apollo.dataadapter.chado.jdbc
Class PureJDBCTransactionWriter

java.lang.Object
  apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

Direct Known Subclasses:

JdbcChadoWriter

public class PureJDBCTransactionWriter
extends java.lang.Object

An alternative to JDBCTransactionWriter that:

• Does not require any triggers to be defined in the database
• Keeps all of the SQL and database access code localized to JdbcChadoAdapter and its subclasses
• Supports two update modes: in-place update and copy-on-write

Version:

$Revision: 1.37 $ $Date: 2009-06-25 17:26:50 $ $Author: gk_fan $

Author:

Jonathan Crabtree

Field Summary

protected ChadoAdapter	adapter
protected boolean	copyOnWrite
protected JdbcChadoAdapter	jdbcAdapter
protected boolean	logApolloTransactions
protected static org.apache.log4j.Logger	logger
protected boolean	logSql
protected boolean	noCommit
protected boolean	useCDS

Constructor Summary

PureJDBCTransactionWriter(ChadoAdapter adapter, JdbcChadoAdapter jdbcAdapter, boolean copyOnWrite, boolean noCommit, boolean useCDS)

Method Summary

protected boolean	addComment(long annotId, Comment comment) Add a comment to the database
protected boolean	addComment(SeqFeatureI feature, AddTransaction t) Comment strings look like this: Only one EST supports this alternative transcript::DATE:Mon Feb 26 18:08:49 CET 2007::TS:1172509728919 With the author in the pub table
protected void	addComments(AnnotatedFeatureI annot) Add all comments from an AnnotatedFeatureI object
protected boolean	addDbXref(long featureId, DbXref dbx)
protected boolean	addDbXref(SeqFeatureI feature, AddTransaction t)
protected void	addDbxrefs(AnnotatedFeatureI annot) Add all dbxrefs from an AnnotatedFeatureI object
protected java.lang.Long	addExon(SeqFeatureI exon, java.lang.String author, java.util.Date date, java.lang.Long transId, int exonNum, apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature, boolean checkExons) Add an exon to a transcript, inserting the exon into the database if it does not already exist.
protected java.lang.Long	addGene(SeqFeatureI gene, java.lang.String author, java.util.Date date, apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature, boolean checkExons) Add a gene to the chado database.
protected java.lang.Long	addSequenceEdit(SequenceEdit seqEdit, java.lang.String author, java.util.Date date)
protected boolean	addSynonym(long annotId, java.lang.String name) Add a synonym to the database
protected boolean	addSynonym(SeqFeatureI feature, AddTransaction t)
protected void	addSynonyms(AnnotatedFeatureI annot) Add all synonyms from an AnnotatedFeatureI object
protected java.lang.Long	addTopLevelAnnot(SeqFeatureI annot, java.lang.String author, java.util.Date date, apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature) Add a top level annotation to the chado database.
protected java.lang.Long	addTranscript(Transcript transcript, java.lang.String author, java.util.Date date, java.lang.Long geneId, long transcriptRank, apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature, boolean checkExons) Add a transcript to the chado database.
protected boolean	commitAddTransaction(java.lang.String transId, AddTransaction t, boolean checkExons)
protected boolean	commitDeleteTransaction(java.lang.String transId, DeleteTransaction dt)
protected boolean	commitTransaction(java.lang.String transId, int numTransactions, Transaction t, boolean checkExons)
boolean	commitTransactions(TransactionManager tm) Write a set of transactions to the database using adapter
protected boolean	commitUpdateParentTransaction(java.lang.String transId, UpdateParentTransaction t)
protected boolean	commitUpdateTransaction(java.lang.String transId, UpdateTransaction ut)
protected boolean	deleteCDS(long featureId)
protected boolean	deleteComment(long annotId, Comment comment)
protected boolean	deleteDbXref(long annotId, DbXref dbXref)
protected boolean	deleteExon(long exonId, long transcriptId) Delete an exon from the database (defaults to not checking if it is a shared exon
protected boolean	deleteExon(long exonId, long transcriptId, boolean checkExon) Delete an exon from the database
protected boolean	deleteGene(long featureId)
protected boolean	deletePolypeptide(long featureId)
protected boolean	deleteSynonym(long annotId, java.lang.String name) Delete a synonym from the database
protected boolean	deleteTranscript(long featureId)
protected boolean	deleteTranscript(long featureId, boolean checkExons)
protected void	fatalError(java.lang.String error)
protected apollo.dataadapter.chado.jdbc.ChadoCds	getCdsCoordinatesFromTranscript(Transcript transcript, int tfmin, int tfmax) Figure out chado CDS coordinates and sequence based on the Apollo transcript.
protected java.lang.String	getChadoCdsName(ApolloNameAdapterI nameAdapter, java.lang.String name)
protected long	getChadoFeatureId(SeqFeatureI feature)
protected long	getChadoIdForFeature(SeqFeatureI f) Retrieve the chado primary key value for a given feature, or -1 if the feature does not exist in the database.
protected int	getChadoIsAnalysis(SeqFeatureI feat) Determine what value to place in the chado feature.is_analysis column for an Apollo feature.
protected int	getChadoLocgroup(long feature_id, apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature)
protected int	getChadoLocgroup(SeqFeatureI feat, apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature) Compute the chado featureloc.locgroup for an Apollo feature.
protected java.lang.String	getChadoPeptideName(ApolloNameAdapterI nameAdapter, java.lang.String name, SeqFeatureI pfeat)
protected java.lang.Long	getChadoPrimaryDbxrefId(SeqFeatureI feat) Determine what to put in the feature.dbxref_id column for an Apollo feature.
protected java.lang.Long	getChadoRelationshipCvTermId(java.lang.String cvName)
protected java.lang.String	getChadoResidues(SeqFeatureI feat) Determine what value to place in the chado feature.residues column for an Apollo feature.
protected AnnotatedFeatureI	getSeqEditRefFeature(SequenceEdit seqEdit)
protected void	logTransactionList(java.util.List tlist)
protected boolean	updateCdsFeatureLocation(long featureId, Transcript transcript, RangeI oldLocn) Update the location of a transcript's CDS and polypeptide.
protected boolean	updateFeatureLocation(long featureId, RangeI oldLocn, apollo.dataadapter.chado.jdbc.ChadoFeatureLoc newLoc) Update the location of a gene-related feature, e.g.
protected boolean	updateFeatureName(long featureId, java.lang.String newName, boolean isName) Update the name
protected boolean	updateFeatureType(long featureId, java.lang.String newType) Update the type
protected boolean	updateOwner(long annotId, java.lang.String newStatus, java.lang.String oldStatus)
protected boolean	updateStatus(long annotId, java.lang.String statusTerm, java.lang.String newStatus, java.lang.String oldStatus)

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

adapter

protected ChadoAdapter adapter

jdbcAdapter

protected JdbcChadoAdapter jdbcAdapter

copyOnWrite

protected boolean copyOnWrite

noCommit

protected boolean noCommit

logApolloTransactions

protected boolean logApolloTransactions

logSql

protected boolean logSql

useCDS

protected boolean useCDS

Constructor Detail

PureJDBCTransactionWriter

public PureJDBCTransactionWriter(ChadoAdapter adapter,
                                 JdbcChadoAdapter jdbcAdapter,
                                 boolean copyOnWrite,
                                 boolean noCommit,
                                 boolean useCDS)

Parameters:

adapter - ChadoAdapter to use for writing changes

jdbcAdapter - JdbcChadoAdapter to use for writing changes

copyOnWrite - Whether to keep a copy of the old object(s) when writing changes.

noCommit - Whether to run in 'no commit' mode.

Method Detail

commitTransactions

public boolean commitTransactions(TransactionManager tm)

Write a set of transactions to the database using adapter

Parameters:

tm - TransactionManager that contains the uncommitted transactions to write.

Returns:

Whether the commit succeeded.

logTransactionList

protected void logTransactionList(java.util.List tlist)

commitTransaction

protected boolean commitTransaction(java.lang.String transId,
                                    int numTransactions,
                                    Transaction t,
                                    boolean checkExons)

Parameters:

checkExons - whether to check database for exons in addExon

getChadoFeatureId

protected long getChadoFeatureId(SeqFeatureI feature)

Returns:

The chado feature_id or -1 if it could not be determined.

commitUpdateParentTransaction

protected boolean commitUpdateParentTransaction(java.lang.String transId,
                                                UpdateParentTransaction t)

commitAddTransaction

protected boolean commitAddTransaction(java.lang.String transId,
                                       AddTransaction t,
                                       boolean checkExons)

Parameters:

checkExons - whether to check database for exons in addExon

addTopLevelAnnot

protected java.lang.Long addTopLevelAnnot(SeqFeatureI annot,
                                          java.lang.String author,
                                          java.util.Date date,
                                          apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature)

Add a top level annotation to the chado database.

Parameters:

annot - Apollo feature that represents the top level annotation

author - Author string from the Apollo transaction.

date - Date from the Apollo transaction.

srcFeature - Chado feature on which the gene is located. May be null.

Returns:

The chado feature.feature_id of the gene feature.

addGene

protected java.lang.Long addGene(SeqFeatureI gene,
                                 java.lang.String author,
                                 java.util.Date date,
                                 apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature,
                                 boolean checkExons)

Add a gene to the chado database.

Parameters:

gene - Apollo feature that represents the gene.

author - Author string from the Apollo transaction.

date - Date from the Apollo transaction.

srcFeature - Chado feature on which the gene is located. May be null.

checkExons - whether to check database for exons in addExon

Returns:

The chado feature.feature_id of the gene feature.

addTranscript

protected java.lang.Long addTranscript(Transcript transcript,
                                       java.lang.String author,
                                       java.util.Date date,
                                       java.lang.Long geneId,
                                       long transcriptRank,
                                       apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature,
                                       boolean checkExons)

Add a transcript to the chado database.

Parameters:

transcript - Apollo feature that represents the transcript/mRNA.

author - Author string from the Apollo transaction.

date - Date from the Apollo transaction.

geneId - Chado feature.feature_id of the gene to which the transcript belongs.

transcriptRank - Rank of the transcript with respect to the gene.

srcFeature - Chado feature on which the transcript is located. May be null.

checkExons - whether to check database for exons in addExon

Returns:

The chado feature.feature_id of the transcript feature.

addExon

protected java.lang.Long addExon(SeqFeatureI exon,
                                 java.lang.String author,
                                 java.util.Date date,
                                 java.lang.Long transId,
                                 int exonNum,
                                 apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature,
                                 boolean checkExons)

Add an exon to a transcript, inserting the exon into the database if it does not already exist.

Parameters:

exon - Apollo feature that represents the exon.

author - Author string from the Apollo transaction.

date - Date from the Apollo transaction.

transId - Chado feature.feature_id of the transcript to which the exon belongs.

exonNum - Index of the exon in the transcript (counting from 0, as per chado feature_relationship.rank)

srcFeature - Chado feature on which the exon is located. May be null.

checkExons - whether to check database for exons in addExon

Returns:

The chado feature.feature_id of the exon feature.

addSynonym

protected boolean addSynonym(SeqFeatureI feature,
                             AddTransaction t)

addComment

protected boolean addComment(SeqFeatureI feature,
                             AddTransaction t)

Comment strings look like this: Only one EST supports this alternative transcript::DATE:Mon Feb 26 18:08:49 CET 2007::TS:1172509728919 With the author in the pub table

addDbxrefs

protected void addDbxrefs(AnnotatedFeatureI annot)

Add all dbxrefs from an AnnotatedFeatureI object

Parameters:

annot - - annotation to store dbxrefs from

addDbXref

protected boolean addDbXref(SeqFeatureI feature,
                            AddTransaction t)

addDbXref

protected boolean addDbXref(long featureId,
                            DbXref dbx)

deleteDbXref

protected boolean deleteDbXref(long annotId,
                               DbXref dbXref)

addSequenceEdit

protected java.lang.Long addSequenceEdit(SequenceEdit seqEdit,
                                         java.lang.String author,
                                         java.util.Date date)

getChadoLocgroup

protected int getChadoLocgroup(SeqFeatureI feat,
                               apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature)

Compute the chado featureloc.locgroup for an Apollo feature.

Parameters:

feat - Apollo feature.

srcFeature - Chado feature on which feat is located (determines locgroup).

getChadoLocgroup

protected int getChadoLocgroup(long feature_id,
                               apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature)

getChadoPrimaryDbxrefId

protected java.lang.Long getChadoPrimaryDbxrefId(SeqFeatureI feat)

Determine what to put in the feature.dbxref_id column for an Apollo feature.

Parameters:

feat - Apollo feature.

getChadoIsAnalysis

protected int getChadoIsAnalysis(SeqFeatureI feat)

Determine what value to place in the chado feature.is_analysis column for an Apollo feature.

Parameters:

feat - Apollo feature.

getChadoResidues

protected java.lang.String getChadoResidues(SeqFeatureI feat)

Determine what value to place in the chado feature.residues column for an Apollo feature.

Parameters:

feat - Apollo feature

getChadoRelationshipCvTermId

protected java.lang.Long getChadoRelationshipCvTermId(java.lang.String cvName)

commitDeleteTransaction

protected boolean commitDeleteTransaction(java.lang.String transId,
                                          DeleteTransaction dt)

deleteExon

protected boolean deleteExon(long exonId,
                             long transcriptId)

Delete an exon from the database (defaults to not checking if it is a shared exon

Parameters:

exonId - - feature.feature_id of the exon

transcriptId - - feature.feature_id of the parent transcript

Returns:

whether the exon was successfully deleted

deleteExon

protected boolean deleteExon(long exonId,
                             long transcriptId,
                             boolean checkExon)

Delete an exon from the database

Parameters:

exonId - - feature.feature_id of the exon

transcriptId - - feature.feature_id of the parent transcript

checkExon - - check to see that this exon is not shared before deletion

Returns:

whether the exon was successfully deleted

deleteTranscript

protected boolean deleteTranscript(long featureId)

deleteTranscript

protected boolean deleteTranscript(long featureId,
                                   boolean checkExons)

deleteCDS

protected boolean deleteCDS(long featureId)

deletePolypeptide

protected boolean deletePolypeptide(long featureId)

deleteGene

protected boolean deleteGene(long featureId)

commitUpdateTransaction

protected boolean commitUpdateTransaction(java.lang.String transId,
                                          UpdateTransaction ut)

updateCdsFeatureLocation

protected boolean updateCdsFeatureLocation(long featureId,
                                           Transcript transcript,
                                           RangeI oldLocn)

Update the location of a transcript's CDS and polypeptide.

Parameters:

featureId - Chado feature id that corresponds to transcript

transcript - Apollo transcript whose peptide has changed

oldLocn - The range of the old CDS feature location. MAY BE NULL.

updateFeatureLocation

protected boolean updateFeatureLocation(long featureId,
                                        RangeI oldLocn,
                                        apollo.dataadapter.chado.jdbc.ChadoFeatureLoc newLoc)

Update the location of a gene-related feature, e.g. exon, transcript, or gene

updateFeatureName

protected boolean updateFeatureName(long featureId,
                                    java.lang.String newName,
                                    boolean isName)

Update the name

updateFeatureType

protected boolean updateFeatureType(long featureId,
                                    java.lang.String newType)

Update the type

fatalError

protected void fatalError(java.lang.String error)

getChadoIdForFeature

protected long getChadoIdForFeature(SeqFeatureI f)

Retrieve the chado primary key value for a given feature, or -1 if the feature does not exist in the database. TODO - move this into the name adapter; could be different for different sites/dbs. see earlier comments

getCdsCoordinatesFromTranscript

protected apollo.dataadapter.chado.jdbc.ChadoCds getCdsCoordinatesFromTranscript(Transcript transcript,
                                                                                 int tfmin,
                                                                                 int tfmax)

Figure out chado CDS coordinates and sequence based on the Apollo transcript. In Apollo the CDS feature coordinates are genomic coordinates corresponding to the 1st base of the start codon and the 1st base of the stop codon, respectively

addSynonyms

protected void addSynonyms(AnnotatedFeatureI annot)

Add all synonyms from an AnnotatedFeatureI object

Parameters:

annot - - annotation to store synonyms from

addSynonym

protected boolean addSynonym(long annotId,
                             java.lang.String name)

Add a synonym to the database

Parameters:

annotId - - Chado ID for owner annotation

name - - Synonym

Returns:

true if successful

deleteSynonym

protected boolean deleteSynonym(long annotId,
                                java.lang.String name)

Delete a synonym from the database

Parameters:

annotId - - Chado ID for owner annotation

name - - Synonym

Returns:

true if successful

addComments

protected void addComments(AnnotatedFeatureI annot)

Add all comments from an AnnotatedFeatureI object

Parameters:

annot - - annotation to store comments from

addComment

protected boolean addComment(long annotId,
                             Comment comment)

Add a comment to the database

Parameters:

annotId - - Chado ID for owner annotation

comment - - Comment object

Returns:

true if successful

deleteComment

protected boolean deleteComment(long annotId,
                                Comment comment)

updateStatus

protected boolean updateStatus(long annotId,
                               java.lang.String statusTerm,
                               java.lang.String newStatus,
                               java.lang.String oldStatus)

updateOwner

protected boolean updateOwner(long annotId,
                              java.lang.String newStatus,
                              java.lang.String oldStatus)

getChadoCdsName

protected java.lang.String getChadoCdsName(ApolloNameAdapterI nameAdapter,
                                           java.lang.String name)

getChadoPeptideName

protected java.lang.String getChadoPeptideName(ApolloNameAdapterI nameAdapter,
                                               java.lang.String name,
                                               SeqFeatureI pfeat)

getSeqEditRefFeature

protected AnnotatedFeatureI getSeqEditRefFeature(SequenceEdit seqEdit)