org.phenotips.studies.family.migrations

Class PhenotipsFamilyMigrations

java.lang.Object

org.phenotips.studies.family.migrations.PhenotipsFamilyMigrations

@Component(roles=PhenotipsFamilyMigrations.class)
@Singleton
public class PhenotipsFamilyMigrations
extends Object

Provides utility methods for migrating patient documents.

Since:

1.3M1

Version:

$Id: 63473de5583a0c44cad705d190229df698aea2b3 $

Constructor Summary

Constructors

Constructor and Description
PhenotipsFamilyMigrations()

Method Summary

Methods

Modifier and Type	Method and Description
com.xpn.xwiki.doc.XWikiDocument	createFamilyDocument(com.xpn.xwiki.doc.XWikiDocument patientXDoc, org.json.JSONObject pedigreeData, String pedigreeImage, com.xpn.xwiki.XWikiContext xcontext, org.hibernate.Session hsession) Creates a new family document for given patient with pedigree data.
String	getOwner(com.xpn.xwiki.doc.XWikiDocument patientDoc) Returns the owner of the patient.
org.json.JSONObject	processPedigree(org.json.JSONObject data, String patientId) Adds to the pedigree JSON: "phenotipsId": patient ID in XWiki; "probandNodeID": 0; "JSON_version": "1.0".
boolean	setFamilyReference(com.xpn.xwiki.doc.XWikiDocument patientDoc, String documentReference, com.xpn.xwiki.XWikiContext xcontext) Sets the reference to the family document in the patient document.
void	updatePedigreeComment(org.json.JSONObject pedigree, String patientId, String commentAddition) Finds a pedigree node linked to patientID and adds the given comment to it's free-text comment.

Methods inherited from class java.lang.Object

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

Constructor Detail

PhenotipsFamilyMigrations

public PhenotipsFamilyMigrations()

Method Detail

createFamilyDocument

public com.xpn.xwiki.doc.XWikiDocument createFamilyDocument(com.xpn.xwiki.doc.XWikiDocument patientXDoc,
                                                   org.json.JSONObject pedigreeData,
                                                   String pedigreeImage,
                                                   com.xpn.xwiki.XWikiContext xcontext,
                                                   org.hibernate.Session hsession)

Creates a new family document for given patient with pedigree data.

Parameters:

patientXDoc - patient document

pedigreeData - pedigree data JSON

pedigreeImage - pedigree SVG image text

xcontext - xwiki context

hsession - hibernate session

Returns:

new family xwiki document or null in case of any errors

setFamilyReference

public boolean setFamilyReference(com.xpn.xwiki.doc.XWikiDocument patientDoc,
                         String documentReference,
                         com.xpn.xwiki.XWikiContext xcontext)

Sets the reference to the family document in the patient document.

Parameters:

patientDoc - patient document

documentReference - family document reference

xcontext - context

Returns:

true if operation was successful, false otherwise (e.g. when family reference creation failed)

processPedigree

public org.json.JSONObject processPedigree(org.json.JSONObject data,
                                  String patientId)

Adds to the pedigree JSON: "phenotipsId": patient ID in XWiki; "probandNodeID": 0; "JSON_version": "1.0".

Parameters:

data - pedigree data

patientId - patient Id

Returns:

processed pedigree JSON object

updatePedigreeComment

public void updatePedigreeComment(org.json.JSONObject pedigree,
                         String patientId,
                         String commentAddition)

Finds a pedigree node linked to patientID and adds the given comment to it's free-text comment.

Parameters:

pedigree - pedigree as JSON

patientId - the PhenoTips patient id

commentAddition - text of comment addition

getOwner

public String getOwner(com.xpn.xwiki.doc.XWikiDocument patientDoc)

Returns the owner of the patient.

Parameters:

patientDoc - patient XDocument

Returns:

owner as string