Add from_extended_prefix_map and get_bioregistry_converter from JSON …

…file. Add support for optional pattern on Record. Add support for delimiter on Converter Fix linux wheel workflows (add openssl-dev dependency for linux wheel builds) Move converter and record out of lib.rs, in a new api.rs file Create fetch.rs file for PrefixMapSources traits and functions to fetch data (from URL, file) Improved tests
biopragmatics · Dec 17, 2023 · 5b2ea76 · 5b2ea76
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diff --git a/.github/workflows/manylinux_build.sh b/.github/workflows/manylinux_build.sh
@@ -1,5 +1,5 @@
 cd /workdir
-yum -y install centos-release-scl-rh
+yum -y install centos-release-scl-rh openssl-devel
 yum -y install llvm-toolset-7.0
 source scl_source enable llvm-toolset-7.0
 curl https://static.rust-lang.org/rustup/dist/%arch%-unknown-linux-gnu/rustup-init --output rustup-init

diff --git a/.github/workflows/musllinux_build.sh b/.github/workflows/musllinux_build.sh
@@ -1,5 +1,5 @@
 cd /workdir
-apk add clang-dev
+apk add clang-dev openssl-dev
 curl https://static.rust-lang.org/rustup/dist/%arch%-unknown-linux-musl/rustup-init --output rustup-init
 chmod +x rustup-init
 ./rustup-init -y --profile minimal

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -41,8 +41,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Generate code coverage
-        run: |
-          cargo tarpaulin -p curies --out xml --verbose --timeout 120
+        run: bash ./scripts/cov.sh
 
       - name: Upload to codecov.io
         uses: codecov/codecov-action@v2

diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,14 @@
+# Rust
 /target/
 Cargo.lock
+
+# Tests
 tarpaulin-report.html
+cobertura.xml
+benchmark.md
+hyperfine_*.deb
+
+# Python
 .venv
 
 # JS
@@ -10,11 +18,10 @@ package-lock.json
 *.lock
 js/LICENSE
 
-# HTML docs generated by mdbook
-lib/docs/docs
+# Docs
 /theme/
 mdbook-admonish.css
 
-# Build scripts
+# Build process
 .github/workflows/manylinux_build_script.sh
 .github/workflows/musllinux_build_script.sh
diff --git a/README.md b/README.md
@@ -19,10 +19,16 @@
         <img src="https://codecov.io/gh/biopragmatics/curies.rs/branch/main/graph/badge.svg" alt="Codecov status" />
     </a>
 </p>
-
 Idiomatic conversion between URIs and compact URIs (CURIEs) in Rust.
 
-## 📥 Install dependencies
+## 📖 Documentation
+
+Checkout the **[biopragmatics.github.io/curies.rs](https://biopragmatics.github.io/curies.rs)** for more details on how to install and use it.
+
+
+## 🧑‍💻 Development
+
+### 📥 Install dependencies
 
 [Rust](https://www.rust-lang.org/tools/install), python 3.8+ and npm are required for development.
 
@@ -35,8 +41,6 @@ cargo install wasm-pack cargo-tarpaulin mdbook mdbook-admonish
 > If you are using VSCode we strongly recommend to install the `rust-lang.rust-analyzer` extension.
 
 
-## Development
-
 ### 🧪 Run tests
 
 Run tests and display prints:
@@ -56,3 +60,4 @@ cargo fmt
 ```shell
 cargo doc --open
 ```
+
diff --git a/js/src/curies.rs → js/src/api.rs b/js/src/curies.rs → js/src/api.rs
@@ -31,6 +31,7 @@ impl RecordJs {
                 uri_prefix,
                 prefix_synonyms: prefix_synonyms_set,
                 uri_prefix_synonyms: uri_prefix_synonyms_set,
+                pattern: None,
             },
         })
     }
@@ -59,15 +60,15 @@ impl ConverterJs {
     #[wasm_bindgen(constructor)]
     pub fn new() -> Result<ConverterJs, JsValue> {
         Ok(Self {
-            converter: Converter::new(),
+            converter: Converter::default(),
         })
     }
 
     #[wasm_bindgen(js_name = addRecord)]
     pub fn add_record(&mut self, record: RecordJs) -> Result<(), JsValue> {
         self.converter
             .add_record(record.record)
-            .map(|_| ())
+            .map(|_| self.converter.build())
             .map_err(|e| JsValue::from_str(&e.to_string()))
     }
 

diff --git a/js/src/lib.rs b/js/src/lib.rs
@@ -2,7 +2,7 @@ use js_sys::Error;
 // #![allow(clippy::unused_unit)]
 use wasm_bindgen::prelude::*;
 
-mod curies;
+mod api;
 
 #[wasm_bindgen(start)]
 pub fn startup() {

diff --git a/lib/Cargo.toml b/lib/Cargo.toml
@@ -17,6 +17,7 @@ serde = { version = "1.0", features = ["derive"] }
 serde_json = "1.0"
 reqwest = { version = "0.11", features = ["blocking", "json"] }
 async-trait = "0.1"
+regex = "1.10"
 
 [dev-dependencies]
 tokio = { version = "1.34", features = ["rt-multi-thread", "macros"] }

diff --git a/lib/docs/contributing.md b/lib/docs/contributing.md
@@ -168,12 +168,12 @@ cargo install cargo-outdated
    cargo outdated
    ```
 
-2. Bump the version in the `Cargo.toml` file in folders `lib/`, `python`, `js`
+2. Bump the version in the `Cargo.toml` file in folders `lib`, `python`, and `js`:
 
    ```bash
    ./scripts/bump.sh 0.0.2
    ```
 
-3. Commit, push, and create a new release on GitHub
+3. Commit, push, and **create a new release on GitHub**.
 
-4. The `build.yml` workflow will automatically build artifacts (binary, pip wheel, npm package), and add them to the new release.
+4. The `build.yml` workflow will automatically build artifacts (pip wheel, npm package), add them to the new release, and publish to public registries (crates.io, PyPI, NPM).
diff --git a/lib/docs/introduction.md b/lib/docs/introduction.md
@@ -13,9 +13,9 @@ Whether you're a developer looking to work with CURIEs (e.g. expand or compress)
 ### ✨ CURIEs management
 
 - 🛠️ **Create** your custom converter
-- 📥 **Import** converters from JSON or JSON-LD context, with helper functions for popular converters, such as `get_obo_converter()`.
-- 🔗 **Expand** CURIEs from their compressed form to URIs.
-- 🗜️ **Compress** URIs to CURIEs.
+- 📥 **Import converters** from JSON or JSON-LD context, with helper functions for popular converters, such as `get_obo_converter()`.
+- 🔗 **Expand CURIEs** from their compressed form to URIs.
+- 🗜️ **Compress URIs** to CURIEs.
 
 ### 📦️ Packaged for multiple interfaces
 

diff --git a/lib/docs/use_javascript.md b/lib/docs/use_javascript.md
@@ -4,6 +4,13 @@
 
 You can easily work with CURIEs from JavaScript, or TypeScript with the [`@biopragmatics/curies`](https://www.npmjs.com/package/@biopragmatics/curies) NPM package.
 
+## 📥️ Install
+
+Install the `npm` package (use `yarn` or `pnpm` if you prefer) to use it from your favorite framework:
+
+```bash
+npm install @biopragmatics/curies
+```
 
 ## 🚀 Use it in bare HTML files
 
@@ -56,14 +63,6 @@ npx http-server
 python -m http.server
 ```
 
-## 📥️ Install
-
-Install the `npm` package (use `yarn` or `pnpm` if you prefer) to use it from your favorite framework:
-
-```bash
-npm install @biopragmatics/curies
-```
-
 ## ⚛️ Use from any JavaScript framework
 
 It can be used from any JavaScript framework, or NodeJS.

diff --git a/lib/docs/use_rust.md b/lib/docs/use_rust.md
@@ -9,17 +9,19 @@ use curies::{Converter, Record};
 use std::collections::HashSet;
 
 fn example() -> Result<(), Box<dyn std::error::Error>> {
-    let mut converter = Converter::new();
+    let mut converter = Converter::default();
 
     let record1 = Record {
         prefix: "doid".to_string(),
         uri_prefix: "http://purl.obolibrary.org/obo/DOID_".to_string(),
         prefix_synonyms: HashSet::from(["DOID".to_string()]),
         uri_prefix_synonyms: HashSet::from(["https://identifiers.org/DOID/"].map(String::from)),
+        pattern: None,
     };
     let record2 = Record::new("obo", "http://purl.obolibrary.org/obo/");
     converter.add_record(record1)?;
     converter.add_record(record2)?;
+    converter.build();
 
     let uri = converter.expand("doid:1234")?;
     println!("Expanded CURIE: {}", uri);