Replaced the trie-rs package by a new ptrie package (it was giving in…

…consistent results). Improve docs, add JS tests with jest

.github/workflows/test.yml

@@ -25,8 +25,6 @@ jobs:
       CARGO_TERM_COLOR: always
     steps:
       - uses: actions/checkout@v4
-        with:
-          submodules: true
       - run: cargo build --all-features
       - run: cargo test
         env:

js/jest.config.ts

@@ -0,0 +1,9 @@
+import type {Config} from 'jest';
+
+const config: Config = {
+  preset: 'ts-jest',
+  verbose: true,
+  // testEnvironment: 'node',
+};
+
+export default config;

js/package.json

@@ -21,7 +21,8 @@
   ],
   "scripts": {
     "fmt": "prettier \"**/*.{ts,tsx,js,cjs,json,md,html}\" --ignore-path .gitignore --write",
-    "test": "wasm-pack build --debug --target nodejs && mocha",
+    "jest" : "jest",
+    "test": "npm run build && jest",
     "build": "rm -rf pkg pkg-web pkg-node && wasm-pack build --release --target web --out-name web && mv pkg pkg-web && wasm-pack build --release --target nodejs --out-name node && mv pkg pkg-node && node build_package.js && rm -r pkg-web pkg-node",
     "start": "http-server ./",
     "release": "npm run build && npm publish ./pkg --access public",
@@ -33,8 +34,12 @@
     ]
   },
   "devDependencies": {
+    "@jest/globals": "^29.7.0",
     "http-server": "^14.1.1",
-    "prettier": "^3.1.0"
+    "jest": "^29.7.0",
+    "prettier": "^3.1.0",
+    "ts-jest": "^29.1.1",
+    "ts-node": "^10.9.2"
   },
   "prettier": {
     "trailingComma": "none",

js/src/api.rs

@@ -1,7 +1,12 @@
 use std::collections::HashSet;
 
-use curies::{sources::get_obo_converter, Converter, Record};
-use js_sys::Promise;
+use curies::{
+    sources::{
+        get_bioregistry_converter, get_go_converter, get_monarch_converter, get_obo_converter,
+    },
+    Converter, Record,
+};
+use js_sys::{Array, Promise};
 use serde::{Deserialize, Serialize};
 use serde_wasm_bindgen::to_value;
 use wasm_bindgen::prelude::*;
@@ -64,11 +69,53 @@ impl ConverterJs {
         })
     }
 
+    #[wasm_bindgen(static_method_of = ConverterJs, js_name = fromPrefixMap)]
+    pub fn from_prefix_map(prefix_map: String) -> Promise {
+        future_to_promise(async move {
+            match Converter::from_prefix_map(&*prefix_map).await {
+                Ok(converter) => Ok(JsValue::from(ConverterJs { converter })),
+                Err(e) => Err(JsValue::from_str(&e.to_string())),
+            }
+        })
+    }
+
+    #[wasm_bindgen(static_method_of = ConverterJs, js_name = fromJsonld)]
+    pub fn from_jsonld(jsonld: String) -> Promise {
+        future_to_promise(async move {
+            match Converter::from_jsonld(&*jsonld).await {
+                Ok(converter) => Ok(JsValue::from(ConverterJs { converter })),
+                Err(e) => Err(JsValue::from_str(&e.to_string())),
+            }
+        })
+    }
+
+    #[wasm_bindgen(static_method_of = ConverterJs, js_name = fromExtendedPrefixMap)]
+    pub fn from_extended_prefix_map(prefix_map: String) -> Promise {
+        future_to_promise(async move {
+            match Converter::from_extended_prefix_map(&*prefix_map).await {
+                Ok(converter) => Ok(JsValue::from(ConverterJs { converter })),
+                Err(e) => Err(JsValue::from_str(&e.to_string())),
+            }
+        })
+    }
+
     #[wasm_bindgen(js_name = addRecord)]
     pub fn add_record(&mut self, record: RecordJs) -> Result<(), JsValue> {
         self.converter
             .add_record(record.record)
-            .map(|_| self.converter.build())
+            .map_err(|e| JsValue::from_str(&e.to_string()))
+    }
+
+    #[wasm_bindgen(js_name = addCurie)]
+    pub fn add_curie(&mut self, prefix: &str, uri_prefix: &str) -> Result<(), JsValue> {
+        self.converter
+            .add_curie(prefix, uri_prefix)
+            .map_err(|e| JsValue::from_str(&e.to_string()))
+    }
+
+    pub fn chain(&self, converter: &ConverterJs) -> Result<ConverterJs, JsValue> {
+        Converter::chain(vec![self.converter.clone(), converter.converter.clone()])
+            .map(|converter| ConverterJs { converter })
             .map_err(|e| JsValue::from_str(&e.to_string()))
     }
 
@@ -84,15 +131,36 @@ impl ConverterJs {
             .map_err(|e| JsValue::from_str(&e.to_string()))
     }
 
+    #[wasm_bindgen(js_name = expandList)]
+    pub fn expand_list(&self, curies: JsValue) -> Result<JsValue, JsValue> {
+        let curies_vec: Vec<String> = serde_wasm_bindgen::from_value(curies)
+            .map_err(|e| JsValue::from_str(&format!("Error converting CURIEs list: {}", e)))?;
+        let js_array = self
+            .converter
+            .expand_list(curies_vec.iter().map(String::as_str).collect())
+            .into_iter()
+            .map(JsValue::from)
+            .collect::<Array>();
+        Ok(JsValue::from(js_array))
+    }
+
+    #[wasm_bindgen(js_name = compressList)]
+    pub fn compress_list(&self, curies: JsValue) -> Result<JsValue, JsValue> {
+        let curies_vec: Vec<String> = serde_wasm_bindgen::from_value(curies)
+            .map_err(|e| JsValue::from_str(&format!("Error converting URIs list: {}", e)))?;
+        let js_array = self
+            .converter
+            .compress_list(curies_vec.iter().map(String::as_str).collect())
+            .into_iter()
+            .map(JsValue::from)
+            .collect::<Array>();
+        Ok(JsValue::from(js_array))
+    }
+
     #[wasm_bindgen(js_name = toString)]
     pub fn to_string(&self) -> String {
         self.converter.to_string()
     }
-
-    // #[wasm_bindgen(js_name = prefixMap)]
-    // pub fn prefix_map(&self) -> Result<JsValue, JsValue> {
-    //     serde_wasm_bindgen::to_value(&self.converter.prefix_map).map_err(|e| e.into())
-    // }
 }
 
 /// Get OBO converter
@@ -108,9 +176,78 @@ pub fn get_obo_converter_js() -> Promise {
     })
 }
 
+/// Get Bioregistry converter
+#[wasm_bindgen(js_name = getBioregistryConverter)]
+pub fn get_bioregistry_converter_js() -> Promise {
+    future_to_promise(async move {
+        match get_bioregistry_converter().await {
+            Ok(converter) => Ok(JsValue::from(ConverterJs { converter })),
+            Err(e) => Err(JsValue::from_str(&format!(
+                "Error getting Bioregistry converter: {e}"
+            ))),
+        }
+    })
+}
+
+/// Get GO converter
+#[wasm_bindgen(js_name = getGoConverter)]
+pub fn get_go_converter_js() -> Promise {
+    future_to_promise(async move {
+        match get_go_converter().await {
+            Ok(converter) => Ok(JsValue::from(ConverterJs { converter })),
+            Err(e) => Err(JsValue::from_str(&format!(
+                "Error getting GO converter: {e}"
+            ))),
+        }
+    })
+}
+
+/// Get Monarch converter
+#[wasm_bindgen(js_name = getMonarchConverter)]
+pub fn get_monarch_converter_js() -> Promise {
+    future_to_promise(async move {
+        match get_monarch_converter().await {
+            Ok(converter) => Ok(JsValue::from(ConverterJs { converter })),
+            Err(e) => Err(JsValue::from_str(&format!(
+                "Error getting Monarch converter: {e}"
+            ))),
+        }
+    })
+}
+
 // impl Into<JsValue> for RecordJs {
 //     fn into(self) -> JsValue {
 //         // JsValue::from_serde(&self).unwrap()
 //         self.to_js()
 //     }
 // }
+
+// NOTE: we cannot easily convert a JS object to a string in Rust, it needs to be done in JS with JSON.stringify()
+// fn get_str_from_obj(obj: JsValue) -> Result<String, JsValue> {
+//     if obj.is_string() {
+//         obj.as_string().ok_or_else(|| JsValue::from_str("String conversion failed"))
+//     } else if obj.is_object() {
+//         let str: String = serde_wasm_bindgen::from_value(obj)
+//             .map_err(|e| JsValue::from_str(&format!("Failed to serialize JSON: {}", e)))?;
+//         Ok(str)
+//     } else {
+//         return Err(JsValue::from_str("Expected a string or a JSON object"));
+//     }
+// }
+
+// #[wasm_bindgen(static_method_of = ConverterJs)]
+// pub fn chain(converters: &JsValue) -> Promise {
+//     future_to_promise(async move {
+//         let converters_vec: Vec<ConverterJs> = serde_wasm_bindgen::from_value(converters).map_err(|e| {
+//             JsValue::from_str(&format!("Error converting converters list: {}", e))
+//         })?;
+//         let rust_converters: Vec<Converter> = converters_vec
+//             .into_iter()
+//             .map(|converter_js| converter_js.converter)
+//             .collect();
+//         match Converter::chain(rust_converters) {
+//             Ok(converter) => Ok(JsValue::from(ConverterJs { converter })),
+//             Err(e) => Err(JsValue::from_str(&e.to_string())),
+//         }
+//     })
+// }

js/tests/curies.test.ts

@@ -0,0 +1,119 @@
+import {describe, expect, test} from '@jest/globals';
+import {Record, Converter, getOboConverter, getBioregistryConverter} from "../pkg/node";
+
+describe('Tests for the curies npm package', () => {
+  // NOTE: `await init()` only needed in browser environment
+
+  test('from empty converter', async () => {
+    const converter = new Converter();
+    const record1 = new Record("DOID", "http://purl.obolibrary.org/obo/DOID_", [], [])
+    converter.addRecord(record1);
+    converter.addCurie("OBO", "http://purl.obolibrary.org/obo/");
+    expect(converter.compress("http://purl.obolibrary.org/obo/DOID_1234")).toBe("DOID:1234");
+    expect(converter.expand("OBO:1234")).toBe("http://purl.obolibrary.org/obo/1234");
+    expect(converter.expandList(["OBO:1234", "DOID:1234", "Wrong:1"])).toEqual([
+      "http://purl.obolibrary.org/obo/1234",
+      "http://purl.obolibrary.org/obo/DOID_1234",
+      undefined
+    ]);
+    expect(converter.compress("http://purl.obolibrary.org/obo/1234")).toBe("OBO:1234");
+    expect(converter.compressList([
+      "http://purl.obolibrary.org/obo/1234",
+      "http://purl.obolibrary.org/obo/DOID_1234",
+      "http://identifiers.org/DOID:1234"
+    ])).toEqual(["OBO:1234", "DOID:1234", undefined]);
+  });
+
+  test('from prefix map', async () => {
+    const converter = await Converter.fromPrefixMap(`{
+      "GO": "http://purl.obolibrary.org/obo/GO_",
+      "DOID": "http://purl.obolibrary.org/obo/DOID_",
+      "OBO": "http://purl.obolibrary.org/obo/"
+    }`);
+    expect(converter.compress("http://purl.obolibrary.org/obo/DOID_1234")).toBe("DOID:1234");
+    expect(converter.expand("DOID:1234")).toBe("http://purl.obolibrary.org/obo/DOID_1234");
+    expect(converter.expandList(["OBO:1234", "DOID:1234", "Wrong:1"])).toEqual([
+      "http://purl.obolibrary.org/obo/1234",
+      "http://purl.obolibrary.org/obo/DOID_1234",
+      undefined
+    ]);
+    expect(converter.compressList([
+      "http://purl.obolibrary.org/obo/1234",
+      "http://purl.obolibrary.org/obo/DOID_1234",
+      "http://identifiers.org/DOID:1234"
+    ])).toEqual(["OBO:1234", "DOID:1234", undefined]);
+  });
+
+  test('from JSON-LD', async () => {
+    const converter = await Converter.fromJsonld(`{
+      "@context": {
+          "GO": "http://purl.obolibrary.org/obo/GO_",
+          "DOID": "http://purl.obolibrary.org/obo/DOID_",
+          "OBO": "http://purl.obolibrary.org/obo/"
+      }
+    }`);
+    expect(converter.compress("http://purl.obolibrary.org/obo/DOID_1234")).toBe("DOID:1234");
+    expect(converter.expand("DOID:1234")).toBe("http://purl.obolibrary.org/obo/DOID_1234");
+  });
+
+  test('from extended prefix map', async () => {
+    const converter = await Converter.fromExtendedPrefixMap(`[
+        {
+          "prefix": "DOID",
+          "prefix_synonyms": [
+              "doid"
+          ],
+          "uri_prefix": "http://purl.obolibrary.org/obo/DOID_",
+          "uri_prefix_synonyms": [
+              "http://bioregistry.io/DOID:"
+          ],
+          "pattern": "^\\\\d+$"
+      },
+      {
+          "prefix": "GO",
+          "prefix_synonyms": [
+              "go"
+          ],
+          "uri_prefix": "http://purl.obolibrary.org/obo/GO_",
+          "pattern": "^\\\\d{7}$"
+      },
+      {
+        "prefix": "OBO",
+        "prefix_synonyms": [
+            "obo"
+        ],
+        "uri_prefix": "http://purl.obolibrary.org/obo/"
+      }
+    ]`);
+    expect(converter.compress("http://bioregistry.io/DOID:1234")).toBe("DOID:1234");
+    expect(converter.expand("doid:1234")).toBe("http://purl.obolibrary.org/obo/DOID_1234");
+  });
+
+  test('get OBO converter', async () => {
+    const converter = await getOboConverter();
+    expect(converter.compress("http://purl.obolibrary.org/obo/DOID_1234")).toBe("DOID:1234");
+    expect(converter.expand("DOID:1234")).toBe("http://purl.obolibrary.org/obo/DOID_1234");
+  });
+
+  test('get Bioregistry converter', async () => {
+    const converter = await getBioregistryConverter();
+    expect(converter.compress("http://purl.obolibrary.org/obo/DOID_1234")).toBe("doid:1234");
+    expect(converter.expand("doid:1234")).toBe("http://purl.obolibrary.org/obo/DOID_1234");
+  });
+
+  test('chain converters', async () => {
+    const customConverter1 = await Converter.fromPrefixMap(`{
+      "DOID": "http://purl.obolibrary.org/obo/SPECIAL_DOID_"
+    }`);
+    const customConverter2 = await Converter.fromPrefixMap(`{
+      "GO": "http://purl.obolibrary.org/obo/SPECIAL_GO_",
+      "DOID": "http://purl.obolibrary.org/obo/DOID_"
+    }`);
+    const bioregistryConverter = await getBioregistryConverter();
+    const converter = bioregistryConverter
+      .chain(customConverter1)
+      .chain(customConverter2)
+    expect(converter.compress("http://purl.obolibrary.org/obo/SPECIAL_DOID_1234")).toBe("DOID:1234");
+  });
+
+});

lib/Cargo.toml

@@ -12,7 +12,7 @@ categories.workspace = true
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-trie-rs = "0.1"
+ptrie = "0.5"
 serde = { version = "1.0", features = ["derive"] }
 serde_json = "1.0"
 reqwest = { version = "0.11", features = ["blocking", "json"] }

lib/docs/SUMMARY.md

@@ -2,6 +2,6 @@
 
 - [Introduction](introduction.md)
 - [Use Rust crate](use_rust.md)
-- [Use Python package](use_python.md)
 - [Use NPM package](use_javascript.md)
+- [Use Python package](use_python.md)
 - [Contributing](contributing.md)