[phenotips/patient-network] bd8b79: PN-239: Allow filtering matches separately by phen...

GitHub noreply at github.com
Mon Jan 22 16:41:24 EST 2018


  Branch: refs/heads/stable-1.1.6
  Home:   https://github.com/phenotips/patient-network
  Commit: bd8b79c46d8f6066c7e803b0a47c1537bb4fb0e8
      https://github.com/phenotips/patient-network/commit/bd8b79c46d8f6066c7e803b0a47c1537bb4fb0e8
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2018-01-22 (Mon, 22 Jan 2018)

  Changed paths:
    M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js
    M matching-notification-ui/src/main/resources/MatchingNotification/UnnotifiedTable.xml

  Log Message:
  -----------
  PN-239: Allow filtering matches separately by phenotypical and genotypical scores

Addressed user comments:
  - rearranged input fields for scores to match the order of fields in the table
  - used floor() instead of round() to round scores in the table to make filtering behave more intuitively
  - un-checked 'expand all" by default


  Commit: 3c62b934aed2e27fb2a59ba42f2caa848e37758c
      https://github.com/phenotips/patient-network/commit/3c62b934aed2e27fb2a59ba42f2caa848e37758c
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2018-01-22 (Mon, 22 Jan 2018)

  Changed paths:
    M similarity-data-impl/src/test/java/org/phenotips/data/similarity/internal/RestrictedPatientSimilarityViewTest.java
    M similarity-genotype-view/src/main/java/org/phenotips/data/similarity/genotype/DefaultPatientGenotype.java
    M similarity-genotype-view/src/main/java/org/phenotips/data/similarity/genotype/DefaultPatientGenotypeSimilarityView.java

  Log Message:
  -----------
  PN-257: VCF variants do not participating in match scoring anymore


  Commit: 747b1c8f722b66b3b30fa87b433a3ef9a09ae0d0
      https://github.com/phenotips/patient-network/commit/747b1c8f722b66b3b30fa87b433a3ef9a09ae0d0
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2018-01-22 (Mon, 22 Jan 2018)

  Changed paths:
    A ui/src/main/resources/PhenoTips/MatchingRunInfo.xml
    A ui/src/main/resources/PhenoTips/MatchingRunInfoClass.xml

  Log Message:
  -----------
  PN-253: Create a configuration table to show the last date+time matching was run


  Commit: 2e4ff4d502887f6dd049edbf2656c262b663b067
      https://github.com/phenotips/patient-network/commit/2e4ff4d502887f6dd049edbf2656c262b663b067
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2018-01-22 (Mon, 22 Jan 2018)

  Changed paths:
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/MatchFinder.java
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/MatchFinderManager.java
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/internal/DefaultMatchFinderManager.java
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/internal/LocalMatchFinder.java
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java
    M pom.xml

  Log Message:
  -----------
  PN-252: Run local matches search only for patients updated/created since last search


  Commit: 1dfa1cfe4710307c5cd3f0121137ab7ce4a9f86b
      https://github.com/phenotips/patient-network/commit/1dfa1cfe4710307c5cd3f0121137ab7ce4a9f86b
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2018-01-22 (Mon, 22 Jan 2018)

  Changed paths:
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/MatchFinderManager.java
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/internal/DefaultMatchFinderManager.java
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/internal/LocalMatchFinder.java
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java
    M pom.xml

  Log Message:
  -----------
  PN-252: Run local matches search only for patients updated/created since last search
Addressing codereview comments


  Commit: e676aaba67b8c1a69aea4c5e57599f91fffeceb7
      https://github.com/phenotips/patient-network/commit/e676aaba67b8c1a69aea4c5e57599f91fffeceb7
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2018-01-22 (Mon, 22 Jan 2018)

  Changed paths:
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/internal/LocalMatchFinder.java

  Log Message:
  -----------
  PN-252: Run local matches search only for patients updated/created since last search

Added more logging and more error catching


  Commit: 7031d30f6e51d9f8039811138ef090684b1623f1
      https://github.com/phenotips/patient-network/commit/7031d30f6e51d9f8039811138ef090684b1623f1
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2018-01-22 (Mon, 22 Jan 2018)

  Changed paths:
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/MatchFinderManager.java
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/internal/DefaultMatchFinderManager.java
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java
    M pom.xml

  Log Message:
  -----------
  PN-252: Run local matches search only for patients updated/created since last search

Simplified the API a bit


  Commit: c560125ed3d858aaf34923e1154f72a9a8a82599
      https://github.com/phenotips/patient-network/commit/c560125ed3d858aaf34923e1154f72a9a8a82599
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2018-01-22 (Mon, 22 Jan 2018)

  Changed paths:
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/internal/DefaultMatchFinderManager.java
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/internal/LocalMatchFinder.java
    R ui/src/main/resources/PhenoTips/MatchingRunInfo.xml
    M ui/src/main/resources/PhenoTips/MatchingRunInfoClass.xml
    A ui/src/main/resources/PhenoTips/MatchingUpdateAndInfo.xml

  Log Message:
  -----------
  PN-252: Run local matches search only for patients updated/created since last search

Added statistics about patients affected by the match


  Commit: fd2e587ea9995a1b569e9cc52bba3fd4f378a05b
      https://github.com/phenotips/patient-network/commit/fd2e587ea9995a1b569e9cc52bba3fd4f378a05b
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2018-01-22 (Mon, 22 Jan 2018)

  Changed paths:
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/MatchFinder.java
    A matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/internal/AbstractMatchFinder.java
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/internal/LocalMatchFinder.java

  Log Message:
  -----------
  PN-252: Run local matches search only for patients updated/created since last search

Refactored code
 - separated common matcher functionality into AbstractMatchFinder
 - extended MatchFinder API to provide more control over matching process


  Commit: 59c329b7308f00c91fe9ffb732c3d247e77e0833
      https://github.com/phenotips/patient-network/commit/59c329b7308f00c91fe9ffb732c3d247e77e0833
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2018-01-22 (Mon, 22 Jan 2018)

  Changed paths:
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/MatchingNotificationManager.java
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/MatchFinderManager.java
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/internal/DefaultMatchFinderManager.java
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java
    M matching-notification-api/src/main/java/org/phenotips/matchingnotification/script/MatchingNotificationScriptService.java

  Log Message:
  -----------
  PN-252: Run local matches search only for patients updated/created since last search
PN-243: Finding local and remote matches should have separate buttons

Back-end changes in various MatchingNotification components to allow better control over what matches are found
(local or remote, all or updated since last matcher run)


  Commit: 7c805c0d407e0e8fc7346f88c62c070f53dee908
      https://github.com/phenotips/patient-network/commit/7c805c0d407e0e8fc7346f88c62c070f53dee908
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2018-01-22 (Mon, 22 Jan 2018)

  Changed paths:
    M pom.xml

  Log Message:
  -----------
  PN-252: Run local matches search only for patients updated/created since last search
PN-243: Finding local and remote matches should have separate buttons

pom.xml update


  Commit: fc2945809a155cfd9b2678ecc5c14dcefdd9fa76
      https://github.com/phenotips/patient-network/commit/fc2945809a155cfd9b2678ecc5c14dcefdd9fa76
  Author: Andrew Misyura <asm at phenotips.org>
  Date:   2018-01-22 (Mon, 22 Jan 2018)

  Changed paths:
    M matching-notification-api/src/main/resources/ApplicationResources.properties
    A matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/findMatches.css
    A matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/findMatches.js
    M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css
    M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/notifiedMatchesTable.js
    M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/unnotifiedMatchesTable.js
    M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/utils.js
    A matching-notification-ui/src/main/resources/MatchingNotification/MatchingRunInfoClass.xml
    A matching-notification-ui/src/main/resources/MatchingNotification/MatchingUpdateAndInfo.xml
    M matching-notification-ui/src/main/resources/MatchingNotification/RequestHandler.xml
    M matching-notification-ui/src/main/resources/MatchingNotification/UnnotifiedTable.xml
    R ui/src/main/resources/PhenoTips/MatchingRunInfoClass.xml
    R ui/src/main/resources/PhenoTips/MatchingUpdateAndInfo.xml

  Log Message:
  -----------
  PN-243: Finding local and remote matches should have separate buttons
PN-252: Run local matches search only for patients updated/created since last search

UI changes:
  - moved "find matches" button from the matching notification page to the "refresh matches" page
  - added separate buttons to find local matches and remore matches, as well as find all matches or only matches for updated patients
  - moved some .xml files around to have them in the same place with other code using common .js files


Compare: https://github.com/phenotips/patient-network/compare/720da881cb44...fc2945809a15


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