[phenotips-notifications] [phenotips/patient-network] bc9b8f: Issue #31: Updated patient phenotype similarity sc...

GitHub noreply at github.com
Wed Jul 30 16:00:20 EDT 2014


  Branch: refs/heads/candidate-genes
  Home:   https://github.com/phenotips/patient-network
  Commit: bc9b8fe830910784f4e62d5d93917b3a04ba1b3a
      https://github.com/phenotips/patient-network/commit/bc9b8fe830910784f4e62d5d93917b3a04ba1b3a
  Author: Orion Buske <orion.buske at gmail.com>
  Date:   2014-07-23 (Wed, 23 Jul 2014)

  Changed paths:
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/DefaultPatientSimilarityView.java
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/DefaultPatientSimilarityViewFactory.java
    M similarity-data-impl/src/test/java/org/phenotips/data/similarity/internal/RestrictedPatientSimilarityViewFactoryTest.java
    M similarity-data-impl/src/test/java/org/phenotips/data/similarity/internal/RestrictedPatientSimilarityViewTest.java

  Log Message:
  -----------
  Issue #31: Updated patient phenotype similarity score to use simGIC score.


  Commit: cdb51f100b068ae4529109fa80ad516d9c294fa9
      https://github.com/phenotips/patient-network/commit/cdb51f100b068ae4529109fa80ad516d9c294fa9
  Author: Orion Buske <orion.buske at gmail.com>
  Date:   2014-07-25 (Fri, 25 Jul 2014)

  Changed paths:
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/DefaultPatientSimilarityViewFactory.java
    A similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/PairCache.java
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/RestrictedGenotypeSimilarityView.java

  Log Message:
  -----------
  Issue #30: Added public methods to control patient similarity caching, and refactored paired-key caching.


  Commit: c7d7701946d112bd845666989b8fd3cdb07f4ddd
      https://github.com/phenotips/patient-network/commit/c7d7701946d112bd845666989b8fd3cdb07f4ddd
  Author: Orion Buske <orion.buske at gmail.com>
  Date:   2014-07-25 (Fri, 25 Jul 2014)

  Changed paths:
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/DefaultPatientSimilarityView.java

  Log Message:
  -----------
  Issue #26: Added boost to similarity score for matching candidate genes.


  Commit: 46a4609bfe35bc50423912b1707e30b3fe9eaf40
      https://github.com/phenotips/patient-network/commit/46a4609bfe35bc50423912b1707e30b3fe9eaf40
  Author: Orion Buske <orion.buske at gmail.com>
  Date:   2014-07-27 (Sun, 27 Jul 2014)

  Changed paths:
    M similarity-data-api/src/main/java/org/phenotips/data/similarity/Genotype.java
    M similarity-data-api/src/main/java/org/phenotips/data/similarity/Variant.java
    A similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/CandidateGene.java
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/DefaultPatientSimilarityView.java
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/DefaultPatientSimilarityViewFactory.java
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/ExomizerGenotype.java
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/ExomizerJobManager.java
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/ExomizerVariant.java
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/PairCache.java
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/RestrictedGenotypeSimilarityView.java
    M similarity-data-impl/src/test/java/org/phenotips/data/similarity/internal/RestrictedPatientSimilarityViewFactoryTest.java
    M similarity-data-impl/src/test/java/org/phenotips/data/similarity/internal/RestrictedPatientSimilarityViewTest.java

  Log Message:
  -----------
  Issue #26: First attempt at incorporating candidate genes. Tweaked scoring to accomodate Exomiser 2. Candidate genes currently show up in json as multiple variants.


  Commit: cce575883a9668401082242258b3943be8ad2d5e
      https://github.com/phenotips/patient-network/commit/cce575883a9668401082242258b3943be8ad2d5e
  Author: Orion Buske <orion.buske at gmail.com>
  Date:   2014-07-27 (Sun, 27 Jul 2014)

  Changed paths:
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/DefaultPatientSimilarityView.java
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/DefaultPatientSimilarityViewFactory.java
    M similarity-data-impl/src/test/java/org/phenotips/data/similarity/internal/RestrictedPatientSimilarityViewFactoryTest.java
    M similarity-data-impl/src/test/java/org/phenotips/data/similarity/internal/RestrictedPatientSimilarityViewTest.java

  Log Message:
  -----------
  Merged in simGIC score branch


  Commit: 806651a7cbddb603ca8ad15e87e451b5eb5a176b
      https://github.com/phenotips/patient-network/commit/806651a7cbddb603ca8ad15e87e451b5eb5a176b
  Author: Orion Buske <orion.buske at gmail.com>
  Date:   2014-07-28 (Mon, 28 Jul 2014)

  Changed paths:
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/DefaultPatientSimilarityView.java

  Log Message:
  -----------
  Improved score memoization


  Commit: eea54ca4e2138e41846f60510399b0a43fb97389
      https://github.com/phenotips/patient-network/commit/eea54ca4e2138e41846f60510399b0a43fb97389
  Author: Orion Buske <orion.buske at gmail.com>
  Date:   2014-07-29 (Tue, 29 Jul 2014)

  Changed paths:
    M similarity-data-api/src/main/java/org/phenotips/data/similarity/Genotype.java
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/ExomizerGenotype.java
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/ExomizerJobManager.java
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/ExomizerVariant.java
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/RestrictedGenotypeSimilarityView.java

  Log Message:
  -----------
  Issue #26: Refactored genotype representation and candidate gene handling. Code not fully tested.


  Commit: 02167c5030e31e5a4796bc0a709d04bd80891c3c
      https://github.com/phenotips/patient-network/commit/02167c5030e31e5a4796bc0a709d04bd80891c3c
  Author: Orion Buske <orion.buske at gmail.com>
  Date:   2014-07-29 (Tue, 29 Jul 2014)

  Changed paths:
    M ui/src/main/resources/PhenoTips/SimilarCases.xml

  Log Message:
  -----------
  Tweaked genotype UI to display only a single score per gene


  Commit: 95d9dcd1ecba5822c72383b81d47307a928ed435
      https://github.com/phenotips/patient-network/commit/95d9dcd1ecba5822c72383b81d47307a928ed435
  Author: Orion Buske <orion.buske at gmail.com>
  Date:   2014-07-29 (Tue, 29 Jul 2014)

  Changed paths:
    A similarity-data-impl/src/main/java/org/phenotips/data/similarity/script/PatientMatchingScriptService.java
    M similarity-data-impl/src/main/resources/META-INF/components.txt

  Log Message:
  -----------
  Issue #30: Initial attempt at exposing script service to control patient matching cache


  Commit: 0e448e7dfce0aa8781b035f13f90ba0f9d92fc95
      https://github.com/phenotips/patient-network/commit/0e448e7dfce0aa8781b035f13f90ba0f9d92fc95
  Author: Orion Buske <orion.buske at gmail.com>
  Date:   2014-07-30 (Wed, 30 Jul 2014)

  Changed paths:
    M similarity-data-impl/src/main/java/org/phenotips/data/similarity/script/PatientMatchingScriptService.java

  Log Message:
  -----------
  Issue #30: Fixed bug after smoke testing clearCache service.


Compare: https://github.com/phenotips/patient-network/compare/bc9b8fe83091^...0e448e7dfce0


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