/*******************************************************************************
 *
 * Leiden Open source Variation Database (LOVD) 3.0 Changelog
 *
 *************/

/*******************
 * 3.0 Alpha 05
 * 2011-10-17
 *********/
 * Fixed bug; When deleting a user, an error occurred because of an invalid
   query to the database.
 * Fixed bug; When creating an individual entry, an error could have been shown
   on the screen.
 * Fixed bug; Registering a user would result into an infinite loop, freezing
   the browser because the code was expecting the user to be logged in.
 * Added new cross and check images in 11x11 and 16x16 and removed the old ones.
 * Added a register user functionality.
 * Added a reCAPTCHA library.
 * Implemented a reCAPTCHA to the user register form.
 * Implemented AJAX calls into the variant submission form so that the HGVS is
   checked instantly and you can convert the position from genomic to the
   transcripts and vice versa.
 * Fixed bug; newly registered submitters are now logged in properly after the
   registration step.
 * Fixed bug; running LOVD in php5 safe mode will no longer cause notices.
 * Added new mail functionalities and implemented them into the registration &
   password reset processes.
 * Improved the compatibility with other database platforms.
 * Changed the wrap length of email body texts from 80 to 70 characters.
 * Implemented the search expression ="" to viewLists, which will match columns
   with no value.
 * Changed PDO to use buffered queries.
 * Changed the standard email headers that are sent with all outgoing mails.
 * Search fields in the viewList now always fit the column.
 * Added a default location_url to the system settings form.
 * User level in the users viewList is now sortable AND searchable.
 * Added some more information about the meaning of the icons on the custom
   column overview if you move your mouse over them.
 * LOVD now distributes an User-Agent string when using certain web calls.
 * Changed URL of bug tracking system, since it has been moved.
 * When installing LOVD, the database URL is now predicted for the user.
 * Fixed problems with advanced searching in viewLists.
 * Made some textual improvements.
 * Improved the PDO wrapper.
 * Fixed bug; Checking the install's URL didn't work during LOVD installation,
   as notices were generated about a missing variable.


/*******************
 * 3.0 Alpha 04
 * 2011-09-02
 *********/
 * For phenotype data entries, the status can now also be set.
 * Fixed bug; The reset password functionality was non functional.
 * The gene's disclaimer will now be shown underneath the viewEntry table.
 * Fixed bug; A gene database's date of creation can no longer be in the future.
 * Curators can now also view custom column information.
 * Added link for changing the columns' order underneath a category's viewList.
 * Added "Genes screened" and "Variants" columns to the individual viewList.
 * Fixed bug; The submitter count and unique variants count were not calculated
   properly by check_update.php.
 * Fixed some numical references to user levels (should be constants).
 * Minimum required PHP version is now 5.1.0, due to the requirement of PDO.
 * LOVD now checks the existence of PDO support and the MySQL driver for PDO,
   then connects to MySQL using PDO. Actually implementing PDO everywhere will
   take some time.
 * Fixed bug; LOVDs that were not installed yet, were throwing notices.
 * Added code for proper authorization of data owners to individuals.php,
   screenings.php and phenotypes.php. The correct user level is not yet assigned
   by lovd_isAuthorized().
 * Fixed some issues with HTML 4.01 compatibility.
 * Fixed bug; lovd_queryDB() did not show the entire query if it was throwing an
   error message about the number of arguments used in the query.
 * Added chromosome to genomic variant viewList.
 * Updated the INSTALL.txt help file.
 * Implemented a custom viewList class, allowing easy implementation of flexible
   viewLists with several different data objects linked to each other.
 * Fixed bug; Added XSS fix to lovd_displayError().
 * Fixed bug; MySQL handles 01 very different than '01' for VARCHAR columns,  so
   lovd_queryDB() will now always quote integers.
 * Implemented the /variants/chr# URL showing a viewList of all genomic variants
   on a specific chromosome.
 * Fixed bug; Non-mandatory selection lists did not have the "(Optional)" suffix
   on data entry forms.
 * Added jeegoocontext drop down menu, written by Erik van den Berg
   (http://www.planitworks.nl/jeegoocontext)
 * Cleaned up inc-upgrade.php; it is no longer supported to upgrade LOVD 3.0
   from earlier than 3.0-pre-21.
 * Added minified jQuery 1.6.2 to the newly created lib/jQuery folder.
 * Added minified jQuery UI 1.8.15-core files (core/mouse/widget/position) &
   sortable file to lib/jQuery.
 * Removed lib/tool-man folder and its contents entirely as it was outdated and
   a solid replacement was found in jQuery UI.
 * Included jQuery & jQuery UI in inc-top.php so they can be accessed everywhere
   in LOVD.
 * Fixed bug; sorting in genes?sortCurator & columns?order now also works for IE
   by using jQuery UI sortable.
   Fixed #1: "Drag and drop sorting does not work in IE 8".
 * Fixed bug; Changed the temporary memory leak fix to a solid permanent fix in
   genes?create, genes?edit & transcripts?create.
 * Renamed 'inc-js-insert_custom_links.php' to 'inc-js-custom_links.php'.
 * Implemented deleteEntry in users?delete & built in a check in users?(un)lock
   to see if a user is already (un)locked.
 * Fixed bug; In phenotype?create it is now mandatory to select a disease, and
   also implemented checks for a valid diseaseid. Also only diseases that have
   custom columns enabled will be selectable now.
 * When an individual has only one disease, you don't have to select the disease
   when creating a new phenotype entry.
 * Implemented one-click navigation from the individual's detailed view to the
   form to add phenotype information on a certain disease.
 * Fixed bug; Couldn't select which genes were screened on screening data entry
   forms.
 * Changed all references to inc-js-insert-custom-links.php to the new name
   inc-js-custom_links.php and removed the old file.
 * Fixed bug; lovd_AJAX_viewListAddNextRow() now works properly in all browsers.
 * Fixed bug; lovd_includeJS() can now also handle files in a different path.
 * Fixed bug; lovd_viewForm() allowed single selection lists to have a "select
   all" link.
 * Fixed bug; Fixed the database structure for transcript variant custom columns
   in object_custom.php.
 * Optimized & cleaned the transcripts?create code.
 * Transcripts/<gene symbol> now also works and is basically the same as the
   /transcripts view with a search on <gene symbol>.
 * Improved navigation between linked data types by adding some extra viewLists
   and links.
 * Implemented a working form to create variants on transcript level.
 * Implemented full submission workflow.


/*******************
 * 3.0 Alpha 03
 * 2011-08-03
 *********/
 * Fixed bug; The verification of the LOVD database URL did not work, actually
   because of a problem in the script on the LOVD website.
 * Fixed bug; When selecting curators for a gene, if the viewList with available
   users was sorted or searched, the users could no longer be selected.
 * Fixed bug; When selecting curators for a gene, clicking on the user's name
   led to execution of javascript outside the scope of the page, resulting in a
   blank page with only "true" on it.
 * Fixed bug; Users can no longer remove a user as curator for a gene, when this
   user has an equal or higher level than themselves.
 * Fixed bug; Fixed notices when not properly selecting a curator for a gene.
 * Added the "Order" column in the custom columns viewList.
 * Simplified the check on the regular expression syntax of a custom column.
 * Fixed bug; On the gene viewEntry pages one of the headers was malformed.
 * Implemented option for curators to sort the list of curators for their genes.
 * Implemented lovd_isAuthorized() for checking a user's authorization for dif-
   ferent data types. Currently, only genes are implemented. The user's level,
   if lower than LEVEL_MANAGER, will no longer be defined in inc-auth.php.
 * Curators of any gene can now also check LOVD's update status. The link to
   this page is now only active for Curators and up.
 * Added navigation for Curators from the gene viewEntry page to forms to edit a
   gene, add a transcript to a gene, and sort the list of curators. Those pages
   are now also opened up to Curators.
 * Minimum MySQL version needed to run LOVD 3.0 is now 4.1.1.
 * Added lovd_php_htmlspecialchars() function that also works recursively.
 * Added array_merge() optimization where possible.
 * Fixed bug; Values of custom columns configured as simple drop down lists were
   lost during edit of the data entry.
 * Fixed bug; On the genomic variant data entry form, "Owner of individual"
   should be "Owner of variant". Also other forms had this error.
   (thanks to Raymond Dalgleish, University of Leicester, UK, for reporting)
 * Links to OMIM are now to OMIM.org and not to the NCBI site anymore.
 * Fixed bug; The user's viewList and viewEntry reported collaborators as being
   curators for the genes they are collaborators for.
 * Implemented lovd_isAuthorized() checks for diseases and transcripts, so that
   curators can correctly be recognized as authorized users.
 * Added virtual user level LEVEL_OWNER, assigned by lovd_isAuthorized() to sub-
   mitters who are owner or creator of a certain data entry.
 * Fixed too big Variant/DBID size on the data entry form.
 * Fixed bug and standardized code for checks on ownerid and statusid.
 * Fixed bug; When all available users had been selected as curator or
   collaborator, you were not able to remove anyone from this list anymore.
 * Fixed bug; Internet Explorer "forgot" which columns where hidden from view in
   viewLists when searching or sorting them.
 * Fixed bug; A change applied to lovd_php_file() in r46 failed on servers with
   PHP 4, so included work around.
 * Checking the user's password for authorization of creates, edits and deletes
   is now handled by class/objects.php.
 * Fixed bug; On input errors, some data entry forms did not delete the password
   after the form was sent back.
 * Fixed bug; All custom columns can now be removed properly.
 * Fixed bug; When a user edits a gene, LOVD checks if there is a known UD number
   in the database. If not, then it generates one through mutalyzer.
 * Implemented a re-ordering functionality of custom columns.
 * Changed the regular expression for gene symbol validity so that it can also
   contain @ and #.
 * Implemented a urldecode and urlencode in genes.php to allow special chars
   to be in the gene symbol and thus in the URL.
 * Implemented automatic exploding of GROUP_CONCAT data based on their name. 
   So '_genes' = array (;) or '__active_diseases' = nested array(;;).
 * Added the temporary memory leak fix from genes?create also to genes?edit &
   transcripts?create.
 * Fixed bug; Variants can be added to a screening again. Still this is only
   possible from the screenings page when you select "Add variant to screening".
 * The proper columns are now loaded also for transcript variants in
   object_custom.php.
 * Implemented tooltips for custom links in viewLists, inside the tooltip is the
   actual link so that they are now clickable without going to the viewEntry.
 * User levels are now properly displayed in user viewLists & viewEntries and
   sortable (not searchable).


/*******************
 * 3.0 Alpha 02
 * 2011-07-05
 *********/
 * Fixed bug; Windows systems will now be able to send mails to the users when
   using reset password.
 * Fixed bug; Appropriate email headers are now added to the LOVD system mail
   function.
 * Fixed bug; Temporary fix for the memory leak in /genes?create.
 * Fixed bug; Order of custom columns is now set correctly when enabled.
 * Create, edit & delete phenotype are now implemented and working properly.
 * User authorization level is now searchable in viewLists.
 * Custom columns can now be removed.
 * Adapted the page for phenotype create a bit.
 * Changed & to W3C compliant &amp; in HTML output.
 * Some LOVD 2.0 -> LOVD 3.0 code standardizations.
 * Some code optimizations.
 * insertEntry() and updateEntry() don't need to implode array values,
   lovd_queryDB() does that for them already.
 * Changed "variant information entry" to "variant entry".
 * Added new logos for gene database create and edit.
 * Removed remaining carriage returns in all files except the
   config.ini.php-lovd.
 * Removed internal LOVD columns from the VariantsOnTranscripts' viewList and
   viewEntry.
 * Fixed bug; Non-shared custom columns couldn't be removed.
 * Used CURRENT_PATH instead of (possibly concatenated) $_PATH_ELEMENTS calls.
 * Added new screening techniques to the "Screening/Technique" column.
 * Fixed bug; The "VariantOnTranscript/RNA" and "VariantOnTranscript/Protein"
   columns were non-mandatory by mistake.
 * Fixed bug; The "updated" column in the genes viewList did not allow for date
   type searching because lovd_getColumnType() did not recognize it.
 * Fixed bug; Notices were thrown when searching in date columns using
   incomplete date ranges.
 * Cleaned out the 2Do.txt file; bugs that had been fixed already were removed.
 * Added anchor in columns viewList.
 * The "Last login" and "Started" columns in the users viewList have been
   shortened to just the dates.
 * Fixed bug; A gene's hidden curators and collaborators should only be viewable
   on that gene's viewEntry page by collaborators or higher.
 * Added panelid and panel_size to the Individuals table, to distinguish between
   individuals and panels.
 * The VariantOnTranscript/DBID field has been removed in favor of the
   VariantOnGenome/DBID field.
 * A new authentication method is introduced, storing the user's passwords even
   more safely as before. The user account password stores are only updated one
   by one, whenever a user logs in.



/*******************
 * 3.0 Alpha 01
 * 2011-05-26
 *********/
 * Initial release to general public.
