[phenotips/phenomecentral.org] 6bc8ba: [maven-release-plugin] prepare for next developmen...

GitHub noreply at github.com
Mon Jul 16 14:53:55 EDT 2018


  Branch: refs/heads/v2
  Home:   https://github.com/phenotips/phenomecentral.org
  Commit: 6bc8ba977747efceebfdbd1f9fd7c8471ae49354
      https://github.com/phenotips/phenomecentral.org/commit/6bc8ba977747efceebfdbd1f9fd7c8471ae49354
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 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: af8ee407a3ae974b5ccfc47d13f4b6363c023780
      https://github.com/phenotips/phenomecentral.org/commit/af8ee407a3ae974b5ccfc47d13f4b6363c023780
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 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: d8a942ed0dee54ecf1c8795172d3530b676cb1bd
      https://github.com/phenotips/phenomecentral.org/commit/d8a942ed0dee54ecf1c8795172d3530b676cb1bd
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 2018)

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

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


  Commit: 771c033ef585fe5c399b368dcfa3b62a32847af6
      https://github.com/phenotips/phenomecentral.org/commit/771c033ef585fe5c399b368dcfa3b62a32847af6
  Author: a-gvo <alina.gvo at gmail.com>
  Date:   2018-07-16 (Mon, 16 Jul 2018)

  Changed paths:
    M pom.xml

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


  Commit: 134d2775a776054c9b18884358856dd4d2d3458e
      https://github.com/phenotips/phenomecentral.org/commit/134d2775a776054c9b18884358856dd4d2d3458e
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2018-07-16 (Mon, 16 Jul 2018)

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

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


  Commit: aa387c225dd817752f8dd86b9ab6a27d7e158240
      https://github.com/phenotips/phenomecentral.org/commit/aa387c225dd817752f8dd86b9ab6a27d7e158240
  Author: Marta Girdea <marta.girdea at gmail.com>
  Date:   2018-07-16 (Mon, 16 Jul 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: 244180f65b0af5a2edb24c462a3b8f6a42677a52
      https://github.com/phenotips/phenomecentral.org/commit/244180f65b0af5a2edb24c462a3b8f6a42677a52
  Author: Marta Girdea <marta.girdea at gmail.com>
  Date:   2018-07-16 (Mon, 16 Jul 2018)

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

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


  Commit: 2263449cc3e7d3b380b5ce7280984ec41688f66b
      https://github.com/phenotips/phenomecentral.org/commit/2263449cc3e7d3b380b5ce7280984ec41688f66b
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 2018)

  Changed paths:
    M rpm/pom.xml

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


  Commit: 01d9ea59dc5200e27a5aee7eb17dde220c091b50
      https://github.com/phenotips/phenomecentral.org/commit/01d9ea59dc5200e27a5aee7eb17dde220c091b50
  Author: Orion Buske <orion at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 2018)

  Changed paths:
    A assets/phenomecentral_logos.svg

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


  Commit: 74435982f7913e07c7638ba49940cdac3cbac815
      https://github.com/phenotips/phenomecentral.org/commit/74435982f7913e07c7638ba49940cdac3cbac815
  Author: katpavlova <katpavlova.ccm at gmail.com>
  Date:   2018-07-16 (Mon, 16 Jul 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: 6bfb4c708368f0f52ec9f22305e5f0cf230971d5
      https://github.com/phenotips/phenomecentral.org/commit/6bfb4c708368f0f52ec9f22305e5f0cf230971d5
  Author: Marta Girdea <marta at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 2018)

  Changed paths:
    M ui/src/main/resources/PhenomeCentral/FooterLinks.xml
    M ui/src/main/resources/data/Consent_forms.xml

  Log Message:
  -----------
  PC-86: Update link to PhenomeCentral consent form. PC-181: Update consent forms


  Commit: 6efdc11ce95609136c81fb94f5cb84768e84c340
      https://github.com/phenotips/phenomecentral.org/commit/6efdc11ce95609136c81fb94f5cb84768e84c340
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2018-07-16 (Mon, 16 Jul 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: bbbdb2831c9745290f6cfa01c8e6aa093d4fbaf1
      https://github.com/phenotips/phenomecentral.org/commit/bbbdb2831c9745290f6cfa01c8e6aa093d4fbaf1
  Author: veronikaslc <veronika.koltunov at gmail.com>
  Date:   2018-07-16 (Mon, 16 Jul 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: 017aa89fa5f5152abe5eebaf273d4809ad9a3e29
      https://github.com/phenotips/phenomecentral.org/commit/017aa89fa5f5152abe5eebaf273d4809ad9a3e29
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 2018)

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

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


  Commit: 3b7092083de34ea81fd56507dd81b435130939cf
      https://github.com/phenotips/phenomecentral.org/commit/3b7092083de34ea81fd56507dd81b435130939cf
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 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: 40fd377bb51577d105f438f71bf08c613d055a92
      https://github.com/phenotips/phenomecentral.org/commit/40fd377bb51577d105f438f71bf08c613d055a92
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 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: 26cc4fdfb597a3d70d3c4b5f1fda9cc38b4d51d2
      https://github.com/phenotips/phenomecentral.org/commit/26cc4fdfb597a3d70d3c4b5f1fda9cc38b4d51d2
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 2018)

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

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


  Commit: 426e3db81f0be1193b765ea297e9103bd1012b47
      https://github.com/phenotips/phenomecentral.org/commit/426e3db81f0be1193b765ea297e9103bd1012b47
  Author: Marta Girdea <marta at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 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: 3a841efc8ed27b31d4dd56bfd7529d8f4479c8ee
      https://github.com/phenotips/phenomecentral.org/commit/3a841efc8ed27b31d4dd56bfd7529d8f4479c8ee
  Author: Marta Girdea <marta.girdea at gmail.com>
  Date:   2018-07-16 (Mon, 16 Jul 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: ce23ed1e4d6766b2910ec48a6eb14647c511541b
      https://github.com/phenotips/phenomecentral.org/commit/ce23ed1e4d6766b2910ec48a6eb14647c511541b
  Author: Marta Girdea <marta.girdea at gmail.com>
  Date:   2018-07-16 (Mon, 16 Jul 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: 7059ee6bfe0f7f4742ca3f3a4bee1bad4f972129
      https://github.com/phenotips/phenomecentral.org/commit/7059ee6bfe0f7f4742ca3f3a4bee1bad4f972129
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 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: 8cf8ed21ed0f6088f5a0d4807d71ab9cf7f3d1f8
      https://github.com/phenotips/phenomecentral.org/commit/8cf8ed21ed0f6088f5a0d4807d71ab9cf7f3d1f8
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 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: 7d55597723bdc6353e82d358a692eecde64c8319
      https://github.com/phenotips/phenomecentral.org/commit/7d55597723bdc6353e82d358a692eecde64c8319
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 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: 7a47fe2bd14b2f843a8939efcf05e3e1dd230157
      https://github.com/phenotips/phenomecentral.org/commit/7a47fe2bd14b2f843a8939efcf05e3e1dd230157
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 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: 22862a19cd56c669a45f1626fc0f3d15ae5d9d83
      https://github.com/phenotips/phenomecentral.org/commit/22862a19cd56c669a45f1626fc0f3d15ae5d9d83
  Author: Orion Buske <orion at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 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: dd5215882b05816a51af6af81d57b5893f536e28
      https://github.com/phenotips/phenomecentral.org/commit/dd5215882b05816a51af6af81d57b5893f536e28
  Author: a-gvo <alina.gvo at gmail.com>
  Date:   2018-07-16 (Mon, 16 Jul 2018)

  Changed paths:
    M war/pom.xml

  Log Message:
  -----------
  PC-233: Included the new remote-matching-core-rest module in the war pom


Compare: https://github.com/phenotips/phenomecentral.org/compare/6bc8ba977747^...dd5215882b05
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