[phenotips-notifications] [phenotips/mendelian-search-application] 1275c8: Initial commit for phenotype matching

GitHub noreply at github.com
Thu Apr 16 14:22:13 EDT 2015


  Branch: refs/heads/master
  Home:   https://github.com/phenotips/mendelian-search-application
  Commit: 1275c8fa561fa8a4457bae64a5fae0a9d4803b27
      https://github.com/phenotips/mendelian-search-application/commit/1275c8fa561fa8a4457bae64a5fae0a9d4803b27
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-03-30 (Mon, 30 Mar 2015)

  Changed paths:
    R api/src/main/java/org/phenotips/mendelianSearch/internal/DefaultMendelianSearchHandler.java
    A api/src/main/java/org/phenotips/mendelianSearch/phenotype/DefaultPatientPhenotypeScorer.java
    A api/src/main/java/org/phenotips/mendelianSearch/phenotype/DefaultPhenotypeScorer.java
    A api/src/main/java/org/phenotips/mendelianSearch/phenotype/PatientPhenotypeScorer.java
    A api/src/main/java/org/phenotips/mendelianSearch/phenotype/PhenotypeScorer.java

  Log Message:
  -----------
  Initial commit for phenotype matching


  Commit: 3e0679ad9a1126d77677696dcade8b8755d7e53d
      https://github.com/phenotips/mendelian-search-application/commit/3e0679ad9a1126d77677696dcade8b8755d7e53d
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M api/pom.xml
    M api/src/main/java/org/phenotips/mendelianSearch/phenotype/DefaultPatientPhenotypeScorer.java
    M api/src/main/java/org/phenotips/mendelianSearch/phenotype/DefaultPhenotypeScorer.java
    M api/src/main/java/org/phenotips/mendelianSearch/phenotype/PatientPhenotypeScorer.java
    M api/src/main/java/org/phenotips/mendelianSearch/phenotype/PhenotypeScorer.java
    A api/src/test/org/phenotips/mendelianSearch/phenotype/DefaultPatientPhenotypeScorerTest.java
    A api/src/test/org/phenotips/mendelianSearch/phenotype/DefaultPhenotypeScorerTest.java
    A api/src/test/org/phenotips/mendelianSearch/phenotype/mocks/MockDisease.java
    A api/src/test/org/phenotips/mendelianSearch/phenotype/mocks/MockHPO.java
    A api/src/test/org/phenotips/mendelianSearch/phenotype/mocks/MockMIM.java
    A api/src/test/org/phenotips/mendelianSearch/phenotype/mocks/MockOntologyTerm.java

  Log Message:
  -----------
  Modifications to phenotype similarity. Added tests and relevant test classes


  Commit: 0c4cd8f35115ccba8bc787e2568cac36ef6bc700
      https://github.com/phenotips/mendelian-search-application/commit/0c4cd8f35115ccba8bc787e2568cac36ef6bc700
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    A api/src/main/java/org/phenotips/mendelianSearch/DefaultMendelianSearch.java
    A api/src/main/java/org/phenotips/mendelianSearch/MendelianSearch.java
    R api/src/main/java/org/phenotips/mendelianSearch/MendelianSearchHandler.java
    A api/src/main/java/org/phenotips/mendelianSearch/genotype/VariantStore.java
    M api/src/main/java/org/phenotips/mendelianSearch/phenotype/DefaultPatientPhenotypeScorer.java
    M api/src/main/java/org/phenotips/mendelianSearch/phenotype/PatientPhenotypeScorer.java
    A api/src/main/java/org/phenotips/mendelianSearch/script/MendelianSearchRequest.java
    M api/src/main/java/org/phenotips/mendelianSearch/script/MendelianSearchScriptService.java
    M api/src/test/org/phenotips/mendelianSearch/phenotype/DefaultPatientPhenotypeScorerTest.java

  Log Message:
  -----------
  Initial prototype for the mendelian search class


  Commit: 70c353ed7ee3c9af7f316eaee2ee45db4ffd74e1
      https://github.com/phenotips/mendelian-search-application/commit/70c353ed7ee3c9af7f316eaee2ee45db4ffd74e1
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M api/pom.xml
    M api/src/main/java/org/phenotips/mendelianSearch/DefaultMendelianSearch.java
    M api/src/main/java/org/phenotips/mendelianSearch/MendelianSearch.java
    A api/src/main/java/org/phenotips/mendelianSearch/genotype/MockVariantStore.java
    M api/src/main/java/org/phenotips/mendelianSearch/genotype/VariantStore.java
    M api/src/main/java/org/phenotips/mendelianSearch/phenotype/DefaultPatientPhenotypeScorer.java
    M api/src/main/java/org/phenotips/mendelianSearch/script/MendelianSearchScriptService.java
    M api/src/main/resources/META-INF/components.txt
    A resources/pom.xml
    A resources/src/main/resources/js/d3.js
    M ui/src/main/resources/PhenoTips/MendelianLivetableResults.xml
    M ui/src/main/resources/PhenoTips/MendelianResults.xml
    M ui/src/main/resources/PhenoTips/MendelianSearch.xml

  Log Message:
  -----------
  Working using phenotype matching and mock variant store


  Commit: 1b7b6f67159f886c1b218dbbe60f72ab10ad96bd
      https://github.com/phenotips/mendelian-search-application/commit/1b7b6f67159f886c1b218dbbe60f72ab10ad96bd
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-04-09 (Thu, 09 Apr 2015)

  Changed paths:
    A api/doc/allclasses-frame.html
    A api/doc/allclasses-noframe.html
    A api/doc/constant-values.html
    A api/doc/deprecated-list.html
    A api/doc/help-doc.html
    A api/doc/index-files/index-1.html
    A api/doc/index-files/index-2.html
    A api/doc/index-files/index-3.html
    A api/doc/index-files/index-4.html
    A api/doc/index-files/index-5.html
    A api/doc/index-files/index-6.html
    A api/doc/index-files/index-7.html
    A api/doc/index.html
    A api/doc/org/phenotips/mendelianSearch/internal/DefaultMendelianSearchHandler.html
    A api/doc/org/phenotips/mendelianSearch/internal/MendelianSearchRequest.html
    A api/doc/org/phenotips/mendelianSearch/internal/class-use/DefaultMendelianSearchHandler.html
    A api/doc/org/phenotips/mendelianSearch/internal/class-use/MendelianSearchRequest.html
    A api/doc/org/phenotips/mendelianSearch/internal/package-frame.html
    A api/doc/org/phenotips/mendelianSearch/internal/package-summary.html
    A api/doc/org/phenotips/mendelianSearch/internal/package-tree.html
    A api/doc/org/phenotips/mendelianSearch/internal/package-use.html
    A api/doc/overview-tree.html
    A api/doc/package-list
    A api/doc/script.js
    A api/doc/stylesheet.css
    M api/src/main/java/org/phenotips/mendelianSearch/genotype/MockVariantStore.java
    M ui/src/main/resources/PhenoTips/MendelianResults.xml

  Log Message:
  -----------
  UI work, styling variant display. Also commiting generated api docs


  Commit: ba131ae90bf8bb4a20313d91f55e52de4138028f
      https://github.com/phenotips/mendelian-search-application/commit/ba131ae90bf8bb4a20313d91f55e52de4138028f
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-04-10 (Fri, 10 Apr 2015)

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

  Log Message:
  -----------
  Removed edit panel from results page, sorted table based on phenotype score, code cleanup


  Commit: 5d21022d1883792097bd2b0a30a294d689dac9fd
      https://github.com/phenotips/mendelian-search-application/commit/5d21022d1883792097bd2b0a30a294d689dac9fd
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-04-10 (Fri, 10 Apr 2015)

  Changed paths:
    R api/src/main/java/org/phenotips/mendelianSearch/DummyResponseScriptService.java

  Log Message:
  -----------
  Removed unused class


  Commit: 976268a4b8fa18ad73468088e142a6c88d21143a
      https://github.com/phenotips/mendelian-search-application/commit/976268a4b8fa18ad73468088e142a6c88d21143a
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-04-13 (Mon, 13 Apr 2015)

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

  Log Message:
  -----------
  Added title to overview section


  Commit: 37d994cccc97fc7fd5fa9efe0f003a4632d731fc
      https://github.com/phenotips/mendelian-search-application/commit/37d994cccc97fc7fd5fa9efe0f003a4632d731fc
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-04-14 (Tue, 14 Apr 2015)

  Changed paths:
    M api/pom.xml
    M api/src/main/java/org/phenotips/mendelianSearch/DefaultMendelianSearch.java
    M api/src/main/java/org/phenotips/mendelianSearch/genotype/MockVariantStore.java
    M api/src/main/java/org/phenotips/mendelianSearch/genotype/VariantStore.java
    M api/src/main/java/org/phenotips/mendelianSearch/script/MendelianSearchScriptService.java
    M api/src/main/resources/META-INF/components.txt

  Log Message:
  -----------
  Support for vairant based search, script service now takes the XWikiRequest


  Commit: fdd4773175fdd1916e54abdbd1e3660cbe5712bb
      https://github.com/phenotips/mendelian-search-application/commit/fdd4773175fdd1916e54abdbd1e3660cbe5712bb
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-04-14 (Tue, 14 Apr 2015)

  Changed paths:
    M api/pom.xml
    M api/src/main/java/org/phenotips/mendelianSearch/DefaultMendelianSearch.java

  Log Message:
  -----------
  var store integration


  Commit: f90583c659043cd7ba2535a9d6626429571471fe
      https://github.com/phenotips/mendelian-search-application/commit/f90583c659043cd7ba2535a9d6626429571471fe
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-04-15 (Wed, 15 Apr 2015)

  Changed paths:
    M ui/src/main/resources/PhenoTips/MendelianLivetableResults.xml
    M ui/src/main/resources/PhenoTips/MendelianResults.xml
    M ui/src/main/resources/PhenoTips/MendelianSearch.xml

  Log Message:
  -----------
  UI updates for demo


  Commit: 77b62f174101e87551d1308c9b419d1ec286e4f8
      https://github.com/phenotips/mendelian-search-application/commit/77b62f174101e87551d1308c9b419d1ec286e4f8
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-04-15 (Wed, 15 Apr 2015)

  Changed paths:
    M api/src/main/java/org/phenotips/mendelianSearch/DefaultMendelianSearch.java
    M api/src/main/java/org/phenotips/mendelianSearch/script/MendelianSearchScriptService.java
    M ui/src/main/resources/PhenoTips/MendelianResults.xml

  Log Message:
  -----------
  Bug fixes


  Commit: 246f854d4ea2c9f3f76163b0de45c75654e84857
      https://github.com/phenotips/mendelian-search-application/commit/246f854d4ea2c9f3f76163b0de45c75654e84857
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-04-16 (Thu, 16 Apr 2015)

  Changed paths:
    M api/src/main/java/org/phenotips/mendelianSearch/DefaultMendelianSearch.java
    M ui/src/main/resources/PhenoTips/MendelianResults.xml
    M ui/src/main/resources/PhenoTips/MendelianSearch.xml

  Log Message:
  -----------
  Final demo version. Box plots no longer appear when dataset is too small


  Commit: aa82c0262903cc73886e8f8e6d77bae4ec4f4750
      https://github.com/phenotips/mendelian-search-application/commit/aa82c0262903cc73886e8f8e6d77bae4ec4f4750
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-04-16 (Thu, 16 Apr 2015)

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

  Log Message:
  -----------
  Minor - changed x axis labels on the box plot


  Commit: e168da7a63d56c0390bb7a6cd5142b94f50f1177
      https://github.com/phenotips/mendelian-search-application/commit/e168da7a63d56c0390bb7a6cd5142b94f50f1177
  Author: mjshepherd <matthewshepherd at live.com>
  Date:   2015-04-16 (Thu, 16 Apr 2015)

  Changed paths:
    R api/doc/allclasses-frame.html
    R api/doc/allclasses-noframe.html
    R api/doc/constant-values.html
    R api/doc/deprecated-list.html
    R api/doc/help-doc.html
    R api/doc/index-files/index-1.html
    R api/doc/index-files/index-2.html
    R api/doc/index-files/index-3.html
    R api/doc/index-files/index-4.html
    R api/doc/index-files/index-5.html
    R api/doc/index-files/index-6.html
    R api/doc/index-files/index-7.html
    R api/doc/index.html
    R api/doc/org/phenotips/mendelianSearch/internal/DefaultMendelianSearchHandler.html
    R api/doc/org/phenotips/mendelianSearch/internal/MendelianSearchRequest.html
    R api/doc/org/phenotips/mendelianSearch/internal/class-use/DefaultMendelianSearchHandler.html
    R api/doc/org/phenotips/mendelianSearch/internal/class-use/MendelianSearchRequest.html
    R api/doc/org/phenotips/mendelianSearch/internal/package-frame.html
    R api/doc/org/phenotips/mendelianSearch/internal/package-summary.html
    R api/doc/org/phenotips/mendelianSearch/internal/package-tree.html
    R api/doc/org/phenotips/mendelianSearch/internal/package-use.html
    R api/doc/overview-tree.html
    R api/doc/package-list
    R api/doc/script.js
    R api/doc/stylesheet.css
    R resources/src/main/resources/js/d3.js

  Log Message:
  -----------
  Removed auto-generated docs and unused D3 file


  Commit: 83875c91c00773f369a98f801ccbe4d6679202bb
      https://github.com/phenotips/mendelian-search-application/commit/83875c91c00773f369a98f801ccbe4d6679202bb
  Author: Matthew Shepherd <mjshepherd at users.noreply.github.com>
  Date:   2015-04-16 (Thu, 16 Apr 2015)

  Changed paths:
    M api/pom.xml
    A api/src/main/java/org/phenotips/mendelianSearch/DefaultMendelianSearch.java
    R api/src/main/java/org/phenotips/mendelianSearch/DummyResponseScriptService.java
    A api/src/main/java/org/phenotips/mendelianSearch/MendelianSearch.java
    R api/src/main/java/org/phenotips/mendelianSearch/MendelianSearchHandler.java
    A api/src/main/java/org/phenotips/mendelianSearch/genotype/MockVariantStore.java
    A api/src/main/java/org/phenotips/mendelianSearch/genotype/VariantStore.java
    R api/src/main/java/org/phenotips/mendelianSearch/internal/DefaultMendelianSearchHandler.java
    A api/src/main/java/org/phenotips/mendelianSearch/phenotype/DefaultPatientPhenotypeScorer.java
    A api/src/main/java/org/phenotips/mendelianSearch/phenotype/DefaultPhenotypeScorer.java
    A api/src/main/java/org/phenotips/mendelianSearch/phenotype/PatientPhenotypeScorer.java
    A api/src/main/java/org/phenotips/mendelianSearch/phenotype/PhenotypeScorer.java
    A api/src/main/java/org/phenotips/mendelianSearch/script/MendelianSearchRequest.java
    M api/src/main/java/org/phenotips/mendelianSearch/script/MendelianSearchScriptService.java
    M api/src/main/resources/META-INF/components.txt
    A api/src/test/org/phenotips/mendelianSearch/phenotype/DefaultPatientPhenotypeScorerTest.java
    A api/src/test/org/phenotips/mendelianSearch/phenotype/DefaultPhenotypeScorerTest.java
    A api/src/test/org/phenotips/mendelianSearch/phenotype/mocks/MockDisease.java
    A api/src/test/org/phenotips/mendelianSearch/phenotype/mocks/MockHPO.java
    A api/src/test/org/phenotips/mendelianSearch/phenotype/mocks/MockMIM.java
    A api/src/test/org/phenotips/mendelianSearch/phenotype/mocks/MockOntologyTerm.java
    A resources/pom.xml
    M ui/src/main/resources/PhenoTips/MendelianLivetableResults.xml
    M ui/src/main/resources/PhenoTips/MendelianResults.xml
    M ui/src/main/resources/PhenoTips/MendelianSearch.xml

  Log Message:
  -----------
  Merge pull request #6 from phenotips/DEMO

Demo


Compare: https://github.com/phenotips/mendelian-search-application/compare/840e636a47a2...83875c91c007


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