org.intermine.bio.dataconversion
Class BioFileConverter

java.lang.Object
  org.intermine.dataconversion.DataConverter
      org.intermine.dataconversion.FileConverter
          org.intermine.bio.dataconversion.BioFileConverter

Direct Known Subclasses:

BioGridConverter, GoConverter, InparanoidConverter, InterProConverter, KeggPathwayConverter, PsiConverter, UniprotKeywordConverter, WormBaseIdentifiersConverter

public abstract class BioFileConverter
extends FileConverter

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

Constructor Summary

BioFileConverter(ItemWriter writer, Model model)
Create a new BioFileConverter.

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

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

Method Summary

Item	createCrossReference(java.lang.String subjectId, java.lang.String value, java.lang.String dataSource, boolean store) Create a new CrossReference.
Item	createSynonym(Item item, java.lang.String value, boolean store) Create a new Synonym.
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 ref 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()
protected Item	makeLocation(java.lang.String chromosomeId, java.lang.String sequenceFeatureId, java.lang.String startString, java.lang.String endString, java.lang.String strand, boolean store) Make a Location between a Feature and a Chromosome.

Methods inherited from class org.intermine.dataconversion.FileConverter

close, getCurrentFile, process, setCurrentFile

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

BioFileConverter

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

Create a new BioFileConverter.

Parameters:

writer - the Writer used to output the resultant items

model - the data model

dataSourceName - the DataSource name

dataSetTitle - the DataSet title

BioFileConverter

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

Create a new BioFileConverter.

Parameters:

writer - the Writer used to output the resultant items

model - the data model

dataSourceName - the DataSource name

dataSetTitle - the DataSet title

ontology - ID of ontology object. if NULL no SO object will be stored

BioFileConverter

public BioFileConverter(ItemWriter writer,
                        Model model)

Create a new BioFileConverter.

Parameters:

writer - the Writer used to output the resultant items

model - the data model

Method Detail

getSequenceOntologyRefId

public java.lang.String getSequenceOntologyRefId()

Returns:

ID represening the Ontology 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 ref with the given details.

Parameters:

title - the DataSet title

dataSourceRefId - the DataSource referenced by the the DataSet

Returns:

the DataSet Item

createSynonym

public Item createSynonym(Item item,
                          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:

item - object

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

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

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

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

makeLocation

protected Item makeLocation(java.lang.String chromosomeId,
                            java.lang.String sequenceFeatureId,
                            java.lang.String startString,
                            java.lang.String endString,
                            java.lang.String strand,
                            boolean store)

Make a Location between a Feature and a Chromosome.

Parameters:

chromosomeId - Chromosome Item identifier

sequenceFeatureId - the Item identifier of the feature

startString - the start position

endString - the end position

strand - the strand

store - if true the location item will be saved in the database

Returns:

the new Location object