[phenotips-notifications] [phenotips/phenotips] 4e72b3: PT-2023: One unified gene section with variants (I...

GitHub noreply at github.com
Sun Oct 25 21:47:53 EDT 2015


  Branch: refs/heads/PT-1280-unified-genes
  Home:   https://github.com/phenotips/phenotips
  Commit: 4e72b3547036f6763c15b8a8480610a3e47726a8
      https://github.com/phenotips/phenotips/commit/4e72b3547036f6763c15b8a8480610a3e47726a8
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-10-25 (Sun, 25 Oct 2015)

  Changed paths:
    M components/export/api/pom.xml
    M components/export/api/src/main/java/org/phenotips/export/internal/DataToCellConverter.java
    M components/export/api/src/main/java/org/phenotips/export/internal/SheetAssembler.java
    M components/export/api/src/main/resources/ApplicationResources.properties
    M components/export/ui/src/main/resources/PhenoTips/ExportJSON.xml
    M components/export/ui/src/main/resources/PhenoTips/ExportPreferences.xml
    M components/patient-data/impl/pom.xml
    M components/patient-data/impl/src/main/java/org/phenotips/data/internal/controller/GeneListController.java
    R components/patient-data/impl/src/main/java/org/phenotips/data/internal/controller/RejectedGeneListController.java
    M components/patient-data/impl/src/main/java/org/phenotips/data/internal/controller/SolvedController.java
    A components/patient-data/impl/src/main/java/org/phenotips/data/internal/controller/VariantListController.java
    M components/patient-data/impl/src/main/resources/ApplicationResources.properties
    M components/patient-data/impl/src/main/resources/META-INF/components.txt
    M components/patient-data/impl/src/test/java/org/phenotips/data/internal/controller/SolvedControllerTest.java
    A components/patient-data/impl/src/test/java/org/phenotips/data/internal/controller/VariantListControllerTest.java
    M components/patient-data/indexing/pom.xml
    A components/patient-data/indexing/src/main/java/org/phenotips/data/indexing/internal/PatientEmptyObjectsRemover.java
    M components/patient-data/indexing/src/main/resources/META-INF/components.txt
    A components/patient-data/indexing/src/test/java/org/phenotips/data/indexing/internal/PatientEmptyObjectsRemoverTest.java
    A components/patient-data/indexing/src/test/java/org/phenotips/data/indexing/internal/PatientEventListenerTest.java
    A components/patient-data/indexing/src/test/java/org/phenotips/data/indexing/internal/SolrPatientIndexerTest.java
    M components/patient-data/migrations/src/main/java/org/phenotips/data/internal/R45391PhenoTips434DataMigration.java
    M components/patient-data/migrations/src/main/java/org/phenotips/data/internal/R50291PhenoTips481DataMigration.java
    A components/patient-data/migrations/src/main/java/org/phenotips/data/internal/R70190PhenoTips1280DataMigration.java
    M components/patient-data/migrations/src/main/resources/META-INF/components.txt
    M components/patient-data/pageobjects/src/main/java/org/phenotips/data/test/po/PatientRecordEditPage.java
    M components/patient-data/pageobjects/src/main/java/org/phenotips/data/test/po/PatientRecordViewPage.java
    A components/patient-data/ui/src/main/resources/PhenoTips/GeneClass.xml
    A components/patient-data/ui/src/main/resources/PhenoTips/GeneVariantClass.xml
    R components/patient-data/ui/src/main/resources/PhenoTips/InvestigationClass.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/PatientClass.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/PatientSheet.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/PatientSheetCode.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/PatientTemplate.xml
    R components/patient-data/ui/src/main/resources/PhenoTips/RejectedGenesClass.xml
    A components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__gene-variants.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__genes.xml
    R components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__rejected_genes.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__solved.xml
    A components/solr-access-service/ui/.gitignore
    M components/vocabularies/hgnc/ui/src/main/resources/PhenoTips/GeneNameService.xml
    M components/widgets/api/src/main/resources/ApplicationResources.properties
    A components/widgets/ui/src/main/resources/PhenoTips/GeneVariantMacros.xml
    M components/widgets/ui/src/main/resources/PhenoTips/TabelarDataMacros.xml
    M components/widgets/ui/src/main/resources/PhenoTips/Widgets.xml

  Log Message:
  -----------
  PT-2023: One unified gene section with variants (Issue #1280). Final commit for codefeview


  Commit: 1aaa88ab5c1c13f783116c4b5e07096566cd39d7
      https://github.com/phenotips/phenotips/commit/1aaa88ab5c1c13f783116c4b5e07096566cd39d7
  Author: Orion Buske <orion.buske at gmail.com>
  Date:   2015-10-25 (Sun, 25 Oct 2015)

  Changed paths:
    M components/export/api/src/main/java/org/phenotips/export/internal/DataToCellConverter.java
    M components/export/api/src/main/resources/ApplicationResources.properties
    M components/patient-data/impl/src/main/java/org/phenotips/data/internal/controller/GeneListController.java
    M components/patient-data/impl/src/main/java/org/phenotips/data/internal/controller/VariantListController.java
    M components/patient-data/impl/src/test/java/org/phenotips/data/internal/controller/VariantListControllerTest.java
    M components/patient-data/indexing/src/test/java/org/phenotips/data/indexing/internal/SolrPatientIndexerTest.java
    M components/widgets/ui/src/main/resources/PhenoTips/GeneVariantMacros.xml

  Log Message:
  -----------
  PT-1280: Updates and fixes to unified gene section

- Cleaned up formatting of patient indexing code
- Added missing fields to gene controller
- Added tests for missing variant objects
- Fixed variant evidence display on firefox (.innerText unsupported)


Compare: https://github.com/phenotips/phenotips/compare/4e72b3547036^...1aaa88ab5c1c


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