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Man, tables take a long time to do in Mediawiki
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‎_wikis/BioJava:BioJavaXDocs.md‎

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@@ -2171,29 +2171,38 @@ second is the mapping name to be used in HQL to query the table, and the
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third column is the class of object you will get when the query returns
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results:
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Table 19.1. Hibernate object-relational mappings. biodatabase Namespace
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SimpleNamespace taxon Taxon SimpleNCBITaxon bioentry BioEntry
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SimpleBioEntry taxon\_name (use properties of NCBITaxon)
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SimpleNCBITaxonName biosequence (including the sequence data) Sequence
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SimpleRichSequence biosequence (excluding the sequence data)
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ThinSequence ThinRichSequence bioentry\_relationship
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BioEntryRelationship SimpleBioEntryRelationship comment Comment
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SimpleComment dbxref CrossRef SimpleCrossRef bioentry\_dbxref (use
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properties of BioEntry) SimpleRankedCrossRef reference DocRef
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SimpleDocRef bioentry\_reference (use properties of BioEntry)
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SimpleRankedDocRef dbxref\_qualifer\_value (use properties of CrossRef)
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SimpleNote bioentry\_qualifier\_value (use properties of BioEntry)
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SimpleNote ontology Ontology ComparableOntology term Term ComparableTerm
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term\_relationship Triple ComparableTriple term\_synonym (use properties
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of Term) String term\_dbxref (use properties of Term)
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SimpleRankedCrossRef seqfeature Feature SimpleRichFeature
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seqfeature\_qualifier\_value (use properties of Feature) SimpleNote
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seqfeature\_dbxref (use properties of Feature) SimpleRankedCrossRef
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seqfeature\_relationship FeatureRelationship
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SimpleRichFeatureRelationship location Location SimpleRichLocation,
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CompoundRichLocation, or EmptyRichLocation location\_qualifier\_value
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(use properties of Location) SimpleNote seqfeature\_path - -
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bioentry\_path - - term\_path - -
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Table 19.1. Hibernate object-relational mappings.
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| BioSQL Table Name | HQL Name to use | Type of returned object |
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|-------------------------------------------|-------------------------------|----------------------------------------------------------------|
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| biodatabase | Namespace | SimpleNamespace |
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| taxon | Taxon | SimpleNCBITaxon |
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| bioentry | BioEntry | SimpleBioEntry |
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| taxon\_name | (use properties of NCBITaxon) | SimpleNCBITaxonName |
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| biosequence (including the sequence data) | Sequence | SimpleRichSequence |
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| biosequence (excluding the sequence data) | ThinSequence | ThinRichSequence |
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| bioentry\_relationship | BioEntryRelationship | SimpleBioEntryRelationship |
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| comment | Comment | SimpleComment |
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| dbxref | CrossRef | SimpleCrossRef |
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| bioentry\_dbxref | (use properties of BioEntry) | SimpleRankedCrossRef |
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| reference | DocRef | SimpleDocRef |
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| bioentry\_reference | (use properties of BioEntry) | SimpleRankedDocRef |
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| dbxref\_qualifer\_value | (use properties of CrossRef) | SimpleNote |
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| bioentry\_qualifier\_value | (use properties of BioEntry) | SimpleNote |
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| ontology | Ontology | ComparableOntology |
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| term | Term | ComparableTerm |
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| term\_relationship | Triple | ComparableTriple |
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| term\_synonym | (use properties of Term) | String |
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| term\_dbxref | (use properties of Term) | SimpleRankedCrossRef |
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| seqfeature | Feature | SimpleRichFeature |
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| seqfeature\_qualifier\_value | (use properties of Feature) | SimpleNote |
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| seqfeature\_dbxref | (use properties of Feature) | SimpleRankedCrossRef |
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| seqfeature\_relationship | FeatureRelationship | SimpleRichFeatureRelationship |
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| location | Location | SimpleRichLocation, CompoundRichLocation, or EmptyRichLocation |
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| location\_qualifier\_value | (use properties of Location) | SimpleNote |
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| seqfeature\_path | nil | nil |
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| bioentry\_path | nil | nil |
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| term\_path | nil | nil |
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### Configuring your application to use Hibernate and BioSQL.
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To configure Hibernate, you must edit the copy you made of the
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hibernate.cfg.xml file. Near the top is a section that looks like this:
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<xml>
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<property name="connection.datasource">java:comp/env/jdbc/YOUR\_JNDI\_DATASOURCE\_GOES\_HERE</property>
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The exact details will vary according to which database you are using.
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</xml> The exact details will vary according to which database you are
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using.
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You will see that the default way of using Hibernate is through a JNDI
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datasource, usually supplied by a servlet container such as Tomcat. In

‎_wikis/BioJava:BioJavaXDocs.mediawiki‎

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The following table describes which object in BioJavaX ends up in which table in BioSQL. The first column is the name of the BioSQL table, the second is the mapping name to be used in HQL to query the table, and the third column is the class of object you will get when the query returns results:
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Table 19.1. Hibernate object-relational mappings.
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biodatabase Namespace SimpleNamespace
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taxon Taxon SimpleNCBITaxon
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bioentry BioEntry SimpleBioEntry
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taxon_name (use properties of NCBITaxon) SimpleNCBITaxonName
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biosequence (including the sequence data) Sequence SimpleRichSequence
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biosequence (excluding the sequence data) ThinSequence ThinRichSequence
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bioentry_relationship BioEntryRelationship SimpleBioEntryRelationship
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comment Comment SimpleComment
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dbxref CrossRef SimpleCrossRef
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bioentry_dbxref (use properties of BioEntry) SimpleRankedCrossRef
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reference DocRef SimpleDocRef
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bioentry_reference (use properties of BioEntry) SimpleRankedDocRef
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dbxref_qualifer_value (use properties of CrossRef) SimpleNote
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bioentry_qualifier_value (use properties of BioEntry) SimpleNote
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ontology Ontology ComparableOntology
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term Term ComparableTerm
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term_relationship Triple ComparableTriple
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term_synonym (use properties of Term) String
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term_dbxref (use properties of Term) SimpleRankedCrossRef
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seqfeature Feature SimpleRichFeature
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seqfeature_qualifier_value (use properties of Feature) SimpleNote
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seqfeature_dbxref (use properties of Feature) SimpleRankedCrossRef
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seqfeature_relationship FeatureRelationship SimpleRichFeatureRelationship
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location Location SimpleRichLocation, CompoundRichLocation, or EmptyRichLocation
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location_qualifier_value (use properties of Location) SimpleNote
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seqfeature_path - -
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bioentry_path - -
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term_path - -
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{|border="1" cellpadding="2"
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!width="200"|BioSQL Table Name
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!width="200"|HQL Name to use
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!width="200"|Type of returned object
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|-
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|biodatabase
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|Namespace
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|SimpleNamespace
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|-
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|taxon
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|Taxon
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|SimpleNCBITaxon
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|-
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|bioentry
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|BioEntry
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|SimpleBioEntry
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|-
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|taxon_name
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|(use properties of NCBITaxon)
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|SimpleNCBITaxonName
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|-
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|biosequence (including the sequence data)
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|Sequence
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|SimpleRichSequence
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|-
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|biosequence (excluding the sequence data)
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|ThinSequence
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|ThinRichSequence
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|-
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|bioentry_relationship
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|BioEntryRelationship
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|SimpleBioEntryRelationship
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|-
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|comment
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|Comment
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|SimpleComment
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|-
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|dbxref
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|CrossRef
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|SimpleCrossRef
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|-
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|bioentry_dbxref
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|(use properties of BioEntry)
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|SimpleRankedCrossRef
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|-
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|reference
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|DocRef
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|SimpleDocRef
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|-
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|bioentry_reference
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|(use properties of BioEntry)
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|SimpleRankedDocRef
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|-
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|dbxref_qualifer_value
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|(use properties of CrossRef)
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|SimpleNote
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|-
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|bioentry_qualifier_value
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|(use properties of BioEntry)
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|SimpleNote
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|-
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|ontology
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|Ontology
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|ComparableOntology
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|-
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|term
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|Term
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|ComparableTerm
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|-
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|term_relationship
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|Triple
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|ComparableTriple
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|-
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|term_synonym
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|(use properties of Term)
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|String
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|-
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|term_dbxref
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|(use properties of Term)
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|SimpleRankedCrossRef
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|-
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|seqfeature
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|Feature
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|SimpleRichFeature
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|-
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|seqfeature_qualifier_value
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|(use properties of Feature)
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|SimpleNote
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|-
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|seqfeature_dbxref
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|(use properties of Feature)
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|SimpleRankedCrossRef
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|-
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|seqfeature_relationship
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|FeatureRelationship
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|SimpleRichFeatureRelationship
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|-
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|location
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|Location
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|SimpleRichLocation, CompoundRichLocation, or EmptyRichLocation
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|-
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|location_qualifier_value
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|(use properties of Location)
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|SimpleNote
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|-
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|seqfeature_path
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|nil
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|nil
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|-
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|bioentry_path
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|nil
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|nil
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|-
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|term_path
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|nil
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|nil
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|}
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=== Configuring your application to use Hibernate and BioSQL. ===
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To configure Hibernate, you must edit the copy you made of the hibernate.cfg.xml file. Near the top is a section that looks like this:
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<xml>
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<property name="connection.datasource">java:comp/env/jdbc/YOUR_JNDI_DATASOURCE_GOES_HERE</property>
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<!-- OR... (for testing only)...
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<property name="connection.password">MYPASSWORD</property>
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<property name="connection.pool_size">20</property>
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-->
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</xml>
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The exact details will vary according to which database you are using.
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You will see that the default way of using Hibernate is through a JNDI datasource, usually supplied by a servlet container such as Tomcat. In this case, you should modify the connection.datasource parameter to reflect the name of your JNDI datasource.

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