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PathParams.051007.pm
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PathParams.051007.pm
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# Copyright SRA International
#
# Distributed under the OSI-approved BSD 3-Clause License.
# See http://ncip.github.com/pathway-interaction-database/LICENSE.txt for details.
package PathParams;
require Exporter;
@ISA = qw(Exporter);
@EXPORT = qw(
ReadParams
CheckParams
);
use strict;
use PWLabel;
use constant ORACLE_LIST_LIMIT => 500;
use constant PRINT => "print";
use constant SHOW => "show";
use constant MACRO_PROCESS => "macro_process";
use constant SKIP_MOL_ID => "skip_mol_id";
use constant SKIP_COMPLEXES => "skip_complexes";
use constant SOURCE_ID => "source_id";
use constant COLLAPSE => "collapse";
use constant COLOR => "color";
use constant VALUE => "value";
use constant CHANNEL => "channel";
use constant CONNECT_MOLECULE => "connect_molecule";
use constant CONNECT_MOL_NAME => "connect_mol_name";
use constant CONNECT_MOL_ID => "connect_mol_id";
use constant CONNECT_MOL_EXT_ID => "connect_mol_ext_id";
use constant PRUNE_MOL_NAME => "prune_mol_name";
use constant PRUNE_MOL_ID => "prune_mol_id";
use constant PRUNE_MOL_EXT_ID => "prune_mol_ext_id";
use constant PATHWAY => "pathway";
use constant PATHWAY_ID => "pathway_id";
use constant PATHWAY_NAME => "pathway_name";
use constant PATHWAY_EXT_ID => "pathway_ext_id";
use constant ATOM_ID => "atom_id";
use constant EVIDENCE_CODE => "evidence_code";
use constant PRUNE_ATOM_ID => "prune_atom_id";
use constant MOLECULE => "molecule";
use constant MOL_NAME => "mol_name";
use constant MOL_ID => "mol_id";
use constant MOL_EXT_ID => "mol_ext_id";
use constant INCLUDE => "include";
use constant EDGE => "edge";
use constant DEGREE_BACK => "degree_back";
use constant DEGREE_FORWARD => "degree_forward";
use constant DB_USER => "db_user";
use constant DB_PASS => "db_pass";
use constant DB_INST => "db_inst";
use constant DB_SCHEMA => "db_schema";
use constant SIM_CYCLE => "sim_cycle";
use constant SIM_MOL_ID => "sim_mol_id";
use constant SIM_OUTPUT => "sim_output";
use constant SIM_METHOD => "sim_method";
use constant SIM_SIMPLE => "sim_simple";
use constant SIM_COMPETE => "sim_compete";
use constant MAX_DEGREE => 5;
my %mol_types = ("CM" => "compound", "CX" => "complex",
"RN" => "rna", "PR" => "protein");
my %id_types = (
"EC" => 1,
"LL" => 1,
"UP" => 1,
"CA" => 1,
"KG" => 1
);
my %printopts = (
"sql" => 1,
"xml" => 1,
"biopax" => 1,
"sbml" => 1,
"lisp" => 1,
"petrinet" => 1,
"sas" => 1,
"dot" => 1,
"template" => 1
);
######################################################################
sub new {
my ($self, $lv) = @_;
my $x = {};
$x->{lv} = $lv;
return bless $x;
}
######################################################################
sub Errors {
my ($self) = @_;
return $self->{errors};
}
######################################################################
sub AddError {
my ($self, $msg) = @_;
#print STDERR "$msg\n";
push @{ $self->{errors} }, $msg;
}
######################################################################
sub Trim {
my ($x) = @_;
$x =~ s/^\s+//;
$x =~ s/\s+$//;
return $x;
}
######################################################################
sub DoDbUser {
my ($self, $user) = @_;
$self->{db}{user} = $user;
}
######################################################################
sub DoDbPass {
my ($self, $pass) = @_;
$self->{db}{pass} = $pass;
}
######################################################################
sub DoDbInst {
my ($self, $inst) = @_;
$self->{db}{inst} = $inst;
}
######################################################################
sub DoDbSchema {
my ($self, $schema) = @_;
$self->{db}{schema} = $schema;
}
######################################################################
sub DoPrint {
my ($self, $what) = @_;
$what = lc(Trim($what));
if (not defined $printopts{$what}) {
$self->AddError("unrecognized print option $what");
return;
}
$self->{print}{$what} = 1;
}
######################################################################
sub DoSourceId {
my ($self, $id) = @_;
$id = lc(Trim($id));
if ($id =~ /^\d+$/) {
$self->{source_id}{$id} = 1;
}
}
######################################################################
sub DoMacroProcess {
my ($self, $name) = @_;
## Don't lower-case; PWLabel retains case-sensitivitiy
$name = Trim($name);
$self->{macroprocess_name}{$name} = 1;
}
######################################################################
sub DoShow {
my ($self, $what) = @_;
$what = lc(Trim($what));
if (
$what eq "atom_id" ||
$what eq "subtype_line" ||
0 ) {
$self->{show}{$what} = 1;
} else {
$self->AddError("unrecognized option $what for show");
return;
}
}
######################################################################
sub DoSkip {
my ($self, $cmd, $mol_id) = @_;
$cmd = lc(Trim($cmd));
if ($cmd eq "complexes") {
$self->{skip}{complexes} = 1;
} elsif ($cmd eq "mol_id") {
$self->{skip}{mol_id}{$mol_id} = 1;
}
}
######################################################################
sub DoCollapse {
my ($self, $cmd) = @_;
$cmd = lc(Trim($cmd));
if ($cmd eq "processes") {
$self->{collapse}{processes} = 1;
} elsif ($cmd eq "molecules") {
$self->{collapse}{molecules} = 1;
} elsif ($cmd eq "subnets") {
$self->{collapse}{subnets} = 1;
} else {
$self->AddError("unrecognized print option $cmd");
return;
}
}
######################################################################
sub DoColor {
my ($self, $number, $color) = @_;
# $boundtype = lc(Trim($boundtype));
$number = lc(Trim($number));
$color = lc(Trim($color));
# if ($boundtype ne "upper" || $boundtype ne "lower") {
# $self->AddError("unrecognized bound $boundtype in color command");
# return;
# }
if ($number !~ /^(-|\+)?\d+(\.\d*)?$/ && $number !~ /^(-|\+)?\.\d+$/) {
$self->AddError("number expected for $number in color command");
return;
}
if ($color !~ /^#?([0-9A-Fa-f]{6})/) {
$self->AddError("six-place hexadecimal color specification " .
"expected for $color");
return;
} else {
$color = $1;
}
$self->{color}{$number} = $color;
}
######################################################################
sub DoSim {
my ($self, $cmd, @vars) = @_;
if ($cmd eq "cycle") {
my $ncycle = Trim(shift @vars);
if ($ncycle !~ /^\d+$/) {
$self->AddError("need numeric argument for 'sim'");
return;
}
$self->{sim}{ncycle} = $ncycle;
} elsif ($cmd eq "mol_id") {
my ($mol_id, $pct) = @vars;
$self->{sim}{mol}{$mol_id} = $pct;
} elsif ($cmd eq "output") {
my $output_type = lc(Trim(shift @vars));
$self->{sim}{output} = $output_type;
} elsif ($cmd eq "method") {
my $meth = lc(Trim(shift @vars));
$self->{sim}{method} = $meth;
if ($meth eq "boolean") {
my $default = shift @vars;
if ($default ne "") {
$self->{sim}{booleandefault} = $default;
}
}
} elsif ($cmd eq "simple") {
my $flag = Trim(shift @vars);
if ($flag ne "0" && $flag ne "" && $flag ne "1") {
$self->AddError("unrecognized sim_simple option $flag");
return;
}
$self->{sim}{simple} = $flag;
} elsif ($cmd eq "compete") {
my $flag = Trim(shift @vars);
if ($flag ne "0" && $flag ne "" && $flag ne "1") {
$self->AddError("unrecognized sim_compete option $flag");
return;
}
$self->{sim}{compete} = $flag;
} else {
$self->AddError("unrecognized sim command $cmd");
return;
}
}
######################################################################
sub DoEdge {
my ($self, @vars) = @_;
my ($interaction_id, $edge_type, $mol_name, $mol_ext_id,
$activity, $location) = @vars;
$interaction_id = Trim($interaction_id);
$edge_type = lc(Trim($edge_type));
$mol_name = Trim($mol_name);
$mol_ext_id = Trim($mol_ext_id);
$activity = lc(Trim($activity));
$location = lc(Trim($location));
if ($interaction_id eq "") {
$self->AddError("missing interaction id in edge command: " .
join("\t", @vars) );
return;
}
if ($edge_type eq "") {
$self->AddError("missing edge type in edge command: " .
join("\t", @vars) );
return;
}
$edge_type = lc($edge_type);
if ($edge_type ne "input" && $edge_type ne "output" &&
$edge_type ne "agent" && $edge_type ne "inhibitor") {
$self->AddError("illegal edge type '$edge_type' in edge command: " .
join("\t", @vars) );
return;
}
if ($mol_name eq "" && $mol_ext_id eq "") {
$self->AddError("must specify mol name and/or mol external id in edge command: " .
join("\t", @vars) );
return;
}
if ($activity) {
$self->{privateactivity}{$activity} = 1;
}
if ($location) {
$self->{privatelocation}{$location} = 1;
}
if ($mol_ext_id =~ /^\d+$/) {
$self->{privatells}{$mol_ext_id} = 1;
}
push @{ $self->{privateedges} }, join("\t", $interaction_id, $edge_type,
$mol_name, $mol_ext_id, $activity, $location);
}
######################################################################
sub DoDegree {
my ($self, $direction, @vars) = @_;
my $n = Trim(shift @vars);
if ($direction ne "back" && $direction ne "forward") {
$self->AddError("unrecognized degree direction");
return;
}
if ($n !~ /^\d+$/) {
$self->AddError("illegal value $n for degree $direction");
return;
} elsif ($n > MAX_DEGREE) {
$self->AddError("value for degree $n exceeds maximum " . MAX_DEGREE);
return;
} else {
$self->{degree}{$direction} = $n;
}
}
######################################################################
sub DoInclude {
my ($self, $what) = @_;
$what = lc(Trim($what));
if ($what eq "complex_uses") {
$self->{include_complex_uses} = 1;
} elsif ($what eq "family_uses") {
$self->{include_family_uses} = 1;
} else {
$self->AddError("Illegal option $what for include");
return;
}
}
######################################################################
sub MouseTrap {
my ($self) = @_;
##! Traps only LocusLink ids for mouse
my (%temp);
for $_ (keys %{ $self->{mol_ext_id} }) {
if (/^\d+$/) {
$temp{$_} = 1;
}
}
for $_ (keys %{ $self->{mol_ext_id_value} }) {
if (/^\d+$/) {
$temp{$_} = 1;
}
}
for $_ (keys %{ $self->{privatells} }) {
$temp{$_} = 1;
}
my @temp = keys %temp;
if (@temp == 0) {
return;
}
my ($db_inst, $db_user, $db_pass, $schema) =
("cgprod", "web", "readonly", "cgap");
my ($db, $sql, $stm, $i, $list);
my ($hs_locus, $mm_locus);
$db = DBI->connect("DBI:Oracle:" . $db_inst, $db_user, $db_pass);
if (not $db or $db->err()) {
print STDERR "Cannot connect to " . $db_user . "@" . $db_inst . "\n";
exit;
}
for($i = 0; $i < @temp; $i += ORACLE_LIST_LIMIT) {
if(($i + ORACLE_LIST_LIMIT - 1) < @temp) {
$list = "'" . join("','", @temp[$i..$i+ORACLE_LIST_LIMIT-1]) . "'";
}
else {
$list = "'" . join("','", @temp[$i..@temp-1]) . "'";
}
$sql = qq!
select
hs.locus_id,
mm.locus_id
from
$schema.hg_entry mm,
$schema.hg_entry hs
where
mm.taxon_id = 10090
and hs.taxon_id = 9606
and hs.entry_id = mm.entry_id
and mm.locus_id in ($list)
!;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
exit;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
exit;
}
while (($hs_locus, $mm_locus) = $stm->fetchrow_array()) {
push @{ $self->{mousetrap}{$mm_locus} }, $hs_locus;
}
}
$db->disconnect();
for $mm_locus (keys %{ $self->{mol_ext_id} }) {
if (defined $self->{mol_ext_id}{$mm_locus}) {
if (defined $self->{mousetrap}{$mm_locus}) {
for $hs_locus (@{ $self->{mousetrap}{$mm_locus} }) {
$self->{mol_ext_id}{$hs_locus} = $self->{mol_ext_id}{$mm_locus};
}
delete $self->{mol_ext_id}{$mm_locus};
if (keys %{ $self->{mol_ext_id}{$mm_locus} } == 0) {
delete $self->{mol_ext_id}{$mm_locus};
}
}
}
}
for $mm_locus (keys %{ $self->{mol_ext_id_value} }) {
if (defined $self->{mol_ext_id_value}{$mm_locus}) {
if (defined $self->{mousetrap}{$mm_locus}) {
for $hs_locus (@{ $self->{mousetrap}{$mm_locus} }) {
for my $subtype (keys %{ $self->{mol_ext_id_value}{$mm_locus} }) {
$self->{mol_ext_id_value}{$hs_locus}{$subtype} =
$self->{mol_ext_id_value}{$mm_locus}{$subtype};
}
}
delete $self->{mol_ext_id_value}{$mm_locus};
if (keys %{ $self->{mol_ext_id_value}{$mm_locus} } == 0) {
delete $self->{mol_ext_id_value}{$mm_locus};
}
}
}
}
}
######################################################################
sub DoChannel {
my ($self, $channel, $molecule) = @_;
my $lv = $self->{lv};
$channel = uc(Trim($channel));
if ($channel eq "") {
$self->AddError("No channel specified for channel command: " .
join("\t", $channel, $molecule));
return;
}
if ($channel !~ /^(A|B)$/) {
$self->AddError("Illegal channel specified for channel command: " .
join("\t", $channel, $molecule));
return;
}
$self->{mol_name}{lc(Trim($molecule))}{channel} = 1;
$self->{mol_ext_id}{lc(Trim($molecule))}{channel} = 1;
$self->{molecule_channel}{lc(Trim($molecule))}{$channel} = 1;
}
######################################################################
sub DoValue {
my ($self, $value, $what, @vars) = @_;
my $lv = $self->{lv};
my ($molid, $name, $extid, $activity, $location);
$value = Trim($value);
if ($value eq "") {
$self->AddError("No value specified for value command: " .
join("\t", $what, $value, @vars));
return;
}
if ($value !~ /^(-|\+)?(\d+)?(\.\d+)?$/) {
$self->AddError("Illegal value specified for value command: " .
join("\t", $what, $value, @vars));
return;
}
if ($what eq "mol_name" || $what eq "molecule") {
($name, $activity, $location) = @vars;
} elsif ($what eq "mol_id") {
($molid, $activity, $location) = @vars;
$molid = Trim($molid);
if ($molid !~ /^\d+$/) {
$self->AddError("illegal molecule id $molid for DoMol");
return;
}
} elsif ($what eq "mol_ext_id" || $what eq "molecule") {
($extid, $activity, $location) = @vars;
} else {
$self->AddError("Illegal molecular specifier for value command: " .
join("\t", $what, $value, @vars));
return;
}
$activity = lc(Trim($activity));
$location = Trim($location);
if ($activity ne "") {
my $lvid = $lv->StringToLabelValue("activity-state", $activity);
if (! $lvid) {
$self->AddError("illegal activity value: $activity");
return;
} else {
# $activity = $lvid;
}
}
if ($location ne "") {
my $lvid = $lv->StringToLabelValue("location", $location);
if (! $lvid) {
$self->AddError("illegal location value: $location");
return;
} else {
# $location = $lvid;
}
}
my $subtype = "$activity\t$location";
if ($what eq "mol_name" || $what eq "molecule") {
$self->{mol_name_value}{lc(Trim($name))}{$subtype} = $value;
$self->{mol_name}{lc(Trim($name))}{value} = 1;
} elsif ($what eq "mol_id") {
$molid = Trim($molid);
$self->{mol_id_value}{$molid}{$subtype} = $value;
} elsif ($what eq "mol_ext_id" || $what eq "molecule") {
$self->{mol_ext_id}{lc(Trim($extid))}{value}{$subtype} = $value;
$self->{mol_ext_id_value}{lc(Trim($extid))}{$subtype} = $value;
}
}
######################################################################
sub DoMol {
my ($self, $op, $what, @vars) = @_;
my ($name, $molid, $extid);
if ($what eq "name") {
($name) = @vars;
$self->{mol_name}{lc(Trim($name))}{$op} = 1;
} elsif ($what eq "id") {
($molid) = @vars;
$molid = Trim($molid);
if ($molid !~ /^\d+$/) {
$self->AddError("illegal molecule id $molid for DoMol");
return;
} else {
if ($op eq "prune") {
$self->{prune_mol_id}{$molid} = 1; ## may still be an unknown molid
} elsif ($op eq "get") {
$self->{mol_id}{$molid} = 1; ## may still be an unknown molid
} elsif ($op eq "connect") {
$self->{connect}{$molid} = 1;
} else {
$self->AddError("unrecognized prune/get/connect action $op");
return;
}
}
} elsif ($what eq "ext_id") {
($extid) = @vars;
$self->{mol_ext_id}{lc(Trim($extid))}{$op} = 1;
} elsif ($what eq "general") {
## by name
($name) = @vars;
$self->{mol_name}{lc(Trim($name))}{$op} = 1;
## by ext id
($extid) = @vars;
$self->{mol_ext_id}{lc(Trim($extid))}{$op} = 1;
} else {
$self->AddError("unrecognized subtype $what for DoMol");
return;
}
}
######################################################################
sub DoAtomId {
my ($self, $what, $atom_id) = @_;
$atom_id = Trim($atom_id);
if ($atom_id =~ /^\*$/) {
if ($what eq "get") {
$self->{atom}{$atom_id} = 1;
}
} elsif ($atom_id =~ /^\d+$/) {
if ($what eq "get") {
$self->{atom}{$atom_id} = 1;
} elsif ($what eq "prune") {
$self->{prune_atom_id}{$atom_id} = 1;
}
} else {
$self->AddError("illegitimate atom id $atom_id");
return;
}
}
######################################################################
sub DoEvidenceCode {
my ($self, $what, $evidence_code) = @_;
$evidence_code = uc(Trim($evidence_code));
if ($evidence_code =~ /^\*$/) {
if ($what eq "get") {
$self->{evidence_code}{$evidence_code} = 1;
}
} elsif ($evidence_code =~ /^[INRT][A-S]{1,2}$/i) {
if ($what eq "get") {
$self->{evidence_code}{$evidence_code} = 1;
}
} else {
$self->AddError("illegitimate evidence_code $evidence_code");
return;
}
}
######################################################################
sub DoPathway {
my ($self, $what, @vars) = @_;
my ($pathway_id, $pathway_ext_id, $pathway_name);
if ($what eq "id") {
($pathway_id) = @vars;
$pathway_id = Trim($pathway_id);
if ($pathway_id !~ /^\d+$/ && $pathway_id ne "*") {
$self->AddError("illegitimate pathway id $pathway_id");
return;
}
$self->{pathway}{id}{$pathway_id} = 1;
} elsif ($what eq "extid") {
($pathway_ext_id) = @vars;
$self->{pathway}{ext_id}{$pathway_ext_id} = 1;
} elsif ($what eq "name") {
($pathway_name) = @vars;
if ($pathway_name !~ /^\s+$/) {
$self->{pathway}{name}{lc(Trim($pathway_name))} = 1;
}
} elsif ($what eq "general") {
($pathway_name) = @vars;
if ($pathway_name !~ /^\s+$/) {
$self->{pathway}{name}{lc(Trim($pathway_name))} = 1;
}
($pathway_ext_id) = @vars;
$self->{pathway}{ext_id}{$pathway_ext_id} = 1;
} else {
$self->AddError("unrecognized subtype $what for DoPathway");
return;
}
}
######################################################################
sub CheckMol {
my ($self, $db) = @_;
if (defined $self->{mol_name}) {
CheckMolName($self, $db);
}
## doing privatells to catch them in mousetrap
if (defined $self->{mol_ext_id} || defined $self->{privatells} ||
defined $self->{mol_ext_id_value}) {
CheckMolExtId($self, $db);
}
for my $x (keys %{ $self->{mol_name} }, keys %{ $self->{mol_ext_id} }) {
if (! defined $self->{molmap}{$x}) {
$self->{no_molmap}{$x} = 1;
}
}
}
######################################################################
sub CheckMolName {
my ($self, $db) = @_;
##!!!!!!! We aren't going to require mol type any longer
my ($sql, $stm);
my ($molid, $molname, $nametype, $moltype, $what, $ll_id, $ll_list);
my ($alias, $alias_list);
my $schema = $self->{db}{schema};
my @temp = keys %{ $self->{mol_name} };
my $list;
$ll_list = 999999;
for(my $i = 0; $i < @temp; $i += ORACLE_LIST_LIMIT) {
if(($i + ORACLE_LIST_LIMIT - 1) < @temp) {
$list = "'" . join("','", @temp[$i..$i+ORACLE_LIST_LIMIT-1]) . "'";
}
else {
$list = "'" . join("','", @temp[$i..@temp-1]) . "'";
}
$list =~ s/,/','/;
$list = lc $list;
# Find alias
$sql = qq!
select
ll_id
from $schema.pw_molecule_search
where lower(symbol) in ($list)
!;
print STDERR "SQL: $sql\n";
$stm = $db->prepare($sql);
if(not $stm) {
$self->AddError("$sql");
$self->AddError("$DBI::errstr");
$self->AddError("prepare call failed");
return;
}
if(!$stm->execute()) {
$self->AddError("$sql");
$self->AddError("$DBI::errstr");
$self->AddError("execute call failed");
return;
}
while (($ll_id) =
$stm->fetchrow_array()) {
$ll_list = $ll_list . ',' . $ll_id;
}
$sql = qq!
select symbol from cgap.ll_gene
where ll_id in ($ll_list)
!;
$stm = $db->prepare($sql);
if(not $stm) {
$self->AddError("$sql");
$self->AddError("$DBI::errstr");
$self->AddError("prepare call failed");
return;
}
if(!$stm->execute()) {
$self->AddError("$sql");
$self->AddError("$DBI::errstr");
$self->AddError("execute call failed");
return;
}
while (($alias) =
$stm->fetchrow_array()) {
$alias = lc(Trim($alias));
$self->{mol_name}{lc(Trim("$alias"))}{"get"} = 1;
$alias_list = $alias_list . ',' . $alias;
$list = $list . "," . "'" . $alias . "'";
}
print STDERR "List: $list\n";
print STDERR "AliasList: $alias_list\n";
## Find exact matches to the name in PID
$sql = qq!
select
n.mol_id,
lower(n.mol_name),
n.name_type,
m.basic_mol_type
from
$schema.pw_mol m,
$schema.pw_mol_name n
where
m.mol_id = n.mol_id
and lower(n.mol_name) in ($list)
!;
$stm = $db->prepare($sql);
if(not $stm) {
$self->AddError("$sql");
$self->AddError("$DBI::errstr");
$self->AddError("prepare call failed");
return;
}
if(!$stm->execute()) {
$self->AddError("$sql");
$self->AddError("$DBI::errstr");
$self->AddError("execute call failed");
return;
}
while (($molid, $molname, $nametype, $moltype) =
$stm->fetchrow_array()) {
$self->{molmap}{$molname}{$molid} = 1;
if (defined $self->{mol_name}{$molname}) {
for $what (keys %{ $self->{mol_name}{$molname} }) {
if ($what eq "prune") {
$self->{prune_mol_id}{$molid} = 1;
} elsif ($what eq "get") {
$self->{mol_id}{$molid} = 1;
} elsif ($what eq "connect") {
$self->{connect}{$molid} = 1;
} elsif ($what eq "value") {
# handled immediately below
} elsif ($what eq "channel") {
# handled immediately below
} else {
$self->AddError("unrecognized action $what in CheckMolName");
return;
}
if (defined $self->{mol_name_value}{$molname}) {
for my $subtype (keys %{ $self->{mol_name_value}{$molname} }) {
$self->{mol_id_value}{$molid}{$subtype} =
$self->{mol_name_value}{$molname}{$subtype};
}
}
if (defined $self->{molecule_channel}{$molname}) {
for my $channel (keys %{ $self->{molecule_channel}{$molname} }) {
$self->{mol_id_channel}{$molid}{$channel} = 1;
}
}
}
}
}
## Find matches of gene names to proteins in PID
$sql = qq!
select
e.mol_id,
lower(g.symbol),
e.id_type,
m.basic_mol_type
from
$schema.pw_mol m,
$schema.pw_ext_mol_id e,
cgap.ll2sp s,
cgap.sp_primary p,
cgap.ll_gene g
where
m.mol_id = e.mol_id
and p.sp_id_or_secondary = e.ext_mol_id
and p.sp_id_or_secondary = s.sp_primary
and s.organism = 'Hs'
and s.ll_id = g.ll_id
and lower(g.symbol) in ($list)
!;
$stm = $db->prepare($sql);
if(not $stm) {
$self->AddError("$sql");
$self->AddError("$DBI::errstr");
$self->AddError("prepare call failed");
return;
}
if(!$stm->execute()) {
$self->AddError("$sql");
$self->AddError("$DBI::errstr");
$self->AddError("execute call failed");
return;
}
while (($molid, $molname, $nametype, $moltype) =
$stm->fetchrow_array()) {
$self->{molmap}{$molname}{$molid} = 1;
if (defined $self->{mol_name}{$molname}) {
for $what (keys %{ $self->{mol_name}{$molname} }) {
if ($what eq "prune") {
$self->{prune_mol_id}{$molid} = 1;
} elsif ($what eq "get") {
$self->{mol_id}{$molid} = 1;
} elsif ($what eq "connect") {
$self->{connect}{$molid} = 1;
} elsif ($what eq "value") {
# handled immediately below
} elsif ($what eq "channel") {
# handled immediately below
} else {
$self->AddError("unrecognized action $what in CheckMolName");
return;
}
if (defined $self->{mol_name_value}{$molname}) {
for my $subtype (keys %{ $self->{mol_name_value}{$molname} }) {
$self->{mol_id_value}{$molid}{$subtype} =
$self->{mol_name_value}{$molname}{$subtype};
}
}
if (defined $self->{molecule_channel}{$molname}) {
for my $channel (keys %{ $self->{molecule_channel}{$molname} }) {
$self->{mol_id_channel}{$molid}{$channel} = 1;
}
}
}
}
}
}
}
######################################################################
sub CheckMolExtId {
my ($self, $db) = @_;
##!! convert Mm locus ids to Hs locus ids
$self->MouseTrap();
my ($sql, $stm);
my ($molid, $extid, $what);
my $schema = $self->{db}{schema};
my @temp = keys %{ $self->{mol_ext_id} };
my $list;
for(my $i = 0; $i < @temp; $i += ORACLE_LIST_LIMIT) {
if(($i + ORACLE_LIST_LIMIT - 1) < @temp) {
$list = "'" . join("','", @temp[$i..$i+ORACLE_LIST_LIMIT-1]) . "'";
}
else {
$list = "'" . join("','", @temp[$i..@temp-1]) . "'";
}
## Find direct matches of ext ids
$sql = qq!
select
e.mol_id,
lower(e.ext_mol_id)
from
$schema.pw_ext_mol_id e
where
lower(e.ext_mol_id) in ($list)
!;
$stm = $db->prepare($sql);
if(not $stm) {