Difference between revisions of "PSU Presentation"
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Connections for the '''Hibernate''' engine are configured in the Spring configuration file | Connections for the '''Hibernate''' engine are configured in the Spring configuration file | ||
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Simple web page to demonstrate displaying a basic feature | Simple web page to demonstrate displaying a basic feature | ||
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Revision as of 21:15, 9 October 2012
This Wiki page is an edited version of Chinmay's presentation.
Sanger Pathogen Sequencing Unit (PSU)
- GeneDB is the organism data and annotation database for the Pathogen Sequencing Unit (PSU) at the Sanger Institute, UK
- Contains 37 organisms, which is expected to grow to 62
- Artemis is an annotation/DNA graphical interface
- PSU is currently migrating to chado schema
- We've implemented a common interface with the two leading open source frameworks: Hibernate and iBatis
Technical - Connections
Connections for the Hibernate engine are configured in the Spring configuration file
<bean id="dataSource" class="org.apache.commons.dbcp.BasicDataSource"> <property name="driverClassName" value="org.postgresql.Driver" /> <property name="url" value="jdbc:postgresql://holly.sanger.ac.uk:5432/chado" /> <property name="username" value="DELIBERATELY_BOGUS_NAME"/> <property name="password" value="WIBBLE" /> </bean> </xml> * Uses a connection pool * Connection to the database is specified graphically, so the '''iBatis''' configuration file has variables for the location: <syntaxhighlight lang="xml"> <property name="JDBC.Driver" value="org.postgresql.Driver"/> <property name="JDBC.ConnectionURL” value="jdbc:postgresql://${chado}"/> <property name="JDBC.Username" value="${username}"/> <property name="JDBC.Password" value="${password}"/> </xml> * provide database location, username & password * select from scrollable list of feature with residues (organisms in separate Postgres schemas) what to open in Artemis =====Technical - Code Generation===== * The shared interface and hibernate implementation were originally generated * There’s no explicit code generation (although the Spring and Hibernate runtimes may use them behinds the scenes) =====Technical - Transactions===== * Transactions are fully supported =====Problems 1, 2, & 3===== Creating a gene <syntaxhighlight lang="java"> genes[0] = new Feature(ORG, GENE, "xfile", false, false, now, now); genes[0].setSeqLen(1029); sequenceDao.persist(genes[0]); FeatureLoc loc = new FeatureLoc(SOURCE_FEATURE, genes[0], 13691, false, 14720, false, (short)1, 0, 0 ,0); sequenceDao.persist(loc); addFeatureProp(genes[0], "description", "A test gene for GMOD meeting"); addSynonymsToFeature(genes[0], "mulder", "scully"); createExon("exon1", genes[0], 13691, 13767, now, 0); createExon("exon2", genes[0], 14687, 14720, now, 1);
Retrieve a gene
Feature f = sequenceDao.getFeatureByUniqueName("xfile"); displayGene(f);
Update a gene
genes[0].setUniqueName("x-file"); sequenceDao.merge(genes[0]);
private Feature createExon(String name, Feature gene, int min, int max, Timestamp now, int rank) { Feature exon = new Feature(ORG, EXON, name, false, false, now, now); exon.setSeqLen(max-min); sequenceDao.persist(exon); FeatureLoc loc = new FeatureLoc(SOURCE_FEATURE, exon, min, false, max, false, (short)1, 0, 0 ,0); sequenceDao.persist(loc); return exon; }
Demo – Sample Problem
Simple web page to demonstrate displaying a basic feature
<st:section name="Naming" id="gene_naming" collapsed="false" collapsible="false" hideIfEmpty="true"> <dl> <dt><b>symbol:</b></dt> <dd>${feature.uniqueName}</dd> </dl> <db:synonym name="synonym" var="name" collection="${feature.featureSynonyms}"> <br /><b>Synonym:</b> <db:list-string collection="${name}" /> </db:synonym> <dt><b>Type:</b></dt> <dd>${feature.cvTerm.name}</dd> <st:section name="Exons" collapsed="false" collapsible="true" hideIfEmpty="true"> <display:table name="exons" uid="tmp" pagesize="30" class="simple" cellspacing="0" cellpadding="4"> <display:column property="uniqueName" title="Exon"/> <display:column property="featureLocsForSrcFeatureId.fmin" title="Start"/> <display:column property="featureLocsForSrcFeatureId.fmax" title="end"/> </display:table> </st:section> <st:section name="cds" collapsible="true"> <b>${feature.residues}</b> </st:section> </xml> [[Category:Middleware Presentations]]