Release Notes - PhenoTips - Version 1.3-milestone-1 - Text format

Sub-task

  • [PT-1149] - Add more fields for candidate genes
  • [PT-1280] - One unified gene section with variants and significance specified per gene
  • [PT-1381] - Add support for storing evidence for candidate genes
  • [PT-1808] - Add manually entered variants to the export
  • [PT-1936] - Push functionality should have a configurable set of fields being pushed
  • [PT-1939] - Should be able to push candidate gene, variant data, phenotypes, diagnoses, age of onset and mode of inheritance
  • [PT-1943] - Reload the cache of consents when new are added
  • [PT-2026] - Design the REST HATEOAS graph for vocabularies
  • [PT-2027] - Create the maven module for the vocabularies REST interface
  • [PT-2028] - Write the needed schema files for the vocabularies REST resources
  • [PT-2029] - Write the interfaces describing the vocabularies REST endpoints
  • [PT-2030] - Implement the "vocabularies" REST endpoint
  • [PT-2031] - Publish the documentation on phenotips.org
  • [PT-2035] - Write unit tests for parental information
  • [PT-2036] - Write integration tests for parental age
  • [PT-2046] - Add unit tests for the Obstetric History controller
  • [PT-2105] - Add a VocabularyExtension @Role
  • [PT-2112] - Add a VocabularyInputTerm interface
  • [PT-2187] - Add a "suggest" relation for linked REST resources
  • [PT-2188] - Store manually entered genes in patient index
  • [PT-2322] - Ping back number of users and cases from all installed PT instances
  • [PT-2335] - Import functionality for gene controller
  • [PT-2336] - Import functionality for variant controller
  • [PT-2412] - Cancer dx is summarized under pedigree symbol
  • [PT-2413] - Administration section for configuring consents
  • [PT-2485] - The migrator fails to migrate patients that have only candidate genes
  • [PT-2486] - The migrator is very slow on large instances
  • [PT-2487] - Empty GeneClass object created by the migrator when no solved gene is specified
  • [PT-2488] - Multiple document versions are created by the migrator
  • [PT-2492] - Cells are shifted left by one after the variants columns in the excel export
  • [PT-2493] - Exception thrown in the Excel export when no Evidence is provided for a variant

Bug

  • [PT-1619] - ExportFilter count does not reflect number of patients that will be exported
  • [PT-2072] - Collapse/expand arrows in the age of onset category do not work
  • [PT-2076] - Automatic phenotypes do not appear in differential
  • [PT-2110] - Validation for date of death should not display anything if valid
  • [PT-2194] - Genotype information section displays duplicate entries erroneously entered
  • [PT-2246] - Missing space in the PDF footer
  • [PT-2247] - Form designer can be broken by some special characters
  • [PT-2284] - Detailed physical phenotype configuration lists Polydactyly twice in the upper extremities section
  • [PT-2290] - Cancer tab looks awkward once vertical scrollbar gets added
  • [PT-2304] - Import functionality is broken in pedigree editor
  • [PT-2312] - Inconsistent appearance of negative phenotypes on patient form (edit mode)
  • [PT-2318] - AbstractSpecializedNCBIEUtilsAccessService calls String.trim() without saving the result
  • [PT-2328] - The monarch patient scorer doesn't work for patients with many phenotypes selected
  • [PT-2331] - Can't import PED files with comment lines
  • [PT-2341] - Maternal and Paternal ethnicity labels are darker
  • [PT-2342] - Orange warning triangle displayed when using only free text phenotypes
  • [PT-2343] - Random test failures for org.phenotips.data.internal.MonarchPatientScorerTest.getScoreSearchesRemotely()
  • [PT-2345] - Collapse/expand arrows in the Global mode of inheritance category do not work
  • [PT-2358] - Workgroup cases no longer displayed for non-members
  • [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-2369] - Can't back up and restore PhenoTips instances with ~1000 pages
  • [PT-2376] - PDF export fails due to OutOfMemory exception
  • [PT-2395] - After push Prenatal and perinatal history items are listed under Clinical symptoms and physical findings
  • [PT-2439] - Reindexing HPO fails
  • [PT-2442] - The monarch patient scorer doesn't work anymore
  • [PT-2460] - Wrong extra indentation for the Allergies label
  • [PT-2468] - The content of textarea fields for multi-object data is not properly displayed in PDF
  • [PT-2474] - OutOfMemoryError thrown when trying to export PDFs on the standalone DMG bundle
  • [PT-2480] - The Push feature may be accidentally removed during upgrades

New Feature

  • [PT-2066] - Add support for recording which twin (A/B) the current patient is

Story

  • [PT-825] - The patient symptoms index should preserve the ontology hierarchy
  • [PT-1161] - Add a REST-full API for accessing vocabularies
  • [PT-1940] - Anonymous usage reporting for PhenoTips instances
  • [PT-1941] - Synchronize consent across instances
  • [PT-1976] - Patient push protocol should support versioning
  • [PT-1993] - Unified genotype section - Entering genes and variants

Task

  • [PT-1315] - Unchecked conversion warnings when building export-api
  • [PT-1362] - Server consent forms need to be queried and responded to as part of push
  • [PT-2083] - Upgrade to Solr 5.3.1
  • [PT-2192] - Add tests for patient indexing
  • [PT-2251] - Upgrade to XWiki 7.1.4
  • [PT-2275] - Add ability to import gene data
  • [PT-2364] - Setting owner of a patient produces a wrong owner id
  • [PT-2420] - When pushing warn user if target PhenoTips instance does not support this push protocol version
  • [PT-2436] - Phenotype sub terms should NOT expand when clicking on N
  • [PT-2440] - Move the hgnc-remote vocabulary in a separate module

Improvement

  • [PT-497] - Add the possibility to reindex OMIM from the administration
  • [PT-1044] - Automatically expand the list of subcategories (if it exists) when selecting YES for a phenotype in the predefined phenotype list
  • [PT-1827] - Make the homepage easily extensible
  • [PT-1844] - Make "create sibling" handle go to the right instead of to the left of the parent link
  • [PT-1928] - Use requirejs to load the pedigree js files
  • [PT-2007] - Improve the pedigree load time by minifying its sources
  • [PT-2049] - Remove yellow on-hover row highlight of a table
  • [PT-2059] - "Enter" should accept first phenotype suggestion
  • [PT-2067] - Allow using Y/N/NA pickers for controlling the "controlled groups" widget
  • [PT-2084] - Enter should accept the selected suggestion
  • [PT-2108] - Optional PatientData should be lazy loaded
  • [PT-2147] - Move the Identifier column to the second place of the All patient record page
  • [PT-2189] - Add new methods for better vocabulary identification
  • [PT-2197] - "Unknown" should be (default) option for Sex field
  • [PT-2227] - Add "thyroid cancer" to the list of cancers in the pedigree node menu
  • [PT-2228] - Make ages easier to read in the cancers tab of the pedigree node menu
  • [PT-2252] - The pedigree image service should support offering to download the file instead of just displaying it
  • [PT-2260] - Shorter URLs: remove the /bin/ part from URLs
  • [PT-2299] - Add a "secure" PatientRepository component that checks access rights before performing an action
  • [PT-2320] - Switch to org.json for JSON processing instead of the unmaintained net.sf.json library
  • [PT-2337] - JSON import does not support non-standard features
  • [PT-2394] - Selecting/deselecting consents should not reset the "Agree to push this data to server" checkbox
  • [PT-2396] - Better language on Push modal
  • [PT-2398] - Upgrade to font-awesome 4.5.0
  • [PT-2426] - Push receiverer component should be included by default in all PhenoTips instances
  • [PT-2435] - Use underscores rather than spaces in pedigree export filenames
  • [PT-2437] - Remove useless tooltip over the "Create new patient" button in the header
  • [PT-2464] - Ability to only specify the year of birth in the patient form
  • [PT-2469] - Improve the look of tabular data in PDF export
  • [PT-2475] - Phenotype details for negative phenotypes should only contain comments

Edit/Copy Release Notes

The text area below allows the project release notes to be edited and copied to another document.