org.phenotips.studies.family.migrations

Class R71498PhenoTips2155DataMigration

java.lang.Object

com.xpn.xwiki.store.migration.hibernate.AbstractHibernateDataMigration

org.phenotips.studies.family.migrations.R71498PhenoTips2155DataMigration

All Implemented Interfaces:

com.xpn.xwiki.store.migration.DataMigration, com.xpn.xwiki.store.migration.hibernate.HibernateDataMigration, com.xpn.xwiki.store.XWikiHibernateBaseStore.HibernateCallback<Object>

@Component
@Named(value="R71498PhenoTips#2155")
@Singleton
public class R71498PhenoTips2155DataMigration
extends com.xpn.xwiki.store.migration.hibernate.AbstractHibernateDataMigration
implements com.xpn.xwiki.store.XWikiHibernateBaseStore.HibernateCallback<Object>

Migration for PhenoTips issue #2155: migrating old family studies data. It is assumed that all old family studies relationships are specified for the proband node. Thus if node A has a relationship to node B, and node B also has a relationship to node A, then no link is made since it is not clear which one is the proband (this case is considered unlikely); such cases should be resolved manually. Otherwise, if there already exists a pedigree for the node which has an old family studies relationship, that relationship is added to that node's pedigree comment. A comment without any pedigree links is also added in case relationship can not be converted to a pedigree in a uniform way, e.g. for "uncle" relationships it is not clear if the uncle is on the maternal or paternal side. In all other cases (no pedigree, relationships are only specified onw-way for one node, and relationship can be one-to-one mapped to a pedigree layout) a new family+pedigree is created and all mentioned patients are linked to the corresponding nodes in that pedigree.

Since:

1.3M4

Version:

$Id: 80155830b6085909f5e6e1f0e2ad80b219ac7bf3 $

Field Summary

Fields inherited from class com.xpn.xwiki.store.migration.hibernate.AbstractHibernateDataMigration

componentManager

Constructor Summary

Constructors

Constructor and Description
R71498PhenoTips2155DataMigration()

Method Summary

Methods

Modifier and Type	Method and Description
Object	doInHibernate(org.hibernate.Session hSession)
String	getDescription()
com.xpn.xwiki.store.migration.XWikiDBVersion	getVersion()
protected void	hibernateMigrate()

Methods inherited from class com.xpn.xwiki.store.migration.hibernate.AbstractHibernateDataMigration

getLiquibaseChangeLog, getName, getPreHibernateLiquibaseChangeLog, getStore, getXWikiContext, migrate, shouldExecute

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

R71498PhenoTips2155DataMigration

public R71498PhenoTips2155DataMigration()

Method Detail

getDescription

public String getDescription()

Specified by:

getDescription in interface com.xpn.xwiki.store.migration.DataMigration

getVersion

public com.xpn.xwiki.store.migration.XWikiDBVersion getVersion()

Specified by:

getVersion in interface com.xpn.xwiki.store.migration.DataMigration

hibernateMigrate

protected void hibernateMigrate()
                         throws com.xpn.xwiki.store.migration.DataMigrationException,
                                com.xpn.xwiki.XWikiException

Specified by:

hibernateMigrate in class com.xpn.xwiki.store.migration.hibernate.AbstractHibernateDataMigration

Throws:

com.xpn.xwiki.store.migration.DataMigrationException

com.xpn.xwiki.XWikiException

doInHibernate

public Object doInHibernate(org.hibernate.Session hSession)
                     throws org.hibernate.HibernateException,
                            com.xpn.xwiki.XWikiException

Specified by:

doInHibernate in interface com.xpn.xwiki.store.XWikiHibernateBaseStore.HibernateCallback<Object>

Throws:

org.hibernate.HibernateException

com.xpn.xwiki.XWikiException