Chore/kill yalc with fire (#629)

* init * more shifting * Move @babel dependencies up to workspace root * Begin updating dependent libraries to use sync'd webpack builds w/ watches * Commit changes before a long weekend * Split packages into platform and extensions * Consolidate how/where we specify file/module type entrypoints * Make it possible to pass in extensions as App props * Resolve viewer's modules * Target for UMD bundle * Add Webpack Stylus loader * Provide WebPack build options for microscopy, vtk, and ui * Better entrypoint for extensions * Push changes up to switch PCs * Fix ESM symlink build for Viewers * Shift docs to root * Specify additional lerna config props * Begin providing basic readme info * Rename example extension folder * Shift links to bottom of doc * First attempt at a netlify deploy preview * Attempt to fix deploy preview build * push workspace enabled to initial command; remove second yarn install; use npx to call gitbook cli commands * Try to use global gitbook-cli * Export node_modules path * More agressive with modifying PATH * Follow deploy log output advice * try again to set bin path * Try swapping bash with a new shell * Try bash -l instead of exec bash * Annd let's try again * and again * We may have figured it out johnny, boy * We need to pull cornerstone-wado-image-loader files from hoisted node_modules * Attempt to fix ticks/escapes * Change copy syntax; try running tests on viewers from root for circleci * Lower version to match circleci image * Try alternative jest-canvas-mock location and version file syntax * Run version command instead of calling node directly * Try alternative jest transform * Set path and enable workspaces * Add codecov flags * Use cpx so our copying finishes? * Get all platform unit tests to run * Run and report individually and in parallel * Try once relying on codecov yaml to split w/ flags * Add projects to split by flags * Generate separate reports * Trigger codecov after everything has finished running; these may not support flags * Use recommended flags from issue comments for codecov * Fix typo * Remove clear flag * Shift back to calling codecov from root * Generate example for codecov issue * Try fixing paths * Simplify * Try using codecov orb * Bump circleci version * Upload core and viewer * Use full string paths * Remove individual codecov calls * Fix dir * Combine files before upload * Escape anchors * tryfix syntax * Escape string literal * Combine lines to reduce path * long paths * Use home alias * Fix filename * Try to see the contents of our cat'd file * Also upload `core` * Try running with aliased folder * Fix path; split PR and Merge unit tests into separate jobs * Set default threshold * Fix typo * Changing to scoped package names * Adding note * Catch more updates * chore(release): publish %s [skip ci] - @ohif/extension-cornerstone@0.0.39-alpha.0 - @ohif/extension-dicom-html@0.0.4-alpha.0 - @ohif/extension-dicom-microscopy@0.0.9-alpha.0 - @ohif/extension-dicom-pdf@0.0.8-alpha.0 - @ohif/extension-vtk@0.1.4-alpha.0 - @ohif/core@0.11.1-alpha.0 - @ohif/i18n@0.2.3-alpha.0 - @ohif/ui@0.2.18-alpha.0 - @ohif/viewer@0.0.22-alpha.0 * Clean up primary readme * Support for dev and dev:* commands * Shift build command; satisfy default PWA build * Remove old scripts * Clean up UI to set webpack scripts * Tidy up project links * Clean duplicate code in UI project * Update UI project's docs * Clean up ui and i18n config * Reduce duplicate code in `@ohif/core` * Fix @ohif/ui versions * bump @ohif/core versions * Redux testkit dep * Remove unused/duplicate config files for projects/packages * ohif-core --> @ohif/core * Safer publish command * chore(release): publish %s [skip ci] - @ohif/extension-cornerstone@0.0.39-alpha.1 - @ohif/extension-dicom-html@0.0.4-alpha.1 - @ohif/extension-dicom-microscopy@0.0.9-alpha.1 - @ohif/extension-dicom-pdf@0.0.8-alpha.1 - @ohif/extension-vtk@0.1.4-alpha.1 - @ohif/core@0.11.1-alpha.1 - @ohif/i18n@0.2.3-alpha.1 - @ohif/ui@0.2.18-alpha.1 - @ohif/viewer@0.0.22-alpha.1 * test version bump * Add global prettier config * chore(release): publish %s [skip ci] - @ohif/viewer@0.0.22-alpha.2 * test lerna publish * Update package.jsons * Fix build scripts * catch changes * chore(release): publish %s [skip ci] - @ohif/extension-cornerstone@0.0.39-alpha.2 - @ohif/extension-dicom-html@0.0.4-alpha.2 - @ohif/extension-dicom-microscopy@0.0.9-alpha.2 - @ohif/extension-dicom-pdf@0.0.8-alpha.2 - @ohif/extension-vtk@0.1.4-alpha.2 - @ohif/core@0.11.1-alpha.2 - @ohif/i18n@0.2.3-alpha.2 - @ohif/ui@0.2.18-alpha.2 - @ohif/viewer@0.0.22-alpha.3 * fix eslint issues caused by eslint 6 and our react-app config * Publish with canary tag * chore(release): publish %s [skip ci] - @ohif/extension-cornerstone@0.0.39-alpha.3 - @ohif/extension-dicom-html@0.0.4-alpha.3 - @ohif/extension-dicom-microscopy@0.0.9-alpha.3 - @ohif/extension-dicom-pdf@0.0.8-alpha.3 - @ohif/extension-vtk@0.1.4-alpha.3 - @ohif/core@0.11.1-alpha.3 - @ohif/i18n@0.2.3-alpha.3 - @ohif/ui@0.2.18-alpha.3 - @ohif/viewer@0.0.22-alpha.4 * chore(release): publish %s [skip ci] - @ohif/extension-cornerstone@0.0.39-alpha.4 - @ohif/extension-dicom-html@0.0.4-alpha.4 - @ohif/extension-dicom-microscopy@0.0.9-alpha.4 - @ohif/extension-dicom-pdf@0.0.8-alpha.4 - @ohif/extension-vtk@0.1.4-alpha.4 - @ohif/core@0.11.1-alpha.4 - @ohif/i18n@0.2.3-alpha.4 - @ohif/ui@0.2.18-alpha.4 - @ohif/viewer@0.0.22-alpha.5 * Simplify build * chore(release): publish %s [skip ci] - @ohif/extension-cornerstone@0.0.39-alpha.5 - @ohif/extension-dicom-html@0.0.4-alpha.5 - @ohif/extension-dicom-microscopy@0.0.9-alpha.5 - @ohif/extension-dicom-pdf@0.0.8-alpha.5 - @ohif/extension-vtk@0.1.4-alpha.5 - @ohif/core@0.11.1-alpha.5 - @ohif/i18n@0.2.3-alpha.5 - @ohif/ui@0.2.18-alpha.5 - @ohif/viewer@0.0.22-alpha.6 * chore(release): publish %s [skip ci] - @ohif/extension-cornerstone@0.0.39-alpha.6 - @ohif/extension-dicom-html@0.0.4-alpha.6 - @ohif/extension-dicom-microscopy@0.0.9-alpha.6 - @ohif/extension-dicom-pdf@0.0.8-alpha.6 - @ohif/extension-vtk@0.1.4-alpha.6 - @ohif/core@0.11.1-alpha.6 - @ohif/i18n@0.2.3-alpha.6 - @ohif/ui@0.2.18-alpha.6 - @ohif/viewer@0.0.22-alpha.7 * Split version and publish * chore(release): publish %s [skip ci] - @ohif/extension-cornerstone@0.0.39-alpha.7 - @ohif/extension-dicom-html@0.0.4-alpha.7 - @ohif/extension-dicom-microscopy@0.0.9-alpha.7 - @ohif/extension-dicom-pdf@0.0.8-alpha.7 - @ohif/extension-vtk@0.1.4-alpha.7 - @ohif/core@0.11.1-alpha.7 - @ohif/i18n@0.2.3-alpha.7 - @ohif/ui@0.2.18-alpha.7 - @ohif/viewer@0.0.22-alpha.8 * Try simplify netlify build * react-viewerbase --> @ohif/ui * add test for stylus loader * Try new way to specify publish path * Use an output folder that won't be ignored * Try move command * fiddle with paths * Dig for some information * Make sure we're in root for our commands * Remove discovery * Setup script-tag example * Fix typo * Move config folder * Update cornerstone extension to use shared/root webpack configs * capture changes * Update extension webpack configs * Don't check in docz output * Fix babel runtime resolution issue * Simplify ui build steps * Push in progress * Shift directories * Get viewer dev path to work * Fix viewer commonjs build * Fix build pwa config for viewers * Make sure our package specific command can be called from root * Update notes * Fix imports and misc. merge notes * Bump wado-image-loader version * Switch up commands to remove webworkers copy * Fix CI config * Fix more broken package references * Add react-dropzone * Persist so e2e test can use * Fix lockfile * Use cypress orb to simplify CI * Fix config * Try again * Install yarn latest for orb * Install yarn a different way * Wait on correct port * Run tests in viewer project * Fix cypress config * Make Cypress happier - use default location * Simplify e2e testing * Capture UI changes since fork * Catch core up * Grab latest deps after merge * Fix broken import * Make sure cornerstone-wado-image-loader resolves to 3+ * Note regarding orbs * Fix refresh on 404 routes * Fix odd error for cornerstone-wado-image-loader * Different target for UMD * Simplify dev script * Try to get fancy with netlify output * Let's do it again * Try to fix measurementTools issue * See if we can get our lerna magic to work on merge to monorepo branch
2019-08-13 15:36:46 -04:00
1 parent cac911f08e
commit 08ff214ea6
@@ -0,0 +1,16 @@
+const path = require('path');
+const merge = require('webpack-merge');
+const webpackCommon = require('./../../../.webpack/webpack.common.js');
+
+//
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+module.exports = (env, argv) => {
+  const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
+
+  return merge(commonConfig, {
+    // https://webpack.js.org/configuration/mode/#mode-development
+    mode: 'development',
+  });
+};
@@ -0,0 +1,39 @@
+const merge = require('webpack-merge');
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.common.js');
+const pkg = require('./../package.json');
+
+const ROOT_DIR = path.join(__dirname, './..');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+module.exports = (env, argv) => {
+  const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
+
+  return merge(commonConfig, {
+    // https://webpack.js.org/configuration/mode/#mode-production
+    mode: 'production',
+    devtool: 'source-map',
+    stats: {
+      colors: true,
+      hash: true,
+      timings: true,
+      assets: true,
+      chunks: false,
+      chunkModules: false,
+      modules: false,
+      children: false,
+      warnings: true,
+    },
+    optimization: {
+      minimize: true,
+      sideEffects: true,
+    },
+    output: {
+      path: ROOT_DIR,
+      library: 'ohifExtensionDicomMicroscopy',
+      libraryTarget: 'umd',
+      filename: pkg.main,
+    },
+  });
+};
@@ -0,0 +1,61 @@
+# Change Log
+
+All notable changes to this project will be documented in this file. See
+[Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+## [0.0.9-alpha.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.0.9-alpha.6...@ohif/extension-dicom-microscopy@0.0.9-alpha.7) (2019-08-08)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+# Change Log
+
+All notable changes to this project will be documented in this file. See
+[Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+## [0.0.9-alpha.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.0.9-alpha.5...@ohif/extension-dicom-microscopy@0.0.9-alpha.6) (2019-08-08)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+# Change Log
+
+All notable changes to this project will be documented in this file. See
+[Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+## [0.0.9-alpha.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.0.9-alpha.4...@ohif/extension-dicom-microscopy@0.0.9-alpha.5) (2019-08-08)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+# Change Log
+
+All notable changes to this project will be documented in this file. See
+[Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+## [0.0.9-alpha.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.0.9-alpha.3...@ohif/extension-dicom-microscopy@0.0.9-alpha.4) (2019-08-08)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+# Change Log
+
+All notable changes to this project will be documented in this file. See
+[Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+## [0.0.9-alpha.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.0.9-alpha.2...@ohif/extension-dicom-microscopy@0.0.9-alpha.3) (2019-08-08)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+# Change Log
+
+All notable changes to this project will be documented in this file. See
+[Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+## [0.0.9-alpha.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.0.9-alpha.1...@ohif/extension-dicom-microscopy@0.0.9-alpha.2) (2019-08-07)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+## [0.0.9-alpha.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.0.9-alpha.0...@ohif/extension-dicom-microscopy@0.0.9-alpha.1) (2019-08-07)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+## 0.0.9-alpha.0 (2019-08-05)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Open Health Imaging Foundation
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
@@ -0,0 +1,34 @@
+# @ohif/extension-dicom-microscopy
+
+![npm (scoped)](https://img.shields.io/npm/v/@ohif/extension-dicom-microscopy.svg?style=flat-square)
+
+<!-- TODO: Simple image or GIF? -->
+
+#### Index
+
+Extension Id: `microscopy`
+
+- [SopClassHandler Module](#sopclasshandler-module)
+- [Viewport Module](#viewport-module)
+
+## SopClassHandler Module
+
+..
+
+## Viewport Module
+
+...
+
+## Resources
+
+### Repositories
+
+...
+
+<!--
+  Links
+  -->
+
+<!-- prettier-ignore-start -->
+
+<!-- prettier-ignore-end -->
@@ -0,0 +1,39 @@
+{
+  "name": "@ohif/extension-dicom-microscopy",
+  "version": "0.0.9-alpha.7",
+  "description": "OHIF extension for Dicom Microscopy",
+  "author": "OHIF",
+  "license": "MIT",
+  "repository": "OHIF/Viewers",
+  "main": "dist/index.umd.js",
+  "module": "src/index.js",
+  "publishConfig": {
+    "access": "public"
+  },
+  "files": [
+    "dist",
+    "README.md"
+  ],
+  "engines": {
+    "node": ">=8",
+    "npm": ">=5"
+  },
+  "scripts": {
+    "dev": "webpack --config .webpack/webpack.dev.js --watch --debug --output-pathinfo",
+    "dev:dicom-microscopy": "yarn run dev",
+    "build": "webpack --config .webpack/webpack.prod.js",
+    "build:package": "yarn run build",
+    "prepublishOnly": "yarn run build",
+    "start": "yarn run dev"
+  },
+  "peerDependencies": {
+    "@ohif/core": "^0.11.1-alpha.0",
+    "react": "^15.0.0 || ^16.0.0",
+    "react-dom": "^15.0.0 || ^16.0.0"
+  },
+  "dependencies": {
+    "@babel/runtime": "^7.5.5",
+    "classnames": "^2.2.6",
+    "dicom-microscopy-viewer": "^0.4.3"
+  }
+}
@@ -0,0 +1,29 @@
+import OHIF from '@ohif/core';
+
+const { utils } = OHIF;
+
+const SOP_CLASS_UIDS = {
+  VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE: '1.2.840.10008.5.1.4.1.1.77.1.6',
+};
+
+const DicomMicroscopySopClassHandler = {
+  id: 'DicomMicroscopySopClassHandlerPlugin',
+  sopClassUids: [SOP_CLASS_UIDS.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE],
+  getDisplaySetFromSeries(series, study, dicomWebClient) {
+    const instance = series.getFirstInstance();
+
+    // Note: We are passing the dicomweb client into each viewport!
+
+    return {
+      plugin: 'microscopy',
+      modality: 'SM',
+      displaySetInstanceUid: utils.guid(),
+      dicomWebClient,
+      sopInstanceUid: instance.getSOPInstanceUID(),
+      seriesInstanceUid: series.getSeriesInstanceUID(),
+      studyInstanceUid: study.getStudyInstanceUID(),
+    };
+  },
+};
+
+export default DicomMicroscopySopClassHandler;
@@ -0,0 +1,103 @@
+import React, { Component } from 'react';
+import ReactResizeDetector from 'react-resize-detector';
+import { api } from 'dicom-microscopy-viewer';
+import debounce from 'lodash.debounce';
+
+const microscopyViewer = api.VLWholeSlideMicroscopyImageViewer;
+
+class DicomMicroscopyViewport extends Component {
+  state = {
+    error: null,
+  };
+
+  viewer = null;
+
+  constructor(props) {
+    super(props);
+
+    this.container = React.createRef();
+
+    this.debouncedResize = debounce(() => {
+      if (this.viewer) this.viewer.resize();
+    }, 100);
+  }
+
+  // install the microscopy renderer into the web page.
+  // you should only do this once.
+  installOpenLayersRenderer(container, displaySet) {
+    const dicomWebClient = displaySet.dicomWebClient;
+
+    const searchInstanceOptions = {
+      studyInstanceUID: displaySet.studyInstanceUid,
+      seriesInstanceUID: displaySet.seriesInstanceUid,
+    };
+
+    dicomWebClient
+      .searchForInstances(searchInstanceOptions)
+      .then(instances => {
+        const promises = [];
+        for (let i = 0; i < instances.length; i++) {
+          const sopInstanceUID = instances[i]['00080018']['Value'][0];
+          const retrieveInstanceOptions = {
+            studyInstanceUID: displaySet.studyInstanceUid,
+            seriesInstanceUID: displaySet.seriesInstanceUid,
+            sopInstanceUID,
+          };
+
+          const promise = dicomWebClient
+            .retrieveInstanceMetadata(retrieveInstanceOptions)
+            .then(metadata => {
+              const imageType = metadata[0]['00080008']['Value'];
+              if (imageType[2] === 'VOLUME') {
+                return metadata[0];
+              }
+            });
+          promises.push(promise);
+        }
+        return Promise.all(promises);
+      })
+      .then(metadata => {
+        metadata = metadata.filter(m => m);
+
+        this.viewer = new microscopyViewer({
+          client: dicomWebClient,
+          metadata,
+          retrieveRendered: false
+        });
+
+        this.viewer.render({ container });
+      });
+  }
+
+  componentDidMount() {
+    const { displaySet } = this.props.viewportData;
+
+    this.installOpenLayersRenderer(this.container.current, displaySet);
+  }
+
+  render() {
+    const style = { width: '100%', height: '100%' };
+    return (
+      <div className={'DicomMicroscopyViewer'} style={style}>
+        {ReactResizeDetector && (
+          <ReactResizeDetector
+            handleWidth
+            handleHeight
+            onResize={this.onWindowResize}
+          />
+        )}
+        {this.state.error ? (
+          <h2>{JSON.stringify(this.state.error)}</h2>
+        ) : (
+          <div style={style} ref={this.container} />
+        )}
+      </div>
+    );
+  }
+
+  onWindowResize = () => {
+    this.debouncedResize();
+  };
+}
+
+export default DicomMicroscopyViewport;
@@ -0,0 +1,16 @@
+import DicomMicroscopySopClassHandler from './DicomMicroscopySopClassHandler.js';
+import DicomMicroscopyViewport from './DicomMicroscopyViewport.js';
+
+export default {
+  /**
+   * Only required property. Should be a unique value across all extensions.
+   */
+  id: 'microscopy',
+
+  getViewportModule() {
+    return DicomMicroscopyViewport;
+  },
+  getSopClassHandlerModule() {
+    return DicomMicroscopySopClassHandler;
+  },
+};