[phenotips/phenotips] 1e1bbd: PT-3076: Upgrade to XWiki 10

GitHub noreply at github.com
Thu Jan 17 12:45:42 EST 2019


  Branch: refs/heads/xwiki-upgrade
  Home:   https://github.com/phenotips/phenotips
  Commit: 1e1bbdfffc8c98b769c365dd0f263ff6c00ab72c
      https://github.com/phenotips/phenotips/commit/1e1bbdfffc8c98b769c365dd0f263ff6c00ab72c
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M pom.xml

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
First step: declare the new XWiki version


  Commit: eb0a96bdd5be1295917c4d903b8e500d6ac69d1f
      https://github.com/phenotips/phenotips/commit/eb0a96bdd5be1295917c4d903b8e500d6ac69d1f
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M components/base-war/pom.xml
    M components/skin/ui/pom.xml
    M resources/ui/pom.xml

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
Use the last available version of the Colibri skin and color themes


  Commit: 00a93389300d0ad4f0a932a64548580449a35df4
      https://github.com/phenotips/phenotips/commit/00a93389300d0ad4f0a932a64548580449a35df4
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M components/application-configuration/ui/src/main/resources/PhenoTips/DBConfigurationClass.xml
    M components/application-configuration/ui/src/main/resources/PhenoTips/DBConfigurationClassDisplayer.xml
    M components/application-configuration/ui/src/main/resources/PhenoTips/LabeledIdentifierConfigurationClass.xml
    M components/application-configuration/ui/src/main/resources/PhenoTips/LabeledIdentifierGlobalSettings.xml
    M components/application-configuration/ui/src/main/resources/PhenoTips/LabeledIdentifierSettings.xml
    M components/application-configuration/ui/src/main/resources/PhenoTips/MenuConfigurationClass.xml
    M components/consents/ui/src/main/resources/PhenoTips/PatientConsent.xml
    M components/consents/ui/src/main/resources/PhenoTips/PatientConsentConfiguration.xml
    M components/default-settings/src/main/resources/PhenoTips/WebPreferences.xml
    M components/default-settings/src/main/resources/WikiManager/WikiUserConfiguration.xml
    M components/default-settings/src/main/resources/XWiki/Admin.xml
    M components/default-settings/src/main/resources/XWiki/XWikiPreferences.xml
    M components/default-settings/src/main/resources/data/WebPreferences.xml
    M components/diagnosis-suggestion/ui/src/main/resources/PhenoTips/DiseasePredictService.xml
    M components/entities/ui/src/main/resources/PhenoTips/EntityBindingClass.xml
    M components/export/ui/src/main/resources/PhenoTips/Export.xml
    M components/export/ui/src/main/resources/PhenoTips/ExportFilter.xml
    M components/export/ui/src/main/resources/PhenoTips/ExportJSON.xml
    M components/export/ui/src/main/resources/PhenoTips/ExportPreferences.xml
    M components/family-studies/ui/src/main/resources/Families/Create.xml
    M components/family-studies/ui/src/main/resources/Families/WebHome.xml
    M components/family-studies/ui/src/main/resources/Families/WebPreferences.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyClass.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyContentTopMenu.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyDataGadget.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyFilters.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyMacros.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyPedigreeInterface.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyRecordField_externalId.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyRecordField_familyReports.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyRecordField_memberReports.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyRecordField_members.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyRecordField_pedigree.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyRecordField_sensitiveInfoWarning.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyRecordSection_about.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyRecordSection_members.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyRecordSection_pedigree.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyRecordSection_reports.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyReferenceClass.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilySelector.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilySheet.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyTemplate.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FormMacros.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/UIX_Field__family_membership.xml
    M components/gene-panels/ui/src/main/resources/PhenoTips/PanelsDisplay.xml
    M components/gene-panels/ui/src/main/resources/PhenoTips/PanelsExport.xml
    M components/gene-panels/ui/src/main/resources/PhenoTips/PanelsGeneStatusObserver.xml
    M components/gene-panels/ui/src/main/resources/PhenoTips/UIX_Field__gene_suggestions.xml
    M components/gene-panels/ui/src/main/resources/PhenoTips/UIX_Section__gene-suggestions.xml
    M components/navigation/ui/src/main/resources/PhenoTips/DBWebHomeSheet.xml
    M components/navigation/ui/src/main/resources/PhenoTips/DatabaseFilters.xml
    M components/navigation/ui/src/main/resources/PhenoTips/LiveTableMacros.xml
    M components/navigation/ui/src/main/resources/PhenoTips/LiveTableResults.xml
    M components/navigation/ui/src/main/resources/XWiki/GadgetClass.xml
    M components/navigation/ui/src/main/resources/XWiki/SearchCode.xml
    M components/navigation/ui/src/main/resources/XWiki/SearchConfig.xml
    M components/navigation/ui/src/main/resources/XWiki/SearchSuggestConfig.xml
    M components/navigation/ui/src/main/resources/data/AllData.xml
    M components/navigation/ui/src/main/resources/data/WebHome.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/AccessRightsManagement.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/AllDataGadget.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/CollaboratorClass.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/FamilyDataGadget.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/MyDataGadget.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/OwnerClass.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/SharedFamilyGadget.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/VisibilityClass.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/VisibilityConfigurationClass.xml
    M components/patient-data-extra/medication/ui/src/main/resources/PhenoTips/MedicationDataClass.xml
    M components/patient-data-extra/medication/ui/src/main/resources/PhenoTips/UIX_Field__medication.xml
    M components/patient-data-sharing/push-ui/src/main/resources/PhenoTips/PushPatient.xml
    M components/patient-data-sharing/push-ui/src/main/resources/PhenoTips/PushPatientConfiguration.xml
    M components/patient-data-sharing/push-ui/src/main/resources/PhenoTips/PushPatientServer.xml
    M components/patient-data-sharing/push-ui/src/main/resources/PhenoTips/PushPatientService.xml
    M components/patient-data-sharing/receiver-ui/src/main/resources/PhenoTips/PhenotipsSourceServerReference.xml
    M components/patient-data-sharing/receiver-ui/src/main/resources/PhenoTips/ReceivePatientConfiguration.xml
    M components/patient-data-sharing/receiver-ui/src/main/resources/PhenoTips/ReceivePatientServer.xml
    M components/patient-data-sharing/receiver-ui/src/main/resources/PhenoTips/ReceivePatientSettings.xml
    M components/patient-data-sharing/receiver-ui/src/main/resources/data/receivePatientData.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/AllDataGadget.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/AllergiesDataClass.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/AllergySearch.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/CheckID.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/CheckLabeledEid.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/CreatePatientRecord.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/ExportMultiplePatients.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/ExportPatient.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/ExternalFileClass.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/ExternalImageClass.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/GeneClass.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/GeneVariantClass.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/JSONImportDialog.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/LabeledEidValidator.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/LabeledIdentifierClass.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/LabledEidTableDataDisplayer.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/ObstetricHistoryClass.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/OntologyVersionClass.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/OpenPatientRecord.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/ParentalInformationClass.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/PatientSheetMacros.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/PatientTemplate.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/PhenotypeCategoryClass.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/PhenotypeDisplay.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/PhenotypeMetaClass.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/RelativeClass.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__additional-documents.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__additional-images-exported.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__additional-images.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__affected_relatives.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__allergies.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__apgar.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__assisted_reproduction.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__charts-exported.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__charts.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__clinical_diagnosis.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__consanguinity.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__date_of_birth.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__date_of_death.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__diagnosis_notes.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__ethnicity.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__exam_date.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__external_id.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__family.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__family_history.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__gender.xml
    M 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
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__genetic_notes.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__gestation.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__global_age_of_onset.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__global_mode_of_inheritance.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__health_card.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__identifier.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__indication_for_referral.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__labeled_eids.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__life_status.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__measurements.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__medical_history.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__miscarriages.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__multiple_gestation.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__obstetric_history.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__omim_id.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__omim_suggestions.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__parental_age.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__parental_names.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__patient_name.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__pedigree-exported.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__pedigree-file.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__phenotype.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__phenotype_suggestions.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__prenatal_development.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__prenatal_phenotype.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__proband_info.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__reports_history.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__required-measurements.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__solved.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__variants.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Section__diagnosis-info.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Section__family-info.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Section__files-info.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Section__genotype.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Section__measurement-info.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Section__medical-history.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Section__patient-info.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Section__phenotype-info.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Section__prenatal-info.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Section__variant-info.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/VCF.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/VariantClass.xml
    M components/patient-measurements/ui/src/main/resources/PhenoTips/ChartGenerator.xml
    M components/patient-measurements/ui/src/main/resources/PhenoTips/ChartService.xml
    M components/patient-measurements/ui/src/main/resources/PhenoTips/ChartServiceMacros.xml
    M components/patient-measurements/ui/src/main/resources/PhenoTips/MeasurementsClass.xml
    M components/patient-measurements/ui/src/main/resources/PhenoTips/PatientToolsService.xml
    M components/pedigree/ui/src/main/resources/PhenoTips/PedigreeClass.xml
    M components/pedigree/ui/src/main/resources/PhenoTips/PedigreeConfiguration.xml
    M components/pedigree/ui/src/main/resources/PhenoTips/PedigreeEditor.xml
    M components/pedigree/ui/src/main/resources/PhenoTips/PedigreeGlobalSettings.xml
    M components/pedigree/ui/src/main/resources/PhenoTips/PedigreeImageService.xml
    M components/pedigree/ui/src/main/resources/PhenoTips/PedigreeInterface.xml
    M components/pedigree/ui/src/main/resources/PhenoTips/PedigreeMacros.xml
    M components/pedigree/ui/src/main/resources/PhenoTips/PedigreeSampleExtension.xml
    M components/pedigree/ui/src/main/resources/PhenoTips/UIX_Field__pedigree.xml
    M components/phenotype-suggest-service/ui/src/main/resources/PhenoTips/DiffDiagnosisService.xml
    M components/record-locking/ui/src/main/resources/PhenoTips/PatientLock.xml
    M components/security/audit/frontend/src/main/resources/PhenoTips/Audit.xml
    M components/security/audit/frontend/src/main/resources/PhenoTips/AuditFilters.xml
    M components/security/audit/frontend/src/main/resources/PhenoTips/AuditLogs.xml
    M components/security/audit/frontend/src/main/resources/PhenoTips/AuditResults.xml
    M components/skin/ui/src/main/resources/ColorThemes/Blue.xml
    M components/skin/ui/src/main/resources/ColorThemes/Kiwi.xml
    M components/skin/ui/src/main/resources/ColorThemes/Maple leaf.xml
    M components/skin/ui/src/main/resources/ColorThemes/Orange.xml
    M components/skin/ui/src/main/resources/ColorThemes/Ruby.xml
    M components/skin/ui/src/main/resources/ColorThemes/Silver leaf.xml
    M components/skin/ui/src/main/resources/Main/WebHome.xml
    M components/skin/ui/src/main/resources/PhenoTips/ContentTopMenu.xml
    M components/skin/ui/src/main/resources/PhenoTips/CreatePatientRecordForm.xml
    M components/skin/ui/src/main/resources/PhenoTips/DocumentMeta.xml
    M components/skin/ui/src/main/resources/PhenoTips/EmbeddableSkin.xml
    M components/skin/ui/src/main/resources/PhenoTips/Skin.xml
    M components/skin/ui/src/main/resources/PhenoTips/SkinCustomization.xml
    M components/skin/ui/src/main/resources/PhenoTips/UIXSheet.xml
    M components/skin/ui/src/main/resources/PhenoTips/UIXTemplate.xml
    M components/skin/ui/src/main/resources/XWiki/PDFClass.xml
    M components/skin/ui/src/main/resources/XWiki/WebHome.xml
    M components/skin/ui/src/main/resources/XWiki/XWikiLogin.xml
    M components/skin/ui/src/main/resources/data/ServerError.xml
    M components/specificity-meter/ui/src/main/resources/PhenoTips/SpecificityMetricWidget.xml
    M components/specificity-meter/ui/src/main/resources/PhenoTips/SpecificityMetricWidgetService.xml
    M components/specificity-meter/ui/src/main/resources/PhenoTips/SpecificityMetricWidgetTranslations.ar.xml
    M components/specificity-meter/ui/src/main/resources/PhenoTips/SpecificityMetricWidgetTranslations.de.xml
    M components/specificity-meter/ui/src/main/resources/PhenoTips/SpecificityMetricWidgetTranslations.es.xml
    M components/specificity-meter/ui/src/main/resources/PhenoTips/SpecificityMetricWidgetTranslations.fr.xml
    M components/specificity-meter/ui/src/main/resources/PhenoTips/SpecificityMetricWidgetTranslations.ja.xml
    M components/specificity-meter/ui/src/main/resources/PhenoTips/SpecificityMetricWidgetTranslations.ru.xml
    M components/specificity-meter/ui/src/main/resources/PhenoTips/SpecificityMetricWidgetTranslations.xml
    M components/studies/ui/src/main/resources/PhenoTips/StudiesMacros.xml
    M components/studies/ui/src/main/resources/PhenoTips/StudyBindingClass.xml
    M components/studies/ui/src/main/resources/PhenoTips/StudyBindingSheet.xml
    M components/studies/ui/src/main/resources/PhenoTips/StudyCases.xml
    M components/studies/ui/src/main/resources/PhenoTips/StudyClass.xml
    M components/studies/ui/src/main/resources/PhenoTips/StudySheet.xml
    M components/studies/ui/src/main/resources/PhenoTips/StudyTemplate.xml
    M components/studies/ui/src/main/resources/Studies/WebHome.xml
    M components/studies/ui/src/main/resources/Studies/WebPreferences.xml
    M components/user-profile-ui/src/main/resources/XWiki/AdminUserProfileSheet.xml
    M components/user-profile-ui/src/main/resources/XWiki/UserProfileSectionClass.xml
    M components/user-profile-ui/src/main/resources/XWiki/UserProfileSectionsClass.xml
    M components/user-profile-ui/src/main/resources/XWiki/XWikiUserPreferencesSheet.xml
    M components/user-profile-ui/src/main/resources/XWiki/XWikiUserProfileSheet.xml
    M components/user-profile-ui/src/main/resources/XWiki/XWikiUserSheet.xml
    M components/users/ui/src/main/resources/Groups/WebHome.xml
    M components/users/ui/src/main/resources/Groups/WebPreferences.xml
    M components/users/ui/src/main/resources/PhenoTips/GroupCases.xml
    M components/users/ui/src/main/resources/PhenoTips/GroupSharedCases.xml
    M components/users/ui/src/main/resources/PhenoTips/GroupsGadget.xml
    M components/users/ui/src/main/resources/PhenoTips/MyGroupsGadget.xml
    M components/users/ui/src/main/resources/PhenoTips/PhenoTipsGroupClass.xml
    M components/users/ui/src/main/resources/PhenoTips/PhenoTipsGroupSheet.xml
    M components/users/ui/src/main/resources/PhenoTips/PhenoTipsGroupTemplate.xml
    M components/utilities/ncbieutils-services/pubmed-suggestions-ui/src/main/resources/PhenoTips/PubMedService.xml
    M components/vocabularies/hpo/ui/src/main/resources/PhenoTips/Detailed physical phenotype configuration.xml
    M components/vocabularies/hpo/ui/src/main/resources/PhenoTips/FormDesigner.xml
    M components/vocabularies/hpo/ui/src/main/resources/PhenoTips/Generic phenotype configuration.de.xml
    M components/vocabularies/hpo/ui/src/main/resources/PhenoTips/Generic phenotype configuration.es.xml
    M components/vocabularies/hpo/ui/src/main/resources/PhenoTips/Generic phenotype configuration.fr.xml
    M components/vocabularies/hpo/ui/src/main/resources/PhenoTips/Generic phenotype configuration.xml
    M components/vocabularies/hpo/ui/src/main/resources/PhenoTips/HPOBranchDisplayer.xml
    M components/vocabularies/hpo/ui/src/main/resources/PhenoTips/PhenotypeMappingClass.xml
    M components/vocabularies/hpo/ui/src/main/resources/PhenoTips/PhenotypeMappingPreview.xml
    M components/vocabularies/hpo/ui/src/main/resources/PhenoTips/PhenotypeMappingSheet.xml
    M components/vocabularies/hpo/ui/src/main/resources/PhenoTips/PhenotypeMappingTemplate.xml
    M components/vocabularies/ui/src/main/resources/PhenoTips/IndexVocabulary.xml
    M components/vocabularies/ui/src/main/resources/PhenoTips/VocabularyRelocationConfiguration.xml
    M components/vocabularies/ui/src/main/resources/PhenoTips/VocabularySourceRelocationClass.xml
    M components/widgets/ui/src/main/resources/Main/MessageSenderMacro.xml
    M components/widgets/ui/src/main/resources/PhenoTips/FontAwesomeIcons.xml
    M components/widgets/ui/src/main/resources/PhenoTips/ImageDisplayer.xml
    M components/widgets/ui/src/main/resources/PhenoTips/JSONMacros.xml
    M components/widgets/ui/src/main/resources/PhenoTips/TabelarDataMacros.xml
    M components/widgets/ui/src/main/resources/PhenoTips/Widgets.xml
    M components/widgets/ui/src/main/resources/PhenoTips/YesNoNAPicker.xml
    M components/widgets/ui/src/main/resources/XWiki/DateTimePicker.xml
    M components/widgets/ui/src/main/resources/XWiki/StringDisplayer.xml
    M resources/ui/src/main/resources/PhenoTips/EthnicitySearch.xml
    M resources/ui/src/main/resources/PhenoTips/PatientPhenotypeExportService.xml
    M resources/ui/src/main/resources/PhenoTips/TouchscreenEvents.xml
    M resources/ui/src/main/resources/PhenoTips/Translations.ar.xml
    M resources/ui/src/main/resources/PhenoTips/Translations.de.xml
    M resources/ui/src/main/resources/PhenoTips/Translations.es.xml
    M resources/ui/src/main/resources/PhenoTips/Translations.fr.xml
    M resources/ui/src/main/resources/PhenoTips/Translations.ja.xml
    M resources/ui/src/main/resources/PhenoTips/Translations.ru.xml
    M resources/ui/src/main/resources/PhenoTips/Translations.xml
    M resources/ui/src/main/resources/PhenoTips/UIX Directory.xml
    M resources/ui/src/main/resources/PhenoTips/WebHome.xml
    M resources/ui/src/main/resources/XWiki/AdminPresentationSheet.xml
    M resources/ui/src/main/resources/XWiki/AdminSheet.xml
    M resources/ui/src/main/resources/XWiki/ConfigurableClass.xml
    M resources/ui/src/main/resources/XWiki/ConfigurableClassMacros.xml
    M resources/ui/src/main/resources/XWiki/ConfigurationClass.xml

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
XDoc source must have mimetypes for attachments, and must not have any dates


  Commit: 35a14f572ddf68ea6845763d46d941ebc47803d0
      https://github.com/phenotips/phenotips/commit/35a14f572ddf68ea6845763d46d941ebc47803d0
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M components/base-war/pom.xml
    M components/consents/api/pom.xml
    M components/consents/rest/pom.xml
    M components/entities/api/pom.xml
    M components/family-studies/api/pom.xml
    M components/family-studies/migrations/pom.xml
    M components/family-studies/rest/pom.xml
    M components/gene-panels/rest/pom.xml
    M components/patient-contacts/pom.xml
    M components/patient-data-extra/medication/api/pom.xml
    M components/patient-data/api/pom.xml
    M components/patient-data/impl/pom.xml
    M components/patient-data/migrations/pom.xml
    M components/patient-data/rest/pom.xml
    M components/patient-tools/pom.xml
    M components/rest-commons/pom.xml
    M components/security/audit/backend/pom.xml
    M components/security/audit/rest/pom.xml
    M components/specificity-meter/api/pom.xml
    M components/users/api/pom.xml
    M components/users/rest/pom.xml
    M components/vocabularies/api/pom.xml
    M components/vocabularies/hgnc-remote/api/pom.xml
    M components/vocabularies/hpo/translation-french/pom.xml
    M components/vocabularies/hpo/translation-german/pom.xml
    M components/vocabularies/hpo/translation-italian/pom.xml
    M components/vocabularies/hpo/translation-russian/pom.xml
    M components/vocabularies/hpo/translation-spanish/pom.xml
    M components/vocabularies/rest/pom.xml
    M distribution/war/pom.xml

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
Make sure we use org.json:json instead of com.tdunning:json, which is the library used by XWiki


  Commit: aa0b05a8d846c6135a36d465c2caa750afff19ea
      https://github.com/phenotips/phenotips/commit/aa0b05a8d846c6135a36d465c2caa750afff19ea
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M components/entity-access-rules/rest/pom.xml
    M components/patient-data/rest/pom.xml
    M components/rest-commons/pom.xml
    R components/rest-commons/src/main/java/org/phenotips/rest/internal/ConfigureISODatesInJson.java
    R components/rest-commons/src/main/java/org/phenotips/rest/internal/ConfigureJsonMapper.java
    R components/rest-commons/src/main/java/org/phenotips/rest/internal/ConfigureNonNullFieldsInJson.java
    A components/rest-commons/src/main/java/org/phenotips/rest/internal/JacksonConverter.java
    A components/rest-commons/src/main/java/org/phenotips/rest/internal/JacksonRepresentation.java
    M components/rest-commons/src/main/resources/META-INF/components.txt
    A components/rest-commons/src/main/resources/META-INF/services/org.restlet.engine.converter.ConverterHelper
    R components/rest-commons/src/test/java/org/phenotips/rest/internal/ConfigureISODatesInJsonTest.java
    M components/vocabularies/rest/pom.xml
    M distribution/war/pom.xml
    M pom.xml

  Log Message:
  -----------
  PT-3861: Upgrade org.restlet
Done


  Commit: 33dd7255cfc68e024d62f408fb8605643ddd8026
      https://github.com/phenotips/phenotips/commit/33dd7255cfc68e024d62f408fb8605643ddd8026
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M components/base-war/pom.xml
    M components/base-war/src/main/webapp/WEB-INF/web.xml
    M components/default-settings/pom.xml
    M components/specificity-meter/api/pom.xml
    M components/vocabularies/api/pom.xml
    M components/vocabularies/chebi/api/pom.xml
    M components/vocabularies/hgnc-remote/api/pom.xml
    M components/vocabularies/hpo/api/pom.xml
    M components/vocabularies/hpo/translation-french/pom.xml
    M components/vocabularies/hpo/translation-german/pom.xml
    M components/vocabularies/hpo/translation-italian/pom.xml
    M components/vocabularies/hpo/translation-russian/pom.xml
    M components/vocabularies/hpo/translation-spanish/pom.xml
    M distribution/hsqldb-database/pom.xml
    M distribution/rpm/pom.xml
    M distribution/war/pom.xml
    M resources/ui/pom.xml

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
Updated build files to include the right dependencies and use the right configuration


  Commit: 199f74d2265be26b21448cc580aa13dd0c5101af
      https://github.com/phenotips/phenotips/commit/199f74d2265be26b21448cc580aa13dd0c5101af
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    R components/base-war/src/main/java/com/xpn/xwiki/api/DeletedDocument.java
    R components/base-war/src/main/java/com/xpn/xwiki/objects/classes/ComputedFieldClass.java
    R components/base-war/src/main/java/com/xpn/xwiki/objects/classes/PropertyClass.java
    M components/base-war/src/main/java/com/xpn/xwiki/store/XWikiHibernateStore.java
    M components/base-war/src/main/java/com/xpn/xwiki/user/impl/xwiki/XWikiAuthServiceImpl.java
    R components/base-war/src/main/java/com/xpn/xwiki/web/TempResourceAction.java
    M components/base-war/src/main/java/com/xpn/xwiki/web/XWikiServletResponse.java
    R components/base-war/src/main/java/com/xpn/xwiki/web/XWikiServletURLFactory.java
    M components/base-war/src/main/java/org/xwiki/url/internal/standard/entity/AbstractEntityResourceReferenceResolver.java
    M components/base-war/src/main/java/org/xwiki/velocity/tools/JSONTool.java
    R components/base-war/src/main/webapp/resources/js/xwiki/table/livetable.css
    M components/base-war/src/main/webapp/resources/js/xwiki/table/livetable.js
    A components/base-war/src/main/webapp/skins/phenotips/attachmentsinline.vm
    A components/base-war/src/main/webapp/skins/phenotips/commentsinline.vm
    A components/base-war/src/main/webapp/skins/phenotips/contentheader.vm
    M components/base-war/src/main/webapp/skins/phenotips/contentview.vm
    A components/base-war/src/main/webapp/skins/phenotips/docextra.vm
    M components/base-war/src/main/webapp/skins/phenotips/edit.vm
    A components/base-war/src/main/webapp/skins/phenotips/editclass.vm
    M components/base-war/src/main/webapp/skins/phenotips/editinline.vm
    A components/base-war/src/main/webapp/skins/phenotips/editobject.vm
    A components/base-war/src/main/webapp/skins/phenotips/editwiki.vm
    A components/base-war/src/main/webapp/skins/phenotips/global.vm
    A components/base-war/src/main/webapp/skins/phenotips/historyinline.vm
    M components/base-war/src/main/webapp/skins/phenotips/htmlheader.vm
    A components/base-war/src/main/webapp/skins/phenotips/javascript.vm
    A components/base-war/src/main/webapp/skins/phenotips/pdfhtmlheader.vm
    M components/base-war/src/main/webapp/skins/phenotips/uorgsuggest.vm
    R components/base-war/src/main/webapp/templates/commentsinline.vm
    R components/base-war/src/main/webapp/templates/displayer_email.vm
    R components/base-war/src/main/webapp/templates/edit.vm
    R components/base-war/src/main/webapp/templates/editclass.vm
    R components/base-war/src/main/webapp/templates/javascript.vm
    M components/base-war/src/main/webapp/templates/macros.vm
    R components/base-war/src/main/webapp/templates/pdfhtmlheader.vm
    M components/patient-access-rules/api/src/test/java/org/phenotips/data/permissions/internal/DefaultPermissionsConfigurationTest.java
    R components/widgets/ui/src/main/resources/Main/MessageSenderMacro.xml

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
Merge overridden upstream files


  Commit: 81a336456b3bae27223414ad4200e88d209abe99
      https://github.com/phenotips/phenotips/commit/81a336456b3bae27223414ad4200e88d209abe99
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M components/family-studies/ui/src/main/resources/Families/WebHome.xml
    M components/navigation/ui/src/main/resources/PhenoTips/LiveTableMacros.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/AllDataGadget.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/SharedFamilyGadget.xml
    M components/patient-data-sharing/push-ui/src/main/resources/PhenoTips/PushPatient.xml
    M components/studies/ui/src/main/resources/PhenoTips/StudiesMacros.xml
    M components/studies/ui/src/main/resources/PhenoTips/StudyCases.xml
    M components/users/ui/src/main/resources/PhenoTips/GroupCases.xml

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
Fixed some deprecated method calls


  Commit: 6f5503784f2c94a69f7bfe997ed52316c8c45969
      https://github.com/phenotips/phenotips/commit/6f5503784f2c94a69f7bfe997ed52316c8c45969
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    A components/base-war/src/main/webapp/resources/js/xwiki/lightbox/back.png
    A components/base-war/src/main/webapp/resources/js/xwiki/lightbox/btnClose.png
    A components/base-war/src/main/webapp/resources/js/xwiki/lightbox/lightbox.css
    A components/base-war/src/main/webapp/resources/js/xwiki/lightbox/lightbox.js
    A components/base-war/src/main/webapp/resources/js/xwiki/usersandgroups/usersandgroups.js
    A components/base-war/src/main/webapp/templates/addnewgroup.vm
    A resources/ui/src/main/resources/XWiki/AdminGroupsSheet.xml
    A resources/ui/src/main/resources/XWiki/AdminUsersSheet.xml

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
Bugfix: managing users and groups requires the Flamingo skin in the latest XWiki verion; use the last version still working with Colibri


  Commit: f40ccdbb1c2b739215cb9b5bce89422e6b93deed
      https://github.com/phenotips/phenotips/commit/f40ccdbb1c2b739215cb9b5bce89422e6b93deed
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M components/base-war/src/main/webapp/WEB-INF/urlrewrite.xml

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
Fixed regression: URLs contain /data/


  Commit: 59a7f7f51d8e6028405912864518b1c12baeb355
      https://github.com/phenotips/phenotips/commit/59a7f7f51d8e6028405912864518b1c12baeb355
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M components/family-studies/ui/src/main/resources/Families/WebHome.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyDataGadget.xml
    M components/navigation/ui/src/main/resources/data/AllData.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/AllDataGadget.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/FamilyDataGadget.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/MyDataGadget.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/SharedFamilyGadget.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/AllDataGadget.xml
    M components/studies/ui/src/main/resources/PhenoTips/StudyCases.xml
    M components/users/ui/src/main/resources/PhenoTips/GroupCases.xml
    M components/users/ui/src/main/resources/PhenoTips/GroupSharedCases.xml

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
Fixed regression: the Actions column on the livetables has a non-functional filter input on top


  Commit: f90dce215270c52070984e576381a977313f2f3e
      https://github.com/phenotips/phenotips/commit/f90dce215270c52070984e576381a977313f2f3e
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M components/base-war/src/main/webapp/resources/uicomponents/widgets/userpicker/userPicker.js

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
Fixed regression: broken display in the user picker


  Commit: 75ca1de7271b09a1d1bdeaadfbaa54739fcab023
      https://github.com/phenotips/phenotips/commit/75ca1de7271b09a1d1bdeaadfbaa54739fcab023
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M components/family-studies/ui/src/main/resources/Families/Create.xml
    M components/skin/ui/src/main/resources/PhenoTips/CreatePatientRecordForm.xml

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
Fixed regression: non-admin users cannot create new patients or families


  Commit: 83857f6400e1f9f016e3130846266b55f9678692
      https://github.com/phenotips/phenotips/commit/83857f6400e1f9f016e3130846266b55f9678692
  Author: Sergiu Dumitriu <sdumitriu at users.noreply.github.com>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M components/consents/ui/src/main/resources/PhenoTips/PatientConsentConfiguration.xml

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10

Regression: Consents can no longer be configured


  Commit: eff03238b0004166d044ce81274a1adfedf643cc
      https://github.com/phenotips/phenotips/commit/eff03238b0004166d044ce81274a1adfedf643cc
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M distribution/war/pom.xml

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
Fixed regression: Most columns are empty in the data tables


  Commit: 76328c697a1f58d4300b613213c3fb6d5c8a727d
      https://github.com/phenotips/phenotips/commit/76328c697a1f58d4300b613213c3fb6d5c8a727d
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M components/base-war/src/main/resources/ApplicationResources.properties

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
Fixed regression: "XWiki is initializing" shows during the first request after starting up PhenoTips


  Commit: 82a40a6b9ff0c24a08ba83a0eaf432eb4a06c340
      https://github.com/phenotips/phenotips/commit/82a40a6b9ff0c24a08ba83a0eaf432eb4a06c340
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M pom.xml

  Log Message:
  -----------
  [misc] Move reporting configuration in the right place


  Commit: f802861df22450678ffc2f8d955a6c9d317abf84
      https://github.com/phenotips/phenotips/commit/f802861df22450678ffc2f8d955a6c9d317abf84
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M components/users/api/src/main/java/org/phenotips/groups/internal/UsersAndGroups.java
    M components/users/ui/src/main/resources/PhenoTips/PhenoTipsGroupSheet.xml
    M components/users/ui/src/main/resources/PhenoTips/PhenoTipsGroupTemplate.xml

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
Fixed regression: broken group avatars in users and groups suggestions


  Commit: 9f85d0a71e45f3866a872737a778e389e3e08e27
      https://github.com/phenotips/phenotips/commit/9f85d0a71e45f3866a872737a778e389e3e08e27
  Author: Marta Girdea <marta.girdea at gmail.com>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M components/patient-data/ui/src/main/resources/PhenoTips/VCF.xml

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10

Fixed regression: The genome reference no longer defaults to the first value defined in the `values` meta property


  Commit: c08b27c9381b1a41fa5c1741dcde45ef1985ab89
      https://github.com/phenotips/phenotips/commit/c08b27c9381b1a41fa5c1741dcde45ef1985ab89
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M components/base-war/src/main/webapp/resources/js/xwiki/lightbox/lightbox.js

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
Fixed regression: editing xgroup memebers from the administration no longer works


  Commit: 5c775d1303df836527c6edb4e806676ba538f78c
      https://github.com/phenotips/phenotips/commit/5c775d1303df836527c6edb4e806676ba538f78c
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2019-01-17 (Thu, 17 Jan 2019)

  Changed paths:
    M components/user-profile-ui/src/main/resources/XWiki/XWikiUserSheet.xml

  Log Message:
  -----------
  PT-3076: Upgrade to XWiki 10
Fixed regression: after registering a new user from the administration, a bare page is displayed


Compare: https://github.com/phenotips/phenotips/compare/fade3d49b9bc...5c775d1303df
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      Functionality will be removed from GitHub.com on January 31st, 2019.


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