IWC showcase

.github/workflows/gh-page-build.yml

@@ -0,0 +1,47 @@
+name: Build and Deploy IWC Website
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install Python Dependencies
+        run: |
+          pip install -r requirements.txt
+
+      - name: Run generate_manifest.py
+        run: python ./scripts/workflow_manifest.py
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+
+      - name: Install NPM Dependencies
+        run: npm install
+        working-directory: ./website
+
+      - name: Build Nuxt 3 Static Site
+        run: npm run generate
+        working-directory: ./website
+        env:
+          NUXT_APP_BASE_URL: /iwc/
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./website/.output/public

.gitignore

@@ -1,3 +1,4 @@
 tool_test_output.html
 tool_test_output.json
 .DS_Store
+workflow_manifest.json

astro.config.mjs

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+import { defineConfig } from 'astro/config';
+import tailwind from "@astrojs/tailwind";
+
+// https://astro.build/config
+export default defineConfig({
+  integrations: [tailwind()]
+});

scripts/workflow_manifest.py

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+import os
+import json
+import yaml
+
+
+def find_and_load_compliant_workflows(directory):
+    """
+    Find all .dockstore.yml files in the given directory and its subdirectories.
+    Read the contents of these files and add the path of the file to the content.
+    Return a list of all collected data.
+
+    """
+    workflow_data = []
+    for root, _, files in os.walk(directory):
+        if ".dockstore.yml" in files:
+            try:
+                dockstore_path = os.path.join(root, ".dockstore.yml")
+                with open(dockstore_path) as f:
+                    workflow_details = yaml.safe_load(f)
+                workflow_details["path"] = root
+                workflow_data.append(workflow_details)
+
+                # Now inspect the details which are something like this:
+                # version: 1.2
+                # workflows:
+                # - name: Velocyto-on10X-from-bundled
+                #   subclass: Galaxy
+                #   publish: true
+                #   primaryDescriptorPath: /Velocyto-on10X-from-bundled.ga
+                #   testParameterFiles:
+                #   - /Velocyto-on10X-from-bundled-tests.yml
+                #   authors:
+                #   - name: Lucille Delisle
+                #     orcid: 0000-0002-1964-4960
+                # - name: Velocyto-on10X-filtered-barcodes
+                #   subclass: Galaxy
+                #   publish: true
+                #   primaryDescriptorPath: /Velocyto-on10X-filtered-barcodes.ga
+                #   testParameterFiles:
+                #   - /Velocyto-on10X-filtered-barcodes-tests.yml
+                #   authors:
+                #   - name: Lucille Delisle
+                #     orcid: 0000-0002-1964-4960
+
+                for workflow in workflow_details["workflows"]:
+                    # For each listed workflow, load the primaryDescriptorPath
+                    # file, which is the actual galaxy workflow.
+                    # strip leading slash from primaryDescriptorPath if present -- these are relative.
+                    workflow_path = os.path.join(
+                        root, workflow["primaryDescriptorPath"].lstrip("/")
+                    )
+                    try:
+                        with open(workflow_path) as f:
+                            workflow["definition"] = json.load(f)
+                    except Exception as e:
+                        print(
+                            f"No workflow file: {os.path.join(root, workflow['primaryDescriptorPath'])}: {e}"
+                        )
+
+                    # also try to load a README.md file for each workflow
+                    try:
+                        with open(os.path.join(root, "README.md")) as f:
+                            workflow["readme"] = f.read()
+                    # catch FileNotFound
+                    except FileNotFoundError:
+                        print(f"No README.md at {os.path.join(root, 'README.md')}")
+                    except Exception as e:
+                        print(
+                            f"Error reading file {os.path.join(root, 'README.md')}: {e}"
+                        )
+
+                    # also try to load a CHANGELOG.md file for each workflow
+                    try:
+                        with open(os.path.join(root, "CHANGELOG.md")) as f:
+                            workflow["changelog"] = f.read()
+                    except FileNotFoundError:
+                        print(f"No CHANGELOG.md at {os.path.join(root, 'CHANGELOG.md')}")
+                    except Exception as e:
+                        print(
+                            f"Error reading file {os.path.join(root, 'CHANGELOG.md')}: {e}"
+                        )
+                    dirname = os.path.dirname(workflow_path).split("/")[-1]
+                    workflow["trsID"] = f"#workflow/github.com/iwc-workflows/{dirname}/{workflow['name'] or 'main'}"
+
+                    workflow_test_path = f"{workflow_path.rsplit('.ga', 1)[0]}-tests.yml"
+                    if os.path.exists(workflow_test_path):
+                        with open(workflow_test_path) as f:
+                            tests = yaml.safe_load(f)
+                        workflow["tests"] = tests
+                    else:
+                        print(f"no test for {workflow_test_path}")
+
+            except Exception as e:
+                print(f"Error reading file {os.path.join(root, '.dockstore.yml')}: {e}")
+
+    return workflow_data
+
+
+def write_to_json(data, filename):
+    """
+    Write the given data into a JSON file with the given filename.
+    """
+    try:
+        with open(filename, "w") as f:
+            json.dump(data, f, indent=4)
+    except Exception as e:
+        print(f"Error writing to file {filename}: {e}")
+
+
+if __name__ == "__main__":
+    workflow_data = find_and_load_compliant_workflows("./workflows")
+    write_to_json(workflow_data, "workflow_manifest.json")

website/.gitignore

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+# Nuxt dev/build outputs
+.output
+.data
+.nuxt
+.nitro
+.cache
+dist
+
+# Node dependencies
+node_modules
+
+# Logs
+logs
+*.log
+
+# Misc
+.DS_Store
+.fleet
+.idea
+
+# Local env files
+.env
+.env.*
+!.env.example

website/.prettierignore

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+# Standard ignores
+**/.git
+**/.svn
+**/.hg
+**/node_modules
+# Ignore the dist folder
+**/dist
+# Don't reformat .json or .yml files included in the project
+*.json
+*.yml

website/README.md

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+# Nuxt 3 Minimal Starter
+
+Look at the [Nuxt 3 documentation](https://nuxt.com/docs/getting-started/introduction) to learn more.
+
+## Setup
+
+Make sure to install the dependencies:
+
+```bash
+# npm
+npm install
+
+# pnpm
+pnpm install
+
+# yarn
+yarn install
+
+# bun
+bun install
+```
+
+## Build workflow manifest
+
+Build the workflow manifest file with
+
+```bash
+python scripts/workflow_manifest.py
+```
+
+## Development Server
+
+Start the development server on `http://localhost:3000`:
+
+```bash
+# npm
+npm run dev
+
+# pnpm
+pnpm run dev
+
+# yarn
+yarn dev
+
+# bun
+bun run dev
+```
+
+## Production
+
+Build the application for production:
+
+```bash
+# npm
+npm run build
+
+# pnpm
+pnpm run build
+
+# yarn
+yarn build
+
+# bun
+bun run build
+```
+
+Locally preview production build:
+
+```bash
+# npm
+npm run preview
+
+# pnpm
+pnpm run preview
+
+# yarn
+yarn preview
+
+# bun
+bun run preview
+```
+
+Check out the [deployment documentation](https://nuxt.com/docs/getting-started/deployment) for more information.

website/app.config.ts

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+export default defineAppConfig({
+    ui: {
+        primary: "amber",
+        gray: "neutral",
+    },
+});

website/app.vue

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+<template>
+    <div>
+        <NuxtLoadingIndicator />
+        <IWCHeader />
+        <main>
+            <NuxtLayout>
+                <NuxtPage />
+            </NuxtLayout>
+        </main>
+    </div>
+</template>

website/components/Author.vue

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+<template>
+    <span class="author">
+        <a v-if="authorUrl !== '#'" :href="authorUrl" target="_blank" rel="noopener noreferrer" class="author-link">
+            {{ author.name }}
+        </a>
+        <span v-else>{{ author.name }}</span>
+    </span>
+</template>
+
+<script setup lang="ts">
+interface Author {
+    name: string;
+    orcid?: string;
+}
+
+const props = defineProps<{
+    author: Author;
+}>();
+
+const authorUrl = computed(() => (props.author.orcid ? `https://orcid.org/${props.author.orcid}` : "#"));
+</script>
+
+<style scoped>
+.author-link {
+    color: inherit;
+    text-decoration: none;
+    border-bottom: 1px dotted currentColor;
+}
+
+.author-link:hover {
+    border-bottom-style: solid;
+}
+</style>

website/components/IWCHeader.vue

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+<template>
+    <header class="shadow-md">
+        <UContainer class="py-4">
+            <div class="flex">
+                <div class="flex flex-grow space-x-2">
+                    <NuxtLink to="/" class="flex items-center space-x-2">
+                        <img src="/iwc_logo.png" alt="IWC Logo" width="64" height="64" />
+                        <span class="text-xl font-semibold">Galaxy IWC - Workflow Library</span>
+                    </NuxtLink>
+                </div>
+                <div class="flex items-center space-x-2">
+                    <NuxtLink to="https://github.com/galaxyproject/iwc/">About</NuxtLink>
+                    <NuxtLink to="https://planemo.readthedocs.io/en/latest/best_practices_workflows.html"
+                        >Development</NuxtLink
+                    >
+                </div>
+            </div>
+        </UContainer>
+    </header>
+</template>