/******************************************************************************* * * LOVD DATABASE CHANGELOG * *************/ /******************* * 1.1.0 Build 13 * 2006-09-14 *********/ * Will now gather sofware versions to help build LOVD v.2.0 compatibility. * Fixed some small HTML errors on four pages and in the manual. * Fixed bug #3; "Setup returns empty screen after first login". Related were errors on other pages appearing when not having a gene selected. * Fixed bug #4; "Does not quote recipient name when sending mail". * Fixed bug #10; "No dot allowed in external link name". * Fixed bug #6; "IP address is not accepted as valid URL". * Fixed bug #7; "Link to reference sequence breaks if no URL filled in". * Fixed bug #9; "Missing icons in LOVD manual". * Fixed bug #8; "Newly created genes have no curator". /******************* * 1.1.0 Build 12 * 2006-07-05 *********/ * Fixed bug; when editing previously added custom links, you could no longer apply the link to the frequency column (thanks to Heidi Schulz, Germany for reporting). * Fixed bug; removed reference to non-existing variable in check_update.php. * Fixed bug; on some configurations, the check for LOVD updates failed. * Fixed bug; minor issue with check on gene symbol. * Fixed bug; when searching through the variants using the public area, the disease and detection technique search terms are not passed on to the next pages. /******************* * 1.1.0 Build 11 * 2006-02-17 *********/ * Fixed bug; links created by the DB submitters custom link to a specific sub- mitter on the list of submitters showed the whole list of submitters for that country, instead of the specific submitter. * Fixed bug; when using a non-numeric HGMD ID, LOVD returned an error about the OMIM Disease ID in stead of the HGMD ID (thanks to Paras Jethwani, Australia for reporting). * Fixed bug; due to the new check on the gene symbol, many legit gene symbols were rejected (bug introduced in Build 10). * Since the HGMD has now changed their query pages, the HGMD numerical ID's all have been replaced by the gene's official gene symbol. LOVD now allows input of non-numeric HGMD ID's and will determine by the type of the given ID which URL to use. * Updated copyright notices to '2004-2006'. /******************* * 1.1.0 Build 10 * 2005-12-21 *********/ * Updated links to HGVS' nomenclature pages to http://www.HGVS.org/mutnomen/. * Removed the additional mention of the country below the full address. The submitters are sorted by country anyway and didn't we ask them for their full address? * When providing multiple external links for the gene homepage, whitespace is now allowed around the semi-colon separating the links. * The gene symbols are more strictly checked, and the database field has been lengthened to 12 characters. Since they are related, two other fields in the user table have been increased in length as well. * Both the manual and LOVD (partially) have been checked for typing errors. * Added a warning to the curator's area that LOVD v.2.0 will drop functionality of the abandoned mutation check feature from the submission page. * Fixed issues with MySQL 5.x (thanks to Paras Jethwani, Australia ) - Checkbox value has to be converted to integer before inserting into MySQL. - Importing text files fails using the shortened import format. * All calls to the static LOVD tables now use the defined constants. * Fixed bug; the presence of the LOVD config table was not checked at install time, possibly resulting in a non-functional LOVD installation directly after install in a hypothetical situation. * Fixed bug; managers could not select themselves as a curator for a gene. * Renamed 'Allowed access to' form field to 'Curator for' and renamed 'Allowed Dbs' column header to 'Curated Dbs'. * Custom links can now also be applied to the Frequency column. * Updated last calls to lovd_magc_unqt() to the newer lovd_magicUnquote(), and removed the lovd_magc_unqt() alias. * Removed the lovd_magc_quot() alias, as it isn't in use anymore. * Updated link format of the Entrez Gene and the HGMD external links. * Added information on the search options for curators to the manual. /******************* * 1.1.0 Build 09 * 2005-11-23 *********/ * Fixed bug; downloading the gene database from the configuration area was not possible due to a malformed mysql query (bug introduced in Build 08). * Fixed bug; summary tables gave wrong percentage of 'Other Substitutions'. * Fixed bug; the 'curate all' function did not work if the PHP register_globals setting was disabled. * Added new option in the configuration area to clean the exonic and intronic data previously imported in the deprecated gene sequence tables. * Fixed broken link from the summary legend to the Quick Reference Guide in the help directory. * Fixed bug; in some cases, the reference sequence parser misplaced and miscal- culated the nucleotide number of the last line of the translated region. * Fixed bug; the reference sequence parser miscalculated the nucleotide number of the last line of the translated region. * The list used to select how many variants you want displayed per page in the curator area, is no longer shortened when you have fewer results than the amount selected. * Fixed bug; when connecting to the MySQL server the hostname used was always 'localhost' regardless of the selected host in the config.ini file. * Fixed bug; actually check if the database hostname was set in the config.ini file. * The LOVD status page now also shows the timezone in which the server resides. * Fixed bug; when no search results are available in the curator area, the total times reported will show '0' in stead of the empty string ''. * Removed redundant variable $_INI['locs'], since this setting has been removed from the config.ini file some time ago. The variable has been replaced by $_SETT['db_config']['location_name']. * Removed redundant variable $_INI['down'], since this setting has been removed from the config.ini file some time ago. The variable has been replaced by $_SETT['db_config']['allow_download']. * Fixed bug; again, the database manager was logged out directly after install. * Included manual with LOVD installation. /******************* * 1.1.0 Build 08 * 2005-08-31 *********/ * Fixed bug; navigating to a different page of a list of mutations (curate or edit) was not possible in some cases. * Fixed bug; the 'noreload' tag responsible for blocking the curation list to reload after successfully curating, duplicating or deleting, did not work for that list. * Updated wording in legend and full legend somewhat. * Added a notification to the variant submission page that all fields, unless specified otherwise, are mandatory. * Fixed bug; free edit could whipe out entire column contents if characters are used that are common in regular expressions. Also added the suggestion to do a download of the database before using free edit. * LOVD now automatically checks for updates when a manager is logged in. For the managers, an icon is shown at the bottom right-hand side of LOVD display- ing information about the update system. When an update is available, direct download links are available. * Replaced old variable name $z_pref by $_SETT['db_status']. * Removed redundant column 'path' from the status table. The install location is now determined dynamically. * Added direct link to LOVD article in the top include. * Replaced old variable name $a_pref by $_INI. * LOVD users can now set the option to refresh the active list of variants when they have added, edited, duplicated or deleted an entry from that list. * Fixed bug; when enabling cookie user authentication, a cookie is immediately sent to authenticate the user for the rest of the session. * Replaced old variable name $auth by $_AUTH. * The disease list on the submission page missed configured diseases with had numbers in their names. * Removed redundant variable $a_legend_data, since the data is contained could also be found in the variable $_SETT['db_config']. * Fixed bug; the error message shown when a bad custom column abbreviation had been filled in, did not mention the fact that uppercase letters were not allowed. * LOVD will now ask for an email address which it can use to send email with. This is necessary, because some SPAM filters refuse messages that have no valid sender address causing LOVD emails to bounce. This email address can be changed on the LOVD Setup page. * Fixed bug; if no detection techniques or phenotypes are set up in the system, the review page prior to completion of a submission of new variants may not show the provided information. * Fixed bug; if no phenotypes are set up in the system, the phenotype filled in by the submitter where not sent to the database. /******************* * 1.1.0 Build 07 * 2005-07-26 *********/ * Forgot some copyright notices, updated everything to '2004-2005'. * Updated the legend of coding DNA reference sequences written by the Reference Sequence Parser. * Fixed bug; after duplication, the form window didn't close anymore because of an JavaScript error (bug introduced in Build 05). * Fixed critical bug; build 06 was uninstallable due to an error in the module for authorization, which logged the Database Administrator out directly after installing LOVD or logging in. /******************* * 1.1.0 Build 06 * 2005-05-04 *********/ * Minor adjustment in checking the format of MySQL table prefix. * Fixed bug; updated handling of allowed gene databases for curators. This also prevents possible problems with genes that have similar names. * Fixed bug; when deleting a curator that was solely assigned to a gene, the gene was left without a curator in stead of assigned to the current user. * Fixed bug; loading data into a gene using the limited set of columns did not work anymore. * Minor adjustment in checking the format of the genesymbol when creating a new gene database. * Fixed bug; reference sequence parser had trouble aligning the up- and downstream sequences. Fixed by adding the first and last lines of the coding DNA sequence, respectively. * The Reference Sequence parser now writes the number of intronic nucleotides at the top of the intronic sequence pages. * On the public variant overview, added some space between the optional notes and the legend. * Fixed bug; errors occured on the summary view under some conditions. * Fixed bug; some odd percentages may have been shown on the summery view; when quering the database for the amount of missense and nonsense mutations, the query did not check for the status set for those mutations. * The Reference Sequence parser now creates the new notation for the sequence numbering after the stop codon as recommended by the HGVS at http://www.genomic.unimelb.edu.au/mdi/mutnomen/recs-DNA.html#number. The new notation is started at a new line. * The mentioned new notation is now sorted properly as well. /******************* * 1.1.0 Build 05 * 2005-03-30 *********/ * Added column 'ID' in the table of the submitter list view (on request). * Updated all links to the LOVD website to www.DMD.nl/LOVD/. * Updated the short legend below the search results a bit. * Added the reference to the LOVD article. * Removed upgrade instructions for LOVD 1.0.2 versions. * Added a small readme for developers. * Reformatted the upgrade script inc-upgrade.php to the new coding standard. More files will be reformatted in the future. * Added 'Times reported' column to the edit and curate pages. Furthermore, the total number of times the current results have been reported is printed below the total number of results. * Reformatted notice-raising code from the edit and curate pages. Although by default, notices are not shown, it does usually indicate sloppy coding. * Added check for PHP error_reporting setting in an attempt to make all notices hidden. * Added a 'clean' header and botton include for common use. * Moved commenly used JavaScript functions into a separate include. * Duplicating an variant entry is no longer by default a full duplicate; the user is now prompted for three possibilities: "Switch alleles", "New paper" or "Full duplicate". Also, duplication is now handled differently internally. * Fixed bug; changing the custom column's order could not be possible depending on the LOVD settings. /******************* * 1.1.0 Build 04 * 2005-02-08 *********/ * Fixed bug; navigating the splitted pages with gene variants did not function with the PHP setting 'register_globals' set to off. * Changed all instances of 'cDNA' to 'coding DNA', according the the new nomen- clature (http://www.genomic.unimelb.edu.au/mdi/mutnomen/). * Fixed bug; using non-alphanumeric characters in the genesymbol of a new data- base breaks this database; checks have been added to check the input. * Fixed bug; some page redirects resulted in automatic logout when the method for user authentication was set not to use cookies. * Added check for correct pattern on configuration variables, to prevent issues i.e. with the database communication. The whole parsing of the config file needs to be rewritten in time. * Fixed bug; the menu include for the configuration and setup area could inter- fere with commenly used existing variable names. * Added functionality for managers to delete a specific gene database. * All references to LocusLink were updated; Entrez Gene will replace LocusLink on March 1st, 2005. * The username field on the login forms now automatically receive focus, making it a little easier to log in. * Fixed bug; the GDB mirror referred to by LOVD was no longer online. LOVD now refers to the gdb.org server. /******************* * 1.1.0 Build 03 * 2004-12-23 *********/ * Fixed two typo's on the public gene index page. * Fixed a few typo's in Reference Sequence Parser. * Fixed bug; all HTML forms with error checking are now also equipped with the lovd_magicUnquote function, which should be called when the form is returned to the user. Not having this function on all forms resulted in problems with certain characters, such as the backspace character or double quote. * Built in possibility to not use cookies as user authentication. This is some- what a security risk, but it is a requested feature and using cookies is turned on by default. * Updated all links and redirects to make sure the session ID is maintained be- tween different pages if cookies are disabled. * Fixed bug; Date of creation of new database was transformed to a format ready to be put in the database even if it had to be returned to the form due to an error. * Fixed typo in uninstaller script. * Removed navigation menu from the full legend because legend.php is loaded in a new window. * Updated navigation menu in public area. * Fixed bug; defining the constants raised notices. * Clearified the confirmation message a bit, which is received when curating all entries at once. * Fixed bug; it appeared that an upgrade to 1.1.0 did upgrade the submitter database table, but a clean 1.1.0 install did not. Upgrading to this build will determine if your installation has the upgraded table; if not, it will be upgraded. * Changed date format created by the Reference Sequence Parser. * Fixed bug; when adding or editing entries and switching database in the back- ground while keeping the window open, an entry was written to the wrong data- base or an entry could be overwritten in a wrong database. /******************* * 1.1.0 Build 02 * 2004-10-27 *********/ * Removed some unnecessary code that remained in the inc-init.php file. * Installation file now takes the LOVD version from inc-init.php, instead of defining the variable by itself. This saves me one step in creating new builds. * Fixed bug; Setup page will now no longer print 'Upgraded ...' when there has never been an upgrade before. * Reference Sequence Parser step 1 is deactivated, since it has not yet been developed. * Fixed bug; downloading the gene table from the config area was broken. * Fixed bug; database location in the system-wide settings was not mandatory. * Fixed bug; emailheaders are put in the inc-init.php, and used by submission, error reporting and registration. Also fixes the issue presented in build 01. * Fixed bug; upgrading could provide a problem due to several pre-release builds. * Including the install lock when installing LOVD is now default. * Fixed typo in setup.php. /******************* * 1.1.0 Build 01 * 2004-10-26 *********/ * LOVD is now released under the GPL license. * Note : All changes made to the LOVD system will now be done with the new PHP Coding Standard I use, based on the PHP::Pear recommendations with a few additions. * Fixed bug; Special characters in the submitter emailaddress caused by several addresses per account are now correctly displayed when viewing submitter data in the curator area and the public area. * Referencing to submitter data has been changed : + Custom link referencing to the public submitter file has been changed. + When submitting a variant without filling in a reference, reference field will contain {DBSubm[1]} where [1] represents the submitter ID. + Added city field to database and submitter registration forms. + Variant tables display "Submitted:COUNTRY;CITY" in the reference field for submitted variants. + Submitterlist is now sorted on country, city and the submitter's last name. * Fixed bug; manager data was not always correctly retreived from the database when sending registration copies by email. * Fixed typo in user management. * Removed all carriage returns from all emailheaders. Allthough this makes LOVD somewhat Linux dependent, it makes sure emails sent by LOVD actually arrive. Read more about this at http://bugs.php.net/bug.php?id=15841. The 'dependency' on Linux will be removed with the next build. * Added email addresses to the submitter list using a function which obfuscates the email addresses by replacing the characters by special HTML, mangling the emailaddresses so that they are safe from spambots. Has been tested for some months before being included in LOVD. * Updated OMIM custom link, since the syntax has been changed by OMIM. * Added new reference sequence parser which creates both genomic and codingDNA reference sequences from just one sequence. For now, you'll have to create the input sequence yourself. The plan is to create the input sequence from a annotated GenBank file or SOAP server. * A link to the scripts directory is provided in the menu now. * Improved structure of library and initiation includes and modified all files accordingly. * Added extra remark on the registration form; registration is not necessary if you only wish to view the public pages. * Created aliases lovd_magicQuote() and lovd_magicUnquote() for functions lovd_magc_quot() and lovd_magc_unqt(). The old functions will be removed in time, when all function calls have been updated. * Added new function; lovd_showInfoTable() will now take over all the manual implementations of the info tables. * Included warnings about the forking of the mutation check functions to the Mutalyzer project. * Added new variable $_SETT that will include basic settings like version, build, preferences and such. Started actually using it, too. * Fixed bug; general legend spoke of 'DB:', which needed to be 'Submitted:'. * $_AUTH will replace $auth. * Added many fields to the database that were available from textfiles only. These fields are both system-wide and gene-specific settings. * Added proper check on homepage url, external links and OMIM disease IDs. * Fixed bug; stop showing 'DNA allele 2' in the general legend for genes hiding the second allele. * Fixed bug; configuration page called a variable which is not available yet without including inc-data.php. * The remaining content of the 'data' directory, formally used to store text files with both gene-specific and general settings, is moved to the root path. This file is config.ini-lovd. * Fixed typo in general legend. * Fixed bug; inc-init.php was generating an non-critical error when installing LOVD. /******************* * 1.0.2 Build 09 * 2004-04-05 *********/ * Fixed bug; Standard input 'c.' in the sequence variation description field of the submission page fooled the check that the field was filled in. * Fixed bug; Detection technique is now a required field and selecting Unknown is now distinguished from not filling in anything. * Fixed bug; Leaving the creation date empty while creating a new database, did not fill in the current date. * Fixed bug; Removed 'u' modifier in the preg_match call used by lovd_link in inc-lib.php since it generated errors in some cases. * Fixed bug; Detection technique was not printed in the emails sent out after submission. * Entry of phenotypes on submission page will now, like the detection technique, be based on entries in the data/legend.txt file if this file is present and if there are phenotypes listed; else the submitter gets a standard entry field. * Improved data entry format for detection technique and phenotype data in the legend.txt file. * Elongated form fields in cDNA reference sequence parser. * The cDNA reference sequence parser now adds anchor names to the exon numbers. * Fixed bug; Maximum length gene name in database increased to 75 (was : 50). * Fixed bug; Reference sequence parser did not generate files or linked to files named according to the settings in the config.ini file. * Included config.ini file as config.ini-lovd and legend.txt as legend.txt-lovd so that upgrading your LOVD installation won't overwrite your old config files. * Fixed bug; When the database version is not known (due to a database error or when not installed yet) the build and version data are not attempted to be displayed in the bottom include. * Fixed bug; Submitters viewed in the setup are now ordered by lastname, firstname and submitter ID. * Fixed bug; When load file is not readable, error message is now different from when the file is not found. * Deleting and curating sequence variants will now cause a window to be opened, just like when editing; this is both faster and more convenient when deleting or curating more than one variant. * Fixed bug; Replaced 'genename' by 'gene symbol' in error message for incorrect DB id. * Fixed bug; Inc-data.php will now only act when $_GET['select_db'] is set. * Fixed bug; When no current database is selected, the legend will no longer try to provide a link to the reference sequence. * Fixed bug; Public database status will no longer generate an query error when a database has no sequence variants stored. * Fixed bug; CSS stylesheet was not used correctly for the coloring of the table rows in the edit and curate views. * Fixed bug; Notices in the included help files did not always display correctly in Internet Explorer. * Fixed bug; Curator area : submitter name in stead of submitter ID is displayed at the bottom of the edit form. /******************* * 1.0.2 Build 08 * 2004-03-04 *********/ * Noreload option for the pop-up window (adding, editing, duplicating) now enabled for all actions (not just add). * Fixed bug; UTF-8 encoding problem in submission page (add.php). * Fixed bug; retreived PubMed data now printed correctly in submission form. * Fixed bug; custom link patters could not contain dots (.). * Fixed bug; create by, create date and possible previous edit by and edit date was not shown on edit form. * Fixed bug; added install path to reference to styles.css on information window of custom links. * Fixed bug; search form on public area got wrecked in previous build, array variable had to be reset for re-use. * Download will now change linebreaks into '
' style tags, removed the quotes around the type value since these cause problems when editing downloaded files in spreadsheets. * Page separation (inc-pages) won't work when register_globals is set to off; applied temporary ugly fix for curator area. * Fixed bug (Curator area); URL used for referring back to search and page settings were built with every entry in the table and links to other pages contained the page variable twice. * Implemented searching in download function. * When searching from edit or curate pages, a download link is presented which allows you to download your search results. * Allowed GeneSymbol_MP23MP35 style Db-ID's for multiplex PCR analysis. * Standard input for DNA, RNA and protein fields is now regarded as empty fields when adding or editing. * Standard input for DNA, RNA and protein fields are now added to empty fields when editing varations as well. * Fixed bug; when there is no header file present for a gene to be included in the public area, the LOVD header was printed twice. * Submission page will automatically highlight the current database when it asks you to select the database you wish to submit a new sequence variation for. * Session now gets started by default in public area - modified all files accordingly. * Added log out functions to all public files not calling int-auth-subs.php. * Added some entries for the public area menu; 'Home', 'Log off' (viewed when logged in), changed 'Register' (now only viewed when nog logged in). * Allowed GeneSymbol_SO23SO35 style Db-ID's for Southern blot analysis. * Fixed bug; List of available gene databases was not ordered properly in /install/uninstall.php, /config/inc-auth.php, /config/index.php, /config/setup.php, /add.php, /index.php. * Fixed bug; Two links in the help pages got broken in build 06. /******************* * 1.0.2 Build 07 * 2004-02-09 *********/ * Fixed bug; upgrade script sometimes printed out wrong versionnumbers. * Fixed bug; pop-up windows from config area failed on Internet Explorer, now provided correct window name. * All calls to the JS lovd_go window pop-up function have been altered and now request a window name; this does imply that shared pop-up windows might occur. * Fixed bug; editing your password (curator and up) no longer logs you off. * Fixed bug; Free Edit only worked for the first match. * Added install path to pref database table. * Fixed bug; Submitters custom link URL no longer contains a double slash. * Fixed bug in initiation script, couldn't get error report emailaddress. * Added small status info on LOVD install on setup page (date of install, date of upgrade, installation path). * Added additional comments about submitting references on the full legend. * Added ability to change the lovd_go window width and height. * Clicking on the custom links on the add and edit forms now opens a new window with more info on the custom link; from this window you can include the pattern to the field. * Lovd_link() will now preg_match accented characters as well, regardless of the set locale; ranges of valid characters were added. * Removed UTF-8 settings for all pages. * Fixed bug; Custom links (e.g. Pubmed) now also work if author has accented characters in his/her name; standard 'c' locale does not support accented characters thus the alnum class in preg_* does not recognize these characters. * Fixed bug in error script, couldn't get error report emailaddress. * Added standard values "c.", "r.", "p." for the dna1, rna and prot fields, respectively (variant form in curator area). * Added visitor IP address and Hostname in LOVD error report. * Public index, search.php and summary.php now call inc-top.php in stead of using own printed top HTML code. * Styles.css removed from Config and Install dirs; common inc-top and inc-top in the Install dir are now referring to one styles.css file. * Added some space in the institute and department columns of the user and submitter tables (from 50 to 75 characters). * Status.php no longer offers itself for download. * Modified format of date printed on top of status.php. * Added menu to top and bottom of public pages. * Improved clarity on register.php a bit. * Added LOVD header to source of inc-top.php and inc-bot.php. /******************* * 1.0.2 Build 06 * 2004-01-29 *********/ * Added DMD_e5e9b ID format to Quick Reference Guide. * Allowed DMD_e5e9b ID format, changed error message with incorrect format. * When curating, the ID is checked, too. * Updated upgrade script, simple db updates (version only) do not need to be configured manually by the programmer anymore. * Bug fixed; List of available databases did not automatically select the current database when switching databases. * Added link from the 'insert exonic data' form to the reference sequence parser. * Link from error message for file load to source directory now opens in a new window. * LOVD now uses UTF-8 page encoding, header is sent and meta data specified. * Register now accepts multiple emailadresses : Your_Name , Colleage_Name . * Updated submitter overview page. * Fixed bug; list of techniques in legend now shows correct additional elaborate information if available. * Download function will now replace \r's and \n's effectively and addslashes() is performed on the values, making sure data is directly re-loadable. * Load data function will get the \r's and \n's back correctly. /******************* * 1.0.2 Build 05 * 2004-01-20 *********/ * Removed (faulty) LOVD footer when LOVD was not yet installed. * Pages other than edit or curate inducing a window for adding variations will now not refresh. * Links within notices on the index page will also send a 'noreload' tag * Help link added to menu. * Colorcoding from edit and curate views now both in old style and new style HTML. * Added notes to edit and curate pages to explain the icons to the left of the entries. * When logging out, the header now shows the LOVD version. * Created update lock in the database and created upgrade script. /******************* * 1.0.2 Build 04 * 2004-01-15 *********/ * Added date of installation and date of update to the pref table. * If installation fails, a rollback will take place. * Fixed bug in error reporting in install script. * Fixed bug in link to LOVD version website. * Added footer copyright message and link to website. * Fixed titles displaying full version and build number. /******************* * 1.0.2 Build 03 * 2004-01-12 *********/ * Removed link on submission page to Excel Sheet for multiple submissions. /******************* * 1.0.2 Build 02 * 2004-01-06 *********/ * Resolved bug in the Quick Reference Guide. /******************* * 1.0.2 * 2003-12-30 *********/ * Initial release.