Release Notes - PhenoTips - Version 1.3-milestone-2 - HTML format

Sub-task

  • [PT-1933] - Allow pushing phenotype details
  • [PT-2052] - Implement missing controller methods
  • [PT-2161] - Birth/Deathdate "hidden" input fields are visible for a short time after opening patient edit page
  • [PT-2288] - Specification
  • [PT-2349] - RESTful API for accessing/managing the owner
  • [PT-2350] - RESTful API for accessing/managing the visibility
  • [PT-2351] - RESTful API for accessing/managing all collaborators
  • [PT-2352] - RESTful API for accessing/managing a specific collaborator
  • [PT-2353] - RESTful API for accessing/managing all permissions in one call
  • [PT-2357] - RESTful API for listing all visibility options
  • [PT-2452] - Apgar scores and twin number cannot be pushed
  • [PT-2457] - Push fails to update phenotypes back to NA values
  • [PT-2459] - Selection of Clinical Symptoms and physical findings triggers pushing of Prenatal and perinatal phenotypes
  • [PT-2508] - Push functionality should also push free text phenotypes
  • [PT-2587] - Administration section for disabling visibility levels
  • [PT-2588] - New API method for listing all visibility levels, including disabled ones
  • [PT-2589] - The `listVisibilityOptions()` method in the permissions service should take into account that some may be disabled
  • [PT-2663] - Update dates-as-entered to the new date JSON format
  • [PT-2687] - Redo functionality is sometimes broken in pedigre editor
  • [PT-2711] - Convert existing pedigree data to new gene format
  • [PT-2716] - Improve pedigree JSON export and import
  • [PT-2731] - Add support for selecting fields from XClasses other than PatientClass in the "Data tables" administration section
  • [PT-2734] - Add support for sorting tables on properties from other xclasses
  • [PT-2736] - Add support for linking to other referenced documents in the All Patients table
  • [PT-2737] - Add links to the creator/author in the All Patients table

Bug

  • [PT-924] - "Right/left hand length" displays an invalid value for measurements performed before the age of 2 years
  • [PT-1818] - Pushed patients appear as "Last modified by Unknown User"
  • [PT-2217] - Abnormal phenotypes not automatically reported or reported incorrectly for some measurements
  • [PT-2245] - Entering a text ending in ) in the "Indication for referral" field will show the last ) in a weird place
  • [PT-2271] - PhenoTips Identifier field is editable but reverts to automatically computed identifier after save
  • [PT-2303] - "None of the above as of today" button is broken in pedigree editor node menu
  • [PT-2307] - Incomplete workgroup creation when uploading a photo and exiting without saving
  • [PT-2362] - Returned access level for other users is wrong when logged in as an administrator
  • [PT-2373] - Date picker month and year are cut off in the XWiki date picker
  • [PT-2378] - Pedigree JSON import always assign the first object as proband (and export fails to specify proband node)
  • [PT-2445] - Consents with blank text are ignored
  • [PT-2458] - Contents of text areas are not properly escaped
  • [PT-2494] - Automatic phenotypes attached to "palpebral fissure length" are backwards
  • [PT-2503] - Issues when pushing free text from Prenatal and perinatal history section
  • [PT-2504] - After upgrade from 1.2 to 1.3, some studies have form configuration set with gene variants hidden
  • [PT-2516] - Pedigree zoom is too sensitive for trackpad use
  • [PT-2519] - Saving a pedigree from some versions of Safari browser generates an invalid SVG image
  • [PT-2525] - "Manage Group Administrators" links to an empty text field
  • [PT-2529] - Info buttons do not work in HPO browser
  • [PT-2530] - Free-text phenotype categories are not saved/created
  • [PT-2532] - Patient data with "open" visibility does not appear in the data table on a workgroup's homepage
  • [PT-2543] - Two extra lines are displayed in the More Actions menu when no push targets are defined
  • [PT-2544] - Labels for checkbox fields in the genes and variants section target the first gene/variant added
  • [PT-2553] - No ip in the info sent by ping back
  • [PT-2560] - Prenatal phenotypes are exported twice in the JSON
  • [PT-2561] - NullPointerException if pushing null/empty JSON
  • [PT-2562] - NullPointerException in vocabulary term creation if 'symbol' field is missing
  • [PT-2563] - Pushing a patient with empty data
  • [PT-2566] - Consent configuration will not allow blank lines in the More Information section
  • [PT-2568] - NullPointerException in feature creation if 'type' or 'observed' field is missing
  • [PT-2573] - Information text areas become 2 columned
  • [PT-2583] - Lists in the consent description completely break the consents ui on the patient record
  • [PT-2584] - PhenoTips doesn't start on older Mac OS X systems without JDK 1.7+ installed
  • [PT-2586] - Patient data with "open" visibility does not appear in the data table on a study's homepage
  • [PT-2593] - Long foot, long palm and large hands are not matched under the musculoskeletal section in the selection summary
  • [PT-2598] - If the patient template doesn't have a VisibilityClass object, changing the default visibility doesn't work
  • [PT-2599] - Exceptions logged when sending emails
  • [PT-2602] - 1.3 code should also support the 1.2 JSON structure, where the rejected and candidate genes are in a different place
  • [PT-2604] - Unable to update patient's DOB and DOD through REST
  • [PT-2607] - After a twin is added some functionality is broken in pedigree editor
  • [PT-2622] - New patient creation prompts for use of deleted Studies
  • [PT-2625] - Date of death is displayed in view mode even when "Date of death unknown" is checked
  • [PT-2631] - Selecting NO for "Abnormal delivery" in the "Prenatal and perinatal history" section fails
  • [PT-2632] - After Save some Prenatal development subcategories are moved to other categories
  • [PT-2633] - Safari global tools label displayed on two lines, almost invisible
  • [PT-2638] - "+ Upload and manage" reports button does not work
  • [PT-2642] - Pedigree editor save behavior gives incorrect feedback and is not error-tolerant
  • [PT-2648] - Support exporting of Clinically Normal status
  • [PT-2656] - Create patient link is not present in the header for non-administrators when browsing groups or studies
  • [PT-2710] - PhenoTips does not start when installed under Program Files on Windows
  • [PT-2713] - Cannot transfer ownership to groups containing " or ~ in their name
  • [PT-2714] - Owner group containing < or ~ in their name aren't displayed correctly
  • [PT-2715] - Cannot attach/display custom images for workgroups containing special characters in their name
  • [PT-2717] - Cannot select a study with special characters in it
  • [PT-2718] - Studies with special characters in their name break the patient record UI
  • [PT-2719] - Bad links generated for studies with special characters in their names in the administration and in the groups using them
  • [PT-2720] - Studies with special characters in their name fail to display the list of workgroups using them
  • [PT-2721] - Bad links generated for workgroup with special characters in their names on the homepage dashboard, administration, and in the studies using them
  • [PT-2722] - Workgroups with special characters in their name fail to display the list of subscribed Studies
  • [PT-2732] - Broken links displayed in livetables for some columns when using "link" type "auto" or "field"
  • [PT-2735] - Cannot filter by more than one type of file for the attachment picker

New Feature

  • [PT-1759] - Add ability to disable access levels across instance
  • [PT-2287] - RESTful API for accessing/managing patient record permissions
  • [PT-2415] - Allow filtering by candidate gene
  • [PT-2615] - Add support for encrypting, decrypting, and hashing data
  • [PT-2616] - Add support for defining transparently encrypted fields in XClasses
  • [PT-2640] - Add generic APIs for working with dominant entities and entity groups

Story

  • [PT-2614] - Better protection of sensitive data

Task

  • [PT-1538] - Date of birth/death in patient JSON does not capture "fuzziness"
  • [PT-1618] - When scrolling downward, the "Quick phenotype search" section overlaps the topmost items
  • [PT-1797] - Hint textboxes for "Matching disorders in OMIM" appear in incorrect positions.
  • [PT-2100] - Warn user when he tries to save gene/variant with empty key field
  • [PT-2443] - Improve the look of push modals and consent form
  • [PT-2448] - Redundant options in the "Select the fields to be exported" dialog
  • [PT-2477] - Add methods to retrieve a collection of patients
  • [PT-2603] - 1.2 to 1.3 gene migration adds one blank space before comment
  • [PT-2612] - Checkboxes "This patient is clinically normal" and "Case solved" should be pushed too
  • [PT-2662] - Disable self-registration

Improvement

  • [PT-2366] - Improve diagnosis and "other phenotypes" suggestions by taking into account global mode of inheritance and global age of onset
  • [PT-2438] - Provide more descriptive warning to users wishing to export to BOADICEA
  • [PT-2454] - Add selection tools ("Select All - None - Invent - Restore initial values") to the modal for pushing a single patient
  • [PT-2455] - Only display options related to actual data fields in the consent configuration UI
  • [PT-2463] - Add ability to enter only year in various pedigree date input fields
  • [PT-2465] - Anonymised pedigree should not show external ID, comments, names and DoB
  • [PT-2470] - Hide empty list of genes from export pdf and patient form when in view mode
  • [PT-2479] - The lines on the pedigree should be thicker
  • [PT-2484] - Better language on Administration: Receive Patient configuration
  • [PT-2498] - Make pedigree editor extensible
  • [PT-2509] - Push dialog improvements
  • [PT-2524] - Patient information asks for "Provincial" Health Card number
  • [PT-2567] - Improve the help text for maternal and paternal ethnicity
  • [PT-2574] - "Unknown" sex shouldn't be displayed in view mode
  • [PT-2585] - Make patient page more visually static and less annoying on load
  • [PT-2590] - Add an API method to get the default visibility
  • [PT-2592] - Cannot easily query all studies using a specific field
  • [PT-2606] - Some unicode characters are not displayed properly within the Pedigree ethnicity suggestions
  • [PT-2641] - Better support for new genes in pedigree editor
  • [PT-2643] - Support pushing data to older servers which only support deprecated patient JSONs
  • [PT-2657] - Add ability to order extensions displayed at the top and bottom of the patient record
  • [PT-2670] - Add a PatientData method for checking if a dictionary data element contains a specific key
  • [PT-2700] - Make the patient-data APIs extend the new entities API
  • [PT-2709] - Let the AuthorizationService accept all types of entities, not just documents
  • [PT-2724] - Add a "secure" PermissionsManager implementation that checks rights before performing any changes
  • [PT-2726] - Provide a Spanish translation of PhenoTips
  • [PT-2730] - Add support for displaying data from XClasses other than PatientClass in the table of patients
  • [PT-2741] - Add a base rest-commons module to be used by the other REST modules
  • [PT-2742] - The REST JSON output should not include null fields
  • [PT-2743] - REST resources should automatically link to related resources
  • [PT-2744] - REST resources should list the methods allowed on self and related resources
  • [PT-2745] - Remove the XML output from the REST resource representations

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