Releases

Category: Releases (51 posts) [RSS]

Jan 16 2017

PhenoTips 1.3 Milestone 5 Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3 Milestone 5 release. The highlights of the release are:

Patient record form

  • When navigating away from a record, a warning is shown if there are unsaved changes
  • Added "Life status" field in the patient form to allow more logical workflow when entering patient data.
  • OMIM diagnosis suggestions are now shown in view mode too.
  • PhenoTips is now storing genes by using Ensembl IDs internally, instead of using gene symbols. 
  • Special wiki markup in several fields used to be interpreted; this has been disabled

Family charts

  • Newly added menu option in the Pedigree Editor allows physicians to quickly mark pedigree node as "Alive & Well" or "Deceased".

Rest api

Bug fixes

  • Cannot specify variant coordinates for variants entered prior to version 1.3M4
  • The Families REST API endpoint does not check permissions properly
  • Global mode of inheritance and Global age of onset cannot be pushed or imported
  • "Chromosome: NA" displayed in the variant summary in edit mode
  • Broken images displayed on the dashboard for groups without a specific image attached to them
  • 'New patient' button often adds multiple patients from one click
  • Legend is broken in pedigree editor
  • An empty family with no pedigree has rights that are too permissive
  • Users shouldn't be allowed to add comments on code pages

See the full list of changes on Jira.

Nov 21 2016

PhenoTips 1.3 Milestone 4 Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3 Milestone 4 release. The highlights of the release are:

Spanish translation of PhenoTips

PhenoTips now supports English and Spanish languages and can be configured to work either in single or multi-language mode, by setting multilingual option in the administration's localization page. Single language mode operates in the language chosen as the default in the administration's localization page.

Phenotips_Administration_Localization_Language.gif

In this version the Spanish version of HPO hasn't been included yet, that will happen in the next milestone. Other translations are under development. If you would like to make PhenoTips available in your language, you can contribute translations at https://crowdin.com/project/phenotips

Pedigree editor

  • Pedigree editor now allows any node to have any gender
  • Adopted individuals can now have their children and partners represented in the pedigree
  • Users are now able to select what traits (disorders, genes, cancers and phenotypes) are reflected in the "affected" column when exporting the PED file of a pedigree
  • Many small improvements such as better scaling of Pedigree legend containing large number of annotations

Other improvements

  • JSON import (symmetric with the Export JSON functionality) is now available on the Patient page for individual patient import and as bulk on the All Patient records page
  • Added chromosome, start position, end position and reference genome as fields for variants
  • Bug fixes in EXCEL export, user interface, etc...

See the full list of changes on Jira.

Oct 17 2016

PhenoTips 1.3 Milestone 3 released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3 Milestone 3 release. The highlights of the release are:

Family charts

Extensive improvements in the pedigree editor now enable physicians to follow/create/update multiple patients within one family in one place. All family members share a single pedigree, accessible either from the patient record or from the newly added Family page.

Almost all of the patient data changes in the pedigree editor will now be reflected on the corresponding patient record and vice versa. An entire family can be constructed within the pedigree editor: existing PhenoTips patient records can be linked to (and unlinked from) individuals in the pedigree and new patient records can be created as well.

The existing access rights functionality enables different physicians to share access to their patients, so one family can contain a collection of patients that are cared for by different clinicians or scientists. The access level for each individual patient is defined in the patient record by the caring physician.

Other improvements

  • Enabled creation/update of multiple patients at once via REST by POSTing a JSONArray with all patients to the /patients endpoint
  • Collaborator names are now visible in the Patient record
  • Embryonal and Fetal onsets are now subterms of a newly added "Antenatal onset" (Global age of onset and the phenotype modifiers)
  • Users are now able to select what traits are reflected in the "affected" column when exporting the pedigree as a PED file
  • Pedigrees can be exported as PNG/SVG directly from the patient record and from the pedigree export dialog
  • Enabled reassignment of the proband in the pedigree editor (P arrow)
  • Added marking to the current patient in the pedigree editor (C arrow)
  • If identifiable from the pedigree, the consanguinity status of a patient is set in their patient record
  • Credits are displayed for the vocabularies in use

Bug fixes

  • When pushing patient data PhenomeCentral rejects logins from clients using newer PhenoTips versions (pushing from 1.3M2 to 1.3M1 fails)
  • Export database as Excel file fails in some cases
  • Patient creation through REST API fails in some cases
  • Corrected the order of phenotypes saved in the "Prenatal and perinatal history" section
  • Phenotypes from systems not found in the mapping, such as "Endocrine" or "Voice", are placed under the heading of "Other"
  • Guest users cannot create patients (on instances that are supposed to allow that)
  • The pedigree editor UI doesn't display fully with the embedded skin
  • Many minor UI fixes in various parts of the application

See the full list of changes on Jira.

Aug 29 2016

PhenoTips 1.3 Milestone 2 released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3 Milestone 2 release. The highlights of the release are:

  • Patient record form
    • User interface improvements
    • Administrators can now disable visibility options globally, for example to remove support for open and hidden records
    • Global mode of inheritance and global age of onset are taken into account when determining suggestions for Diagnosis and "other phenotypes"
  • All Patient Records page
    • Added ability to filter by candidate gene
    • The author and creator columns now link to the actual user pages
  • Pedigree editor improvements
    • Added ability to select confirmed causal genes and to display rejected genes
    • Add ability to enter only year in pedigree date fields
    • Improved pedigree JSON export and import
  • REST APIs
    • A new RESTful API for accessing/managing patient record permissions, enabling users to access/manage patient record permissions: the owner, visibility, and collaborators
    • The XML output has been removed, only JSON is now returned by the REST services
    • Related resources are now more consistently linked, to support better discoverability
    • Allowed methods (GET, POST, PUT, DELETE...) are now listed for all resource links, reflecting both the methods supported by each resource, as well as the rights of the authenticated user
  • Push functionality improvements:
    • More user friendly interface
    • Most of patient data can be pushed except Date of death unknown, Pedigree, Medical reports, Obstetric history, Copy number variants and Additional files
    • Previously entered data can be cleared when pushing again after deleting it
  • Packaging
    • The Mac OS X .dmg package should now start when only the JRE is installed (previously it sometimes failed when JDK 1.6 was installed, but only the JRE for 1.7 or 1.8)
    • When installed on Windows, PhenoTips data is now stored under the current user's home directory by default, allowing installation under Program Files
    • User self-registration is disabled by default, an administrator must either re-enable self-registration or create user accounts
    • The PhenoTips interface is now translated in Spanish (support for the Spanish translation of HPO is on the way). Want to see PhenoTips translated in another language? Please contribute!

See the full list of changes on Jira.

Jun 21 2016

PhenoTips 1.2.5 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.2.5 release. This is a bugfix release, with minor changes in functionality. The following fixes are in this release:

  • PT-2639 - Add support for importing pedigree into 1.2.x from JSON data created by a 1.3.x instance
  • PT-2633 - Safari global tools label displayed on two lines, almost invisible
  • PT-2632 - After Save some Prenatal development subcategories are moved to other categories
  • PT-2631 - Selecting NO for "Abnormal delivery" in the "Prenatal and perinatal history" section fails
  • PT-2622 - New patient creation prompts for use of deleted Studies
  • PT-2607 - After a twin is added some functionality is broken in pedigree editor
  • PT-2606 - Some unicode characters are not displayed properly within the Pedigree ethnicity suggestions
  • PT-2605 - When pushing individual records to a 1.3 server some PII fields get pushed as well
  • PT-2600 - PR seem to be granted to every user
  • PT-2599 - Exceptions logged when sending emails
  • PT-2598 - If the patient template doesn't have a VisibilityClass object, changing the default visibility doesn't work
  • PT-2593 - Long foot, long palm and large hands are not matched under the musculoskeletal section in the selection summary
  • PT-2586 - Patient data with "open" visibility does not appear in the data table on a study's homepage
  • PT-2584 - PhenoTips doesn't start on older Mac OS X systems without JDK 1.7+ installed
  • PT-2543 - Two extra lines are displayed in the More Actions menu when no push targets are defined
  • PT-2532 - Patient data with "open" visibility does not appear in the data table on a workgroup's homepage
  • PT-2530 - Free-text phenotype categories are not saved/created
  • PT-2519 - Saving a pedigree from some versions of Safari browser generates an invalid SVG image
  • PT-2516 - Pedigree zoom is too sensitive for trackpad use
  • PT-2458 - Contents of text areas are not properly escaped
  • PT-2373 - Date picker month and year are cut off in the XWiki date picker
  • PT-2362 - Returned access level for other users is wrong when logged in as an administrator
  • PT-2245 - Entering a text ending in ) in the "Indication for referral" field will show the last ) in a weird place
  • PT-924 - "Right/left hand length" displays an invalid value for measurements performed before the age of 2 years

May 06 2016

PhenoTips 1.2.4 (stable) released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.2.4 release. This is a bugfix release, with minor changes in functionality. The following fixes are in this release:

  • PT-2494 - Automatic phenotypes attached to "palpebral fissure length" are backwards
  • PT-2480 - The Push feature may be accidentally removed during upgrades
  • PT-2474 - OutOfMemoryError thrown when trying to export PDFs on the standalone DMG bundle
  • PT-2468 - The content of textarea fields for multi-object data is not properly displayed in PDF
  • PT-2464 - Ability to only specify the year of birth in the patient form
  • PT-2463 - Add ability to enter only year in various pedigree date input fields
  • PT-2460 - Wrong extra indentation for the Allergies label
  • PT-2439 - Reindexing HPO fails
  • PT-2378 - Pedigree JSON import always assign the first object as proband (and export fails to specify proband node)
  • PT-2376 - PDF export fails due to OutOfMemory exception
  • PT-2369 - Can't back up and restore PhenoTips instances with 1000 pages
  • PT-2361 - Filtering on tables with patients does not return any of the patient records where a specific object/property present as a filter is missing
  • PT-2358 - Workgroup cases no longer displayed for non-members
  • PT-2341 - Maternal and Paternal ethnicity labels are darker
  • PT-2331 - Can't import PED files with comment lines
  • PT-2328 - The monarch patient scorer doesn't work for patients with many phenotypes selected
  • PT-2312 - Inconsistent appearance of negative phenotypes on patient form (edit mode)
  • PT-2284 - Detailed physical phenotype configuration lists Polydactyly twice in the upper extremities section
  • PT-2246 - Missing space in the PDF footer

Apr 27 2016

PhenoTips 1.3 Milestone 1 released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3 Milestone 1 release. The highlights of the release are:

  • Improved support for recording genes and variants
  • Added support for configuring and recording consents obtained from the patient
  • Almost all patient data can now be exported and re-imported via JSON
  • A new REST API for accessing vocabularies
  • Added an "Unknown" option for the patient sex, selected by default
  • Added support for recording twin number (A/B/Other) for patients from a multiple gestation
  • Each PhenoTips instance sends anonymous general installation and usage data back to phenotips.org for statistics (see below for details)
  • Push functionality improvements:
    • Push receiver component is now included by default, although no remote instances are allowed to push by default
    • Consents from the remote server are queried and displayed before pushing a patient record
    • Added verification if the source and target PhenoTips instances support the same push protocol version
    • Added ability to push almost all patient data such as genes, variant data, phenotypes, diagnoses, age of onset and mode of inheritance
  • Pedigree improvements:
    • Improved the pedigree load time
    • The pedigree image service now supports downloading the file instead of just displaying it
    • Moved "create sibling" handle to the right of the parent link
    • Ages are now easier to read in the cancers tab
    • Cancer dx is summarized under pedigree symbol
    • Added "thyroid cancer"
    • Added ability to import PED files with comment lines
  • Other improvements:
    • Automatically expand the list of subcategories (if it exists) when selecting YES for a phenotype
    • Pressing Enter now select the first phenotype suggestion from the drop-down
    • Made shorter URLs by removing the /bin/ part of the URL
    • Upgraded to Solr 5.3.1
    • Upgraded to XWiki 7.1.4
  •  Bug fixes:
    • Failure when reindexing HPO from the default URL
    • The monarch patient scorer didn't work at all anymore
    • The monarch patient scorer didn't work for patients with many phenotypes selected
    • Can't back up and restore PhenoTips instances with 1000 pages
    • Import functionality broken in pedigree editor
    • PDF export fails due to OutOfMemory exception
    • Automatically selected phenotypes, for example by abnormal measurements, do not appear in differential
    • Inconsistent appearance of negative phenotypes on patient form
    • Detailed physical phenotype configuration lists Polydactyly twice in the upper extremities section

As mentioned above, starting with this version, each PhenoTips instance sends regular "pings" with general information about itself to a central server located at https://stats.phenotips.org/. The information consists of:

  • Technical data, such as OS, java version and vendor, servlet container, database used, PhenoTips version, enabled extensions, which enable us to focus our efforts on the most popular configurations and know when it's a good time to switch to a new version or drop compatibilities without affecting our users
  • Generic usage data: number of users, number of patient records, which will be used, in an aggregated form, in grant applications to receive funding that allows us to continue developing PhenoTips as free software.

PhenoTips installations running in closed networks without access to the internet will not be able to send any data to our stats server. This does not affect in any way the functioning of the software.

See the full list of changes on Jira.

Dec 13 2015

PhenoTips 1.2.2 (stable) released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.2.2 release. This is a bugfix release, with minor changes in functionality. The following fixes are in this release:

  • PT-2264 - Wrong URL returned after creating a patient via the REST API
  • PT-2272 - Can't open two history windows at the same time
  • PT-2229 - Pedigree is broken in older IE browsers
  • PT-2248 - "None of the above as of today" button does not blank out the "As of" fields for patients without birth date
  • PT-2249 - The pedigree image service fails to generate PNGs for pedigrees created with 1.2.1
  • PT-2250 - The pedigree generates invalid SVG in IE9
  • PT-2254 - The patient node abnormality graphics do not fill the entire node shape with large number of abnormalities
  • PT-2255 - "Apply colour gradient to nodes" option causes improper look of saved pedigrees and missing pedigrees in exported PDFs
  • PT-2265 - Panning around pedigree editor is sometimes broken

Nov 16 2015

PhenoTips 1.2.1 (stable) released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.2.1 release. This is a bugfix release, with minor changes in functionality. The following fixes are in this release:

  • PT-2221 - After upgrading the RPM distribution from 1.1 to 1.2, gene names cannot be searched
  • PT-2222 - After upgrading from 1.1 to 1.2, several extensions are marked as invalid
  • PT-2240 - Proband information cannot be edited in the pedigree anymore
  • PT-2241 - JS error in IE9 when closing the pedigree editor

Nov 04 2015

PhenoTips 1.2 (stable) released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.2 release. The highlights of the release, since 1.1, are:

  • Added a REST-ful API for accessing patient data
  • PhenoTips now requires logging in by default
  • An optional "Consent" dialog is available, although not enabled by default, which controls which fields are displayed in the patient record
  • Added "Other" as an option for the patient's sex
  • Multiple global mode of inheritance values can be selected instead of just one
  • Support for recording allergies
  • Support for recording medication data (optional extension)
  • Improvements to the Prenatal and perinatal section, including
    • support for recording mother's obstetric history,
    • more assisted reproduction options,
    • maternal and paternal age at birth, multiple gestation,
    • additional prenatal, neonatal and perinatal phenotypes
  • Measurements improvements:
    • Update the measurements data with the new WHO data set
    • Added growth charts for BMI and Head Circumference for children older than 3 years
    • Growth charts now mention their source
  • Ability to see more suggested phenotypes or diagnoses in a browsable list of pages
  • The phenotype categories are collapsed by default, making it a bit more obvious that not all the checkboxes must be selected
  • Improved phenotype search suggestions
  • Performance and search results improvements for the gene name service
  • Updated the OMIM index with the latest version
    • This also fixes a regression, the local patient record specificity score works again
    • Now the official name is recorded separately from the other synonyms
  • Diagnosis suggestions were broken by non-standard (free text) phenotypes
  • Users can comment on patient records
  • Allow "locking" a record to prevent any further editing, until it is "unlocked" (optional extension)
  • The last modification date is now shown by default in the All data table
  • The "All data" table sometimes didn't show all the records
  • Pedigree improvements:
    • A new Print feature which allows printing the pedigree on multiple pages
    • A new plain black and white color scheme for pedigrees,
    • Better synchronization with the information entered in the patient record
    • Cross-browser compatibility for the pedigree has been improved
    • Added edit pedigree button to the view patient page
    • Included pregnancy as an option for the new child menu
    • Added the ability to record and display notes on diagnosed cancers
    • The "Comments" box appears in all tabs of a node's menu, not just the clinical tab
    • Improved icons for the new child menu
  • A simpler user profile, without some of the unused features such as sending messages, recent activity, watchlists and user networks
  • Many smaller improvements and bugfixes throughout the application
  • The license has changed: PhenoTips is now available under the AGPL 3.0 license
  • Upgraded XWiki to 7.1.2, which requires an application container that supports the Servlet v3.0 specification
  • The DMG package is now signed
The license of PhenoTips changed from LGPL 2.1 to AGPL 3.0.
This version of PhenoTips now requires an application container that supports the Servlet v3.0 specification. In particular, this means that Tomcat 6, the version available in RHEL/CentOS 6.x, is no longer supported, and Tomcat 7 is required. In RHEL/CentOS 6.x, this can be installed from the EPEL repository.