Release notes

Release Notes - PhenoTips - Version 1.4-milestone-1 - HTML format

Sub-task

  • [PT-1750] - Pedigree: Add ability to shade nodes by phenotype
  • [PT-2414] - Add tests for the family locking module
  • [PT-2671] - Add a RecordConfigurationModule role
  • [PT-2672] - Make the RecordConfiguration, RecordSection and RecordElement interfaces mutable
  • [PT-2673] - Update the DefaultRecordConfigurationManager to use the RecordConfigurationModules
  • [PT-2674] - Make the RecordConfigurationManager support more than one type of record
  • [PT-2675] - Add a RecordConfigurationModule for patient records
  • [PT-2676] - Add a RecordConfigurationModule for studies
  • [PT-2677] - Add a RecordConfigurationModule for consents
  • [PT-3029] - API changes for supporting vocabulary categories
  • [PT-3030] - Modify DefaultVocabularyManager to support searching in vocabulary categories
  • [PT-3039] - Modify each vocabulary to report the categories it supports
  • [PT-3040] - Implement the new category search methods
  • [PT-3080] - Move any consents-related code to a new consents module
  • [PT-3097] - Update SolrService to use category search methods
  • [PT-3098] - Extend REST API
  • [PT-3107] - Switch to standard XWiki pagination look for gene panels
  • [PT-3275] - Improve info text in pedigree legend box
  • [PT-3323] - Add a RecordConfigurationModule for family records
  • [PT-3334] - Switch from Jena2 to Jena3

Bug

  • [PT-2092] - Unable to remove collaborator after modifying owner
  • [PT-2815] - Family updates and patient JSON updates should be performed under the correct user
  • [PT-2860] - Pushed record does not get assigned to the chosen remote work group
  • [PT-3199] - 'Present' column in exported excel is blank for some cases
  • [PT-3208] - In pedigree editor export JSON the very first patient is marked as proband
  • [PT-3220] - Cannot administer users on virtual instances
  • [PT-3221] - Gene Comments panel is too short, Strategy panel too long
  • [PT-3223] - Variant Interpretation column lacks human-readable UI strings
  • [PT-3229] - LifeStatusController does not handle life status changes well on import
  • [PT-3235] - Pedigree editor may be broken after a node is deleted
  • [PT-3236] - Reindexing HGNC through REST fails if url isn't provided
  • [PT-3239] - Unclickable labels for several administrative section elements
  • [PT-3257] - Problem when user removes self as managing collaborator
  • [PT-3260] - The permissions REST API always returns the 'owner' access level for collaborators with administrative rights on a patient record, regardless of the recorded collaborator level
  • [PT-3261] - Unable to import 10 patients through import JSON option
  • [PT-3265] - getTerm in HGNC vocabulary should match on exact input provided
  • [PT-3272] - Upon deletion of a pedigree node, its carrier genes are still present in the legend
  • [PT-3273] - Gene strategies and variant evidence have an extra semicolon when exported to Excel
  • [PT-3278] - Export doesn't take into account the filters for genes and for clinical diagnosis
  • [PT-3279] - "Delete all x" option does not work in the Advanced Search and in the Export dialog
  • [PT-3280] - In filters (both Patient/family table and Export dialog), the spacing between labels and inputs is confusing
  • [PT-3284] - Suggest widgets for vocabularies do not work on the filters for groups' owned and shared cases tables, and for study cases
  • [PT-3287] - In the advanced data filters, when filtering by more than one owner no results are returned
  • [PT-3294] - A phenotype can appear as both positive and negative in the "Current selection" in certain conditions
  • [PT-3295] - Selecting from the quick search suggestions a phenotype that is already selected and had details attached appears to cause the loss of the details
  • [PT-3297] - Phenotype details re-appear in view mode, with no pre-notice in edit mode about the extra data
  • [PT-3305] - Empty family tables displayed on the homepage when the permissions module is not installed
  • [PT-3306] - No patients table displayed on the homepage when the permissions module is not installed
  • [PT-3307] - A&W box does not clear in some situations, causing problems with export to png
  • [PT-3308] - Export to PNG SVG initiated in pedigree editor is missing person's details other than internalID
  • [PT-3309] - Remove quotation marks from Export PNG/SVG buttons
  • [PT-3313] - Not all patients are shown in the "All Patients" table when the permissions module is not installed
  • [PT-3315] - Phenotypes from the predefined list disappear from phenotype selection after JSON import from edit mode
  • [PT-3319] - Long custom entries in the genes table cause layout issues
  • [PT-3320] - Pedigree node hover boxes do not fade out when they should in some cases
  • [PT-3338] - In the excel export, paternal ethnicity should be left, maternal ethnicity should be right
  • [PT-3345] - When importing a new patient, a new owner object is created even if the owner already exists
  • [PT-3353] - Terms added from the ontology browser are always added in the main clinical symptoms section, regardless of where the browser was triggered from
  • [PT-3354] - Genes that are confirmed negative should NOT be coloured in the pedigree
  • [PT-3355] - Some functionality is broken in IE9 (most notably pedigree editor can not be opened)
  • [PT-3357] - In pedigree editor do not show A&W options on hoverboxes for patients which are read-only for current user

New Feature

  • [PT-2496] - Extract HPO terms from "Indication for referral" and "Medical history" and display them as phenotype suggestions
  • [PT-3020] - Vocabulary types
  • [PT-3343] - 'Owner' and 'visibility' should be available for displaying in the patients table
  • [PT-3344] - Collaborators should be available for displaying in the patients table, and filterable in the advanced filters
  • [PT-3358] - Service for annotating freeform text with HPO terms using CTakes

Story

  • [PT-2669] - Make the patient record form easier to configure from other modules

Task

  • [PT-1366] - The vocabulary reindexing operation should not leave the system in a bad state at any moment
  • [PT-1393] - Improve pedigree node colouring and legend
  • [PT-1403] - Replace all usages of the deprecated ScriptServices with the new ontology access services
  • [PT-2323] - Refactor the REST service to use the delete method from PatientRepository
  • [PT-3051] - Allow assigning Alive and Well status to a group of people in pedigree editor
  • [PT-3086] - Add option to filter out genes that have been ruled out in gene panels
  • [PT-3196] - Deprecate SolrService and use the Vocabularies RESTful API instead
  • [PT-3207] - Require Java 1.8
  • [PT-3210] - Refactor the patient permissions UIX to use the RESTful API for permissions
  • [PT-3211] - Move the differential phenotype suggestions service into a separate component
  • [PT-3214] - Write Tests for Patient Data
  • [PT-3228] - Upgrade to Solr 6.5.1
  • [PT-3245] - Cannot install PhenoTips on systems with java < 1.8.101
  • [PT-3253] - Cleanup diagnoses titles in All Patient Data view
  • [PT-3264] - Remove Touchscreen drag and drop JavaScriptExtention
  • [PT-3311] - TermsForGene.toJSON should create a summary for each term instead of calling term.toJSON
  • [PT-3312] - The homepage gadgets title should display the title parameter, not the document title
  • [PT-3314] - When the permissions module is not installed, do not show the 'owner' and 'visibility' advanced filters
  • [PT-3324] - Refactor the Permissions manager dialog to enable extending it with custom sharing options
  • [PT-3328] - Fail the build if there are dependency misconfigurations
  • [PT-3349] - Remove FAMILIES SHARED WITH ME widget from the home page
  • [PT-3352] - By default negative genes should be excluded from Gene panel suggestions

Improvement

  • [PT-2925] - Expose XWikiDocument in Patient class (via Entities API)
  • [PT-3127] - Rearrange pedigree import dialog to put the options above the actual file selection
  • [PT-3186] - Improve advanced data filtering form
  • [PT-3187] - Rename "Disorders" column in the excel export file
  • [PT-3212] - Rename Molecular diagnosis to Final diagnosis
  • [PT-3215] - Add info button to already selected final and clinical diagnoses
  • [PT-3216] - Add info button to selected phenotypes
  • [PT-3230] - Modify "by disease" to "by final diagnosis" in advanced data filter and both export dialogs
  • [PT-3240] - Remove redundant options from Excel export dialog
  • [PT-3248] - Rename "disorders" to "final diagnosis" in pedigree editor
  • [PT-3262] - Improve the look of the export dialog
  • [PT-3267] - Save pedigree user preferences
  • [PT-3276] - Merge 2 APGAR scores options into one in Push dialog
  • [PT-3277] - In the excel export, move Variants between Genes and Genetic data notes
  • [PT-3282] - Allow pushing/exporting/importing medical reports
  • [PT-3286] - When hovering an individual in the pedigree, highlight all its abnormalities/annotations in the legend
  • [PT-3304] - "New patient" button in the browse patient page should be underlined on mouse hover
  • [PT-3310] - Remove comma from text displayed in JSON import dialog
  • [PT-3329] - Enable checkstyle for test code
  • [PT-3330] - Allow pushing/exporting/importing additional images
  • [PT-3332] - Allow pushing/exporting/importing additional documents
  • [PT-3346] - Filter panel should remain collapsed until user who closed it opens it again

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