[phenotips-notifications] [phenotips/phenotips] a030b6: PT-1548: Merge family-studies component from famil...

GitHub noreply at github.com
Mon Dec 21 17:30:54 EST 2015


  Branch: refs/heads/PT-1548
  Home:   https://github.com/phenotips/phenotips
  Commit: a030b61e9e059a9b21a54c71f99fda4f342e1b99
      https://github.com/phenotips/phenotips/commit/a030b61e9e059a9b21a54c71f99fda4f342e1b99
  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/main/java/org/phenotips/studies/family/Family.java
    A 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/FamilyUtils.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/JsonAdapter.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/Pedigree.java
    R components/family-studies/api/src/main/java/org/phenotips/studies/family/Processing.java
    R components/family-studies/api/src/main/java/org/phenotips/studies/family/Validation.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/events/AbstractFamilyEvent.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/events/FamilyEvent.java
    A 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/FamilyUtilsImpl.java
    A 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/PedigreeUtils.java
    R components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/ProcessingImpl.java
    R components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/StatusResponse.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/SvgUpdater.java
    R components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/ValidationImpl.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/XWikiFamily.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/XWikiFamilyPermissions.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/XWikiFamilyRepository.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/export/FamilySearchResult.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/internal/export/XWikiFamilyExport.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/listener/FamilyDeletingListener.java
    R components/family-studies/api/src/main/java/org/phenotips/studies/family/listener/PatientLinkListener.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/listener/PermissionsChangeListener.java
    A components/family-studies/api/src/main/java/org/phenotips/studies/family/response/JSONResponse.java
    A 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/resources/ApplicationResources.properties
    M components/family-studies/api/src/main/resources/META-INF/components.txt
    M components/family-studies/pom.xml
    M components/family-studies/ui/pom.xml
    A components/family-studies/ui/src/main/resources/Family/CreateFamily.xml
    A components/family-studies/ui/src/main/resources/Family/WebHome.xml
    A components/family-studies/ui/src/main/resources/PhenoTips/AddRemovePatientToFamily.xml
    R components/family-studies/ui/src/main/resources/PhenoTips/CreateFamily.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyClass.xml
    A components/family-studies/ui/src/main/resources/PhenoTips/FamilyContentTopMenu.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyPedigreeInterface.xml
    M components/family-studies/ui/src/main/resources/PhenoTips/FamilyReference.xml
    A components/family-studies/ui/src/main/resources/PhenoTips/FamilySearch.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/UIX_Field__family_membership.xml

  Log Message:
  -----------
  PT-1548: Merge family-studies component from family-studies branch (aggregated commits by @antonkatz and @itaiGershtansky)


  Commit: 70511912eaa1217bfc4b1987ee325038a4b921fa
      https://github.com/phenotips/phenotips/commit/70511912eaa1217bfc4b1987ee325038a4b921fa
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/navigation/ui/src/main/resources/PhenoTips/SuggestPatientsService.xml

  Log Message:
  -----------
  PT-2179: Mark patients associated with another family in the patient suggest widget
Fixed


  Commit: 5d675534a356a60b74bf8588f24656933f3573ba
      https://github.com/phenotips/phenotips/commit/5d675534a356a60b74bf8588f24656933f3573ba
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    A 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/PedigreeImageService.xml

  Log Message:
  -----------
  PT-1548: Merge patient-data component changes from family-studies branch (aggregated commits by @antonkatz and @itaiGershtansky)


  Commit: be6326a8061cebb173d1296ea543be50850a64fe
      https://github.com/phenotips/phenotips/commit/be6326a8061cebb173d1296ea543be50850a64fe
  Author: Anton Kats <antonkats at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/skin/ui/src/main/resources/PhenoTips/DocumentMeta.xml

  Log Message:
  -----------
  PT-1548: Added menu to the family sheet


  Commit: a4b50ca9cdf293d9e90ec4dd8db1652cfe87d15f
      https://github.com/phenotips/phenotips/commit/a4b50ca9cdf293d9e90ec4dd8db1652cfe87d15f
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    A components/family-studies/ui/src/main/resources/PhenoTips/FamilyDataGadget.xml
    A components/family-studies/ui/src/main/resources/PhenoTips/SharedFamilyGadget.xml
    M components/skin/ui/src/main/resources/PhenoTips/Skin.xml

  Log Message:
  -----------
  Integrating changes from Anton's commit 5bd437602a3239b0e11806132c9c75b4b0ea567b to use new gadgets


  Commit: 4a0c6d3f9a603a3ddd71272075329d50c660372a
      https://github.com/phenotips/phenotips/commit/4a0c6d3f9a603a3ddd71272075329d50c660372a
  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
    A components/pedigree/resources/src/main/resources/pedigree/externalEndpoints.js
    A 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/model/export.js
    M components/pedigree/resources/src/main/resources/pedigree/model/import.js
    M components/pedigree/resources/src/main/resources/pedigree/model/positionedGraph.js
    A components/pedigree/resources/src/main/resources/pedigree/patientDataLoader.js
    M components/pedigree/resources/src/main/resources/pedigree/pedigree.js
    R components/pedigree/resources/src/main/resources/pedigree/probandDataLoader.js
    M components/pedigree/resources/src/main/resources/pedigree/saveLoadEngine.js
    M components/pedigree/resources/src/main/resources/pedigree/undoRedoManager.js
    M components/pedigree/resources/src/main/resources/pedigree/versionUpdater.js
    M components/pedigree/resources/src/main/resources/pedigree/view.js
    M components/pedigree/resources/src/main/resources/pedigree/view/abstractHoverbox.js
    M components/pedigree/resources/src/main/resources/pedigree/view/abstractNode.js
    M components/pedigree/resources/src/main/resources/pedigree/view/abstractPerson.js
    M components/pedigree/resources/src/main/resources/pedigree/view/abstractPersonVisuals.js
    M components/pedigree/resources/src/main/resources/pedigree/view/legend.js
    M components/pedigree/resources/src/main/resources/pedigree/view/nodeMenu.js
    M components/pedigree/resources/src/main/resources/pedigree/view/nodetypeSelectionBubble.js
    M components/pedigree/resources/src/main/resources/pedigree/view/okCancelDialogue.js
    M components/pedigree/resources/src/main/resources/pedigree/view/person.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personHoverbox.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personVisuals.js
    M components/pedigree/resources/src/main/resources/pedigree/view/templateSelector.js
    M components/pedigree/resources/src/main/resources/pedigree/view/workspace.js
    M components/pedigree/ui/src/main/resources/PhenoTips/UIX_Field__pedigree.xml

  Log Message:
  -----------
  PT-1548: Pedigree editor changes to enable family-studies


  Commit: d979ea37b3358b84de03f03aa82121ab71b41e99
      https://github.com/phenotips/phenotips/commit/d979ea37b3358b84de03f03aa82121ab71b41e99
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/family-studies/api/pom.xml
    M components/family-studies/pom.xml
    M components/family-studies/ui/pom.xml

  Log Message:
  -----------
  PT-1548: Updated various family-studies pom.xml versions to 1.3


  Commit: c9d970de47450a714dc896406bcc1b350e3446af
      https://github.com/phenotips/phenotips/commit/c9d970de47450a714dc896406bcc1b350e3446af
  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/FamilyDataGadget.xml
    M components/skin/ui/src/main/resources/PhenoTips/Skin.xml

  Log Message:
  -----------
  PT-1548: Family gadget improvement
Fixed new family link and made style consistent with new patient link
Note: using condensed "create-fam" name to get around XWiki title length limits


  Commit: 438355660b6408281f2a90ef0c79dec035ba3eec
      https://github.com/phenotips/phenotips/commit/438355660b6408281f2a90ef0c79dec035ba3eec
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

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

  Log Message:
  -----------
  PT-1548: Fixes to family-studies to pass style-checks and use existing authorization API


  Commit: d46c03487a2fbaca617481a963474570e34025ad
      https://github.com/phenotips/phenotips/commit/d46c03487a2fbaca617481a963474570e34025ad
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2015-12-21 (Mon, 21 Dec 2015)

  Changed paths:
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__consanguinity.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__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__global_mode_of_inheritance.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__pedigree-file.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__proband_info.xml
    M components/pedigree/ui/src/main/resources/PhenoTips/UIX_Field__pedigree.xml

  Log Message:
  -----------
  PT-1548: Moved Pedigree section to be right after family section


  Commit: aa4f5a3d222277d2150847f2ecdd032d3a00f760
      https://github.com/phenotips/phenotips/commit/aa4f5a3d222277d2150847f2ecdd032d3a00f760
  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/editor.css
    M components/pedigree/resources/src/main/resources/pedigree/view/importSelector.js

  Log Message:
  -----------
  PT-2088: Improve UI on Pedigree import dialog
Fixed


  Commit: 3f5c095365eb5651046cda23cf9da2fb4ab7d37a
      https://github.com/phenotips/phenotips/commit/3f5c095365eb5651046cda23cf9da2fb4ab7d37a
  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/editor.css

  Log Message:
  -----------
  PT-2103: Merge Templates and Import functions in pedigree editor
Initial commit


  Commit: 30cc2a8570c33370c6eec319ab1afab04ecb2f62
      https://github.com/phenotips/phenotips/commit/30cc2a8570c33370c6eec319ab1afab04ecb2f62
  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: 8b5d10085491edc039b97ce7b482b3926786304e
      https://github.com/phenotips/phenotips/commit/8b5d10085491edc039b97ce7b482b3926786304e
  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: 6f16769c7c1e8f08d4cd0e4265d7670e64280916
      https://github.com/phenotips/phenotips/commit/6f16769c7c1e8f08d4cd0e4265d7670e64280916
  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: b31b98cdbbbc9523d98f27b431b4660aa7319f8c
      https://github.com/phenotips/phenotips/commit/b31b98cdbbbc9523d98f27b431b4660aa7319f8c
  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: f403db4fe871a0b14db031f5a35f0e7318448adf
      https://github.com/phenotips/phenotips/commit/f403db4fe871a0b14db031f5a35f0e7318448adf
  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: 1b75ce200dc6d83856258c0680d379fd7aac8647
      https://github.com/phenotips/phenotips/commit/1b75ce200dc6d83856258c0680d379fd7aac8647
  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: 1ff3c860ddfc91942a5ec785b7ed32a1bebc2e8f
      https://github.com/phenotips/phenotips/commit/1ff3c860ddfc91942a5ec785b7ed32a1bebc2e8f
  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: d9f52fad0fa7cb685db8396492c305d8a45f316d
      https://github.com/phenotips/phenotips/commit/d9f52fad0fa7cb685db8396492c305d8a45f316d
  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:
  -----------
  PT-1548: Fix for family search api to allow search by any part of a family name, not just beginning


  Commit: d1867468ffe87796ca438207f0a7fdb200d8baef
      https://github.com/phenotips/phenotips/commit/d1867468ffe87796ca438207f0a7fdb200d8baef
  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: e1a24d96d3b1f6f7352e8f71a9c734271906b81d
      https://github.com/phenotips/phenotips/commit/e1a24d96d3b1f6f7352e8f71a9c734271906b81d
  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/Family/CreateFamily.xml
    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
    M components/patient-data/ui/src/main/resources/PhenoTips/ExportPatient.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
    A 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
    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: Move assigning a patient to a family from patient form to pedigree section
- refactored script services
- disable editing of FamilyID filed in the Family history and pedigree section
- new patient drop legend to allow dragging and dropping unassigned patients to pedigree nodes


  Commit: 4e6ae5f7e145fd7e684c3261ab74daef579843e8
      https://github.com/phenotips/phenotips/commit/4e6ae5f7e145fd7e684c3261ab74daef579843e8
  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: a825dda3d01b7c9f545a501fb991066f09114bee
      https://github.com/phenotips/phenotips/commit/a825dda3d01b7c9f545a501fb991066f09114bee
  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: a95bead43087d9327e31905a123440b3c82368cb
      https://github.com/phenotips/phenotips/commit/a95bead43087d9327e31905a123440b3c82368cb
  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
    M components/pedigree/resources/src/main/resources/pedigree/view/templateSelector.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: 0271ecd40da747f35833c286409f33cdbdea2052
      https://github.com/phenotips/phenotips/commit/0271ecd40da747f35833c286409f33cdbdea2052
  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)


  Commit: f2f2d48602cc02a7146d49aaa0cf78faa4dba15f
      https://github.com/phenotips/phenotips/commit/f2f2d48602cc02a7146d49aaa0cf78faa4dba15f
  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/Family.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/script/FamilyScriptService.java
    M components/patient-data/api/src/main/java/org/phenotips/data/PatientRepository.java
    M components/patient-data/impl/src/main/java/org/phenotips/data/internal/PhenoTipsPatientRepository.java
    M pom.xml

  Log Message:
  -----------
  PT-2236: Add action buttons to the pedigree thumbnail displayed on the patient page
Added remove functionality to family- and patient- repositories


  Commit: 757ac5e47c0141e80cb9de477e0ad77e8a4d69e5
      https://github.com/phenotips/phenotips/commit/757ac5e47c0141e80cb9de477e0ad77e8a4d69e5
  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/view/person.js

  Log Message:
  -----------
  PT-1548: Re-enable editing of proband node in pedigree editor (reverse PT-2163)


  Commit: f33741db93f31e2ec88c44cf051c93397f778a37
      https://github.com/phenotips/phenotips/commit/f33741db93f31e2ec88c44cf051c93397f778a37
  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/view/nodeMenu.js

  Log Message:
  -----------
  [misc] Fixed pedigree editor node menu causing some internal prototype exceptions due to bad DOM searches


Compare: https://github.com/phenotips/phenotips/compare/a0520388f8b5...f33741db93f3


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