Local::QueryLog * modify substitute_placeholders method to handle bind params containing parens-within-parens * modify Local::DBIxSimple, RDBO & RDBO::Manager to join bind params on null-byte instead of comma to avoid breaking split on bind params which already contain commas * protect placeholder substitution from vars containing question-mark * protect SQL::Abstract::Tree query formatting from control characters (eg parens, question-marks) * append undef's to end of @bind for any trailing table cols with default values (eg timestamp cols) * substitute NULL for undef bind params * simplify _warn_handler() logic, returns early if not required

LIMS::Local::QueryLog - fix permissions issue with previous commit (9171b6a & bf60ec8); format queries for console & log file using SQL::Abstract::Tree

Local::QueryLog * combine development queries (SELECT's, UPDATE's, etc) into single file * replace SELECT query log file names with simpler schema (development.sql, deployment.sql) * adapt log_rotate.pl script for changes to Local::QueryLog

preparation for migration to Deb9 * replace Log::Dispatch::File::Rolling log-file format - package broken due to removal of _make_handle method in Log::Dispatch::File * update Makefile.PL

Major update to print run function: * print run returns single pdf instead of html page, to allow individual report page headers and numbers * avoided breaking section summaries across new page in report * moved report page numbering to footer.html * expanded horizontal space for "Amended report by" details * fixed error in PDF::WebKit->configure options format Other updates: * exempted print_run from Devel::Cycle code block in devel mode (already exempt in deployment) * debug() returns undef instead of '0' so .tt doesn't display return value * stopped logging process_size in QueryLog - was activated by script errors * moved notification about danger of using 2nd tab for record update to top of file * fixed time zone setting in new message notification log (was not allowing for BST) * fixed error in chart loading function, now only loads in required lab section instad of all Fix added 7th Nov: * added NCH PNH (PB) to turnaround times audit category (was included in PB category)

patched QueryLog again to return query logging function to console for devel server; email address changes

genomics sample linkage form; xsd validation for genomics_xml.pl; bugfix for audit/turnaround_percentile.tt - subtraction only performed if values exist

patched genomic_xml script - error in gel_id generation; moved receiving_system & receiving_facility hl7 items to object constructor; reverted QueryLog to return if fastcgi - logging process size was killing print run - change introduced on live system 23/3/16

bugfix - previous change to QueryLog stopped all sql logging by setting gglobal SKIP_LOG_QUERY inside code block

logging fastcgi process size

changed user message handling: * site.status.tt calls ajax/seek_new_messsages as jQuery on page load * site/status.tt calls new_messages.cgi every minute until 1 min before session timeout * set idle-timeout value in session user_profile, created at new login if no existing user profile * user session user_profile idle-timeout value in LIMS::_authen_config $authen_timeout sub * new $LIMS::Local::QueryLog::SKIP_LOG_QUERY to avoid logging specific queries (eg ajax/seek_new_messages) * updated new_messages.cgi with logging and formatted return msg to same as ajax/seek_new_messages

patient merge includes demographics data; moved mech.htm to scripts dir

added process size logging facility to fastcgi process; authorised/incomplete records worklist displays outstanding lab tests; added cd SCRIPT_DIR to fcgi script so git version info loaded when restarted from outside HILIS4 dir

minor adjustment to QueryLog formatting to make process-size easier to read

cosmetic changes to _warn_handler and minor performance enhancement by accessing elements of coderef directly, not via temporary vars (, , etc)