[phenotips-notifications] [phenotips/phenotips] 43f668: Initial commit

GitHub noreply at github.com
Mon Oct 19 14:53:53 EDT 2015


  Branch: refs/heads/PT-1950
  Home:   https://github.com/phenotips/phenotips
  Commit: 43f6685309d571bda02eeb081969e91c17b722e5
      https://github.com/phenotips/phenotips/commit/43f6685309d571bda02eeb081969e91c17b722e5
  Author: Sergiu Dumitriu <sergiu at xwiki.org>
  Date:   2012-12-14 (Fri, 14 Dec 2012)

  Changed paths:
    A data/en_product1.xml
    A data/en_product2.xml
    A data/negative_phenotype_annotation.tab
    A data/omim_prelevance.txt
    A data/phenotype_annotation.tab
    A pom.xml
    A src/main/java/edu/toronto/cs/cidb/oo/DisorderData.java
    A src/main/java/edu/toronto/cs/cidb/oo/DisorderDataBuilder.java
    A src/main/java/edu/toronto/cs/cidb/oo/Main.java
    A src/main/java/edu/toronto/cs/cidb/oo/OOSaxParser.java

  Log Message:
  -----------
  Initial commit


  Commit: ff71211ca52bb06ddeed9d620c94998cc1a222ea
      https://github.com/phenotips/phenotips/commit/ff71211ca52bb06ddeed9d620c94998cc1a222ea
  Author: Marta Girdea <marta.girdea at gmail.com>
  Date:   2012-12-14 (Fri, 14 Dec 2012)

  Changed paths:
    M src/main/java/edu/toronto/cs/cidb/oo/DisorderDataBuilder.java

  Log Message:
  -----------
  generated keywords for indexing


  Commit: 1972658a4e507bbb3e32cb715518a5db7f5c2cb3
      https://github.com/phenotips/phenotips/commit/1972658a4e507bbb3e32cb715518a5db7f5c2cb3
  Author: Marta Girdea <marta.girdea at gmail.com>
  Date:   2012-12-14 (Fri, 14 Dec 2012)

  Changed paths:
    M src/main/java/edu/toronto/cs/cidb/oo/DisorderDataBuilder.java

  Log Message:
  -----------
  replaced dashes with underscores in fields names


  Commit: 43485faff42b628ad8b5ed1619912c0c93921d8e
      https://github.com/phenotips/phenotips/commit/43485faff42b628ad8b5ed1619912c0c93921d8e
  Author: Marta Girdea <marta.girdea at gmail.com>
  Date:   2012-12-14 (Fri, 14 Dec 2012)

  Changed paths:
    M src/main/java/edu/toronto/cs/cidb/oo/DisorderDataBuilder.java

  Log Message:
  -----------
  fixed field name (for consistency). added "not_keywords" field only if negative phenotypes exist.


  Commit: 3f55fbfe82254223fb2272703f611672dbb23687
      https://github.com/phenotips/phenotips/commit/3f55fbfe82254223fb2272703f611672dbb23687
  Author: Sergiu Dumitriu <sergiu at xwiki.org>
  Date:   2012-12-20 (Thu, 20 Dec 2012)

  Changed paths:
    M src/main/java/edu/toronto/cs/cidb/oo/DisorderData.java
    M src/main/java/edu/toronto/cs/cidb/oo/DisorderDataBuilder.java
    M src/main/java/edu/toronto/cs/cidb/oo/Main.java

  Log Message:
  -----------
  Adjusted boost values


  Commit: 30256c7a6a647ca901638367a1e8273264c9ca3a
      https://github.com/phenotips/phenotips/commit/30256c7a6a647ca901638367a1e8273264c9ca3a
  Author: Sergiu Dumitriu <sergiu at xwiki.org>
  Date:   2013-01-07 (Mon, 07 Jan 2013)

  Changed paths:
    M pom.xml
    M src/main/java/edu/toronto/cs/cidb/oo/DisorderDataBuilder.java

  Log Message:
  -----------
  Index the actual specified symptoms separately


  Commit: 327743b5bdfa615dd637ae74eb0fa72e1067f15d
      https://github.com/phenotips/phenotips/commit/327743b5bdfa615dd637ae74eb0fa72e1067f15d
  Author: Marta Girdea <marta.girdea at gmail.com>
  Date:   2014-01-16 (Thu, 16 Jan 2014)

  Changed paths:
    M src/main/java/edu/toronto/cs/cidb/oo/DisorderData.java
    M src/main/java/edu/toronto/cs/cidb/oo/DisorderDataBuilder.java
    M src/main/java/edu/toronto/cs/cidb/oo/Main.java
    A src/main/java/edu/toronto/cs/cidb/oo/OmimDBBuilder.java
    A src/main/java/edu/toronto/cs/cidb/oo/OmimSourceParser.java
    A src/main/java/edu/toronto/cs/cidb/oo/RecordData.java
    A src/main/java/edu/toronto/cs/cidb/oo/TSVParser.java
    A src/main/java/edu/toronto/cs/util/maps/AbstractCollectionMap.java
    A src/main/java/edu/toronto/cs/util/maps/AbstractMapOperator.java
    A src/main/java/edu/toronto/cs/util/maps/AbstractNumericValueMap.java
    A src/main/java/edu/toronto/cs/util/maps/AddMapOperator.java
    A src/main/java/edu/toronto/cs/util/maps/CounterMap.java
    A src/main/java/edu/toronto/cs/util/maps/DivideMapOperator.java
    A src/main/java/edu/toronto/cs/util/maps/DoubleMap.java
    A src/main/java/edu/toronto/cs/util/maps/IntegerMap.java
    A src/main/java/edu/toronto/cs/util/maps/IntegerSumMap.java
    A src/main/java/edu/toronto/cs/util/maps/ListMap.java
    A src/main/java/edu/toronto/cs/util/maps/MapOperator.java
    A src/main/java/edu/toronto/cs/util/maps/MultiplyMapOperator.java
    A src/main/java/edu/toronto/cs/util/maps/NumericValueMap.java
    A src/main/java/edu/toronto/cs/util/maps/SetMap.java
    A src/main/java/edu/toronto/cs/util/maps/SubtractMapOperator.java
    A src/main/java/edu/toronto/cs/util/maps/SumMap.java

  Log Message:
  -----------
  More fields indexed


  Commit: 8bbab361072d0b4ff4977f671fe5445f10dfca5e
      https://github.com/phenotips/phenotips/commit/8bbab361072d0b4ff4977f671fe5445f10dfca5e
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2014-10-02 (Thu, 02 Oct 2014)

  Changed paths:
    M pom.xml
    R src/main/java/edu/toronto/cs/cidb/oo/DisorderData.java
    R src/main/java/edu/toronto/cs/cidb/oo/DisorderDataBuilder.java
    R src/main/java/edu/toronto/cs/cidb/oo/Main.java
    R src/main/java/edu/toronto/cs/cidb/oo/OOSaxParser.java
    R src/main/java/edu/toronto/cs/cidb/oo/OmimDBBuilder.java
    R src/main/java/edu/toronto/cs/cidb/oo/OmimSourceParser.java
    R src/main/java/edu/toronto/cs/cidb/oo/RecordData.java
    R src/main/java/edu/toronto/cs/cidb/oo/TSVParser.java
    R src/main/java/edu/toronto/cs/util/maps/AbstractCollectionMap.java
    R src/main/java/edu/toronto/cs/util/maps/AbstractMapOperator.java
    R src/main/java/edu/toronto/cs/util/maps/AbstractNumericValueMap.java
    R src/main/java/edu/toronto/cs/util/maps/AddMapOperator.java
    R src/main/java/edu/toronto/cs/util/maps/CounterMap.java
    R src/main/java/edu/toronto/cs/util/maps/DivideMapOperator.java
    R src/main/java/edu/toronto/cs/util/maps/DoubleMap.java
    R src/main/java/edu/toronto/cs/util/maps/IntegerMap.java
    R src/main/java/edu/toronto/cs/util/maps/IntegerSumMap.java
    R src/main/java/edu/toronto/cs/util/maps/ListMap.java
    R src/main/java/edu/toronto/cs/util/maps/MapOperator.java
    R src/main/java/edu/toronto/cs/util/maps/MultiplyMapOperator.java
    R src/main/java/edu/toronto/cs/util/maps/NumericValueMap.java
    R src/main/java/edu/toronto/cs/util/maps/SetMap.java
    R src/main/java/edu/toronto/cs/util/maps/SubtractMapOperator.java
    R src/main/java/edu/toronto/cs/util/maps/SumMap.java
    A src/main/java/org/phenotips/oo/DisorderData.java
    A src/main/java/org/phenotips/oo/DisorderDataBuilder.java
    A src/main/java/org/phenotips/oo/Main.java
    A src/main/java/org/phenotips/oo/OOSaxParser.java
    A src/main/java/org/phenotips/oo/OmimDBBuilder.java
    A src/main/java/org/phenotips/oo/OmimSourceParser.java
    A src/main/java/org/phenotips/oo/RecordData.java
    A src/main/java/org/phenotips/oo/TSVParser.java
    A src/main/java/org/phenotips/util/maps/AbstractCollectionMap.java
    A src/main/java/org/phenotips/util/maps/AbstractMapOperator.java
    A src/main/java/org/phenotips/util/maps/AbstractNumericValueMap.java
    A src/main/java/org/phenotips/util/maps/AddMapOperator.java
    A src/main/java/org/phenotips/util/maps/CounterMap.java
    A src/main/java/org/phenotips/util/maps/DivideMapOperator.java
    A src/main/java/org/phenotips/util/maps/DoubleMap.java
    A src/main/java/org/phenotips/util/maps/IntegerMap.java
    A src/main/java/org/phenotips/util/maps/IntegerSumMap.java
    A src/main/java/org/phenotips/util/maps/ListMap.java
    A src/main/java/org/phenotips/util/maps/MapOperator.java
    A src/main/java/org/phenotips/util/maps/MultiplyMapOperator.java
    A src/main/java/org/phenotips/util/maps/NumericValueMap.java
    A src/main/java/org/phenotips/util/maps/SetMap.java
    A src/main/java/org/phenotips/util/maps/SubtractMapOperator.java
    A src/main/java/org/phenotips/util/maps/SumMap.java

  Log Message:
  -----------
  [misc] Use org.phenotips as the package name / groupId


  Commit: c9ce143e48a77e81679064084f15d098323a784a
      https://github.com/phenotips/phenotips/commit/c9ce143e48a77e81679064084f15d098323a784a
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-06-29 (Mon, 29 Jun 2015)

  Changed paths:
    A components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  Initial commit of some setup


  Commit: 2477dc3ca9f06ec5d34dcb27148241254725b9ab
      https://github.com/phenotips/phenotips/commit/2477dc3ca9f06ec5d34dcb27148241254725b9ab
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-06-29 (Mon, 29 Jun 2015)

  Changed paths:
    A components/patient-data-extra/medication/api/pom.xml
    A components/patient-data-extra/medication/api/src/main/java/org/phenotips/data/Medication.java
    A components/patient-data-extra/medication/api/src/main/java/org/phenotips/data/MedicationEffect.java
    A components/patient-data-extra/medication/api/src/main/java/org/phenotips/data/internal/controller/MedicationController.java
    A components/patient-data-extra/medication/api/src/main/resources/META-INF/components.txt
    A components/patient-data-extra/medication/api/src/test/java/org/phenotips/data/MedicationControllerTest.java
    A components/patient-data-extra/medication/api/src/test/java/org/phenotips/data/MedicationEffectTest.java
    A components/patient-data-extra/medication/api/src/test/java/org/phenotips/data/MedicationTest.java
    A components/patient-data-extra/medication/pom.xml
    A components/patient-data-extra/medication/ui/.gitignore
    A components/patient-data-extra/medication/ui/pom.xml
    A components/patient-data-extra/medication/ui/src/main/resources/PhenoTips/MedicationDataClass.xml
    A components/patient-data-extra/medication/ui/src/main/resources/PhenoTips/UIX_Field__medication.xml
    A components/patient-data-extra/pom.xml
    M components/patient-data-sharing/push-ui/src/main/resources/PhenoTips/PushPatient.xml
    M components/patient-data/impl/src/main/java/org/phenotips/data/internal/controller/SexController.java
    M components/patient-data/impl/src/main/resources/ApplicationResources.properties
    M components/patient-data/pageobjects/src/main/java/org/phenotips/data/test/po/PatientRecordEditPage.java
    R components/patient-data/ui/src/main/resources/PhenoTips/MedicationDataClass.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/PatientClass.xml
    R components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__medication.xml
    M components/patient-measurements/api/src/main/resources/ApplicationResources.properties
    M components/pedigree/resources/src/main/resources/pedigree/model/baseGraph.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/pedigree.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/importSelector.js
    M components/pedigree/resources/src/main/resources/pedigree/view/nodetypeSelectionBubble.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personVisuals.js
    M components/pom.xml
    M components/record-locking/api/src/main/java/org/phenotips/recordLocking/PatientRecordLockManager.java
    M components/record-locking/api/src/main/java/org/phenotips/recordLocking/internal/DefaultPatientRecordLockManager.java
    M components/record-locking/api/src/main/java/org/phenotips/recordLocking/internal/authorization/LockedAuthorizationModule.java
    M components/record-locking/api/src/main/java/org/phenotips/recordLocking/script/RecordLockingService.java
    M components/record-locking/api/src/test/java/org/phenotips/recordLocking/script/RecordLockingScriptTest.java

  Log Message:
  -----------
  Merge branch 'master' into DefaultPatientByExternalIdResourceImpl-tests


  Commit: e668aa4a17a750b732ffb664a69fd686582403d2
      https://github.com/phenotips/phenotips/commit/e668aa4a17a750b732ffb664a69fd686582403d2
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-06-30 (Tue, 30 Jun 2015)

  Changed paths:
    M components/patient-data/rest/pom.xml

  Log Message:
  -----------
  Added test deps and changed min coverage for dev


  Commit: 7750b78954c3df77a5189dc11d9663a0f798cfe5
      https://github.com/phenotips/phenotips/commit/7750b78954c3df77a5189dc11d9663a0f798cfe5
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-06-30 (Tue, 30 Jun 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  Set up getting instances of injected classes


  Commit: f9e9c26fecf75d589c0a3ab5f88dcdf566689ce3
      https://github.com/phenotips/phenotips/commit/f9e9c26fecf75d589c0a3ab5f88dcdf566689ce3
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-03 (Fri, 03 Jul 2015)

  Changed paths:
    M components/patient-data/rest/pom.xml

  Log Message:
  -----------
  Changed POM to include wiki test component dependency


  Commit: 6bf840332060a5f175a43e5b72f5c47c9febb166
      https://github.com/phenotips/phenotips/commit/6bf840332060a5f175a43e5b72f5c47c9febb166
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-03 (Fri, 03 Jul 2015)

  Changed paths:
    A components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/ConfigureISODatesInJsonTest.java

  Log Message:
  -----------
  Added Test for ConfigureISODatesInJson OnEvent method


  Commit: 34d8b857ea8378c8cb19a9c87e086d0af635bb48
      https://github.com/phenotips/phenotips/commit/34d8b857ea8378c8cb19a9c87e086d0af635bb48
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-03 (Fri, 03 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/ConfigureISODatesInJsonTest.java

  Log Message:
  -----------
  Added Test for object contruction of ConfigureISODatesInJson class


  Commit: 6499e09ebb5457fb5c6712dc6a50392ff74fb75e
      https://github.com/phenotips/phenotips/commit/6499e09ebb5457fb5c6712dc6a50392ff74fb75e
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-03 (Fri, 03 Jul 2015)

  Changed paths:
    M components/patient-data/rest/pom.xml

  Log Message:
  -----------
  Added javax.servlet dependancy


  Commit: b6e0ca6ed755a5b9af2cf35390faca5cc09bbf38
      https://github.com/phenotips/phenotips/commit/b6e0ca6ed755a5b9af2cf35390faca5cc09bbf38
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-03 (Fri, 03 Jul 2015)

  Changed paths:
    A components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  DefaultPatientResourceImpl tests


  Commit: 49f2a62edd932dec265fef00fbb80993bbb01276
      https://github.com/phenotips/phenotips/commit/49f2a62edd932dec265fef00fbb80993bbb01276
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-03 (Fri, 03 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  completed test coverage of DefaultPatientResourceImplTest


  Commit: e3637ea4ee209313f558fb1bc9c8a05b1f66e0f0
      https://github.com/phenotips/phenotips/commit/e3637ea4ee209313f558fb1bc9c8a05b1f66e0f0
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-03 (Fri, 03 Jul 2015)

  Changed paths:
    M components/patient-data/rest/pom.xml

  Log Message:
  -----------
  changed minimum coverage to avoid build failure


  Commit: 5f54ed673bcee996e3403a22bd8ef4c64eb49a3e
      https://github.com/phenotips/phenotips/commit/5f54ed673bcee996e3403a22bd8ef4c64eb49a3e
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-03 (Fri, 03 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  Added comment header to DefaultPatientResourceImplTest class


  Commit: 7c4002c0785c52db6419194c8eeb6a101500a0d4
      https://github.com/phenotips/phenotips/commit/7c4002c0785c52db6419194c8eeb6a101500a0d4
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-03 (Fri, 03 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  Removed a few unused statements


  Commit: f262018bc3fa866cd709b7aeb0c32c5d9340e76e
      https://github.com/phenotips/phenotips/commit/f262018bc3fa866cd709b7aeb0c32c5d9340e76e
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-03 (Fri, 03 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  changed Reflections to getInstance for mocking of injected fields


  Commit: da57246c2d6c8c4e0b537ab261c490b69ce0ddb6
      https://github.com/phenotips/phenotips/commit/da57246c2d6c8c4e0b537ab261c490b69ce0ddb6
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-03 (Fri, 03 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/ConfigureISODatesInJsonTest.java

  Log Message:
  -----------
  added static imports for Mockito.when and Mockito.verify


  Commit: 9b093294f7798e11c88353c75da2aff4d8d5e60d
      https://github.com/phenotips/phenotips/commit/9b093294f7798e11c88353c75da2aff4d8d5e60d
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-03 (Fri, 03 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImpl.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultPatientResourceImpl.java
    M components/patient-measurements/api/src/main/resources/measurementsChartsConfigurations.properties
    M components/patient-measurements/api/src/main/resources/org/phenotips/measurements/internal/bmi.csv
    M components/patient-measurements/api/src/main/resources/org/phenotips/measurements/internal/hc.csv
    M components/patient-measurements/api/src/main/resources/org/phenotips/measurements/internal/weight.csv
    M components/patient-measurements/api/src/test/java/org/phenotips/measurements/internal/BMITest.java
    M components/patient-measurements/api/src/test/java/org/phenotips/measurements/internal/HeadCircumferenceTest.java
    M components/patient-measurements/api/src/test/java/org/phenotips/measurements/internal/WeightTest.java

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/master' into rest-patient-resource-test


  Commit: 2c6b6b0786f077d20bf9de83bdfa18914a2a0b87
      https://github.com/phenotips/phenotips/commit/2c6b6b0786f077d20bf9de83bdfa18914a2a0b87
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-03 (Fri, 03 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  Added test for new logger message in deletePatient


  Commit: 215c3c2723669664bf7bfec554fe4750e08d9a6c
      https://github.com/phenotips/phenotips/commit/215c3c2723669664bf7bfec554fe4750e08d9a6c
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-06 (Mon, 06 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  hasAccess now checks for real DocumentReferences instead of null values


  Commit: a3e57a6664e9fba8a312ae4df7fd5c3f64ada032
      https://github.com/phenotips/phenotips/commit/a3e57a6664e9fba8a312ae4df7fd5c3f64ada032
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-06 (Mon, 06 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  Removed ReflectionUtils.setFieldValue calls in deletePatient tests


  Commit: 34e1be6a2a1766326ade2c324569c88322a10955
      https://github.com/phenotips/phenotips/commit/34e1be6a2a1766326ade2c324569c88322a10955
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-07 (Tue, 07 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  changed set up and added another test


  Commit: ec4213a8d517a04d20a094b6cbd45ecbae3b10db
      https://github.com/phenotips/phenotips/commit/ec4213a8d517a04d20a094b6cbd45ecbae3b10db
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-07 (Tue, 07 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  Whitespace/formating changes


  Commit: 90c38ed1ac291fa970b72e57e03f86b1a1a39a0a
      https://github.com/phenotips/phenotips/commit/90c38ed1ac291fa970b72e57e03f86b1a1a39a0a
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-07 (Tue, 07 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  Removed unnecessary URI field


  Commit: 7836ebf7b6c3fd64aded22a485ef7dfff7d6d5ba
      https://github.com/phenotips/phenotips/commit/7836ebf7b6c3fd64aded22a485ef7dfff7d6d5ba
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-08 (Wed, 08 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  Make use of XWikiContext.TYPE_PROVIDER field


  Commit: 46a8df99cd8aab6f7cef72f466110c35b92696eb
      https://github.com/phenotips/phenotips/commit/46a8df99cd8aab6f7cef72f466110c35b92696eb
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-08 (Wed, 08 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/ConfigureISODatesInJsonTest.java

  Log Message:
  -----------
  Use getInstance() instead of calling constructor


  Commit: b6d86a3bd987548a909acdcfd3bfad372ed45126
      https://github.com/phenotips/phenotips/commit/b6d86a3bd987548a909acdcfd3bfad372ed45126
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-08 (Wed, 08 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  added test for getting patient properly


  Commit: 6f99f1acc57b6c713e4417f3b4b679130bf45005
      https://github.com/phenotips/phenotips/commit/6f99f1acc57b6c713e4417f3b4b679130bf45005
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-08 (Wed, 08 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  Added test for getting a patient that isn't found


  Commit: 151738270f6ac734ee520a8d5adc396b79599bb3
      https://github.com/phenotips/phenotips/commit/151738270f6ac734ee520a8d5adc396b79599bb3
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-08 (Wed, 08 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  Added test for not finding a patient while updating


  Commit: 4b359b44c17130e686758ab26407dd8be1d01b0b
      https://github.com/phenotips/phenotips/commit/4b359b44c17130e686758ab26407dd8be1d01b0b
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-08 (Wed, 08 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  Added test for updating patient with no access


  Commit: 5fbae300805341248576f6d3cb364b6a8b1de8db
      https://github.com/phenotips/phenotips/commit/5fbae300805341248576f6d3cb364b6a8b1de8db
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-09 (Thu, 09 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  test for json not having id feild when updating


  Commit: 6b4591d7a7adf9b5928a6c8c6fda03e851a0c402
      https://github.com/phenotips/phenotips/commit/6b4591d7a7adf9b5928a6c8c6fda03e851a0c402
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-09 (Thu, 09 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  fixed typo


  Commit: 6a05865e729bdc49ef1b8ab08d29cd17930809a6
      https://github.com/phenotips/phenotips/commit/6a05865e729bdc49ef1b8ab08d29cd17930809a6
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-09 (Thu, 09 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  removed useless test


  Commit: 564bd9eff4820b674276141e957857f3a247b3f3
      https://github.com/phenotips/phenotips/commit/564bd9eff4820b674276141e957857f3a247b3f3
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-09 (Thu, 09 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  test for throwing exception while updating from json


  Commit: df8312a6d1349f84e251ab374ffdcf6390049a9b
      https://github.com/phenotips/phenotips/commit/df8312a6d1349f84e251ab374ffdcf6390049a9b
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-09 (Thu, 09 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  fixed typo


  Commit: 9ed5be1a23b9fcb9aee56a02f0d5d12ab47fd85e
      https://github.com/phenotips/phenotips/commit/9ed5be1a23b9fcb9aee56a02f0d5d12ab47fd85e
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-09 (Thu, 09 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  test successful update of patient


  Commit: f3c31c23cbf31fffa7374a4722034db7fbedd927
      https://github.com/phenotips/phenotips/commit/f3c31c23cbf31fffa7374a4722034db7fbedd927
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-09 (Thu, 09 Jul 2015)

  Changed paths:
    M .gitignore
    M components/default-settings/src/main/resources/XWiki/XWikiPreferences.xml
    M components/navigation/api/src/main/resources/ApplicationResources.properties
    M components/navigation/pageobjects/src/main/java/org/phenotips/navigation/test/po/AllRecordsPage.java
    M components/navigation/pageobjects/src/main/java/org/phenotips/navigation/test/po/HomePage.java
    M components/navigation/tests/src/test/it/org/phenotips/navigation/test/ui/HomePageTest.java
    M components/patient-data-extra/medication/api/pom.xml
    M components/patient-data-extra/medication/api/src/main/java/org/phenotips/data/Medication.java
    M components/patient-data-extra/medication/api/src/main/java/org/phenotips/data/MedicationEffect.java
    M components/patient-data-extra/medication/api/src/main/java/org/phenotips/data/internal/controller/MedicationController.java
    M components/patient-data-extra/medication/api/src/test/java/org/phenotips/data/MedicationControllerTest.java
    M components/patient-data-extra/medication/api/src/test/java/org/phenotips/data/MedicationEffectTest.java
    M components/patient-data-extra/medication/api/src/test/java/org/phenotips/data/MedicationTest.java
    A components/patient-data-sharing/push-api/src/test/java/org/phenotips/data/push/internal/DefaultPushServerInfoTest.java
    A components/patient-data-sharing/push-api/src/test/java/org/phenotips/data/push/internal/DefaultPushServerSendPatientResponseTest.java
    M components/patient-data/api/src/main/java/org/phenotips/data/PatientData.java
    M components/patient-data/impl/src/main/java/org/phenotips/data/internal/controller/MetaDataController.java
    M components/patient-data/pageobjects/src/main/java/org/phenotips/data/test/po/PatientRecordEditPage.java
    M components/patient-data/pageobjects/src/main/java/org/phenotips/data/test/po/PatientRecordViewPage.java
    M components/patient-data/rest/pom.xml
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/DateTimeAdapter.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/DomainObjectFactory.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/PatientByExternalIdResource.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/PatientResource.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/PatientsResource.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/Relations.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/ConfigureISODatesInJson.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultDomainObjectFactory.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImpl.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultPatientResourceImpl.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImpl.java
    A components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultDomainObjectFactoryTest.java
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java
    M components/patient-data/tests/src/test/it/org/phenotips/data/test/ui/AllTests.java
    M components/patient-data/tests/src/test/it/org/phenotips/data/test/ui/PatientRecordTest.java
    M components/patient-data/ui/src/main/resources/PhenoTips/VariantClass.xml
    M components/patient-measurements/api/src/main/resources/measurementsChartsConfigurations.properties
    M components/patient-measurements/api/src/main/resources/org/phenotips/measurements/internal/bmi.csv
    M components/patient-measurements/api/src/main/resources/org/phenotips/measurements/internal/hc.csv
    M components/patient-measurements/api/src/main/resources/org/phenotips/measurements/internal/weight.csv
    M components/patient-measurements/api/src/test/java/org/phenotips/measurements/internal/BMITest.java
    M components/patient-measurements/api/src/test/java/org/phenotips/measurements/internal/HeadCircumferenceTest.java
    M components/patient-measurements/api/src/test/java/org/phenotips/measurements/internal/WeightTest.java
    M components/pedigree/resources/src/main/resources/pedigree/editor.css
    M components/pedigree/resources/src/main/resources/pedigree/view/templateSelector.js
    M components/pedigree/ui/src/main/resources/PhenoTips/PedigreeGlobalSettings.xml
    M components/record-locking/api/src/main/java/org/phenotips/recordLocking/PatientRecordLockManager.java
    M components/record-locking/api/src/main/java/org/phenotips/recordLocking/internal/DefaultPatientRecordLockManager.java
    M components/record-locking/api/src/main/java/org/phenotips/recordLocking/internal/authorization/LockedAuthorizationModule.java
    M components/record-locking/api/src/main/java/org/phenotips/recordLocking/script/RecordLockingService.java
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.fdt
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.fdx
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.fnm
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.nvd
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.nvm
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.si
    R resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene41_0.doc
    R resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene41_0.pos
    R resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene41_0.tim
    R resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene41_0.tip
    A resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene50_0.doc
    A resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene50_0.pos
    A resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene50_0.tim
    A resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene50_0.tip
    R resources/solr-configuration/src/main/resources/hpo/data/index/segments.gen
    M resources/solr-configuration/src/main/resources/hpo/data/index/segments_2
    M resources/solr-configuration/src/main/resources/hpo/data/spellchecker/_0.cfe
    M resources/solr-configuration/src/main/resources/hpo/data/spellchecker/_0.cfs
    M resources/solr-configuration/src/main/resources/hpo/data/spellchecker/_0.si
    R resources/solr-configuration/src/main/resources/hpo/data/spellchecker/segments.gen
    A resources/solr-configuration/src/main/resources/hpo/data/spellchecker/segments_3
    R resources/solr-configuration/src/main/resources/hpo/data/spellchecker/segments_4

  Log Message:
  -----------
  merge


  Commit: 4fd57f8db552e0cdf0af0e1ad13d495092acbdbe
      https://github.com/phenotips/phenotips/commit/4fd57f8db552e0cdf0af0e1ad13d495092acbdbe
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-09 (Thu, 09 Jul 2015)

  Changed paths:
    M .gitignore
    M components/default-settings/src/main/resources/XWiki/XWikiPreferences.xml
    M components/navigation/api/src/main/resources/ApplicationResources.properties
    M components/navigation/pageobjects/src/main/java/org/phenotips/navigation/test/po/AllRecordsPage.java
    M components/navigation/pageobjects/src/main/java/org/phenotips/navigation/test/po/HomePage.java
    M components/navigation/tests/src/test/it/org/phenotips/navigation/test/ui/HomePageTest.java
    M components/patient-data-extra/medication/api/pom.xml
    M components/patient-data-extra/medication/api/src/main/java/org/phenotips/data/Medication.java
    M components/patient-data-extra/medication/api/src/main/java/org/phenotips/data/MedicationEffect.java
    M components/patient-data-extra/medication/api/src/main/java/org/phenotips/data/internal/controller/MedicationController.java
    M components/patient-data-extra/medication/api/src/test/java/org/phenotips/data/MedicationControllerTest.java
    M components/patient-data-extra/medication/api/src/test/java/org/phenotips/data/MedicationEffectTest.java
    M components/patient-data-extra/medication/api/src/test/java/org/phenotips/data/MedicationTest.java
    A components/patient-data-sharing/push-api/src/test/java/org/phenotips/data/push/internal/DefaultPushServerInfoTest.java
    A components/patient-data-sharing/push-api/src/test/java/org/phenotips/data/push/internal/DefaultPushServerSendPatientResponseTest.java
    M components/patient-data/api/src/main/java/org/phenotips/data/PatientData.java
    M components/patient-data/impl/src/main/java/org/phenotips/data/internal/controller/MetaDataController.java
    M components/patient-data/pageobjects/src/main/java/org/phenotips/data/test/po/PatientRecordEditPage.java
    M components/patient-data/pageobjects/src/main/java/org/phenotips/data/test/po/PatientRecordViewPage.java
    M components/patient-data/rest/pom.xml
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/DateTimeAdapter.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/DomainObjectFactory.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/PatientByExternalIdResource.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/PatientResource.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/PatientsResource.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/Relations.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/ConfigureISODatesInJson.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultDomainObjectFactory.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImpl.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultPatientResourceImpl.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImpl.java
    A components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultDomainObjectFactoryTest.java
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java
    M components/patient-data/tests/src/test/it/org/phenotips/data/test/ui/AllTests.java
    M components/patient-data/tests/src/test/it/org/phenotips/data/test/ui/PatientRecordTest.java
    M components/patient-data/ui/src/main/resources/PhenoTips/VariantClass.xml
    M components/patient-measurements/api/src/main/resources/measurementsChartsConfigurations.properties
    M components/patient-measurements/api/src/main/resources/org/phenotips/measurements/internal/bmi.csv
    M components/patient-measurements/api/src/main/resources/org/phenotips/measurements/internal/hc.csv
    M components/patient-measurements/api/src/main/resources/org/phenotips/measurements/internal/weight.csv
    M components/patient-measurements/api/src/test/java/org/phenotips/measurements/internal/BMITest.java
    M components/patient-measurements/api/src/test/java/org/phenotips/measurements/internal/HeadCircumferenceTest.java
    M components/patient-measurements/api/src/test/java/org/phenotips/measurements/internal/WeightTest.java
    M components/pedigree/resources/src/main/resources/pedigree/editor.css
    M components/pedigree/resources/src/main/resources/pedigree/view/templateSelector.js
    M components/pedigree/ui/src/main/resources/PhenoTips/PedigreeGlobalSettings.xml
    M components/record-locking/api/src/main/java/org/phenotips/recordLocking/PatientRecordLockManager.java
    M components/record-locking/api/src/main/java/org/phenotips/recordLocking/internal/DefaultPatientRecordLockManager.java
    M components/record-locking/api/src/main/java/org/phenotips/recordLocking/internal/authorization/LockedAuthorizationModule.java
    M components/record-locking/api/src/main/java/org/phenotips/recordLocking/script/RecordLockingService.java
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.fdt
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.fdx
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.fnm
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.nvd
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.nvm
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.si
    R resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene41_0.doc
    R resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene41_0.pos
    R resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene41_0.tim
    R resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene41_0.tip
    A resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene50_0.doc
    A resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene50_0.pos
    A resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene50_0.tim
    A resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene50_0.tip
    R resources/solr-configuration/src/main/resources/hpo/data/index/segments.gen
    M resources/solr-configuration/src/main/resources/hpo/data/index/segments_2
    M resources/solr-configuration/src/main/resources/hpo/data/spellchecker/_0.cfe
    M resources/solr-configuration/src/main/resources/hpo/data/spellchecker/_0.cfs
    M resources/solr-configuration/src/main/resources/hpo/data/spellchecker/_0.si
    R resources/solr-configuration/src/main/resources/hpo/data/spellchecker/segments.gen
    A resources/solr-configuration/src/main/resources/hpo/data/spellchecker/segments_3
    R resources/solr-configuration/src/main/resources/hpo/data/spellchecker/segments_4

  Log Message:
  -----------
  Merge branch 'DeanWay-DefaultPatientByExternalIdResourceImpl-tests' into DefaultPatientByExternalIdResourceImpl-tests


  Commit: 2188d59971494e22993010c610193578bb8d61c1
      https://github.com/phenotips/phenotips/commit/2188d59971494e22993010c610193578bb8d61c1
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-09 (Thu, 09 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  clean up


  Commit: 8746a8cbf037a5a0262deab12c64870cdb38a455
      https://github.com/phenotips/phenotips/commit/8746a8cbf037a5a0262deab12c64870cdb38a455
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-09 (Thu, 09 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  added test for private checking multiple method


  Commit: 27211eac8c889e1188186880c1d1982cd007115e
      https://github.com/phenotips/phenotips/commit/27211eac8c889e1188186880c1d1982cd007115e
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-09 (Thu, 09 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  clean up variables


  Commit: c4b615767d74008d0cde85bc9577552dea448392
      https://github.com/phenotips/phenotips/commit/c4b615767d74008d0cde85bc9577552dea448392
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-09 (Thu, 09 Jul 2015)

  Log Message:
  -----------
  Merge branch 'master' into DefaultPatientByExternalIdResourceImpl-tests


  Commit: c291948950cded56b3e228489656b34c523a13f2
      https://github.com/phenotips/phenotips/commit/c291948950cded56b3e228489656b34c523a13f2
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-09 (Thu, 09 Jul 2015)

  Log Message:
  -----------
  Merge branch 'master' into DefaultPatientByExternalIdResourceImpl-tests


  Commit: ae3e0fc8d28908f772a591bd7d571440507acd0c
      https://github.com/phenotips/phenotips/commit/ae3e0fc8d28908f772a591bd7d571440507acd0c
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-09 (Thu, 09 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  test for checkMultiplePatients throwing QueryException


  Commit: 37220a458ce72f0ae2c0009c5ab427e50d7e5beb
      https://github.com/phenotips/phenotips/commit/37220a458ce72f0ae2c0009c5ab427e50d7e5beb
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-10 (Fri, 10 Jul 2015)

  Changed paths:
    M components/default-settings/src/main/resources/XWiki/XWikiPreferences.xml
    M components/navigation/api/src/main/resources/ApplicationResources.properties
    M components/navigation/pageobjects/src/main/java/org/phenotips/navigation/test/po/AllRecordsPage.java
    M components/navigation/pageobjects/src/main/java/org/phenotips/navigation/test/po/HomePage.java
    M components/navigation/tests/src/test/it/org/phenotips/navigation/test/ui/HomePageTest.java
    M components/patient-data-extra/medication/api/pom.xml
    M components/patient-data-extra/medication/api/src/main/java/org/phenotips/data/Medication.java
    M components/patient-data-extra/medication/api/src/main/java/org/phenotips/data/MedicationEffect.java
    M components/patient-data-extra/medication/api/src/main/java/org/phenotips/data/internal/controller/MedicationController.java
    M components/patient-data-extra/medication/api/src/test/java/org/phenotips/data/MedicationControllerTest.java
    M components/patient-data-extra/medication/api/src/test/java/org/phenotips/data/MedicationEffectTest.java
    M components/patient-data-extra/medication/api/src/test/java/org/phenotips/data/MedicationTest.java
    A components/patient-data-sharing/push-api/src/test/java/org/phenotips/data/push/internal/DefaultPushServerInfoTest.java
    A components/patient-data-sharing/push-api/src/test/java/org/phenotips/data/push/internal/DefaultPushServerSendPatientResponseTest.java
    M components/patient-data/api/src/main/java/org/phenotips/data/PatientData.java
    M components/patient-data/impl/src/main/java/org/phenotips/data/internal/controller/MetaDataController.java
    M components/patient-data/pageobjects/src/main/java/org/phenotips/data/test/po/PatientRecordEditPage.java
    M components/patient-data/pageobjects/src/main/java/org/phenotips/data/test/po/PatientRecordViewPage.java
    M components/patient-data/rest/pom.xml
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/DateTimeAdapter.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/DomainObjectFactory.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/PatientByExternalIdResource.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/PatientResource.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/PatientsResource.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/Relations.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/ConfigureISODatesInJson.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultDomainObjectFactory.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImpl.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultPatientResourceImpl.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImpl.java
    A components/patient-data/rest/src/test/java/org/phenotips/data/rest/DateTimeAdapterTest.java
    A components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultDomainObjectFactoryTest.java
    M components/patient-data/tests/src/test/it/org/phenotips/data/test/ui/AllTests.java
    M components/patient-data/tests/src/test/it/org/phenotips/data/test/ui/PatientRecordTest.java
    M components/patient-data/ui/src/main/resources/PhenoTips/VariantClass.xml
    M components/pedigree/resources/src/main/resources/pedigree/editor.css
    M components/pedigree/resources/src/main/resources/pedigree/view/templateSelector.js
    M components/pedigree/ui/src/main/resources/PhenoTips/PedigreeGlobalSettings.xml
    M components/record-locking/api/src/main/java/org/phenotips/recordLocking/PatientRecordLockManager.java
    M components/record-locking/api/src/main/java/org/phenotips/recordLocking/internal/DefaultPatientRecordLockManager.java
    M components/record-locking/api/src/main/java/org/phenotips/recordLocking/internal/authorization/LockedAuthorizationModule.java
    M components/record-locking/api/src/main/java/org/phenotips/recordLocking/script/RecordLockingService.java
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.fdt
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.fdx
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.fnm
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.nvd
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.nvm
    M resources/solr-configuration/src/main/resources/hpo/data/index/_0.si
    R resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene41_0.doc
    R resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene41_0.pos
    R resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene41_0.tim
    R resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene41_0.tip
    A resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene50_0.doc
    A resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene50_0.pos
    A resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene50_0.tim
    A resources/solr-configuration/src/main/resources/hpo/data/index/_0_Lucene50_0.tip
    R resources/solr-configuration/src/main/resources/hpo/data/index/segments.gen
    M resources/solr-configuration/src/main/resources/hpo/data/index/segments_2
    M resources/solr-configuration/src/main/resources/hpo/data/spellchecker/_0.cfe
    M resources/solr-configuration/src/main/resources/hpo/data/spellchecker/_0.cfs
    M resources/solr-configuration/src/main/resources/hpo/data/spellchecker/_0.si
    R resources/solr-configuration/src/main/resources/hpo/data/spellchecker/segments.gen
    A resources/solr-configuration/src/main/resources/hpo/data/spellchecker/segments_3
    R resources/solr-configuration/src/main/resources/hpo/data/spellchecker/segments_4

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/master' into rest-patient-resource-test


  Commit: 252587eff9f373c73d9d44fcc6ce069ac6d50fd6
      https://github.com/phenotips/phenotips/commit/252587eff9f373c73d9d44fcc6ce069ac6d50fd6
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-10 (Fri, 10 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  Updated tests for throws changes


  Commit: 1f1875bc019128f0b3c44ead92c83908c472c30f
      https://github.com/phenotips/phenotips/commit/1f1875bc019128f0b3c44ead92c83908c472c30f
  Author: Tarang <tarang.marathe at gmail.com>
  Date:   2015-07-10 (Fri, 10 Jul 2015)

  Changed paths:
    A components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  initial addPatient and listPatient tests

changed addPatient tests
addPatient and listPatients tests


  Commit: 080d9f4f8c61c539d4095a92904db8e1c3f9840b
      https://github.com/phenotips/phenotips/commit/080d9f4f8c61c539d4095a92904db8e1c3f9840b
  Author: Tarang <tarang.marathe at gmail.com>
  Date:   2015-07-10 (Fri, 10 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  added exception status checks


  Commit: 6336c675344d835a87cbaac5f64653f6390111d5
      https://github.com/phenotips/phenotips/commit/6336c675344d835a87cbaac5f64653f6390111d5
  Author: Tarang <tarang.marathe at gmail.com>
  Date:   2015-07-10 (Fri, 10 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  added exception checking


  Commit: 711fa70b4fa79eec3973030ed66198911b3d5367
      https://github.com/phenotips/phenotips/commit/711fa70b4fa79eec3973030ed66198911b3d5367
  Author: Tarang <tarang.marathe at gmail.com>
  Date:   2015-07-10 (Fri, 10 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  completed listPatientsDefaultBehaviour test

completed listPatientsDefaultBehaviour test

corrected typo


  Commit: a2b769799ce4af784b67e22cb9946d0a0992c4b3
      https://github.com/phenotips/phenotips/commit/a2b769799ce4af784b67e22cb9946d0a0992c4b3
  Author: Tarang <tarang.marathe at gmail.com>
  Date:   2015-07-10 (Fri, 10 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  license added


  Commit: 301dc6b6744162e66ad6b8cfbc3e9342dbdb7014
      https://github.com/phenotips/phenotips/commit/301dc6b6744162e66ad6b8cfbc3e9342dbdb7014
  Author: Tarang <tarang.marathe at gmail.com>
  Date:   2015-07-10 (Fri, 10 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  listPatients error handling

fixed test for listPatients error handling

rebasing


  Commit: b21d0806ae6fe08c090d14733a44bbe12bca3503
      https://github.com/phenotips/phenotips/commit/b21d0806ae6fe08c090d14733a44bbe12bca3503
  Author: Tarang <tarang.marathe at gmail.com>
  Date:   2015-07-10 (Fri, 10 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  removed throws XWikiRestException


  Commit: e81c9398d6d68636d08a3c4e362aa7312baf6d79
      https://github.com/phenotips/phenotips/commit/e81c9398d6d68636d08a3c4e362aa7312baf6d79
  Author: Tarang <tarang.marathe at gmail.com>
  Date:   2015-07-10 (Fri, 10 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  removed unused classes


  Commit: 74e68a3f2e990fa65de453195852f292e0ffb019
      https://github.com/phenotips/phenotips/commit/74e68a3f2e990fa65de453195852f292e0ffb019
  Author: Tarang <tarang.marathe at gmail.com>
  Date:   2015-07-10 (Fri, 10 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  improved exception status checking


  Commit: f6d5b6680787222b72131e1a95ec660a5aa76247
      https://github.com/phenotips/phenotips/commit/f6d5b6680787222b72131e1a95ec660a5aa76247
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-13 (Mon, 13 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  uses real document reference now


  Commit: f1852e139255a89b9bc998909bef76682fe59c46
      https://github.com/phenotips/phenotips/commit/f1852e139255a89b9bc998909bef76682fe59c46
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-13 (Mon, 13 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/ConfigureISODatesInJsonTest.java

  Log Message:
  -----------
  Improved method for checking that and ApplicationStartedEvent is added by ConfigureISODatesInJson


  Commit: 5d732a814d7771b8ac18807ebab3c9044e9c1b35
      https://github.com/phenotips/phenotips/commit/5d732a814d7771b8ac18807ebab3c9044e9c1b35
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-13 (Mon, 13 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  Improved test method names


  Commit: 84e49db1a8fd75b7fa8e9931f8a22bca7eed3514
      https://github.com/phenotips/phenotips/commit/84e49db1a8fd75b7fa8e9931f8a22bca7eed3514
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-13 (Mon, 13 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  Expanded tests on normal Behavior of DefaultPatientResourceImpl methods


  Commit: 926ed479b29415c5eb9ca9b90d5c6e17b05be418
      https://github.com/phenotips/phenotips/commit/926ed479b29415c5eb9ca9b90d5c6e17b05be418
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-15 (Wed, 15 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  changed method name to make more sense


  Commit: 05426f2e6242392df9ee22aad2b934c8c6b1fdb1
      https://github.com/phenotips/phenotips/commit/05426f2e6242392df9ee22aad2b934c8c6b1fdb1
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-15 (Wed, 15 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  private method checks for when it is called on all other public methods


  Commit: b70ddd82396ceb68594f5cd0df23883cb1cb6e9f
      https://github.com/phenotips/phenotips/commit/b70ddd82396ceb68594f5cd0df23883cb1cb6e9f
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-16 (Thu, 16 Jul 2015)

  Changed paths:
    M README.md
    A components/base-war/src/main/webapp/resources/js/scriptaculous/dragdrop.js
    M components/jodatime-service/pom.xml
    M components/patient-data-extra/medication/api/pom.xml
    M components/patient-data/api/src/main/java/org/phenotips/data/Patient.java
    M components/patient-data/api/src/main/java/org/phenotips/data/PatientDataController.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/DateTimeAdapter.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/PatientByExternalIdResource.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/PatientResource.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/PatientsResource.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImpl.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultPatientResourceImpl.java
    M components/patient-data/rest/src/main/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImpl.java
    A components/patient-data/rest/src/test/java/org/phenotips/data/rest/DateTimeAdapterTest.java
    M components/pedigree/resources/src/main/resources/pedigree/view.js
    M components/pedigree/resources/src/main/resources/pedigree/view/legend.js
    M components/specificity-meter/ui/src/main/resources/PhenoTips/SpecificityMetricWidget.xml
    M pom.xml

  Log Message:
  -----------
  Merge branch 'master' into DefaultPatientByExternalIdResourceImpl-tests


  Commit: 2ef47647d867c40cc72aa984280dc18e1d3f4cdb
      https://github.com/phenotips/phenotips/commit/2ef47647d867c40cc72aa984280dc18e1d3f4cdb
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-16 (Thu, 16 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  removed XWikiException


  Commit: 2927fc581b0cc7e6c2a7d1aab257054269e21a11
      https://github.com/phenotips/phenotips/commit/2927fc581b0cc7e6c2a7d1aab257054269e21a11
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-16 (Thu, 16 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  fixed imports


  Commit: 925d60a727262119431aa1dcc5a3d12770eaba6d
      https://github.com/phenotips/phenotips/commit/925d60a727262119431aa1dcc5a3d12770eaba6d
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-16 (Thu, 16 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  Verify use of DomainObjectFactory


  Commit: 4c865f07cc3b0a758b8b47ae9eb10cac0ee11ca6
      https://github.com/phenotips/phenotips/commit/4c865f07cc3b0a758b8b47ae9eb10cac0ee11ca6
  Author: Tarang <tarang.marathe at gmail.com>
  Date:   2015-07-16 (Thu, 16 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  added user access test for listPatients


  Commit: 3c2fff432d89a84e235597bef48256b561afe48a
      https://github.com/phenotips/phenotips/commit/3c2fff432d89a84e235597bef48256b561afe48a
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-16 (Thu, 16 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  Check for initial logger message only once


  Commit: f4bd20296b17d81fb37862daaf0bb93f981b614c
      https://github.com/phenotips/phenotips/commit/f4bd20296b17d81fb37862daaf0bb93f981b614c
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-16 (Thu, 16 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  Reordered tests for readability(Tests for the same method grouped together)


  Commit: 87e6a16d793e704ba479c422401e07e6c8d185d7
      https://github.com/phenotips/phenotips/commit/87e6a16d793e704ba479c422401e07e6c8d185d7
  Author: JKereliuk <j.kereliuk at mail.utoronto.ca>
  Date:   2015-07-16 (Thu, 16 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  Merge pull request #1 from DeanWay/DefaultPatientByExternalIdResourceImpl-tests

Default patient by external id resource impl tests


  Commit: c02e35990ca8646f612db5376c9f3daaeda79b3d
      https://github.com/phenotips/phenotips/commit/c02e35990ca8646f612db5376c9f3daaeda79b3d
  Author: Tarang <tarang.marathe at gmail.com>
  Date:   2015-07-16 (Thu, 16 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  additonal user access test


  Commit: 14cc73cb7d805bbfedcbbde94ba64db3e1875ac1
      https://github.com/phenotips/phenotips/commit/14cc73cb7d805bbfedcbbde94ba64db3e1875ac1
  Author: Tarang <tarang.marathe at gmail.com>
  Date:   2015-07-17 (Fri, 17 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  improved listPatientsNoUserAccess


  Commit: 3a28e3ca7a56d0bc0d9260ab64601ac5109a6927
      https://github.com/phenotips/phenotips/commit/3a28e3ca7a56d0bc0d9260ab64601ac5109a6927
  Author: DeanWay <deanway93 at gmail.com>
  Date:   2015-07-21 (Tue, 21 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/ConfigureISODatesInJsonTest.java

  Log Message:
  -----------
  Remove unnecessary cast


  Commit: ac54a29c98af71c2d07c7201d6abd8eb2072151d
      https://github.com/phenotips/phenotips/commit/ac54a29c98af71c2d07c7201d6abd8eb2072151d
  Author: Tarang <tarang.marathe at gmail.com>
  Date:   2015-07-22 (Wed, 22 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  number of record tests


  Commit: ec775646de4f71b44f82790642eada9c7376b203
      https://github.com/phenotips/phenotips/commit/ec775646de4f71b44f82790642eada9c7376b203
  Author: Tarang <tarang.marathe at gmail.com>
  Date:   2015-07-22 (Wed, 22 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  fixed array Object lengths


  Commit: 94ad682b8d6b030b463400b3f61c23c87e486bd0
      https://github.com/phenotips/phenotips/commit/94ad682b8d6b030b463400b3f61c23c87e486bd0
  Author: Tarang <tarang.marathe at gmail.com>
  Date:   2015-07-23 (Thu, 23 Jul 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  edge cases for record lookup


  Commit: e5def923bfa43b9a23b21ba2a33133fa660253dd
      https://github.com/phenotips/phenotips/commit/e5def923bfa43b9a23b21ba2a33133fa660253dd
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-08-21 (Fri, 21 Aug 2015)

  Changed paths:
    A components/navigation/ui/src/main/resources/PhenoTips/DashboardGadgets.xml

  Log Message:
  -----------
  Issue #1769: Moved dashboard gadgets into UIX extensions in separate file


  Commit: 58681becb14450e69e694d4ed3f8ea541c09f9a9
      https://github.com/phenotips/phenotips/commit/58681becb14450e69e694d4ed3f8ea541c09f9a9
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-08-21 (Fri, 21 Aug 2015)

  Changed paths:
    M components/navigation/ui/src/main/resources/data/WebHome.xml

  Log Message:
  -----------
  Issue #1769: Added UIX extension point to homepage


  Commit: e84d34f92dcac290b87a20627208b021c6391d87
      https://github.com/phenotips/phenotips/commit/e84d34f92dcac290b87a20627208b021c6391d87
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-08-21 (Fri, 21 Aug 2015)

  Changed paths:
    M components/navigation/ui/src/main/resources/data/WebHome.xml

  Log Message:
  -----------
  Issue #1769: Removed original gadgets from data.WebHome


  Commit: a997fa0dcc08980eaccb829aa8569dc4312ed941
      https://github.com/phenotips/phenotips/commit/a997fa0dcc08980eaccb829aa8569dc4312ed941
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-08-21 (Fri, 21 Aug 2015)

  Changed paths:
    M components/navigation/ui/src/main/resources/PhenoTips/DashboardGadgets.xml
    M components/navigation/ui/src/main/resources/data/WebHome.xml

  Log Message:
  -----------
  Issue #1769: Added parent to PhenoTips.DashboardGadgets and titles will not be displayed if empty


  Commit: d5e725bc3b58967360b8bded820f64ee91ba7275
      https://github.com/phenotips/phenotips/commit/d5e725bc3b58967360b8bded820f64ee91ba7275
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-08-25 (Tue, 25 Aug 2015)

  Changed paths:
    M components/navigation/ui/src/main/resources/data/WebHome.xml

  Log Message:
  -----------
  Issue #1769: Addressing comment in WebHome


  Commit: af877fc61d8627ad7c8a57f7ebe88387237aacc3
      https://github.com/phenotips/phenotips/commit/af877fc61d8627ad7c8a57f7ebe88387237aacc3
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-08-25 (Tue, 25 Aug 2015)

  Changed paths:
    R components/navigation/ui/src/main/resources/PhenoTips/DashboardGadgets.xml
    A components/navigation/ui/src/main/resources/PhenoTips/WelcomeMessageGadget.xml
    A components/patient-access-rules/ui/src/main/resources/PhenoTips/AllDataGadget.xml
    A components/patient-access-rules/ui/src/main/resources/PhenoTips/MyDataGadget.xml
    A components/users/ui/src/main/resources/PhenoTips/GroupsGadget.xml

  Log Message:
  -----------
  Issue #1769: Moved individual gadgets to their own documents


  Commit: 2fc355fb57608c4e123195b405fd68042a2ab177
      https://github.com/phenotips/phenotips/commit/2fc355fb57608c4e123195b405fd68042a2ab177
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-08-25 (Tue, 25 Aug 2015)

  Changed paths:
    M components/navigation/ui/src/main/resources/PhenoTips/WelcomeMessageGadget.xml
    M components/navigation/ui/src/main/resources/data/WebHome.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/AllDataGadget.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/MyDataGadget.xml
    M components/users/ui/src/main/resources/PhenoTips/GroupsGadget.xml

  Log Message:
  -----------
  Issue #1769: Welcome message is configurable from admin, gadget title are now specified in document titles


  Commit: 23ac41216db86fae15e1845baa114deeaac2d47e
      https://github.com/phenotips/phenotips/commit/23ac41216db86fae15e1845baa114deeaac2d47e
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-08-25 (Tue, 25 Aug 2015)

  Changed paths:
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/MyDataGadget.xml

  Log Message:
  -----------
  Issue #1769: minor typo fix


  Commit: 15852da6603eff2354cbf1accd432a398d17f57e
      https://github.com/phenotips/phenotips/commit/15852da6603eff2354cbf1accd432a398d17f57e
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-08-26 (Wed, 26 Aug 2015)

  Changed paths:
    R components/navigation/ui/src/main/resources/PhenoTips/WelcomeMessageGadget.xml
    M components/navigation/ui/src/main/resources/data/WebHome.xml

  Log Message:
  -----------
  Issue #1769: Removed welcome message gadget


  Commit: 10cb1eadb21f3d6e239e4e9d8b0a593cbe10a4fe
      https://github.com/phenotips/phenotips/commit/10cb1eadb21f3d6e239e4e9d8b0a593cbe10a4fe
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-08-27 (Thu, 27 Aug 2015)

  Changed paths:
    M components/pedigree/resources/src/main/resources/pedigree/controller.js
    M components/pedigree/resources/src/main/resources/pedigree/disorder.js
    M components/pedigree/resources/src/main/resources/pedigree/filesaver/FileSaver.js
    M components/pedigree/resources/src/main/resources/pedigree/hpoTerm.js
    M components/pedigree/resources/src/main/resources/pedigree/model/baseGraph.js
    M components/pedigree/resources/src/main/resources/pedigree/model/dynamicGraph.js
    M components/pedigree/resources/src/main/resources/pedigree/model/edgeOptimization.js
    M components/pedigree/resources/src/main/resources/pedigree/model/export.js
    M components/pedigree/resources/src/main/resources/pedigree/model/helpers.js
    M components/pedigree/resources/src/main/resources/pedigree/model/import.js
    M components/pedigree/resources/src/main/resources/pedigree/model/ordering.js
    M components/pedigree/resources/src/main/resources/pedigree/model/positionedGraph.js
    M components/pedigree/resources/src/main/resources/pedigree/model/queues.js
    M components/pedigree/resources/src/main/resources/pedigree/model/xcoordclass.js
    M components/pedigree/resources/src/main/resources/pedigree/pedigree.js
    A components/pedigree/resources/src/main/resources/pedigree/pedigreeApp.js
    M components/pedigree/resources/src/main/resources/pedigree/pedigreeDate.js
    A components/pedigree/resources/src/main/resources/pedigree/pedigreeEditorParameters.js
    M components/pedigree/resources/src/main/resources/pedigree/preferencesManager.js
    A components/pedigree/resources/src/main/resources/pedigree/probandDataLoader.js
    M components/pedigree/resources/src/main/resources/pedigree/saveLoadEngine.js
    R components/pedigree/resources/src/main/resources/pedigree/undoRedo.js
    A 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/abstractNodeVisuals.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/ageCalc.js
    M components/pedigree/resources/src/main/resources/pedigree/view/cancersLegend.js
    A components/pedigree/resources/src/main/resources/pedigree/view/childlessBehavior.js
    A components/pedigree/resources/src/main/resources/pedigree/view/childlessBehaviorVisuals.js
    M components/pedigree/resources/src/main/resources/pedigree/view/datepicker.js
    M components/pedigree/resources/src/main/resources/pedigree/view/disorderLegend.js
    M components/pedigree/resources/src/main/resources/pedigree/view/exportSelector.js
    M components/pedigree/resources/src/main/resources/pedigree/view/geneLegend.js
    M components/pedigree/resources/src/main/resources/pedigree/view/graphicHelpers.js
    M components/pedigree/resources/src/main/resources/pedigree/view/hpoLegend.js
    M components/pedigree/resources/src/main/resources/pedigree/view/importSelector.js
    M components/pedigree/resources/src/main/resources/pedigree/view/legend.js
    M components/pedigree/resources/src/main/resources/pedigree/view/lineSet.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/partnership.js
    M components/pedigree/resources/src/main/resources/pedigree/view/partnershipHoverbox.js
    M components/pedigree/resources/src/main/resources/pedigree/view/partnershipVisuals.js
    M components/pedigree/resources/src/main/resources/pedigree/view/person.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personGroup.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personGroupHoverbox.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personGroupVisuals.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personHoverbox.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personPlaceholder.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personPlaceholderVisuals.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personVisuals.js
    M components/pedigree/resources/src/main/resources/pedigree/view/readonlyHoverbox.js
    M components/pedigree/resources/src/main/resources/pedigree/view/saveLoadIndicator.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/PedigreeEditor.xml

  Log Message:
  -----------
  Issue #1870: Use RequireJS to load the pedigree files


  Commit: 5f85071d7124eb3f34a59274abfc29fba4c2fb30
      https://github.com/phenotips/phenotips/commit/5f85071d7124eb3f34a59274abfc29fba4c2fb30
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-08-28 (Fri, 28 Aug 2015)

  Changed paths:
    M components/pedigree/resources/src/main/resources/pedigree/disorder.js
    M components/pedigree/resources/src/main/resources/pedigree/editor.css
    M components/pedigree/resources/src/main/resources/pedigree/filesaver/FileSaver.js
    M components/pedigree/resources/src/main/resources/pedigree/model/baseGraph.js
    M components/pedigree/resources/src/main/resources/pedigree/model/edgeOptimization.js
    M components/pedigree/resources/src/main/resources/pedigree/model/positionedGraph.js
    M components/pedigree/resources/src/main/resources/pedigree/pedigree.js
    M components/pedigree/resources/src/main/resources/pedigree/pedigreeApp.js
    M components/pedigree/resources/src/main/resources/pedigree/pedigreeDate.js
    M components/pedigree/resources/src/main/resources/pedigree/versionUpdater.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/abstractNodeVisuals.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/disorderLegend.js
    M components/pedigree/resources/src/main/resources/pedigree/view/exportSelector.js
    M components/pedigree/resources/src/main/resources/pedigree/view/graphicHelpers.js
    M components/pedigree/resources/src/main/resources/pedigree/view/importSelector.js
    M components/pedigree/resources/src/main/resources/pedigree/view/legend.js
    M components/pedigree/resources/src/main/resources/pedigree/view/lineSet.js
    M components/pedigree/resources/src/main/resources/pedigree/view/nodeMenu.js
    M components/pedigree/resources/src/main/resources/pedigree/view/okCancelDialogue.js
    M components/pedigree/resources/src/main/resources/pedigree/view/partnership.js
    M components/pedigree/resources/src/main/resources/pedigree/view/partnershipHoverbox.js
    M components/pedigree/resources/src/main/resources/pedigree/view/partnershipVisuals.js
    M components/pedigree/resources/src/main/resources/pedigree/view/person.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personGroup.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personGroupHoverbox.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personHoverbox.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personPlaceholderHoverbox.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personVisuals.js
    M components/pedigree/resources/src/main/resources/pedigree/view/readonlyHoverbox.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:
  -----------
  Issue #1870: Errors in commit


  Commit: ff0e4f76b20ed74e8e5f4b6c88914b840249a16b
      https://github.com/phenotips/phenotips/commit/ff0e4f76b20ed74e8e5f4b6c88914b840249a16b
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-08-28 (Fri, 28 Aug 2015)

  Changed paths:
    M components/pedigree/resources/pom.xml
    A components/pedigree/resources/src/main/resources/pedigree/build.js
    A components/pedigree/resources/src/main/resources/pedigree/minified/pedigree.min.js
    M components/pedigree/resources/src/main/resources/pedigree/pedigreeApp.js
    A components/pedigree/resources/src/main/resources/pedigree/requireConfigs/optimizerConfig.js
    A components/pedigree/resources/src/main/resources/pedigree/requireConfigs/runtimeConfig.js
    M components/pedigree/ui/src/main/resources/PhenoTips/PedigreeEditor.xml

  Log Message:
  -----------
  Issue: Minify Pedigree


  Commit: 9eb561e388d6dcd0c63d6430472729b99d43c43c
      https://github.com/phenotips/phenotips/commit/9eb561e388d6dcd0c63d6430472729b99d43c43c
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-08-31 (Mon, 31 Aug 2015)

  Changed paths:
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/AllDataGadget.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/MyDataGadget.xml
    M components/users/ui/src/main/resources/PhenoTips/GroupsGadget.xml

  Log Message:
  -----------
  Issue #1769: Fixed build failure. Added parent to new xml files


  Commit: 67d4b062b7cdef6f3c225db3abe7fcf19018ed04
      https://github.com/phenotips/phenotips/commit/67d4b062b7cdef6f3c225db3abe7fcf19018ed04
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-08-31 (Mon, 31 Aug 2015)

  Changed paths:
    M components/pedigree/resources/pom.xml
    R components/pedigree/resources/src/main/resources/pedigree/build.js
    R components/pedigree/resources/src/main/resources/pedigree/minified/pedigree.min.js
    A components/pedigree/resources/src/main/resources/pedigree/requireConfigs/build.js

  Log Message:
  -----------
  PT-2007: Minify Pedigree -- Minified pedigree will not be created in src directory


  Commit: 138d2cc9503ab69aebb5cf647954def45521b0c1
      https://github.com/phenotips/phenotips/commit/138d2cc9503ab69aebb5cf647954def45521b0c1
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-09-11 (Fri, 11 Sep 2015)

  Changed paths:
    M components/patient-data/ui/src/main/resources/PhenoTips/PatientSheetCode.xml

  Log Message:
  -----------
  PT-2049: Remove yellow on-hover row highlight of a table. Fixed


  Commit: 1a195b8565f478181a70601c4dfbb874a967e2d2
      https://github.com/phenotips/phenotips/commit/1a195b8565f478181a70601c4dfbb874a967e2d2
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-18 (Fri, 18 Sep 2015)

  Changed paths:
    A components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  Merge branch 'DefaultPatientByExternalIdResourceImpl-tests' of https://github.com/JKereliuk/phenotips


  Commit: 62803ca8228e4024c221a795905f2d5cc20ed80c
      https://github.com/phenotips/phenotips/commit/62803ca8228e4024c221a795905f2d5cc20ed80c
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-18 (Fri, 18 Sep 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientByExternalIdResourceImplTest.java

  Log Message:
  -----------
  [cleanup] Applied codestyle


  Commit: 6ecc33959067337e75a8905633580d3eec7e785a
      https://github.com/phenotips/phenotips/commit/6ecc33959067337e75a8905633580d3eec7e785a
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-19 (Sat, 19 Sep 2015)

  Changed paths:
    M components/vocabularies/hpo/ui/src/main/resources/PhenoTips/HPOBranchDisplayer.xml

  Log Message:
  -----------
  PT-2065: JS errors related to bad CSS selectors triggered when editing patient records
Fixed


  Commit: 160dcdf3d4912e838b46035315d3df3c6b210fee
      https://github.com/phenotips/phenotips/commit/160dcdf3d4912e838b46035315d3df3c6b210fee
  Author: Sergiu Dumitriu <sdumitriu at users.noreply.github.com>
  Date:   2015-09-20 (Sun, 20 Sep 2015)

  Changed paths:
    A components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/ConfigureISODatesInJsonTest.java
    A components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  Merge pull request #1802 from DeanWay/rest-patient-resource-test

Patient data REST api tests (ConfigureISODatesInJson and DefaultPatientResourceImpl)


  Commit: f7ba03887837c52214a76751b433769ac3b43191
      https://github.com/phenotips/phenotips/commit/f7ba03887837c52214a76751b433769ac3b43191
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-21 (Mon, 21 Sep 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  [cleanup] Applied codestyle


  Commit: 2d3bba5d5eda8e7685efed9f61044c36d305c3e4
      https://github.com/phenotips/phenotips/commit/2d3bba5d5eda8e7685efed9f61044c36d305c3e4
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-21 (Mon, 21 Sep 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  [cleanup] Improved method names


  Commit: 074f43abd329c5f2d13ccd1ce48f71135834c878
      https://github.com/phenotips/phenotips/commit/074f43abd329c5f2d13ccd1ce48f71135834c878
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-21 (Mon, 21 Sep 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientResourceImplTest.java

  Log Message:
  -----------
  [cleanup] Removed unnecessary tests


  Commit: a3483666d53591720930223be111fce1fcc794b9
      https://github.com/phenotips/phenotips/commit/a3483666d53591720930223be111fce1fcc794b9
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-22 (Tue, 22 Sep 2015)

  Changed paths:
    M components/patient-data/impl/src/main/java/org/phenotips/data/internal/controller/PrenatalPerinatalHistoryController.java
    M components/patient-data/ui/src/main/resources/PhenoTips/PatientClass.xml
    M components/patient-data/ui/src/main/resources/PhenoTips/UIX_Field__multiple_gestation.xml
    M components/widgets/ui/src/main/resources/PhenoTips/Widgets.xml

  Log Message:
  -----------
  PT-2066: Add support for recording which twin (A/B) the current patient is
PT-2067: Allow using Y/N/NA pickers for controlling the "controlled groups" widget
Done


  Commit: f16e39c683e7bea0d36b3c5340c02cd3114d5d1d
      https://github.com/phenotips/phenotips/commit/f16e39c683e7bea0d36b3c5340c02cd3114d5d1d
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-22 (Tue, 22 Sep 2015)

  Changed paths:
    M components/widgets/ui/src/main/resources/PhenoTips/Widgets.xml
    M components/widgets/ui/src/main/resources/PhenoTips/YesNoNAPicker.xml

  Log Message:
  -----------
  [cleanup] Sync xobjects with their xclasses


  Commit: 77896d37497e9a617282fe1d8830aed2b5d7078b
      https://github.com/phenotips/phenotips/commit/77896d37497e9a617282fe1d8830aed2b5d7078b
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2015-09-22 (Tue, 22 Sep 2015)

  Changed paths:
    M components/patient-data/ui/src/main/resources/PhenoTips/PatientSheetCode.xml

  Log Message:
  -----------
  PT-2049: Remove yellow on-hover row highlight of a table. Removed commented code.


  Commit: 57fd69046e9c5a921599a24e66102ec4d554b6f7
      https://github.com/phenotips/phenotips/commit/57fd69046e9c5a921599a24e66102ec4d554b6f7
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-23 (Wed, 23 Sep 2015)

  Changed paths:
    M components/patient-data/ui/src/main/resources/PhenoTips/AllergiesDataClass.xml

  Log Message:
  -----------
  PT-2074: Inconsistent indentation in the Allergies list
Fixed


  Commit: e737e178bda38d3e59778738c9580b7cb86d2dc2
      https://github.com/phenotips/phenotips/commit/e737e178bda38d3e59778738c9580b7cb86d2dc2
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2015-09-24 (Thu, 24 Sep 2015)

  Changed paths:
    M components/pedigree/resources/src/main/resources/pedigree/editor.css
    M components/pedigree/resources/src/main/resources/pedigree/view/ageCalc.js
    M components/pedigree/resources/src/main/resources/pedigree/view/nodeMenu.js

  Log Message:
  -----------
  PT-1917: Updated cancer section in the pedigre editor (some rewordings, added "none of the above" button).


  Commit: 59b5f9cae8c2c408c70c05929a624431a700a3b7
      https://github.com/phenotips/phenotips/commit/59b5f9cae8c2c408c70c05929a624431a700a3b7
  Author: Sergiu Dumitriu <sdumitriu at users.noreply.github.com>
  Date:   2015-09-24 (Thu, 24 Sep 2015)

  Changed paths:
    M components/pedigree/resources/src/main/resources/pedigree/editor.css
    M components/pedigree/resources/src/main/resources/pedigree/view/ageCalc.js
    M components/pedigree/resources/src/main/resources/pedigree/view/nodeMenu.js

  Log Message:
  -----------
  Merge pull request #1893 from phenotips/issue-1859

PT-1917: Updated cancer section in the pedigree editor


  Commit: 99b2b170b2753c43356a99c9bd6f2d286576ac49
      https://github.com/phenotips/phenotips/commit/99b2b170b2753c43356a99c9bd6f2d286576ac49
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-25 (Fri, 25 Sep 2015)

  Changed paths:
    M distribution/hsqldb-database/pom.xml

  Log Message:
  -----------
  PT-2077: The ability to push patients to another server is no longer available
Fixed


  Commit: 62644cf93f85cee243820dab2d02857ab84bc084
      https://github.com/phenotips/phenotips/commit/62644cf93f85cee243820dab2d02857ab84bc084
  Author: Sergiu Dumitriu <sdumitriu at users.noreply.github.com>
  Date:   2015-09-25 (Fri, 25 Sep 2015)

  Changed paths:
    M components/patient-data/ui/src/main/resources/PhenoTips/PatientSheetCode.xml

  Log Message:
  -----------
  Merge pull request #1888 from veronikaslc/PT-2049

PT-2049: Remove yellow on-hover row highlight of a table


  Commit: 04bd63a3f65ab4b240177e9a5ab7e6f68435db26
      https://github.com/phenotips/phenotips/commit/04bd63a3f65ab4b240177e9a5ab7e6f68435db26
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-26 (Sat, 26 Sep 2015)

  Changed paths:
    A components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  Merge branch 'master' of https://github.com/tmarathe/phenotips


  Commit: 52d339924f1fe94cd7c1a7391f1ed9d323c9a44f
      https://github.com/phenotips/phenotips/commit/52d339924f1fe94cd7c1a7391f1ed9d323c9a44f
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-26 (Sat, 26 Sep 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  [cleanup] Applied codestyle


  Commit: 1681a46ae08ef5c75336eb8f4c10482064be6230
      https://github.com/phenotips/phenotips/commit/1681a46ae08ef5c75336eb8f4c10482064be6230
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-26 (Sat, 26 Sep 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/DefaultPatientsResourceImplTest.java

  Log Message:
  -----------
  [misc] Fixed bad test


  Commit: 39477c4d004d15acff7abeb2e4dd77031c7c3a68
      https://github.com/phenotips/phenotips/commit/39477c4d004d15acff7abeb2e4dd77031c7c3a68
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-26 (Sat, 26 Sep 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/ConfigureISODatesInJsonTest.java

  Log Message:
  -----------
  [cleanup] Applied codestyle


  Commit: c97bab61fbc5c8183c4b741dc1527a5e01df3f0b
      https://github.com/phenotips/phenotips/commit/c97bab61fbc5c8183c4b741dc1527a5e01df3f0b
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-26 (Sat, 26 Sep 2015)

  Changed paths:
    M components/patient-data/rest/src/test/java/org/phenotips/data/rest/internal/ConfigureISODatesInJsonTest.java

  Log Message:
  -----------
  [misc] Rewrite test so that it doesn't alter the Restlet engine, since other tests require a valid engine


  Commit: a81720eed5ccd72aee26a688bdc2544e40cff643
      https://github.com/phenotips/phenotips/commit/a81720eed5ccd72aee26a688bdc2544e40cff643
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-26 (Sat, 26 Sep 2015)

  Changed paths:
    M components/pedigree/resources/src/main/resources/pedigree/controller.js
    M components/pedigree/resources/src/main/resources/pedigree/disorder.js
    M components/pedigree/resources/src/main/resources/pedigree/editor.css
    M components/pedigree/resources/src/main/resources/pedigree/filesaver/FileSaver.js
    M components/pedigree/resources/src/main/resources/pedigree/hpoTerm.js
    M components/pedigree/resources/src/main/resources/pedigree/model/baseGraph.js
    M components/pedigree/resources/src/main/resources/pedigree/model/dynamicGraph.js
    M components/pedigree/resources/src/main/resources/pedigree/model/edgeOptimization.js
    M components/pedigree/resources/src/main/resources/pedigree/model/export.js
    M components/pedigree/resources/src/main/resources/pedigree/model/helpers.js
    M components/pedigree/resources/src/main/resources/pedigree/model/import.js
    M components/pedigree/resources/src/main/resources/pedigree/model/ordering.js
    M components/pedigree/resources/src/main/resources/pedigree/model/positionedGraph.js
    M components/pedigree/resources/src/main/resources/pedigree/model/queues.js
    M components/pedigree/resources/src/main/resources/pedigree/model/xcoordclass.js
    M components/pedigree/resources/src/main/resources/pedigree/pedigree.js
    A components/pedigree/resources/src/main/resources/pedigree/pedigreeApp.js
    M components/pedigree/resources/src/main/resources/pedigree/pedigreeDate.js
    A components/pedigree/resources/src/main/resources/pedigree/pedigreeEditorParameters.js
    M components/pedigree/resources/src/main/resources/pedigree/preferencesManager.js
    A components/pedigree/resources/src/main/resources/pedigree/probandDataLoader.js
    M components/pedigree/resources/src/main/resources/pedigree/saveLoadEngine.js
    R components/pedigree/resources/src/main/resources/pedigree/undoRedo.js
    A 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/abstractNodeVisuals.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/ageCalc.js
    M components/pedigree/resources/src/main/resources/pedigree/view/cancersLegend.js
    A components/pedigree/resources/src/main/resources/pedigree/view/childlessBehavior.js
    A components/pedigree/resources/src/main/resources/pedigree/view/childlessBehaviorVisuals.js
    M components/pedigree/resources/src/main/resources/pedigree/view/datepicker.js
    M components/pedigree/resources/src/main/resources/pedigree/view/disorderLegend.js
    M components/pedigree/resources/src/main/resources/pedigree/view/exportSelector.js
    M components/pedigree/resources/src/main/resources/pedigree/view/geneLegend.js
    M components/pedigree/resources/src/main/resources/pedigree/view/graphicHelpers.js
    M components/pedigree/resources/src/main/resources/pedigree/view/hpoLegend.js
    M components/pedigree/resources/src/main/resources/pedigree/view/importSelector.js
    M components/pedigree/resources/src/main/resources/pedigree/view/legend.js
    M components/pedigree/resources/src/main/resources/pedigree/view/lineSet.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/partnership.js
    M components/pedigree/resources/src/main/resources/pedigree/view/partnershipHoverbox.js
    M components/pedigree/resources/src/main/resources/pedigree/view/partnershipVisuals.js
    M components/pedigree/resources/src/main/resources/pedigree/view/person.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personGroup.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personGroupHoverbox.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personGroupVisuals.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personHoverbox.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personPlaceholder.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personPlaceholderHoverbox.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personPlaceholderVisuals.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personVisuals.js
    M components/pedigree/resources/src/main/resources/pedigree/view/readonlyHoverbox.js
    M components/pedigree/resources/src/main/resources/pedigree/view/saveLoadIndicator.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/PedigreeEditor.xml

  Log Message:
  -----------
  Merge branch 'Issue-#1870' of https://github.com/mjshepherd/phenotips


  Commit: d2c3ae9b091abe5ad6d725aa39d934bdd6eacb82
      https://github.com/phenotips/phenotips/commit/d2c3ae9b091abe5ad6d725aa39d934bdd6eacb82
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-27 (Sun, 27 Sep 2015)

  Changed paths:
    M components/pedigree/resources/src/main/resources/pedigree/pedigreeEditorParameters.js
    M components/pedigree/resources/src/main/resources/pedigree/view/person.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personVisuals.js
    M components/pedigree/resources/src/main/resources/pedigree/view/templateSelector.js

  Log Message:
  -----------
  [misc] Re-commit changes lost when rewriting the pedigree using require.js


  Commit: 61153434e95dc8f86c68e080fd3de64ab352e102
      https://github.com/phenotips/phenotips/commit/61153434e95dc8f86c68e080fd3de64ab352e102
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-27 (Sun, 27 Sep 2015)

  Changed paths:
    M components/pedigree/resources/src/main/resources/pedigree/pedigreeEditorParameters.js
    M components/pedigree/resources/src/main/resources/pedigree/view/nodeMenu.js
    M components/pedigree/resources/src/main/resources/pedigree/view/personVisuals.js

  Log Message:
  -----------
  [cleanup] Fixed indentation + typos


  Commit: c6830dc197c3b157d054686d1eed10593791c95f
      https://github.com/phenotips/phenotips/commit/c6830dc197c3b157d054686d1eed10593791c95f
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-09-28 (Mon, 28 Sep 2015)

  Changed paths:
    M components/widgets/ui/src/main/resources/PhenoTips/Widgets.xml

  Log Message:
  -----------
  PT-2059: "Enter" should accept first phenotype suggestion


  Commit: 0afba38623647f22ba008d3adc8030d23f402c02
      https://github.com/phenotips/phenotips/commit/0afba38623647f22ba008d3adc8030d23f402c02
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-09-28 (Mon, 28 Sep 2015)

  Changed paths:
    M components/widgets/ui/src/main/resources/PhenoTips/Widgets.xml

  Log Message:
  -----------
  PT-2058: Phenotype search should regain focus after selecting suggestion


  Commit: 3e2d952735710fe17064c8a5e00265341eb774c9
      https://github.com/phenotips/phenotips/commit/3e2d952735710fe17064c8a5e00265341eb774c9
  Author: Sergiu Dumitriu <sdumitriu at users.noreply.github.com>
  Date:   2015-09-28 (Mon, 28 Sep 2015)

  Changed paths:
    M components/widgets/ui/src/main/resources/PhenoTips/Widgets.xml

  Log Message:
  -----------
  Merge pull request #1895 from mjshepherd/PT-2058

PT-2058: Phenotype search should regain focus after selecting suggestion


  Commit: 19b255fdb156a95ca78989f5f3edc01c20e0260b
      https://github.com/phenotips/phenotips/commit/19b255fdb156a95ca78989f5f3edc01c20e0260b
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-09-28 (Mon, 28 Sep 2015)

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

  Log Message:
  -----------
  PT-2080: Unable to add notes on "affected" cancer after reload if notes field was blank before reload


  Commit: 8ece64f8b770c650617b004cb2f71e779709ddcf
      https://github.com/phenotips/phenotips/commit/8ece64f8b770c650617b004cb2f71e779709ddcf
  Author: Sergiu Dumitriu <sdumitriu at users.noreply.github.com>
  Date:   2015-09-28 (Mon, 28 Sep 2015)

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

  Log Message:
  -----------
  Merge pull request #1896 from mjshepherd/PT-2080

PT-2080: Unable to add notes on "affected" cancer after reload if notes field was blank before reload


  Commit: 03ba221906d62a01ac93a6d491d8d517653a0470
      https://github.com/phenotips/phenotips/commit/03ba221906d62a01ac93a6d491d8d517653a0470
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-29 (Tue, 29 Sep 2015)

  Changed paths:
    M pom.xml

  Log Message:
  -----------
  PT-2083: Upgrade to Solr 5.3.1
Done


  Commit: 3b2f1ca049775cbdc4ee4b064d04f80320756820
      https://github.com/phenotips/phenotips/commit/3b2f1ca049775cbdc4ee4b064d04f80320756820
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-09-30 (Wed, 30 Sep 2015)

  Changed paths:
    M components/patient-data/ui/src/main/resources/PhenoTips/PatientSheetCode.xml
    M components/widgets/ui/src/main/resources/PhenoTips/Widgets.xml

  Log Message:
  -----------
  PT-2084: Enter should accept the selected suggestion
Done


  Commit: 784bd09b3c96d648af7f2d8bd9969bdb4d4dbacb
      https://github.com/phenotips/phenotips/commit/784bd09b3c96d648af7f2d8bd9969bdb4d4dbacb
  Author: Sergiu Dumitriu <sdumitriu at users.noreply.github.com>
  Date:   2015-09-30 (Wed, 30 Sep 2015)

  Changed paths:
    M components/widgets/ui/src/main/resources/PhenoTips/Widgets.xml

  Log Message:
  -----------
  Merge pull request #1894 from mjshepherd/PT-2059

PT-2059: "Enter" should accept first phenotype suggestion


  Commit: 69d199eb6d6df5928fef6392719c8c51cba440c8
      https://github.com/phenotips/phenotips/commit/69d199eb6d6df5928fef6392719c8c51cba440c8
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-01 (Thu, 01 Oct 2015)

  Changed paths:
    M pom.xml

  Log Message:
  -----------
  [misc] Update dependencies


  Commit: 936825849cb92ba7da46598d633a9f0855af5e59
      https://github.com/phenotips/phenotips/commit/936825849cb92ba7da46598d633a9f0855af5e59
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-01 (Thu, 01 Oct 2015)

  Changed paths:
    M pom.xml

  Log Message:
  -----------
  [misc] Update main class declaration after changing packages


  Commit: 303b092b0e28e0d09c717dc5eed6555c3d0246a5
      https://github.com/phenotips/phenotips/commit/303b092b0e28e0d09c717dc5eed6555c3d0246a5
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-01 (Thu, 01 Oct 2015)

  Changed paths:
    A .gitattributes
    A .gitignore

  Log Message:
  -----------
  [misc] Added git configuration files


  Commit: ba568daebc5a43e0a6700567dfe62fe71ef38e0c
      https://github.com/phenotips/phenotips/commit/ba568daebc5a43e0a6700567dfe62fe71ef38e0c
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-01 (Thu, 01 Oct 2015)

  Changed paths:
    M data/en_product1.xml
    R data/en_product2.xml
    A data/en_product2_prev.xml
    M data/negative_phenotype_annotation.tab
    M data/phenotype_annotation.tab

  Log Message:
  -----------
  [misc] Update data files


  Commit: 529978bdfc538ba8214944c79142394edafc2c5f
      https://github.com/phenotips/phenotips/commit/529978bdfc538ba8214944c79142394edafc2c5f
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-02 (Fri, 02 Oct 2015)

  Changed paths:
    M pom.xml

  Log Message:
  -----------
  [misc] Start bringing the omim indexer closer to being merged with the main PhenoTips codebase


  Commit: 65d63957ea3aaee33193a8890fdef73762f68b3a
      https://github.com/phenotips/phenotips/commit/65d63957ea3aaee33193a8890fdef73762f68b3a
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-02 (Fri, 02 Oct 2015)

  Changed paths:
    M src/main/java/org/phenotips/oo/OmimSourceParser.java

  Log Message:
  -----------
  [cleanup] Use try-with-resources


  Commit: 14d3fed9c8c9eacd5fb7632471f3e4dd1a1ffdd6
      https://github.com/phenotips/phenotips/commit/14d3fed9c8c9eacd5fb7632471f3e4dd1a1ffdd6
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-02 (Fri, 02 Oct 2015)

  Changed paths:
    M src/main/java/org/phenotips/oo/DisorderDataBuilder.java
    M src/main/java/org/phenotips/oo/Main.java
    M src/main/java/org/phenotips/oo/RecordData.java
    M src/main/java/org/phenotips/oo/TSVParser.java
    M src/main/java/org/phenotips/util/maps/AbstractCollectionMap.java
    M src/main/java/org/phenotips/util/maps/AbstractMapOperator.java
    M src/main/java/org/phenotips/util/maps/AbstractNumericValueMap.java
    M src/main/java/org/phenotips/util/maps/ListMap.java
    M src/main/java/org/phenotips/util/maps/NumericValueMap.java
    M src/main/java/org/phenotips/util/maps/SetMap.java

  Log Message:
  -----------
  [cleanup] Applied codestyle


  Commit: fc0db3273520f9d84a9eb8d187179c8c5478621a
      https://github.com/phenotips/phenotips/commit/fc0db3273520f9d84a9eb8d187179c8c5478621a
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-02 (Fri, 02 Oct 2015)

  Changed paths:
    M src/main/java/org/phenotips/oo/OOSaxParser.java

  Log Message:
  -----------
  [cleanup] Removed unneeded method


  Commit: 891ad56b60f0defe3da3d7975395c880bbc18833
      https://github.com/phenotips/phenotips/commit/891ad56b60f0defe3da3d7975395c880bbc18833
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-02 (Fri, 02 Oct 2015)

  Changed paths:
    R src/main/java/org/phenotips/oo/OmimDBBuilder.java

  Log Message:
  -----------
  [cleanup] Removed unused class


  Commit: 377b916343b3717755fa25d35204f56a392f2d49
      https://github.com/phenotips/phenotips/commit/377b916343b3717755fa25d35204f56a392f2d49
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-02 (Fri, 02 Oct 2015)

  Changed paths:
    M src/main/java/org/phenotips/oo/RecordData.java
    R src/main/java/org/phenotips/util/maps/AbstractCollectionMap.java
    R src/main/java/org/phenotips/util/maps/AbstractMapOperator.java
    R src/main/java/org/phenotips/util/maps/AbstractNumericValueMap.java
    R src/main/java/org/phenotips/util/maps/AddMapOperator.java
    R src/main/java/org/phenotips/util/maps/CounterMap.java
    R src/main/java/org/phenotips/util/maps/DivideMapOperator.java
    R src/main/java/org/phenotips/util/maps/DoubleMap.java
    R src/main/java/org/phenotips/util/maps/IntegerMap.java
    R src/main/java/org/phenotips/util/maps/IntegerSumMap.java
    R src/main/java/org/phenotips/util/maps/ListMap.java
    R src/main/java/org/phenotips/util/maps/MapOperator.java
    R src/main/java/org/phenotips/util/maps/MultiplyMapOperator.java
    R src/main/java/org/phenotips/util/maps/NumericValueMap.java
    R src/main/java/org/phenotips/util/maps/SetMap.java
    R src/main/java/org/phenotips/util/maps/SubtractMapOperator.java
    R src/main/java/org/phenotips/util/maps/SumMap.java

  Log Message:
  -----------
  [cleanup] Removed classes already present in a dependency


  Commit: a0b3229eec183aa39e50ba343902b79e4795d73b
      https://github.com/phenotips/phenotips/commit/a0b3229eec183aa39e50ba343902b79e4795d73b
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-02 (Fri, 02 Oct 2015)

  Changed paths:
    M src/main/java/org/phenotips/oo/DisorderData.java
    M src/main/java/org/phenotips/oo/DisorderDataBuilder.java
    M src/main/java/org/phenotips/oo/Main.java
    M src/main/java/org/phenotips/oo/OOSaxParser.java
    M src/main/java/org/phenotips/oo/OmimSourceParser.java
    M src/main/java/org/phenotips/oo/RecordData.java
    M src/main/java/org/phenotips/oo/TSVParser.java

  Log Message:
  -----------
  [cleanup] Added license headers


  Commit: f0ed7e1988fadd34819d535129e56fb447f1c55f
      https://github.com/phenotips/phenotips/commit/f0ed7e1988fadd34819d535129e56fb447f1c55f
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2015-10-03 (Sat, 03 Oct 2015)

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

  Log Message:
  -----------
  PT-2089: In pedigree BOADICEA export non-monozyg. twins are exported as siblings


  Commit: 8b757b8d35124d7053c50a98777898acc731bdc4
      https://github.com/phenotips/phenotips/commit/8b757b8d35124d7053c50a98777898acc731bdc4
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-03 (Sat, 03 Oct 2015)

  Changed paths:
    M src/main/java/org/phenotips/oo/OmimSourceParser.java

  Log Message:
  -----------
  [cleanup] Improved codestyle


  Commit: 3f2ffc8acaf5fb5734e775ff02adbb2d9faba3e3
      https://github.com/phenotips/phenotips/commit/3f2ffc8acaf5fb5734e775ff02adbb2d9faba3e3
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2015-10-04 (Sun, 04 Oct 2015)

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

  Log Message:
  -----------
  PT-2087: In pedigree editor comments box appears on all tabs of a node's menu


  Commit: 8440fd4165ad153d1e2df3857901d27b568e89be
      https://github.com/phenotips/phenotips/commit/8440fd4165ad153d1e2df3857901d27b568e89be
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-04 (Sun, 04 Oct 2015)

  Changed paths:
    M components/pedigree/resources/pom.xml
    M components/pedigree/resources/src/main/resources/pedigree/pedigreeApp.js
    A components/pedigree/resources/src/main/resources/pedigree/requireConfigs/build.js
    A components/pedigree/resources/src/main/resources/pedigree/requireConfigs/optimizerConfig.js
    A components/pedigree/resources/src/main/resources/pedigree/requireConfigs/runtimeConfig.js
    M components/pedigree/ui/src/main/resources/PhenoTips/PedigreeEditor.xml

  Log Message:
  -----------
  Merge branch 'minifyPedigree' of https://github.com/mjshepherd/phenotips


  Commit: 609b4a66034667198e0596b0a40ff199c1ace351
      https://github.com/phenotips/phenotips/commit/609b4a66034667198e0596b0a40ff199c1ace351
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-04 (Sun, 04 Oct 2015)

  Changed paths:
    M components/pedigree/resources/pom.xml

  Log Message:
  -----------
  [cleanup] Improve build configuration codestyle


  Commit: 28293d0b66533dc22c80382d0e562c14c3349ef1
      https://github.com/phenotips/phenotips/commit/28293d0b66533dc22c80382d0e562c14c3349ef1
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-05 (Mon, 05 Oct 2015)

  Changed paths:
    M components/pedigree/resources/pom.xml
    A components/pedigree/resources/src/main/build/build.js
    A components/pedigree/resources/src/main/build/optimizerConfig.js
    R components/pedigree/resources/src/main/resources/pedigree/requireConfigs/build.js
    R components/pedigree/resources/src/main/resources/pedigree/requireConfigs/optimizerConfig.js

  Log Message:
  -----------
  PT-2007: Minify Pedigree
Better location for build configuration resources


  Commit: 0e451e62944d9561b6349538dd0549c815a11a83
      https://github.com/phenotips/phenotips/commit/0e451e62944d9561b6349538dd0549c815a11a83
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-05 (Mon, 05 Oct 2015)

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

  Log Message:
  -----------
  PT-2087: The comments box should appear in all tabs of a node's menu
Fixed typo which cased JS errors and misbehaving comments field in the Cencers tab


  Commit: dca3972cb2a2a0f792cd016c58b3c91c771a7a85
      https://github.com/phenotips/phenotips/commit/dca3972cb2a2a0f792cd016c58b3c91c771a7a85
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-05 (Mon, 05 Oct 2015)

  Changed paths:
    M pom.xml
    M src/main/java/org/phenotips/oo/Main.java
    M src/main/java/org/phenotips/oo/OmimSourceParser.java
    M src/main/java/org/phenotips/oo/TSVParser.java

  Log Message:
  -----------
  [misc] Use online resources for indexing
+ removed prelevance information from the index, since it is no longer useful


  Commit: 9ca27ee46f18a72f88ae835a6fa7c6c927d154b0
      https://github.com/phenotips/phenotips/commit/9ca27ee46f18a72f88ae835a6fa7c6c927d154b0
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-05 (Mon, 05 Oct 2015)

  Changed paths:
    R src/main/java/org/phenotips/oo/DisorderData.java
    R src/main/java/org/phenotips/oo/DisorderDataBuilder.java
    R src/main/java/org/phenotips/oo/OOSaxParser.java
    R src/main/java/org/phenotips/oo/RecordData.java

  Log Message:
  -----------
  [cleanup] Removed legacy sources


  Commit: 9a766fa7b6277ad028e1691a920eec22fd5e7f92
      https://github.com/phenotips/phenotips/commit/9a766fa7b6277ad028e1691a920eec22fd5e7f92
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-05 (Mon, 05 Oct 2015)

  Changed paths:
    M src/main/java/org/phenotips/oo/Main.java

  Log Message:
  -----------
  [misc] store the full link to genereviews for backwards compatibility


  Commit: a083706b6ca523cf79c544da53b03cd345fd10c5
      https://github.com/phenotips/phenotips/commit/a083706b6ca523cf79c544da53b03cd345fd10c5
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-05 (Mon, 05 Oct 2015)

  Changed paths:
    M src/main/java/org/phenotips/oo/Main.java

  Log Message:
  -----------
  [cleanup] Define more constants


  Commit: 0f8b7045065274e01a1d1f0cb399d037ad2b4791
      https://github.com/phenotips/phenotips/commit/0f8b7045065274e01a1d1f0cb399d037ad2b4791
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-05 (Mon, 05 Oct 2015)

  Changed paths:
    M src/main/java/org/phenotips/oo/Main.java
    R src/main/java/org/phenotips/oo/TSVParser.java

  Log Message:
  -----------
  [cleanup] Use commons-csv for parsing mim2gene instead of a custom class


  Commit: 2a98ec846698777c1762cbcb2c19400658921072
      https://github.com/phenotips/phenotips/commit/2a98ec846698777c1762cbcb2c19400658921072
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-05 (Mon, 05 Oct 2015)

  Changed paths:
    M pom.xml

  Log Message:
  -----------
  [misc] Fixed dependencies


  Commit: a518c7f0c8861907af9ad9412500781a62fbaf64
      https://github.com/phenotips/phenotips/commit/a518c7f0c8861907af9ad9412500781a62fbaf64
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-05 (Mon, 05 Oct 2015)

  Changed paths:
    M src/main/java/org/phenotips/oo/Main.java
    M src/main/java/org/phenotips/oo/OmimSourceParser.java

  Log Message:
  -----------
  [misc] Move all loading code into one class


  Commit: 971937b9670843ebb26454cd3af5e443caf7aac0
      https://github.com/phenotips/phenotips/commit/971937b9670843ebb26454cd3af5e443caf7aac0
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-05 (Mon, 05 Oct 2015)

  Changed paths:
    M src/main/java/org/phenotips/oo/OmimSourceParser.java

  Log Message:
  -----------
  [cleanup] Removed code duplication


  Commit: 9bbae9241c2b70fe87e300da4d159268ae53ee67
      https://github.com/phenotips/phenotips/commit/9bbae9241c2b70fe87e300da4d159268ae53ee67
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-06 (Tue, 06 Oct 2015)

  Changed paths:
    R data/en_product1.xml
    R data/en_product2_prev.xml
    R data/negative_phenotype_annotation.tab
    R data/omim_prelevance.txt
    R data/phenotype_annotation.tab

  Log Message:
  -----------
  [misc] Removed local data


  Commit: 6c3847f766925153f0e63f0ee18ceb7c6450e4a7
      https://github.com/phenotips/phenotips/commit/6c3847f766925153f0e63f0ee18ceb7c6450e4a7
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-06 (Tue, 06 Oct 2015)

  Changed paths:
    M src/main/java/org/phenotips/oo/OmimSourceParser.java

  Log Message:
  -----------
  [cleanup] Applied codestyle, use a proper logger


  Commit: c967c448f1170d88c54a45488edd9d4f755ecaf3
      https://github.com/phenotips/phenotips/commit/c967c448f1170d88c54a45488edd9d4f755ecaf3
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-06 (Tue, 06 Oct 2015)

  Changed paths:
    A components/vocabularies/omim/api/src/main/java/org/phenotips/oo/Main.java
    A components/vocabularies/omim/api/src/main/java/org/phenotips/oo/OmimSourceParser.java
    R src/main/java/org/phenotips/oo/Main.java
    R src/main/java/org/phenotips/oo/OmimSourceParser.java

  Log Message:
  -----------
  [misc] Move classes in the right place


  Commit: 96f30c6c4371136b6efd480e179deaf75d502155
      https://github.com/phenotips/phenotips/commit/96f30c6c4371136b6efd480e179deaf75d502155
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-06 (Tue, 06 Oct 2015)

  Changed paths:
    R .gitattributes
    R .gitignore
    R components/vocabularies/omim/api/src/main/java/org/phenotips/oo/Main.java
    R pom.xml

  Log Message:
  -----------
  [misc] Prepare for merging: deleted files that won't be needed anymore


  Commit: cd18a265d5e7af220dfabddd2208c92ba1d3aa05
      https://github.com/phenotips/phenotips/commit/cd18a265d5e7af220dfabddd2208c92ba1d3aa05
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-06 (Tue, 06 Oct 2015)

  Changed paths:
    A components/vocabularies/omim/api/src/main/java/org/phenotips/oo/OmimSourceParser.java

  Log Message:
  -----------
  Merge orphanet-omim


  Commit: baa30a5a02c6f879d12f0a8426932299e1bbe6bf
      https://github.com/phenotips/phenotips/commit/baa30a5a02c6f879d12f0a8426932299e1bbe6bf
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-06 (Tue, 06 Oct 2015)

  Changed paths:
    M components/vocabularies/omim/api/pom.xml

  Log Message:
  -----------
  [misc] Declared the used dependencies


  Commit: d4c2b1e16139f7eff7714c7b78b3a93e2dc56c93
      https://github.com/phenotips/phenotips/commit/d4c2b1e16139f7eff7714c7b78b3a93e2dc56c93
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-06 (Tue, 06 Oct 2015)

  Changed paths:
    M components/vocabularies/omim/api/src/main/java/org/phenotips/oo/OmimSourceParser.java
    M components/vocabularies/omim/api/src/main/java/org/phenotips/vocabulary/internal/solr/MendelianInheritanceInMan.java

  Log Message:
  -----------
  PT-497: Add the possibility to reindex OMIM from the administration
First step, phenotype ancestors aren't included yet


  Commit: d537992b9b7db449058bac58c9272048c5f426f3
      https://github.com/phenotips/phenotips/commit/d537992b9b7db449058bac58c9272048c5f426f3
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-06 (Tue, 06 Oct 2015)

  Changed paths:
    M components/vocabularies/omim/api/src/main/java/org/phenotips/oo/OmimSourceParser.java

  Log Message:
  -----------
  [cleanup] Added javadoc


  Commit: 4654b0ff1257f52f15f5be7fab7d758c2aa91ef4
      https://github.com/phenotips/phenotips/commit/4654b0ff1257f52f15f5be7fab7d758c2aa91ef4
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-06 (Tue, 06 Oct 2015)

  Changed paths:
    M components/vocabularies/omim/api/src/main/java/org/phenotips/oo/OmimSourceParser.java
    M components/vocabularies/omim/api/src/main/java/org/phenotips/vocabulary/internal/solr/MendelianInheritanceInMan.java

  Log Message:
  -----------
  [cleanup] Don't expose more information than needed


  Commit: b2612e105b00060721225fd10e9f9f92d9bd8fa6
      https://github.com/phenotips/phenotips/commit/b2612e105b00060721225fd10e9f9f92d9bd8fa6
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-06 (Tue, 06 Oct 2015)

  Changed paths:
    M components/vocabularies/omim/api/src/main/java/org/phenotips/oo/OmimSourceParser.java
    M components/vocabularies/omim/api/src/main/java/org/phenotips/vocabulary/internal/solr/MendelianInheritanceInMan.java

  Log Message:
  -----------
  PT-497: Add the possibility to reindex OMIM from the administration
Phenotype ancestors are now indexed as well


  Commit: dd24e0551a920d4fca372a6f0eae74c237dad7ca
      https://github.com/phenotips/phenotips/commit/dd24e0551a920d4fca372a6f0eae74c237dad7ca
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-06 (Tue, 06 Oct 2015)

  Changed paths:
    M components/vocabularies/omim/api/src/main/java/org/phenotips/oo/OmimSourceParser.java
    M components/vocabularies/omim/api/src/main/java/org/phenotips/vocabulary/internal/solr/MendelianInheritanceInMan.java

  Log Message:
  -----------
  PT-497: Add the possibility to reindex OMIM from the administration
Allow specifying the location of the OMIM source


  Commit: 69f6915de406876517e65bc1674f588ce4b3aefb
      https://github.com/phenotips/phenotips/commit/69f6915de406876517e65bc1674f588ce4b3aefb
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-06 (Tue, 06 Oct 2015)

  Changed paths:
    R components/vocabularies/omim/api/src/main/java/org/phenotips/oo/OmimSourceParser.java
    M components/vocabularies/omim/api/src/main/java/org/phenotips/vocabulary/internal/solr/MendelianInheritanceInMan.java
    A components/vocabularies/omim/api/src/main/java/org/phenotips/vocabulary/internal/solr/OmimSourceParser.java

  Log Message:
  -----------
  [cleanup] Moved class in the right package


  Commit: 0ba45d948338473493a94faf2f946949caf74ca3
      https://github.com/phenotips/phenotips/commit/0ba45d948338473493a94faf2f946949caf74ca3
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-06 (Tue, 06 Oct 2015)

  Changed paths:
    M components/vocabularies/omim/api/src/main/java/org/phenotips/vocabulary/internal/solr/OmimSourceParser.java

  Log Message:
  -----------
  PT-497: Add the possibility to reindex OMIM from the administration
Make sure single valued fields only have one value


  Commit: 88cb93d97e523db9d97c85486c3d8bc1795242e6
      https://github.com/phenotips/phenotips/commit/88cb93d97e523db9d97c85486c3d8bc1795242e6
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-06 (Tue, 06 Oct 2015)

  Changed paths:
    M components/vocabularies/omim/api/src/main/java/org/phenotips/vocabulary/internal/solr/OmimSourceParser.java

  Log Message:
  -----------
  PT-497: Add the possibility to reindex OMIM from the administration
Protect against NPE when the OMIM-Phenotype mapping uses a more recent version of HPO than what's currently indexed


  Commit: a60856ecf08b08de66a0c28b5ee12acd26085889
      https://github.com/phenotips/phenotips/commit/a60856ecf08b08de66a0c28b5ee12acd26085889
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-06 (Tue, 06 Oct 2015)

  Changed paths:
    M components/vocabularies/omim/api/src/main/java/org/phenotips/vocabulary/internal/solr/MendelianInheritanceInMan.java
    M components/vocabularies/omim/api/src/main/java/org/phenotips/vocabulary/internal/solr/OmimSourceParser.java
    M resources/solr-configuration/src/main/resources/omim/conf/schema.xml

  Log Message:
  -----------
  PT-497: Add the possibility to reindex OMIM from the administration
Store the current version


  Commit: d0d356c7807cdd501979f991775f43533fbba215
      https://github.com/phenotips/phenotips/commit/d0d356c7807cdd501979f991775f43533fbba215
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-06 (Tue, 06 Oct 2015)

  Changed paths:
    M resources/solr-configuration/src/main/resources/omim/conf/schema.xml
    M resources/solr-configuration/src/main/resources/omim/conf/solrconfig.xml

  Log Message:
  -----------
  PT-497: Add the possibility to reindex OMIM from the administration
Improved schema


  Commit: f2c6c50761ad95ae51f33fcf311312f546a2bbe0
      https://github.com/phenotips/phenotips/commit/f2c6c50761ad95ae51f33fcf311312f546a2bbe0
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-07 (Wed, 07 Oct 2015)

  Changed paths:
    A resources/solr-configuration/src/main/resources/omim/data/index/_0.cfe
    A resources/solr-configuration/src/main/resources/omim/data/index/_0.cfs
    A resources/solr-configuration/src/main/resources/omim/data/index/_0.si
    A resources/solr-configuration/src/main/resources/omim/data/index/_1.cfe
    A resources/solr-configuration/src/main/resources/omim/data/index/_1.cfs
    A resources/solr-configuration/src/main/resources/omim/data/index/_1.si
    A resources/solr-configuration/src/main/resources/omim/data/index/_2.cfe
    A resources/solr-configuration/src/main/resources/omim/data/index/_2.cfs
    A resources/solr-configuration/src/main/resources/omim/data/index/_2.si
    A resources/solr-configuration/src/main/resources/omim/data/index/_3.cfe
    A resources/solr-configuration/src/main/resources/omim/data/index/_3.cfs
    A resources/solr-configuration/src/main/resources/omim/data/index/_3.si
    A resources/solr-configuration/src/main/resources/omim/data/index/_4.cfe
    A resources/solr-configuration/src/main/resources/omim/data/index/_4.cfs
    A resources/solr-configuration/src/main/resources/omim/data/index/_4.si
    A resources/solr-configuration/src/main/resources/omim/data/index/_5.cfe
    A resources/solr-configuration/src/main/resources/omim/data/index/_5.cfs
    A resources/solr-configuration/src/main/resources/omim/data/index/_5.si
    A resources/solr-configuration/src/main/resources/omim/data/index/_6.cfe
    A resources/solr-configuration/src/main/resources/omim/data/index/_6.cfs
    A resources/solr-configuration/src/main/resources/omim/data/index/_6.si
    A resources/solr-configuration/src/main/resources/omim/data/index/_7.cfe
    A resources/solr-configuration/src/main/resources/omim/data/index/_7.cfs
    A resources/solr-configuration/src/main/resources/omim/data/index/_7.si
    R resources/solr-configuration/src/main/resources/omim/data/index/_x.fdt
    R resources/solr-configuration/src/main/resources/omim/data/index/_x.fdx
    R resources/solr-configuration/src/main/resources/omim/data/index/_x.fnm
    R resources/solr-configuration/src/main/resources/omim/data/index/_x.nvd
    R resources/solr-configuration/src/main/resources/omim/data/index/_x.nvm
    R resources/solr-configuration/src/main/resources/omim/data/index/_x.si
    R resources/solr-configuration/src/main/resources/omim/data/index/_x_Lucene41_0.doc
    R resources/solr-configuration/src/main/resources/omim/data/index/_x_Lucene41_0.pos
    R resources/solr-configuration/src/main/resources/omim/data/index/_x_Lucene41_0.tim
    R resources/solr-configuration/src/main/resources/omim/data/index/_x_Lucene41_0.tip
    R resources/solr-configuration/src/main/resources/omim/data/index/segments.gen
    A resources/solr-configuration/src/main/resources/omim/data/index/segments_4
    R resources/solr-configuration/src/main/resources/omim/data/index/segments_b
    R resources/solr-configuration/src/main/resources/omim/data/spellchecker/_18.cfe
    R resources/solr-configuration/src/main/resources/omim/data/spellchecker/_18.cfs
    R resources/solr-configuration/src/main/resources/omim/data/spellchecker/_18.si
    A resources/solr-configuration/src/main/resources/omim/data/spellchecker/_2.cfe
    A resources/solr-configuration/src/main/resources/omim/data/spellchecker/_2.cfs
    A resources/solr-configuration/src/main/resources/omim/data/spellchecker/_2.si
    R resources/solr-configuration/src/main/resources/omim/data/spellchecker/segments.gen
    R resources/solr-configuration/src/main/resources/omim/data/spellchecker/segments_11
    A resources/solr-configuration/src/main/resources/omim/data/spellchecker/segments_9

  Log Message:
  -----------
  PT-497: Add the possibility to reindex OMIM from the administration
New OMIM index


  Commit: fa9d9f29c6dbea560820fa6c8482bd8385a0a351
      https://github.com/phenotips/phenotips/commit/fa9d9f29c6dbea560820fa6c8482bd8385a0a351
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-07 (Wed, 07 Oct 2015)

  Changed paths:
    M resources/solr-configuration/src/main/resources/omim/conf/schema.xml

  Log Message:
  -----------
  [cleanup] Removed unneeded whitespace


  Commit: 57bd8123b449503a75db947e71a76c0e7492934e
      https://github.com/phenotips/phenotips/commit/57bd8123b449503a75db947e71a76c0e7492934e
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-07 (Wed, 07 Oct 2015)

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

  Log Message:
  -----------
  PT-497: Add the possibility to reindex OMIM from the administration
Added reindex button in the administration section


  Commit: e6fcb4df1e5bdc712a82687a7c674add9d2e52c1
      https://github.com/phenotips/phenotips/commit/e6fcb4df1e5bdc712a82687a7c674add9d2e52c1
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-07 (Wed, 07 Oct 2015)

  Changed paths:
    M .gitignore

  Log Message:
  -----------
  [misc] Always ignore Solr locks


  Commit: d1c9ce4c0fe757329816bce3463182652cbda681
      https://github.com/phenotips/phenotips/commit/d1c9ce4c0fe757329816bce3463182652cbda681
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-07 (Wed, 07 Oct 2015)

  Changed paths:
    M components/vocabularies/omim/api/src/main/java/org/phenotips/vocabulary/internal/solr/OmimSourceParser.java

  Log Message:
  -----------
  PT-497: Add the possibility to reindex OMIM from the administration
Bugfix: ancestors weren't actually stored


  Commit: 44ed0e267bdf3b8d9a5ea1b1a182214063108440
      https://github.com/phenotips/phenotips/commit/44ed0e267bdf3b8d9a5ea1b1a182214063108440
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-07 (Wed, 07 Oct 2015)

  Changed paths:
    M components/vocabularies/omim/api/src/main/java/org/phenotips/vocabulary/internal/solr/MendelianInheritanceInMan.java

  Log Message:
  -----------
  PT-2097: Display only the official title for OMIM diseases
Also search in synonyms.

(cherry picked from commit 9b3c973dcc88715bef5268aa6de49fd2953a78bb)


  Commit: f87954698cd2056c709a990848d117011d44f8e6
      https://github.com/phenotips/phenotips/commit/f87954698cd2056c709a990848d117011d44f8e6
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2015-10-07 (Wed, 07 Oct 2015)

  Changed paths:
    M components/pedigree/resources/src/main/resources/pedigree/editor.css
    M components/pedigree/resources/src/main/resources/pedigree/view/nodeMenu.js

  Log Message:
  -----------
  PT-1917: Fix cancer notes icon clickable when it should not be; minor UI update


  Commit: 90872f58b0d6301647acd07e83d9bd91a9f62409
      https://github.com/phenotips/phenotips/commit/90872f58b0d6301647acd07e83d9bd91a9f62409
  Author: root <root at sickkids.sickkids.ca>
  Date:   2015-10-08 (Thu, 08 Oct 2015)

  Changed paths:
    M components/export/ui/src/main/resources/PhenoTips/ExportFilter.xml

  Log Message:
  -----------
  Issue PT-1619: ExportFilter count does not reflect number of patients that will be exported.


  Commit: 8b01bb5a7df1e920f492a4917da32764acb4580a
      https://github.com/phenotips/phenotips/commit/8b01bb5a7df1e920f492a4917da32764acb4580a
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-08 (Thu, 08 Oct 2015)

  Changed paths:
    M pom.xml

  Log Message:
  -----------
  [misc] Various Maven plugin updates


  Commit: ed0763415843dcb31f4aecde9c5aea84ddcd97f5
      https://github.com/phenotips/phenotips/commit/ed0763415843dcb31f4aecde9c5aea84ddcd97f5
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-09 (Fri, 09 Oct 2015)

  Changed paths:
    M components/navigation/ui/src/main/resources/data/WebHome.xml
    A components/patient-access-rules/ui/src/main/resources/PhenoTips/AllDataGadget.xml
    A components/patient-access-rules/ui/src/main/resources/PhenoTips/MyDataGadget.xml
    A components/users/ui/src/main/resources/PhenoTips/GroupsGadget.xml

  Log Message:
  -----------
  Merge branch 'Issue-#1769' of https://github.com/mjshepherd/phenotips


  Commit: 1a98ee7cac793b09867fd37dffead71e118e9a8f
      https://github.com/phenotips/phenotips/commit/1a98ee7cac793b09867fd37dffead71e118e9a8f
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-09 (Fri, 09 Oct 2015)

  Changed paths:
    M components/navigation/ui/src/main/resources/data/WebHome.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/AllDataGadget.xml
    M components/patient-access-rules/ui/src/main/resources/PhenoTips/MyDataGadget.xml

  Log Message:
  -----------
  PT-1827: Make the homepage easily extensible
Reduce the usage of the {{html}} macro


  Commit: fc77f52eb7337f4d9d75752579c323ec35d868c8
      https://github.com/phenotips/phenotips/commit/fc77f52eb7337f4d9d75752579c323ec35d868c8
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-09 (Fri, 09 Oct 2015)

  Changed paths:
    M components/navigation/ui/src/main/resources/data/WebHome.xml

  Log Message:
  -----------
  [cleanup] Improved codestyle


  Commit: 3bf771d024c8c03c9b7f8f0dd8cb4f75d85fb5b4
      https://github.com/phenotips/phenotips/commit/3bf771d024c8c03c9b7f8f0dd8cb4f75d85fb5b4
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-09 (Fri, 09 Oct 2015)

  Changed paths:
    M components/navigation/ui/src/main/resources/data/WebHome.xml

  Log Message:
  -----------
  [misc] Sync xobjects with their xclasses


  Commit: 3b7abf40e4907df863ecb34122fec2e10cd7f418
      https://github.com/phenotips/phenotips/commit/3b7abf40e4907df863ecb34122fec2e10cd7f418
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-10 (Sat, 10 Oct 2015)

  Changed paths:
    A components/vocabularies/api/src/main/java/org/phenotips/vocabulary/VocabularyInputTerm.java

  Log Message:
  -----------
  PT-2112: Add a VocabularyInputTerm interface
Done


  Commit: 8195610d29eace873ee34687efb9fc471813de0e
      https://github.com/phenotips/phenotips/commit/8195610d29eace873ee34687efb9fc471813de0e
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-10 (Sat, 10 Oct 2015)

  Changed paths:
    M components/vocabularies/api/src/main/java/org/phenotips/vocabulary/VocabularyInputTerm.java
    A components/vocabularies/api/src/main/java/org/phenotips/vocabulary/internal/solr/VocabularyExtension.java

  Log Message:
  -----------
  PT-2105: Add a VocabularyExtension @Role
Done


  Commit: d331b8df81954a369b6fa1c9df8e04a314b42984
      https://github.com/phenotips/phenotips/commit/d331b8df81954a369b6fa1c9df8e04a314b42984
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-10 (Sat, 10 Oct 2015)

  Changed paths:
    A components/vocabularies/api/src/main/java/org/phenotips/vocabulary/VocabularyExtension.java
    R components/vocabularies/api/src/main/java/org/phenotips/vocabulary/internal/solr/VocabularyExtension.java

  Log Message:
  -----------
  PT-2105: Add a VocabularyExtension @Role
Moved in the right package


  Commit: 5b0b3a6e9c073e764cdf04dfec020c1ba5111b8f
      https://github.com/phenotips/phenotips/commit/5b0b3a6e9c073e764cdf04dfec020c1ba5111b8f
  Author: Sergiu Dumitriu <sdumitriu at users.noreply.github.com>
  Date:   2015-10-11 (Sun, 11 Oct 2015)

  Changed paths:
    M components/export/ui/src/main/resources/PhenoTips/ExportFilter.xml

  Log Message:
  -----------
  Merge pull request #1899 from phenotips/PT-1619

Issue PT-1619: ExportFilter count does not reflect number of patients…


  Commit: 39834e6dd7d41def473f894c4d162a11c700cef6
      https://github.com/phenotips/phenotips/commit/39834e6dd7d41def473f894c4d162a11c700cef6
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-12 (Mon, 12 Oct 2015)

  Changed paths:
    A components/default-settings/src/main/resources/PhenoTips/WebPreferences.xml
    M components/widgets/ui/src/main/resources/XWiki/DateTimePicker.xml

  Log Message:
  -----------
  PT-2120: When allowing guests to view data, many styles, scripts and UI elements are broken


  Commit: d0e3eb407e68306b2128ea7b34e63866d2918bcd
      https://github.com/phenotips/phenotips/commit/d0e3eb407e68306b2128ea7b34e63866d2918bcd
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-13 (Tue, 13 Oct 2015)

  Changed paths:
    M components/widgets/ui/src/main/resources/XWiki/DateTimePicker.xml

  Log Message:
  -----------
  [misc] Sync xobjects with their xclass


  Commit: e20926b42fbcd6a577e07f66569dbc1d31de9ee9
      https://github.com/phenotips/phenotips/commit/e20926b42fbcd6a577e07f66569dbc1d31de9ee9
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-13 (Tue, 13 Oct 2015)

  Changed paths:
    M components/widgets/ui/src/main/resources/XWiki/DateTimePicker.xml

  Log Message:
  -----------
  [cleanup] Cleanup whitespace


  Commit: 969e435452a065f3b4d448f0f30d7b24fba8e774
      https://github.com/phenotips/phenotips/commit/969e435452a065f3b4d448f0f30d7b24fba8e774
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-13 (Tue, 13 Oct 2015)

  Changed paths:
    M components/xwiki-translation-manager/src/main/java/org/phenotips/translation/TranslationManager.java

  Log Message:
  -----------
  PT-2122: The TranslationManager component cannot be used
Fixed


  Commit: 4da93779d7b0391077768a726b57b81a85966e1c
      https://github.com/phenotips/phenotips/commit/4da93779d7b0391077768a726b57b81a85966e1c
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-13 (Tue, 13 Oct 2015)

  Changed paths:
    M components/xwiki-translation-manager/src/main/java/org/phenotips/translation/TranslationManager.java

  Log Message:
  -----------
  [misc] Mark new role as unstable API


  Commit: 5a2c818f727affd5f76dcfdc18f9f972a92bd071
      https://github.com/phenotips/phenotips/commit/5a2c818f727affd5f76dcfdc18f9f972a92bd071
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-13 (Tue, 13 Oct 2015)

  Changed paths:
    A components/xwiki-translation-manager/src/main/resources/META-INF/components.txt
    R components/xwiki-translation-manager/src/main/resources/components.txt

  Log Message:
  -----------
  PT-2122: The TranslationManager component cannot be used
Really fixed


  Commit: f40bc96be38089f88723e019f374a2a6844197a0
      https://github.com/phenotips/phenotips/commit/f40bc96be38089f88723e019f374a2a6844197a0
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-14 (Wed, 14 Oct 2015)

  Changed paths:
    M components/patient-access-rules/api/pom.xml
    M components/patient-access-rules/api/src/main/java/org/phenotips/data/permissions/internal/AbstractAccessLevel.java
    M components/patient-access-rules/api/src/main/java/org/phenotips/data/permissions/internal/AbstractVisibility.java
    M components/patient-access-rules/api/src/test/java/org/phenotips/data/permissions/internal/access/EditAccessLevelTest.java
    M components/patient-access-rules/api/src/test/java/org/phenotips/data/permissions/internal/access/ManageAccessLevelTest.java
    M components/patient-access-rules/api/src/test/java/org/phenotips/data/permissions/internal/access/NoAccessLevelTest.java
    M components/patient-access-rules/api/src/test/java/org/phenotips/data/permissions/internal/access/OwnerAccessLevelTest.java
    M components/patient-access-rules/api/src/test/java/org/phenotips/data/permissions/internal/access/ViewAccessLevelTest.java
    M components/patient-access-rules/api/src/test/java/org/phenotips/data/permissions/internal/visibility/HiddenVisibilityTest.java
    M components/patient-access-rules/api/src/test/java/org/phenotips/data/permissions/internal/visibility/OpenVisibilityTest.java
    M components/patient-access-rules/api/src/test/java/org/phenotips/data/permissions/internal/visibility/PrivateVisibilityTest.java
    M components/patient-access-rules/api/src/test/java/org/phenotips/data/permissions/internal/visibility/PublicVisibilityTest.java

  Log Message:
  -----------
  [misc] Use the new TranslationManager instead of XWiki's LocalizationManager


  Commit: 25a17e3a9b15dd926c7294cce60f8100a4fc56b4
      https://github.com/phenotips/phenotips/commit/25a17e3a9b15dd926c7294cce60f8100a4fc56b4
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-14 (Wed, 14 Oct 2015)

  Changed paths:
    M components/patient-tools/pom.xml
    M components/patient-tools/src/main/java/org/phenotips/tools/FormField.java

  Log Message:
  -----------
  [misc] Use the new TranslationManager instead of XWiki's LocalizationManager


  Commit: c7c2e4f3b75890d4fae8642f54a23ff178c7b9d0
      https://github.com/phenotips/phenotips/commit/c7c2e4f3b75890d4fae8642f54a23ff178c7b9d0
  Author: Marta Girdea <marta.girdea at gmail.com>
  Date:   2015-10-14 (Wed, 14 Oct 2015)

  Changed paths:
    M components/patient-data/ui/src/main/resources/PhenoTips/PedigreeImageService.xml

  Log Message:
  -----------
  PT-2132: Requesting raster export of pedigree images fails

Fixed


  Commit: bc6a7b272f02f113aac24a2a10effc06b74492b8
      https://github.com/phenotips/phenotips/commit/bc6a7b272f02f113aac24a2a10effc06b74492b8
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-15 (Thu, 15 Oct 2015)

  Changed paths:
    M components/patient-data/ui/src/main/resources/PhenoTips/PatientSheetCode.xml

  Log Message:
  -----------
  PT-2110: Validation for date of death should not display anything if valid
Fixed.


  Commit: 6ec9428edadb14d700f5edc31f1aae05f1952529
      https://github.com/phenotips/phenotips/commit/6ec9428edadb14d700f5edc31f1aae05f1952529
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-16 (Fri, 16 Oct 2015)

  Changed paths:
    M components/navigation/ui/src/main/resources/data/WebHome.xml

  Log Message:
  -----------
  PT-2147: Move the Identifier column to the second place of the All patient record page
Done


  Commit: dedbb0d9149e3eb18a465b8f824cb6ac5ea489c9
      https://github.com/phenotips/phenotips/commit/dedbb0d9149e3eb18a465b8f824cb6ac5ea489c9
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2015-10-18 (Sun, 18 Oct 2015)

  Changed paths:
    M components/widgets/ui/src/main/resources/PhenoTips/ImageDisplayer.xml
    M components/widgets/ui/src/main/resources/PhenoTips/TabelarDataMacros.xml
    M components/widgets/ui/src/main/resources/PhenoTips/Widgets.xml

  Log Message:
  -----------
  [misc] Sync xobjects with their current xclass


  Commit: 919ff74ed79fdc5d24b8b620ff2858a104618ad7
      https://github.com/phenotips/phenotips/commit/919ff74ed79fdc5d24b8b620ff2858a104618ad7
  Author: Denys Pavlov <denys.pavlov at gmail.com>
  Date:   2015-10-19 (Mon, 19 Oct 2015)

  Changed paths:
    A components/vocabularies/orphanet/api/pom.xml
    A components/vocabularies/orphanet/api/src/main/java/org/phenotips/vocabulary/internal/solr/Orphanet.java
    A components/vocabularies/orphanet/api/src/main/resources/META-INF/components.txt
    A components/vocabularies/orphanet/pom.xml
    A components/vocabularies/orphanet/ui/pom.xml
    A components/vocabularies/orphanet/ui/src/main/resources/PhenoTips/OrphanetInfoService.xml

  Log Message:
  -----------
  Added ORPHANET vocabulary skeleton


  Commit: d5a41ba093942f73569d8806d8b9fa8637ca043b
      https://github.com/phenotips/phenotips/commit/d5a41ba093942f73569d8806d8b9fa8637ca043b
  Author: Denys Pavlov <denys.pavlov at gmail.com>
  Date:   2015-10-19 (Mon, 19 Oct 2015)

  Changed paths:
    M components/vocabularies/api/pom.xml
    A components/vocabularies/api/src/main/java/org/phenotips/vocabulary/internal/solr/AbstractOWLSolrVocabulary.java
    M components/vocabularies/orphanet/api/pom.xml
    A components/vocabularies/orphanet/api/src/checkstyle/checkstyle-suppressions.xml
    M components/vocabularies/orphanet/api/src/main/java/org/phenotips/vocabulary/internal/solr/Orphanet.java
    A resources/solr-configuration/src/main/resources/orphanet/conf/protwords.txt
    A resources/solr-configuration/src/main/resources/orphanet/conf/schema.xml
    A resources/solr-configuration/src/main/resources/orphanet/conf/solrconfig.xml
    A resources/solr-configuration/src/main/resources/orphanet/conf/stopwords.txt
    A resources/solr-configuration/src/main/resources/orphanet/conf/synonyms.txt
    A resources/solr-configuration/src/main/resources/orphanet/core.properties

  Log Message:
  -----------
  added OWL parser to parse Orphanet to Solr


  Commit: 19ec3fb2cebb166baf1e14de5844f8fc68e60cc8
      https://github.com/phenotips/phenotips/commit/19ec3fb2cebb166baf1e14de5844f8fc68e60cc8
  Author: Denys Pavlov <denys.pavlov at gmail.com>
  Date:   2015-10-19 (Mon, 19 Oct 2015)

  Changed paths:
    M components/vocabularies/orphanet/api/pom.xml
    M components/vocabularies/pom.xml
    M distribution/war/pom.xml

  Log Message:
  -----------
  adding orphanet to all the poms.


  Commit: 4bd03c77d6315203d0fe281efc41c81512c6acde
      https://github.com/phenotips/phenotips/commit/4bd03c77d6315203d0fe281efc41c81512c6acde
  Author: Denys Pavlov <denys.pavlov at gmail.com>
  Date:   2015-10-19 (Mon, 19 Oct 2015)

  Changed paths:
    M components/patient-data/ui/pom.xml
    M components/vocabularies/api/src/main/java/org/phenotips/vocabulary/internal/solr/AbstractOWLSolrVocabulary.java

  Log Message:
  -----------
  added logging on orphanet solr error, including xar in distribution


  Commit: dab3b771e95ef57a8cd1b9426ef90f308734ce6b
      https://github.com/phenotips/phenotips/commit/dab3b771e95ef57a8cd1b9426ef90f308734ce6b
  Author: Denys Pavlov <denys.pavlov at gmail.com>
  Date:   2015-10-19 (Mon, 19 Oct 2015)

  Changed paths:
    M components/vocabularies/orphanet/api/src/main/java/org/phenotips/vocabulary/internal/solr/Orphanet.java
    M resources/solr-configuration/src/main/resources/orphanet/conf/schema.xml

  Log Message:
  -----------
  fix solr schema


  Commit: 2ccfb0c9bdc4d794b5375fd7b14c359a80fff4f9
      https://github.com/phenotips/phenotips/commit/2ccfb0c9bdc4d794b5375fd7b14c359a80fff4f9
  Author: Denys Pavlov <denys.pavlov at gmail.com>
  Date:   2015-10-19 (Mon, 19 Oct 2015)

  Changed paths:
    M components/vocabularies/orphanet/api/src/main/java/org/phenotips/vocabulary/internal/solr/Orphanet.java
    A resources/solr-configuration/src/main/resources/orphanet/data/index/_1.fdt
    A resources/solr-configuration/src/main/resources/orphanet/data/index/_1.fdx
    A resources/solr-configuration/src/main/resources/orphanet/data/index/_1.fnm
    A resources/solr-configuration/src/main/resources/orphanet/data/index/_1.nvd
    A resources/solr-configuration/src/main/resources/orphanet/data/index/_1.nvm
    A resources/solr-configuration/src/main/resources/orphanet/data/index/_1.si
    A resources/solr-configuration/src/main/resources/orphanet/data/index/_1_1.liv
    A resources/solr-configuration/src/main/resources/orphanet/data/index/_1_Lucene50_0.doc
    A resources/solr-configuration/src/main/resources/orphanet/data/index/_1_Lucene50_0.pos
    A resources/solr-configuration/src/main/resources/orphanet/data/index/_1_Lucene50_0.tim
    A resources/solr-configuration/src/main/resources/orphanet/data/index/_1_Lucene50_0.tip
    A resources/solr-configuration/src/main/resources/orphanet/data/index/segments_4
    A resources/solr-configuration/src/main/resources/orphanet/data/spellchecker/_1.cfe
    A resources/solr-configuration/src/main/resources/orphanet/data/spellchecker/_1.cfs
    A resources/solr-configuration/src/main/resources/orphanet/data/spellchecker/_1.si
    A resources/solr-configuration/src/main/resources/orphanet/data/spellchecker/segments_7

  Log Message:
  -----------
  added indexed solr data, removed reference to local filesystem


  Commit: 29367319fdd9ed63545372a98db66149e912f47c
      https://github.com/phenotips/phenotips/commit/29367319fdd9ed63545372a98db66149e912f47c
  Author: Denys Pavlov <denys.pavlov at gmail.com>
  Date:   2015-10-19 (Mon, 19 Oct 2015)

  Changed paths:
    M components/vocabularies/orphanet/ui/src/main/resources/PhenoTips/OrphanetInfoService.xml
    M resources/solr-configuration/src/main/resources/orphanet/conf/schema.xml

  Log Message:
  -----------
  returning json, not storing extra solr fields


  Commit: 90e5d9058689e3ea64aede1528fc7134120a71f1
      https://github.com/phenotips/phenotips/commit/90e5d9058689e3ea64aede1528fc7134120a71f1
  Author: Denys Pavlov <denys.pavlov at gmail.com>
  Date:   2015-10-19 (Mon, 19 Oct 2015)

  Changed paths:
    M components/vocabularies/orphanet/api/src/main/java/org/phenotips/vocabulary/internal/solr/Orphanet.java

  Log Message:
  -----------
  cleaned up URI for fetching Orphanet OWL


  Commit: ee06e887e500dbfbc63505ddf3909b83b9a2440e
      https://github.com/phenotips/phenotips/commit/ee06e887e500dbfbc63505ddf3909b83b9a2440e
  Author: Denys Pavlov <denys.pavlov at gmail.com>
  Date:   2015-10-19 (Mon, 19 Oct 2015)

  Changed paths:
    M components/vocabularies/orphanet/api/pom.xml
    M components/vocabularies/orphanet/pom.xml
    M components/vocabularies/orphanet/ui/pom.xml

  Log Message:
  -----------
  upgrading orphanet to 1.3-SNAPSHOT


  Commit: 4999008f31e8ac6e9bbf024575440f81781d4235
      https://github.com/phenotips/phenotips/commit/4999008f31e8ac6e9bbf024575440f81781d4235
  Author: Denys Pavlov <denys.pavlov at gmail.com>
  Date:   2015-10-19 (Mon, 19 Oct 2015)

  Log Message:
  -----------
  Merge branch 'PT-1950' of github.com:phenotips/phenotips into PT-1950


Compare: https://github.com/phenotips/phenotips/compare/16b4d13b5e08...4999008f31e8


More information about the notifications mailing list