Release Notes - PhenoTips - Version 1.4-milestone-4 - HTML format

Sub-task

  • [PT-3507] - In pedigree, allow adding existing patients and creating new patients which are not linked to any pedigree node
  • [PT-3607] - Phase 1: Show the number of genes, sort by it in descending order and display an icon for nonstandard terms
  • [PT-3626] - Include vocabularies installed as extensions when getting the list of vocabularies
  • [PT-3627] - Cannot reindex vocabularies with special characters in their source URL
  • [PT-3628] - Cannot reindex a vocabulary from a source included inside a jar
  • [PT-3629] - Cannot reindex an installed vocabulary from a source included inside a jar
  • [PT-3637] - Gene panels: Add Rejected Candidate to Exclude Negative Genes filter
  • [PT-3641] - Add info button to Mode of inheritance
  • [PT-3650] - Display rejected genes with a strike-through
  • [PT-3699] - Provide API for adding patients to the family

Bug

  • [PT-1738] - Inputting an identical identifier in a new patient record and saving displays wrong error message
  • [PT-2938] - When a patient is deleted the "push to remote servers" data is not removed
  • [PT-3348] - Typed gene name doesn't get replaced with the proper Ensembl ID after displaying gene information
  • [PT-3464] - Logging out while in edit mode can lock the object for 30 minutes
  • [PT-3513] - Bugs in pedigree patient drop legend and unlinked patient handling
  • [PT-3544] - Free text entered as an ethnicity does not get suggested anymore
  • [PT-3558] - Export as JSON is missing the Referrer (report creator) info
  • [PT-3560] - Text mining kills local instance after few new records are entered
  • [PT-3561] - Remove the owner filter from the Workgroup Cases table since it doesn't work
  • [PT-3577] - Group cases are not displayed in Admin/Group/Cases
  • [PT-3580] - Lookup fields in advanced filters and export/push dialog need to have a uniform look
  • [PT-3585] - Newly added genes and variants do not have correct delete urls
  • [PT-3586] - Nonstandard features get copied to features array in the pedigree JSON representation
  • [PT-3590] - PED export omits cancers entered in the new cancer tab
  • [PT-3591] - Labeled external identifier fields should be shown in Advanced filter panel only if they are allowed and defined
  • [PT-3597] - Cannot delete a family via REST
  • [PT-3609] - Users that are not subscribed to any studies cannot see when a patient record belongs to a study
  • [PT-3610] - View-only collaborators are presented with the option to change the study of a patient record
  • [PT-3625] - Non-functional "Go to search page" displayed in the quick-search results
  • [PT-3630] - PhenoTips doesn't run on Java 9
  • [PT-3632] - Upon successful reindexing corresponding vocabulary fields turn into edit mode
  • [PT-3645] - Phenotype suggestions aren't displayed if OMIM suggestions aren't enabled
  • [PT-3648] - PhenoTips won't run on Windows if username contains space character
  • [PT-3653] - DetailsDialog date picker should be attached to the date input
  • [PT-3654] - Problems when SAVE button is disabled
  • [PT-3657] - Edit mode is not detected correctly by scrollValidation
  • [PT-3664] - Remove the top owner filter from the Shared Workgroup Cases table

New Feature

  • [PT-3379] - Families should support members that are not assigned to an individual in the pedigree
  • [PT-3605] - Add a REST service for accessing patients by labeled external identifiers
  • [PT-3646] - Validate entered PubMed ID and display details about the article
  • [PT-3662] - New API for working with connections (predicates) between entities
  • [PT-3693] - Add the ability to record parent's names
  • [PT-3694] - Add support for auditing who viewed and edited records

Task

  • [PT-1645] - New patient link in browse all patients page should have cursor pointer
  • [PT-3515] - Add ability to show external identifiers in place of internal ones in the Patient and Family record forms
  • [PT-3563] - DetailsDialog and DetailsDialogGroup should permit to save form data
  • [PT-3564] - Add the option for adding a date picker in DetailsDialog and DetailsDialogGroup
  • [PT-3571] - Resolve text mining issues and turn it on by default
  • [PT-3574] - Clearing Referrer and Last Author fields in familie's advanced filters does not automatically refresh the results
  • [PT-3575] - Better name for labeled identifiers
  • [PT-3589] - Make same visual arrangements in PED export dialog as in pedigree legend
  • [PT-3594] - Don't append a free text option if input has exact match in suggestion list
  • [PT-3595] - All "mandatory" and "checked" form elements should be added to checked list in scrollValidation on "xwiki:dom:updated"
  • [PT-3596] - Add the option to populate the date picker with last entered date in DetailsDialog
  • [PT-3598] - Remove space between the menu and the permissions block
  • [PT-3624] - Upgrade XWiki to 7.4.6
  • [PT-3658] - When initializing FuzzyDatePicker from fuzzyInput data, update the fuzzy-date input with that data
  • [PT-3659] - Display a pencil icon in top right corner of DetailsDialog on loss of focus
  • [PT-3660] - If the DetailsDialog contains no data, "no additional information" should be displayed on loss of focus
  • [PT-3661] - Remove the APIs for entity groups
  • [PT-3695] - Pedigree editor UI elements that are related to linking patient records to families made easily accessible programatically to editor add-ons

Improvement

  • [PT-2430] - Update vocabulary version upon successful reindexing
  • [PT-3266] - Add alternative names, inheritance, onset, and prevalence in ORDO diagnosis infobox
  • [PT-3384] - Improve the look of Gene panels section
  • [PT-3430] - Remove or replace all occurrences of the word "node" from the pedigree UI
  • [PT-3476] - Add owner, collaborators and visibility to family directory filters
  • [PT-3484] - Gene lookup should provide free text option at the bottom as the other lookups do
  • [PT-3485] - Permissions dialog: clicking on the new owner field should automatically select Transfer ownership to another user or group
  • [PT-3531] - Gray out Cancer tab for view only users
  • [PT-3566] - Disable SAVE button and autosave while saving record is in the process
  • [PT-3592] - Homepage gadget extra action icons should be bigger
  • [PT-3602] - Add "Rejected candidate" gene and rename Negative to Tested negative status
  • [PT-3623] - Allow new vocabularies to be installed as extensions
  • [PT-3639] - Remove "Global" from Global mode of inheritance and Global age of onset
  • [PT-3643] - Improve labeling/default for variants in Genotype section
  • [PT-3651] - Add ability to consent/push/export genes and variants separately
  • [PT-3668] - Display human-readable symptoms and not symptoms in ORDO and OMIM diagnosis info-boxes
  • [PT-3669] - Rename Gene Panel as "Suggested Genes"
  • [PT-3673] - Rename "Report date" to "Creation date" in the "browse all" table for consistency
  • [PT-3696] - Include inaccessible records when checking the uniqueness of the external id
  • [PT-3698] - Filtering for non-positive boolean values should also work when no value at all is set

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