Release Notes - PhenoTips - Version 1.3-milestone-3 - Text format

Sub-task

  • [PT-1565] - Add markings to current patient node and modify markings for proband
  • [PT-1566] - Store an indication to the proband
  • [PT-1567] - Create UI for indicating proband
  • [PT-1572] - Add pedigree legend to the family page
  • [PT-1575] - Update pedigree SVG for each family member to correctly mark current patient
  • [PT-1587] - Display in pedigree
  • [PT-2088] - Improve UI on Pedigree import dialog
  • [PT-2103] - Merge Templates and Import functions on Pedigree
  • [PT-2231] - Add Family external identifier to the Family history and pedigree section
  • [PT-2232] - Remove "FAMILY" and "PEDIGREE" labels from Family history and pedigree section
  • [PT-2233] - Move functionality of patient-family assignment from Patient form to Pedigree editor
  • [PT-2234] - Replace the full pedigree with its thumbnail in the Family history and pedigree section
  • [PT-2236] - Add ability to delete families and add action buttons to the pedigree thumbnail
  • [PT-2309] - Disable old family studies impementation
  • [PT-2326] - Pedigree image missing in patient's Export PDF
  • [PT-2339] - Migrate internal pedigree JSON to new format supporting phenotype details
  • [PT-2399] - Add a DocumentLock class
  • [PT-2400] - Add a LockManager component
  • [PT-2401] - Add a LockModule component
  • [PT-2402] - Implement BasicEditLockModule
  • [PT-2403] - Implement FamilyLockModule
  • [PT-2404] - Add a LockScriptService
  • [PT-2405] - Change edit.vm to use the new LockScriptService
  • [PT-2406] - Add a new xwiki-locks Maven module
  • [PT-2417] - Implement PatientFamilyLockModule
  • [PT-2418] - Implement FamilyMembersLockModule
  • [PT-2419] - Implement PatientLockModule
  • [PT-2424] - Implement PatientSelfLockModule
  • [PT-2425] - Implement FamilySelfLockModule
  • [PT-2537] - Patient assignment on a newly imported pedigree template
  • [PT-2538] - Better warning messages in pedigree editor (part1)
  • [PT-2539] - Correct "unlink patient" button label in pedigree editor
  • [PT-2618] - Create proposal: REST-full API for accessing family studies
  • [PT-2619] - Implement: REST-full API for accessing family studies
  • [PT-2779] - Deprecate UIX_Field__genes
  • [PT-2812] - Improve how family permissions are automatically updated
  • [PT-2834] - Pedigree PED export will crash when any cancers are selected for export
  • [PT-2839] - Cannot upgrade RPM installations from older versions to 1.3M3

Bug

  • [PT-1577] - Checkbox text in various OK/Cancel dialogues in pedigree editor is not clickable
  • [PT-1768] - Phenotypes from systems not found in the mapping, such as "Endocrine" or "Voice", are placed under the heading of "Other"
  • [PT-2133] - Unable to specify relationship as 'separated' in pedigree editor
  • [PT-2180] - Clicking "Create new" [patient record for individual] in the pedigree editor generates a new record even if the user clicks "Cancel" in the confirmation box
  • [PT-2305] - Issue with My Families
  • [PT-2372] - Family record is in a weird state once the last member is removed
  • [PT-2384] - Pedigree is missing on exported PDF
  • [PT-2387] - Adding a twin to an individual causes the loss of patient's cancer-related info and the twin's last name at birth isn't added
  • [PT-2397] - Selected subterms move from the "Delivery" to the "Prenatal Development" section after save
  • [PT-2451] - All Prenatal and perinatal history free text ends up in PERINATAL COMPLICATIONS after save
  • [PT-2510] - The node menu cannot be accessed to edit an individial in the pedigree under some circumstances
  • [PT-2512] - Diseases entered for individuals in the pedigree are lost after saving and reopening the pedigree
  • [PT-2535] - Two users can edit a pedigree for different patients sharing the same family
  • [PT-2629] - Unable to save family pedigree if user has no right to edit at least one node
  • [PT-2727] - Delete button next to pedigree thumbnail on patient page does not work when the "family id" is not present
  • [PT-2749] - Comments box becomes too small when variant is added to a gene
  • [PT-2754] - Some radio buttons in pedigree node menu do not behave correctly
  • [PT-2755] - Printed pedigree doesn't include genes in the legend
  • [PT-2756] - Cannot export patients as Excel
  • [PT-2758] - Guest users cannot create patients
  • [PT-2759] - The pedigree editor UI doesn't display fully with the embeddable skin
  • [PT-2760] - Unnecessary underline text decoration on hover for texts without links in the patient table
  • [PT-2764] - Embryonal and Fetal onsets are no longer displayed
  • [PT-2774] - VocabularyTerm#getDistanceTo often fails to compute the distance between two terms
  • [PT-2778] - Family permissions are not consistently updated to reflect member patient permissions
  • [PT-2786] - Patient creation through REST API is broken
  • [PT-2787] - Different fonts on Save and Cancel buttons in the page menu
  • [PT-2789] - Pressing "None of the above.." button doesn't clear "As of" drop down value
  • [PT-2810] - Fixed-width icons aren't really fixed width
  • [PT-2829] - Can not push patients to some older PhenoTips servers

New Feature

  • [PT-2827] - Allow users to comment on family records

Story

  • [PT-1557] - Setting/displaying proband for a family (pedigree specifically)
  • [PT-1563] - Save data on the pedigree to the linked patient record
  • [PT-2237] - Family page requirements

Task

  • [PT-910] - Allow changing the proband node in pedigree
  • [PT-1460] - Synchronize patient data between Phenotips and pedigree editor
  • [PT-1555] - List families on the home page
  • [PT-1585] - Checkbox and message - privacy warning on each load
  • [PT-1698] - Vocabularies should auto-generate their Solr configuration at startup
  • [PT-1794] - Add a delete button to the top of the edit page
  • [PT-2153] - Support for negative phenotypes and phenotype details in pedigree editor
  • [PT-2154] - Migrate existing pedigrees
  • [PT-2160] - Move the modal with warning of sensitive information to the middle of the screen and add CLOSE button to it
  • [PT-2171] - Default Family identifier to proband last name
  • [PT-2172] - Make family page configurable
  • [PT-2179] - Mark patients associated with another family in the pedigree lookup when attempting to link a pedigree node to an existing patient
  • [PT-2314] - Session for pedigree
  • [PT-2316] - Modify labels on the home page
  • [PT-2317] - Non standard terms entered in the Clinical tab in pedigree editor are not saved
  • [PT-2392] - Twins last name at birth is not added, as it would be if a non-twin sibling were created
  • [PT-2597] - Improve pedigree JSON export and import
  • [PT-2647] - API for exposing a family's proband
  • [PT-2684] - Expose the proband as a field in the FamilyClass
  • [PT-2694] - Family page menus should be consistent with patient record menus
  • [PT-2695] - Display a table of all families in Families/WebHome
  • [PT-2729] - Delete family when deleting its last patient
  • [PT-2733] - Display the family id with link to family page in the table of all patients
  • [PT-2761] - Add UI for switching between supported languages
  • [PT-2802] - Add the ability to create and browse families from the global tool bar
  • [PT-2807] - Allow creating/updating multiple patients at once via REST
  • [PT-2808] - JSON tool should parse to org.json.JSONArray/org.json.JSONObject, not net.sf.json.JSON
  • [PT-2813] - Use exceptions (when appropriate) for error reporting in family studies code

Improvement

  • [PT-1559] - Aggregate reports (ex. pdfs) of individual patients under the family page
  • [PT-1573] - Navigation from pedigree should be smart in chosing the action
  • [PT-2141] - Unable to update Genotype information, date of birth and date of death from the pedigree node
  • [PT-2168] - Family history and pedigree section improvements
  • [PT-2230] - Allow exporting pedigree as an image from within pedigree editor
  • [PT-2239] - Pedigree editor improvements
  • [PT-2315] - Separate proband indicator and deceased person indicator
  • [PT-2332] - Better looking tabs in pedigree editor node menu
  • [PT-2434] - The consanguinity status of a patient should be set when identifiable from the pedigree
  • [PT-2489] - Empty consent section should be hidden in view mode
  • [PT-2507] - Display vocabulary credits
  • [PT-2521] - Generating the pedigree image in PNG format fails on the family page
  • [PT-2534] - Family studies code should be more bullet-proof
  • [PT-2572] - Move edit button to the header of the variant grid
  • [PT-2626] - Hide empty Family history and pedigree section
  • [PT-2664] - If a collaborator is assigned to a patient record show the collaborator's user name
  • [PT-2723] - Users should be able to select what traits are reflected in the "affected" column when exporting the PED file of a pedigree
  • [PT-2763] - Suggest dialogs should hide when they lose focus
  • [PT-2767] - Allow creating empty patient records via REST without passing any data
  • [PT-2775] - Vocabulary#getTerms should return the terms in the same order as the requested IDs
  • [PT-2776] - VocabularyTerm#getAncestors should return the ancestors ordered from the most specific to the most generic
  • [PT-2782] - Individual controllers should not save the patient document directly
  • [PT-2788] - Hide sections with empty data
  • [PT-2796] - Family script service should use current user credentials
  • [PT-2798] - Improve new pedigree creation UI and data flow
  • [PT-2809] - Improve the style of the menu on the patient and family directories
  • [PT-2816] - Improve family studies back-end code (refactor on top of Entities part1)
  • [PT-2818] - Life status does not transfer correctly from pedigree to patient records
  • [PT-2825] - Correct wording in pedigree incorrect drag error message
  • [PT-2826] - Change cursor for pedigree thumbnail to arrow if user has only view rights
  • [PT-2828] - Fix typos: "form" is used instead of "from" in several places in the pedigree editor

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