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Merged
ielis merged 5 commits into from
Dec 10, 2025
Merged

Work on Pointer #78

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427bc15
Work on `Pointer`.
ielis Dec 5, 2025
d6f6872
Merge branch 'main' into dd/node-materializer
ielis Dec 8, 2025
c70587c
Show examples for escaping and unescaping.
ielis Dec 8, 2025
b7fefb1
Update the docs.
ielis Dec 9, 2025
04041a3
Linting
SmartMonkey-git Dec 10, 2025
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4 changes: 2 additions & 2 deletions src/parsing/parseable_nodes.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@ impl ParsableNode<Disease> for Disease {
if let Value::Object(map) = &node.inner
&& node
.pointer()
.segments()
.iter_segments()
.into_iter()
.any(|seg| seg.to_lowercase() == "diseases")
&& map.contains_key("term")
Expand All @@ -102,7 +102,7 @@ impl ParsableNode<Diagnosis> for Diagnosis {
if let Value::Object(map) = &node.inner
&& node
.pointer()
.segments()
.iter_segments()
.into_iter()
.any(|seg| seg.to_lowercase() == "interpretations")
&& map.contains_key("disease")
Expand Down
88 changes: 45 additions & 43 deletions src/patches/patch_engine.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -103,12 +103,14 @@ impl PatchEngine {
patches.sort_by(|p1, p2| match (p1, p2) {
(PatchInstruction::Add { .. }, PatchInstruction::Remove { .. }) => Ordering::Less,
(PatchInstruction::Remove { .. }, PatchInstruction::Add { .. }) => Ordering::Greater,
(PatchInstruction::Add { at: at1, .. }, PatchInstruction::Add { at: at2, .. }) => {
at1.segments().count().cmp(&at2.segments().count())
}
(PatchInstruction::Remove { at: at1 }, PatchInstruction::Remove { at: at2 }) => {
at1.segments().count().cmp(&at2.segments().count())
}
(PatchInstruction::Add { at: at1, .. }, PatchInstruction::Add { at: at2, .. }) => at1
.iter_segments()
.count()
.cmp(&at2.iter_segments().count()),
(PatchInstruction::Remove { at: at1 }, PatchInstruction::Remove { at: at2 }) => at1
.iter_segments()
.count()
.cmp(&at2.iter_segments().count()),
_ => Ordering::Equal,
});
}
Expand Down Expand Up @@ -168,7 +170,7 @@ mod tests {
let phenostr = sample_phenopacket();
let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Add {
at: Pointer::new("/metaData"),
at: Pointer::from("/metaData"),
value: json!({"created": "2024-01-01"}),
},
vec![],
Expand All @@ -187,7 +189,7 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Add {
at: Pointer::new("/subject/timeAtLastEncounter"),
at: Pointer::from("/subject/timeAtLastEncounter"),
value: json!({"age": "P30Y"}),
},
vec![],
Expand All @@ -206,7 +208,7 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Remove {
at: Pointer::new("/subject/dateOfBirth"),
at: Pointer::from("/subject/dateOfBirth"),
},
vec![],
));
Expand All @@ -223,7 +225,7 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Remove {
at: Pointer::new("/diseases/0/onset"),
at: Pointer::from("/diseases/0/onset"),
},
vec![],
));
Expand All @@ -241,8 +243,8 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Move {
from: Pointer::new("/subject/dateOfBirth"),
to: Pointer::new("/subject/birthDate"),
from: Pointer::from("/subject/dateOfBirth"),
to: Pointer::from("/subject/birthDate"),
},
vec![],
));
Expand All @@ -260,8 +262,8 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Move {
from: Pointer::new("/diseases/0/onset"),
to: Pointer::new("/ageOfOnset"),
from: Pointer::from("/diseases/0/onset"),
to: Pointer::from("/ageOfOnset"),
},
vec![],
));
Expand All @@ -279,8 +281,8 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Duplicate {
from: Pointer::new("/subject/id"),
to: Pointer::new("/subject/patientId"),
from: Pointer::from("/subject/id"),
to: Pointer::from("/subject/patientId"),
},
vec![],
));
Expand All @@ -298,8 +300,8 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Duplicate {
from: Pointer::new("/diseases/0/term"),
to: Pointer::new("/diagnosisTerm"),
from: Pointer::from("/diseases/0/term"),
to: Pointer::from("/diagnosisTerm"),
},
vec![],
));
Expand All @@ -318,11 +320,11 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Add {
at: Pointer::new("/subject/karyotypicSex"),
at: Pointer::from("/subject/karyotypicSex"),
value: Value::String("XY".to_string()),
},
vec![PatchInstruction::Add {
at: Pointer::new("/subject/taxonomy"),
at: Pointer::from("/subject/taxonomy"),
value: json!({"id": "NCBITaxon:9606", "label": "Homo sapiens"}),
}],
));
Expand All @@ -340,16 +342,16 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Add {
at: Pointer::new("/metaData"),
at: Pointer::from("/metaData"),
value: json!({"created": "2024-01-01"}),
},
vec![
PatchInstruction::Remove {
at: Pointer::new("/subject/dateOfBirth"),
at: Pointer::from("/subject/dateOfBirth"),
},
PatchInstruction::Move {
from: Pointer::new("/subject/sex"),
to: Pointer::new("/subject/gender"),
from: Pointer::from("/subject/sex"),
to: Pointer::from("/subject/gender"),
},
],
));
Expand All @@ -369,10 +371,10 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Remove {
at: Pointer::new("/subject/sex"),
at: Pointer::from("/subject/sex"),
},
vec![PatchInstruction::Add {
at: Pointer::new("/subject/gender"),
at: Pointer::from("/subject/gender"),
value: Value::String("MALE".to_string()),
}],
));
Expand All @@ -390,11 +392,11 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Move {
from: Pointer::new("/diseases/0"),
to: Pointer::new("/primaryDiagnosis"),
from: Pointer::from("/diseases/0"),
to: Pointer::from("/primaryDiagnosis"),
},
vec![PatchInstruction::Add {
at: Pointer::new("/primaryDiagnosis/confirmed"),
at: Pointer::from("/primaryDiagnosis/confirmed"),
value: Value::Bool(true),
}],
));
Expand Down Expand Up @@ -423,7 +425,7 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Add {
at: Pointer::new("/schemaVersion"),
at: Pointer::from("/schemaVersion"),
value: Value::Number(Number::from_f64(2.0f64).unwrap()),
},
vec![],
Expand All @@ -441,11 +443,11 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Duplicate {
from: Pointer::new("/subject"),
to: Pointer::new("/backup"),
from: Pointer::from("/subject"),
to: Pointer::from("/backup"),
},
vec![PatchInstruction::Remove {
at: Pointer::new("/subject/dateOfBirth"),
at: Pointer::from("/subject/dateOfBirth"),
}],
));

Expand All @@ -464,7 +466,7 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Add {
at: Pointer::new("/phenotypicFeatures/0/severity"),
at: Pointer::from("/phenotypicFeatures/0/severity"),
value: json!({"label": "severe"}),
},
vec![],
Expand All @@ -485,7 +487,7 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Add {
at: Pointer::new("/diseases/0/onset/iso8601"),
at: Pointer::from("/diseases/0/onset/iso8601"),
value: json!({"iso8601duration": "P10Y"}),
},
vec![],
Expand All @@ -506,7 +508,7 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Add {
at: Pointer::new("/notes"),
at: Pointer::from("/notes"),
value: Value::String(
"Patient has \"complex\" symptoms; requires care.".to_string(),
),
Expand All @@ -526,12 +528,12 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Move {
from: Pointer::new("/subject/sex"),
to: Pointer::new("/subject/biologicalSex"),
from: Pointer::from("/subject/sex"),
to: Pointer::from("/subject/biologicalSex"),
},
vec![PatchInstruction::Move {
from: Pointer::new("/subject/id"),
to: Pointer::new("/patientIdentifier"),
from: Pointer::from("/subject/id"),
to: Pointer::from("/patientIdentifier"),
}],
));

Expand All @@ -550,10 +552,10 @@ mod tests {

let patch = Patch::new(NonEmptyVec::with_rest(
PatchInstruction::Remove {
at: Pointer::new("/subject/sex"),
at: Pointer::from("/subject/sex"),
},
vec![PatchInstruction::Add {
at: Pointer::new("/subject/sex"),
at: Pointer::from("/subject/sex"),
value: Value::String("FEMALE".to_string()),
}],
));
Expand All @@ -569,7 +571,7 @@ mod tests {
let minimal = json!({"id": "test"});

let patch = Patch::new(NonEmptyVec::with_single_entry(PatchInstruction::Add {
at: Pointer::new("/subject"),
at: Pointer::from("/subject"),
value: json!({"id": "patient.1"}),
}));

Expand Down
6 changes: 3 additions & 3 deletions src/rules/resources.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ mod test_curies_have_resources {
label: "Seizure".into(),
},
Default::default(),
Pointer::new("/phenotypicFeatures/0/type"),
Pointer::from("/phenotypicFeatures/0/type"),
)];
let resources = [];
let data = (List(&ocs), List(&resources));
Expand Down Expand Up @@ -109,12 +109,12 @@ impl ReportFromContext for CuriesHaveResourcesReport {

impl CompileReport for CuriesHaveResourcesReport {
fn compile_report(&self, full_node: &dyn Node, lint_violation: &LintViolation) -> ReportSpecs {
let resources_ptr = Pointer::new("/metaData/resources");
let resources_ptr = Pointer::from("/metaData/resources");
let span = if let Some(resources_range) = full_node.span_at(&resources_ptr).cloned() {
resources_range
} else {
// `metaData` lacks the `resources` field itself.
let metadata_ptr = Pointer::new("/metaData");
let metadata_ptr = Pointer::from("/metaData");
full_node.span_at(&metadata_ptr)
.cloned()
.expect("We assume `metaData` is always in the `Node` because we validate the basic phenopacket invariants before running this rule")
Expand Down
2 changes: 1 addition & 1 deletion src/tree/mod.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,4 @@ pub mod node;
pub mod node_repository;
pub mod pointer;
pub mod traits;
pub(crate) mod utils;
mod utils;
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