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Nov 08 2018

PhenoTips 1.4.1 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.4.1 release. In this is release, the following defects have been addressed:

Bugs

  • PT-3821 - SimpleJSON representation of pedigrees is incompatible between PhenoTips 1.3 and 1.4 when cancers are included
  • PT-3865 - When the family template already specifies a default owner, new families end up having two owners
  • PT-3872 - Sometimes livetable's "Loading" animation disappears before the data is actualy loaded
  • PT-3877 - Wrong PhenoTips version reported in JSONs exported from PhenomeCentral
  • PT-3878 - Solved status does not return correctly
  • PT-3880 - The standalone and DMG packages do not run on Java 11
  • PT-3881 - Pedigree editor may fail to load some pedigrees with multi-generation relationships

Improvements

  • PT-3873 - Built-in suggestions for groups should only suggest PhenoTips work groups
  • PT-3874 - Allow disabling filters on the All Families table
  • PT-3875 - Remove non-negative ID filter for improved table performance
  • PT-3876 - Improve data table performance by not using substring match for visibility filters

See the full list of changes in JIRA

PhenoTips 1.4 (stable) released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.4 release. Here are the highlights of the release:

Home page

  • Now displaying homepage gadget extra actions as icons only (instead of text)
  • Active Groups gadget is replaced by a new My Groups gadget
  • Added link to browse all owned patient records on the My Patients gadget
  • Added owner column to the Patients/Families Shared With Me gadgets
HomePage.png

Patient and family directories

  • Owner, Visibility and Collaborators are now available for displaying as columns in the patients table (only the Owner column is displayed by default)
  • Advanced filters are replaced with the new Filters panel located on the far left side of All patient records and All family records pages
  • Collaborators and Studies are added to the patient's FILTERS panel
  • User groups can now be entered into the Owner and Collaborator filter fields along with the user names
PatientsFilteredByOwner.png

Patient and family data

  • Added ability to show external identifiers in place of internal ones as the title of Patient and Family record
  • New option to remove the corresponding patient record when deleting an individual from the pedigree
  • Added Export PDF to family records
  • Families now support members that are not assigned to an individual in the pedigree
  • Uniqueness check for family external ID
  • Renamed Molecular diagnosis to Final diagnosis
  • Free-text diagnoses in patient form and in pedigree editor are now supported
  • Support for multiple external identifiers per patient
  • Added an option to list family members on the patient record form
  • Removed "Global" from Global mode of inheritance and Global age of onset
  • Added alternative names, inheritance, onset, and prevalence in ORDO diagnosis info-box
  • Display human-readable symptoms and not symptoms in ORDO and OMIM diagnosis info-boxes
  • Added validation of PubMed IDs and details about the article are now shown
  • Added info button to mode of inheritance, selected phenotypes, clinical and final diagnoses
  • Added Rejected candidate gene status
  • Renamed Negative to Tested negative gene status
  • Gene lookup now supports free text option at the bottom as the other lookups do
  • Improved layout of the Gene suggestions section (formerly known as Gene panels section)
  • By default tested negative and rejected candidate genes are removed from Gene suggestions section
SuggestedGenesGenotypeInformationDiagnosisSections.png
  • Improved labeling/default for variants in Genotype section
  • Added functionality for displaying additional tabs on records
  • Added ability to enter groups in the owner and collaborator fields of the filtering panel, push and permission dialogs
  • More robust save functionality

Pedigree editor

  • Coloring of disorders, phenotypes and genes can be turned on/off for the whole group or per individual item in the pedigree legend
  • Improved pedigree legend box
  • All abnormalities/annotations associated with a person are highlighted in the legend while hovering over an individual's symbol in the pedigree
  • New and improved cancers UI in pedigree editor
  • Pedigree editor is now using a standardized vocabulary for cancers
  • Applied the same visual arrangements in PED export dialog as in pedigree legend
  • Allowed assigning Alive and Well status to a group of people
  • SVG output of the pedigree editor is now scrollable
PedigreeColouring.png

Push/Export/Import

  • Improved and more user friendly export dialog
  • Push dialog now displays consented fields only
  • Added ability to push, export and import medical reports, additional images and documents
  • Various fixes involving Excel export file
  • The XAR export on family pages now includes the records for all family members
PushExportDialog.png

Vocabularies

  • Added support for vocabulary categories
    • instead of searching only a specific vocabulary, for example "OMIM", it is now possible to search in all vocabularies of a certain type, for example "diseases"
    • added REST API endpoints /vocabularies/categories; vocabularies/categories/{category}; vocabularies/categories/{category}?suggest)
  • More robust vocabulary reindexing operation is no longer leaving system in a bad state (e.g. after failure)
  • Suggest widgets for vocabularies are now working on the filters for groups' owned and shared cases tables, and for study cases
  • Gene suggestions are now showing the exact input provided (if found) as a first option
  • Administrators can permanently redefine the location of vocabulary sources

Permissions

  • Several improvements in case permissions module is not installed:
    • Patients and family tables are now displayed on the homepage
    • Fields 'owner' and 'visibility' are removed from advanced filters
    • All patients are now shown in the "Browse Patients" table
  • Permissions manager dialog can be extended with custom sharing options
  • Removal of one's own account as managing collaborator no longer throws exceptions
  • Implemented family permissions
  • Improved Permissions dialog (user and group fields are now merged into only one field)

ModifyPermissionsDialog.png

REST API

  • Allowed method PATCH on patient resources
  • Allowed explicit updates, overwrites and merges when updating patient records
  • Added REST API for family permissions

Translations

  • Added support for French, German and Russian HPO translations

Administration/System

  • Added support for auditing of:
    • viewed and edited records
    • permissions and data sharing
    • push events 

      AccessLogs.png

  • Added ability to:
    • configure additional default and/or optional external identifiers
    • define if external identifiers should be unique
    • display external identifiers in place of internal ones in the Patient and Family page

      ExternalIDConfiguration.png

  • Group administrators are now called Group managers
  • Added ability to consent/push/export genes and variants separately
  • Upgraded XWiki to 7.4.6
  • Java 1.8 is now required
  • Text mining and new vocabularies can now be installed as extensions

New PhenoTips extension: Text mining

  • Text mining provides extraction of HPO terms from "Indication for referral" and "Medical history" and displayed as phenotype suggestions under SUGGESTIONS FROM CLINICAL NOTES box

    TextMining.png

Bug fixes

  • Families shared with me are missing some families with shared patients
  • Drop-down autocomplete doesn't follow the search bar in pedigree editor
  • Layout issue in the first tab of the pedigree editor node menu
  • Gene panels should display HGNC gene symbol rather that its alias
  • Loading spinner doesn't display properly in export modal
  • Pedigree editor breaks when using non-default date input format
  • When using dd-mm-yyyy for pedigree date format (both input and display), using decades in the pedigree breaks the editor
  • Genes should be stored internally as Ensembl IDs, not HGNC IDs
  • Corrected problem with missing person's details when exporting pedigree to PNG and SVG
  • Corrected several problems involving entering phenotype details
  • Some occasional failures to save records have been averted
  • Clicking N/A on a dropdown prenatal phenotype doesn't do the same on the duplicate
  • Different/inconsistent behavior when filtering in Advanced data filtering and Export
  • Users can remove from a family patients that they can't normally access
  • The consanguinity status of a patient isn't set when identifiable from the pedigree
  • Non-categorized custom phenotypes disappear from saved patient record
  • Filtering by gene doesn't work as expected in advanced filters, push and export
  • Guest users cannot access the families that they create
  • Unable to import pedigree using BOADICEA format
  • Family permission dialog cannot be moved around
  • Pedigree action buttons not looking good when scaling down below 90%
  • When using the embeddable skin, the "New Patient" button on the homepage doesn't work
  • Some labels not shown on family form
  • Delete pedigree button label is white in some cases
  • 0 values for the Obstetric History fields are lost in the JSON export
  • OMIM was no longer reindexable
  • After reindexing vocabularies, spellchecked suggestions no longer work
  • Patient/Family search widget does not work for guest users
  • Records created by guest users should be accessible to everyone
  • The SVG rasterizer service caches the first requested size of the generated image
  • Variants cannot be deleted via the REST patient API
  • Gray out Cancer tab for view only users
  • View-only collaborators were wrongly presented with the option to change the study of a patient record
  • Users that are not subscribed to any studies cannot see when a patient record belongs to a study
  • When a patient is deleted, the "pushed to remote servers" data is not removed
  • Cannot delete a family via REST
  • Group cases are not displayed in Admin/Group/Cases
  • Free text entered as an ethnicity does not get suggested anymore
  • Nonstandard features get copied to features array in the pedigree JSON representation
  • Export as JSON is missing the Referrer (report creator) info
  • Phenotype suggestions aren't displayed if OMIM suggestions aren't enabled
  • Non-functional "Go to search page" displayed in the quick-search results
  • PED export omits cancers entered in the new cancer tab
  • Clearing Referrer and Last Author fields in families' advanced filters does not automatically refresh the results
  • Bugs in pedigree patient drop legend and unlinked patient handling
  • Typed gene name doesn't get replaced with the proper Ensembl ID after displaying gene information
  • Logging out while in edit mode can lock the object for 30 minutes
  • Unauthenticated users can edit the PatientTemplate and FamilyTemplate
  • PhenoTips won't run on Windows if username contains space character
  • PhenoTips doesn't run on Java 9+
  • XSS vulnerability in patient form data
  • Creating a new family member using the "Add family member" button in pedigree editor does not add new patient to the family
  • Switching languages while editing patient record causes strange behavior
  • Reindexing ORDO with the default source URL always ends up with a very old version of ORDO

Oct 26 2018

PhenoTips 1.4 Release Candidate 4 Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.4 RC4 release.
In this is release, the following items have been done:

New Feature

  • PT-3829 - Enable auditing push events

Improvements

  • PT-3837 - Clarify the meaning of the "CNP" variant classification for CNVs
    Improvement
  • PT-2520 - Make the SVG output of the pedigree editor scrollable
  • PT-3851 - The XAR export on family pages should include the records for all family members
  • PT-3822 - Text mining should be available as an extension rather than part of PhenoTips install

Defects

  • PT-3824 - Creating a new family member using the "Add family member" button in pedigree editor does not add new patient to the family
  • PT-3826 - Switching languages while editing patient record causes strange behaviour
  • PT-3840 - Server logs are flooded with "deprecated parseContent" warnings
  • PT-3844 - Reindexing ORDO fails
  • PT-3845 - Changing a vocabulary source doesn't work
  • PT-3846 - Broken "Is a type of" displayed in the term info box for ORDO terms
  • PT-3847 - After reindexing ORDO, the vocabulary version is no longer known
  • PT-3848 - Reindexing ORDO with the default source URL always ends up with a very old version of ORDO

See the full list of changes in JIRA