[phenotips/phenomecentral.org] 1f2fd7: PC-86: Update link to PhenomeCentral consent form....

GitHub noreply at github.com
Mon Jul 16 15:09:38 EDT 2018


  Branch: refs/heads/v2
  Home:   https://github.com/phenotips/phenomecentral.org
  Commit: 1f2fd702d1fcfc6710e394d35a33af06044093d7
      https://github.com/phenotips/phenomecentral.org/commit/1f2fd702d1fcfc6710e394d35a33af06044093d7
  Author: Marta Girdea <marta at phenotips.org>
  Date:   2018-07-16 (Mon, 16 Jul 2018)

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


  Commit: 9dad42ce660df0cbd65c35589b14d62ded0ce928
      https://github.com/phenotips/phenomecentral.org/commit/9dad42ce660df0cbd65c35589b14d62ded0ce928
  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: f6326a1425bfab52d72f886fe9882244de856216
      https://github.com/phenotips/phenomecentral.org/commit/f6326a1425bfab52d72f886fe9882244de856216
  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: 9ead984403e32becb5b6594ac32e020c4cf89b3a
      https://github.com/phenotips/phenomecentral.org/commit/9ead984403e32becb5b6594ac32e020c4cf89b3a
  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: 06ab42fad7cad027662697c95f1032067835ade0
      https://github.com/phenotips/phenomecentral.org/commit/06ab42fad7cad027662697c95f1032067835ade0
  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: 14ea14b2e9495f76ae17947b714e3e3a97314471
      https://github.com/phenotips/phenomecentral.org/commit/14ea14b2e9495f76ae17947b714e3e3a97314471
  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: 5499c6a5481f593b3aafb6cb08a8f5a358ffc68f
      https://github.com/phenotips/phenomecentral.org/commit/5499c6a5481f593b3aafb6cb08a8f5a358ffc68f
  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: 7365823a4d1258334e1e07173c34cba146e260e4
      https://github.com/phenotips/phenomecentral.org/commit/7365823a4d1258334e1e07173c34cba146e260e4
  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: fb26e59947953e04fa5bbbe8f2e671e5336d1527
      https://github.com/phenotips/phenomecentral.org/commit/fb26e59947953e04fa5bbbe8f2e671e5336d1527
  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: 51caa8511a4b855b8d53f073b2f17e8f1532d0d7
      https://github.com/phenotips/phenomecentral.org/commit/51caa8511a4b855b8d53f073b2f17e8f1532d0d7
  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: 55d74759f952c416b778335549dc00495254e158
      https://github.com/phenotips/phenomecentral.org/commit/55d74759f952c416b778335549dc00495254e158
  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: bbd58667dd22b3b0564b0b5dea2c7b061b974cca
      https://github.com/phenotips/phenomecentral.org/commit/bbd58667dd22b3b0564b0b5dea2c7b061b974cca
  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: 93bb2c6ea993ad53a046228b3db714abf1b1373d
      https://github.com/phenotips/phenomecentral.org/commit/93bb2c6ea993ad53a046228b3db714abf1b1373d
  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: 9a170a47a421982574ab2499cd4243df31848990
      https://github.com/phenotips/phenomecentral.org/commit/9a170a47a421982574ab2499cd4243df31848990
  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: a7b9890ac54a1e2567a60db418ddb5398db3c2c7
      https://github.com/phenotips/phenomecentral.org/commit/a7b9890ac54a1e2567a60db418ddb5398db3c2c7
  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: a7122a0f806ff1658417de2b55d542e25b253e86
      https://github.com/phenotips/phenomecentral.org/commit/a7122a0f806ff1658417de2b55d542e25b253e86
  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/dd5215882b05...a7122a0f806f
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