Release Notes - PhenoTips - Version 1.4-milestone-3 - HTML format

Sub-task

  • [PT-2884] - Move pedigree updating code from versionUpdater.js to a migrator
  • [PT-2998] - Create IdentifierClass. Fields: label (String), value (String)
  • [PT-2999] - Add administration section
  • [PT-3000] - Create UIX for displaying identifiers
  • [PT-3001] - Write controllers
  • [PT-3002] - Implement searching by identifiers in "Advanced filters"
  • [PT-3339] - Modify the JSON serialization of consent objects to include the actual fields affected by the consent, if any
  • [PT-3340] - When generating the list of available fields to push, filter out any fields associated with consents that have not been granted at the previous step
  • [PT-3423] - Implement a migrator from old internal pedigree format to new
  • [PT-3424] - Implement a migrator from auto-generated internal pedigree format to new
  • [PT-3431] - Update format of stored/serialized pedigrees
  • [PT-3470] - Fix checkstyle violations for the entity-access-rules-api module
  • [PT-3501] - Store numeric age of diagnosis for cancers

Bug

  • [PT-2175] - Extended negative prenatal phenotypes never stored
  • [PT-2238] - Exception while saving a patient
  • [PT-2391] - Clicking N/A on a dropdown prenatal phenotype doesn't do the same on the duplicate
  • [PT-3082] - Excel export list EnsembleIDs in "Gene name" and "Gene symbol" columns
  • [PT-3104] - Different/inconsistent behavior when filtering in Advanced data filtering and Export
  • [PT-3335] - Obstetric History doesn't appear as an exportable/pushable information in the export preferences dialogs
  • [PT-3347] - Parental age at EDD doesn't appear to be exportable in the excel format
  • [PT-3442] - Users can remove from a family patients that they can't normally access
  • [PT-3450] - Filtering by member in the phenotips-groups macro ignores the Administrators subgroup
  • [PT-3455] - The consanguinity status of a patient isn't set when identifiable from the pedigree
  • [PT-3460] - Non-categorized custom phenotypes disappear from saved patient record
  • [PT-3473] - Filtering by gene doesn't work as expected in advanced filters, push and export
  • [PT-3479] - Guest users cannot access the families that they create
  • [PT-3481] - Unable to import pedigree using BOADICEA format
  • [PT-3486] - Family permission dialog cannot be moved around
  • [PT-3488] - Pedigree action buttons not looking good when scaling down below 90%
  • [PT-3493] - When using the PT embeddable skin, the "New Patient" button on the homepage doesn't work
  • [PT-3503] - Labels not shown on family form
  • [PT-3505] - Delete pedigree button label is white in some cases
  • [PT-3524] - 0 values for the Obstetric History fields are lost in the JSON export
  • [PT-3533] - OMIM is no longer reindexable
  • [PT-3534] - After reindexing vocabularies, spellchecked suggestions no longer work
  • [PT-3536] - Patient/Family search widget does not work for guest users
  • [PT-3542] - Records created by guest users should be accessible to everyone
  • [PT-3543] - The SVG rasterizer service caches the first requested size of the generated image
  • [PT-3565] - Variants cannot be deleted via the REST patient API
  • [PT-3579] - Unable to add collaborator
  • [PT-3587] - Measurement section isn't functioning

New Feature

  • [PT-3285] - When deleting an individual linked to a patient record from the pedigree, offer the option to also remove the corresponding patient record
  • [PT-3351] - REST Service for suggesting both users and workgroups simultaneously
  • [PT-3399] - Add a REST service for suggesting patients matching an input
  • [PT-3440] - Add the option to list other family members on the Patient record
  • [PT-3451] - Add "My groups" gadget on the homepage
  • [PT-3463] - Add a REST service for suggesting families matching an input
  • [PT-3529] - New API for providing metadata about entities
  • [PT-3532] - Add support for German and Russian HPO translations
  • [PT-3554] - Create a script that would enable upload of vcf file to the given patient

Story

  • [PT-1995] - Multiple external IDs per patient
  • [PT-3576] - Display the save actions for added tabs by default

Task

  • [PT-870] - Add a link to browse all owned patient records on the "my patients" gadget
  • [PT-2044] - Push patient module lacks tests
  • [PT-2617] - Change internal representation of pedigrees
  • [PT-3072] - Create a Gene class to hold gene info
  • [PT-3189] - Implement indexing of OncoTree
  • [PT-3359] - Replace "Patient" with "PrimaryEntity" in the permissions module
  • [PT-3477] - Script service for PrimaryEntityResolver
  • [PT-3491] - Replace Active Groups gadget with My Groups Gadget on homepage
  • [PT-3492] - Include the French HPO in the build
  • [PT-3518] - Add functionality for displaying additional tabs
  • [PT-3535] - Rename group administrators to group managers
  • [PT-3537] - Move DetailsDialog and DetailsDialogGroup to widgets
  • [PT-3550] - Hide ontologizer warnings on startup
  • [PT-3553] - Update gene table code to be able to handle displaying multiple gene tables
  • [PT-3556] - Validate all "mandatory" and "checked" form elements on scroll
  • [PT-3568] - Text mining should be disabled by default until we figure out why it is slowing down the system
  • [PT-3569] - Text mining should be running only when "Indication for referral" or "Medical history" fields are edited
  • [PT-3570] - Decrease the frequency of auto save from 10 seconds to 1 minute

Improvement

  • [PT-2446] - Consents administration: don't allow setting a consent as required for certain fields if it is already mandatory
  • [PT-2471] - Push dialog should display consented fields only
  • [PT-2936] - Adjust the alignment of variants editing fields
  • [PT-2986] - The "Perinatal complications" subsection (under the "Prenatal and perinatal history" section) is no longer shown on the patient form
  • [PT-3274] - Add Export PDF option to the More Action menu of the Family Page
  • [PT-3350] - Add ability to enter groups in the owner and collaborator fields of the filtering panel
  • [PT-3435] - Auditability of permissions and data sharing
  • [PT-3454] - Uniqueness check for family external ID (JS/UI only)
  • [PT-3474] - Add owner column to browse all families page
  • [PT-3480] - Better sizing of the livetable actions column
  • [PT-3502] - Improve the formatting of free text in diagnosis section
  • [PT-3517] - Use lighter shade of gray for placeholder text displayed in the genetic variants fields
  • [PT-3545] - Improve robustness of phenotype specificity scorer
  • [PT-3549] - Display homepage gadget extra actions as icons only instead of text

The text area below allows the project release notes to be copied to another document.