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. The migrator can only auto-generate a family/pedigree if there is no existing pedigree, all members of the family are owned by the same user, and all members of the family can be included in restricted pedigree shape (or a subset of the shape) as described below: < >--*--< > < >--*--< > | | +-----+-----+ | | | | | < > <...> ---*---

| +---+---+------------+---... | | | / \ < > <...> <...> <...> <...> - R denotes "root" patient (not necessarily the proband) - R may have at most one partner, P - at most 3 generations: root patient, root parents and root children - at most one partner for the root patient (P) - R may have some siblings or twins, none of which should have a child - P's parents are only related to P (and possibly as grandparents to P+R's children) - R's parents are only related to R and R's siblings (and possibly as grandparents to R+P's children) - all other nodes are children of R and P, can't be related to any other node other than R, P or other children as twins (or their parents as grandchilren) - "supported" relations are PARENT/CHILD/TWIN/SIBLING (because all other relationships 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) - there may be other patients which are only linked by non-supported relation types (e.g a patient which is only an uncle of someone - but not a parent or child or sibling of anyone). Those patients are added as comments to the generated pedigree. - a pedigree must have the root patient, and at least one more patient, which can be either a child, a parent or a partner. It may also have more relatives, as long as they fit the shape outlined above. It is assumed that the proband is the patient in the family with the earliest PT document creation time (not necessarily the "root" patient in the pedigree above). 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. Additionally and independently of the above, if a node in an existing pedigree has an external ID of an existing PhenoTips record, that patient is linked to the pedigree node (unless that patient is a member of another family or is also referenced from another pedigree).

Since:

1.3M4

Version:

$Id: 87568bf9aeeacc5d5dbce33a2d4f3e7f12bde25b $

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