistoryItem item,
int index,
int parent_operation_id)
throws java.sql.SQLException
write
public void write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermCopyHistoryItem item,
int index,
int parent_operation_id)
throws java.sql.SQLException
write
public void write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermMoveHistoryItem item,
int index,
int parent_operation_id)
throws java.sql.SQLException
buildImpliedDeletes
private void buildImpliedDeletes(org.bdgp.apps.dagedit.datamodel.Term term,
java.util.Vector deleted,
java.util.Vector impliedDeletes)
write
public void write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermRelationshipHistoryItem item,
int index,
int parent_operation_id)
throws java.sql.SQLException
write
public void write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermDeleteHistoryItem item,
int index,
int parent_operation_id)
throws java.sql.SQLException
write
public void write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.HistoryItem item,
int index,
int parent_operation_id)
throws DataAdapterException,
java.sql.SQLException
write
public void write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermAddHistoryItem item,
int index,
int parent_operation_id)
throws java.sql.SQLException
getDatabaseIDForTerm
protected int getDatabaseIDForTerm(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term term)
throws java.sql.SQLException
write
public void write(java.sql.Statement stmt,
int session_id,
org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem item,
int index,
int parent_operation_id)
throws java.sql.SQLException
addDbxref
protected void addDbxref(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term target,
org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.DbxrefEdit edit,
int operation_id,
int synonym_edit_id,
int synonym_id,
int definition_edit_id,
int definition_id)
throws java.sql.SQLException
deleteDbxref
protected void deleteDbxref(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term target,
org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.DbxrefEdit edit,
int operation_id,
int synonym_edit_id,
int synonym_id,
int definition_edit_id,
int definition_id)
throws java.sql.SQLException
writeDbxrefs
protected void writeDbxrefs(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term target,
org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.DbxrefEdit edit,
int operation_id,
int session_id,
int synonym_edit_id,
int synonym_id,
int definition_edit_id,
int definition_id)
throws java.sql.SQLException
writeSynonyms
protected void writeSynonyms(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term target,
org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.SynonymEdit edit,
int operation_id,
int session_id)
throws java.sql.SQLException
getTermCategories
public java.util.Vector getTermCategories()
throws DataAdapterException
- Specified by:
getTermCategories in interface DEDataAdapterI
buildRelTypeList
private void buildRelTypeList(java.sql.Statement stmt)
throws java.sql.SQLException
getRelTypeIndex
protected java.util.Hashtable getRelTypeIndex(java.sql.Statement stmt)
throws java.sql.SQLException
buildCatList
private void buildCatList(java.sql.Statement stmt)
throws java.sql.SQLException
getCategoryIndex
protected java.util.Hashtable getCategoryIndex(java.sql.Statement stmt)
throws java.sql.SQLException
writeCategories
protected void writeCategories(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term target,
org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.CategoryEdit edit,
int operation_id,
int session_id,
java.util.Hashtable catIndex)
throws java.sql.SQLException
writeDefinition
protected int writeDefinition(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term target)
throws java.sql.SQLException
writeComment
protected void writeComment(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term target)
throws java.sql.SQLException
writeTermText
protected void writeTermText(java.sql.Statement stmt,
org.bdgp.apps.dagedit.datamodel.Term target)
throws java.sql.SQLException
formatString
protected java.lang.String formatString(java.lang.String in)
getSupportedOperations
public IOOperation[] getSupportedOperations()
getUI
public DataAdapterUI getUI(IOOperation op)
getConnection
public java.sql.Connection getConnection()
throws java.sql.SQLException,
java.lang.ClassNotFoundException
changePassword
public void changePassword(java.lang.String newPassword)
throws DataAdapterException
init
public void init()
init
public void init(java.lang.String driver,
java.lang.String url)
init
public void init(java.lang.String driver,
java.lang.String url,
java.lang.String username,
java.lang.String password)
setSaveComment
public void setSaveComment(java.lang.String saveComment)
readTerms
public void readTerms(java.sql.Connection con)
throws java.sql.SQLException,
java.lang.ClassNotFoundException
readTerms
public void readTerms(java.sql.Connection con,
boolean showProgress)
throws java.sql.SQLException,
java.lang.ClassNotFoundException
getRoot
public org.bdgp.apps.dagedit.datamodel.DEEditHistory getRoot()
throws DataAdapterException
- Specified by:
getRoot in interface DEDataAdapterI
getRoot
public org.bdgp.apps.dagedit.datamodel.DEEditHistory getRoot(boolean showProgress)
throws DataAdapterException
getRoot
public org.bdgp.apps.dagedit.datamodel.DEEditHistory getRoot(java.sql.Connection con,
boolean showProgress)
throws DataAdapterException
getAllTerms
public java.util.Vector getAllTerms()
getStateInformation
public java.util.Properties getStateInformation()
- Specified by:
getStateInformation in interface DEDataAdapterI
setStateInformation
public void setStateInformation(java.util.Properties props)
- Specified by:
setStateInformation in interface DEDataAdapterI