[phenotips/phenomecentral.org] f377df: [maven-release-plugin] prepare for next developmen...

GitHub noreply at github.com
Mon Oct 15 12:44:32 EDT 2018


  Branch: refs/heads/stable-1.1.x-on-PT-1.4
  Home:   https://github.com/phenotips/phenomecentral.org
  Commit: f377dffeeb7df946900821963828f57fb00f82e5
      https://github.com/phenotips/phenomecentral.org/commit/f377dffeeb7df946900821963828f57fb00f82e5
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M hsqldb-database/pom.xml
    M pom.xml
    M rpm/pom.xml
    M standalone/pom.xml
    M ui/pom.xml
    M war/pom.xml

  Log Message:
  -----------
  [maven-release-plugin] prepare for next development iteration


  Commit: 55afa0b646807f7f498254f74952dc1c5b557dc3
      https://github.com/phenotips/phenomecentral.org/commit/55afa0b646807f7f498254f74952dc1c5b557dc3
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M rpm/pom.xml

  Log Message:
  -----------
  [misc] Increased the document cache size, since certain migrations may fail if the cache is too small (also for the RPM package)


  Commit: df1777a57cae53f6aabb8e1c5a097db2a9b02e59
      https://github.com/phenotips/phenomecentral.org/commit/df1777a57cae53f6aabb8e1c5a097db2a9b02e59
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M ui/src/main/resources/PhenomeCentral/RegistrationWiki.xml

  Log Message:
  -----------
  [misc] Enabling autologin doesn't work


  Commit: d45c8fe393024daea1481f95395eef7943186852
      https://github.com/phenotips/phenomecentral.org/commit/d45c8fe393024daea1481f95395eef7943186852
  Author: a-gvo <alina.gvo at gmail.com>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M pom.xml

  Log Message:
  -----------
  PC-187: Changed the patient-network and remote-matching versions to 1.2-SNAPSHOT.


  Commit: e57111b73bebd1fd9acde1fb5f4aadc78c818311
      https://github.com/phenotips/phenomecentral.org/commit/e57111b73bebd1fd9acde1fb5f4aadc78c818311
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M rpm/src/main/resources/exomiser_cron.py

  Log Message:
  -----------
  [bugfix] Create exomiser output directory if not already exist


  Commit: 2894e854c9fc97023cd6c3e6f2449dbbe03cdd5a
      https://github.com/phenotips/phenomecentral.org/commit/2894e854c9fc97023cd6c3e6f2449dbbe03cdd5a
  Author: Marta Girdea <marta.girdea at gmail.com>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M ui/src/main/resources/ColorThemes/Flat.xml

  Log Message:
  -----------
  PC-197: "Patient ID" and "Create" overlap when using split screen

Quick fix. The right fix is an overall responsive layout.


  Commit: a9a7a80b37fda108c646c708b0d90ba210a4e804
      https://github.com/phenotips/phenomecentral.org/commit/a9a7a80b37fda108c646c708b0d90ba210a4e804
  Author: Marta Girdea <marta.girdea at gmail.com>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M ui/src/main/resources/ColorThemes/Flat.xml

  Log Message:
  -----------
  [misc] applied codestyle


  Commit: ddd19d7d0b8c27a5a95edeab40d2a737175c1c40
      https://github.com/phenotips/phenomecentral.org/commit/ddd19d7d0b8c27a5a95edeab40d2a737175c1c40
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M rpm/pom.xml

  Log Message:
  -----------
  [misc] Fixed failing CI build


  Commit: d1e1bb4ab807a036c813bf6549f4a52a8d91a443
      https://github.com/phenotips/phenomecentral.org/commit/d1e1bb4ab807a036c813bf6549f4a52a8d91a443
  Author: Orion Buske <orion at phenotips.org>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    A assets/phenomecentral_logos.svg

  Log Message:
  -----------
  [asset] Added PhenomeCentral logo svg


  Commit: b387a5212a93bda58aa2cb1dc8b259e8fcf12d25
      https://github.com/phenotips/phenomecentral.org/commit/b387a5212a93bda58aa2cb1dc8b259e8fcf12d25
  Author: katpavlova <katpavlova.ccm at gmail.com>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M war/src/main/webapp/resources/js/xwiki/usersandgroups/nonactiveusers.js

  Log Message:
  -----------
  PC-175: Fix typo and make string translatable, wrap existing UI with escape tool


  Commit: 56eb6888f9862775a7c7bda3aaf5f9fa4b6dc3cd
      https://github.com/phenotips/phenomecentral.org/commit/56eb6888f9862775a7c7bda3aaf5f9fa4b6dc3cd
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M pom.xml
    M rpm/pom.xml
    M standalone/pom.xml
    M standalone/src/assemble/application.xml
    M ui/pom.xml
    M ui/src/main/resources/PhenoTips/AllDataGadget.xml
    M ui/src/main/resources/PhenoTips/GroupsGadget.xml
    M ui/src/main/resources/PhenoTips/MyDataGadget.xml
    M ui/src/main/resources/PhenoTips/PatientTemplate.xml
    M war/pom.xml

  Log Message:
  -----------
  [misc] Upgrading phenotips dependency to 1.4-SNAPSHOT


  Commit: ec1531c11f5e11d333cc8334827b15e28e5a092e
      https://github.com/phenotips/phenomecentral.org/commit/ec1531c11f5e11d333cc8334827b15e28e5a092e
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M rpm/pom.xml
    A rpm/src/main/resources/ctakes.xml
    M ui/src/main/resources/PhenoTips/AllDataGadget.xml
    M ui/src/main/resources/PhenoTips/MyDataGadget.xml

  Log Message:
  -----------
  [misc] Upgrading phenotips dependency to 1.4-SNAPSHOT
Addressing codereview comments


  Commit: a96f9a878bb8ca0dcf8161aff5ab10f443f39130
      https://github.com/phenotips/phenomecentral.org/commit/a96f9a878bb8ca0dcf8161aff5ab10f443f39130
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M pom.xml
    M war/pom.xml

  Log Message:
  -----------
  [misc] More changes needed for upgrading to PhenoTips 1.4-SNAPSHOT


  Commit: 34091ac29466ee4e97a662e20dbe0e15b186be51
      https://github.com/phenotips/phenomecentral.org/commit/34091ac29466ee4e97a662e20dbe0e15b186be51
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M ui/src/main/resources/PhenoTips/AllDataGadget.xml
    M ui/src/main/resources/PhenoTips/FamilyDataGadget.xml
    R ui/src/main/resources/PhenoTips/GroupsGadget.xml
    M ui/src/main/resources/PhenoTips/PublicDataGadget.xml
    M ui/src/main/resources/PhenoTips/SharedFamilyGadget.xml
    M ui/src/main/resources/PhenoTips/UIX_Field__omim_suggestions.xml

  Log Message:
  -----------
  [misc] More changes needed for upgrading to PhenoTips 1.4-SNAPSHOT


  Commit: 8d2ef0c8d3335e03968b89825146cdc8e28e85bd
      https://github.com/phenotips/phenomecentral.org/commit/8d2ef0c8d3335e03968b89825146cdc8e28e85bd
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M standalone/src/main/resources/start.sh

  Log Message:
  -----------
  [misc] Increase the amount of allocated memory and remove the PermSize configuration, since it's no longer valid on Java8


  Commit: 1bffaab663042f024210c902d91e1734b866261a
      https://github.com/phenotips/phenomecentral.org/commit/1bffaab663042f024210c902d91e1734b866261a
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

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

  Log Message:
  -----------
  [misc] Removed deprecated field from the consents configuration


  Commit: 80699ce2ed80fb2bb3ee512584def5eb912772bf
      https://github.com/phenotips/phenomecentral.org/commit/80699ce2ed80fb2bb3ee512584def5eb912772bf
  Author: Marta Girdea <marta at phenotips.org>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    R ui/src/main/resources/PhenoTips/PatientAccessRightsManagement.xml
    A ui/src/main/resources/PhenomeCentral/JournalSubmission.xml

  Log Message:
  -----------
  PC-185: Reimplement the 'submission to journal' feature
Reimplemented as an extension of the AccessRightsManager widget, instead of modifying the code of the widget directly.
IMPORTANT: Depends on PT-3324, so it will work only if PhenomeCentral is built on top of a PhenoTips version where either PR #2379 or PR #2380 is merged.
TODOs:
* the list of journals is still hardcoded
* the UI is not translatable.


  Commit: dab70c12572527857ed0ad71139f70c34abc8011
      https://github.com/phenotips/phenomecentral.org/commit/dab70c12572527857ed0ad71139f70c34abc8011
  Author: Marta Girdea <marta.girdea at gmail.com>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M ui/src/main/resources/PhenomeCentral/JournalSubmission.xml

  Log Message:
  -----------
  PC-185: Reimplement the 'submission to journal' feature

[Addressing code review comments] Added missing `parent` for extension document.


  Commit: ae4cd978a7917e683004b79c9b6049e83acd1224
      https://github.com/phenotips/phenomecentral.org/commit/ae4cd978a7917e683004b79c9b6049e83acd1224
  Author: Marta Girdea <marta.girdea at gmail.com>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M ui/src/main/resources/PhenomeCentral/JournalSubmission.xml

  Log Message:
  -----------
  PC-185: Reimplement the 'submission to journal' feature

Ensure the journal submission is shown only for patients, not families. Families cannot be submitted to the journal at the moment.


  Commit: 30d82763aa6ff147375a6a9807b6850a22bde09c
      https://github.com/phenotips/phenomecentral.org/commit/30d82763aa6ff147375a6a9807b6850a22bde09c
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    A ui/src/main/resources/PhenomeCentral/Journal.xml
    M ui/src/main/resources/PhenomeCentral/JournalSubmission.xml

  Log Message:
  -----------
  PC-185: Reimplement the 'submission to journal' feature
The list of journals isn't hardcoded anymore


  Commit: 6e7ed7811edd55edd1c96617626473b671b5082c
      https://github.com/phenotips/phenomecentral.org/commit/6e7ed7811edd55edd1c96617626473b671b5082c
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M ui/src/main/resources/PhenomeCentral/JournalSubmission.xml

  Log Message:
  -----------
  PC-185: Reimplement the 'submission to journal' feature
Bugfix: wrong access level was granted


  Commit: b13d4df06a3f9789a22daf51405c371bbc6e1b34
      https://github.com/phenotips/phenomecentral.org/commit/b13d4df06a3f9789a22daf51405c371bbc6e1b34
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M ui/src/main/resources/PhenomeCentral/JournalSubmission.xml

  Log Message:
  -----------
  [bulletproofing] Check if `console` exists first before using it, for IE compatibility


  Commit: d2870f96c96f6cd74273dbfaf190e214f21bd77f
      https://github.com/phenotips/phenomecentral.org/commit/d2870f96c96f6cd74273dbfaf190e214f21bd77f
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M ui/src/main/resources/PhenomeCentral/Journal.xml
    M ui/src/main/resources/PhenomeCentral/JournalSubmission.xml

  Log Message:
  -----------
  [cleanup] Mark code documents as hidden


  Commit: a42183aaebb800003b11115f557a02585d104d25
      https://github.com/phenotips/phenomecentral.org/commit/a42183aaebb800003b11115f557a02585d104d25
  Author: Orion Buske <orion at phenotips.org>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    A assets/Montserrat-Bold.ttf
    A assets/Montserrat-Regular.ttf
    M assets/phenomecentral_logos.svg

  Log Message:
  -----------
  [assets] Added PhenomeCentral logo fonts (and removed svg references to other fonts)


  Commit: c72bdb36eb2c6daf8cc9c3a7c0af5c9bdd3aa33c
      https://github.com/phenotips/phenomecentral.org/commit/c72bdb36eb2c6daf8cc9c3a7c0af5c9bdd3aa33c
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2018-10-15 (Mon, 15 Oct 2018)

  Changed paths:
    M ui/src/main/resources/Families/WebHome.xml
    M ui/src/main/resources/PhenoTips/AllDataGadget.xml
    R ui/src/main/resources/PhenoTips/DBWebHomeSheet.xml
    R ui/src/main/resources/PhenoTips/DatabaseFilters.xml
    M ui/src/main/resources/PhenoTips/FamilyDataGadget.xml
    R ui/src/main/resources/PhenoTips/FamilyFilters.xml
    R ui/src/main/resources/PhenoTips/GroupCases.xml
    R ui/src/main/resources/PhenoTips/GroupSharedCases.xml
    M ui/src/main/resources/PhenoTips/MyDataGadget.xml
    M ui/src/main/resources/PhenoTips/MyGroupsGadget.xml
    M ui/src/main/resources/PhenoTips/PatientTemplate.xml
    M ui/src/main/resources/PhenoTips/PublicDataGadget.xml
    M ui/src/main/resources/PhenoTips/SharedFamilyGadget.xml
    R ui/src/main/resources/PhenoTips/StudyCases.xml
    M ui/src/main/resources/data/WebHome.xml
    M war/pom.xml

  Log Message:
  -----------
  [misc] More changes needed for upgrading to PhenoTips 1.4-SNAPSHOT


Compare: https://github.com/phenotips/phenomecentral.org/compare/19b50381b6cd...c72bdb36eb2c
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