1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
use crate::sbml::Layout;
use crate::{BinaryOp, BooleanNetwork, FnUpdate, Monotonicity};
use std::collections::HashMap;
use std::io::{Error, Write};
impl BooleanNetwork {
pub fn to_sbml(&self, layout: Option<&Layout>) -> String {
let mut buffer: Vec<u8> = Vec::new();
self.write_as_sbml(layout, &mut buffer)
.expect("Cannot write model to SBML.");
String::from_utf8(buffer).expect("Invalid UTF formatting in string.")
}
pub fn write_as_sbml(&self, layout: Option<&Layout>, out: &mut dyn Write) -> Result<(), Error> {
write!(
out,
"<?xml version='1.0' encoding='UTF-8' standalone='no'?>"
)?;
write!(out, "<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" layout:required=\"false\" level=\"3\" qual:required=\"true\" xmlns:layout=\"http://www.sbml.org/sbml/level3/version1/layout/version1\" version=\"1\" xmlns:qual=\"http://www.sbml.org/sbml/level3/version1/qual/version1\">")?;
write!(out, "<model>")?;
if let Some(layout) = layout {
if !layout.is_empty() {
write_layout(out, layout)?;
}
}
self.write_species(out)?;
self.write_transitions(out)?;
write!(out, "</model>")?;
write!(out, "</sbml>")?;
Ok(())
}
fn write_species(&self, out: &mut dyn Write) -> Result<(), Error> {
write!(out, "<qual:listOfQualitativeSpecies xmlns:qual=\"http://www.sbml.org/sbml/level3/version1/qual/version1\">")?;
for v in self.variables() {
write!(out, "<qual:qualitativeSpecies qual:maxLevel=\"1\" qual:constant=\"false\" qual:name=\"{}\" qual:id=\"{}\"/>", self[v].get_name(), self[v].get_name())?;
}
write!(out, "</qual:listOfQualitativeSpecies>")?;
Ok(())
}
fn write_transitions(&self, out: &mut dyn Write) -> Result<(), Error> {
write!(out, "<qual:listOfTransitions xmlns:qual=\"http://www.sbml.org/sbml/level3/version1/qual/version1\">")?;
for id in self.variables() {
let var_name = self[id].get_name();
write!(out, "<qual:transition qual:id=\"tr_{}\">", var_name)?;
write!(out, "<qual:listOfInputs>")?;
for r in self.regulators(id) {
let r_var_name = self[r].get_name();
let regulation = self.graph.find_regulation(r, id);
let monotonicity = regulation.and_then(|r| r.monotonicity);
let observability = regulation.map(|r| r.is_observable());
let sign = match monotonicity {
None => "unknown",
Some(Monotonicity::Activation) => "positive",
Some(Monotonicity::Inhibition) => "negative",
};
let essential = if let Some(true) = observability {
"true"
} else {
"false"
};
write!(out, "<qual:input qual:qualitativeSpecies=\"{}\" qual:transitionEffect=\"none\" qual:sign=\"{}\" qual:id=\"tr_{}_in_{}\" essential=\"{}\"/>", r_var_name, sign, var_name, r_var_name, essential)?;
}
write!(out, "</qual:listOfInputs>")?;
write!(out, "<qual:listOfOutputs>")?;
write!(out, "<qual:output qual:qualitativeSpecies=\"{}\" qual:transitionEffect=\"assignmentLevel\" qual:id=\"tr_{}_out\"/>", var_name, var_name)?;
write!(out, "</qual:listOfOutputs>")?;
if let Some(update_function) = self.get_update_function(id) {
write!(out, "<qual:listOfFunctionTerms>")?;
if let FnUpdate::Const(value) = update_function {
let value = if *value { "1" } else { "0" };
write!(out, "<qual:defaultTerm qual:resultLevel=\"{}\"/>", value)?;
} else {
write!(out, "<qual:defaultTerm qual:resultLevel=\"0\"/>")?;
write!(out, "<qual:functionTerm qual:resultLevel=\"1\">")?;
write!(out, "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">")?;
self.write_update_function(out, update_function)?;
write!(out, "</math>")?;
write!(out, "</qual:functionTerm>")?;
}
write!(out, "</qual:listOfFunctionTerms>")?;
}
write!(out, "</qual:transition>")?;
}
write!(out, "</qual:listOfTransitions>")?;
Ok(())
}
fn write_update_function(&self, out: &mut dyn Write, function: &FnUpdate) -> Result<(), Error> {
match function {
FnUpdate::Const(true) => write!(out, "<true/>")?,
FnUpdate::Const(false) => write!(out, "<false/>")?,
FnUpdate::Var(id) => {
write!(
out,
"<apply><eq/><ci>{}</ci><cn type=\"integer\">1</cn></apply>",
self.get_variable_name(*id)
)?;
}
FnUpdate::Not(inner) => {
write!(out, "<apply><not/>")?;
self.write_update_function(out, inner)?;
write!(out, "</apply>")?;
}
FnUpdate::Binary(op, l, r) => {
let op = match op {
BinaryOp::Imp => "implies",
BinaryOp::And => "and",
BinaryOp::Or => "or",
BinaryOp::Xor => "xor",
BinaryOp::Iff => "eq",
};
write!(out, "<apply><{}/>", op)?;
self.write_update_function(out, l)?;
self.write_update_function(out, r)?;
write!(out, "</apply>")?;
}
FnUpdate::Param(id, args) => {
write!(out, "<apply><csymbol>{}</csymbol>", self[*id].get_name())?;
for arg in args {
write!(out, "<ci>{}</ci>", self[*arg].get_name())?;
}
write!(out, "</apply>")?;
}
}
Ok(())
}
}
fn write_layout(out: &mut dyn Write, layout: &HashMap<String, (f64, f64)>) -> Result<(), Error> {
write!(out, "<layout:listOfLayouts xmlns:layout=\"http://www.sbml.org/sbml/level3/version1/layout/version1\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">")?;
write!(out, "<layout:layout layout:id=\"__layout__\">")?;
write!(out, "<layout:listOfAdditionalGraphicalObjects>")?;
for (name, (x, y)) in layout {
write!(
out,
"<layout:generalGlyph layout:id=\"_ly_{}\" layout:reference=\"{}\">",
name, name
)?;
write!(out, "<layout:boundingBox>")?;
write!(
out,
"<layout:position layout:x=\"{}\" layout:y=\"{}\"/>",
x, y
)?;
write!(
out,
"<layout:dimensions layout:height=\"25\" layout:width=\"45\"/>"
)?;
write!(out, "</layout:boundingBox>")?;
write!(out, "</layout:generalGlyph>")?;
}
write!(out, "</layout:listOfAdditionalGraphicalObjects>")?;
write!(out, "</layout:layout>")?;
write!(out, "</layout:listOfLayouts>")?;
Ok(())
}
#[cfg(test)]
mod tests {
use crate::BooleanNetwork;
use pretty_assertions::assert_eq;
use std::collections::HashMap;
use std::convert::TryFrom;
#[test]
fn test_sbml_export() {
let model = BooleanNetwork::try_from(
"
a -? a
c -? a
# This regulation is used in the function and therefore must
# use our custom `essential` attribute in order to preserved
# that it is in fact not essential.
a ->? b
a ->? c
b -| c
# Also some comments are allowed
c -| d
$a: a & (p(c) => (c | c))
$b: p(a) <=> q(a, a)
# Notice that a regulates c but does not appear in the function!
$c: q(b, b) => !(b ^ r)
",
)
.unwrap();
let mut expected_layout = HashMap::new();
expected_layout.insert("a".to_string(), (1.0, 2.0));
expected_layout.insert("b".to_string(), (1.5, 2.8));
expected_layout.insert("c".to_string(), (1542.123, -4.333));
expected_layout.insert("d".to_string(), (121.776, 2.0));
let sbml = model.to_sbml(Some(&expected_layout));
let (actual, layout) = BooleanNetwork::try_from_sbml(&sbml).unwrap();
assert_eq!(model, actual);
assert_eq!(expected_layout, layout);
}
}
