[phenotips-notifications] [phenotips/phenotips] 31e4ca: PT-1548: Merge family-studies component from famil...

GitHub noreply at github.com
Mon Dec 21 10:31:49 EST 2015


  Branch: refs/heads/PT-2233
  Home:   https://github.com/phenotips/phenotips
  Commit: 31e4cae860ea3ddf97b5e658073f3392754770fb
      https://github.com/phenotips/phenotips/commit/31e4cae860ea3ddf97b5e658073f3392754770fb
  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: 357131a8e18839070e3aaf3385fbea54c19f8573
      https://github.com/phenotips/phenotips/commit/357131a8e18839070e3aaf3385fbea54c19f8573
  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: 83dbd258b742162b6aa8dc5d8bf4b1d1bdb8719c
      https://github.com/phenotips/phenotips/commit/83dbd258b742162b6aa8dc5d8bf4b1d1bdb8719c
  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: 2fa7d860620841ba8b51aa723c2e1dffd4884c18
      https://github.com/phenotips/phenotips/commit/2fa7d860620841ba8b51aa723c2e1dffd4884c18
  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: cdd9b43697bd55b5723bbb4923768f3c79a8295b
      https://github.com/phenotips/phenotips/commit/cdd9b43697bd55b5723bbb4923768f3c79a8295b
  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: 985e7c2237ab793fb623f132e22fda80a175ec8d
      https://github.com/phenotips/phenotips/commit/985e7c2237ab793fb623f132e22fda80a175ec8d
  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: bf7073ad0e5291c66c8b470073a08acee1e61de1
      https://github.com/phenotips/phenotips/commit/bf7073ad0e5291c66c8b470073a08acee1e61de1
  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: 2f69775f8b3dc795735cfad3c6a1a51d23f35529
      https://github.com/phenotips/phenotips/commit/2f69775f8b3dc795735cfad3c6a1a51d23f35529
  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: 40557b5b22400d55af7a6ca537d4c5b8be2dae07
      https://github.com/phenotips/phenotips/commit/40557b5b22400d55af7a6ca537d4c5b8be2dae07
  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: 8a810422a77a83665299fa35fba5e1e245446369
      https://github.com/phenotips/phenotips/commit/8a810422a77a83665299fa35fba5e1e245446369
  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: 2b6192c5b794f7dd64b80025afdcb18989ef2b67
      https://github.com/phenotips/phenotips/commit/2b6192c5b794f7dd64b80025afdcb18989ef2b67
  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: 6803cca8e2c690d091d8426fd947e96d9d14d657
      https://github.com/phenotips/phenotips/commit/6803cca8e2c690d091d8426fd947e96d9d14d657
  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: a9e8e963a870bc253b0f40d51fc5c07a1e66db5b
      https://github.com/phenotips/phenotips/commit/a9e8e963a870bc253b0f40d51fc5c07a1e66db5b
  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: ca6795e1d36613d85c2106ca4e1b2ce83a6b06fe
      https://github.com/phenotips/phenotips/commit/ca6795e1d36613d85c2106ca4e1b2ce83a6b06fe
  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: 8b4e2b532f85861e38a46cc44fdf8fbf7c8332b6
      https://github.com/phenotips/phenotips/commit/8b4e2b532f85861e38a46cc44fdf8fbf7c8332b6
  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: 37f8ffe10647cae099754aa8812715ef8cefdd44
      https://github.com/phenotips/phenotips/commit/37f8ffe10647cae099754aa8812715ef8cefdd44
  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: c5d044ac2e6b3c27a722c230174cbc4c878b38d9
      https://github.com/phenotips/phenotips/commit/c5d044ac2e6b3c27a722c230174cbc4c878b38d9
  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: 926684511ffa76a4b9dae5a8d946fc759dde7f02
      https://github.com/phenotips/phenotips/commit/926684511ffa76a4b9dae5a8d946fc759dde7f02
  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: 3a66feb2570efe8215b8c3000452575801e4f365
      https://github.com/phenotips/phenotips/commit/3a66feb2570efe8215b8c3000452575801e4f365
  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: 4782c1a4b20fd161bd17e6964c950131e4eb041a
      https://github.com/phenotips/phenotips/commit/4782c1a4b20fd161bd17e6964c950131e4eb041a
  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: bb06dafddc5b494339e3cd6f37ca4257d593bfec
      https://github.com/phenotips/phenotips/commit/bb06dafddc5b494339e3cd6f37ca4257d593bfec
  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: df4129337dd13282f253d6777161d8404a816031
      https://github.com/phenotips/phenotips/commit/df4129337dd13282f253d6777161d8404a816031
  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: 2e911d44ca54500fceec06dee65d67187a0275fe
      https://github.com/phenotips/phenotips/commit/2e911d44ca54500fceec06dee65d67187a0275fe
  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: 1c30b004f308dca7311c2e402cce535b7ee9cade
      https://github.com/phenotips/phenotips/commit/1c30b004f308dca7311c2e402cce535b7ee9cade
  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: ede945067d6b3960a890b9aa7417c63a6822e958
      https://github.com/phenotips/phenotips/commit/ede945067d6b3960a890b9aa7417c63a6822e958
  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: 6d50dfb7b1e5060786c3770484ef09a66e284885
      https://github.com/phenotips/phenotips/commit/6d50dfb7b1e5060786c3770484ef09a66e284885
  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: 4e4f566415765e0950a033c288c691fabbd5a4c5
      https://github.com/phenotips/phenotips/commit/4e4f566415765e0950a033c288c691fabbd5a4c5
  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: 65331849da9f9e9db18c4ad551f42df6711bf635
      https://github.com/phenotips/phenotips/commit/65331849da9f9e9db18c4ad551f42df6711bf635
  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: d05c78bf89ac3e9cc5c510943989bd7fc1156862
      https://github.com/phenotips/phenotips/commit/d05c78bf89ac3e9cc5c510943989bd7fc1156862
  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: 2f3a84124346754f8bf88d3cc3fb197b27790b83
      https://github.com/phenotips/phenotips/commit/2f3a84124346754f8bf88d3cc3fb197b27790b83
  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: 2bd18efa44df3e4a8de4bf1ccbe0244698e0fcb0
      https://github.com/phenotips/phenotips/commit/2bd18efa44df3e4a8de4bf1ccbe0244698e0fcb0
  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/8e53d5dd303c...2bd18efa44df


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