Add common use cases

src/materializer.rs

@@ -11,7 +11,7 @@ use phenopackets::schema::v2::core::{
 pub(crate) struct NodeMaterializer;
 
 impl NodeMaterializer {
-    pub fn materialize_nodes(&mut self, dyn_node: &DynamicNode, repo: &mut NodeRepository) {
+    pub fn materialize_nodes(&self, dyn_node: &DynamicNode, repo: &mut NodeRepository) {
         if let Some(oc) = OntologyClass::parse(dyn_node) {
             Self::push_to_repo(oc, dyn_node, repo);
         } else if let Some(pf) = PhenotypicFeature::parse(dyn_node) {

src/patches/traits.rs

@@ -15,7 +15,7 @@ pub trait PatchFromContext {
     ) -> Result<Box<dyn RegisterablePatch>, FromContextError>;
 }
 
-impl<T: CompilePatches + Send + RulePatch> RegisterablePatch for T {
+impl<T: CompilePatches + RulePatch> RegisterablePatch for T {
     fn compile_patches(&self, value: &dyn Node, lint_violation: &LintViolation) -> Vec<Patch> {
         CompilePatches::compile_patches(self, value, lint_violation)
     }
@@ -30,6 +30,6 @@ pub trait RulePatch: PatchFromContext + RegisterablePatch + CompilePatches {
 }
 
 /// Tries to compile patches for a given rule.
-pub trait CompilePatches: Send + Sync {
+pub trait CompilePatches {
     fn compile_patches(&self, node: &dyn Node, lint_violation: &LintViolation) -> Vec<Patch>;
 }

src/phenolint.rs

@@ -53,7 +53,7 @@ impl Phenolint {
 }
 
 impl Lint<str> for Phenolint {
-    fn lint(&mut self, phenostr: &str, patch: bool, quiet: bool) -> LintResult {
+    fn lint(&self, phenostr: &str, patch: bool, quiet: bool) -> LintResult {
         let mut report = LintReport::default();
 
         let (values, spans, input_type) = match PhenopacketParser::to_abstract_tree(phenostr) {
@@ -142,7 +142,7 @@ impl Lint<str> for Phenolint {
 }
 
 impl Lint<PathBuf> for Phenolint {
-    fn lint(&mut self, phenopath: &PathBuf, patch: bool, quit: bool) -> LintResult {
+    fn lint(&self, phenopath: &PathBuf, patch: bool, quit: bool) -> LintResult {
         let phenodata = match fs::read(phenopath) {
             Ok(phenodata) => phenodata,
             Err(err) => {
@@ -155,7 +155,7 @@ impl Lint<PathBuf> for Phenolint {
 }
 
 impl Lint<[u8]> for Phenolint {
-    fn lint(&mut self, phenodata: &[u8], patch: bool, quit: bool) -> LintResult {
+    fn lint(&self, phenodata: &[u8], patch: bool, quit: bool) -> LintResult {
         let (phenostr, input_type) = match PhenopacketParser::to_string(phenodata) {
             Ok(phenostr) => phenostr,
             Err(err) => {

src/report/traits.rs

@@ -8,12 +8,12 @@ pub trait RuleReport: ReportFromContext + RegisterableReport + CompileReport {
     const RULE_ID: &'static str;
 }
 
-pub trait RegisterableReport {
+pub trait RegisterableReport: Send + Sync {
     fn compile_report(&self, value: &dyn Node, lint_violation: &LintViolation) -> ReportSpecs;
     fn rule_id(&self) -> String;
 }
 
-impl<T: CompileReport + Send + RuleReport> RegisterableReport for T {
+impl<T: CompileReport + RuleReport> RegisterableReport for T {
     fn compile_report(&self, value: &dyn Node, lint_violation: &LintViolation) -> ReportSpecs {
         CompileReport::compile_report(self, value, lint_violation)
     }

src/rules/traits.rs

@@ -9,7 +9,7 @@ pub trait LintRule: RuleFromContext + Send + Sync {
     fn check_erased(&self, board: &NodeRepository) -> Vec<LintViolation>;
 }
 
-pub trait RuleMetaData: Send + Sync {
+pub trait RuleMetaData {
     fn rule_id(&self) -> &str;
 }
 
@@ -19,12 +19,12 @@ pub trait RuleFromContext {
         Self: Sized;
 }
 
-pub trait RuleCheck: Send + Sync + 'static {
+pub trait RuleCheck: 'static {
     type Data<'a>: LintData<'a> + ?Sized;
     fn check(&self, data: Self::Data<'_>) -> Vec<LintViolation>;
 }
 
-impl<T> LintRule for T
+impl<T: Send + Sync> LintRule for T
 where
     T: RuleCheck + RuleFromContext + RuleMetaData,
     for<'a> <T as RuleCheck>::Data<'a>: Sized,

src/traits.rs

@@ -1,5 +1,5 @@
 use crate::error::LintResult;
 
 pub trait Lint<T: ?Sized> {
-    fn lint(&mut self, phenodata: &T, patch: bool, quit: bool) -> LintResult;
+    fn lint(&self, phenodata: &T, patch: bool, quit: bool) -> LintResult;
 }

tests/use_cases.rs

@@ -0,0 +1,30 @@
+use phenolint::LinterContext;
+use phenolint::phenolint::Phenolint;
+use phenolint::traits::Lint;
+use serde_json::json;
+use std::path::PathBuf;
+use std::sync::OnceLock;
+
+static PHENOLINT: OnceLock<Phenolint> = OnceLock::new();
+
+#[test]
+fn lint_minimal_valid_phenopacket() {
+    let phenolint = PHENOLINT.get_or_init(init_phenolint);
+
+    let value = json!({
+        "id": "phenopacket",
+    });
+    let payload_str = serde_json::to_string(&value).unwrap();
+
+    // TODO: is it absolutely necessary for `lint` to take `&mut self`?
+    let result = phenolint.lint(payload_str.as_str(), true, true);
+
+    // TODO: assert properly
+    eprintln!("{:?}", result);
+}
+
+fn init_phenolint() -> Phenolint {
+    let context = LinterContext::new(Some(PathBuf::from("tests/assets/hp.toy.json")));
+    let rule_ids = vec!["CURIE001".into(), "INTER001".into()];
+    Phenolint::new(context, rule_ids)
+}