[phenotips/phenotips] 33fa4a: PT-3368: Extend Entities API

GitHub noreply at github.com
Tue Jan 23 23:45:47 EST 2018


  Branch: refs/heads/PT-2640-entities-1.4
  Home:   https://github.com/phenotips/phenotips
  Commit: 33fa4a930f297cacdb2580c2c4f1180a70a5b593
      https://github.com/phenotips/phenotips/commit/33fa4a930f297cacdb2580c2c4f1180a70a5b593
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

  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-3368: Extend Entities API

Added AbstractPrimaryEntityGroupWithParameters


  Commit: ee3386079b9fa0e29b70ac4473ea412d21472a4b
      https://github.com/phenotips/phenotips/commit/ee3386079b9fa0e29b70ac4473ea412d21472a4b
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Binding group G to interface and not implementation


  Commit: 995568f5ef229ffe136ede9602c5bdc1a877115b
      https://github.com/phenotips/phenotips/commit/995568f5ef229ffe136ede9602c5bdc1a877115b
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Saving class property of member in a container group


  Commit: 3f72d6857cc558b5cb22c163927523e24b70879a
      https://github.com/phenotips/phenotips/commit/3f72d6857cc558b5cb22c163927523e24b70879a
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Setting member parameters in container


  Commit: 600619637e0a94d4a3e74a3641e94ea49159ad34
      https://github.com/phenotips/phenotips/commit/600619637e0a94d4a3e74a3641e94ea49159ad34
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Bugfix - getMembersOfType()


  Commit: ec3cf33afa1ac6b2c61422558f9ae304b88a2d92
      https://github.com/phenotips/phenotips/commit/ec3cf33afa1ac6b2c61422558f9ae304b88a2d92
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

  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-3368: Extend Entities API

Replaced AbstractPrimaryEntityGroupWithParameters with AbstractContainerPrimaryEntityGroupWithParameters


  Commit: 97f7c05ed051a8a09bf4617c6ed5f89305670fd2
      https://github.com/phenotips/phenotips/commit/97f7c05ed051a8a09bf4617c6ed5f89305670fd2
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

  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-3368: Extend Entities API

Added constructor(DocumentReference) to the primary entity tree


  Commit: 9ab637ac21d02e4383be6607b9f20188e68cc2c7
      https://github.com/phenotips/phenotips/commit/9ab637ac21d02e4383be6607b9f20188e68cc2c7
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Bugfix - taking the first non-null manager


  Commit: 05da39fe5581981161f92d6bbb61cd73fe60d793
      https://github.com/phenotips/phenotips/commit/05da39fe5581981161f92d6bbb61cd73fe60d793
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Bugfix - AbstractPrimaryEntityGroupManager.getGroupsForEntity()


  Commit: 5be79a3518607ea27aaa7695cc785a3977af7682
      https://github.com/phenotips/phenotips/commit/5be79a3518607ea27aaa7695cc785a3977af7682
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Added @role to PatientEntityManager


  Commit: 5a172320d6d32892817b63e25b88359e39ec172d
      https://github.com/phenotips/phenotips/commit/5a172320d6d32892817b63e25b88359e39ec172d
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

  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-3368: Extend Entities API

Added PrimaryEntityProperty and AbstractPrimaryEntityProperty


  Commit: 5e4f1688f7725b98a1487bc3f0f42709f71a44ce
      https://github.com/phenotips/phenotips/commit/5e4f1688f7725b98a1487bc3f0f42709f71a44ce
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Fixed AbstractContainerPrimaryEntityGroupManager.getGroupsForEntity()


  Commit: 722373ffa606f3d726a77425b13c39f64e37283c
      https://github.com/phenotips/phenotips/commit/722373ffa606f3d726a77425b13c39f64e37283c
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Changed message level about missing entity manager from error to info


  Commit: b6684fe05f00c026bffa97721de68db6ad7de41e
      https://github.com/phenotips/phenotips/commit/b6684fe05f00c026bffa97721de68db6ad7de41e
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Fixed location of PrimaryEntityProperty in entity tree


  Commit: c3871e3fefb6aabe532a9f8d9319531ecebb7c57
      https://github.com/phenotips/phenotips/commit/c3871e3fefb6aabe532a9f8d9319531ecebb7c57
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Removing property from PrimaryEntityProperty when set parameter is null


  Commit: 72fbb324afc5be80d5fd18ec9ca1511981ea105d
      https://github.com/phenotips/phenotips/commit/72fbb324afc5be80d5fd18ec9ca1511981ea105d
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Fixed documentation - PrimaryEntityManager.get() doesn't throw exceptions


  Commit: c35935555bdb6db8b3378a5f0f15f0e619821ce8
      https://github.com/phenotips/phenotips/commit/c35935555bdb6db8b3378a5f0f15f0e619821ce8
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

  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-3368: Extend Entities API: made PrimaryEntityGroup not to extend PrimaryEntity


  Commit: ba2e44084df22748997ae5f192ff7f8a163e094e
      https://github.com/phenotips/phenotips/commit/ba2e44084df22748997ae5f192ff7f8a163e094e
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

  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-3368: Extend Entities API

Renamed PrimaryEntityGroup->PrimaryEntityGroupManager


  Commit: 2da3427c581eca3430acc148659956657baf2a36
      https://github.com/phenotips/phenotips/commit/2da3427c581eca3430acc148659956657baf2a36
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

  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-3368: Extend Entities API

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: 88fec9801dd0fe57bf1350cb6d8a270999750a08
      https://github.com/phenotips/phenotips/commit/88fec9801dd0fe57bf1350cb6d8a270999750a08
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Added PrimaryEntityGroupManager.CLASS_XPROPERTY


  Commit: 72cb8d7f38e5cd830bddaa712564b3471a5fd3ca
      https://github.com/phenotips/phenotips/commit/72cb8d7f38e5cd830bddaa712564b3471a5fd3ca
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Using local serializer instead of full+split


  Commit: 26784dd8c2425a5020e066148adbf2d93978ff1b
      https://github.com/phenotips/phenotips/commit/26784dd8c2425a5020e066148adbf2d93978ff1b
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

  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-3368: Extend Entities API

Added PrimaryEntityGroupManager.removeAllMembers(group, members)


  Commit: 07f3dfccb4b31b894aebd559d4817984f205f23c
      https://github.com/phenotips/phenotips/commit/07f3dfccb4b31b894aebd559d4817984f205f23c
  Author: ItaiGershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

  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-3368: Extend Entities API

Added PrimaryEntityGroupManager.isMember(group, member)


  Commit: fb7c5179f15110f3626be59454af6de745eaeb75
      https://github.com/phenotips/phenotips/commit/fb7c5179f15110f3626be59454af6de745eaeb75
  Author: Itai Gershtansky <itaig.phenotips at gmail.com>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Added a comment - isMember() can be implemented more efficiently in AbstractPrimaryEntityGroupManager


  Commit: 253441088c2bbe2967a84ac084fe6f7b90610ab4
      https://github.com/phenotips/phenotips/commit/253441088c2bbe2967a84ac084fe6f7b90610ab4
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API: updated code after rebase

- fixed checkstyle
- now using new getXDocument() method


  Commit: ea0f84672a05785d1f1ce1923e863c8bdeea5cda
      https://github.com/phenotips/phenotips/commit/ea0f84672a05785d1f1ce1923e863c8bdeea5cda
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Refactored Entity Properties (Property no longer implements a Group interface, effectively hiding
methods that should not be used on a property)


  Commit: f2f5efde581b3431ebe3040f5836ce72ad3d286f
      https://github.com/phenotips/phenotips/commit/f2f5efde581b3431ebe3040f5836ce72ad3d286f
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

  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/AbstractExternalPrimaryEntityGroupManager.java
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractInternalPrimaryEntityGroupManager.java
    M components/entities/api/src/main/java/org/phenotips/entities/internal/AbstractPrimaryEntityGroupManager.java

  Log Message:
  -----------
  PT-3368: Extend Entities API

Removed getMembersOfType() since in the new/current design all members always have the same known type; improved comments


  Commit: b2d850116a3e144d3012a36e5853d979f4152ac7
      https://github.com/phenotips/phenotips/commit/b2d850116a3e144d3012a36e5853d979f4152ac7
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2018-01-23 (Tue, 23 Jan 2018)

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

  Log Message:
  -----------
  PT-3368: Extend Entities API

Lazy initialization of member and group managers, which should resolve ComponentManager is null
problems when a GroupManager is initialized before ApplicationStartedEvent is sent (e.g.
when a manager is used in some event listener which is initialized early)


Compare: https://github.com/phenotips/phenotips/compare/159257c4e1fe...b2d850116a3e


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