Releases

Category: Releases (59 posts) [RSS]

Nov 30 2018

PhenoTips 1.3.9 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3.9 release.
In this is release, the following defects have been addressed:

  • PT-3826 - Switching languages while editing patient record causes strange behaviour
  • PT-3848 - Reindexing ORDO with the default source URL always ends up with a very old version of ORDO
  • PT-3872 - Sometimes livetable's "Loading" animation disapears before the data is actualy loaded
  • PT-3877 - Wrong phenotips version reported in jsons exported from PhenomeCentral
  • PT-3882 - ContactInfo does not parse a string with multiple emails
  • PT-3837 - Clarify the meaning of the "CNP" variant classification in the Copy Number Variants section
  • PT-3876 - Improve data table performance by not using substring match for visibility filters

See the full list of changes in JIRA

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

May 14 2018

PhenoTips 1.3.7 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3.7 release.
In this is release, the following items have been addressed:

Improvements

PT-3285 - Added option to delete patient record when deleting the corresponding individual in the pedigree
PT-3454 - Uniqueness check for family's external ID
PT-3545 - Improve robustness of phenotype specificity scorer
PT-3517 - Lighter shade of gray for placeholder text displayed in the genetic variants fields

Defects

PT-3656 - Pushing patient record and assigning it to one of user group does not work
PT-3667 - Unauthenticated users can edit the PatientTemplate and FamilyTemplate
PT-2391 - Clicking N/A on a dropdown prenatal phenotype doesn't do the same on the duplicate
PT-3464 - Logging out while in edit mode can lock the object for 30 minutes
PT-3543 - The SVG rasterizer service caches the first requested size of the generated image
PT-3552 - XSS vulnerability in patient form data
PT-3558 - JSON export missing the Referrer (the report creator) info
PT-3565 - Variants cannot be deleted via the REST patient API
PT-3597 - Cannot delete a family via REST
PT-3585 - Newly added genes and variants have incorrect delete urls
PT-3609 - Users who aren't subscribed to any study unable to 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-3648 - PhenoTips won't run on Windows if username contains space character
PT-3586 - Free text phenotypes get copied to features array in the pedigree JSON representation
PT-3588 - Free text phenotypes in pedigree JSON of non-patient node gets duplicated with every save
PT-3664 - Remove the top owner filter from the Shared Workgroup Cases table 

See the full list of changes in JIRA.

Feb 26 2018

PhenoTips 1.4 Milestone 3 Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.4 Milestone 3 release. The highlights of the release are:

New Features and Improvements

Patient data

  • Support for Multiple external IDs per patient
  • Added option to list family members on the Patient record form
  • The "Perinatal complications" subsection (under the "Prenatal and perinatal history" section) is now shown on the patient form
  • Added functionality for displaying additional tabs
  • Added ability to enter groups in the owner and collaborator fields of the filtering panel, push and permission dialogs
  • Decreased the frequency of auto save from 10 seconds to 1 minute

Families and pedigrees

  • New option to remove the corresponding patient record when deleting an individual from the pedigree
  • Added Export PDF option to the More Action menu of the Family Page
  • Uniqueness check for family external ID

Navigation pages

  • Now displaying homepage gadget extra actions as icons only instead of text
  • Active Groups gadget is replaced with new My Groups gadget on homepage
  • Added link to browse all owned patient records on the My patients gadget
  • Added owner column to browse all families page

Translations

  • Added support for French, German and Russian HPO translations

Consents

  • Disallow setting mandatory consent as required
  • Push dialog now displays consented fields only

Text mining

  • Text mining now runs only when "Indication for referral" or "Medical history" fields are edited
  • Text mining is temporarily disabled by default

Administration

  • Auditability of permissions and data sharing
  • Implemented indexing of OncoTree
  • Group administrators are now called Group managers

Defects

PT-2175 - Extended negative prenatal phenotypes never stored
PT-2238 - Some occasional failures to save records have been averted
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

See the full list of changes in JIRA.

Nov 17 2017

PhenoTips 1.3.6 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3.6 release.
In this is release, the following items have been addressed:

Improvements

PT-3490 - Upgrade to Solr 5.5.5

Defects

PT-2986 - The "Perinatal complications" subsection (under the "Prenatal and perinatal history" section) is no longer shown on the patient form
PT-3442 - Users can remove from a family patients that they can't normally access
PT-3499 - "Browse groups" button is missing from the "My Groups" gadget

Oct 24 2017

PhenoTips 1.3.5 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3.5 release.
In this is release, the following items have been addressed:

New Feature

PT-3451 - Add a "My groups" gadget on the homepage

Bug fixes and improvements

PT-3104 - Different/inconsistent behavior when filtering in Advanced data filtering and Export
PT-3450 - Filtering by member in the phenotips-groups macro ignores the Administrators subgroup
PT-3452 - Enable support for free-text diagnoses in the patient record form and in the pedigree editor
PT-3460 - Non-categorized custom phenotypes disappear from saved patient record

Oct 17 2017

PhenoTips 1.4 Milestone 2 Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.4 Milestone 2 release. The highlights of the release are:

Patient data

  • Patient records can be filtered by the study they belong to
  • Improved look and functionality of patient and family directories
  • New and improved cancers UI in pedigree editor
  • Pedigree editor is now using standardized vocabulary for cancers
  • By default negative phenotypes are removed from Gene panel section
  • Free-text diagnoses in patient form and in pedigree editor are now supported
  • Implemented family permissions

REST API

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

Vocabularies

  • Administrators can permanently redefine the location of vocabulary sources
  • Improved vocabulary reindex process

Text mining

  • Administrators can configure the text-mining service either locally (CTAKES) or remotely through services.phenotips.org (CTAKES and NCR)

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
  • Under high load, no HPO terms are extracted from clinical notes
  • Loading spinner doesn't display properly in export modal
  • Pedigree editor breaks when using non-default date input format
  • In some cases, using a decade for DOB in a pedigree breaks the editor
  • 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
  • Problems with guest users:
    - missing "owner" access on guest-owned patient records
    - wrong failure reported when deleting records

See the full list of changes in JIRA.

Sep 22 2017

PhenoTips 1.3.3 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3.3 release. In this is release, the following issues have been resolved:

Pedigree editor:

  • PT-3272 - Upon deletion of a pedigree node, its carrier genes are still present in the legend
  • PT-3320 - Pedigree node hover boxes do not fade out when they should in some cases
  • PT-3321 - Drop-down autocomplete doesn't follow the search bar in pedigree editor
  • PT-3355 - Some functionality is broken in IE9 (most notably pedigree editor can not be opened)
  • PT-3385 - Unauthenticated users can't save new pedigree
  • PT-3438 - Pedigree editor breaks when using non-default date input format
  • PT-3248 - Rename "disorders" to "final diagnosis" in pedigree editor
  • PT-3275 - Improve info text in pedigree legend box
  • PT-3357 - In pedigree editor do not show A&W options on hoverboxes for patients which are read-only for current user

Family charts:

  • PT-2804 - All families should only list current user's families
  • PT-2815 - Family updates and patient JSON updates should be performed under the correct user
  • PT-2824 - "Families shared with me" are missing some families with shared patients

Patient records:

  • 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-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-3408 - Wrong failure reported when guest users delete their records
  • PT-3416 - Loading spinner doesn't display properly in export modal
  • PT-3377 - Remove negative phenotypes from Gene panel section

See the full list of changes on JIRA.

Aug 23 2017

PhenoTips 1.4 Milestone 1 Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.4 Milestone 1 release. The highlights of the release are:

Pedigree editor

  • Colouring 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 person are highlighted in the legend while hovering over an individual's symbol in the pedigree
  • Allowed assigning "Alive and Well" status to a group of people
  • Corrected problem with missing person's details when exporting to PNG and SVG

PedigreeColouring.png

Patient and family records

Data tables

  • New and improved data filtering: Advanced filters are replaced with FILTERS panel located on the far left side of All patient/family records pages
  • Collaborators are added to the patient's FILTERS panel
  • 'Owner', 'Visibility' and "Collaborators" are now available for displaying in the patients table (they are not shown by default)

AdvancedFilters.png

Patient form

  • Text mining: HPO terms are now extracted from "Indication for referral" and "Medical history" and displayed as phenotype suggestions under SUGGESTIONS FROM CLINICAL NOTES box
  • Renamed "Molecular diagnosis" to "Final diagnosis"
  • Added info button to selected phenotypes, clinical and final diagnoses
  • Improved layout of the Gene panels section
  • Added new option to filter out genes that have been ruled out in gene panels (turned on by default)
  • Corrected several problems involving entering phenotype details

TextMining.png

GenePanels.png

Push/Export/Import

  • Added ability to push, export and import medical reports, additional images and documents
  • Improved and more user friendly export dialog
  • Various fixes involving Excel export file

ExportDialog.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

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

Other

  • Java 1.8 is now required
  • Removed FAMILIES SHARED WITH ME widget from the home page
  • Gene Panels JSON is now more concise

See the full list of changes in JIRA.