package RequestForm::DB; use LIMS::Local::QueryLibrary; use DateTime::Format::MySQL; use LIMS::Local::Utils; use Path::Tiny; use FindBin; use Data::Dumper; use lib '/home/raj/perl-lib'; use Local::DB; use RequestForm::Test; # test_schema() for test scripts use RequestForm::Class; # provides Moo, Local::MooX::Types & LIMS::Local::Debug::p has dbname => ( is => 'ro', isa => String, required => 1 ); # uclh, hilis4, etc has sql_lib => ( is => 'lazy' ); # returns SQL::Library obj has dbix => ( is => 'lazy' ); # returns DBIx::Simple object sub _build_dbix { my $self = shift; my $db = $self->dbname; # dbname = uclh, leeds, etc $db =~ s/leeds/hilis4/; # leeds -> hilis4 symlink doesn't work on innodb tables return Local::DB->dbix($db) unless $db eq 'test'; # test needs sqlite db initialising: my $dbix = $self->init_test_db(); # return in memory sqlite dbix object return $dbix; } sub _build_sql_lib { my $lib = path($FindBin::Bin, '..', 'sql.lib')->realpath; LIMS::Local::QueryLibrary->new({ lib => $lib }); } sub init_test_db { # returns dbix object using in-memory sqlite db my $self = shift; my $dbix = Local::DB->dbix({ dsn => 'dbi:SQLite:dbname=:memory:' }); my @schema = test_schema(); # RequestForm::Test do { $dbix->dbh->do($_) || die $dbix->error } for @schema; # $dbix->error doesn't work here # TODO: only needed in 004_basic_function.t but called for all - ? possible to share dbix { # initialise patients table with patient #2 from patients.conf: my $src = patient_data(); # my $cols = $self->get_cols('patients'); # can't call dbix() yet, _build_dbix hasn't finished my $info = $dbix->query("PRAGMA table_info(patients)")->hashes; # warn Dumper $info; my @cols = grep { $_ ne 'id' } map $_->{name}, @$info; # warn Dumper \@cols; my $patient = $src->[1]; # dpp $data; my %data; $data{$_} = $patient->{$_} for @cols; # warn Dumper \%data; # dob from components: $data{dob} = join '-', @{$patient}{qw(year month day)}; # warn Dumper \%data; $dbix->insert('patients', \%data); } return $dbix; } sub save_params { my $self = shift; my $vars = shift; # p $vars; # get field names from request_form table: my $cols = $self->get_cols('request_form'); # p $cols; my %h = map +($_ => $vars->{$_}), @$cols; # p %h; my $db = $self->dbix(); $db->insert('request_form', \%h); } sub search_patient { my ($self, $nhs_number) = @_; # p $nhs_number; my $db = $self->dbix(); my $data = $db->select('patients', '*', { nhs_number => $nhs_number })->hash; return $data; } sub get_referral_sources { my ($self, $str) = @_; # part of referral_location (string) my $db = $self->dbix(); my $lib = $self->sql_lib; my $sql = $lib->retr('referral_sources'); my $data = $db->query( $sql, $str )->hashes; # p $vars; return $data; } sub get_previous_cml_monitoring { my ($self, $nhs_number) = @_; my $db = $self->dbix(); my $lib = $self->sql_lib; my $sql = $lib->retr('previous_cml_monitoring'); my $query = $db->query( $sql, $nhs_number ); my (@data, $last_result); # get bcr-abl results in reverse chronological order: while ( my $ref = $query->hash ) { # p $ref; # registration date to DT object: my $reg_date = DateTime::Format::MySQL->parse_date($ref->{registered}); # extract bcr-abl:abl ratio if exists: my ($ratio) = $ref->{result} =~ /(BCR-ABL : ABL ratio = .*%)/; # date of last result is reg date of most recent bcr-abl ratio: $last_result = $reg_date if ( $ratio and ! $last_result ); # set result to bcr-abl:abl ratio, otherwise keep original: push @data, { registered => $reg_date, result => $ratio || $ref->{result}, }; } my %h = ( date_last => $last_result, results => \@data, ); # p %h; return \%h; } sub get_userid { my ($self, $username) = @_; my $db = $self->dbix(); $db->select('users', 'id', { username => $username })->into(my $user_id); return $user_id; } sub get_cols { my ($self, $table) = @_; my $db = $self->dbname; my $meta = $db eq 'test' ? $self->get_meta_for_sqlite($table) : $self->get_meta_for_mysql($table); # p $meta; return [ keys %$meta ]; } sub get_meta_for_mysql { my ($self, $table) = @_; my $dbh = $self->dbix; my $t = $dbh->query("show columns from $table")->hashes; # p $t; my %meta = map { $_->{field} => $_ } @$t; # p %meta; return \%meta; } sub get_meta_for_sqlite { my ($self, $table) = @_; # warn $table; my $dbh = $self->dbix; my $t = $dbh->query("PRAGMA table_info($table)")->hashes; my %meta = map { $_->{name} => $_ } @$t; # warn Dumper \%meta; return \%meta; } 1;