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Jul 12 2018

PhenoTips 1.4 Release Candidate 1 Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.4 RC1 release.
In this is release, the following items have been done:

New Feature

PT-3711 - Administrators can browse and filter audited events

Improvements

PT-3581 - Prevent opening same patient/family in multiple tabs from pedigree editor and patient form
PT-3671 - User and group search rest service should be case insensitive
PT-3683 - Modify colour of "Affected" status to a darker shade
PT-3741 - Display group title in the suggest group element
PT-3742 - Add uniqueness ID check configuration to Administration
PT-3753 - Display family members by default on Patient and Family forms
PT-3754 - Display Suggested Genes section by default

Bug fixes

PT-3706 - Measurements don't work for non-admin users
PT-3708 - Automatic layout may leave pedigree in an un-saveable and un-exportable state
PT-3718 - Pedigree editor should warn user about unsaved changes before closing
PT-3727 - Undo/redo functionality in pedigree editor may misbehave when un-linked patients are involved
PT-3717 - Show internal/external family ID under Family history according to configuration for ID in the Admin module
PT-3728 - Pedigree editor should "show external ID instead of internal" as per setting in the Admin module
PT-2134 - When creating a new patient within pedigree editor, the system does not ask if the patient is a part of a study
PT-2850 - In pedigree, unlinked patients may lose data entered in cancers tab
PT-3523 - Difficult to click on patient link in Pedigree Editor in some cases
PT-3530 - "Delete all" button deletes only one of the abnormalities in pedigree editor
PT-3600 - Autocomplete/suggest inputs in the pedigree node popover retain input between different nodes
PT-3674 - When removing genes from a person in pedigree editor, all associated gene variants need to be removed too
PT-3680 - Patient info lost after pedigree JSON import
PT-3700 - Broken homepage displayed after upgrading from older versions
PT-3701 - Clicking on the creation date from records on the homepage leads to a Not Found page
PT-3703 - The "required" flag for a field is ignored when a patient record is populated from the pedigree
PT-3704 - The id uniqueness is not checked when a patient record is populated from the pedigree editor
PT-3705 - On "quit-and-save" pedigree complains that a family has no members if all members are unlinked
PT-3707 - In pedigree n-person symbols should not be highlighted as a valid drag target for linking patient records
PT-3710 - Pedigree import should not import patient records which are not already in the family, but keep those who are
PT-3716 - Import/export functionality in pedigree does not handle group of people
PT-3729 - Unable to remove pedigree node linked to the current patient in pedigree editor
PT-3731 - Non-admin users see uninterpreted code instead of the default workgroup image
PT-3736 - "Create new patient" button doesn't work after being prompted to save changes
PT-3738 - $services.groups.getGroupsForUser returns just a few of the user's workgroups
PT-3743 - If Date Of Birth is marked as required, only year of birth will be enforced
PT-3746 - Passing a group to EntityAccessManager.isAdministrator triggers an XWiki permissions cache bug
PT-3748 - Unable to transfer ownership to another user or group in a certain situation
PT-3749 - Saving and loading pedigree may fail if current user has no view rights for some of the patients in the family
PT-3752 - Pedigree editor does not prompt for save if patient is added to an existing family and left unliked
PT-3761 - Unable to save pedigree nor export it into PhenoTips JSON format
PT-3762 - Patients added to a family with no pedigree outside of pedigree editor do not show up when pedigree is created

See the full list of changes in JIRA.

Jun 15 2018

PhenoTips 1.4 Milestone 4 Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.4 Milestone 4 release. The highlights of the release are:

Improvements

Patients data

  • Families now support members that are not assigned to an individual in the pedigree
  • Added owner, collaborators and visibility to family directory filters
  • Renamed "Report date" to "Creation date" on the landing page
  • Permissions: Clicking on the new owner field automatically select "Transfer ownership to another user or group"
  • Added info button to Mode of inheritance
  • 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 Rejected candidate gene status
  • Renamed Negative to Tested negative status
  • Gene lookup now supports free text option at the bottom as the other lookups do
  • Improved labeling/default for variants in Genotype section
  • Gene panels section:
      - renamed section title to Suggested Genes
      - now more user friendly
      - shows the number of genes associated with each phenotype,
      - sorts phenotypes by number of associated genes in descending order,
      - nonstandard terms are marked with an icon
      - rejected genes are now displayed with a strike-through
      - Rejected Candidate is added to existing Exclude Negative Genes filter
  • Same visual arrangements in PED export dialog as in pedigree legend
  • More robust save functionality
  • Uniform look for lookup fields in advanced filters and export/push dialog

Administration/System

  • Added ability to consent/push/export genes and variants separately
  • Vocabulary version is now updated upon successful reindexing
  • New vocabularies can be installed as extensions
  • New support for auditing who viewed and edited records
  • Added ability to show external identifiers in place of internal ones in the Patient and Family record forms
  • Upgraded XWiki to 7.4.6

Defects

  • Problems when reindexing vocabularies:
      - an installed vocabulary from a source included inside a jar
      - a vocabulary from a source included inside a jar
      - vocabularies with special characters in their source URL
  • Gray out Cancer tab for view only users
  • View-only collaborators are 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 "push to remote servers" data is not removed
  • Cannot delete a family via REST
  • Group cases are not displayed in Admin/Group/Cases
  • Resolve text mining issues and turn it on by default
  • Free text option appended to the phenotype lookup, when input (phenotype) has exact match in the suggestion list
  • 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

See the full list of changes in JIRA.

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.