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chore: Clean up unused files, imports, and work on getting end-to-end tests and unit tests running (#2272)

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Erik Ziegler authored and GitHub committed 2021-03-01 16:52:54 +01:00
1 parent 414ebc6850
commit 0db81b30f3
374 files changed
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extensions/dicom-microscopy/.webpack/webpack.dev.js
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const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
const SRC_DIR = path.join(__dirname, '../src');
const DIST_DIR = path.join(__dirname, '../dist');
module.exports = (env, argv) => {
return webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
};
extensions/dicom-microscopy/.webpack/webpack.prod.js
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const webpack = require('webpack');
const merge = require('webpack-merge');
const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.commonjs.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, {
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: 'OHIFExtDicomMicroscopy',
libraryTarget: 'umd',
libraryExport: 'default',
filename: pkg.main,
},
plugins: [
new webpack.optimize.LimitChunkCountPlugin({
maxChunks: 1
})
]
});
};
extensions/dicom-microscopy/CHANGELOG.md
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# Change Log
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [0.50.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.8...@ohif/extension-dicom-microscopy@0.50.9) (2020-04-02)
**Note:** Version bump only for package @ohif/extension-dicom-microscopy
## [0.50.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.7...@ohif/extension-dicom-microscopy@0.50.8) (2020-03-31)
**Note:** Version bump only for package @ohif/extension-dicom-microscopy
## [0.50.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.6...@ohif/extension-dicom-microscopy@0.50.7) (2020-03-09)
**Note:** Version bump only for package @ohif/extension-dicom-microscopy
## [0.50.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.5...@ohif/extension-dicom-microscopy@0.50.6) (2019-09-26)
### Bug Fixes
* Add some code splitting for PWA build ([#937](https://github.com/OHIF/Viewers/issues/937)) ([8938035](https://github.com/OHIF/Viewers/commit/8938035))
## [0.50.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.4...@ohif/extension-dicom-microscopy@0.50.5) (2019-09-10)
### Bug Fixes
* simplify runtime-extension usage ([ac5dbda](https://github.com/OHIF/Viewers/commit/ac5dbda))
## [0.50.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.3...@ohif/extension-dicom-microscopy@0.50.4) (2019-09-04)
**Note:** Version bump only for package @ohif/extension-dicom-microscopy
## [0.50.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.2...@ohif/extension-dicom-microscopy@0.50.3) (2019-09-04)
### Bug Fixes
* measurementsAPI issue caused by production build ([#842](https://github.com/OHIF/Viewers/issues/842)) ([49d3439](https://github.com/OHIF/Viewers/commit/49d3439))
## [0.50.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.1...@ohif/extension-dicom-microscopy@0.50.2) (2019-09-03)
### Bug Fixes
* **dicom-microscopy:** Update dicom-microscopy-viewer to 0.6.1 to fix Google Cloud usage with WSI images ([#843](https://github.com/OHIF/Viewers/issues/843)) ([dbaf5c5](https://github.com/OHIF/Viewers/commit/dbaf5c5))
## [0.50.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.0-alpha.10...@ohif/extension-dicom-microscopy@0.50.1) (2019-08-14)
**Note:** Version bump only for package @ohif/extension-dicom-microscopy
# [0.50.0-alpha.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.0.9-alpha.9...@ohif/extension-dicom-microscopy@0.50.0-alpha.10) (2019-08-14)
**Note:** Version bump only for package @ohif/extension-dicom-microscopy
## [0.0.9-alpha.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.0.9-alpha.8...@ohif/extension-dicom-microscopy@0.0.9-alpha.9) (2019-08-14)
**Note:** Version bump only for package @ohif/extension-dicom-microscopy
## 0.0.9-alpha.8 (2019-08-14)
**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.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
extensions/dicom-microscopy/LICENSE
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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.
extensions/dicom-microscopy/README.md
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# @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 -->
extensions/dicom-microscopy/package.json
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{
"name": "@ohif/extension-dicom-microscopy",
"version": "0.50.9",
"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": ">=10",
"npm": ">=6",
"yarn": ">=1.16.0"
},
"scripts": {
"dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --debug --output-pathinfo",
"dev:dicom-microscopy": "yarn run dev",
"build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
"build:package": "yarn run build",
"start": "yarn run dev"
},
"peerDependencies": {
"@ohif/core": "^0.50.0",
"react": "^16.11.0",
"react-dom": "^16.11.0"
},
"dependencies": {
"@babel/runtime": "7.7.6",
"classnames": "^2.2.6",
"dicom-microscopy-viewer": "^0.6.1"
}
}
extensions/dicom-microscopy/src/DicomMicroscopySopClassHandler.js
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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;
extensions/dicom-microscopy/src/DicomMicroscopyViewport.js
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import React, { Component } from 'react';
import ReactResizeDetector from 'react-resize-detector';
import debounce from 'lodash.debounce';
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(async metadata => {
metadata = metadata.filter(m => m);
const { api } = await import(
/* webpackChunkName: "dicom-microscopy-viewer" */ 'dicom-microscopy-viewer'
);
const microscopyViewer = api.VLWholeSlideMicroscopyImageViewer;
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;
extensions/dicom-microscopy/src/index.js
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import React from 'react';
import DicomMicroscopySopClassHandler from './DicomMicroscopySopClassHandler.js';
const Component = React.lazy(() => {
return import('./DicomMicroscopyViewport');
});
const DicomMicroscopyViewport = props => {
return (
<React.Suspense fallback={<div>Loading...</div>}>
<Component {...props} />
</React.Suspense>
);
};
export default {
/**
* Only required property. Should be a unique value across all extensions.
*/
id: 'microscopy',
getViewportModule() {
return DicomMicroscopyViewport;
},
getSopClassHandlerModule() {
return DicomMicroscopySopClassHandler;
},
};