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PathwayXML.pm
executable file
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PathwayXML.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 PathwayXML;
require Exporter;
@ISA = qw(Exporter);
#@EXPORT = qw(
#);
use strict;
use Pathway;
use DBI;
use constant ORACLE_LIST_LIMIT => 500;
use constant MAX_LONG_LEN => 16384;
my $INCOMING;
my $OUTGOING;
my $pathway_type;
my $subnet_type;
######################################################################
sub new {
my ($self, $db, $schema, $pw, $lv) = @_;
my $x = {};
$x->{db} = $db;
$x->{pw} = $pw;
$x->{lv} = $lv;
$x->{schema} = $schema;
$db->{LongReadLen} = MAX_LONG_LEN;
# InitializePartOf($x);
# InitializeFamilyMember($x);
$pathway_type = $lv->StringToLabelValue("process-type", "pathway");
$subnet_type = $lv->StringToLabelValue("process-type", "subnet");
return bless $x;
}
######################################################################
######################################################################
######################################################################
##
## spec by degree
##
######################################################################
######################################################################
sub AtomsOfDegree {
my ($self, $direction, $degree, $prune_mol_hash,
$prune_atom_hash) = @_;
my $db = $self->{db};
my $pw = $self->{pw};
my $lv = $self->{lv};
my $SCHEMA = $self->{schema};
my $retval = 'not assigned';
if ($degree < 1) {
return;
}
## !!! Initial fill of $pw has been pruned for mols,
## but duplicate atoms have not been detected and pruned
$INCOMING = $lv->StringToLabelValue("edge-type", "incoming-edge");
$OUTGOING = $lv->StringToLabelValue("edge-type", "outgoing-edge");
my ($atoms_in, $mols_in, %mols_out, $prune_mol_list);
my ($layer, $atom_id);
my (%consumed, %produced, $producedCount);
if ($prune_mol_hash) {
$prune_mol_list = join(",", keys %{ $prune_mol_hash });
}
$atoms_in = {};
my $atomidlist;
my $first =1;
for $atom_id (@{ $pw->Atoms() }) {
$$atoms_in{$atom_id} = 1;
if ($first == 1) {
$atomidlist = $atom_id;
$first = 0;
} else {
$atomidlist = $atomidlist . ',' . $atom_id;
}
}
$retval = FindInsAndOuts($self, $pw->Atoms(), \%produced, \%consumed);
$producedCount = scalar(keys %produced);
for ($layer = 1; $layer <= $degree; $layer++) {
if (scalar(keys %consumed) > 0 &&
($direction eq "back" || $direction eq "both")) {
# return "In consumed\n";
$mols_in = join(",", keys %consumed);
$retval = "$atomidlist MOLS: $mols_in";
# return $retval;
undef %consumed;
$retval = OneDegreeDirection($self, "back", $atomidlist, $prune_mol_list,
$prune_mol_hash, $prune_atom_hash,
$mols_in, \%consumed, $atoms_in, $layer);
# return "After OneDegreeDirection-back $retval\n";
#print STDERR "direction = back, mols_in = $mols_in, mols_out = " .
#join(",", keys %consumed) . "\n";
}
if (scalar(keys %produced) > 0 &&
($direction eq "forward" || $direction eq "both")) {
$mols_in = join(",", keys %produced);
undef %produced;
# return $mols_in;
$retval = OneDegreeDirection($self, "forward", $atomidlist, $prune_mol_list,
$prune_mol_hash, $prune_atom_hash,
$mols_in, \%produced, $atoms_in, $layer);
#print STDERR "direction = forward, mols_in = $mols_in, mols_out = " .
#join(",", keys %produced) . "\n";
}
}
return $retval;
}
######################################################################
sub OneDegreeDirection {
my ($self, $direction, $atomidlist, $prune_mol_list, $prune_mol_hash,
$prune_atom_hash,
$mols_in, $mols_out, $atoms_in, $layer, $source_id_list, $evidence_code_list) = @_;
my $db = $self->{db};
my $pw = $self->{pw};
my $lv = $self->{lv};
my $SCHEMA = $self->{schema};
my ($atom_id, %new_atoms, %pro, %con);
my $retval = NAOD($self, $direction, $atomidlist, $prune_mol_list,
$prune_atom_hash, $mols_in,
$atoms_in, \%new_atoms, $pw, $lv);
if (scalar(keys %new_atoms) == 0) {
return 'none';
}
$retval = FillAtoms($self, join(",", keys %new_atoms), $evidence_code_list);
if ($prune_mol_hash && scalar(keys %{ $prune_mol_hash }) > 0) {
$pw->PruneMol($prune_mol_hash);
}
FindInsAndOuts($self, [keys %new_atoms], \%pro, \%con);
if ($direction eq "back" || $direction eq "both") {
for (keys %con) {
$$mols_out{$_} = 1;
}
}
if ($direction eq "forward" || $direction eq "both") {
for (keys %pro) {
$$mols_out{$_} = 1;
}
}
for $atom_id (keys %new_atoms) {
$pw->SetLayer($atom_id, $layer);
$$atoms_in{$atom_id} = 1;
}
return $retval;
}
######################################################################
sub FindInsAndOuts {
my ($self, $atom_set, $produced, $consumed) = @_;
my $db = $self->{db};
my $pw = $self->{pw};
my $lv = $self->{lv};
my $SCHEMA = $self->{schema};
my ($atom_id, $edge, $label, $consumedCount, $retval);
$consumedCount = 0;
for $atom_id (@{ $atom_set }) {
for $edge (@{ $pw->Edges($atom_id) }) {
for $label (@{ $pw->EdgeLabel($atom_id, $edge) }) {
if ($lv->IsA($label, $INCOMING)) {
$$consumed{$pw->EdgeMol($atom_id, $edge)} = 1;
}
if ($lv->IsA($label, $OUTGOING)) {
$$produced{$pw->EdgeMol($atom_id, $edge)} = 1;
}
}
}
}
}
######################################################################
sub DirectionsMatch {
my ($self, $spec, $a_lab, $b_lab) = @_;
my $db = $self->{db};
my $pw = $self->{pw};
my $lv = $self->{lv};
my $SCHEMA = $self->{schema};
## point of view is from "a": "back" means from b to a
## (hence b should have an outgoing edge and a an incoming)
if ($spec eq "both") {
return 1;
}
my ($a_lv, $b_lv);
my ($a_in, $a_out, $b_in, $b_out) = (0, 0, 0, 0);
for $a_lv (@{ $a_lab }) {
if ($lv->IsA($a_lv, $INCOMING)) {
$a_in = 1;
} elsif ($lv->IsA($a_lv, $OUTGOING)) {
$a_out = 1;
}
}
for $b_lv (@{ $b_lab }) {
if ($lv->IsA($b_lv, $INCOMING)) {
$b_in = 1;
} elsif ($lv->IsA($b_lv, $OUTGOING)) {
$b_out = 1;
}
}
if ($spec eq "back") {
if ($a_in && $b_out) {
return 1;
} else {
return 0;
}
} elsif ($spec eq "forward") {
if ($a_out && $b_in) {
return 1;
} else {
return 0;
}
}
}
sub NAOD {
my ($self, $direction, $atomidlist, $prune_mol_list, $prune_atom_hash,
$mols_in, $atoms_in,
$atoms_out) = @_;
my $db = $self->{db};
my $pw = $self->{pw};
my $lv = $self->{lv};
my $SCHEMA = $self->{schema};
my $pw2 = $self->{pw};
my ($i, $first, $atom_id, $stm, $sql, $list, @atom_list, $new_atoms);
my %atoms;
my @atomarray = split(/,/,$atomidlist);
for (my $j = 0; $j < @atomarray; $j++) {
$atoms{$atomarray[$j]} = 1;
}
# for($i = 0; $i < @atomarray; $i += ORACLE_LIST_LIMIT) {
# if(($i + ORACLE_LIST_LIMIT - 1) < @atomarray) {
# $list = join(",", @atomarray[$i..$i+ORACLE_LIST_LIMIT-1]);
#}
#else {
# $list = join(",", @atomarray[$i..@atomarray-1]);
#}
# $list = $atom_list[0];
#return $list;
if ($direction eq "back") {
$sql = qq!
select
c.atom_1
from
$SCHEMA.pw_connect c
where
c.atom_2 in ($atomidlist)
and c.precedence in ('11','10')
union
select
c.atom_2
from
$SCHEMA.pw_connect c
where
c.atom_1 in ($atomidlist)
and c.precedence in ('11','01')
!;
}
# return $sql ;
if ($direction eq "forward") {
$sql = qq!
select
c.atom_1
from
$SCHEMA.pw_connect c
where
c.atom_2 in ($atomidlist)
and c.precedence in ('11','01')
union
select
c.atom_2
from
$SCHEMA.pw_connect c
where
c.atom_1 in ($atomidlist)
and c.precedence in ('11','10')
!;
}
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
die;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
die;
}
$first = 1;
while (($atom_id) =
$stm->fetchrow_array()) {
if ($atoms{$atom_id} == 1) {} else {
if ($first == 1) {
$first = 0;
$new_atoms = $atom_id;
} else {
$new_atoms = $new_atoms . ',' . $atom_id;
}
$$atoms_out{$atom_id} = 1;
}
}
$stm->finish();
# }
return $new_atoms;
}
######################################################################
sub NewAtomsOfDegree {
my ($self, $direction, $prune_mol_list, $prune_atom_hash,
$mols_in, $atoms_in,
$atoms_out) = @_;
my $db = $self->{db};
my $pw = $self->{pw};
my $lv = $self->{lv};
my $SCHEMA = $self->{schema};
my $pw2 = $self->{pw};
## atoms_in are already added to $pw
my ($sql, $stm, $stm2);
my ($atom_id, $edge_seq_id, $mol_id, $mol_lv, $edge_lv, $atomidlist, $ptm_id);
my (%mol_inst, %edge_inst, %ptm_inst);
my ($i, @mol_list, $list, $prune_clause);
my ($ptm_expression_id, $uniprot_acc, $mod_type, $residue, $pos);
if ($prune_mol_list) {
$prune_clause = "and e.mol_id not in ($prune_mol_list)";
1 } else {
$prune_clause = "";
}
##
## First, fetch all atoms that share a mol_id with the seed list
##
@mol_list = split ",", $mols_in;
for($i = 0; $i < @mol_list; $i += ORACLE_LIST_LIMIT) {
if(($i + ORACLE_LIST_LIMIT - 1) < @mol_list) {
$list = join(",", @mol_list[$i..$i+ORACLE_LIST_LIMIT-1]);
}
else {
$list = join(",", @mol_list[$i..@mol_list-1]);
}
$sql = qq!
select
e.atom_id, e.edge_seq_id, e.mol_id, m.label_value_id, el.label_value_id
from
$SCHEMA.pw_edge e,
$SCHEMA.pw_mol_label m,
$SCHEMA.pw_edge_label el
where
e.atom_id = m.atom_id (+)
and e.edge_seq_id = m.edge_seq_id (+)
and e.atom_id = el.atom_id
and e.edge_seq_id = el.edge_seq_id
and e.mol_id in ($list)
$prune_clause
!;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
die;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
die;
}
while (($atom_id, $edge_seq_id, $mol_id, $mol_lv, $edge_lv) =
$stm->fetchrow_array()) {
if ($pw->HasAtom($atom_id)) {
next;
}
# if ((defined $self->{atomsinsource}) &&
#if ((defined $self->{source_id}) &&
# !(defined $self->{atomsinsource}{$atom_id})) {
# next;
#}
# if ((defined $self->{atomsinevidence}) &&
#if ((defined $self->{evidence_code}) &&
# !(defined $self->{atomsinevidence}{$atom_id})) {
# next;
#}
if ($prune_atom_hash && defined $$prune_atom_hash{$atom_id}) {
next;
}
$mol_inst{$atom_id}{$edge_seq_id}{$mol_id}{$mol_lv} = 1;
$edge_inst{$atom_id}{$edge_seq_id}{$edge_lv} = $mol_id;
}
}
my ($candidate_atom, $candidate_edge, $candidate_inst);
my ($inst, $hit);
for $atom_id (keys %edge_inst) {
$hit = 0;
for $edge_seq_id (keys %{ $mol_inst{$atom_id} }) {
for $mol_id (keys %{ $mol_inst{$atom_id}{$edge_seq_id} }) {
my $ptms = $ptm_inst{$atom_id}{$edge_seq_id};
$inst = Pathway::MolInstToString($mol_id,
[ keys %{ $mol_inst{$atom_id}{$edge_seq_id}{$mol_id} } ]);
# $inst = $pw->NormalMolInstString($atom_id, $edge_seq_id);
$sql = qq!
select
pep.ptm_type,
pep.ptm_residue,
pep.ptm_pos
from
$SCHEMA.pw_edge_modification pem,
$SCHEMA.pw_ptm_expression pep
where
atom_id = $atom_id
and edge_id = $edge_seq_id
and pem.ptm_expression_id = pep.ptm_expression_id
!;
$stm2 = $db->prepare($sql);
if(not $stm2) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
die;
}
if(!$stm2->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
die;
}
my $ptm_string;
my $first = 1;
while (($mod_type, $residue, $pos) =
$stm2->fetchrow_array()) {
if ($first == 1) {
$first = 0;
$ptm_string = "$pos$residue$mod_type";
} else {
$ptm_string = $ptm_string . "," . "$pos$residue$mod_type";
}
}
$inst = $inst . $ptm_string;
for $candidate_atom (@{ $pw->MolUse($mol_id) }) {
if (! defined $$atoms_in{$candidate_atom}) {
next;
}
for $candidate_edge (@{ $pw->Edges($candidate_atom) }) {
$candidate_inst = $pw->NormalMolInstString(
$candidate_atom, $candidate_edge);
# $atomidlist = $atomidlist . "PTM: $ptm_string Atom: $atom_id Edge: $edge_seq_id Cand: $candidate_atom $candidate_edge Inst: $inst Cand: $candidate_inst<BR>";
if ($inst eq $candidate_inst) {
if (DirectionsMatch($self, $direction,
$pw->EdgeLabel($candidate_atom, $candidate_edge),
[ keys %{ $edge_inst{$atom_id}{$edge_seq_id} } ])) {
$hit = 1;
# $atomidlist = $atomidlist . "HIT!";
} else {
}
}
}
}
}
}
if ($hit) {
$$atoms_out{$atom_id} = 1;
}
}
return $atomidlist;
}
######################################################################
######################################################################
##
## spec by molecules
##
######################################################################
######################################################################
######################################################################
sub RecursiveGetContainingComplexes {
my ($self, $seed_mol_list, $cumulative_mol_list, $added_mol_list) = @_;
my $db = $self->{db};
my $pw = $self->{pw};
my $lv = $self->{lv};
my $SCHEMA = $self->{schema};
my ($sql, $stm, $list, $complex_mol_id, $i);
for($i = 0; $i < @{ $seed_mol_list }; $i += ORACLE_LIST_LIMIT) {
if(($i + ORACLE_LIST_LIMIT - 1) < @{ $seed_mol_list }) {
$list = join(",", @{ $seed_mol_list }[$i..$i+ORACLE_LIST_LIMIT-1]);
}
else {
$list = join(",", @{ $seed_mol_list }[$i..@{ $seed_mol_list } - 1]);
}
$sql = qq!
select
c.complex_mol_id
from
$SCHEMA.pw_complex_component c
where
c.component_mol_id in ($list)
!;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
die;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
die;
}
while (($complex_mol_id) = $stm->fetchrow_array()) {
if (! defined $$cumulative_mol_list{$complex_mol_id}) {
$$cumulative_mol_list{$complex_mol_id} = 1;
$$added_mol_list{$complex_mol_id} = 1;
}
}
}
}
######################################################################
sub GetContainingComplexes {
my ($self, $mol_list_in, $cumulative_mol_list) = @_;
my $db = $self->{db};
my $pw = $self->{pw};
my $lv = $self->{lv};
my $SCHEMA = $self->{schema};
my $seed_mol_list = $mol_list_in;
my %added_mol_list;
for my $mol_id (@{ $seed_mol_list }) {
$$cumulative_mol_list{$mol_id} = 1;
}
while (1) {
RecursiveGetContainingComplexes($self, $seed_mol_list, $cumulative_mol_list,
\%added_mol_list);
if (scalar(keys %added_mol_list) == 0) {
last;
}
$seed_mol_list = [ keys %added_mol_list ];
undef %added_mol_list;
}
}
######################################################################
sub AtomsOfMols {
my ($self, $mol_list, $include_complex_uses) = @_;
my $db = $self->{db};
my $pw = $self->{pw};
my $lv = $self->{lv};
my $SCHEMA = $self->{schema};
my ($sql, $stm);
my ($atom_id, %atoms, $i, $list);
my @mol_list = split ",", $mol_list;
if ($include_complex_uses) {
my %cumulative_mol_list;
GetContainingComplexes($self, \@mol_list, \%cumulative_mol_list);
@mol_list = keys %cumulative_mol_list;
}
for($i = 0; $i < @mol_list; $i += ORACLE_LIST_LIMIT) {
if(($i + ORACLE_LIST_LIMIT - 1) < @mol_list) {
$list = join(",", @mol_list[$i..$i+ORACLE_LIST_LIMIT-1]);
}
else {
$list = join(",", @mol_list[$i..@mol_list-1]);
}
$sql = qq!
select
e.atom_id
from
$SCHEMA.pw_edge e
where
e.mol_id in ($list)
!;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
die;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
die;
}
while (($atom_id) = $stm->fetchrow_array()) {
$atoms{$atom_id} = 1;
}
}
FillAtoms($self, join(",", keys %atoms));
}
######################################################################
######################################################################
##
## MacroProcess
##
######################################################################
######################################################################
######################################################################
sub FillMacroProcesses {
my ($self, $lvid_list, $evidence_code_list, $source_id_list) = @_;
my $db = $self->{db};
my $pw = $self->{pw};
my $lv = $self->{lv};
my $SCHEMA = $self->{schema};
my ($sql, $stm);
my ($lvid, $atom_id, %atom_ids);
if ($lvid_list eq "") {
return;
}
my $source_clause = '';
my $source_spec = join(",", @{ $source_id_list });
my $sourceNumber = $#{$source_id_list};
if (($sourceNumber > -1) || ($source_spec > 1)) {
$source_clause = "and atom_id in (" .
"select a.atom_id from $SCHEMA.pw_atom a " .
"where a.atom_source_id in " .
"(" . $source_spec . ") )";
}
$sql = qq!
select
atom_id
from
$SCHEMA.pw_atom_condition
where
label_value_id in ($lvid_list)
$source_clause
!;
# return $sql;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
die;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
die;
}
while (($atom_id) = $stm->fetchrow_array()) {
$atom_ids{$atom_id} = 1;
}
$sql = qq!
select
atom_id
from
$SCHEMA.pw_atom_label
where
label_value_id in ($lvid_list)
$source_clause
!;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
die;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
die;
}
while (($atom_id) = $stm->fetchrow_array()) {
## Add code for source and evidence
# if ((defined $self->{source_id}) &&
# !(defined $self->{atomsinsource}{$atom_id})) {
# next;
#}
#if ((defined $self->{evidence_code}) &&
# !(defined $self->{atomsinevidence}{$atom_id})) {
# next;
#}
$atom_ids{$atom_id} = 1;
}
my $retval = $self->FillAtoms(join(",", keys %atom_ids), $evidence_code_list, $source_id_list);
return $retval;
}
######################################################################
######################################################################
##
## Atoms only
##
######################################################################
######################################################################
######################################################################
sub FillAtoms {
my ($self, $atom_list, $evidence_code_list, $source_id_list) = @_;
my $db = $self->{db};
my $pw = $self->{pw};
my $lv = $self->{lv};
my $SCHEMA = $self->{schema};
my (%temp, $a);
if ($atom_list ne '') {
my $retval = $self->AtomSearch($db, $SCHEMA, $atom_list, $evidence_code_list, $source_id_list);
# return $retval;
}
if ($atom_list eq "*") {
GetEdgesForAtoms($self, "*");
GetAtomsAndLabelsForAtoms($self, "*");
GetMoleculesForAtoms($self, "*");
GetEvidenceForAtoms($self, "*");
GetReferencesForAtoms($self, "*");
GetNotesForAtoms($self, "*");
} else {
my @atom_list = split(",", $atom_list);
my ($i, $list);
for($i = 0; $i < @atom_list; $i += ORACLE_LIST_LIMIT) {
if(($i + ORACLE_LIST_LIMIT - 1) < @atom_list) {
$list = join(",", @atom_list[$i..$i+ORACLE_LIST_LIMIT-1]);
}
else {
$list = join(",", @atom_list[$i..@atom_list-1]);
}
GetEdgesForAtoms($self, $list);
GetAtomsAndLabelsForAtoms($self, $list);
GetMoleculesForAtoms($self, $list);
GetPathwaysForAtoms($self, $list);
GetEvidenceForAtoms($self, $list);
GetReferencesForAtoms($self, $list);
GetNotesForAtoms($self, $list);
}
}
}
######################################################################
sub GetAtomBasics {
my ($self, $atom_id) = @_;
my $db = $self->{db};
my $pw = $self->{pw};
my $lv = $self->{lv};
my $SCHEMA = $self->{schema};
my ($organism, $atom_source_id, $source_name);
my ($sql, $stm);
$sql = qq!
select
a.organism,
a.atom_source_id,
s.source_name
from
$SCHEMA.pw_atom a,
$SCHEMA.pw_source s
where
a.atom_id = $atom_id
and a.atom_source_id = s.source_id
!;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
die;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
die;
}
while (($organism, $atom_source_id, $source_name) =
$stm->fetchrow_array()) {
last;
}
$stm->finish();
return ($organism, $atom_source_id, $source_name);
}
######################################################################
sub GetAbstractions {
my ($self, $atoms) = @_;
my $db = $self->{db};
my $pw = $self->{pw};
my $lv = $self->{lv};
my $SCHEMA = $self->{schema};
if (keys %{ $atoms } < 1) {
return;
}
my $abs = join(",", keys %{ $atoms });
my ($sql, $stm);
my ($atom_id, $pathway_id, $pathway_name, $ext_pathway_id);
$sql = qq!
select distinct
a.atom_id, p.pathway_id, p.pathway_name, p.ext_pathway_id
from
$SCHEMA.pw_abstraction a,
$SCHEMA.pw_pathway p
where
a.atom_id in ($abs)
and (p.pathway_id = a.pathway_id or
p.ext_pathway_id = a.ext_pathway_id
)
!;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
die;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
die;
}
while (($atom_id, $pathway_id, $pathway_name, $ext_pathway_id) =
$stm->fetchrow_array()) {
$pw->AddAbstraction($atom_id, $pathway_id, $pathway_name,
$ext_pathway_id);
}
}
######################################################################
sub GetAtomsAndLabelsForAtoms {
my ($self, $atom_list) = @_;
my $db = $self->{db};
my $pw = $self->{pw};
my $lv = $self->{lv};
my $SCHEMA = $self->{schema};
my ($sql, $stm);
my ($atom_id, $label_value_id, $atom_source_id, $negative_flag);
my ($name, $value);
my ($atom_clause);
if ($atom_list eq "*") {
$atom_clause = "";
} else {
$atom_clause = "and al.atom_id in ($atom_list)";
}
$sql = qq!
select
al.atom_id, al.label_value_id, a.atom_source_id
from
$SCHEMA.pw_atom_label al,
$SCHEMA.pw_atom a
where
a.atom_id = al.atom_id
$atom_clause
!;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
die;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
die;
}
my %abstractions;
while (($atom_id, $label_value_id, $atom_source_id) =
$stm->fetchrow_array()) {
$pw->AddAtomLabel($atom_id, $label_value_id);
## ($name, $value) = split /\t/, $lvhash{$label_value_id};
($name, $value) = $lv->LabelValueToString($label_value_id);
if ($name eq "process-type") {
$pw->AddAtom($atom_id, $label_value_id);
if ($label_value_id eq $pathway_type ||
$label_value_id eq $subnet_type) {
$abstractions{$atom_id} = 1;
}
$pw->AddAtomSource($atom_id, $atom_source_id);
}
}
if (keys %abstractions) {
$self->GetAbstractions(\%abstractions);
}
if ($atom_list eq "*") {
$atom_clause = "";
} else {
$atom_clause = "where al.atom_id in ($atom_list)";
}
##
## Now conditions
##
$sql = qq!