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createFamilyDocument(XWikiDocument, JSONObject, String, XWikiContext, Session) - Method in class org.phenotips.studies.family.migrations.PhenotipsFamilyMigrations

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

D

doInHibernate(Session) - Method in class org.phenotips.studies.family.migrations.R71496PhenoTips2339DataMigration

doInHibernate(Session) - Method in class org.phenotips.studies.family.migrations.R71498PhenoTips2155DataMigration

doInHibernate(Session) - Method in class org.phenotips.studies.family.migrations.R71500PhenoTips2944DataMigration

doInHibernate(Session) - Method in class org.phenotips.studies.family.migrations.R71503PhenoTips1393DataMigration

doInHibernate(Session) - Method in class org.phenotips.studies.family.migrations.R71505PhenoTips3402DataMigration

Searches for all family documents that contain a XWikiRights object, and removes the objects.

doInHibernate(Session) - Method in class org.phenotips.studies.family.migrations.R71506PhenoTips3292DataMigration

doInHibernate(Session) - Method in class org.phenotips.studies.family.migrations.R71507PhenoTips3423DataMigration

doInHibernate(Session) - Method in class org.phenotips.studies.family.migrations.R71508PhenoTips3424DataMigration

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getDescription() - Method in class org.phenotips.studies.family.migrations.R71496PhenoTips2339DataMigration

getDescription() - Method in class org.phenotips.studies.family.migrations.R71497PhenoTips2154DataMigration

getDescription() - Method in class org.phenotips.studies.family.migrations.R71498PhenoTips2155DataMigration

getDescription() - Method in class org.phenotips.studies.family.migrations.R71500PhenoTips2944DataMigration

getDescription() - Method in class org.phenotips.studies.family.migrations.R71503PhenoTips1393DataMigration

getDescription() - Method in class org.phenotips.studies.family.migrations.R71505PhenoTips3402DataMigration

getDescription() - Method in class org.phenotips.studies.family.migrations.R71506PhenoTips3292DataMigration

getDescription() - Method in class org.phenotips.studies.family.migrations.R71507PhenoTips3423DataMigration

getDescription() - Method in class org.phenotips.studies.family.migrations.R71508PhenoTips3424DataMigration

getOwner(XWikiDocument) - Method in class org.phenotips.studies.family.migrations.PhenotipsFamilyMigrations

Returns the owner of the patient.

getVersion() - Method in class org.phenotips.studies.family.migrations.R71496PhenoTips2339DataMigration

getVersion() - Method in class org.phenotips.studies.family.migrations.R71497PhenoTips2154DataMigration

getVersion() - Method in class org.phenotips.studies.family.migrations.R71498PhenoTips2155DataMigration

getVersion() - Method in class org.phenotips.studies.family.migrations.R71500PhenoTips2944DataMigration

getVersion() - Method in class org.phenotips.studies.family.migrations.R71503PhenoTips1393DataMigration

getVersion() - Method in class org.phenotips.studies.family.migrations.R71505PhenoTips3402DataMigration

getVersion() - Method in class org.phenotips.studies.family.migrations.R71506PhenoTips3292DataMigration

getVersion() - Method in class org.phenotips.studies.family.migrations.R71507PhenoTips3423DataMigration

getVersion() - Method in class org.phenotips.studies.family.migrations.R71508PhenoTips3424DataMigration

H

hibernateMigrate() - Method in class org.phenotips.studies.family.migrations.R71496PhenoTips2339DataMigration

hibernateMigrate() - Method in class org.phenotips.studies.family.migrations.R71497PhenoTips2154DataMigration

hibernateMigrate() - Method in class org.phenotips.studies.family.migrations.R71498PhenoTips2155DataMigration

hibernateMigrate() - Method in class org.phenotips.studies.family.migrations.R71500PhenoTips2944DataMigration

hibernateMigrate() - Method in class org.phenotips.studies.family.migrations.R71503PhenoTips1393DataMigration

hibernateMigrate() - Method in class org.phenotips.studies.family.migrations.R71505PhenoTips3402DataMigration

hibernateMigrate() - Method in class org.phenotips.studies.family.migrations.R71506PhenoTips3292DataMigration

hibernateMigrate() - Method in class org.phenotips.studies.family.migrations.R71507PhenoTips3423DataMigration

hibernateMigrate() - Method in class org.phenotips.studies.family.migrations.R71508PhenoTips3424DataMigration

O

org.phenotips.studies.family.migrations - package org.phenotips.studies.family.migrations

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PhenotipsFamilyMigrations - Class in org.phenotips.studies.family.migrations

Provides utility methods for migrating patient documents.

PhenotipsFamilyMigrations() - Constructor for class org.phenotips.studies.family.migrations.PhenotipsFamilyMigrations

processPedigree(JSONObject, String) - Method in class org.phenotips.studies.family.migrations.PhenotipsFamilyMigrations

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

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R71496PhenoTips2339DataMigration - Class in org.phenotips.studies.family.migrations

Migration for PhenoTips issue PT-2339: support for negative phenotypes and phenotype details in pedigree editor.

R71496PhenoTips2339DataMigration() - Constructor for class org.phenotips.studies.family.migrations.R71496PhenoTips2339DataMigration

R71497PhenoTips2154DataMigration - Class in org.phenotips.studies.family.migrations

Migration for PhenoTips issue #2154: migrating existing pedigrees into families with one member.

R71497PhenoTips2154DataMigration() - Constructor for class org.phenotips.studies.family.migrations.R71497PhenoTips2154DataMigration

R71498PhenoTips2155DataMigration - Class in org.phenotips.studies.family.migrations

Migration for PhenoTips issue #2155: migrating old family studies data.

R71498PhenoTips2155DataMigration() - Constructor for class org.phenotips.studies.family.migrations.R71498PhenoTips2155DataMigration

R71500PhenoTips2944DataMigration - Class in org.phenotips.studies.family.migrations

Migration for PhenoTips issue PT-2944: translate existing gene data in pedigree from gene name to Ensembl gene IDs.

R71500PhenoTips2944DataMigration() - Constructor for class org.phenotips.studies.family.migrations.R71500PhenoTips2944DataMigration

R71503PhenoTips1393DataMigration - Class in org.phenotips.studies.family.migrations

Migration for PhenoTips issue PT-1393: Improve pedigree node colouring and legend.

R71503PhenoTips1393DataMigration() - Constructor for class org.phenotips.studies.family.migrations.R71503PhenoTips1393DataMigration

R71505PhenoTips3402DataMigration - Class in org.phenotips.studies.family.migrations

Migration for PhenoTips issue PT-3402: Search for documents with families that have XWikiRights objects and remove the objects.

R71505PhenoTips3402DataMigration() - Constructor for class org.phenotips.studies.family.migrations.R71505PhenoTips3402DataMigration

R71506PhenoTips3292DataMigration - Class in org.phenotips.studies.family.migrations

Migration for PhenoTips issue PT-3292: linking existing cancers to their OncoTree identifiers.

R71506PhenoTips3292DataMigration() - Constructor for class org.phenotips.studies.family.migrations.R71506PhenoTips3292DataMigration

R71507PhenoTips3423DataMigration - Class in org.phenotips.studies.family.migrations

Migrate from old internal pedigree format to the new.

R71507PhenoTips3423DataMigration() - Constructor for class org.phenotips.studies.family.migrations.R71507PhenoTips3423DataMigration

R71508PhenoTips3424DataMigration - Class in org.phenotips.studies.family.migrations

Migrate internal representation of pedigrees stored in the auto-generated SimpleJSON format.

R71508PhenoTips3424DataMigration() - Constructor for class org.phenotips.studies.family.migrations.R71508PhenoTips3424DataMigration

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setFamilyReference(XWikiDocument, String, XWikiContext) - Method in class org.phenotips.studies.family.migrations.PhenotipsFamilyMigrations

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

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updatePedigree(JSONObject, Map<String, String>, Map<String, String>) - Method in class org.phenotips.studies.family.migrations.PhenotipsFamilyMigrations

Asigns nodes to PhenoTips records and adds comments to nodes.

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