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Hibernate Presentation

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Chado API via Java & Hibernate, Robert Bruggner, VectorBase.org. This Wiki page is an edited version of Robert's presentation.

Overview
  • Background
  • Quick Hibernate Overview
  • Hibernate Connectivity and O/R Mapping Example
  • GMOD Demo

Also see Comparison of XORT and Hibernate for Chado Reporting.

Background
  • VectorBase
    • A bioinformatic resource center for invertebrate vectors of human pathogens
  • Responsible for storage and display of multiple organisms’ genomes
    • Anopheles gambiae, Aedes aegypti, Ixodes scapularis, Culex pipiens and so on....
  • Want to store data for many organisms- Chado a natural choice
  • Ensembl Genome Browser already used for A. gambiae
    • Wrote Ensembl API Database adaptor for Chado... Not maintainable.
  • Use Both Databases
    • Transfer genomic data from Ensembl to Chado
    • Search Engine and Indexer using Lucene
    • Run DAS
    • Export data via ChadoXML and GFF3
  • Need API for Database I/O
Hibernate Background
  • They say: “A powerful, high performance object/relational persistence and query service.”
  • Automates the persistence of plain old Java objects (POJO)
    • User maps their POJO properties to database tables via XML (HBM File).
    • There are Hibernate tools that generate HBMs
      • Configurable in the sense that one can create get & set tables where the methods map one-to-one to fields.
  • Persist a specific object by storing it the database.
  • Intelligent Database I/O
    • Smart detection of Dirty Properties when performing Save / Update / Delete.
    • Cascadable Save / Update / Delete for complex objects.
  • Everything's done within the scope of a transaction.
Hibernate Database Connectivity
  • Configure Hibernate in hibernate.cfg.xml
  • Define a Data Source
    • We use a simple, single JDBC connection Chado
    • Can be configured to use a connection pool or data source accessible by the Java Naming and Directory Interface (JNDI).
    • Define a connection “dialect”
    • org.hibernate.dialect.PostgreSQLDialect
  • Describe the relationship between Java objects and database tables
    • Use XML to describe where to store POJO property data in the database
  • Create a new Hibernate Session based on the configuration
  • Begin a transaction to start performing work
POJO and HBM Example file - CV
 public class CV {
 
    private int cv_id
    private String name;
    private String definition;
 
    public property gettersandsetters() {
            ....
    }
 
    public boolean equals(CV comparaCV) {
         ....
    }
    public int hashCode(){
         ...
    }
 }
 <hibernate-mapping>
 
    <class name="org.vectorbase.chadoAPI.chadoObjects.CV" table="cv">
 
    <id name="cv_id" column="cv_id" unsaved-value="undefined">
 
    <generator class="sequence">
 
    <param name="sequence">cv_cv_id_seq</param>
 
    </generator>
 
    </id>	
 
    <property name="name" column=”name” type="java.lang.String” not-null="true"/>
 
    <property name="definition" column=”definition” type="java.lang.String”/>
 
    </class>
 </hibernate-mapping>
HBM Example CVTerm
 public class CVTerm {
 
    private int cvterm_id;
 
    private CV cv;
 
    private String name;
 
    private String definition;
 
    private DBXref dbxref;
 
    private int is_obsolete;
 
    private int is_relationshiptype;
 
   .....
 
}
 <hibernate-mapping>
 
    <class name="org.vectorbase.chadoAPI.chadoObjects.CVTerm" table="cvterm">
 
    <id name="cvterm_id" column="cvterm_id" unsaved-value="undefined">
 
    <generator class="sequence">
 
    <param name="sequence">cvterm_cvterm_id_seq</param>
 
    </generator>
 
    </id>
 
    <many-to-one name="cv" class="org.vectorbase.chadoAPI.chadoObjects.CV" column="cv_id" 
            not-null="true" cascade="save-update"/>
 
    <property name="name" not-null="true" type="java.lang.String"/>
 
    <property name="definition"/>
 
    <one-to-one name="dbxref" class="org.vectorbase.chadoAPI.chadoObjects.DBXref" cascade="all"/>
 
    <property name="is_obsolete"/>
 
    <property name="is_relationshiptype"/>
 
    </class>
  </hibernate-mapping>
Hibernate Object Retrieve

One can use Java, Hibernate Query Language, or SQL, this example uses HQL

 import org.hibernate.Session;
 import org.vectorbase.chadoAPI.CVTerm;
 import org.vectorbase.chadoAPI.CV;
 
 // Load the configuration from hibernate.cfg.xml
 
 // Build a session factory first (not shown)
 
 // Get the session based on the configuration and begin transaction
 Session session = HibernateSessionFactory.getCurrentSession();
 session.beginTransaction();
 
 // Load a CVTerm by its ID
 CVTerm cvt = (CVTerm) session.get(CVTerm.class,1);
 
 // Load a CVTerm using HQL
 CVTerm cvt = session.createQuery(“from CVTerm where name=?).setString(0,”name”).uniqueResult();
 
 // Print out the name of the cvterm
 System.out.println(cvt.getName());
 
 // Get the cv that the cvterm is associated with
 // Hibernate doesn’t return the cv_id - it returns a CV Object.
 CV cv = cvt.getCv();
 
 // Print out the cv’s name
 System.out.println(cv.getName());
Hibernate Object Update
 import org.hibernate.Session;
 import org.vectorbase.chadoAPI.CVTerm;
 
 // Load the configuration from hibernate.cfg.xml
 
 // Build a session factory first (not shown)
 
 // Get the session based on the configuration and begin transaction
 Session session = HibernateSessionFactory.getCurrentSession();
 session.beginTransaction();
 
 // Load a CVTerm by its ID
 CVTerm cvt = (CVTerm) session.get(CVTerm.class,1);
 
 // Change cvt’s name
 cvt.setName(New CVTerm name”);
 
 // Save!
 // Generated SQL updates “Dirty” properties (name, in this case)
 session.save(cvt);
 
 // Commit data to database
 session.commit();
Hibernate Save
 import org.hibernate.Session;
 import org.vectorbase.chadoAPI.CVTerm;
 import org.vectorbase.chadoAPI.CV;
 
 // Load the configuration from hibernate.cfg.xml
 // Build a session factory first and get begin transaction (not shown)
 
 // Make a new CV
 CV new_cv = new CV();
 new_cv.setName(New CV”);
 new_cv.setDefinition(New CV Def”);
 
 // Make a new cvterm for that cv
 CVTerm new_cvterm = new CVTerm();
 new_cvterm.setName(New CVTerm Name);
 // ..... save dbxref etc......
 
 // Add that CVTerm to our new CV
 new_cv.addCVTerm(new_cvterm);
 
 // Save the new data...
 // Hibernate recognizes that it has to first save new_cv, then save new_cvterm.
 session.save(new_cvterm);
 
 session.commit();
 
 // You can see the new id’s assigned by the database
 System.out.println(new_cv.getCv_id());
 System.out.println(new_cvterm.getCvterm_id());
Inheritance
 <hibernate-mapping>
 
     <class name="org.vectorbase.chadoAPI.chadoObjects.Feature" table="feature" discriminator-
  value="not null">
 
     <id name="feature_id" column="feature_id" unsaved-value="undefined">
 
    <generator class="sequence">
 
    <param name="sequence">feature_feature_id_seq</param>
 
    </generator>
 
     </id>	
 
      <discriminator column="type_id" type="integer" insert="false"/>
 
     <many-to-one name="dbxref" class="org.vectorbase.chadoAPI.chadoObjects.DBXref" 
                  column="dbxref_id" cascade="all"/>
 
     <many-to-one name="organism" class="org.vectorbase.chadoAPI.chadoObjects.Organism" 
                  column="organism_id" not-null="true" cascade="save-update"/>
 
     <property name="name"/>
                  .....
 
 <hibernate-mapping>	
 
     <subclass name="org.vectorbase.chadoAPI.chadoFeatures.Gene" 
          extends="org.vectorbase.chadoAPI.chadoObjects.Feature" discriminator-value="767">
 
     </subclass>
 </hibernate-mapping>

Write custom methods for specific sub-classes

ChadoAPI
  • POJO Mappings
    • CV, CVTerm, DB, DBXref, Feature, FeatureCVTerm, FeatureDBXref, FeatureLoc, FeatureProp, FeatureRelationship, FeatureSynonym, Organism, Pub, Synonym
  • Extended Features
    • Chromosome, Gene, Transcript, Exon, Protein
  • Constants
    • CVTerms, FeatureFeatureRelationships, Ontologies
  • Special
    • ChadoAdapter
Problem 1 - GMOD Example
 // Set up our session and begin transaction
 Session session = HibernateUtil.getSessionFactory().getCurrentSession();
 session.beginTransaction();
 
 // Make a chado adpator and load up some utility objects
 ChadoAdaptor ca = new ChadoAdaptor();
 Chromosome c = ca.fetchChromosomeByUniqueName("fake_chromosome");
 Pub null_pub = ca.fetchPubByPubID(1);
 Organism agambiae = ca.fetchOrganismByScientificName("Anopheles","gambiae");
 
 // Begin GMOD Demo Code
 
 // Make our new gene;
 Gene xfile = new Gene();
 xfile.setOrganism(agambiae);
 xfile.setUniquename("xfile");
 xfile.setDescription("A test gene for GMOD meeting");
 
 /* Set the location of our gene. No need to set coordinates because they'll be updated
   * based on the exon boundaries. 
   */
 FeatureLoc xfile_loc = new FeatureLoc();
 xfile_loc.setSrcfeature(c);
 xfile_loc.setStrand(1);
 xfile.setFeatureLoc(xfile_loc);
 
 // Add synonyms to xfile
 xfile.createNewFeatureSynonym("mulder", null_pub, CVTerms.EXACT_SYNONYM);
 xfile.createNewFeatureSynonym("scully", null_pub, CVTerms.EXACT_SYNONYM);
Problem 2 - GMOD Example
 // Create a new transcript for our gene.
 Transcript t = xfile.createGeneTranscript("xfile-RA");
 
 // Create some exons for that transcript.
 t.createTranscriptExon("xfile:1", 13691, 13767);
 t.createTranscriptExon("xfile:2", 14687, 14720);
 
 // Save our new gene
 session.save(xfile);
 System.out.println("xfile feature_id is " + xfile.getFeature_id());
 
 // Fetch our saved gene from the database
 Gene xfile_r = ca.fetchGeneByUniqueName("xfile");
 System.out.println("symbol: " + xfile_r.getUniquename());
 System.out.print("synonyms: ");
 for (FeatureSynonym fs : xfile_r.getFeatureSynonyms()){
 
         System.out.print(fs.getSynonym().getName() + " ");
 }
 
 System.out.println("description: " + xfile_r.getDescription());
 System.out.println("type: " + xfile_r.getType().getName());
 
 for (Transcript tx : xfile_r.fetchAllTranscripts()){
     for (Exon e : tx.fetchAllExons()){
          System.out.println(e.getUniquename() + " Start:\t" + e.getFeatureLoc().getFmin());
          System.out.println(e.getUniquename() + " End:\t" + e.getFeatureLoc().getFmax());
          System.out.println("\tSrcFeatureID: " + e.getFeatureLoc().getSrcfeature().getFeature_id());
     }
     System.out.println(">" + tx.getUniquename());
     System.out.println(tx.generateTranscriptSequenceFromExons().toUpperCase());
 }
Problems 3, 4, & 5 - GMOD Update & Delete
 // Lets update our name...
 xfile_r.setUniquename("x-file");
 
 session.save(xfile_r);
 
 // Not part of the ChadoAdaptor utility object, but a good example of HQL
 List<Gene> genes = (List<Gene>)session.createQuery("from Gene where uniquename like ?").setString(0,”x-%).list();
 
 for (Gene g : genes){
 
    System.out.println(g.getFeature_id() + 
                          "\t" + g.getUniquename() + 
                          "\t" + g.getOrganism().getGenus() +
                          " " + g.getOrganism().getSpecies());
 }
 
 // Deleting... hmm...
 Gene delete_me = ca.fetchGeneByUniqueName("x-ray");
 session.delete(delete_me);
 
 // All Finished
 session.getTransaction().commit();


What Hibernate Does Well
  • Hibernate can be configured to perform specialized functions
    • For example, it has its own notion of a cascade
  • Flexible with respect to language
    • Java, Hibernate Query Language, or SQL
  • Any JDBC driver
Acknowledgements
  • VectorBase People
    • Frank Collins, EO Stinson, Ryan Butler
  • GMOD
  • NIAID