Release Notes - PhenoTips - Version 1.3-milestone-5 - HTML format

Sub-task

  • [PT-2113] - Implement SolrVocabularyInputTerm
  • [PT-2777] - Write a migrator to translate existing gene data from HGNC id to Ensembl Id
  • [PT-2785] - Store genes internally as Ensembl IDs
  • [PT-2929] - Update the pedigree editor to work with Ensembl IDs instead of gene symbols
  • [PT-2942] - Export both gene name and Ensembl id in the patient JSON
  • [PT-2944] - Write a migrator to translate existing gene data in pedigrees
  • [PT-2945] - Complete A&W feature
  • [PT-2979] - Use VocabularyExtensions when reindexing vocabularies
  • [PT-2988] - Add "life_status" field to patient class
  • [PT-2989] - Add UI extension for displaying life_status in the patient form
  • [PT-2990] - Remove "Date of death unknown" from UI
  • [PT-2991] - Write a migrator to populate life status
  • [PT-2992] - Update the lifestatus controllers to take this property into account instead of date of death
  • [PT-2994] - DoD should be displayed only if patient is deceased

Bug

  • [PT-1787] - Using two consecutive dashes -- in the patient's identifier field will display it striked out in view mode
  • [PT-2069] - Two dashed lines in OMIM list creates strikethrough
  • [PT-2932] - Push field selection dialogue flashes annoyingly when opened
  • [PT-2949] - Cannot specify variant coordinates for variants entered pre-1.3M4
  • [PT-2950] - "Chromosome: NA" displayed in the variant summary in edit mode
  • [PT-2953] - Broken images displayed on the dashboard for groups without a specific image attached to them
  • [PT-2955] - In the 'browse all patients' page, 'New patient' button often adds multiple patients from one click
  • [PT-2961] - Legend is broken in pedigree editor
  • [PT-2967] - Entering ethnicities or allergies with a pipe | in them will actually split the value in two
  • [PT-2968] - Adding phenotype details for non-standard phenotypes may fail when the term contains characters not valid in an URL
  • [PT-2971] - An empty family with no pedigree has rights that are too permissive
  • [PT-2980] - Global mode of inheritance and Global age of onset cannot be pushed / imported
  • [PT-2984] - Cannot tab out of gene field if correct gene name is entered
  • [PT-3003] - Users shouldn't be allowed to add comments on code pages

New Feature

  • [PT-2821] - Allow to retrieve multiple patients at once via REST, given a list of (internal or external) IDs
  • [PT-2987] - "Life status" field in the patient form

Story

  • [PT-2012] - Store genes internally as Ensembl gene IDs

Task

  • [PT-1814] - Warn users of unsaved data loss
  • [PT-2014] - A&W in the pedigree

Improvement

  • [PT-2889] - Drop "living" from "Other living affected relatives”
  • [PT-2899] - When switching to another language while editing warn user of potential data loss
  • [PT-2951] - Improve warning message when deleting a single pedigree node results in removal of many other nodes
  • [PT-2957] - Improve the aspect of the language selection menu
  • [PT-2966] - By default all studies should be selectable
  • [PT-2976] - Show OMIM diagnosis suggestions in view mode
  • [PT-2996] - Update JSONTool usage in velocity code

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