org.intermine.bio.dataconversion
Class BioDBConverter

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

Direct Known Subclasses:

ChadoDBConverter

public abstract class BioDBConverter
extends DBConverter

A DBConverter with helper methods for bio sources.

Constructor Summary

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

BioDBConverter(Database database, Model tgtModel, ItemWriter writer, java.lang.String dataSourceName, java.lang.String dataSetTitle)
Create a new BioDBConverter object.

Method Summary

Item	createSynonym(java.lang.String subjectId, java.lang.String value, boolean store) Create a new Synonym.
protected Item	getChromosome(java.lang.String identifier, int taxonId) Make a Chromosome Item, then store and return it.
Item	getDataSetItem(int taxonId) Return the DataSet Item created from the dataSetTitle.
Item	getDataSetItem(java.lang.String title, Item dataSourceItem) Return a DataSource item for the given name
Item	getDataSetItem(java.lang.String title, java.lang.String url, java.lang.String description, Item dataSourceItem) Return a DataSource item with the given details.
abstract java.lang.String	getDataSetTitle(int taxonId) Return the DataSet title for a given taxon id.
Item	getDataSourceItem() Return the DataSource Item created from the dataSourceName.
Item	getDataSourceItem(java.lang.String name) Return a DataSet item for the given title
java.lang.String	getDataSourceName() Return the data source name set by setDataSourceName().
Item	getOrganismItem(int taxonId) The Organism item created from the taxon id passed to the constructor.
java.lang.String	getSequenceOntologyRefId()
protected Item	makeLocation(java.lang.String chromosomeId, java.lang.String locatedSequenceFeatureId, int start, int end, int strand, int taxonId) Make a Location Relation between a LocatedSequenceFeature and a Chromosome.
void	setDataSourceName(java.lang.String name) Set the name of the DataSource Item to create for this converter.

Methods inherited from class org.intermine.dataconversion.DBConverter

getDatabase, process

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

Constructor Detail

BioDBConverter

public BioDBConverter(Database database,
                      Model tgtModel,
                      ItemWriter writer,
                      java.lang.String dataSourceName,
                      java.lang.String dataSetTitle)

Create a new BioDBConverter object. The constructor will automatically create a DataConverterStoreHook for this converter that sets DataSet references and collections.

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

dataSourceName - the DataSource name

dataSetTitle - the DataSet title

BioDBConverter

public BioDBConverter(Database database,
                      Model tgtModel,
                      ItemWriter writer)

Create a new BioDBConverter object. The constructor will automatically create a DataConverterStoreHook for this converter that sets DataSet references and collections.

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

Method Detail

setDataSourceName

public void setDataSourceName(java.lang.String name)

Set the name of the DataSource Item to create for this converter.

Parameters:

name - the name

getDataSourceName

public java.lang.String getDataSourceName()

Return the data source name set by setDataSourceName().

Returns:

the data source name

getDataSetItem

public Item getDataSetItem(int taxonId)

Return the DataSet Item created from the dataSetTitle.

Parameters:

taxonId - the taxon id of the to use when creating the DataSet

Returns:

the DataSet Item

getDataSourceItem

public Item getDataSourceItem()

Return the DataSource Item created from the dataSourceName.

Returns:

the DataSource Item

makeLocation

protected Item makeLocation(java.lang.String chromosomeId,
                            java.lang.String locatedSequenceFeatureId,
                            int start,
                            int end,
                            int strand,
                            int taxonId)

Make a Location Relation between a LocatedSequenceFeature and a Chromosome.

Parameters:

chromosomeId - Chromosome Item identifier

locatedSequenceFeatureId - the Item identifier of the feature

start - the start position

end - the end position

strand - the strand

taxonId - the taxon id to use when finding the Chromosome for the Location

Returns:

the new Location object

getOrganismItem

public Item getOrganismItem(int taxonId)

The Organism item created from the taxon id passed to the constructor.

Parameters:

taxonId - NCBI taxonomy id of organism to create

Returns:

the Organism Item

getDataSourceItem

public Item getDataSourceItem(java.lang.String name)

Return a DataSet item for the given title

Parameters:

name - the DataSet name

Returns:

the DataSet Item

getDataSetItem

public Item getDataSetItem(java.lang.String title,
                           Item dataSourceItem)

Return a DataSource item for the given name

Parameters:

title - the DataSet title

dataSourceItem - the DataSource referenced by the the DataSet

Returns:

the DataSet Item

getDataSetTitle

public abstract java.lang.String getDataSetTitle(int taxonId)

Return the DataSet title for a given taxon id.

Parameters:

taxonId - the taxon id

Returns:

the title

getDataSetItem

public Item getDataSetItem(java.lang.String title,
                           java.lang.String url,
                           java.lang.String description,
                           Item dataSourceItem)

Return a DataSource item with the given details.

Parameters:

title - the DataSet title

url - the new url field, or null if the url shouldn't be set

description - the new description field, or null if the field shouldn't be set

dataSourceItem - the DataSource referenced by the the DataSet

Returns:

the DataSet Item

getChromosome

protected Item getChromosome(java.lang.String identifier,
                             int taxonId)
                      throws ObjectStoreException

Make a Chromosome Item, then store and return it. The Item is held in a Map so this method can be called multiple times.

Parameters:

identifier - the chromsome identifier

taxonId - the id of the organism

Returns:

the Chromsome Item

Throws:

ObjectStoreException - if an Item can't be stored

createSynonym

public Item createSynonym(java.lang.String subjectId,
                          java.lang.String value,
                          boolean store)
                   throws org.xml.sax.SAXException,
                          ObjectStoreException

Create a new Synonym. Keeps a map of already processed synonyms, ignores duplicates. The "store" param should be true only if the subject has already been stored. Storing a synonym first can signficantly slow down the build process.

Parameters:

subjectId - id representing the object (eg. Gene) this synonym describes.

value - the Synonym value

store - if true, will store item

Returns:

the synonym item or null if this is a duplicate

Throws:

ObjectStoreException - if the synonym can't be stored

org.xml.sax.SAXException - if the synonym can't be stored

getSequenceOntologyRefId

public java.lang.String getSequenceOntologyRefId()

Returns:

ID represening the Ontology object