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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