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
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
use std::fmt::Display;
use std::fmt::Formatter;
use std::fmt::Result as FmtResult;
use std::fmt::Write;
use std::str::FromStr;

use pest::iterators::Pair;
use url::Url;

use crate::ast::*;
use crate::share::Share;
use crate::share::Cow;
use crate::share::Redeem;
use crate::error::Error;
use crate::error::Result;
use crate::parser::FromPair;
use crate::parser::Rule;


/// A clause appearing in a header frame.
///
/// Header clauses are used to add metadata to OBO documents. They are all
/// optional, but every document should *at least* contain a `FormatVersion`
/// clause, to help with interoperability and to make sure the semantics of
/// the right OBO specification are in use.
///
/// # Comparison
/// `HeaderClause` implements `PartialOrd` following the semantics of the OBO
/// specification: clauses will compare based on their serialization order
/// rather than on their alphabetic order; clauses of the same kind will be
/// ranked in the alphabetic order.
#[derive(Clone, Debug, Eq, Hash, PartialEq, PartialOrd, Ord)]
pub enum HeaderClause {
    FormatVersion(UnquotedString),
    DataVersion(UnquotedString),
    Date(NaiveDateTime),
    SavedBy(UnquotedString),
    AutoGeneratedBy(UnquotedString),
    Import(Import),
    Subsetdef(SubsetIdent, QuotedString),
    SynonymTypedef(SynonymTypeIdent, QuotedString, Option<SynonymScope>),
    DefaultNamespace(NamespaceIdent),
    NamespaceIdRule(UnquotedString),
    Idspace(IdentPrefix, Url, Option<QuotedString>),
    TreatXrefsAsEquivalent(IdentPrefix),
    TreatXrefsAsGenusDifferentia(IdentPrefix, RelationIdent, ClassIdent),
    TreatXrefsAsReverseGenusDifferentia(IdentPrefix, RelationIdent, ClassIdent),
    TreatXrefsAsRelationship(IdentPrefix, RelationIdent),
    TreatXrefsAsIsA(IdentPrefix),
    TreatXrefsAsHasSubclass(IdentPrefix),
    // FIXME(@althonos): Add support for hidden comment and qualifiers.
    PropertyValue(PropertyValue),
    Remark(UnquotedString),
    Ontology(UnquotedString),
    OwlAxioms(UnquotedString),
    Unreserved(UnquotedString, UnquotedString),
}

impl Display for HeaderClause {
    fn fmt(&self, f: &mut Formatter) -> FmtResult {
        use self::HeaderClause::*;
        match self {
            FormatVersion(ref version) =>
                f.write_str("format-version: ").and(version.fmt(f)),
            DataVersion(version) => f.write_str("data-version: ").and(version.fmt(f)),
            Date(date) => f.write_str("date: ").and(date.fmt(f)),
            SavedBy(person) => f.write_str("saved-by: ").and(person.fmt(f)),
            AutoGeneratedBy(thing) => f.write_str("auto-generated-by: ").and(thing.fmt(f)),
            Import(import) => f.write_str("import: ").and(import.fmt(f)),
            Subsetdef(subset, desc) => f
                .write_str("subsetdef: ")
                .and(subset.fmt(f))
                .and(f.write_char(' '))
                .and(desc.fmt(f)),
            SynonymTypedef(syntype, desc, optscope) => {
                f.write_str("synonymtypedef: ")
                    .and(syntype.fmt(f))
                    .and(f.write_char(' '))
                    .and(desc.fmt(f))?;
                match optscope {
                    Some(scope) => f.write_char(' ').and(scope.fmt(f)),
                    None => Ok(()),
                }
            }
            DefaultNamespace(ns) => f.write_str("default-namespace: ").and(ns.fmt(f)),
            NamespaceIdRule(r) => f.write_str("namespace-id-rule: ").and(r.fmt(f)),
            Idspace(prefix, url, optdesc) => {
                f.write_str("idspace: ")
                    .and(prefix.fmt(f))
                    .and(f.write_char(' '))
                    .and(url.fmt(f))?;
                match optdesc {
                    Some(desc) => f.write_char(' ').and(desc.fmt(f)),
                    None => Ok(()),
                }
            }
            TreatXrefsAsEquivalent(prefix) => f
                .write_str("treat-xrefs-as-equivalent: ")
                .and(prefix.fmt(f)),
            TreatXrefsAsGenusDifferentia(prefix, rel, cls) => f
                .write_str("treat-xrefs-as-genus-differentia: ")
                .and(prefix.fmt(f))
                .and(f.write_char(' '))
                .and(rel.fmt(f))
                .and(f.write_char(' '))
                .and(cls.fmt(f)),
            TreatXrefsAsReverseGenusDifferentia(prefix, rel, cls) => f
                .write_str("treat-xrefs-as-reverse-genus-differentia: ")
                .and(prefix.fmt(f))
                .and(f.write_char(' '))
                .and(rel.fmt(f))
                .and(f.write_char(' '))
                .and(cls.fmt(f)),
            TreatXrefsAsRelationship(prefix, rel) => f
                .write_str("treat-xrefs-as-relationship: ")
                .and(prefix.fmt(f))
                .and(f.write_char(' '))
                .and(rel.fmt(f)),
            TreatXrefsAsIsA(prefix) => f
                .write_str("treat-xrefs-as-is_a: ")
                .and(prefix.fmt(f)),
            TreatXrefsAsHasSubclass(prefix) => f
                .write_str("treat-xrefs-as-has-subclass: ")
                .and(prefix.fmt(f)),
            PropertyValue(pv) => f.write_str("property_value: ").and(pv.fmt(f)),
            Remark(remark) => f.write_str("remark: ").and(remark.fmt(f)),
            Ontology(ont) => f.write_str("ontology: ").and(ont.fmt(f)),
            OwlAxioms(axioms) => f.write_str("owl-axioms: ").and(axioms.fmt(f)),
            Unreserved(key, value) => key.fmt(f).and(f.write_str(": ")).and(value.fmt(f)),
        }
    }
}

impl<'i> FromPair<'i> for HeaderClause {
    const RULE: Rule = Rule::HeaderClause;
    unsafe fn from_pair_unchecked(pair: Pair<'i, Rule>) -> Result<Self> {
        let mut inner = pair.into_inner();
        let tag = inner.next().unwrap();
        match tag.as_rule() {
            Rule::FormatVersionTag => {
                let version = UnquotedString::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::FormatVersion(version))
            }
            Rule::DataVersionTag => {
                let version = UnquotedString::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::DataVersion(version))
            }
            Rule::DateTag => {
                let date = NaiveDateTime::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::Date(date))
            }
            Rule::SavedByTag => {
                let person = UnquotedString::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::SavedBy(person))
            }
            Rule::AutoGeneratedByTag => {
                let soft = UnquotedString::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::AutoGeneratedBy(soft))
            }
            Rule::ImportTag => {
                let import = Import::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::Import(import))
            }
            Rule::SubsetdefTag => {
                let subset = SubsetIdent::from_pair_unchecked(inner.next().unwrap())?;
                let desc = QuotedString::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::Subsetdef(subset, desc))
            }
            Rule::SynonymTypedefTag => {
                let id = SynonymTypeIdent::from_pair_unchecked(inner.next().unwrap())?;
                let desc = QuotedString::from_pair_unchecked(inner.next().unwrap())?;
                let scope = match inner.next() {
                    Some(pair) => Some(SynonymScope::from_pair_unchecked(pair)?),
                    None => None,
                };
                Ok(HeaderClause::SynonymTypedef(id, desc, scope))
            }
            Rule::DefaultNamespaceTag => {
                let id = NamespaceIdent::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::DefaultNamespace(id))
            }
            Rule::NamespaceIdRuleTag => {
                let value = UnquotedString::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::NamespaceIdRule(value))
            }
            Rule::IdspaceTag => {
                let prefix = IdentPrefix::from_pair_unchecked(inner.next().unwrap())?;
                let url = Url::from_pair_unchecked(inner.next().unwrap())?;
                let desc = match inner.next() {
                    Some(pair) => Some(QuotedString::from_pair_unchecked(pair)?),
                    None => None,
                };
                Ok(HeaderClause::Idspace(prefix, url, desc))
            }
            Rule::TreatXrefsAsEquivalentTag => {
                let prefix = IdentPrefix::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::TreatXrefsAsEquivalent(prefix))
            }
            Rule::TreatXrefsAsGenusDifferentiaTag => {
                let prefix = IdentPrefix::from_pair_unchecked(inner.next().unwrap())?;
                let rel = RelationIdent::from_pair_unchecked(inner.next().unwrap())?;
                let cls = ClassIdent::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::TreatXrefsAsGenusDifferentia(prefix, rel, cls))
            }
            Rule::TreatXrefsAsReverseGenusDifferentiaTag => {
                let prefix = IdentPrefix::from_pair_unchecked(inner.next().unwrap())?;
                let rel = RelationIdent::from_pair_unchecked(inner.next().unwrap())?;
                let cls = ClassIdent::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::TreatXrefsAsReverseGenusDifferentia(
                    prefix, rel, cls,
                ))
            }
            Rule::TreatXrefsAsRelationshipTag => {
                let prefix = IdentPrefix::from_pair_unchecked(inner.next().unwrap())?;
                let rel = RelationIdent::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::TreatXrefsAsRelationship(prefix, rel))
            }
            Rule::TreatXrefsAsIsATag => {
                let prefix = IdentPrefix::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::TreatXrefsAsIsA(prefix))
            }
            Rule::TreatXrefsAsHasSubclassTag => {
                let prefix = IdentPrefix::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::TreatXrefsAsHasSubclass(prefix))
            }
            Rule::PropertyValueTag => {
                let pv = PropertyValue::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::PropertyValue(pv))
            }
            Rule::RemarkTag => {
                let remark = UnquotedString::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::Remark(remark))
            }
            Rule::OntologyTag => {
                let ont = UnquotedString::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::Ontology(ont))
            }
            Rule::OwlAxiomsTag => {
                let axioms = UnquotedString::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::OwlAxioms(axioms))
            }
            Rule::Unreserved => {
                let tag = UnquotedString::from_str(tag.as_str())?;
                let value = UnquotedString::from_pair_unchecked(inner.next().unwrap())?;
                Ok(HeaderClause::Unreserved(tag, value))
            }
            _ => unreachable!(),
        }
    }
}
impl_fromstr!(HeaderClause);

#[cfg(test)]
mod tests {

    use pretty_assertions::assert_eq;
    use super::*;

    #[test]
    fn from_str() {
        let actual = HeaderClause::from_str("format-version: 1.2").unwrap();
        let expected = HeaderClause::FormatVersion(UnquotedString::new(String::from("1.2")));
        assert_eq!(actual, expected);

        let actual = HeaderClause::from_str("subsetdef: GO_SLIM \"GO Slim\"").unwrap();
        let expected = HeaderClause::Subsetdef(
            SubsetIdent::from(UnprefixedIdent::new("GO_SLIM")),
            QuotedString::new("GO Slim"),
        );
        assert_eq!(actual, expected);

        let actual = HeaderClause::from_str("date: 17:03:2019 20:16").unwrap();
        let expected = HeaderClause::Date(NaiveDateTime::new(17, 3, 2019, 20, 16));
        assert_eq!(actual, expected);

        let actual =
            HeaderClause::from_str("namespace-id-rule: * XAO:$sequence(7,5000,9999999)$").unwrap();
        let expected = HeaderClause::NamespaceIdRule(
            UnquotedString::new("* XAO:$sequence(7,5000,9999999)$"),
        );
        assert_eq!(actual, expected);

        let actual = HeaderClause::from_str("treat-xrefs-as-relationship: TEST rel").unwrap();
        let expected = HeaderClause::TreatXrefsAsRelationship(
            IdentPrefix::new("TEST"),
            RelationIdent::from(UnprefixedIdent::new("rel"))
        );
        assert_eq!(actual, expected);

        let actual =
            HeaderClause::from_str("tag: value").unwrap();
        let expected = HeaderClause::Unreserved(
            UnquotedString::new("tag"),
            UnquotedString::new("value"),
        );
        assert_eq!(actual, expected);
    }

    #[test]
    fn partial_cmp() {

        macro_rules! assert_lt {
            ($l:ident, $r:ident) => (
                assert!($l < $r, "'{}' < '{}' is not true!", $l, $r)
            )
        }

        let fv1 = HeaderClause::FormatVersion(UnquotedString::new("1.4"));
        let fv2 = HeaderClause::FormatVersion(UnquotedString::new("2"));
        assert_lt!(fv1, fv2);

        let dv1 = HeaderClause::DataVersion(UnquotedString::new("1.4"));
        let dv2 = HeaderClause::DataVersion(UnquotedString::new("2"));
        assert_lt!(dv1, dv2);

        assert_lt!(fv1, dv1);
        assert_lt!(fv1, dv2);
        assert_lt!(fv2, dv1);
        assert_lt!(fv2, dv2);
    }
}