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

platform/core/src/utils/updateMetaDataManager.js

@@ -0,0 +1,101 @@
+import { WadoRsMetaDataBuilder } from '../classes/metadata/WadoRsMetaDataBuilder';
+import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
+import getWADORSImageId from './getWADORSImageId';
+
+function getRadiopharmaceuticalInfoMetaData(instance) {
+  const radiopharmaceuticalInfo = instance.radiopharmaceuticalInfo;
+
+  if (instance.modality !== 'PT' || !radiopharmaceuticalInfo) {
+    return;
+  }
+
+  return new WadoRsMetaDataBuilder()
+    .addTag('00181072', radiopharmaceuticalInfo.radiopharmaceuticalStartTime)
+    .addTag('00181074', radiopharmaceuticalInfo.radionuclideTotalDose)
+    .addTag('00181075', radiopharmaceuticalInfo.radionuclideHalfLife)
+    .toJSON();
+}
+
+const getWadoRsInstanceMetaData = (study, series, instance) => {
+  return new WadoRsMetaDataBuilder()
+    .addTag('00080016', instance.sopClassUid)
+    .addTag('00080018', instance.sopInstanceUid)
+    .addTag('00080021', series.seriesDate)
+    .addTag('00080031', series.seriesTime)
+    .addTag('0008103e', series.seriesDescription)
+    .addTag('00080060', series.modality)
+    .addTag('00101010', study.patientAge)
+    .addTag('00101020', study.patientSize)
+    .addTag('00101030', study.patientWeight)
+    .addTag('0020000d', study.studyInstanceUid)
+    .addTag('00081030', study.studyDescription)
+    .addTag('00100010', study.patientName)
+    .addTag('00100020', study.patientId)
+    .addTag('00080020', study.studyDate)
+    .addTag('00080030', study.studyTime)
+    .addTag('00080050', study.accessionNumber)
+    .addTag('00200013', instance.instanceNumber)
+    .addTag('00180050', instance.sliceThickness)
+    .addTag('0020000e', series.seriesInstanceUid)
+    .addTag('00200011', series.seriesNumber)
+    .addTag('00200032', instance.imagePositionPatient, true)
+    .addTag('00200037', instance.imageOrientationPatient, true)
+    .addTag('00200052', instance.frameOfReferenceUID)
+    .addTag('00201041', instance.sliceLocation)
+    .addTag('00280002', instance.samplesPerPixel)
+    .addTag('00280004', instance.photometricInterpretation)
+    .addTag('00280006', instance.planarConfiguration)
+    .addTag('00280010', instance.rows)
+    .addTag('00280011', instance.columns)
+    .addTag('00280030', instance.pixelSpacing, true)
+    .addTag('00280034', instance.pixelAspectRatio, true)
+    .addTag('00280100', instance.bitsAllocated)
+    .addTag('00280101', instance.bitsStored)
+    .addTag('00280102', instance.highBit)
+    .addTag('00280103', instance.pixelRepresentation)
+    .addTag('00280106', instance.smallestPixelValue)
+    .addTag('00280107', instance.largestPixelValue)
+    .addTag('00281050', instance.windowCenter, true)
+    .addTag('00281051', instance.windowWidth, true)
+    .addTag('00281052', instance.rescaleIntercept)
+    .addTag('00281053', instance.rescaleSlope)
+    .addTag('00281054', instance.rescaleType)
+    .addTag('00281101', instance.redPaletteColorLookupTableDescriptor)
+    .addTag('00281102', instance.greenPaletteColorLookupTableDescriptor)
+    .addTag('00281103', instance.bluePaletteColorLookupTableDescriptor)
+    .addTag('00281201', instance.redPaletteColorLookupTableData)
+    .addTag('00281202', instance.greenPaletteColorLookupTableData)
+    .addTag('00281203', instance.bluePaletteColorLookupTableData)
+    .addTag('00540016', getRadiopharmaceuticalInfoMetaData(instance))
+    .toJSON();
+};
+
+export default function updateMetaDataManager(study) {
+  study.seriesList.forEach(series => {
+    series.instances.forEach(instance => {
+      // Cache just images that are going to be loaded via WADO-RS
+      if (
+        instance.imageRendering !== 'wadors' &&
+        instance.thumbnailRendering !== 'wadors'
+      ) {
+        return;
+      }
+
+      const metaData = getWadoRsInstanceMetaData(study, series, instance);
+      const numberOfFrames = instance.numberOfFrames || 1;
+
+      // We can share the same metaData with all frames because it doesn't have
+      // any frame specific data, such as frameNumber, pixelData, offset, etc.
+      // WADO-RS frame number is 1-based
+      for (let frameNumber = 0; frameNumber < numberOfFrames; frameNumber++) {
+        const imageId = getWADORSImageId(instance, frameNumber);
+
+        // TODO Drop dependency on this
+        cornerstoneWADOImageLoader.wadors.metaDataManager.add(
+          imageId,
+          metaData
+        );
+      }
+    });
+  });
+}