use std::mem::replace;
use std::str::FromStr;
use std::string::ToString;
use std::collections::HashMap;
use fastobo::ast::ClassIdent;
use fastobo::ast::HeaderFrame;
use fastobo::ast::HeaderClause;
use fastobo::ast::EntityFrame;
use fastobo::ast::Ident;
use fastobo::ast::QuotedString;
use fastobo::ast::Synonym;
use fastobo::ast::OboDoc;
use fastobo::ast::SynonymScope;
use fastobo::ast::TermClause;
use fastobo::ast::TypedefClause;
use fastobo::ast::InstanceClause;
use fastobo::ast::TermFrame;
use fastobo::ast::IsoDateTime;
use fastobo::ast::InstanceFrame;
use fastobo::ast::TypedefFrame;
use fastobo::ast::Line;
use fastobo::ast::UnquotedString;
use fastobo::ast::Xref;
use fastobo::ast::XrefList;
use fastobo::ast::RelationIdent;
use fastobo::ast::PrefixedIdent;
use fastobo::ast::SubsetIdent;
use fastobo::ast::InstanceIdent;
use fastobo::ast::PropertyValue;
use fastobo::ast::Url;
use fastobo::semantics::Identified;
use fastobo::semantics::Orderable;
use fastobo::visit::VisitMut;
use fastobo::visit::IdCompactor;
use crate::constants::property::dc;
use crate::constants::property::iao;
use crate::constants::property::obo_in_owl;
use crate::constants::property::rdfs;
use crate::model::Graph;
use crate::model::Meta;
use crate::model::Node;
use crate::model::NodeType;
use crate::model::BasicPropertyValue;
use crate::model::DefinitionPropertyValue;
use crate::model::SynonymPropertyValue;
use crate::model::XrefPropertyValue;
use super::FromGraph;
use crate::error::Error;
use crate::error::Result;
impl FromGraph<Graph> for OboDoc {
fn from_graph(graph: Graph) -> Result<Self> {
let mut entities = HashMap::new();
for node in graph.nodes.into_iter() {
if let Some(frame) = <Option<EntityFrame>>::from_graph(node)? {
entities.insert(frame.as_id().clone(), frame);
}
}
for edge in graph.edges.iter() {
let id_sub = Ident::from_str(&edge.sub)?;
let id_pred = RelationIdent::from_str(&edge.pred)?;
let id_obj = Ident::from_str(&edge.obj)?;
if &edge.pred == "is_a" || &edge.pred == "subPropertyOf" || &edge.pred == "subClassOf" {
match entities.get_mut(&id_sub) {
Some(EntityFrame::Term(ref mut frame)) => {
let c = TermClause::IsA(From::from(id_obj));
frame.push(Line::from(c));
}
Some(EntityFrame::Typedef(ref mut frame)) => {
let c = TypedefClause::IsA(From::from(id_obj));
frame.push(Line::from(c));
}
Some(EntityFrame::Instance(_)) => {
return Err(Error::invalid_instance_clause("is_a"));
},
None => (),
}
} else if &edge.pred == "inverseOf" {
match entities.get_mut(&id_sub) {
Some(EntityFrame::Typedef(ref mut frame)) => {
let c = TypedefClause::InverseOf(From::from(id_obj));
frame.push(Line::from(c));
}
Some(EntityFrame::Term(ref mut frame)) => {
return Err(Error::invalid_term_clause("inverse_of"));
}
Some(EntityFrame::Instance(_)) => {
return Err(Error::invalid_instance_clause("inverse_of"));
},
None => (),
}
} else {
match entities.get_mut(&id_sub) {
Some(EntityFrame::Term(ref mut frame)) => {
let c = TermClause::Relationship(id_pred, From::from(id_obj));
frame.push(Line::from(c));
}
Some(EntityFrame::Typedef(ref mut frame)) => {
let c = TypedefClause::Relationship(id_pred, From::from(id_obj));
frame.push(Line::from(c));
}
Some(EntityFrame::Instance(ref mut frame)) => {
let c = InstanceClause::Relationship(id_pred, From::from(id_obj));
frame.push(Line::from(c));
}
None => (),
}
}
}
for eq in graph.equivalent_nodes_sets.iter() {
for node in eq.node_ids.iter() {
let node_id = Ident::from_str(&node)?;
match entities.get_mut(&node_id) {
Some(EntityFrame::Term(ref mut frame)) => {
for node in eq.node_ids.iter().filter(|&n| n != node) {
let id = ClassIdent::from_str(&node)?;
frame.push(Line::from(TermClause::EquivalentTo(id)));
}
}
Some(EntityFrame::Typedef(ref mut frame)) => {
for node in eq.node_ids.iter().filter(|&n| n != node) {
let id = RelationIdent::from_str(&node)?;
frame.push(Line::from(TypedefClause::EquivalentTo(id)));
}
}
Some(EntityFrame::Instance(_)) => {
return Err(Error::invalid_instance_clause("equivalent_to"));
},
None => (),
}
}
}
for dr in graph.domain_range_axioms.iter() {
let id = Ident::from_str(&dr.predicate_id)?;
if let Some(EntityFrame::Typedef(ref mut frame)) = entities.get_mut(&id) {
for domain in dr.domain_class_ids.iter() {
let domain_id = ClassIdent::from_str(&domain)?;
frame.push(Line::from(TypedefClause::Domain(domain_id)));
}
for range in dr.range_class_ids.iter() {
let range_id = ClassIdent::from_str(&range)?;
frame.push(Line::from(TypedefClause::Range(range_id)));
}
}
}
let mut header = FromGraph::from_graph(*graph.meta)?;
let mut entities = entities.into_iter().map(|(_, v)| v).collect();
let mut doc = OboDoc::with_header(header).and_entities(entities);
doc.sort();
IdCompactor::new().visit_doc(&mut doc);
Ok(doc)
}
}