1. 01 Oct, 2015 2 commits
  2. 24 Sep, 2015 1 commit
  3. 23 Sep, 2015 1 commit
  4. 21 Sep, 2015 4 commits
  5. 18 Sep, 2015 4 commits
  6. 08 Sep, 2015 1 commit
  7. 02 Sep, 2015 1 commit
  8. 01 Sep, 2015 1 commit
  9. 28 Aug, 2015 1 commit
  10. 31 Jul, 2015 2 commits
  11. 28 Jul, 2015 1 commit
  12. 24 Jul, 2015 1 commit
  13. 23 Jul, 2015 2 commits
  14. 22 Jul, 2015 1 commit
  15. 21 Jul, 2015 3 commits
  16. 17 Jul, 2015 2 commits
    • Fokkema's avatar
      Reviewed r602: · af58c15c
      Fokkema authored
      - Minor changes to the manual; clarifications, minor fixes.
      - Whitespace changes induced by editor.
      - Changed all mentions of "id" to "ID" when the abbreviation was meant (and not field names).
      
      
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@605 a7477d18-a37e-46de-aef1-57953c184492
      af58c15c
    • Fokkema's avatar
      Reviewed r595 and fixed two bugs: · bd8a341f
      Fokkema authored
      - Removed gene update on individual create, because it can't have variants.
      - Fixed typos in the comments.
      - Applied coding standards.
      - Removed useless array_unique() calls.
      - Removed incorrect comments.
      - In gene updates for screenings, the individual status is now checked as well.
      - In gene update for a new screening, looking for variants of the current screening will do no good because there can be none - looking for variants belonging to the individual instead.
      - Removed duplicate gene updated when editing a screening.
      - When confirming variants with a screening or removing variants from a screening, only run the gene update for the affected variants.
      - Greatly simplified the gene update code for transcripts create, edit and delete, since the gene symbol is already known in a variable.
      - Fixed bug; Fixed proper check whether you're in a submission when confirming variants.
      - Fixed bug;  Editing a transcript entry didn't update the "Last edited by" and "Date last edited" fields.
      
      
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@604 a7477d18-a37e-46de-aef1-57953c184492
      bd8a341f
  17. 15 Jul, 2015 1 commit
  18. 10 Jul, 2015 3 commits
  19. 08 Jul, 2015 3 commits
    • Fokkema's avatar
      Reviewed r592: · 745c0ae2
      Fokkema authored
      - Fixed bug; A normal import using a file with gene information didn't work anymore, because the gene's checkFields() was run and rejected one field.
      - Merged two consecutive updateEntry() calls into one.
      - Fixed bug; Only run setUpdatedDate() for entries that are at least LEVEL_MARKED.
      - When ScreeningsToVariants is affected, actually the screening should define the setUpdatedDate() call, not the variant.
      
      
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@599 a7477d18-a37e-46de-aef1-57953c184492
      745c0ae2
    • Fokkema's avatar
      Updated Objects::checkFields() to included a feature in... · 0a655043
      Fokkema authored
      Updated Objects::checkFields() to included a feature in Object_Custom::checkFields() which reports valid options when a field's given value is not in a selection list's set of options.
      
      
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@598 a7477d18-a37e-46de-aef1-57953c184492
      0a655043
    • Fokkema's avatar
      Reviewed r587: · 1831bd32
      Fokkema authored
      - Minor edits of comments.
      - Make sure we *always* check only the first of grouped statusses, instead of relying on PHP's type casting during comparison of text and integers.
      - Rather a short-hand if than lots of code repeated.
      - Fixed notices in unique variant view when owner is unknown.
      
      
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@597 a7477d18-a37e-46de-aef1-57953c184492
      1831bd32
  20. 07 Jul, 2015 1 commit
    • Fokkema's avatar
      Reviewed r586: · 8b9bfb72
      Fokkema authored
      - Fixed the construction of the selection list in class/object_genes.php.
      - Fixed the ID check in class/object_transcript_variants.php.
      - Many changes in import.php:
        * Fixed indentation and use of tabs instead of spaces.
        * Improved comments and fixed many typos in comments and messages printed to the screen.
        * Removed redundant function lovd_calculateDiffScore().
        * Standardized variable names and applied standard coding styles here and there.
        * The lovd_isAuthorized() function did not receive proper authorization object names for variant edits, thus returned a "Access denied" for all curators editing variants.
        * Removed some leftover commented code.
        * The code reporting edits of columns not allowed to be edited, was repeated for each section. Pulled it out and put it in one place.
        * Added htmlspecialchars() where needed in error messages printed on the screen to prevent XSS attacks through file uploads.
        * Standardized code a bit that reports unallowed edits of linking tables, but it now reports errors incorrectly - will be fixed later.
        * Put back some code specifically for inserts, back to the code block for inserts.
        * Fixed bug; When having todo's other than insert or update, the $nDataTotal count was wrong, and the progress bar completed too soon.
        * Rewrote an extensive switch() statement to a simple strpos() check.
      
      
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@596 a7477d18-a37e-46de-aef1-57953c184492
      8b9bfb72
  21. 02 Jul, 2015 1 commit
  22. 01 Jul, 2015 1 commit
  23. 30 Jun, 2015 2 commits