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Changes for second draft of KSaplingDBD.xml #171

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Changes for second draft of KSaplingDBD.xml #171

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130 changes: 69 additions & 61 deletions lib/ModelSEED/ModelSEEDScripts/generateTablesForKbase.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -218,22 +218,21 @@ sub doBiochemistryAndMapping {
# formula (string): a pH-neutral formula for the compound
# label (string): primary name of the compound, for use in displaying
# reactions
# msid (string): common modeling ID of this compound
# source-id (string): common modeling ID of this compound
# uncharged-formula (string): a electrically neutral formula for the compound
#
{
my $a = {
id => 'uuid',
msid => 'id',
mass => 'mass',
'mod-date' => 'modDate',
abbr => 'abbreviation',
'default-charge' => 'defaultCharge',
'deltaG' => 'deltaG',
id => 'uuid',
'source-id' => 'id',
mass => 'mass',
'mod-date' => 'modDate',
abbr => 'abbreviation',
'charge' => 'defaultCharge',
'deltaG' => 'deltaG',
'deltaG-error' => 'deltaGErr',
formula => 'formula',
label => 'name',
'uncharged-formula' => 'unchargedFormula',
formula => 'formula',
label => 'name',
};
tie my %columns, 'Tie::Hash::Sorted', 'Hash' => $a;
buildTable("$directory/compound.dtx", \%columns, $biochemObj->compounds);
Expand All @@ -253,11 +252,11 @@ sub doBiochemistryAndMapping {
{
my $a = {
id => 'uuid',
msid => 'id',
'is-minimal' => 'isMinimal',
'is-defined' => 'isMinimal',
'mod-date' => 'modDate',
name => 'name',
type => 'type',
description => 'type',
'source-id' => 'id',
};
tie my %columns, 'Tie::Hash::Sorted', 'Hash' => $a;
buildTable("$directory/media.dtx", \%columns, $biochemObj->media);
Expand All @@ -278,24 +277,24 @@ sub doBiochemistryAndMapping {
# thermodynamic-reversibility (char): computed reversibility of this reaction
# in a pH-neutral environment
# abbr (string): abbreviated name of this reaction
# msid (string): common modeling ID of this reaction
# source-id (string): common modeling ID of this reaction
# name (string): descriptive name of this reaction
# status (string): string indicating additional information about this
# reaction, generally indicating whether the reaction
# is balanced and/or accurate
{
my $a = {
id => 'uuid',
'default-protons' => 'defaultProtons',
deltaG => 'deltaG',
'deltaG-error' => 'deltaGErr',
direction => 'direction',
'mod-date' => 'modDate',
id => 'uuid',
'default-protons' => 'defaultProtons',
deltaG => 'deltaG',
'deltaG-error' => 'deltaGErr',
direction => 'direction',
'mod-date' => 'modDate',
'thermodynamic-reversibility' => 'thermoReversibility',
abbr => 'abbreviation',
msid => 'id',
name => 'name',
status => 'status',
abbr => 'abbreviation',
'source-id' => 'id',
name => 'name',
status => 'status',
};
tie my %columns, 'Tie::Hash::Sorted', 'Hash' => $a;
buildTable("$directory/reaction.dtx", \%columns, $biochemObj->reactions);
Expand Down Expand Up @@ -343,16 +342,14 @@ sub doBiochemistryAndMapping {
# from-link (string): id of the source Media.
# to-link (string): id of the target Compound.
# concentration (float): concentration of the compound in the media
# maximum-flux (float): maximum flux of the compound for this media
# minimum-flux (float): minimum flux of the compound for this media
# concentraiton-units (string) ;
#
{
my $a = {
'from-link' => 'media_uuid',
'to-link' => 'compound_uuid',
concentration => 'concentration',
'maximum-flux' => 'maxFlux',
'minimum-flux' => 'minFlux',
'concentration-units' => sub { 'mmol/L' },
};
tie my %columns, 'Tie::Hash::Sorted', 'Hash' => $a;
my $mediaCompounds = [];
Expand All @@ -362,8 +359,6 @@ sub doBiochemistryAndMapping {
media_uuid => $media->uuid,
compound_uuid => $mediacpd->compound_uuid,
concentration => $mediacpd->concentration,
maxFlux => $mediacpd->maxFlux,
minFlux => $mediacpd->minFlux,
};
push(@$mediaCompounds, $hash);
}
Expand Down Expand Up @@ -486,7 +481,6 @@ sub doBiochemistryAndMapping {
'to-link' => 'localized_compound',
coefficient => 'coefficient',
cofactor => 'isCofactor',
'is-transport' => 'isTransport',
};
tie my %columns, 'Tie::Hash::Sorted', 'Hash' => $a;
my $reagents = [];
Expand Down Expand Up @@ -626,37 +620,46 @@ sub doModel {
##
## Model
{
# TODO : Fix feature-count, must be # of features w/ reactions
# Generate feature-count
my $features = {};
my $mdlrxns = $model->modelreactions;
foreach my $rxn (@$mdlrxns) {
my $proteins = $rxn->modelReactionProteins;
foreach my $protein (@$proteins) {
my $subunits = $protein->modelReactionProteinSubunits;
foreach my $subunit (@$subunits) {
my $genes = $subunit->modelReactionProteinSubunitGenes;
foreach my $gene (@$genes) {
my $feature = $gene->feature;
$features->{$feature->id} = 1;
}
}
}
}
my $a = {
id => 'uuid',
'mod-date' => 'modDate',
name => 'name',
'reaction-count' => sub {
return scalar(@{$_[0]->modelreactions});
},
'compound-count' => sub {
return scalar(@{$_[0]->modelcompounds});
},
'annotation-count' => sub {
return scalar(@{$_[0]->modelcompounds});
},
'annotation-count' => sub {
return scalar(@{$_[0]->annotation->features});
},
status => 'status',
version => 'version',
type => 'type',
id => 'uuid',
'mod-date' => 'modDate',
name => 'name',
'reaction-count' => sub { scalar( @{ $_[0]->modelreactions } ) },
'compound-count' => sub { scalar( @{ $_[0]->modelcompounds } ) },
'feature-count' => sub { scalar( keys %$features ); },
status => 'status',
version => 'version',
type => 'type',
'source-id' => 'id',
};
tie my %columns, 'Tie::Hash::Sorted', 'Hash' => $a;
buildTable("$directory/Model.dtx", \%columns, [$model], $append);
}
## LocationInstance ( ModelCompartment )
{
my $a = {
id => 'uuid',
'compartment-index' => 'compartmentIndex',
pH => 'pH',
potential => 'potential',
label => 'label',
id => 'uuid',
index => 'compartmentIndex',
pH => 'pH',
potential => 'potential',
label => 'label',
};
tie my %columns, 'Tie::Hash::Sorted', 'Hash' => $a;
buildTable("$directory/LocationInstance.dtx", \%columns, $model->modelcompartments, $append);
Expand All @@ -665,19 +668,23 @@ sub doModel {
{
my $mdl_cpds = $model->modelcompounds;
my $a = {
id => 'uuid',
charge => 'charge',
formula => 'formula',
id => 'uuid',
charge => 'charge',
formula => 'formula',
deltaG => sub { $_[0]->compound->deltaG },
'deltaG-error' => sub { $_[0]->compound->deltaGErr },
'source-id' => sub { $_[0]->compound->id },
};
tie my %columns, 'Tie::Hash::Sorted', 'Hash' => $a;
buildTable("$directory/CompoundInstance.dtx", \%columns, $mdl_cpds, $append);
}
## ReactionInstance ( ModelReaction )
{
my $a = {
id => 'uuid',
direction => 'direction',
proton => 'protons',
id => 'uuid',
direction => 'direction',
proton => 'protons',
'source-id' => sub { $_[0]->reaction->id },
};
tie my %columns, 'Tie::Hash::Sorted', 'Hash' => $a;
buildTable("$directory/ReactionInstance.dtx", \%columns, $model->modelreactions, $append);
Expand All @@ -695,6 +702,7 @@ sub doModel {
lipid => 'lipid',
protein => 'protein',
'mod-date' => 'modDate',
'source-id' => 'id',
};
my $b = {
id => 'uuid',
Expand Down