galaxy-charts 0.0.21 → 0.0.23

package/docs/.vitepress/cache/deps/vue.js

@@ -1,344 +0,0 @@
-import {
-  BaseTransition,
-  BaseTransitionPropsValidators,
-  Comment,
-  DeprecationTypes,
-  EffectScope,
-  ErrorCodes,
-  ErrorTypeStrings,
-  Fragment,
-  KeepAlive,
-  ReactiveEffect,
-  Static,
-  Suspense,
-  Teleport,
-  Text,
-  TrackOpTypes,
-  Transition,
-  TransitionGroup,
-  TriggerOpTypes,
-  VueElement,
-  assertNumber,
-  callWithAsyncErrorHandling,
-  callWithErrorHandling,
-  camelize,
-  capitalize,
-  cloneVNode,
-  compatUtils,
-  compile,
-  computed,
-  createApp,
-  createBaseVNode,
-  createBlock,
-  createCommentVNode,
-  createElementBlock,
-  createHydrationRenderer,
-  createPropsRestProxy,
-  createRenderer,
-  createSSRApp,
-  createSlots,
-  createStaticVNode,
-  createTextVNode,
-  createVNode,
-  customRef,
-  defineAsyncComponent,
-  defineComponent,
-  defineCustomElement,
-  defineEmits,
-  defineExpose,
-  defineModel,
-  defineOptions,
-  defineProps,
-  defineSSRCustomElement,
-  defineSlots,
-  devtools,
-  effect,
-  effectScope,
-  getCurrentInstance,
-  getCurrentScope,
-  getCurrentWatcher,
-  getTransitionRawChildren,
-  guardReactiveProps,
-  h,
-  handleError,
-  hasInjectionContext,
-  hydrate,
-  hydrateOnIdle,
-  hydrateOnInteraction,
-  hydrateOnMediaQuery,
-  hydrateOnVisible,
-  initCustomFormatter,
-  initDirectivesForSSR,
-  inject,
-  isMemoSame,
-  isProxy,
-  isReactive,
-  isReadonly,
-  isRef,
-  isRuntimeOnly,
-  isShallow,
-  isVNode,
-  markRaw,
-  mergeDefaults,
-  mergeModels,
-  mergeProps,
-  nextTick,
-  normalizeClass,
-  normalizeProps,
-  normalizeStyle,
-  onActivated,
-  onBeforeMount,
-  onBeforeUnmount,
-  onBeforeUpdate,
-  onDeactivated,
-  onErrorCaptured,
-  onMounted,
-  onRenderTracked,
-  onRenderTriggered,
-  onScopeDispose,
-  onServerPrefetch,
-  onUnmounted,
-  onUpdated,
-  onWatcherCleanup,
-  openBlock,
-  popScopeId,
-  provide,
-  proxyRefs,
-  pushScopeId,
-  queuePostFlushCb,
-  reactive,
-  readonly,
-  ref,
-  registerRuntimeCompiler,
-  render,
-  renderList,
-  renderSlot,
-  resolveComponent,
-  resolveDirective,
-  resolveDynamicComponent,
-  resolveFilter,
-  resolveTransitionHooks,
-  setBlockTracking,
-  setDevtoolsHook,
-  setTransitionHooks,
-  shallowReactive,
-  shallowReadonly,
-  shallowRef,
-  ssrContextKey,
-  ssrUtils,
-  stop,
-  toDisplayString,
-  toHandlerKey,
-  toHandlers,
-  toRaw,
-  toRef,
-  toRefs,
-  toValue,
-  transformVNodeArgs,
-  triggerRef,
-  unref,
-  useAttrs,
-  useCssModule,
-  useCssVars,
-  useHost,
-  useId,
-  useModel,
-  useSSRContext,
-  useShadowRoot,
-  useSlots,
-  useTemplateRef,
-  useTransitionState,
-  vModelCheckbox,
-  vModelDynamic,
-  vModelRadio,
-  vModelSelect,
-  vModelText,
-  vShow,
-  version,
-  warn,
-  watch,
-  watchEffect,
-  watchPostEffect,
-  watchSyncEffect,
-  withAsyncContext,
-  withCtx,
-  withDefaults,
-  withDirectives,
-  withKeys,
-  withMemo,
-  withModifiers,
-  withScopeId
-} from "./chunk-XYSSNQS4.js";
-import "./chunk-G3PMV62Z.js";
-export {
-  BaseTransition,
-  BaseTransitionPropsValidators,
-  Comment,
-  DeprecationTypes,
-  EffectScope,
-  ErrorCodes,
-  ErrorTypeStrings,
-  Fragment,
-  KeepAlive,
-  ReactiveEffect,
-  Static,
-  Suspense,
-  Teleport,
-  Text,
-  TrackOpTypes,
-  Transition,
-  TransitionGroup,
-  TriggerOpTypes,
-  VueElement,
-  assertNumber,
-  callWithAsyncErrorHandling,
-  callWithErrorHandling,
-  camelize,
-  capitalize,
-  cloneVNode,
-  compatUtils,
-  compile,
-  computed,
-  createApp,
-  createBlock,
-  createCommentVNode,
-  createElementBlock,
-  createBaseVNode as createElementVNode,
-  createHydrationRenderer,
-  createPropsRestProxy,
-  createRenderer,
-  createSSRApp,
-  createSlots,
-  createStaticVNode,
-  createTextVNode,
-  createVNode,
-  customRef,
-  defineAsyncComponent,
-  defineComponent,
-  defineCustomElement,
-  defineEmits,
-  defineExpose,
-  defineModel,
-  defineOptions,
-  defineProps,
-  defineSSRCustomElement,
-  defineSlots,
-  devtools,
-  effect,
-  effectScope,
-  getCurrentInstance,
-  getCurrentScope,
-  getCurrentWatcher,
-  getTransitionRawChildren,
-  guardReactiveProps,
-  h,
-  handleError,
-  hasInjectionContext,
-  hydrate,
-  hydrateOnIdle,
-  hydrateOnInteraction,
-  hydrateOnMediaQuery,
-  hydrateOnVisible,
-  initCustomFormatter,
-  initDirectivesForSSR,
-  inject,
-  isMemoSame,
-  isProxy,
-  isReactive,
-  isReadonly,
-  isRef,
-  isRuntimeOnly,
-  isShallow,
-  isVNode,
-  markRaw,
-  mergeDefaults,
-  mergeModels,
-  mergeProps,
-  nextTick,
-  normalizeClass,
-  normalizeProps,
-  normalizeStyle,
-  onActivated,
-  onBeforeMount,
-  onBeforeUnmount,
-  onBeforeUpdate,
-  onDeactivated,
-  onErrorCaptured,
-  onMounted,
-  onRenderTracked,
-  onRenderTriggered,
-  onScopeDispose,
-  onServerPrefetch,
-  onUnmounted,
-  onUpdated,
-  onWatcherCleanup,
-  openBlock,
-  popScopeId,
-  provide,
-  proxyRefs,
-  pushScopeId,
-  queuePostFlushCb,
-  reactive,
-  readonly,
-  ref,
-  registerRuntimeCompiler,
-  render,
-  renderList,
-  renderSlot,
-  resolveComponent,
-  resolveDirective,
-  resolveDynamicComponent,
-  resolveFilter,
-  resolveTransitionHooks,
-  setBlockTracking,
-  setDevtoolsHook,
-  setTransitionHooks,
-  shallowReactive,
-  shallowReadonly,
-  shallowRef,
-  ssrContextKey,
-  ssrUtils,
-  stop,
-  toDisplayString,
-  toHandlerKey,
-  toHandlers,
-  toRaw,
-  toRef,
-  toRefs,
-  toValue,
-  transformVNodeArgs,
-  triggerRef,
-  unref,
-  useAttrs,
-  useCssModule,
-  useCssVars,
-  useHost,
-  useId,
-  useModel,
-  useSSRContext,
-  useShadowRoot,
-  useSlots,
-  useTemplateRef,
-  useTransitionState,
-  vModelCheckbox,
-  vModelDynamic,
-  vModelRadio,
-  vModelSelect,
-  vModelText,
-  vShow,
-  version,
-  warn,
-  watch,
-  watchEffect,
-  watchPostEffect,
-  watchSyncEffect,
-  withAsyncContext,
-  withCtx,
-  withDefaults,
-  withDirectives,
-  withKeys,
-  withMemo,
-  withModifiers,
-  withScopeId
-};
-//# sourceMappingURL=vue.js.map

package/docs/.vitepress/cache/deps/vue.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": [],
-  "sourcesContent": [],
-  "mappings": "",
-  "names": []
-}

package/docs/.vitepress/config.mts

@@ -1,55 +0,0 @@
-import { defineConfig } from 'vitepress'
-
-// https://vitepress.dev/reference/site-config
-export default defineConfig({
-  appearance: "dark",
-  base: "/galaxy-charts/",
-  title: "Galaxy Charts",
-  description: "Documentation for Galaxy Charts",
-  themeConfig: {
-    // https://vitepress.dev/reference/default-theme-config
-    logo: '/galaxy-charts.svg',
-    nav: [
-      { text: 'Home', link: '/' },
-    ],
-
-    sidebar: [
-      {
-        text: 'Introduction',
-        items: [
-          { text: 'What is Galaxy Charts?', link: '/content/introduction' },
-          { text: 'Getting Started', link: '/content/installation' },
-          { text: 'Connect to Galaxy', link: '/content/configuration' },
-        ]
-      },
-      {
-        text: 'XML Wrapper',
-        items: [
-            { text: 'Introduction', link: '/content/xml-introduction' },
-            { text: 'Framework', link: '/content/xml-framework' },
-            { text: 'Data Sources', link: '/content/xml-datasources' },
-            { text: 'Sections', link: '/content/xml-sections' },
-            { text: 'Inputs', link: '/content/xml-inputs' },
-        ]
-      },
-      {
-        text: 'Vue Component',
-        items: [
-            { text: 'Introduction', link: '/content/vue-introduction' },
-            { text: 'Utilities', link: '/content/vue-utilities' }
-        ]
-      },
-      {
-        text: 'Deploy to Galaxy',
-        items: [
-            { text: 'Build and Publish', link: '/content/deploy-plugin' },
-            { text: 'Submit Pull Request', link: '/content/deploy-request' },
-        ]
-      },
-    ],
-
-    socialLinks: [
-      { icon: 'github', link: 'https://github.com/galaxyproject/galaxy-charts' }
-    ]
-  }
-})

package/docs/.vitepress/theme/index.js

@@ -1,7 +0,0 @@
-// docs/.vitepress/theme/index.js or index.ts
-import DefaultTheme from 'vitepress/theme'
-import './tailwind.css'  // Ensure this file exists and includes your Tailwind imports
-
-export default {
-  ...DefaultTheme,
-}

package/docs/.vitepress/theme/tailwind.css

@@ -1,7 +0,0 @@
-@tailwind base;
-@tailwind components;
-@tailwind utilities;
-
-.VPNavBarTitle a span {
-    color: #E30A17;
-}

package/docs/content/configuration.md

@@ -1,45 +0,0 @@
-# Connect to Galaxy
-
-Galaxy Charts can be used to develop visualizations independently of Galaxy. However, to access Galaxy datasets, metadata, or run jobs, the visualization may need to connect to the Galaxy API.
-
-To connect the Galaxy Charts standalone application to a Galaxy instance (either local or public), provide the following environment variables when running Galaxy Charts:
-
-- **`GALAXY_KEY`**: Your Galaxy API key.
-- **`GALAXY_ROOT`**: The Galaxy server URL e.g. `https://usegalaxy.org` for Galaxy main.
-
-Run the following command, replacing `MY_API_KEY` and `MY_GALAXY_SERVER` with your own values:
-
-```bash
-GALAXY_KEY=MY_API_KEY GALAXY_ROOT=MY_GALAXY_SERVER npm run dev
-```
-
-## Making Requests to the Galaxy API
-
-Once connected to Galaxy, you can make API requests by importing `GalaxyApi` as follows:
-
-```javascript
-import { GalaxyApi } from "galaxy-charts";
-
-async function fetchGalaxyVersion() {
-  try {
-    const { response, data } = await GalaxyApi().GET("/api/version");
-    console.log("API Version:", data);
-  } catch (error) {
-    console.error("Error fetching Galaxy version:", error);
-  }
-}
-
-fetchGalaxyVersion();
-```
-
-`GalaxyApi` supports `GET`, `POST` and `PUT` requests.
-
-## How to Obtain an API Key
-
-1. Go to your Galaxy instance and sign in.
-2. Click on your username in the top navigation bar, then select **Preferences**.
-3. Scroll down to the **Manage API Key** section to create and access your personal API key.
-
-::: warning NOTE
-Keep your API key secure, just like your login credentials.
-:::

package/docs/content/deploy-plugin.md

@@ -1,22 +0,0 @@
----
-outline: deep
----
-
-# Building and Publishing Your Visualization
-
-Once your visualization is complete and ready for deployment to Galaxy, you can publish it to `npm` and [submit a pull](deploy-request) request to the Galaxy development repository.
-
-## Configure the Package Name
-
-1. Open the `package.json` file in your project.
-2. Update the `name` field to specify a unique package name.
-3. Adjust the `version` field if needed.
-
-## Build and Publish to npm
-
-To build and publish your package to `npm`, run the following commands from your project’s root directory:
-
-```bash
-npm run build
-npm publish
-```

package/docs/content/deploy-request.md

@@ -1,65 +0,0 @@
----
-outline: deep
----
-
-# Submit a Pull Request to Galaxy
-
-With your visualization published to `npm`, the next step is to submit a pull request to the Galaxy development repository. This pull request should include your XML wrapper file and, optionally, a logo file in `png` format.
-
-Note: Replace `MY_VISUALIZATION` with your visualization name in the following instructions.
-
-## Step 1: Fork and Clone the Galaxy Repository
-
-Fork the Galaxy repository available at [Galaxy Project on GitHub](https://github.com/galaxyproject/galaxy) and clone it to your local machine.
-
-## Step 2: Create a Branch for Your Visualization
-
-Create a new branch specifically for your visualization:
-
-```bash
-git branch MY_VISUALIZATION
-git checkout MY_VISUALIZATION
-```
-
-## Step 3: Set Up Your Visualization Directory
-
-1. Create a directory for your visualization in the Galaxy repository at `config/plugins/visualizations/MY_VISUALIZATION`.
-
-2. Copy the XML file (`MY_VISUALIZATION.xml`) generated during development into a subdirectory named config:
-
-```plaintext
-config/plugins/visualizations/MY_VISUALIZATION/config/MY_VISUALIZATION.xml
-```
-
-## Step 4: Verify XML Requirements and Data Sources
-
-1. Ensure the `requirements` section in your XML file specifies the correct `npm` package name and version.
-2. Confirm the `data_sources` section in the XML lists the appropriate datatype extension(s) compatible with your visualization.
-
-## Step 5: Add an Optional Logo
-
-Optionally, include a logo file (logo.png) for your visualization by placing it in a static subdirectory:
-
-```plaintext
-config/plugins/visualizations/MY_VISUALIZATION/static/logo.png
-```
-
-## Step 6: Update the Gulpfile
-
-In the Galaxy root directory, open `client/gulpfile.js` and add the name of your visualization to the `INSTALL_PLUGIN_BUILD_IDS` list.
-
-## Step 7: Run Galaxy and Test Your Visualization
-
-1. **Start Galaxy** by running the following command:
-
-    ```bash
-    ./run.sh
-    ```
-
-2. **Upload a test file**  to your Galaxy history, ensuring it has the correct data type for your visualization.
-
-3. **Open your visualization** from the Activity Bar to view and test your uploaded dataset.
-
-## :tada: Thank you for your contribution!
-
-Following these steps will prepare your visualization for integration with Galaxy. Once everything is set up, you can submit your pull request.

package/docs/content/installation.md

@@ -1,42 +0,0 @@
-# Getting Started
-
-Follow these steps to start developing a new visualization for Galaxy.
-
-## 1. Set Up Your Repository
-
-1. Sign in to your [GitHub](https://github.com) account.
-2. Go to the [Galaxy Charts Starter](https://github.com/guerler/galaxy-charts-starter) repository.
-3. Click on **Use this template** and select **Create a new repository**.
-4. Name your new repository (e.g., `MY_VISUALIZATION`), then complete the setup by clicking **Create repository**.
-
-## 2. Clone Your Repository
-
-Open a terminal window and clone your newly created repository:
-
-```bash
-git clone https://github.com/USERNAME/MY_VISUALIZATION
-```
-Replace USERNAME with your GitHub username and MY_VISUALIZATION with your repository name.
-
-## 3. Initialize Your Visualization Project
-
-Navigate to your project directory and set up the environment:
-```bash
-cd MY_VISUALIZATION
-npm install
-npm run dev
-```
-
-## 4. Next Steps
-
-Open a web browser and navigate to the localhost URL displayed in your terminal (typically in the format `http://localhost:PORT`):
-
-<div class="flex justify-around items-center p-1">
-  <img class="border-2 rounded border-gray-100" src="/galaxy-charts-starter.jpg" alt="starter" width="80%">
-</div>
-
-Congratulations! Your Galaxy visualization repository is set up and ready for development. Follow the instructions on the splash screen and refer to these docs as you build your custom visualization.
-
-When you’re ready to publish, refer to the [Deploy to Galaxy](deploy-plugin.html) section to share your visualization with the Galaxy community.
-
-Thank you for your contribution!

package/docs/content/introduction.md

@@ -1,45 +0,0 @@
----
-outline: deep
----
-
-# What is Galaxy Charts?
-
-Galaxy Charts is a powerful visualization plugin framework built specifically for the Galaxy platform. Designed with modern web development tools, Galaxy Charts uses the following technologies to create a flexible and dynamic environment for developing visualizations:
-
-<div class="grid grid-cols-5 gap-12 text-center my-10">
-    <div class="flex flex-col items-center">
-        <img src="/vite.svg" alt="vite" class="w-16 h-16">
-        <span class="font-bold mt-2">Vite</span>
-    </div>
-    <div class="flex flex-col items-center">
-        <img src="/vitest.svg" alt="vitest" class="w-16 h-16">
-        <span class="font-bold mt-2">Vitest</span>
-    </div>
-    <div class="flex flex-col items-center">
-        <img src="/vue.svg" alt="vue" class="w-16 h-16">
-        <span class="font-bold mt-2">Vue 3</span>
-    </div>
-    <div class="flex flex-col items-center">
-        <img src="/naive-ui.svg" alt="naive-ui" class="w-16 h-16">
-        <span class="font-bold mt-2">Naive UI</span>
-    </div>
-    <div class="flex flex-col items-center">
-        <img src="/tailwind.svg" alt="tailwind" class="w-16 h-16">
-        <span class="font-bold mt-2">Tailwind CSS</span>
-    </div>
-</div>
-
-With Galaxy Charts, you can develop visualizations locally in Vue, taking advantage of advanced tooling like hot-reloading for instant feedback, efficient bundling for optimized performance, and other modern features. This setup enables a streamlined and responsive development experience.
-
-<div class="flex justify-around items-center p-1">
-  <img class="border-2 rounded border-gray-100" src="/galaxy-charts-demo.gif" alt="demo" width="80%">
-</div>
-
-### Key Features
-
-- **Local and Remote Data Access**: Load data locally or connect to a remote Galaxy instance to access data providers and resources through the Galaxy API, giving you flexibility in sourcing data.
-- **Automated Testing**: Test your visualization thoroughly in the local environment, ensuring it’s fully functional and bug-free before deploying it to Galaxy.
-- **Enhanced Development Workflow**: By integrating state-of-the-art development tools, Galaxy Charts provides a smooth and efficient workflow that significantly reduces the time and effort needed to build complex visualizations.
-
-In short, Galaxy Charts transforms and simplifies the process of developing and deploying visualizations on the Galaxy platform, offering an unparalleled experience for developers working in the Galaxy ecosystem.
-

package/docs/content/vue-introduction.md

@@ -1,38 +0,0 @@
-# Vue Component
-
-The `GalaxyCharts` core component is used to embed a JavaScript-based visualization by placing the visualization code within its `#default` slot. This component parses static `config` options and the XML visualization wrapper to render both the viewport and input form.
-
-```vue
-<script setup>
-import { GalaxyCharts } from "galaxy-charts";
-
-// Configuration of your visualization
-const config = {
-    dataset_id: "MY_DATASET_ID",
-    dataset_url: "MY_DATASET_URL",
-    settings: {},
-};
-
-// XML wrapper of your visualization
-const xml = "MY_VISUALIZATION.xml";
-</script>
-
-<template>
-    <GalaxyCharts :config="config" :xml="xml">
-        <template #default="{ datasetId, datasetUrl, root, settings, specs, tracks }">
-            <!-- Place your plugin code here! -->
-        </template>
-    </GalaxyCharts>
-</template>
-```
-
-## Overview of Slot Values
-
-| Variable | Description |
-|----------|-------------|
-|**datasetId**| The ID of the main dataset to be visualized. Every visualization requires a primary dataset, although additional datasets can be added later if needed.|
-|**datasetUrl**| The URL of the dataset to be visualized. The entire dataset may be requested for visualization, or only parts/metadata may be retrieved via the Galaxy API.|
-|**root**| The proxy route to the Galaxy server (default is '/').|
-|**settings**| Configuration settings specific to the visualization, as declared in the XML wrapper.|
-|**specs**| Static specification values defined in the XML wrapper.|
-|**tracks**| Track configuration values for the visualization, as specified in the XML wrapper.|