package LIMS; =begin # doesn't work under production env use vars '$svk_revision'; BEGIN { # get svk equivalent of svnversion - hit only once during startup: unless ($ENV{HARNESS_ACTIVE}) { # crashes it $svk_revision = `svk info | grep 'Revision:' | awk '{print \$2}'`; } } our $VERSION = $svk_revision; =cut use Moose; extends 'LIMS::Titanium'; with ( # 'LIMS::Model::Roles::QueryLogger', 'LIMS::Controller::Roles::DataMap', ); #use strict; #use warnings; #use base 'LIMS::Titanium'; # std CPAN Titanium with some additional modules loaded use Data::Dumper; use Time::HiRes qw(gettimeofday tv_interval); use DateTime; DateTime->DefaultLocale('en_GB'); # set default locale for app use Scalar::Util qw(weaken); # use POSIX qw(strftime); # only required by CAP::LogDispatch callback use LIMS::RDBO; # returns LIMS::DB->new_or_cached via init_db() use LIMS::Validate; # returns validation profile use LIMS::Local::Debug; use LIMS::Local::Utils; use LIMS::Local::Config; use LIMS::Local::QueryLog qw( set_querylog_args ); use LIMS::Local::LogDispatch; =begin # test don't work - sub cgiapp_get_query { my $self = shift; require CGI::Simple; # note, uploads are disabled by default in CGI::Simple return CGI::Simple->new(); } =cut #------------------------------------------------------------------------------- # OVERRIDE METHODS #------------------------------------------------------------------------------- sub cgiapp_init { my $self = shift; # DEBUG $self->query; # needs to be after Log::Dispatch setup if ($self->{have_turned_dbi_trace_on}) { # eg in fcgi script - comment to enable my $msg = sprintf 'PID: %s; TIMESTAMP: %s', $$, DateTime->now( time_zone => 'local' )->datetime; DBI->trace_msg($msg, 0); # warn $msg; } # set Time::HiRes base-line; needs to be before Log::Dispatch setup $self->param( t0 => [gettimeofday] ); # CAP::DBI - load dbh into object - replaced with own dbh() method now # my $dbi = $self->_dbh_config; $self->dbh_config( $dbi ); # configure plugins: $self->_configure_plugins; # everything protected except forgotten password, logout & AJAX functions: # (need 'logout' or will have to login an expired session 1st to logout!!) $self->authen->protected_runmodes( qr/^(?!password_|logout|do_ajax)/ ); $self->debug($self->query); # needs to be done after plugin config #require LIMS::Local::DevelCycle; # warn Devel::Cycle::find_cycle($self); #my $out = LIMS::Local::DevelCycle::find($self); warn $out if $out; } #------------------------------------------------------------------------------- sub setup { my $self = shift; $self->run_modes( login => 'login', AUTOLOAD => \&_exception, ); # warn Dumper $self->run_modes; } #------------------------------------------------------------------------------- sub cgiapp_prerun { my $self = shift; # check access route is permitted (ie direct or via portal): return $self->redirect('/') unless $self->_check_portal_referral(); $self->tt_params( app_url => $self->query->url, url_with_path => $self->query->url(-path_info=>1), # also works in template c.query.utl(path_info=1); # VERSION => $VERSION, # doesn't work under production env # action => (split '/', $self->query->path_info)[1], # using c.query.path_info.match('^/' _ link) instead ); $self->_create_user_profile() if $self->authen->username && ! defined $self->session->param('UserProfile'); # $self->debug($self->session->dump); $self->_set_active_link(); # redirect to hello page if new login: if ( $self->authen->is_new_login ) { return $self->redirect( $self->query->url . '/login/hello' ); } # pass username to QueryLog for sql logging: LIMS::Local::QueryLog::set_querylog_args({user => $self->authen->username}); # pass config args to errorhandler (needs admin email, smtp, etc): LIMS::Local::ErrorHandler::set_errorhandler_args({ cfg => $self->cfg('settings'), user => $self->authen->username, }); # otherwise CAD-loaded classes can't find it for package-wide authorization: $self->run_modes( authz_forbidden => 'forbidden' ); # alternative to $self->authen->protected_runmodes: # $self->authen->username ? # $self->authen->redirect_after_login : # $self->authen->redirect_to_login; } #------------------------------------------------------------------------------- sub cgiapp_postrun { } #------------------------------------------------------------------------------- sub teardown { my $self = shift; $self->session->flush; # recommended action } #------------------------------------------------------------------------------- # for model methods, return (or if 1st call then create & return) a db object: sub lims_db { shift->{__lims_db} ||= LIMS::RDBO->init_db } # should be the *only* call in whole app sub dbh { shift->lims_db->dbh } # for Controller methods requiring the dbh eg session_config() #------------------------------------------------------------------------------- # drop-in replacements for CAP::ConfigAuto (cfg & config) - using L::Local::Config now sub config { my $self = shift; my $cfg = LIMS::Local::Config->instance; if (@_) { my $section = shift; return $cfg->{$section}; } else { return $cfg; } } # alias for config() used by CAP::ConfigAuto: sub cfg { shift->config(@_) } #------------------------------------------------------------------------------- # RUNMODES #------------------------------------------------------------------------------- sub login { my $self = shift; # for destination in login.tt - query->self_url with query_string args removed: $self->tt_params( destination_url => $self->query->url(-path_info=>1) ); $self->_limerick(); return $self->tt_process('login/default.tt'); } #------------------------------------------------------------------------------- # PRIVATE METHODS #------------------------------------------------------------------------------- sub _configure_plugins { my $self = shift; # load config from config file: my $cfg = $self->cfg; #------------------------------------------------------------------------------- # override default template_name_generator method: $cfg->{tt_config}->{TEMPLATE_NAME_GENERATOR} = _tmpl_name_generator(); # should be able to do this in config? # $self->tt_config( $cfg->{tt_config} ); # now loading TT as class method __PACKAGE__->tt_config( $cfg->{tt_config} ); # (singleton) instead of object method #------------------------------------------------------------------------------- # configure CAP::Session - uses CGI::Session; gets cookie or hidden field # session id from $cgi; add CGI_SESSION_OPTIONS (cgi method, session driver, # etc) to session_config(): $cfg->{session_config}->{CGI_SESSION_OPTIONS} = $self->_set_cgisession_options(); $self->session_config( %{ $cfg->{session_config} } ); #------------------------------------------------------------------------------- # configure CAP::Authentication: $cfg->{authen_cfg}->{DRIVER} = # override $cfg->{authen_cfg}->{DRIVER} = [] $ENV{ROSEDB_DEVINIT} =~ /devinit_devel/ # use 'Dummy' login for devel ? 'Dummy' # ! $ENV{HARNESS_ACTIVE} : [ 'Generic', sub { $self->model('User')->verify_credentials(@_) } ]; $self->authen->config( $cfg->{authen_cfg} ); # $self->debug($cfg->{authen_cfg}); #------------------------------------------------------------------------------- # ValidateRM/DFV config: $self->param( dfv_defaults => $cfg->{dfv_defaults} ); #------------------------------------------------------------------------------- # CAP::MessageStack config: $self->capms_config( -automatic_clearing => 1, # removed from session after display -classification_param_name => 'class', # default = 'classification' ); #------------------------------------------------------------------------------- FormValidator::Simple->set_messages( $self->messages('form_validator') ); #------------------------------------------------------------------------------- # configure CAP::Authorization: # push @{ $cfg->{authz_cfg}->{DRIVER} }, ( DBH => $self->dbh ); # $self->authz->config( $cfg->{authz_cfg} ); my $obj = $self; weaken $obj; # or we get circular ref inside authz config() # only used for package-wide auth ie __PACKAGE__->authz->authz_runmodes() $self->authz->config( DRIVER => [ 'Generic', sub { # Generic driver recieves username as 1st arg (don't need it here): my ($username, $action) = @_; # warn $action; return $obj->user_can($action); # using user_can() to validate } ], # FORBIDDEN_RUNMODE => 'forbidden', # doesn't work with CA::Dispatch for # class-wide authz, so defining authz_forbidden rm in prerun() instead ); #------------------------------------------------------------------------------- # CAP::Flash config: using CAP::MessageStack & self->flash() as drop-in replacement # my $flash_config = $cfg->{flash}; # $self->flash_config( @$flash_config ); # using CGI::Session::Flash & $self->flash #------------------------------------------------------------------------------- # CAP::LogDispatch config (needs to be after session & authen configs): # $self->_cap_logdispatch_setup; # comment out if using LIMS::Local::LogDispatch instead #------------------------------------------------------------------------------- # experimental - to stop large build-up of 'form_state_cap_form_state_<32-digits> # => 172800' in session table (but still in _SESSION_EXPIRE_LIST from CGI::Session) # TODO: actually dangerous if params expire - all will be null so params updated as such # $self->form_state->config( expires => '+30m'); # puts form_state into url } #------------------------------------------------------------------------------- # add CGI_SESSION_OPTIONS (cgi method, session driver, etc) to session_config(): sub _set_cgisession_options { my $self = shift; my $cfg = $self->cfg; # override $cfg->{settings}->{db_session_serializer} to a readable format # if running test suite: $cfg->{settings}->{db_session_serializer} = 'default' if $ENV{HARNESS_ACTIVE}; my %CGI_SESSION_OPTIONS = ( db => [ 'driver:MySQL;serializer:'.$cfg->{settings}->{db_session_serializer}, $self->query, { Handle => $self->dbh }, ], # need IDFile, IDInit & IDIncr in session_options_file if using id:incr file => [ 'driver:File;serializer:'.$cfg->{settings}->{file_session_serializer}, $self->query, $cfg->{session_options_file}, ], ); # select CGI_SESSION_OPTIONS driver method from settings.txt (db or file): my $session_driver # sessions dir if lims_server.pl = $ENV{SERVER_SOFTWARE} =~ /HTTP::Server::Simple/ ? $cfg->{settings}->{session_driver} : 'db'; # sessions table for production or test harness return $CGI_SESSION_OPTIONS{$session_driver}; } #------------------------------------------------------------------------------- sub _check_portal_referral { my $self = shift; # $self->stash( REMOTE_ADDR => $ENV{REMOTE_ADDR} ); # to check mod_rpaf is working return 1 # return OK if already logged in or hidden form param supplied: if $self->authen->username || $self->query->param('is_portal_access') || $ENV{SERVER_PORT} == 8080; # VPN access on non-approved IP addr # get array(ref) of permitted direct-entry IP addresses: my $permitted = $self->get_yaml_file('local_addr'); # $self->debug($cfg); # will return true only if REMOTE_ADDR matches a permitted ip address: return ( grep { $ENV{REMOTE_ADDR} =~ /^$_/ } @$permitted ); } #------------------------------------------------------------------------------- sub _set_active_link { my $self = shift; # use Data::Dumper; # warn Dumper $self->query->path_info; my $default = 'search'; # default link # get 'class' arg (if exists) from url eg /foo/bar/1 - class = 'foo': my $class = ( split '/', $self->query->path_info )[1] || return $default; # for classes that don't correspond directly to nav links: my $mapped = { # class nav-link patient => 'register', # request => 'register', # TODO: matches also 'unlock' & 'email_record' config => 'admin', }; my $active_link = $mapped->{$class} || $class || $default; $self->tt_params( active_link => $active_link ); # warn $active_link; } #------------------------------------------------------------------------------- =begin # doesn't work with LIMS::Local::Config->instance method sub _cap_logdispatch_setup { # using LIMS::Local::LogDispatch instead my $self = shift; my $cfg = $self->cfg; # warn Dumper $cfg; # can't have $self in a callback: my $t0 = $self->param('t0'); my $user = $self->authen->username; $cfg->{log_dispatch}{LOG_DISPATCH_OPTIONS} = { callbacks => sub { my %h = @_; chomp $h{message}; my $timestamp = strftime "[%d-%b-%Y %H:%M:%S]", localtime; return sprintf "%s %s %s [%.4f sec]\n", $timestamp, uc $user, $h{message}, tv_interval $t0, [gettimeofday]; }, }; # warn Dumper $cfg->{log_dispatch}; $self->log_config( $cfg->{log_dispatch} ); } =cut #------------------------------------------------------------------------------- # called from cgiapp_prerun only if authen->username exists && profile doesn't: sub _create_user_profile { my $self = shift; my %args = ( col => 'username', value => $self->authen->username, ); # get users' details from users table, or die (can't use error() as session # doesn't exist yet, so user_can() call from tmpl fails): my $user_details = $self->model('User')->get_user_details(\%args) || die 'no user details found in _create_user_profile()'; # first look for custom permissions: my $user_permissions = # arrayref $self->model('User')->get_user_permissions($user_details->id); # if no custom permissions, load default settings for this users' group: if (! @$user_permissions) { $user_permissions = $self->model('User')->get_user_group_functions($user_details->group_id); } # get list of function_names from user_permissions object: my @functions = map { $_->function->function_name } @$user_permissions; # user_profile object to hashref - don't force_load or dies on login table my $profile = $user_details->as_tree; # $self->debug($profile); # stuff functions list into $profile: $profile->{functions} = \@functions; # $self->debug($profile); # set session & authen user profile: $self->session->param( UserProfile => $profile ); # TODO (lot of work) can probably replace this with: $self->authen->store->save(yooza_profile => $profile); # for CAP::Authen LOGIN_SESSION_TIMEOUT { # update userid col of sessions table: my $args = { session_id => $self->session->id, userid => $self->authen->username, }; $self->model('User')->update_session_userid($args); # also updates last_login } unless ( $profile->{designation} eq 'administrator' ) { # || ! $ENV{MOD_PERL}; # register successful login (except db admin): $self->model('User')->register_login($self->session); } } # ?? only works if rm = requested, not forwarded (use LIMS::get_template_name for that) sub _tmpl_name_generator { return sub { my $self = shift; # my $self->tt_template_name(1); # causes infinate loop -> out-of-memory error my $rm = $self->get_current_runmode; # warn $rm; my $module = ref $self; # warn $module; # remove LIMS & LIMS/Controller from $module: my @segments = grep $_ !~ 'LIMS|Controller', split '::', $module; my $catfile = File::Spec->catfile(@segments, $rm); my $tmpl = lc $catfile . '.tt'; # $self->debug('auto-generated template: ' . $tmpl); return $tmpl; }; } #------------------------------------------------------------------------------- sub _limerick { my $self = shift; my $src_file = $self->cfg('path_to_app_root') . '/src/lib/lear.txt'; return 0 unless (-e $src_file); require LIMS::Local::Drollness; # to avoid compile-time error if absent my $data = LIMS::Local::Drollness::limerick($src_file); $self->tt_params( limerick => $data ); } #------------------------------------------------------------------------------- # returns dbh object (and sets authen_cfg driver - not any more): =begin # replaced with own dbh() method now sub _dbh_config { my $self = shift; # Rose::DB method: # my $driver = 'dbi_driver'; # not using now, replaced with Generic & sub {} return LIMS::DB->new_or_cached->retain_dbh; # need retain_dbh or get: =begin ERROR' for request '/hmds/admin/user_location': Error executing class callback in init stage: Can't connect to data source 'LIMS::DB::__RoseDBPrivate__::Rose::DB::MySQL=HASH(0x9a810f4)' because I can't work out what driver to use (it doesn't seem to contain a 'dbi:driver:' prefix and the DBI_DRIVER env var is not set) at /home/raj/perl5/lib/perl5/CGI/Application/Plugin/DBH.pm line 42 =cut # $dbi->trace(1, './logs/trace.log'); # best switched on in LIMS::DB::dbi_connect # switch on profiling: #use DBI::Profile; #$dbi->{Profile} = DBI::Profile->new(); #$dbi->{Profile} = 2; =begin # DBIC method: use lib '/home/raj/www/apps/LIMS/tags/legacy/lib'; use LIMS::Schema; $self->dbh_config( $cfg->{'dbh_params'} ); # add schema to object - move to own class - load as needed: $self->param( schema => LIMS::Schema->connect(@{ $cfg->{dbh_params} }) ); $cfg->{'dbic_driver'}->[2] = $self->param('schema'); # SCHEMA my $driver = 'dbic_driver'; =cut =begin # using DRIVER = "Generic, sub {}" now - set in _configure_plugins() # override DBH => undef in $self->cfg->{dbi_driver}: @{ $self->cfg->{dbi_driver} }[2] = $db; $self->cfg->{authen_cfg}{DRIVER} = $self->cfg->{$driver}; =cut # return $db; # moved to top #} #------------------------------------------------------------------------------- sub _debug_path { my ($self, $method) = @_; if (! $method) { my @caller = caller(1); # warn $caller[3]; ($method) = $caller[3] =~ /.*::(.*)/; # greedy matching ensures last } # done in LOG_DISPATCH_OPTIONS callbacks sub now: # my $timings = # sprintf "%s, %.4f sec", $method, tv_interval $self->param('t0'), [gettimeofday]; $self->debug($method); # DEBUG( $timings ); } #------------------------------------------------------------------------------- # never gets called if using CA::Dispatch - CAD uses its own error handling for # non-existent rms sub _exception { my ($self, $intended_runmode) = @_; # $obj->_dump_path('_exception'); # my $output = "Looking for '$intended_runmode', but found 'AUTOLOAD' instead"; $self->tt_params( mode => 'Error', # title msg => $intended_runmode, title => 'Unknown Action', ); return $self->tt_process('site/exception.tt'); } 1; __END__ # uses CAP::TT tt_template_name method to return path to template # alternative to TEMPLATE_NAME_GENERATOR in tt_config - should be able to handle # forwarded rm's; requires tmpl name to match module path # (eg Admin::Screen::default() => admin/screen/default.tt): =begin sub _get_template_name { my $self = shift; # eg LIMS/Admin/Screen/Test/default.tmpl my @segments = grep $_ !~ 'LIMS|Controller', split '/', $self->tt_template_name(1); my $tmpl = File::Spec->catfile(@segments); $tmpl =~ s/tmpl/tt/; # using tt suffix return lc $tmpl; # DEBUG 'auto-generated template: ' . $tmpl; } =cut