[phenotips/phenotips] c121c7: PT-2640-entities: Added AbstractPrimaryEntityGroup...

GitHub noreply at github.com
Fri Feb 24 02:55:27 EST 2017


  Branch: refs/heads/PT-2640-entities
  Home:   https://github.com/phenotips/phenotips
  Commit: c121c7c49d22e8d5246f84a579c357c3d15bb59e
      https://github.com/phenotips/phenotips/commit/c121c7c49d22e8d5246f84a579c357c3d15bb59e
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityGroup.java
    A components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityGroupWithParameters.java

  Log Message:
  -----------
  PT-2640-entities: Added AbstractPrimaryEntityGroupWithParameters.


  Commit: a24858c1b9032a42e79c6aada1bd82eed3e9cb2c
      https://github.com/phenotips/phenotips/commit/a24858c1b9032a42e79c6aada1bd82eed3e9cb2c
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractContainerPrimaryEntityGroupManager.java

  Log Message:
  -----------
  PT-2640-entities: Binding group G to interface and not implementation.


  Commit: a844bc211740230245ec8c2be42d0fa9d0cac55a
      https://github.com/phenotips/phenotips/commit/a844bc211740230245ec8c2be42d0fa9d0cac55a
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractContainerPrimaryEntityGroup.java

  Log Message:
  -----------
  PT-2640-entities: Saving class property of member in a container group.


  Commit: c07c3e06401e1116d84bbd5b1b046e542024d024
      https://github.com/phenotips/phenotips/commit/c07c3e06401e1116d84bbd5b1b046e542024d024
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractContainerPrimaryEntityGroup.java

  Log Message:
  -----------
  PT-2640-entities: setting member parameters in container.


  Commit: b87913254f26487a244d2e6ff4362dfc6cd0ac30
      https://github.com/phenotips/phenotips/commit/b87913254f26487a244d2e6ff4362dfc6cd0ac30
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractContainerPrimaryEntityGroup.java

  Log Message:
  -----------
  PT-2640-entities: bugfix - getMembersOfType().


  Commit: 4d349de0400ab9976d71b1a97f68f90f2eae4aa0
      https://github.com/phenotips/phenotips/commit/4d349de0400ab9976d71b1a97f68f90f2eae4aa0
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    A components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractContainerPrimaryEntityGroupWithParameters.java
    R components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityGroupWithParameters.java

  Log Message:
  -----------
  PT-2640-entities: replaced AbstractPrimaryEntityGroupWithParameters with AbstractContainerPrimaryEntityGroupWithParameters.


  Commit: 23078540e8e6b4b01583d2ecc56fe3ebbd4c6aa6
      https://github.com/phenotips/phenotips/commit/23078540e8e6b4b01583d2ecc56fe3ebbd4c6aa6
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractContainerPrimaryEntityGroup.java
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntity.java
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityGroup.java

  Log Message:
  -----------
  PT-1987-projects: Added constructor(DocumentReference) to the primary entity tree.


  Commit: 7094e2fcedb2502a94bfee5dbb9ea7a8cd1786e1
      https://github.com/phenotips/phenotips/commit/7094e2fcedb2502a94bfee5dbb9ea7a8cd1786e1
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/pom.xml

  Log Message:
  -----------
  PT-1987-projects: removed unnecessary dependency.


  Commit: 097865256de0a6dd08d97c7c790279de4fce0f2f
      https://github.com/phenotips/phenotips/commit/097865256de0a6dd08d97c7c790279de4fce0f2f
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityGroup.java

  Log Message:
  -----------
  PT-1987-projects: bugfix - taking the first non-null manager.


  Commit: 225c86c30573cc06d3c93e8697eface22326b64e
      https://github.com/phenotips/phenotips/commit/225c86c30573cc06d3c93e8697eface22326b64e
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityGroupManager.java

  Log Message:
  -----------
  PT-1987-projects: bugfix - AbstractPrimaryEntityGroupManager.getGroupsForEntity().


  Commit: 0532d7e79e545f21f36f5afc9fea5ba52f70b133
      https://github.com/phenotips/phenotips/commit/0532d7e79e545f21f36f5afc9fea5ba52f70b133
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/patient-data/impl/src/main/java/org/phenotips/data/internal/PatientEntityManager.java

  Log Message:
  -----------
  PT-1987-projects - Added @role to PatientEntityManager.


  Commit: 79d46d36635b075304c6ae6a8bb03acdb7119977
      https://github.com/phenotips/phenotips/commit/79d46d36635b075304c6ae6a8bb03acdb7119977
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    A components/entities/api/src/main/java/org/phenotips/entities/PrimaryEntityProperty.java
    A components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityProperty.java

  Log Message:
  -----------
  PT-1987-projects: Added PrimaryEntityProperty and AbstractPrimaryEntityProperty.


  Commit: 9b54608ccbaac39e0d265e4a8ebb8a05e293749f
      https://github.com/phenotips/phenotips/commit/9b54608ccbaac39e0d265e4a8ebb8a05e293749f
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractContainerPrimaryEntityGroupManager.java

  Log Message:
  -----------
  PT-1987-projects: Fixed AbstractContainerPrimaryEntityGroupManager.getGroupsForEntity().


  Commit: 7f1e960ce493f6c105dab24181fcc9113db43e87
      https://github.com/phenotips/phenotips/commit/7f1e960ce493f6c105dab24181fcc9113db43e87
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityGroup.java

  Log Message:
  -----------
  PT-1987-projects: Changed message level about missing entity manager from error to info.


  Commit: f6cfa05b96a30de7a86a2dbd5397ede7016303a4
      https://github.com/phenotips/phenotips/commit/f6cfa05b96a30de7a86a2dbd5397ede7016303a4
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/PrimaryEntityProperty.java

  Log Message:
  -----------
  PT-1987-projects: Fixed location of PrimaryEntityProperty in entity tree.


  Commit: 48c4befc34f3169dfc37a0723cd2acc97ef493a7
      https://github.com/phenotips/phenotips/commit/48c4befc34f3169dfc37a0723cd2acc97ef493a7
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityProperty.java

  Log Message:
  -----------
  PT-1987-projects: removing property from PrimaryEntityProperty when set parameter is null.


  Commit: 30afa870bbdc50e1ef78a8ced63cb18718cf6a6c
      https://github.com/phenotips/phenotips/commit/30afa870bbdc50e1ef78a8ced63cb18718cf6a6c
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/PrimaryEntityManager.java

  Log Message:
  -----------
  PT-1987-projects: Fixed documentation - PrimaryEntityManager.get() doesn't throw exceptions.


  Commit: 6f318e4f971b32e670bb90f30fcc9a9d46882e89
      https://github.com/phenotips/phenotips/commit/6f318e4f971b32e670bb90f30fcc9a9d46882e89
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/PrimaryEntityGroup.java
    R components/entities/api/src/main/java/org/phenotips/entities/PrimaryEntityGroupManager.java
    M components/entities/api/src/main/java/org/phenotips/entities/PrimaryEntityProperty.java
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractContainerPrimaryEntityGroup.java
    R components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractContainerPrimaryEntityGroupManager.java
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractContainerPrimaryEntityGroupWithParameters.java
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityGroup.java
    R components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityGroupManager.java
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityProperty.java

  Log Message:
  -----------
  PT-1987-projects: Made PrimaryEntityGroup not to extend PrimaryEntity.


  Commit: 583dc583cf4cfa89c2859cf3fb673a99f06ec987
      https://github.com/phenotips/phenotips/commit/583dc583cf4cfa89c2859cf3fb673a99f06ec987
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/PrimaryEntity.java

  Log Message:
  -----------
  PT-1987-projects: added TODO.


  Commit: 6a25c1dc846c5e59a5bdff106a983d2fbfc2b441
      https://github.com/phenotips/phenotips/commit/6a25c1dc846c5e59a5bdff106a983d2fbfc2b441
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    R components/entities/api/src/main/java/org/phenotips/entities/PrimaryEntityGroup.java
    A components/entities/api/src/main/java/org/phenotips/entities/PrimaryEntityGroupManager.java
    M components/entities/api/src/main/java/org/phenotips/entities/PrimaryEntityProperty.java
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractContainerPrimaryEntityGroup.java
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityGroup.java

  Log Message:
  -----------
  PT-1987-projects: Renamed PrimaryEntityGroup->PrimaryEntityGroupManager.


  Commit: 8d5619a82136acb5b2a3f31a53177af5a206c609
      https://github.com/phenotips/phenotips/commit/8d5619a82136acb5b2a3f31a53177af5a206c609
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    R components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractContainerPrimaryEntityGroup.java
    R components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractContainerPrimaryEntityGroupWithParameters.java
    A components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractExternalPrimaryEntityGroupManager.java
    A components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractInternalPrimaryEntityGroupManager.java
    R components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityGroup.java
    A components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityGroupManager.java
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityProperty.java

  Log Message:
  -----------
  PT-1987-projects: Refactored entity group manager tree:
1. Renamed two types of groups to internal/external
2. Incorporated 'with parameter' property into the internal group manager (the WithType class removed)
3. Pulled AbstractPrimaryEntityGroup common to two group managers, handling operations unrelated to implementation.


  Commit: 81a220962af70e3c0808f2cc3352902e57521b0d
      https://github.com/phenotips/phenotips/commit/81a220962af70e3c0808f2cc3352902e57521b0d
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/PrimaryEntityGroupManager.java

  Log Message:
  -----------
  PT-2640-entities: added PrimaryEntityGroupManager.CLASS_XPROPERTY (cherry-pick fix).


  Commit: 4a0ee739ef35933f185d5e8453fa9f1d5eab2d1e
      https://github.com/phenotips/phenotips/commit/4a0ee739ef35933f185d5e8453fa9f1d5eab2d1e
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/PrimaryEntity.java
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntity.java
    M components/specificity-meter/api/src/main/java/org/phenotips/data/script/PatientSpecificityScriptService.java

  Log Message:
  -----------
  PT-2640-entities: added PrimaryEntity.getFullName().


  Commit: 5762c59e383e427ef4449f847f6b118ac7e79f30
      https://github.com/phenotips/phenotips/commit/5762c59e383e427ef4449f847f6b118ac7e79f30
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractInternalPrimaryEntityGroupManager.java

  Log Message:
  -----------
  PT-2640-entities: Using local serializer instead of full+split.


  Commit: 19052a5ed50de48007aa70c730861e96b782534f
      https://github.com/phenotips/phenotips/commit/19052a5ed50de48007aa70c730861e96b782534f
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/PrimaryEntityGroupManager.java
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityGroupManager.java

  Log Message:
  -----------
  PT-2640-entities: added PrimaryEntityGroupManager.removeAllMembers(group, members).


  Commit: 39d591a89757d0d89760e574fe380494ec827221
      https://github.com/phenotips/phenotips/commit/39d591a89757d0d89760e574fe380494ec827221
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/PrimaryEntityGroupManager.java
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityGroupManager.java

  Log Message:
  -----------
  PT-2640-entities: Added PrimaryEntityGroupManager.isMember(group, member).


  Commit: 7ff030e5c0ad0deb4d66912accf1b2dcaefa8c1e
      https://github.com/phenotips/phenotips/commit/7ff030e5c0ad0deb4d66912accf1b2dcaefa8c1e
  Author: Itai Gershtansky <itaig.phenotips at gmail.com>
  Date:   2017-02-24 (Fri, 24 Feb 2017)

  Changed paths:
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityGroupManager.java

  Log Message:
  -----------
  Update AbstractPrimaryEntityGroupManager.java

PT-2640-entities: Added a comment - isMember() can be implemented more efficiently.


Compare: https://github.com/phenotips/phenotips/compare/9edffdfc1852...7ff030e5c0ad


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