1. 01 Oct, 2019 1 commit
  2. 05 Sep, 2019 1 commit
  3. 27 Aug, 2019 1 commit
  4. 03 Nov, 2017 1 commit
  5. 25 Jul, 2017 1 commit
  6. 20 Jul, 2017 1 commit
  7. 06 Dec, 2016 1 commit
  8. 09 Sep, 2016 1 commit
  9. 08 Sep, 2016 1 commit
  10. 01 Sep, 2016 4 commits
    • Ivo Fokkema's avatar
      Reviewed #117: · 03d5476d
      Ivo Fokkema authored
      - Removed inc-lib-diseases.php since it's not a library and it's only used in one place. Copied the data over there, and applied coding styles (lists of data for option lists we often keep in $_SETT).
      - Simplified VL column definition, you only need to provide the field type if you don't have a physical field for that data.
      - Simplified the inc-upgrade.php call, so there's only one ALTER TABLE run.
      - Simplified changelog a bit, it's for the users and not for the programmers :)
    • mkroon's avatar
      Fix editing tissues field for diseases and updated DB model. · 15943f43
      mkroon authored
      * Bugfix, stored values for tissues field of diseases were not
        displayed when editing form.
      * Updated tissues field in DB to TEXT format (since multiple values
        may be selected from a large array).
      * Reverted pretty display of tissues field in viewEntry and viewList to
        make it consistent with custom column select fields.
    • mkroon's avatar
      Added option groups feature to select fields in form generator. · bfd76530
      mkroon authored
      * Set option groups for diseases's tissues field.
      * Made tissue field for diseases multi-selectable.
    • mkroon's avatar
  11. 20 Jul, 2016 1 commit
    • mkroon's avatar
      New column widths for major edit/create forms. · 0d1a3658
      mkroon authored
      After trial and error, the major edit and create forms are displayed
      nicely with a column width of 35% for the labels and 65% for the input
      fields. This means that most labels are on a single line and all
      standard input elements do not exceed the table borders. The changes
      are applied to all forms of the major objects (diseases, genes, etc.).
      These figures are suitable for standard edit and create forms where
      the table has a width of 760px with 14px reserved for the middle column
      with help links, and when select boxes have the standard 75 characters
      width for their content and text boxes have a width of 50 cols. This is
      tested in Chromium and Firefox.
  12. 08 Feb, 2016 1 commit
  13. 05 Feb, 2016 1 commit
  14. 02 Feb, 2016 1 commit
    • mkroon's avatar
      Made sure all numeric fields in viewlists are right-aligned. · 956427a2
      mkroon authored
      Left-aligned numeric fields:
      1.  (x) Genes > View all genes: {Transcripts, Variants, Unique variants}
      2.  (x) Transcripts > View transcripts: {ID, Variants}
      3.  (x) Variants > View genomic variants: {Variant ID, Frequency?}
      4.  (x) Individuals > View individuals: {Individual ID, Variants, Panel Size}
      5.  (x) Diseases > View diseases: {ID, OMIM ID}
      6.  (x) Genes > View GPR78 gene > Active transcripts: {ID, Variants}
      7.  (x) Transcripts > View transcripts of gene GPR78: {ID, Variants}
      8.  (x) Variants > View unique variants in GPR78: {Reported, Exon?, Frequency?}
      9.  (x) Variants > View all transcript variants in GPR78: {Exon?, Frequency?}
      10. (x) Variants > View genomic variant # > Variant on transcripts: {Exon?}
      11. (x) Variants > Full data view for GPR78: {Exon?, Frequency?, Panel size}
      12. (x) Submit > Select screening to add variant to: {Screening ID, Variants found}
      13. (x) Screenings > View screenings: {Screening ID, Individual ID, Variants found}
      14. (x) Screenings > View screenings that screened gene GPR78: {Screening ID, Individual ID, Variants found}
      15. (x) Individuals > View individual # > Screenings: {Screening ID, Variants found}
      Fixed by altering aColumnsViewList attributes of object_* classes by
      adding CSS:
          'view' => array('Phenotypes', 80, 'style="text-align : right;"'),
  15. 08 Dec, 2015 1 commit
  16. 19 Oct, 2015 1 commit
  17. 07 May, 2015 1 commit
  18. 29 Jan, 2015 1 commit
  19. 18 Oct, 2014 1 commit
  20. 26 Feb, 2014 1 commit
  21. 13 Dec, 2013 1 commit
    • Ivo Fokkema's avatar
      Merged with NGS_diagnostics branch: · 6348906e
      Ivo Fokkema authored
      - class/template.php now also loads the JeeGoo files in the clean template, so that menu's are also available in windows with the clean template.
      - Fixed notices in the data listings caused by incorrect search expressions.
      - Added support for FLOAT columns:
        * FLOAT columns could not be searched in a numeric way.
        * Added proper checks in checkFields() for FLOAT columns.
      - Improved ViewList and ViewEntry for diseases associated with many genes:
        * Increased the group_concat() output size in diseases.php, to be able to cope with a possible long list of genes a disease is associated to.
        * The disease VL now shortens the list of associated genes to 22, and in case there are more, it shows 20 genes and mentions the number of genes not shown.
        * The disease VE now shows the total number of genes associated with the disease, and shortens the list of associated genes to 22. If there are more, you can click a link to instantly view the entire list.
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@375 a7477d18-a37e-46de-aef1-57953c184492
  22. 09 Sep, 2013 1 commit
  23. 20 Jun, 2013 2 commits
    • Ivo Fokkema's avatar
      Fixed two bugs in previous commit: · bb45cefa
      Ivo Fokkema authored
      - Added DISTINCT to geneid in disease VE query, such that the gene symbols are not repeated that much.
      - Added proper checks on statusid for the numbers of individuals and phenotypes in the disease VL and VE.
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@309 a7477d18-a37e-46de-aef1-57953c184492
    • Ivo Fokkema's avatar
      Created phenotype data view per disease and improved data linking: · 169ab86e
      Ivo Fokkema authored
      - Some numbers on the gene homepage (public variants, hidden variants) are now clickable in case you are authorized to see these subsets.
      - The disease listing now shows the number of phenotype entries associated with each disease.
      - The disease detailed view now shows the number of individuals reported having this disease, and the number of phenotype entries associated with this disease. The latter is a link leading to the phenotype data listing.
      - Also, the individuals viewlist is only loaded when individuals are known to be associated with the disease in question.
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@308 a7477d18-a37e-46de-aef1-57953c184492
  24. 30 May, 2013 1 commit
    • Ivo Fokkema's avatar
      Released 3.0-05: · 1063eab2
      Ivo Fokkema authored
      - The list of diseases now shows the number of individuals in the database linked to these diseases.
      - The list of individuals on the disease detailed view is now split in pages and can be navigated.
      - Fixed bug; On large installations, the check_update.php script took quite some time and locked the session of the current user.
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@302 a7477d18-a37e-46de-aef1-57953c184492
  25. 19 Dec, 2012 1 commit
    • Ivo Fokkema's avatar
      Fixed a large amount of bugs and improved code for enabling default custom columns: · 4b94b0cf
      Ivo Fokkema authored
      - Added Selenium unit test for the creation of a disease, linked to a gene.
      - Implemented lovd_addAllDefaultCustomColumns() that adds custom columns to genes and diseases alike, whether new or existing. It replaces lovd_addAllDefaultCustomColumnsForGene().
      - Implemented lovd_addAllDefaultCustomColumns() for newly created diseases, replacing custom code.
      - Fixed bug; The wrong field was highlighted when trying to create a disease with a name already existing in the database.
      - Fixed bug; Genes created when importing SeattleSeq files didn't get their Entrez Gene and OMIM IDs stored.
      - Fixed problem with creating genes and transcripts when importing SeattleSeq annotated files with MySQL's strict mode on.
      - Reformatted the variant mapper a bit; improved variable names and added comments, changed structure just a bit.
      - Fixed problem with creating transcripts by the variant mapper with MySQL's strict mode on.
      - Fixed bug; Mapping variants to transcripts not yet in LOVD failed because of a bug introduced in r256.
      - Fixed bug; The RNA field was not predicted when mapping variants onto transcripts not yet in LOVD.
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@271 a7477d18-a37e-46de-aef1-57953c184492
  26. 11 Oct, 2012 1 commit
    • Ivo Fokkema's avatar
      Released 3.0-beta-09: · 912afaa4
      Ivo Fokkema authored
      - Fixed bug; Creating a personal data download for a user without submitted data, generated an error.
      - Fixed bug; In a full data download the Variants_On_Transcripts section also contained data from the Variants_On_Genome section.
      - Fixed bug; An owner of a screening could not be changed by editing the field.
      - Adapted more checkFields() calls to pass $zData through as an argument, rather than globaling it.
      - Adapted more getForm() calls to return the form data immediately if already run before.
      - Fixed notice when trying to import unknown data type files.
      - Added link to the import page from the setup area.
      - Added the inline gene switch icon to SVN, previously forgot to upload it.
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@237 a7477d18-a37e-46de-aef1-57953c184492
  27. 04 Oct, 2012 1 commit
    • Ivo Fokkema's avatar
      New draft of the import script: · 35c55063
      Ivo Fokkema authored
      - Import is only allowed by managers right now, because security checks are missing.
      - Import now processes Screenings, Screenings_To_Genes and Variants_On_Genome.
      - LOVD_Custom's checkSelectedInput() now works with import.php's non-array values as well.
      - LOVD_Object's checkFields() now checks, for non-custom column select fields, if the selected value(s) actually match the input list. This should always be true, but if users are manipulating LOVD forms, this may have in the worst case scenario, caused query errors while inserting or editing data.
        * This means that imports are now also checked for valid input in select fields.
        * Because of this change, specific checks have been removed from the checkFields() of LOVD_Custom, LOVD_Disease, LOVD_Gene, LOVD_GenomeVariant and LOVD_Screening.
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@234 a7477d18-a37e-46de-aef1-57953c184492
  28. 28 Sep, 2012 1 commit
    • Ivo Fokkema's avatar
      Committed second draft version of the import code: · d45f21a2
      Ivo Fokkema authored
      - Finished handling category Diseases.
      - Now handles categories Genes_To_Diseases and Individuals.
      - The column headers are checked for mandatory custom columns.
      - Improved lovd_endLine() so that is can be used more often to kill the import if we're getting a lot of errors.
      - The import calculates a percentile difference between the data in the database and the data in the file, in case we're running an update (not yet implemented).
      - Repeated data in the import file is now properly detected.
      - Errors returned by the Object::checkFields() now mention the field ID instead of the name on the form.
      - Diseases bearing the same name are no longer allowed.
      - Improved the efficiency of the Disease's object's checkFields().
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@232 a7477d18-a37e-46de-aef1-57953c184492
  29. 27 Sep, 2012 1 commit
    • Ivo Fokkema's avatar
      Fixed installation bug and made LOVD useful in strict mode, also preparing for the import feature: · 914785cb
      Ivo Fokkema authored
      - Adapted all checkFields() calls to allow for the passing of $zData, a requirement for the import code.
      - Edited the checkFields() of the diseases object to handle full data checking by the import script.
      - Fixed bug; LOVD 3.0-beta-08 was actually non-installable due to a change in table structure while the installation process was not updated accordingly.
      - LOVD is now also installable with MySQL's strict mode on. Closes #17: "installation error LOVD".
      - Increased efficiency of the checkFields() calls by the individuals and screenings objects by using data from $this->aFormData instead of running new queries.
      - Increased efficiency of the getForm() calls by the individuals, screenings and genomic variants objects by returning the previously generated form immediately, if available.
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@231 a7477d18-a37e-46de-aef1-57953c184492
  30. 31 Aug, 2012 1 commit
    • Ivo Fokkema's avatar
      Big commit with many, many fixes: · 82137fad
      Ivo Fokkema authored
      - Committed the authorization unit test changes made by iclugtenburg.
      - Slightly improved the manual, after remarks by users.
      - Updated the refseq parser:
        * Fixed problem in parsing the reference sequence ID out of the file.
        * Will now also work behind a proxy server or with PHP's fopen wrappers off.
      - Improved the description of the individual's panel ID on the data entry form.
      - Proxy servers requiring Basic authentication are now also handled correctly; a username and password can be set in the LOVD system settings.
      - Curators were not able to delete any data, although links to do so were shown in the menu.
      - Reviewed r221; Minor edits.
      - Reviewed r222; Fixed 2 problems:
        * Fixed bug; The public, submitters and sometimes curators could no longer see the connection to an individual from a variant's page.
        * Restored the correct sorting order of diseases on the gene homepage.
      - Reviewed r223; Fixed 2 problems and other minor edits:
        * Restored the correct sorting of diseases in the "create phenotype" list.
        * Many changes improving the efficiency and readability of the code.
        * Fixed bug; The screenings overview lost the column "genes screened".
      - Reviewed r224; Fixed some problems:
        * Restored the correct sorting order of diseases on the individuals viewlist, and made use of abbreviations if available.
        * Many changes improving the efficiency and readability of the code.
        * Fixed bug; The number of variants reported on the screening VE was not correct if multiple genes had been screened.
      - Improved submission messages here and there with minor textual changes or additions, hoping to clarify the path more.
      - Improved possibly unclear error message on system settings form.
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@226 a7477d18-a37e-46de-aef1-57953c184492
  31. 29 Aug, 2012 1 commit
    • Ivar Lugtenburg's avatar
      Made some minor other changes & quick fixes: · 686fcec4
      Ivar Lugtenburg authored
      - Combined the variants_found and "Variants found" columns into one column in screenings viewList.
      - The individual viewEntry now contains a list of diseases and the diseases viewList below has been removed.
      - Added some new options to the tab menu and fixed the occasional disappearance of older ones.
      - Quick fix for object_diseases.php
      - Quick fix for the new lovd_saveWork() function in inc-lib-init.php.
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@224 a7477d18-a37e-46de-aef1-57953c184492
  32. 27 Aug, 2012 1 commit
    • Ivar Lugtenburg's avatar
      Fixed 1 bug, revised some authorization matters and added some extra functionalities: · ba9bf69f
      Ivar Lugtenburg authored
      - Fixed bug; The search fields on custom columns no longer produce an unexpected "Bad syntax error".
      - It is now possible to add and remove custom columns to the "Healthy/Control" disease.
      - When hovering your mouse over a search field, the current search expression will be explained in more detail in the popup.
      - No longer possible to add both a disease AND 'Healthy/Control' to a individual.
      - Added color highlighting for marked and non-public entries in viewLists.
      - Changed all viewEntry options to the new Jeegoo menu implementation.
      - Curators can now create diseases, but can only do so when they connect them to their own gene(s).
      - Curators can now edit diseases, but can only do so when they are connected to their own gene(s).
      - Curators can now remove diseases, but can only do so when they are not connected to other genes than their own gene(s).
      - The screenings & individuals pages now have gene specific page, which shows the entries that have been screened for the currdb gene.
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@222 a7477d18-a37e-46de-aef1-57953c184492
  33. 20 Jul, 2012 1 commit
    • Ivo Fokkema's avatar
      Added the special "Healthy/Control" disease, fixed 5 bugs, other minor improvements: · c04d33f1
      Ivo Fokkema authored
      - The standard LOVD user can now no longer be edited, deleted, locked or booted from the system.
      - You can now tag healthy controls as such by applying the "Healthy/Control" disease to the individual in question. This disease may not be viewed, edited or deleted, but its columns can be seen and configured. However, since there is no VE for this disease, there is no link to these views.
      - Fixed bug; Visiting a variants VE removed the currdb.
      - A column's form_type can now be 65535 characters long (TEXT) instead of 255 (VARCHAR), so we can put in longer help texts.
      - Fixed bug; A zero is now valid input for a mandatory column.
      - Fixed bug; If a multiple selection list contained a value of zero, it was incorrectly selected by itself due to some PHP strangeness.
      - Several gene's fields are now HTML enabled; Text for own disclaimer, Page header, Page footer, Notes for the LOVD gene homepage, and Notes for the variant listings.
      - On a user's detailed view, the genes this user is curator or collaborator of, are now clickable. A curator or collaborator may now also see which genes he/she is collaborator of.
      - Fixed bug; Invalid search expressions caused one or two PHP errors as well as generate a normal LOVD error message.
      - Fixed bug; During installation an error was printed on the screen when LOVD tries to authorize the user.
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@213 a7477d18-a37e-46de-aef1-57953c184492
  34. 19 Jul, 2012 1 commit
    • Ivar Lugtenburg's avatar
      Fixed 4 bugs, made some minor changes & code cleanups: · 237fe70e
      Ivar Lugtenburg authored
       - Fixed bug; The human-readable refseq would always ignore the setup settings and choose the same (default) Mutalyzer server.
       - Fixed bug; The check on the DBID during variant create/edit now only accepts gene symbols that are actually present in the LOVD.
       - Fixed bug; In some cases the variant create/edit forms would give a javascript error.
       - Fixed bug; Since Mutalyzer changed how upstream/downstream positions are described, protein predictions could produce weird errors.
       - Protein prediction on the variant create and edit form can now return multiple warnings/errors returned by Mutalyzer.
       - Status columns are now automatically hidden if the users do not have all view privileges on that entry.
       - Implemented the "Show contents to public" and "Show field on submission form" options for custom columns, so that they are actually hidden when deselected.
       - Variant DBID's kan now only be filled in by Curators, Managers and Administrators.
       - The OMIM ID field now has a check to ensure that the number is 6 digits and that the first digit is at least a 1 or higher.
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@205 a7477d18-a37e-46de-aef1-57953c184492
  35. 13 Jul, 2012 1 commit
    • Ivo Fokkema's avatar
      Finished/improved the download format, fixed some bugs and made some more minor improvements: · af777611
      Ivo Fokkema authored
      - Fixed bug; Internet Explorer users couldn't configure new curators for genes or use the Mutalyzer mapping / variant checking features.
      - Improved the full download format; it now includes more data (genes, transcripts, and diseases), and also includes the relationships between individuals and diseases, screenings and genes, and screenings and variants.
      - Submitters are no longer allowed to add submissions without adding individual data also.
      - Fixed bug; On a disease's detailed view, in the list of genes the disease is linked to, genes without an OMIM ID were left out.
      - The Status column has been added to more data overviews, if the user is authorized to see this column.
      - Fixed bug; lovd_isAuthorized() now also degrades users back to LEVEL_SUBMITTER if these users already were LEVEL_CURATOR or LEVEL_COLLABORATOR but were not authorized by the new lovd_isAuthorized() call.
      - Slightly improved (simplified) the code for selecting a "currdb" database.
      - When there was no signature, no session was started, which could lead into really awkward behavior before and during installation.
      - Some whitespace fixes here and there.
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@202 a7477d18-a37e-46de-aef1-57953c184492
  36. 06 Jul, 2012 1 commit
    • Ivo Fokkema's avatar
      Big update to the manual, and many minor other changes: · cf1f618a
      Ivo Fokkema authored
      - Did a lot of work on the manual:
        * Fixed some markup problems in the manual.
        * Figures in the manual now have prettier captions and have a background with right frame instead of a somewhat loose frame.
        * Per section, added markings of required user level and since when this feature is included in LOVD.
        * Added chapter "LOVD Setup" to the manual, with sections "LOVD system settings", "System logs" and "Uninstalling LOVD".
        * Added chapter "Gene databases" to the manual, with sections "Creating a new gene database", "The gene homepage", "Editing a gene database" and "Deleting a gene database".
      - When searching for a gene symbol on the "Create a new gene" form, LOVD now also searches for aliases if no match is found.
      - From the gene data entry form, you can now open a new window to create new disease entries.
      - Decreased size of some multiple selection lists, since they were too big in my point of view.
      - From the individual data entry form, managers can now open a new window to create new disease entries. Other users get a note that they can include a missing disease in the individual's remarks field, such that a manager can configure the requested disease in the LOVD.
      - Enabled the link to the RefSeq parser from the genes data entry form. Also added a prediction of the output file name. Only problem there is that we can't really predict that name since it depends on the transcript chosen. The RefSeq parser will have to be adapted to create a file that points to the several possible refseq files.
      - Some whitespace problems fixed, mostly because I'm testing the PhpStorm IDE and I configured it to fix it automatically in edited files.
      git-svn-id: https://humgenprojects.lumc.nl/svn/LOVD3/trunk@200 a7477d18-a37e-46de-aef1-57953c184492