Release Notes - PhenoTips - Version 1.4-milestone-2 - HTML format

Sub-task

  • [PT-3292] - Migrator for existing pedigree cancer data
  • [PT-3293] - New cancers UI in pedigree editor
  • [PT-3360] - Add a PhenoTips.VocabularySourceRelocationClass XClass
  • [PT-3361] - Add Vocabulary#getSourceLocation
  • [PT-3362] - Add VocabularySourceRelocationService
  • [PT-3363] - Add an administration section for defining vocabulary source relocations
  • [PT-3364] - Modify the reindex page to use getSourceLocation instead of getDefaultSourceLocation
  • [PT-3365] - Modify existing vocabularies and vocabulary extensions to use the relocation service for each additional resource URL used
  • [PT-3383] - UIX points for generic entity sheets in patient record
  • [PT-3392] - Better column selection for homepage gadgets
  • [PT-3393] - Improve the links displayed for each patient and family in the homepage gadgets
  • [PT-3397] - Display action links (edit,delete) in the patient and family gadgets on the homepage
  • [PT-3400] - The permissions UIX should have the extension point org.phenotips.entitySheet.before
  • [PT-3401] - Make the wording in the permssions dialog more generic (e.g. "case"->"record") to capture both patients and families
  • [PT-3411] - Rename the PatientAccessRightsManagement UIX to AccessRightsManagement
  • [PT-3412] - Refactor the AccessRightsManagement UIX (variable and method names, translation keys, etc) to be more generic, i.e. not refer to patients specifically
  • [PT-3413] - Add support for family entities in the AccessRightsManagement code
  • [PT-3414] - Add UIX points for generic entity sheets in family record
  • [PT-3417] - Add administration section for configuring the text-mining service
  • [PT-3418] - Read and use the service URL from application configuration if available
  • [PT-3457] - Unable to open node that contains cancers with unspecified age
  • [PT-3458] - Patient sheet suggest pickers should accept free text
  • [PT-3459] - PedigreeProcessor should not ignore free-text disorder terms
  • [PT-3461] - Pedigree crashes when patient sheet has free-text disorders
  • [PT-3462] - Custom disorders are not displayed correctly in view and edit mode
  • [PT-3466] - Add options for using CTAKES and NCR remotely through services.phenotips.org
  • [PT-3469] - Remove the old PermissionsManagerScriptService

Bug

  • [PT-2804] - All families should only list current user's families
  • [PT-2824] - Families shared with me are missing some families with shared patients
  • [PT-3321] - Drop-down autocomplete doesn't follow the search bar in pedigree editor
  • [PT-3366] - In pedigree editor node menu first tab has some layout problems
  • [PT-3374] - Gene panels should display gene symbol from HGNC rather that its alias
  • [PT-3385] - Unauthenticated users can't save new pedigree
  • [PT-3387] - Suggestions from clinical notes are sometimes misaligned
  • [PT-3405] - Guest users should have "owner" access on guest-owned patient records
  • [PT-3408] - Wrong failure reported when guest users delete their records
  • [PT-3410] - Under high load, no HPO terms are extracted from clinical notes
  • [PT-3416] - Loading spinner doesn't display properly in export modal
  • [PT-3428] - BROWSE RELATED TERMS button does not work in pedigree editor
  • [PT-3438] - Pedigree editor breaks when using non-default date input format
  • [PT-3444] - DefaultCollaborator objects with null user cannot be added to any hashed collection
  • [PT-3446] - In some cases, using a decade for DOB in a pedigree breaks the editor
  • [PT-3447] - DefaultOwner objects with null user cannot be compared
  • [PT-3449] - When using dd-mm-yyyy for pedigree date format (both input and display), using decades in the pedigree breaks the editor
  • [PT-3452] - Enable support for free-text diagnoses in patient form and in pedigree editor
  • [PT-3467] - Genes should be stored internally as Ensembl IDs, not HGNC IDs

New Feature

  • [PT-2224] - Use a standardized vocabulary for cancers in the pedigree editor
  • [PT-3341] - Allow administrators to permanently redefine the location of vocabulary sources
  • [PT-3381] - REST API for family permissions
  • [PT-3386] - Administrators should be able to choose between multiple services used for text annotation

Task

  • [PT-1466] - Allow filtering patient records by the study they belong to
  • [PT-2624] - Implement family permissions
  • [PT-3034] - Allow method PATCH on patient resources
  • [PT-3226] - Reimplement the data access restrictions as AuthorizationModules
  • [PT-3382] - Integrate permission dialog with family record
  • [PT-3402] - Add an authorisation module for allowing the owner and collaborators of family member (patient) records to access the family record and pedigree
  • [PT-3409] - Make FamilyRepository a PrimaryEntityManager
  • [PT-3419] - Re-enable the FAMILIES SHARED WITH ME widget on the home page
  • [PT-3441] - Create a PrimaryEntityResolver
  • [PT-3443] - Refactor PatientAccessHelper and PermissionsManager implementations to fix dependency issue

Improvement

  • [PT-3081] - Updating patient records should allow explicit updates, overwrites and merges
  • [PT-3271] - Improve vocabulary reindex process
  • [PT-3376] - Live tables: replace "Reported by" column with "Owner"
  • [PT-3377] - Remove negative phenotypes from Gene panel section
  • [PT-3380] - Make families basic entities
  • [PT-3394] - Improve the links displayed for each family in the families directory
  • [PT-3395] - Improve the look of the livetable actions
  • [PT-3396] - Improve the usefulness of the data and links in the homepage gadgets related to patients and families
  • [PT-3415] - Remove useless notification "Added HP:#######" displayed when accepting a text-mining suggestion
  • [PT-3427] - Open patients with private families should not show the pedigree at all for non-collaborators
  • [PT-3471] - Make the patients and families script services more similar to the underlying entity repository interface

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