org.intermine.bio.dataconversion
Class BioDirectoryConverter

java.lang.Object
  org.intermine.dataconversion.DataConverter
      org.intermine.dataconversion.DirectoryConverter
          org.intermine.bio.dataconversion.BioDirectoryConverter

Direct Known Subclasses:

PdbConverter, UniprotConverter

public abstract class BioDirectoryConverter
extends DirectoryConverter

A DirectoryConverter that automatically sets the dataSets collection of objects as they are stored.

Constructor Summary

BioDirectoryConverter(ItemWriter writer, Model model, java.lang.String dataSourceName, java.lang.String dataSetTitle)
Create a new BioDirectoryConverter.

BioDirectoryConverter(ItemWriter writer, Model model, java.lang.String dataSourceName, java.lang.String dataSetTitle, java.lang.String ontology)
Create a new BioDirectoryConverter.

Method Summary

Item	createCrossReference(java.lang.String subjectId, java.lang.String value, java.lang.String dataSource, boolean store) Create a new CrossReference.
Item	createSynonym(java.lang.String subjectId, java.lang.String value, boolean store) Create a new Synonym.
java.lang.String	getDataSet(java.lang.String title, java.lang.String dataSourceRefId) Return a DataSet item with the given details.
java.lang.String	getDataSource(java.lang.String name) Return a DataSource item for the given title
java.lang.String	getOrganism(java.lang.String taxonId) The Organism item created from the taxon id passed to the constructor.
java.lang.String	getSequenceOntologyRefId()
void	setDataSet(java.lang.String refId) Update the dataset reference Id.

Methods inherited from class org.intermine.dataconversion.DirectoryConverter

close, 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

BioDirectoryConverter

public BioDirectoryConverter(ItemWriter writer,
                             Model model,
                             java.lang.String dataSourceName,
                             java.lang.String dataSetTitle)

Create a new BioDirectoryConverter.

Parameters:

writer - the Writer used to output the resultant items

model - the data model

dataSourceName - the DataSource name

dataSetTitle - the DataSet title

BioDirectoryConverter

public BioDirectoryConverter(ItemWriter writer,
                             Model model,
                             java.lang.String dataSourceName,
                             java.lang.String dataSetTitle,
                             java.lang.String ontology)

Create a new BioDirectoryConverter.

Parameters:

writer - the Writer used to output the resultant items

model - the data model

dataSourceName - the DataSource name

dataSetTitle - the DataSet title

Method Detail

setDataSet

public void setDataSet(java.lang.String refId)

Update the dataset reference Id. Overwrites the one set in the constructor. Needed for Uniprot which has a few different datasets.

Parameters:

refId - ID representing dataset object

getDataSource

public java.lang.String getDataSource(java.lang.String name)

Return a DataSource item for the given title

Parameters:

name - the DataSource name

Returns:

the DataSource Item

getDataSet

public java.lang.String getDataSet(java.lang.String title,
                                   java.lang.String dataSourceRefId)

Return a DataSet item with the given details.

Parameters:

title - the DataSet title

dataSourceRefId - the DataSource referenced by the the DataSet

Returns:

the DataSet Item

getOrganism

public java.lang.String getOrganism(java.lang.String taxonId)

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

Parameters:

taxonId - NCBI taxonomy id of organism to create

Returns:

the refId representing the Organism Item

createCrossReference

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

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

Parameters:

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

value - identifier

dataSource - external database

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

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