feat: Add Static WADO display (#2499)
* Rebased to have just the static view changes * Changes based on the PR * Couple more changes for the PR * Removed an extraneous log * Fix the study worklist display when returning to the page * Added some documentation on the static wado data source setup, and a bounds check change on the Queue test which was failing * PR updates - change the undefined study description to '' and remove the aws deploy * Fixed the e2e tests to actually pass/fail correctly on actual results
This commit is contained in:
Bill Wallace authored and Alireza committed
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@@ -25,10 +25,10 @@ describe('Queue', () => {
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const start = Date.now();
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timer(threshold).then(now => {
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const elapsed = now - start;
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expect(elapsed >= threshold && elapsed < 2 * threshold).toBe(true);
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expect(elapsed >= threshold && elapsed <= 2 * threshold).toBe(true);
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});
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const end = await timer(threshold);
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expect(end - start > 2 * threshold).toBe(true);
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expect(end - start >= 2 * threshold).toBe(true);
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expect(mockedTimeout).toBeCalledTimes(2);
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});
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it('should prevent task execution when queue limit is reached', async () => {
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@@ -189,3 +189,42 @@ below:
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https://github.com/OHIF/Viewers/tree/master/platform/viewer/public/html-templates
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[config-files]:
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https://github.com/OHIF/Viewers/tree/master/platform/viewer/public/config
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## Static Files
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There is a binay DICOM to static file generator, which provides easily served
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binary files. The files are all compressed in order to reduce space signifcantly,
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and are pre-computed for the files required for OHIF, so that the performance
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of serving the files is just the read from disk/write to http stream time, without
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any extra processing time.
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The project for the static wado files is located here:
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[static-wado]: https://github.com/wayfarer3130/static-wado
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It can be compiled with Java and Gradle, and then run against a set of dicom,
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in the example located in /dicom/study1 outputting to /dicomweb, and then a
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server run against that data, like this:
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```
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git clone https://github.com/wayfarer3130/static-wado.git
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cd static-wado
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./gradlew installDist
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StaticWado/build/install/StaticWado/bin/StaticWado -d /dicomweb /dicom/study1
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cd /dicomweb
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npx http-server -p 5000 --cors -g
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```
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There is then a dev environment in the platform/viewer directory which can be run
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against those files, like this:
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```
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cd platform/viewer
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yarn dev:static
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```
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Additional studies can be added to the dicomweb by re-running the StaticWado command.
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It will create a single studies.gz index file (JSON DICOM file, compressed)
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containing an index of all studies created. There is then a small extension
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to OHIF which performs client side indexing.
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The StaticWado command also knows how to deploy a client and dicomweb directory
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to Amazon s3, which can then server files up directly. There is another
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build setup build:aws in the viewer package.json to create such a deployment.
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@@ -76,7 +76,17 @@ function create({
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You can take a look at `dicomweb` data source implementation to get an idea
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`extensions/default/src/DicomWebDataSource/index.js`
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## Static WADO Client
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If the configuration for the data source has the value staticWado set, then it
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is assumed that queries for the studies return a super-set of the studies, as
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it is assumed to be returning a static list. The StaticWadoClient performs the
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search functionality manually, by interpretting the query parameters and then
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applying them to the returned response. This functionality may be useful for
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other types of DICOMweb back ends, where they are capable of performing queries,
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but don't allow for querying certain types of fields. However, that only works
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as long as the size of the studies list isn't too large that client side
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selectiton isn't too expensive.
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## DicomMetadataStore
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In `OHIF-v3` we have a central location for the metadata of studies and they are located
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@@ -1,6 +1,6 @@
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/* CUSTOM OHIF SCROLLBAR */
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.ohif-scrollbar {
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scrollbar-color: #0944b3 transparent;
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scrollbar-color: #3E5967 transparent;
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}
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.ohif-scrollbar::-webkit-scrollbar {
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@@ -14,10 +14,12 @@
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.ohif-scrollbar::-webkit-scrollbar-thumb {
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@apply rounded;
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@apply bg-primary-main;
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background-color: #3e5967;
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}
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.ohif-scrollbar::-webkit-scrollbar-thumb:window-inactive {
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@apply bg-primary-main;
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background-color: #3e5967;
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}
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/* INVISIBLE SCROLLBAR */
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@@ -105,7 +105,7 @@ const StudyBrowser = ({
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})}
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</ButtonGroup>
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</div>
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<div className="flex flex-col flex-1 overflow-auto invisible-scrollbar">
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<div className="flex flex-col flex-1 overflow-auto ohif-scrollbar">
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{getTabContent()}
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</div>
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</React.Fragment>
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@@ -167,7 +167,7 @@ StudyBrowser.propTypes = {
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),
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};
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const noop = () => {};
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const noop = () => { };
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StudyBrowser.defaultProps = {
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onClickTab: noop,
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@@ -1,12 +1,12 @@
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//We are keeping the hardcoded results values for the study list tests
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//this is intended to be running in a controled docker environment with test data.
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describe('OHIF Study List', function() {
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context('Desktop resolution', function() {
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before(function() {
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describe('OHIF Study List', function () {
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context('Desktop resolution', function () {
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before(function () {
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cy.openStudyList();
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});
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beforeEach(function() {
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beforeEach(function () {
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cy.viewport(1750, 720);
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cy.initStudyListAliasesOnDesktop();
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//Clear all text fields
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@@ -21,31 +21,42 @@ describe('OHIF Study List', function() {
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//cy.get('@modalities')
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});
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it('searches Patient Name with exact string', function() {
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it('Displays several studies initially', function () {
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cy.waitStudyList();
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cy.get('@searchResult2').should($list => {
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expect($list.length).to.be.greaterThan(1);
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expect($list).to.contain('Juno');
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expect($list).to.contain('832040');
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});
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});
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it('searches Patient Name with exact string', function () {
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cy.get('@PatientName').type('Juno');
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//Wait result list to be displayed
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cy.waitStudyList();
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cy.get('@searchResult').should($list => {
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cy.get('@searchResult2').should($list => {
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expect($list.length).to.be.eq(1);
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expect($list).to.contain('Juno');
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});
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});
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it('searches MRN with exact string', function() {
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/* TODO - re-enable this once the test server is fixed to allow searching by mrn
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it('searches MRN with exact string', function () {
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cy.get('@MRN').type('0000003');
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//Wait result list to be displayed
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cy.waitStudyList();
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cy.get('@searchResult').should($list => {
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cy.get('@searchResult2').should($list => {
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expect($list.length).to.be.eq(1);
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expect($list).to.contain('0000003');
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});
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});
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*/
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it('searches Accession with exact string', function() {
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it('searches Accession with exact string', function () {
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cy.get('@AccessionNumber').type('0000155811');
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//Wait result list to be displayed
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cy.waitStudyList();
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cy.get('@searchResult').should($list => {
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cy.get('@searchResult2').should($list => {
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expect($list.length).to.be.eq(1);
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expect($list).to.contain('0000155811');
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});
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@@ -56,7 +67,7 @@ describe('OHIF Study List', function() {
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cy.get('@modalities').type('Ct');
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//Wait result list to be displayed
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cy.waitStudyList();
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cy.get('@searchResult').should($list => {
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cy.get('@searchResult2').should($list => {
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expect($list.length).to.be.greaterThan(1);
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expect($list).to.contain('CT');
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});
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@@ -68,7 +79,7 @@ describe('OHIF Study List', function() {
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cy.get('@StudyDescription').type('PETCT');
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//Wait result list to be displayed
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cy.waitStudyList();
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cy.get('@searchResult').should($list => {
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cy.get('@searchResult2').should($list => {
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expect($list.length).to.be.eq(1);
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expect($list).to.contain('PETCT');
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});
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@@ -92,7 +103,7 @@ describe('OHIF Study List', function() {
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})
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.then(numStudies => {
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//Compare to the number of Rows in the search result
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cy.get('@searchResult').then($searchResult => {
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cy.get('@searchResult2').then($searchResult => {
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let countResults = $searchResult.length;
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expect(numStudies.text()).to.be.eq(countResults.toString());
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});
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@@ -18,12 +18,16 @@
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"proxy": "http://localhost:8042",
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"scripts": {
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"build:viewer": "cross-env NODE_ENV=production yarn run build",
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"build:dev": "cross-env NODE_ENV=development yarn run build",
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"build:aws": "cross-env NODE_ENV=development APP_CONFIG=config/aws_static.js yarn run build && gzip -9 -r dist",
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"build:viewer:ci": "cross-env NODE_ENV=production PUBLIC_URL=/ APP_CONFIG=config/netlify.js QUICK_BUILD=true yarn run build",
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"build:viewer:qa": "cross-env NODE_ENV=production APP_CONFIG=config/google.js yarn run build",
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"build:viewer:demo": "cross-env NODE_ENV=production APP_CONFIG=config/demo.js HTML_TEMPLATE=rollbar.html QUICK_BUILD=true yarn run build",
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"build": "node --max_old_space_size=4096 ./../../node_modules/webpack/bin/webpack.js --progress --config .webpack/webpack.pwa.js",
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"dev": "cross-env NODE_ENV=development webpack serve --config .webpack/webpack.pwa.js",
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"dev:orthanc": "cross-env NODE_ENV=development PROXY_TARGET=/dicom-web PROXY_DOMAIN=http://localhost:8042 APP_CONFIG=config/docker_nginx-orthanc.js webpack serve --config .webpack/webpack.pwa.js",
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"dev:dcm4chee": "cross-env NODE_ENV=development APP_CONFIG=config/local_dcm4chee.js webpack serve --config .webpack/webpack.pwa.js",
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"dev:static": "cross-env NODE_ENV=development APP_CONFIG=config/local_static.js webpack serve --config .webpack/webpack.pwa.js",
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"dev:viewer": "yarn run dev",
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"start": "yarn run dev",
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"test:e2e": "cypress open",
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@@ -0,0 +1,159 @@
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window.config = {
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routerBasename: '/',
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// whiteLabelling: {},
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extensions: [],
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modes: [],
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showStudyList: true,
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// filterQueryParam: false,
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dataSources: [
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{
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friendlyName: 'dcmjs DICOMWeb Server',
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namespace: 'org.ohif.default.dataSourcesModule.dicomweb',
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sourceName: 'dicomweb',
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configuration: {
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name: 'DCM4CHEE',
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// Something here to check build
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wadoUriRoot: 'https://myserver.com/dicomweb',
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qidoRoot: 'https://myserver.com/dicomweb',
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wadoRoot: 'https://myserver.com/dicomweb',
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qidoSupportsIncludeField: false,
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supportsReject: false,
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imageRendering: 'wadors',
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thumbnailRendering: 'wadors',
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enableStudyLazyLoad: true,
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supportsFuzzyMatching: false,
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supportsWildcard: false,
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staticWado: true,
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},
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},
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{
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friendlyName: 'dicom json',
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namespace: 'org.ohif.default.dataSourcesModule.dicomjson',
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sourceName: 'dicomjson',
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configuration: {
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name: 'json',
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},
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},
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{
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friendlyName: 'dicom local',
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namespace: 'org.ohif.default.dataSourcesModule.dicomlocal',
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sourceName: 'dicomlocal',
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configuration: {},
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},
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],
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httpErrorHandler: error => {
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// This is 429 when rejected from the public idc sandbox too often.
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console.warn(error.status);
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// Could use services manager here to bring up a dialog/modal if needed.
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console.warn('test, navigate to https://ohif.org/');
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},
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// whiteLabeling: {
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// /* Optional: Should return a React component to be rendered in the "Logo" section of the application's Top Navigation bar */
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// createLogoComponentFn: function (React) {
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// return React.createElement(
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// 'a',
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// {
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// target: '_self',
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// rel: 'noopener noreferrer',
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// className: 'text-purple-600 line-through',
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// href: '/',
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// },
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// React.createElement('img',
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// {
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// src: './customLogo.svg',
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// className: 'w-8 h-8',
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// }
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// ))
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// },
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// },
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defaultDataSourceName: 'dicomweb',
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hotkeys: [
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{
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commandName: 'incrementActiveViewport',
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label: 'Next Viewport',
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keys: ['right'],
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},
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{
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commandName: 'decrementActiveViewport',
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label: 'Previous Viewport',
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keys: ['left'],
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},
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{ commandName: 'rotateViewportCW', label: 'Rotate Right', keys: ['r'] },
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{ commandName: 'rotateViewportCCW', label: 'Rotate Left', keys: ['l'] },
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{ commandName: 'invertViewport', label: 'Invert', keys: ['i'] },
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{
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commandName: 'flipViewportVertical',
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label: 'Flip Horizontally',
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keys: ['h'],
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},
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{
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commandName: 'flipViewportHorizontal',
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label: 'Flip Vertically',
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keys: ['v'],
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},
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{ commandName: 'scaleUpViewport', label: 'Zoom In', keys: ['+'] },
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{ commandName: 'scaleDownViewport', label: 'Zoom Out', keys: ['-'] },
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{ commandName: 'fitViewportToWindow', label: 'Zoom to Fit', keys: ['='] },
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{ commandName: 'resetViewport', label: 'Reset', keys: ['space'] },
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{ commandName: 'nextImage', label: 'Next Image', keys: ['down'] },
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{ commandName: 'previousImage', label: 'Previous Image', keys: ['up'] },
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{
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commandName: 'previousViewportDisplaySet',
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label: 'Previous Series',
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keys: ['pagedown'],
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},
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{
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commandName: 'nextViewportDisplaySet',
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label: 'Next Series',
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keys: ['pageup'],
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},
|
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{ commandName: 'setZoomTool', label: 'Zoom', keys: ['z'] },
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// ~ Window level presets
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{
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commandName: 'windowLevelPreset1',
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label: 'W/L Preset 1',
|
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keys: ['1'],
|
||||
},
|
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{
|
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commandName: 'windowLevelPreset2',
|
||||
label: 'W/L Preset 2',
|
||||
keys: ['2'],
|
||||
},
|
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{
|
||||
commandName: 'windowLevelPreset3',
|
||||
label: 'W/L Preset 3',
|
||||
keys: ['3'],
|
||||
},
|
||||
{
|
||||
commandName: 'windowLevelPreset4',
|
||||
label: 'W/L Preset 4',
|
||||
keys: ['4'],
|
||||
},
|
||||
{
|
||||
commandName: 'windowLevelPreset5',
|
||||
label: 'W/L Preset 5',
|
||||
keys: ['5'],
|
||||
},
|
||||
{
|
||||
commandName: 'windowLevelPreset6',
|
||||
label: 'W/L Preset 6',
|
||||
keys: ['6'],
|
||||
},
|
||||
{
|
||||
commandName: 'windowLevelPreset7',
|
||||
label: 'W/L Preset 7',
|
||||
keys: ['7'],
|
||||
},
|
||||
{
|
||||
commandName: 'windowLevelPreset8',
|
||||
label: 'W/L Preset 8',
|
||||
keys: ['8'],
|
||||
},
|
||||
{
|
||||
commandName: 'windowLevelPreset9',
|
||||
label: 'W/L Preset 9',
|
||||
keys: ['9'],
|
||||
},
|
||||
],
|
||||
};
|
||||
@@ -20,8 +20,8 @@ window.config = {
|
||||
imageRendering: 'wadouri',
|
||||
thumbnailRendering: 'wadouri',
|
||||
enableStudyLazyLoad: true,
|
||||
supportsFuzzyMatching: true,
|
||||
supportsWildcard: true,
|
||||
supportsFuzzyMatching: false,
|
||||
supportsWildcard: false,
|
||||
},
|
||||
},
|
||||
],
|
||||
|
||||
@@ -0,0 +1,158 @@
|
||||
window.config = {
|
||||
routerBasename: '/',
|
||||
// whiteLabelling: {},
|
||||
extensions: [],
|
||||
modes: [],
|
||||
showStudyList: true,
|
||||
// filterQueryParam: false,
|
||||
dataSources: [
|
||||
{
|
||||
friendlyName: 'dcmjs DICOMWeb Server',
|
||||
namespace: 'org.ohif.default.dataSourcesModule.dicomweb',
|
||||
sourceName: 'dicomweb',
|
||||
configuration: {
|
||||
name: 'DCM4CHEE',
|
||||
wadoUriRoot: 'http://localhost:5000',
|
||||
qidoRoot: 'http://localhost:5000',
|
||||
wadoRoot: 'http://localhost:5000',
|
||||
qidoSupportsIncludeField: false,
|
||||
supportsReject: false,
|
||||
imageRendering: 'wadors',
|
||||
thumbnailRendering: 'wadors',
|
||||
enableStudyLazyLoad: true,
|
||||
supportsFuzzyMatching: false,
|
||||
supportsWildcard: false,
|
||||
staticWado: true,
|
||||
},
|
||||
},
|
||||
{
|
||||
friendlyName: 'dicom json',
|
||||
namespace: 'org.ohif.default.dataSourcesModule.dicomjson',
|
||||
sourceName: 'dicomjson',
|
||||
configuration: {
|
||||
name: 'json',
|
||||
},
|
||||
},
|
||||
{
|
||||
friendlyName: 'dicom local',
|
||||
namespace: 'org.ohif.default.dataSourcesModule.dicomlocal',
|
||||
sourceName: 'dicomlocal',
|
||||
configuration: {},
|
||||
},
|
||||
],
|
||||
httpErrorHandler: error => {
|
||||
// This is 429 when rejected from the public idc sandbox too often.
|
||||
console.warn(error.status);
|
||||
|
||||
// Could use services manager here to bring up a dialog/modal if needed.
|
||||
console.warn('test, navigate to https://ohif.org/');
|
||||
},
|
||||
// whiteLabeling: {
|
||||
// /* Optional: Should return a React component to be rendered in the "Logo" section of the application's Top Navigation bar */
|
||||
// createLogoComponentFn: function (React) {
|
||||
// return React.createElement(
|
||||
// 'a',
|
||||
// {
|
||||
// target: '_self',
|
||||
// rel: 'noopener noreferrer',
|
||||
// className: 'text-purple-600 line-through',
|
||||
// href: '/',
|
||||
// },
|
||||
// React.createElement('img',
|
||||
// {
|
||||
// src: './customLogo.svg',
|
||||
// className: 'w-8 h-8',
|
||||
// }
|
||||
// ))
|
||||
// },
|
||||
// },
|
||||
defaultDataSourceName: 'dicomweb',
|
||||
hotkeys: [
|
||||
{
|
||||
commandName: 'incrementActiveViewport',
|
||||
label: 'Next Viewport',
|
||||
keys: ['right'],
|
||||
},
|
||||
{
|
||||
commandName: 'decrementActiveViewport',
|
||||
label: 'Previous Viewport',
|
||||
keys: ['left'],
|
||||
},
|
||||
{ commandName: 'rotateViewportCW', label: 'Rotate Right', keys: ['r'] },
|
||||
{ commandName: 'rotateViewportCCW', label: 'Rotate Left', keys: ['l'] },
|
||||
{ commandName: 'invertViewport', label: 'Invert', keys: ['i'] },
|
||||
{
|
||||
commandName: 'flipViewportVertical',
|
||||
label: 'Flip Horizontally',
|
||||
keys: ['h'],
|
||||
},
|
||||
{
|
||||
commandName: 'flipViewportHorizontal',
|
||||
label: 'Flip Vertically',
|
||||
keys: ['v'],
|
||||
},
|
||||
{ commandName: 'scaleUpViewport', label: 'Zoom In', keys: ['+'] },
|
||||
{ commandName: 'scaleDownViewport', label: 'Zoom Out', keys: ['-'] },
|
||||
{ commandName: 'fitViewportToWindow', label: 'Zoom to Fit', keys: ['='] },
|
||||
{ commandName: 'resetViewport', label: 'Reset', keys: ['space'] },
|
||||
{ commandName: 'nextImage', label: 'Next Image', keys: ['down'] },
|
||||
{ commandName: 'previousImage', label: 'Previous Image', keys: ['up'] },
|
||||
{
|
||||
commandName: 'previousViewportDisplaySet',
|
||||
label: 'Previous Series',
|
||||
keys: ['pagedown'],
|
||||
},
|
||||
{
|
||||
commandName: 'nextViewportDisplaySet',
|
||||
label: 'Next Series',
|
||||
keys: ['pageup'],
|
||||
},
|
||||
{ commandName: 'setZoomTool', label: 'Zoom', keys: ['z'] },
|
||||
// ~ Window level presets
|
||||
{
|
||||
commandName: 'windowLevelPreset1',
|
||||
label: 'W/L Preset 1',
|
||||
keys: ['1'],
|
||||
},
|
||||
{
|
||||
commandName: 'windowLevelPreset2',
|
||||
label: 'W/L Preset 2',
|
||||
keys: ['2'],
|
||||
},
|
||||
{
|
||||
commandName: 'windowLevelPreset3',
|
||||
label: 'W/L Preset 3',
|
||||
keys: ['3'],
|
||||
},
|
||||
{
|
||||
commandName: 'windowLevelPreset4',
|
||||
label: 'W/L Preset 4',
|
||||
keys: ['4'],
|
||||
},
|
||||
{
|
||||
commandName: 'windowLevelPreset5',
|
||||
label: 'W/L Preset 5',
|
||||
keys: ['5'],
|
||||
},
|
||||
{
|
||||
commandName: 'windowLevelPreset6',
|
||||
label: 'W/L Preset 6',
|
||||
keys: ['6'],
|
||||
},
|
||||
{
|
||||
commandName: 'windowLevelPreset7',
|
||||
label: 'W/L Preset 7',
|
||||
keys: ['7'],
|
||||
},
|
||||
{
|
||||
commandName: 'windowLevelPreset8',
|
||||
label: 'W/L Preset 8',
|
||||
keys: ['8'],
|
||||
},
|
||||
{
|
||||
commandName: 'windowLevelPreset9',
|
||||
label: 'W/L Preset 9',
|
||||
keys: ['9'],
|
||||
},
|
||||
],
|
||||
};
|
||||
@@ -49,6 +49,7 @@ function DataSourceWrapper(props) {
|
||||
total: 0,
|
||||
resultsPerPage: 25,
|
||||
pageNumber: 1,
|
||||
location: 'Not a valid location, causes first load to occur',
|
||||
});
|
||||
const [isLoading, setIsLoading] = useState(false);
|
||||
|
||||
@@ -68,6 +69,7 @@ function DataSourceWrapper(props) {
|
||||
total: studies.length,
|
||||
resultsPerPage: queryFilterValues.resultsPerPage,
|
||||
pageNumber: queryFilterValues.pageNumber,
|
||||
location,
|
||||
});
|
||||
|
||||
setIsLoading(false);
|
||||
@@ -77,7 +79,6 @@ function DataSourceWrapper(props) {
|
||||
// Cache invalidation :thinking:
|
||||
// - Anytime change is not just next/previous page
|
||||
// - And we didn't cross a result offset range
|
||||
const isFirstLoad = data.studies.length === 0 && !isLoading;
|
||||
const isSamePage = data.pageNumber === queryFilterValues.pageNumber;
|
||||
const previousOffset =
|
||||
Math.floor((data.pageNumber * data.resultsPerPage) / STUDIES_LIMIT) *
|
||||
@@ -85,11 +86,12 @@ function DataSourceWrapper(props) {
|
||||
const newOffset =
|
||||
Math.floor(
|
||||
(queryFilterValues.pageNumber * queryFilterValues.resultsPerPage) /
|
||||
STUDIES_LIMIT
|
||||
STUDIES_LIMIT
|
||||
) *
|
||||
(STUDIES_LIMIT - 1);
|
||||
const isDataInvalid =
|
||||
isFirstLoad || !isSamePage || newOffset !== previousOffset;
|
||||
const isLocationUpdated = data.location !== location;
|
||||
const isDataInvalid = !isSamePage || !isLoading &&
|
||||
(newOffset !== previousOffset || isLocationUpdated);
|
||||
|
||||
if (isDataInvalid) {
|
||||
getData();
|
||||
|
||||
@@ -55,8 +55,8 @@ function Local() {
|
||||
return acc.concat(mods)
|
||||
}, [])
|
||||
|
||||
const fistLocalDataSource = localDataSources[0]
|
||||
const dataSource = fistLocalDataSource.createDataSource({})
|
||||
const firstLocalDataSource = localDataSources[0]
|
||||
const dataSource = firstLocalDataSource.createDataSource({})
|
||||
|
||||
const onDrop = async (acceptedFiles) => {
|
||||
const studies = await filesToStudies(acceptedFiles, dataSource)
|
||||
|
||||
Reference in new issue
Block a user