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
This commit is contained in:
Danny Brown authored and GitHub committed 2019-08-13 15:36:46 -04:00
1 parent cac911f08e
commit 08ff214ea6
919 files changed
+45652 -52097

No files matched your search

@@ -0,0 +1,39 @@
import { redux } from "@ohif/core";
import store from "./../../store";
const { setViewportActive } = redux.actions;
const actions = {
updateViewportDisplaySet: ({ direction }) => {
// TODO
// console.warn('updateDisplaySet: ', direction);
},
updateActiveViewport: ({ viewports, direction }) => {
const { viewportSpecificData, activeViewportIndex } = viewports;
const maxIndex = Object.keys(viewportSpecificData).length - 1;
let newIndex = activeViewportIndex + direction;
newIndex = newIndex > maxIndex ? 0 : newIndex;
newIndex = newIndex < 0 ? maxIndex : newIndex;
store.dispatch(setViewportActive(newIndex));
}
};
const definitions = {
// Next/Previous active viewport
incrementActiveViewport: {
commandFn: actions.updateActiveViewport,
storeContexts: ["viewports"],
options: { direction: 1 }
},
decrementActiveViewport: {
commandFn: actions.updateActiveViewport,
storeContexts: ["viewports"],
options: { direction: -1 }
}
};
export default {
definitions,
defaultContext: "VIEWER"
};
@@ -0,0 +1,8 @@
import commandsModule from './commandsModule.js';
export default {
id: 'generic-viewer-commands',
getCommandsModule() {
return commandsModule;
},
};
@@ -0,0 +1,356 @@
import { connect } from 'react-redux';
import { MeasurementTable } from '@ohif/ui';
import OHIF from '@ohif/core';
import moment from 'moment';
import cornerstone from 'cornerstone-core';
//
import jumpToRowItem from './jumpToRowItem.js';
import getMeasurementLocationCallback from './../../lib/getMeasurementLocationCallback';
const { setViewportSpecificData } = OHIF.redux.actions;
const { MeasurementApi } = OHIF.measurements;
function groupBy(list, props) {
return list.reduce((a, b) => {
(a[b[props]] = a[b[props]] || []).push(b);
return a;
}, {});
}
function getAllTools() {
const config = OHIF.measurements.MeasurementApi.getConfiguration();
let tools = [];
config.measurementTools.forEach(
toolGroup => (tools = tools.concat(toolGroup.childTools))
);
return tools;
}
function getMeasurementText(measurementData) {
const { location, description } = measurementData;
let text = '...';
if (location) {
text = location;
if (description) {
text += `(${description})`;
}
}
return text;
}
function getDataForEachMeasurementNumber(
measurementNumberList,
timepoints,
displayFunction
) {
const data = [];
// on each measurement number we should get each measurement data by available timepoint
measurementNumberList.forEach(measurement => {
timepoints.forEach(timepoint => {
const eachData = {
displayText: '...',
};
if (measurement.timepointId === timepoint.timepointId) {
eachData.displayText = displayFunction(measurement);
}
data.push(eachData);
});
});
return data;
}
function convertMeasurementsToTableData(toolCollections, timepoints) {
const config = OHIF.measurements.MeasurementApi.getConfiguration();
const toolGroups = config.measurementTools;
const tools = getAllTools();
const tableMeasurements = toolGroups.map(toolGroup => {
return {
groupName: toolGroup.name,
groupId: toolGroup.id,
measurements: [],
};
});
Object.keys(toolCollections).forEach(toolId => {
const toolMeasurements = toolCollections[toolId];
const tool = tools.find(tool => tool.id === toolId);
const { displayFunction } = tool.options.measurementTable;
// Group by measurementNumber so we can display then all in the same line
const groupedMeasurements = groupBy(toolMeasurements, 'measurementNumber');
Object.keys(groupedMeasurements).forEach(groupedMeasurementsIndex => {
const measurementNumberList =
groupedMeasurements[groupedMeasurementsIndex];
const measurementData = measurementNumberList[0];
const {
measurementNumber,
lesionNamingNumber,
toolType,
} = measurementData;
const measurementId = measurementData._id;
//check if all measurements with same measurementNumber will have same LABEL
const tableMeasurement = {
itemNumber: lesionNamingNumber,
label: getMeasurementText(measurementData),
measurementId,
measurementNumber,
lesionNamingNumber,
toolType,
hasWarnings: false, //TODO
warningTitle: '', //TODO
isSplitLesion: false, //TODO
warningList: [], //TODO
data: getDataForEachMeasurementNumber(
measurementNumberList,
timepoints,
displayFunction
),
};
// find the group object for the tool
const toolGroupMeasurements = tableMeasurements.find(group => {
return group.groupId === tool.toolGroup;
});
// inject the new measurement for this measurementNumer
toolGroupMeasurements.measurements.push(tableMeasurement);
});
});
// Sort measurements by lesion naming number
tableMeasurements.forEach(tm => {
tm.measurements.sort((m1, m2) =>
m1.lesionNamingNumber > m2.lesionNamingNumber ? 1 : -1
);
});
return tableMeasurements;
}
function convertTimepointsToTableData(timepoints) {
if (!timepoints || !timepoints.length) {
return [];
}
return [
{
label: 'Study date:',
key: 'StudyDate',
date: moment(timepoints[0].latestDate).format('DD-MMM-YY'),
},
];
}
const mapStateToProps = state => {
const { timepoints, measurements } = state.timepointManager;
return {
timepoints: convertTimepointsToTableData(timepoints),
measurementCollection: convertMeasurementsToTableData(
measurements,
timepoints
),
timepointManager: state.timepointManager,
viewports: state.viewports,
};
};
const mapDispatchToProps = dispatch => {
return {
dispatchRelabel: (event, measurementData, viewportsState) => {
const activeViewportIndex =
(viewportsState && viewportsState.activeViewportIndex) || 0;
const enabledElements = cornerstone.getEnabledElements();
if (!enabledElements || enabledElements.length <= activeViewportIndex) {
OHIF.log.error('Failed to find the enabled element');
return;
}
const { element } = enabledElements[activeViewportIndex];
const eventData = {
event: {
clientX: event.clientX,
clientY: event.clientY,
},
element,
};
const { toolType, measurementId } = measurementData;
const tool = MeasurementApi.Instance.tools[toolType].find(measurement => {
return measurement._id === measurementId;
});
const options = {
skipAddLabelButton: true,
editLocation: true,
};
// Clone the tool not to set empty location initially
const toolForLocation = Object.assign({}, tool, { location: null });
getMeasurementLocationCallback(eventData, toolForLocation, options);
},
dispatchEditDescription: (event, measurementData, viewportsState) => {
const activeViewportIndex =
(viewportsState && viewportsState.activeViewportIndex) || 0;
const enabledElements = cornerstone.getEnabledElements();
if (!enabledElements || enabledElements.length <= activeViewportIndex) {
OHIF.log.error('Failed to find the enabled element');
return;
}
const { element } = enabledElements[activeViewportIndex];
const eventData = {
event: {
clientX: event.clientX,
clientY: event.clientY,
},
element,
};
const { toolType, measurementId } = measurementData;
const tool = MeasurementApi.Instance.tools[toolType].find(measurement => {
return measurement._id === measurementId;
});
const options = {
editDescriptionOnDialog: true,
};
getMeasurementLocationCallback(eventData, tool, options);
},
dispatchJumpToRowItem: (
measurementData,
viewportsState,
timepointManagerState,
options
) => {
const actionData = jumpToRowItem(
measurementData,
viewportsState,
timepointManagerState,
dispatch,
options
);
actionData.viewportSpecificData.forEach(viewportSpecificData => {
const { viewportIndex, displaySet } = viewportSpecificData;
dispatch(setViewportSpecificData(viewportIndex, displaySet));
});
const { toolType, measurementNumber } = measurementData;
const measurementApi = MeasurementApi.Instance;
Object.keys(measurementApi.tools).forEach(toolType => {
const measurements = measurementApi.tools[toolType];
measurements.forEach(measurement => {
measurement.active = false;
});
});
const measurementsToActive = measurementApi.tools[toolType].filter(
measurement => {
return measurement.measurementNumber === measurementNumber;
}
);
measurementsToActive.forEach(measurementToActive => {
measurementToActive.active = true;
});
measurementApi.syncMeasurementsAndToolData();
cornerstone.getEnabledElements().forEach(enabledElement => {
cornerstone.updateImage(enabledElement.element);
});
// Needs to update viewports.layout state to set layout
//const layout = actionData.layout;
//dispatch(setLayout(layout))
// Needs to update viewports.activeViewportIndex to the first updated viewport
//const viewportIndex = actionData.viewportIndex;
//dispatch(setViewportActive(viewportIndex));
// Needs to update timepointsManager.measurements state to set active measurementId
// TODO: Not yet implemented
//dispatch(setActiveMeasurement(measurementData.measurementId))
// (later): Needs to set some property on state.extensions.cornerstone to synchronize viewport scrolling
},
};
};
const mergeProps = (propsFromState, propsFromDispatch, ownProps) => {
return {
timepoints: propsFromState.timepoints,
measurementCollection: propsFromState.measurementCollection,
selectedMeasurementNumber: ownProps.selectedMeasurementNumber,
...propsFromDispatch,
onItemClick: (event, measurementData) => {
// TODO: Add timepointId to .data for measurementData?
// TODO: Tooltype should be on the level below? This should
// provide the entire row item?
const viewportsState = propsFromState.viewports;
const timepointManagerState = propsFromState.timepointManager;
// TODO: invertViewportTimepointsOrder should be stored in / read from user preferences
// TODO: childToolKey should come from the measurement table when it supports child tools
const options = {
invertViewportTimepointsOrder: false,
childToolKey: null,
};
propsFromDispatch.dispatchJumpToRowItem(
measurementData,
viewportsState,
timepointManagerState,
options
);
},
onRelabelClick: (event, measurementData) => {
const viewportsState = propsFromState.viewports;
propsFromDispatch.dispatchRelabel(event, measurementData, viewportsState);
},
onEditDescriptionClick: (event, measurementData) => {
const viewportsState = propsFromState.viewports;
propsFromDispatch.dispatchEditDescription(
event,
measurementData,
viewportsState
);
},
onDeleteClick: (event, measurementData) => {
const { MeasurementHandlers } = OHIF.measurements;
MeasurementHandlers.onRemoved({
detail: {
toolType: measurementData.toolType,
measurementData: {
_id: measurementData.measurementId,
lesionNamingNumber: measurementData.lesionNamingNumber,
measurementNumber: measurementData.measurementNumber,
},
},
});
},
};
};
const ConnectedMeasurementTable = connect(
mapStateToProps,
mapDispatchToProps,
mergeProps
)(MeasurementTable);
export default ConnectedMeasurementTable;
@@ -0,0 +1,23 @@
import ConnectedMeasurementTable from './ConnectedMeasurementTable.js';
export default {
id: 'measurements-table',
getPanelModule() {
return {
menuOptions: [
{
icon: 'list',
label: 'Measurements',
target: 'measurement-panel',
},
],
components: [
{
id: 'measurement-panel',
component: ConnectedMeasurementTable,
},
],
defaultContext: ['VIEWER'],
};
},
};
@@ -0,0 +1,111 @@
import { measurements, utils } from "@ohif/core";
const { MeasurementApi } = measurements;
const { studyMetadataManager } = utils;
// TODO: Move this function to OHIF itself so we can use it on the OHIF measurment table (when it is finished)
/**
* Activates a set of measurements
*
* @param measurementData
* @param viewportsState
* @param timepointManagerState
* @param options
*/
export default function jumpToRowItem(
measurementData,
viewportsState,
timepointManagerState,
options = { invertViewportTimepointsOrder: false, childToolKey: null }
) {
const numViewports = viewportsState.layout.viewports.length;
const numTimepoints = timepointManagerState.timepoints.length;
const { measurements, timepoints } = timepointManagerState;
const numViewportsToUpdate = Math.min(numTimepoints, numViewports);
const { toolType, measurementNumber } = measurementData;
if (options.invertViewportTimepointsOrder) {
timepoints.reverse();
}
const measurementsForToolGroup = measurements[toolType];
// Retrieve the measurements data
const measurementsToJumpTo = [];
for (let i = 0; i < numViewportsToUpdate; i++) {
const { timepointId } = timepoints[i];
const dataAtThisTimepoint = measurementsForToolGroup.find(entry => {
return (
entry.timepointId === timepointId &&
entry.measurementNumber === measurementNumber
);
});
if (!dataAtThisTimepoint) {
measurementsToJumpTo.push(null);
continue;
}
let measurement = dataAtThisTimepoint;
const { tool } = MeasurementApi.getToolConfiguration(toolType);
if (options.childToolKey) {
measurement = dataAtThisTimepoint[options.childToolKey];
} else if (Array.isArray(tool.childTools)) {
const key = tool.childTools.find(key => !!dataAtThisTimepoint[key]);
measurement = dataAtThisTimepoint[key];
}
measurementsToJumpTo.push(measurement);
}
// TODO: Add a single viewports state action which allows
// - viewportData to be set
// - layout to be set
// - activeViewport to be set
// Needs to update viewports.viewportData state to set image set data
const displaySetContainsSopInstance = (displaySet, sopInstanceUid) =>
displaySet.images.find(
image => image.getSOPInstanceUID() === sopInstanceUid
);
const viewportSpecificData = [];
measurementsToJumpTo.forEach((data, viewportIndex) => {
// Skip if there is no measurement to jump
if (!data) {
return;
}
const study = studyMetadataManager.get(data.studyInstanceUid);
if (!study) {
throw new Error("Study not found.");
}
const displaySet = study.findDisplaySet(displaySet => {
return displaySetContainsSopInstance(displaySet, data.sopInstanceUid);
});
if (!displaySet) {
throw new Error("Display set not found.");
}
displaySet.sopInstanceUid = data.sopInstanceUid;
if (data.frameIndex) {
displaySet.frameIndex = data.frameIndex;
}
viewportSpecificData.push({
viewportIndex,
displaySet
});
});
return {
viewportSpecificData,
layout: [] // TODO: if we need to change layout, we should return this here
};
}
@@ -0,0 +1,4 @@
import GenericViewerCommands from './GenericViewerCommands/index.js';
import MeasurementsPanel from './MeasurementsPanel/index.js';
export { GenericViewerCommands, MeasurementsPanel };