org.intermine.bio.dataconversion
Class ChadoDBConverter

java.lang.Object
  org.intermine.dataconversion.DataConverter
      org.intermine.dataconversion.DBConverter
          org.intermine.bio.dataconversion.BioDBConverter
              org.intermine.bio.dataconversion.ChadoDBConverter

Direct Known Subclasses:

GenomeDBConverter

public class ChadoDBConverter
extends BioDBConverter

DataConverter to read from a Chado database into items

Field Summary

protected static org.apache.log4j.Logger

LOG

Constructor Summary

ChadoDBConverter(Database database, Model tgtModel, ItemWriter writer)
Create a new ChadoDBConverter object.

Method Summary

ChadoProcessor	findProcessor(java.lang.Class<? extends ChadoProcessor> cls) Look at the list of completed processors and return the processor of the given type.
java.util.Map<java.lang.Integer,OrganismData>	getChadoIdToOrgDataMap() Return a map from chado organism_id to OrganismData object for all the organisms that we are processing
protected java.util.Map<OrganismData,java.lang.Integer>	getChadoOrganismIds(java.sql.Connection conn) Return a map from chado organism id to OrganismData for the organisms in the organism table in chado.
java.util.List<ChadoProcessor>	getCompletedProcessors()
protected java.sql.Connection	getConnection() Get the connection to use when processing.
java.lang.String	getDataSetTitle(int taxonId) Default implementation that makes a data set title based on the data source name.
java.util.Set<OrganismData>	getOrganismsToProcess() Return the OrganismData objects for the organisms listed in the source configuration.
void	process() Process the data from the Database and write to the ItemWriter.
void	setOrganisms(java.lang.String organisms) Set the taxon ids to use when creating the Organism Item for the new features.
void	setProcessors(java.lang.String processors) Set the class names of the ChadoProcessors to run.

Methods inherited from class org.intermine.bio.dataconversion.BioDBConverter

createSynonym, getChromosome, getDataSetItem, getDataSetItem, getDataSetItem, getDataSourceItem, getDataSourceItem, getDataSourceName, getOrganismItem, getSequenceOntologyRefId, makeLocation, setDataSourceName

Methods inherited from class org.intermine.dataconversion.DBConverter

getDatabase

Methods inherited from class org.intermine.dataconversion.DataConverter

addUniqueItemId, alias, createItem, getItemWriter, getModel, getUniqueItemId, newId, setStoreHook, store, store, store, store, store

Methods inherited from class java.lang.Object

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

Field Detail

LOG

protected static final org.apache.log4j.Logger LOG

Constructor Detail

ChadoDBConverter

public ChadoDBConverter(Database database,
                        Model tgtModel,
                        ItemWriter writer)
                 throws java.sql.SQLException

Create a new ChadoDBConverter object.

Parameters:

database - the database to read from

tgtModel - the Model used by the object store we will write to with the ItemWriter

writer - an ItemWriter used to handle the resultant Items

Throws:

java.sql.SQLException - if we fail to get a database connection

Method Detail

setOrganisms

public void setOrganisms(java.lang.String organisms)

Set the taxon ids to use when creating the Organism Item for the new features. Only features from chado with these organisms will be processed.

Parameters:

organisms - a space separated list of the organism abbreviations or taxon ids to look up in the organism table eg. "Dmel Dpse"

setProcessors

public void setProcessors(java.lang.String processors)

Set the class names of the ChadoProcessors to run.

Parameters:

processors - a space separated list of the fully-qualified class names of module processors to run

getChadoIdToOrgDataMap

public java.util.Map<java.lang.Integer,OrganismData> getChadoIdToOrgDataMap()

Return a map from chado organism_id to OrganismData object for all the organisms that we are processing

Returns:

the Map

getConnection

protected java.sql.Connection getConnection()

Get the connection to use when processing.

Returns:

the Connection, or null while testing

process

public void process()
             throws java.lang.Exception

Process the data from the Database and write to the ItemWriter. Query from database and write items to the writer.

Specified by:

process in class DBConverter

Throws:

java.lang.Exception - if there is a problem while processing

getChadoOrganismIds

protected java.util.Map<OrganismData,java.lang.Integer> getChadoOrganismIds(java.sql.Connection conn)
                                                                     throws java.sql.SQLException

Return a map from chado organism id to OrganismData for the organisms in the organism table in chado. This is a protected method so that it can be overriden for testing

Parameters:

conn - the db connection

organismsToProcess2 -

Returns:

a Map from abbreviation to chado organism_id

Throws:

java.sql.SQLException - if the is a database problem

getOrganismsToProcess

public java.util.Set<OrganismData> getOrganismsToProcess()

Return the OrganismData objects for the organisms listed in the source configuration.

Returns:

the organismsToProcess

findProcessor

public ChadoProcessor findProcessor(java.lang.Class<? extends ChadoProcessor> cls)

Look at the list of completed processors and return the processor of the given type. If there is none or more than one, throw a RuntimeException

Parameters:

cls - the class

Returns:

the ChadoProcessor

getDataSetTitle

public java.lang.String getDataSetTitle(int taxonId)

Default implementation that makes a data set title based on the data source name. Return the DataSet title for a given taxon id.

Specified by:

getDataSetTitle in class BioDBConverter

Parameters:

taxonId - the taxon id

Returns:

the title

getCompletedProcessors

public java.util.List<ChadoProcessor> getCompletedProcessors()

Returns:

the completedProcessors