test: Add tests for python and JS with pytest and jest. Update some g…

…h actions versions

.github/workflows/test.yml

@@ -24,8 +24,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-        with:
-          submodules: true
       - run: |
           rustup update
           cargo install cargo-tarpaulin
@@ -34,6 +32,24 @@ jobs:
         env:
           RUST_BACKTRACE: 1
 
+  test-js:
+    name: 🟨 Tests JavaScript
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - run: |
+          rustup update
+          ./scripts/test-js.sh
+
+  test-python:
+    name: 🐍 Tests Python
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - run: |
+          rustup update
+          ./scripts/test-python.sh
+
   cov:
     name: ☂️ Coverage
     runs-on: ubuntu-latest
@@ -47,7 +63,7 @@ jobs:
           cargo tarpaulin -p nanopub --out xml --exclude-files lib/src/error.rs --verbose --timeout 120
 
       - name: Upload to codecov.io
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v4
         with:
           fail_ci_if_error: true
           token: ${{secrets.CODECOV_TOKEN}}
@@ -78,10 +94,10 @@ jobs:
       - run: bash ./scripts/docs-build.sh
 
       - name: Setup Pages
-        uses: actions/configure-pages@v3
+        uses: actions/configure-pages@v4
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v3
         with:
           path: './target/doc'
 
@@ -103,7 +119,7 @@ jobs:
       with:
         python-version: ${{ env.STABLE_PYTHON_VERSION }}
 
-    - uses: actions/setup-java@v3
+    - uses: actions/setup-java@v4
       with:
         distribution: 'temurin' # See 'Supported distributions' for available options
         java-version: '21'

.gitignore

@@ -1,4 +1,3 @@
-.venv
 target/
 Cargo.lock
 tarpaulin-report.html
@@ -7,9 +6,16 @@ tarpaulin-report.html
 node_modules/
 pkg*/
 package-lock.json
+yarn.lock
+pnpm-lock.yaml
 *.lock
 js/LICENSE.txt
 
+# Python
+.venv
+__pycache__/
+.pytest_cache
+
 # HTML docs generated by mdbook
 lib/docs/docs
 /theme/

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

@@ -1,7 +1,7 @@
 {
   "version": "0.0.0",
   "name": "@nanopub/sign",
-  "description": "JavaScript bindings for the Nanopub rust toolkit",
+  "description": "JavaScript bindings for the Nanopub toolkit writen in Rust",
   "license": "MIT",
   "homepage": "https://github.com/vemonet/nanopub-rs",
   "module": "web.js",
@@ -21,7 +21,9 @@
   ],
   "scripts": {
     "fmt": "prettier \"**/*.{ts,tsx,js,cjs,json,md,html}\" --ignore-path .gitignore --write",
-    "test": "wasm-pack build --debug --target nodejs && mocha",
+    "old-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 +35,12 @@
     ]
   },
   "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/tests/nanopub.test.ts

@@ -0,0 +1,48 @@
+import {describe, expect, test} from '@jest/globals';
+import {Nanopub, NpProfile} from "../pkg/node";
+
+const privKey=`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`;
+const orcid="https://orcid.org/0000-0000-0000-0000";
+const unsignedRdf = `@prefix : <http://purl.org/nanopub/temp/mynanopub#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix dc: <http://purl.org/dc/terms/> .
+@prefix pav: <http://purl.org/pav/> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix np: <http://www.nanopub.org/nschema#> .
+@prefix npx: <http://purl.org/nanopub/x/> .
+@prefix ex: <http://example.org/> .
+
+:Head {
+  : np:hasAssertion :assertion ;
+    np:hasProvenance :provenance ;
+    np:hasPublicationInfo :pubinfo ;
+    a np:Nanopublication .
+}
+
+:assertion {
+  ex:mosquito ex:transmits ex:malaria .
+}
+
+:provenance {
+  :assertion prov:hadPrimarySource <http://dx.doi.org/10.3233/ISU-2010-0613> .
+}
+
+:pubinfo {
+  : dc:created "2014-07-24T18:05:11+01:00"^^xsd:dateTime ;
+    pav:createdBy <http://orcid.org/0000-0002-1267-0234> ;
+    a npx:ExampleNanopub .
+}`
+
+describe('Tests for the curies npm package', () => {
+  // NOTE: `await init()` only needed in browser environment
+
+  test('publish np', async () => {
+    const profile = new NpProfile(privKey, orcid, "Your Name", "");
+    const np = await new Nanopub(unsignedRdf).publish(profile);
+
+    console.log("Published Nanopub:", np.info());
+    expect(np.info().published).toBeDefined();
+    // expect(np.info().trusty_hash).toBe("RAE9traVUygMTJ-k8E1_pVNy3gtf7uUvtHJtPeU64WpA4");
+  });
+
+});

lib/docs/contributing.md

@@ -83,14 +83,16 @@ cd nanopub-rs
 git checkout -b add-my-contribution
 ```
 
-###  🧪 Run tests
+###  🧪 Test Rust crate
 
-Run tests for all packages:
+Run tests for the rust crate:
 
 ```bash
 cargo test
 ```
 
+~~~admonish example title="Testing options"
+
 Display prints:
 
 ```bash
@@ -109,25 +111,20 @@ If tests panic without telling on which test it failed:
 cargo test -- --test-threads=1
 ```
 
+~~~
+
 Test the `nanopub` crate with code coverage:
 
 ```bash
 cargo tarpaulin -p nanopub --out html
 ```
 
-Test signing a nanopublication with the CLI:
-
-```bash
-cd cli
-cargo run -- sign ../lib/tests/resources/nanopub_test_blank.trig
-```
-
-### 🐍 Run python
+### 🐍 Test Python package
 
-Build the pip package, and run the `python/try.py` script:
+Build the pip package and run `pytest` tests:
 
 ```bash
-./scripts/run-python.sh
+./scripts/test-python.sh
 ```
 
 Or just run the script:
@@ -137,12 +134,12 @@ source .venv/bin/activate
 python python/try.py
 ```
 
-### 🟨 Run JavaScript
+### 🟨 Test JavaScript package
 
-Build the npm package:
+Build the npm package and run `jest` tests:
 
 ```bash
-./scripts/run-js.py
+./scripts/test-js.sh
 ```
 
 Start a web server to access the dev webpage:
@@ -153,6 +150,21 @@ python -m http.server 3000 --directory ./js
 
 Open [localhost:3000](http://localhost:3000) in your web browser.
 
+### ⌨️ Test CLI
+
+Test signing a nanopublication with the commandline interface:
+
+```bash
+cd cli
+cargo run -- sign ../lib/tests/resources/nanopub_test_blank.trig
+```
+
+### 🌈 Run all tests
+
+```bash
+./scripts/test-all.sh
+```
+
 ### ✨ Format
 
 ```bash

lib/docs/use_python.md

@@ -5,9 +5,9 @@
 You can easily publish Nanopubs from Python.
 
 
-```admonish info title="Build a Nanopublication"
+~~~admonish info title="Build a Nanopublication"
 This package takes an already prepared Nanopublication RDF string as input. If you want to build a Nanopublication programmatically, use the [`nanopub`](https://fair-workflows.github.io/nanopub) pip package. You can then feed the serialized RDF of the built Nanopub to this package functions.
-```
+~~~
 
 ## 📥️ Install
 

lib/tests/nanopub_test.rs

@@ -42,6 +42,22 @@ async fn publish_proteinatlas() -> Result<(), Box<dyn Error>> {
     Ok(())
 }
 
+#[tokio::test]
+async fn publish_already_signed() -> Result<(), Box<dyn Error>> {
+    let np_rdf = fs::read_to_string("./tests/resources/signed.simple1-rsa.trig")?;
+    let np = Nanopub::new(&np_rdf)?.publish(None, Some("")).await?;
+    assert!(np.info.published.is_some());
+    Ok(())
+}
+
+#[tokio::test]
+async fn publish_unsigned_no_profile_error() -> Result<(), Box<dyn Error>> {
+    let np_rdf = fs::read_to_string("./tests/resources/simple1-rsa.trig")?;
+    let np = Nanopub::new(&np_rdf)?.publish(None, None).await;
+    assert!(np.is_err());
+    Ok(())
+}
+
 #[test]
 fn sign_nanopub_blank() -> Result<(), Box<dyn Error>> {
     let np_rdf = fs::read_to_string("./tests/resources/nanopub_test_blank.trig")?;

python/tests/__init__.py

@@ -0,0 +1 @@
+"""Tests."""

python/tests/test_nanopub.py

@@ -0,0 +1,70 @@
+import pytest
+from nanopub_sign import Nanopub, NpProfile, get_np_server
+
+rdf_str = """@prefix : <http://purl.org/nanopub/temp/mynanopub#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix dc: <http://purl.org/dc/terms/> .
+@prefix pav: <http://purl.org/pav/> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix np: <http://www.nanopub.org/nschema#> .
+@prefix npx: <http://purl.org/nanopub/x/> .
+@prefix ex: <http://example.org/> .
+
+:Head {
+	: np:hasAssertion :assertion ;
+		np:hasProvenance :provenance ;
+		np:hasPublicationInfo :pubinfo ;
+		a np:Nanopublication .
+}
+
+:assertion {
+	ex:mosquito ex:transmits ex:malaria .
+}
+
+:provenance {
+	:assertion prov:hadPrimarySource <http://dx.doi.org/10.3233/ISU-2010-0613> .
+}
+
+:pubinfo {
+	: dc:created "2014-07-24T18:05:11+01:00"^^xsd:dateTime ;
+		pav:createdBy <http://orcid.org/0000-0002-1267-0234> ;
+		a npx:ExampleNanopub .
+}"""
+
+private_key = """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"""
+
+# Instantiate nanopub profile
+profile = NpProfile(
+    private_key=private_key,
+    orcid_id="https://orcid.org/0000-0000-0000-0000",
+    name="",
+    introduction_nanopub_uri=""
+)
+
+def test_check():
+    np = Nanopub.check(rdf_str)
+    assert not np.info()["trusty_hash"]
+    assert not np.info()["published"]
+
+def test_sign():
+    np = Nanopub.sign(
+        rdf=rdf_str,
+        profile=profile,
+    )
+    assert np.info()["trusty_hash"]
+    assert not np.info()["published"]
+
+def test_publish():
+    np = Nanopub.publish(
+        rdf=rdf_str,
+        profile=profile,
+        server_url=None,
+    )
+    # print("Published", np.info())
+    # print(np.get_rdf())
+    assert np.info()["trusty_hash"]
+    assert np.info()["published"]
+
+def test_get_np_server():
+    print(f"Random server: {get_np_server()}")
+    assert len(get_np_server()) > 3

scripts/test-all.sh

@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+set -e
+
+cargo test
+
+./scripts/test-js.sh
+./scripts/test-python.sh