[phenotips-notifications] [phenotips/phenotips] 99e9aa: PT-2234: Replace the full pedigree with its thumbn...

GitHub noreply at github.com
Mon Dec 21 10:29:27 EST 2015


  Branch: refs/heads/PT-2233
  Home:   https://github.com/phenotips/phenotips
  Commit: 99e9aae3186da1d0ea00620a8a8d7c8c2ac8858c
      https://github.com/phenotips/phenotips/commit/99e9aae3186da1d0ea00620a8a8d7c8c2ac8858c
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/pedigree/api/src/main/resources/ApplicationResources.properties
    M components/pedigree/ui/src/main/resources/PhenoTips/UIX_Field__pedigree.xml

  Log Message:
  -----------
  PT-2234: Replace the full pedigree with its thumbnail in the Family history and pedigree section


  Commit: dfac592f8c9e9501611f9263d8938eb011579d7a
      https://github.com/phenotips/phenotips/commit/dfac592f8c9e9501611f9263d8938eb011579d7a
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/family-studies/ui/src/main/resources/PhenoTips/UIX_Field__family_membership.xml
    M components/pedigree/ui/src/main/resources/PhenoTips/UIX_Field__pedigree.xml

  Log Message:
  -----------
  PT-2232: Remove FAMILY label from Family history and pedigree section; remove PEDIGREE label from patient page


  Commit: 10225e454ff8f5e77e8fb04d4b837d1364ed18aa
      https://github.com/phenotips/phenotips/commit/10225e454ff8f5e77e8fb04d4b837d1364ed18aa
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/export/XWikiFamilyExport.java
    M components/family-studies/ui/src/main/resources/PhenoTips/UIX_Field__family_membership.xml

  Log Message:
  -----------
  PT-2231: Add Family external identifier to the Family history and pedigree section
Fixed


  Commit: 54c0ebb579f6c05209071b629b75d040fc08ac8a
      https://github.com/phenotips/phenotips/commit/54c0ebb579f6c05209071b629b75d040fc08ac8a
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/pedigree/resources/src/main/resources/pedigree/model/dynamicGraph.js
    M components/pedigree/resources/src/main/resources/pedigree/view.js
    M components/pedigree/resources/src/main/resources/pedigree/view/workspace.js

  Log Message:
  -----------
  [misc] Minor pedigree editor bugfixes


  Commit: 3152db3a27f803045b1a5f4f14b6b2c72b56132b
      https://github.com/phenotips/phenotips/commit/3152db3a27f803045b1a5f4f14b6b2c72b56132b
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/pedigree/resources/src/main/resources/pedigree/controller.js
    M components/pedigree/resources/src/main/resources/pedigree/editor.css
    M components/pedigree/resources/src/main/resources/pedigree/pedigree.js
    M components/pedigree/resources/src/main/resources/pedigree/saveLoadEngine.js
    M components/pedigree/resources/src/main/resources/pedigree/view/exportSelector.js
    M components/pedigree/resources/src/main/resources/pedigree/view/importSelector.js
    A components/pedigree/resources/src/main/resources/pedigree/view/tabbedSelector.js
    A components/pedigree/resources/src/main/resources/pedigree/view/tabbedSelectorTab.js
    M components/pedigree/resources/src/main/resources/pedigree/view/templateSelector.js
    M components/pedigree/resources/src/main/resources/pedigree/view/workspace.js

  Log Message:
  -----------
  PT-2103: Merge Templates and Import functions in pedigree editor
New tabbed dialogue and behaviour fixes


  Commit: 4c757a96ba5e367d9960fa8ea4f5a602224869eb
      https://github.com/phenotips/phenotips/commit/4c757a96ba5e367d9960fa8ea4f5a602224869eb
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/pedigree/resources/src/main/resources/pedigree/familyDataLoader.js

  Log Message:
  -----------
  PT-2160: Move the modal with warning about sensitive information to the middle of the screen and add "close" button
Fixed


  Commit: ce892ce1f94749dd819cb0b7bdbe972fa1f789ea
      https://github.com/phenotips/phenotips/commit/ce892ce1f94749dd819cb0b7bdbe972fa1f789ea
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/pedigree/resources/src/main/resources/pedigree/undoRedoManager.js

  Log Message:
  -----------
  [misc] Fixed unsaved change warning when the pedigree editor is just opened and no changes have been made

Fixed.


  Commit: 0cc27d3eed0fd4c31185beca188b084ce6fa04f9
      https://github.com/phenotips/phenotips/commit/0cc27d3eed0fd4c31185beca188b084ce6fa04f9
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyTemplate.xml

  Log Message:
  -----------
  [misc] Updated FamilyTemplate to the latest FamilyClass definition


  Commit: 055562ccc0773de481a71e1c1547e40341e6a628
      https://github.com/phenotips/phenotips/commit/055562ccc0773de481a71e1c1547e40341e6a628
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/export/XWikiFamilyExport.java

  Log Message:
  -----------
  [misc] Fix for family search api to allow search by any part of a family name, not just beginning


  Commit: 76b19b5a5ef34ec8c3a6883d5c412a1971ffa368
      https://github.com/phenotips/phenotips/commit/76b19b5a5ef34ec8c3a6883d5c412a1971ffa368
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/pedigree/resources/src/main/resources/pedigree/view/nodeMenu.js
    M components/pedigree/resources/src/main/resources/pedigree/view/person.js
    M components/pedigree/resources/src/main/resources/pedigree/view/printEngine.js

  Log Message:
  -----------
  PT-1548: Fix for patient URL generators when family pedigree is opened


  Commit: c4582577cfdd98fa3388152bc9888a169ef53cc6
      https://github.com/phenotips/phenotips/commit/c4582577cfdd98fa3388152bc9888a169ef53cc6
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    R components/family-studies/ui/src/main/resources/PhenoTips/AddRemovePatientToFamily.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyPedigreeInterface.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/UIX_Field__family_membership.xml

  Log Message:
  -----------
  [family-studies for PT-2233]: moving AddRemovePatientToFamily script service to the FamilyPedigreeInterface services.


  Commit: a27f41a9c741fe28fb08f18a421851a5ea20eb69
      https://github.com/phenotips/phenotips/commit/a27f41a9c741fe28fb08f18a421851a5ea20eb69
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/family-studies/ui/src/main/resources/PhenoTips/UIX_Field__family_membership.xml

  Log Message:
  -----------
  PT-2233: Disable editing of FamilyID filed in the Family history and pedigree section.


  Commit: 5a9d6a9682fd4fafd17ce990aef5ed3d5ebc0dff
      https://github.com/phenotips/phenotips/commit/5a9d6a9682fd4fafd17ce990aef5ed3d5ebc0dff
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/family-studies/ui/src/main/resources/Family/CreateFamily.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyPedigreeInterface.xml
    M components/pedigree/resources/src/main/resources/pedigree/editor.css
    M components/pedigree/resources/src/main/resources/pedigree/externalEndpoints.js
    M components/pedigree/resources/src/main/resources/pedigree/familyDataLoader.js
    M components/pedigree/resources/src/main/resources/pedigree/saveLoadEngine.js
    A components/pedigree/resources/src/main/resources/pedigree/view/familySelector.js

  Log Message:
  -----------
  PT-2233: Move assigning a patient to a family from patient form to pedigree section.


  Commit: 8ef5c780ac31101ad572cd9e47a7cb4958f1940b
      https://github.com/phenotips/phenotips/commit/8ef5c780ac31101ad572cd9e47a7cb4958f1940b
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/PedigreeUtils.java
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/script/FamilyScriptService.java
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyPedigreeInterface.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/ExportPatient.xml
    M components/pedigree/resources/src/main/resources/pedigree/editor.css
    M components/pedigree/resources/src/main/resources/pedigree/pedigree.js
    M components/pedigree/resources/src/main/resources/pedigree/view/familySelector.js
    A components/pedigree/resources/src/main/resources/pedigree/view/patientDropLegend.js
    M components/pedigree/resources/src/main/resources/pedigree/view/person.js

  Log Message:
  -----------
  PT-2233: Drop a patient to a node if assigning to an existing family


  Commit: 9bbea11c51f4a261eb8bc364a00b1f0665c8a3e0
      https://github.com/phenotips/phenotips/commit/9bbea11c51f4a261eb8bc364a00b1f0665c8a3e0
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/PedigreeUtils.java
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/XWikiFamilyRepository.java
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/script/FamilyScriptService.java
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyPedigreeInterface.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/UIX_Field__family_membership.xml
    M components/pedigree/resources/src/main/resources/pedigree/controller.js
    M components/pedigree/resources/src/main/resources/pedigree/editor.css
    M components/pedigree/resources/src/main/resources/pedigree/externalEndpoints.js
    M components/pedigree/resources/src/main/resources/pedigree/familyDataLoader.js
    M components/pedigree/resources/src/main/resources/pedigree/model/dynamicGraph.js
    M components/pedigree/resources/src/main/resources/pedigree/pedigree.js
    M components/pedigree/resources/src/main/resources/pedigree/saveLoadEngine.js
    M components/pedigree/resources/src/main/resources/pedigree/versionUpdater.js
    M components/pedigree/resources/src/main/resources/pedigree/view/familySelector.js
    M components/pedigree/resources/src/main/resources/pedigree/view/patientDropLegend.js
    M components/pedigree/resources/src/main/resources/pedigree/view/templateSelector.js
    M components/pedigree/resources/src/main/resources/pedigree/view/workspace.js

  Log Message:
  -----------
  PT-2233: Refactoring code to latest changes in family-studies, highlighting droppable nodes


  Commit: 172c91b0a800cc2a2cfd2caec52d299d0a5ace3c
      https://github.com/phenotips/phenotips/commit/172c91b0a800cc2a2cfd2caec52d299d0a5ace3c
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/patient-data/ui/src/main/resources/PhenoTips/ExportPatient.xml
    M components/pedigree/resources/src/main/resources/pedigree/editor.css
    M components/pedigree/resources/src/main/resources/pedigree/view/familySelector.js
    M components/pedigree/resources/src/main/resources/pedigree/view/patientDropLegend.js

  Log Message:
  -----------
  PT-2233: Fix for ExportPatient script service to accept family id as a request parameter.


  Commit: 40d17f588811d55e53fd6d9bc5af519098c6b614
      https://github.com/phenotips/phenotips/commit/40d17f588811d55e53fd6d9bc5af519098c6b614
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/pedigree/resources/src/main/resources/pedigree/controller.js
    M components/pedigree/resources/src/main/resources/pedigree/view/patientDropLegend.js

  Log Message:
  -----------
  PT-2233: Add 'do not show again' button to pedigree sharing warning dialog'


  Commit: 2ad1d2cf0da001154c09b0137c4698ce24b17540
      https://github.com/phenotips/phenotips/commit/2ad1d2cf0da001154c09b0137c4698ce24b17540
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/family-studies/api/pom.xml
    A components/family-studies/api/src/checkstyle/checkstyle-suppressions.xml
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/Family.java
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/FamilyRepository.java
    R components/family-studies/api/src/main/java/org/phenotips/studies/family/JsonAdapter.java
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/Pedigree.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/PedigreeProcessor.java
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/DefaultPedigree.java
    R components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/JsonAdapterImpl.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/PedigreeProcessorImpl.java
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/PedigreeUtils.java
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/SvgUpdater.java
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/XWikiFamily.java
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/XWikiFamilyPermissions.java
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/XWikiFamilyRepository.java
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/export/XWikiFamilyExport.java
    R components/family-studies/api/src/main/java/org/phenotips/studies/family/response/JSONResponse.java
    R components/family-studies/api/src/main/java/org/phenotips/studies/family/response/StatusResponse.java
    M components/family-studies/api/src/main/java/org/phenotips/studies/family/script/FamilyScriptService.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/script/JSONResponse.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/script/PedigreeScriptService.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/script/response/AbstractJSONResponse.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/script/response/AlreadyHasFamilyResponse.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/script/response/FamilyInfoJSONResponse.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/script/response/InternalErrorResponse.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/script/response/InvalidFamilyIdResponse.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/script/response/InvalidInputJSONResponse.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/script/response/InvalidPatientIdResponse.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/script/response/NotEnoughPermissionsOnFamilyResponse.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/script/response/NotEnoughPermissionsOnPatientResponse.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/script/response/OKJSONResponse.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/script/response/PatientContainedMultipleTimesInPedigreeResponse.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/script/response/PatientHasNoFamilyResponse.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/script/response/ValidLinkJSONResponse.java
    M components/family-studies/api/src/main/resources/ApplicationResources.properties
    M components/family-studies/api/src/main/resources/META-INF/components.txt
    M components/family-studies/ui/src/main/resources/Family/CreateFamily.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilySheet.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/UIX_Field__family_membership.xml
    M components/navigation/ui/src/main/resources/PhenoTips/SuggestPatientsService.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/ExportPatient.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/PedigreeImageService.xml
    M components/pedigree/ui/src/main/resources/PhenoTips/UIX_Field__pedigree.xml

  Log Message:
  -----------
  PT-1548: Refactoring code
- separate FamilyScriptService and PedigreeScriptService
- refactor responses
- refactor to better reflect new design when having a pedigree implies necessarily having a family


  Commit: 3540d408361d083b4f49428945636e52f6f42add
      https://github.com/phenotips/phenotips/commit/3540d408361d083b4f49428945636e52f6f42add
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyPedigreeInterface.xml
    M components/pedigree/resources/src/main/resources/pedigree/controller.js
    M components/pedigree/resources/src/main/resources/pedigree/editor.css
    M components/pedigree/resources/src/main/resources/pedigree/externalEndpoints.js
    A components/pedigree/resources/src/main/resources/pedigree/familyData.js
    R components/pedigree/resources/src/main/resources/pedigree/familyDataLoader.js
    M components/pedigree/resources/src/main/resources/pedigree/model/dynamicGraph.js
    M components/pedigree/resources/src/main/resources/pedigree/patientDataLoader.js
    M components/pedigree/resources/src/main/resources/pedigree/pedigree.js
    M components/pedigree/resources/src/main/resources/pedigree/saveLoadEngine.js
    M components/pedigree/resources/src/main/resources/pedigree/versionUpdater.js
    M components/pedigree/resources/src/main/resources/pedigree/view/familySelector.js
    M components/pedigree/resources/src/main/resources/pedigree/view/legend.js
    M components/pedigree/resources/src/main/resources/pedigree/view/patientDropLegend.js
    M components/pedigree/resources/src/main/resources/pedigree/view/person.js
    M components/pedigree/resources/src/main/resources/pedigree/view/saveLoadIndicator.js

  Log Message:
  -----------
  PT-2233: Move assigning a patient to a family from patient form to pedigree section
- refactor JS and script service to reflect new design when having a pedigree implies necessarily having a family
- refactor drop legend


  Commit: 8e53d5dd303ca80a9f6c4307b62e953ea8aa48d2
      https://github.com/phenotips/phenotips/commit/8e53d5dd303ca80a9f6c4307b62e953ea8aa48d2
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/pedigree/ui/src/main/resources/PhenoTips/PedigreeEditor.xml

  Log Message:
  -----------
  [misc] Force pedigree editor to load fa-icons (fixes no fa-icons on family page pedigree; may also fix SUP-8)


Compare: https://github.com/phenotips/phenotips/compare/908a227f2231...8e53d5dd303c


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