apollo.dataadapter.chado
Class ChadoAdapter

java.lang.Object
  org.bdgp.io.AbstractDataAdapter
      apollo.dataadapter.AbstractApolloAdapter
          apollo.dataadapter.chado.ChadoAdapter

All Implemented Interfaces:

ApolloDataAdapterI, org.bdgp.io.DataAdapter, org.bdgp.io.VisualDataAdapter

public class ChadoAdapter
extends AbstractApolloAdapter

A data adapter that allows Apollo to communicate with a Chado-compliant relational database. Note that this class is one of two adapter classes required by the Apollo data adapter specification; the other one is ChadoAdapterGUI.

This data adapter was written primarily as an exercise to help me to learn the Chado schema (as it was implemented at TIGR in late 2003.) Therefore there are numerous caveats, of which a few are listed below:

• The adapter has been tested only with Sybase, although it was designed with other DBMSs in mind.
• The adapter supports two versions of the Chado schema, which we refer to as "pre_fmb" and "fmb"; the latter should correspond to the "FlyBase Migration Build" freeze of Chado. The adapter looks for a table present in one version but not the other in order to determine the schema version.
• The adapter only supports read access. Write access will hopefully be forthcoming.
• The adapter currently allows the user to select only a single sequence for display. (By "sequence" we mean any Chado feature.)
• The adapter loads the entire sequence and all of its annotations before displaying anything. (i.e., there is no support for on-demand or delayed data loading.)
• Extensive hard-coding can be observed in the set of annotations that the data adapter attempts to load. Most of these data types (except for the gene models themselves, which should follow the Chado spec. fairly closely) are also TIGR-specific.

Finally, here are some thoughts on two additional topics; the first is the question of SO-compliance, and the second is the issue of how to refactor the adapter to make it more configurable. 1. SO compliance: the adapter is definitely *not* SO-compliant, although it could probably be made to work with a SO-enabled version of Chado simply by looking up the cvterm_ids for the crucial elements of the central dogma on which the gene representation depends (e.g. exon, transcript, etc.) Handling inheritance properly and dynamically discovering the relationships between SO terms by querying the database, however, is likely to be a more challenging undertaking. In other words, getting it to work should be easy, but getting it to work right is likely to be hard. (Isn't this always the way?) 2. Making the adapter more configurable. Good progress has already been made on this front in terms of setting up the architecture to allow connections to different types of Chado databases (Sybase, PostgresQL, etc.), although this has not been tested. What the adapter really needs is a way for the user (or Apollo "administrator" or application programmer) to configure what annotations should be read from different data sources. One thing that significantly impeded efforts to use Apollo here at TIGR is the fact that Apollo supports only one tiers file for each data adapter. This is fine if you only have a couple of different databases, but we have tens or hundreds, each with different data, and we would really like to be able to configure the display on a finer-grained basis than is allowed by the current setup.

Version:

$Revision: 1.53 $ $Date: 2009-06-20 03:49:40 $ $Author: jcrabtree $

Author:

Jonathan Crabtree

See Also:

ChadoAdapterGUI

Field Summary

static java.lang.String	CHADO_DB
static java.lang.String	DRIVER_CLASS
static java.lang.String	JDBC_URL
protected static org.apache.log4j.Logger	logger
static java.lang.String	PASSWORD
protected java.util.Properties	stateInfo The current driver properties set by the GUI in the most recent call to setStateInformation.
protected org.bdgp.io.IOOperation[]	SUPPORTED_OPS Array containing the list of IO operations supported by this adapter; currently the adapter supports read-only access to a Chado database.
static java.lang.String	USERNAME

Fields inherited from class apollo.dataadapter.AbstractApolloAdapter

curation_set, region, style

Fields inherited from class org.bdgp.io.AbstractDataAdapter

listeners

Fields inherited from interface apollo.dataadapter.ApolloDataAdapterI

OP_APPEND_DATA, OP_READ_DATA, OP_READ_RAW_ANALYSIS, OP_READ_SEQUENCE, OP_WRITE_DATA

Constructor Summary

ChadoAdapter()

Method Summary

java.lang.Boolean	addToCurationSet()
void	commitChanges(CurationSet curation) Writes back curation set via jdbc, using the curations sets transactions
ChadoDatabase	getActiveDatabase() Returns active database.
CurationSet	getCurationSet() returns a saved CurationSet.
java.lang.String	getGFFSource()
java.lang.String	getRawAnalysisResults(java.lang.String id)
SequenceI	getSequence(DbXref dbxref)
SequenceI	getSequence(DbXref dbxref, int start, int end)
SequenceI	getSequence(java.lang.String id) Strings for input types
protected void	getSequenceList(java.lang.String featType, java.util.Vector uniquenames, java.util.Vector descriptions) Read a list of sequence IDs and descriptions into two parallel Vectors.
java.util.Vector	getSequences(DbXref[] dbxref)
java.util.Vector	getSequences(DbXref[] dbxref, int[] start, int[] end)
java.util.Properties	getStateInformation() State info Properties carries all the info needed for the adapter to do its query This is an alternative to setDataInput.
Style	getStyle() A chado database can set its own style.
org.bdgp.io.IOOperation[]	getSupportedOperations() Returns a list of all operations supported by this data adapter
java.lang.String	getType() From org.bdgp.io.DataAdapter.
org.bdgp.io.DataAdapterUI	getUI(org.bdgp.io.IOOperation op) Returns a user interface for the requested IOOperation.
boolean	hasLinkData() Return true - this means that the features potentially have synteny data associated with them and then can be used in the synteny viewer this follows the game model of embedding links in the features
void	init() From org.bdgp.io.DataAdapter interface.
void	setDbLoginForDefaultDb(java.lang.String login) Created to modify the login/username from the command line
void	setDbPassAndActiveForDb(java.lang.String chadoDb, java.lang.String pass) Set password to pass for the chadoDB identified by chadoDb and set this DB as active Created to modify the password from the command line
void	setDbPassForDb(java.lang.String chadoDb, java.lang.String pass) Set password to pass for the chadoDB identified by chadoDb Created to modify the password from the command line
void	setDbPassForDefaultDb(java.lang.String pass) Created to modify the password from the command line
void	setFlatFileWriteMode(boolean flatFileWriteMode) Used to set the flat file write mode flag from the command line.
void	setGFFSource(java.lang.String gffSource)
void	setStateInformation(java.util.Properties p) This should set StateInformation object! see StateInformation for Strings to use for keys.

Methods inherited from class apollo.dataadapter.AbstractApolloAdapter

cacheUI, canWriteData, clearOldData, clearStateInformation, commitChanges, commitChanges, commitChanges, commitChanges, commitChanges, getAdapters, getCachedUI, getChildAdapter, getChildAdapter, getCurationState, getDatabase, getDataInput, getDefaultStyle, getFilename, getInput, getInputType, getName, getNameAdapter, getNumberOfChildAdapters, getSpecies, isComposite, loadNewSpeciesFromLink, operationIsSupported, rollbackAnnotations, rollbackAnnotations, setCuration, setCurationNumber, setCurationState, setDatabase, setDataInput, setDataLoadListener, setInput, setInputType, setLocation, setName, setPadLeft, setPadRight, setRegion, setSpecies, setStyle

Methods inherited from class org.bdgp.io.AbstractDataAdapter

addProgressListener, fireProgressEvent, removeProgressListener, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.bdgp.io.VisualDataAdapter

addProgressListener, fireProgressEvent, removeProgressListener

Field Detail

logger

protected static final org.apache.log4j.Logger logger

DRIVER_CLASS

public static java.lang.String DRIVER_CLASS

JDBC_URL

public static java.lang.String JDBC_URL

CHADO_DB

public static java.lang.String CHADO_DB

USERNAME

public static java.lang.String USERNAME

PASSWORD

public static java.lang.String PASSWORD

stateInfo

protected java.util.Properties stateInfo

The current driver properties set by the GUI in the most recent call to setStateInformation.

SUPPORTED_OPS

protected org.bdgp.io.IOOperation[] SUPPORTED_OPS

Array containing the list of IO operations supported by this adapter; currently the adapter supports read-only access to a Chado database.

Constructor Detail

ChadoAdapter

public ChadoAdapter()

Method Detail

hasLinkData

public boolean hasLinkData()

Return true - this means that the features potentially have synteny data associated with them and then can be used in the synteny viewer this follows the game model of embedding links in the features

Specified by:

hasLinkData in interface ApolloDataAdapterI

Overrides:

hasLinkData in class AbstractApolloAdapter

getStateInformation

public java.util.Properties getStateInformation()

Description copied from interface: ApolloDataAdapterI

State info Properties carries all the info needed for the adapter to do its query This is an alternative to setDataInput. For most cases setDataInput should be sufficient. This should return StateInformation

Specified by:

getStateInformation in interface ApolloDataAdapterI

Overrides:

getStateInformation in class AbstractApolloAdapter

setStateInformation

public void setStateInformation(java.util.Properties p)

Description copied from interface: ApolloDataAdapterI

This should set StateInformation object! see StateInformation for Strings to use for keys.

Specified by:

setStateInformation in interface ApolloDataAdapterI

Overrides:

setStateInformation in class AbstractApolloAdapter

getStyle

public Style getStyle()

A chado database can set its own style. Override the superclass method to get style from the ChadoDatabase configuration file.

Specified by:

getStyle in interface ApolloDataAdapterI

Overrides:

getStyle in class AbstractApolloAdapter

getCurationSet

public CurationSet getCurationSet()
                           throws ApolloAdapterException

Description copied from interface: ApolloDataAdapterI

returns a saved CurationSet.

Specified by:

getCurationSet in interface ApolloDataAdapterI

Overrides:

getCurationSet in class AbstractApolloAdapter

Throws:

ApolloAdapterException

commitChanges

public void commitChanges(CurationSet curation)
                   throws ApolloAdapterException

Writes back curation set via jdbc, using the curations sets transactions

Specified by:

commitChanges in interface ApolloDataAdapterI

Overrides:

commitChanges in class AbstractApolloAdapter

Throws:

ApolloAdapterException

addToCurationSet

public java.lang.Boolean addToCurationSet()
                                   throws ApolloAdapterException

Specified by:

addToCurationSet in interface ApolloDataAdapterI

Overrides:

addToCurationSet in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getSequence

public SequenceI getSequence(java.lang.String id)
                      throws ApolloAdapterException

Description copied from interface: ApolloDataAdapterI

Strings for input types

Specified by:

getSequence in interface ApolloDataAdapterI

Overrides:

getSequence in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getSequence

public SequenceI getSequence(DbXref dbxref)
                      throws ApolloAdapterException

Specified by:

getSequence in interface ApolloDataAdapterI

Overrides:

getSequence in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getSequence

public SequenceI getSequence(DbXref dbxref,
                             int start,
                             int end)
                      throws ApolloAdapterException

Specified by:

getSequence in interface ApolloDataAdapterI

Overrides:

getSequence in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getSequences

public java.util.Vector getSequences(DbXref[] dbxref)
                              throws ApolloAdapterException

Specified by:

getSequences in interface ApolloDataAdapterI

Overrides:

getSequences in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getSequences

public java.util.Vector getSequences(DbXref[] dbxref,
                                     int[] start,
                                     int[] end)
                              throws ApolloAdapterException

Specified by:

getSequences in interface ApolloDataAdapterI

Overrides:

getSequences in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getRawAnalysisResults

public java.lang.String getRawAnalysisResults(java.lang.String id)
                                       throws ApolloAdapterException

Specified by:

getRawAnalysisResults in interface ApolloDataAdapterI

Overrides:

getRawAnalysisResults in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getType

public java.lang.String getType()

Description copied from class: AbstractApolloAdapter

From org.bdgp.io.DataAdapter. Default implementation returns "". Override this to return a string describing the data adapter. The reason for the default implementation is that as far as I can tell getType is not used by apollo nor org.bdgp, so seems silly to require it. Am i missing something?

Specified by:

getType in interface org.bdgp.io.DataAdapter

Overrides:

getType in class AbstractApolloAdapter

getSupportedOperations

public org.bdgp.io.IOOperation[] getSupportedOperations()

Description copied from interface: org.bdgp.io.DataAdapter

Returns a list of all operations supported by this data adapter

init

public void init()

Description copied from class: AbstractApolloAdapter

From org.bdgp.io.DataAdapter interface. no-op default implementation. A data adapter should override this if it needs to do some initialization.

Specified by:

init in interface org.bdgp.io.DataAdapter

Overrides:

init in class AbstractApolloAdapter

getUI

public org.bdgp.io.DataAdapterUI getUI(org.bdgp.io.IOOperation op)

Description copied from interface: org.bdgp.io.VisualDataAdapter

Returns a user interface for the requested IOOperation. Most VisualDataAdapters will return a different user interface for each supported IOOperation.

getSequenceList

protected void getSequenceList(java.lang.String featType,
                               java.util.Vector uniquenames,
                               java.util.Vector descriptions)
                        throws ApolloAdapterException

Read a list of sequence IDs and descriptions into two parallel Vectors. The sequence IDs must be values from the chado column feature.uniquename, but the descriptions can be any unique human-readable string that adequately describes the corresponding sequence.

Parameters:

featType - The type of sequence to retrive from the feature table (e.g., 'assembly', 'super-contig')

uniquenames - Vector that will hold the sequence IDs (values from the chado column feature.uniquename)

descriptions - Vector that will hold the human-readable descriptions for the sequences named in uniquenames

Throws:

ApolloAdapterException

getActiveDatabase

public ChadoDatabase getActiveDatabase()

Returns active database. if active database has not been set, return default database

setDbPassForDefaultDb

public void setDbPassForDefaultDb(java.lang.String pass)

Created to modify the password from the command line

Parameters:

pass - : Default Db new password

setDbLoginForDefaultDb

public void setDbLoginForDefaultDb(java.lang.String login)

Created to modify the login/username from the command line

Parameters:

login - : Default Db new login/username.

setFlatFileWriteMode

public void setFlatFileWriteMode(boolean flatFileWriteMode)

Used to set the flat file write mode flag from the command line.

Parameters:

login - : Default Db new login/username.

getGFFSource

public java.lang.String getGFFSource()

setGFFSource

public void setGFFSource(java.lang.String gffSource)

setDbPassForDb

public void setDbPassForDb(java.lang.String chadoDb,
                           java.lang.String pass)
                    throws java.lang.Exception

Set password to pass for the chadoDB identified by chadoDb Created to modify the password from the command line

Parameters:

chadoDb -

pass -

Throws:

java.lang.Exception

setDbPassAndActiveForDb

public void setDbPassAndActiveForDb(java.lang.String chadoDb,
                                    java.lang.String pass)
                             throws java.lang.Exception

Set password to pass for the chadoDB identified by chadoDb and set this DB as active Created to modify the password from the command line

Parameters:

chadoDb -

pass -

Throws:

java.lang.Exception