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: d9736db952d95f164c83b8d4baa602934467fcd0 $

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 pedigree, 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.
Set<String>	updatePedigree(org.json.JSONObject pedigree, Map<String,String> externalIdToPhenotipsId, Map<String,String> commentsByPhenotipsId) Asigns nodes to PhenoTips records and adds comments to nodes.

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 pedigree,
                                  String patientId)

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

Parameters:

pedigree - pedigree JSON, supposedly in 1.2.x format

patientId - patient Id

Returns:

processed pedigree JSON object

updatePedigree

public Set<String> updatePedigree(org.json.JSONObject pedigree,
                         Map<String,String> externalIdToPhenotipsId,
                         Map<String,String> commentsByPhenotipsId)

Asigns nodes to PhenoTips records and adds comments to nodes. - Finds all nodes with the given external IDs and - if not already linked to a PT record - links them to the given PT record - For each node linked to a PT record (including nodes linked in step1 above) appends the comment provided

Parameters:

pedigree - pedigree as JSON. The pedigree will be modified in place

externalIdToPhenotipsId - a map of externalIDs which, if found in pedigree, should be linked to the corresponding phenotips records

commentsByPhenotipsId - a map of phenotips ids to comments that shouldbe added for those nodes. The list may include nodes linked based on the `externalIdToPhenotipsId` list

Returns:

a set of phenotips IDs that were newly linked based on externalID

getOwner

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

Returns the owner of the patient.

Parameters:

patientDoc - patient XDocument

Returns:

owner as string