Merge branch 'master' of github.com:ImagingDataCommons/slim into feat…

…/bump-to-0.35

.gitignore

@@ -10,6 +10,7 @@
 
 # testing
 /coverage
+.env
 
 # production
 /build

README.md

@@ -81,11 +81,87 @@ Users can authenticate and authorize the application to access data via [OpenID
 
 ## Configuration
 
+### Server Configuration
+
 The app can be configured via a `public/config/{name}.js` JavaScript configuration file (see for example the default `public/config/local.js`).
 Please refer to the [AppConfig.d.ts](src/AppConfig.d.ts) file for configuration options.
 
 The configuration can be changed at build-time using the `REACT_APP_CONFIG` environment variable.
 
+### Handling Mixed Content and HTTPS
+
+When deploying SLIM with HTTPS, you may encounter mixed content scenarios where your PACS/VNA server returns HTTP URLs in its responses. This commonly occurs when:
+
+- The PACS server populates bulkdataURI fields with internal HTTP URLs
+- Your viewer is running on HTTPS but needs to communicate with services that respond with HTTP URLs
+- You're using a reverse proxy that terminates SSL
+
+To handle these scenarios, SLIM provides the `upgradeInsecureRequests` option in the server configuration:
+
+```js
+window.config = {
+  servers: [{
+    id: "local",
+    url: "https://your-server.com/dcm4chee-arc/aets/MYAET/rs",
+    upgradeInsecureRequests: true  // Enable automatic HTTP -> HTTPS upgrade
+  }]
+}
+```
+
+When `upgradeInsecureRequests` is set to `true` and at least one of your URLs (service URL, QIDO, WADO, or STOW prefixes) uses HTTPS, the viewer will automatically:
+
+1. Add the `Content-Security-Policy: upgrade-insecure-requests` header to requests
+2. Attempt to upgrade any HTTP responses to HTTPS
+
+This feature was implemented in response to [issue #159](https://github.com/ImagingDataCommons/slim/issues/159) where PACS servers would return HTTP bulkdata URIs even when accessed via HTTPS.
+
+### Messages/Popups Configuration
+
+Configure message popup notifications that appear at the top of the screen. By default, all message popups are enabled.
+
+```javascript
+window.config = {
+  // ... other config options ...
+  messages: {
+    disabled: ['warning', 'info'], // Disable specific message types
+    duration: 5, // Show messages for 5 seconds
+    top: 100 // Show 100px from top of screen
+  }
+}
+```
+
+Options:
+- `disabled`: Disable specific message types or all messages
+- `duration`: How long messages are shown (in seconds)
+- `top`: Distance from top of screen (in pixels)
+
+Available message types:
+- `success` - Green popups
+- `error` - Red popups  
+- `warning` - Yellow popups
+- `info` - Blue popups
+
+Examples:
+```javascript
+// Disable specific types with custom duration and position
+messages: {
+  disabled: ['warning', 'info'],
+  duration: 5, // Show for 5 seconds
+  top: 50 // Show 50px from top
+}
+```
+
+```javascript
+// Disable all popups
+messages: {
+  disabled: true
+}
+```
+
+Default values if not specified:
+- `duration`: 5 seconds
+- `top`: 100 pixels
+
 ## Deployment
 
 Download the latest release from [github.com/imagingdatacommons/slim/releases](https://github.com/imagingdatacommons/slim/releases) and then run the following commands to install build dependencies and build the app:
@@ -223,7 +299,6 @@ Create an [OIDC client ID for web application](https://developers.google.com/ide
 Note that Google's OIDC implementation does currently not yet support the authorization code grant type with PKCE challenge for private clients.
 For the time being, the legacy implicit grand type has to be used.
 
-
 ## Development
 
 To install requirements and run the app for local development, run the following commands:

docs/CHANGELOG.md

@@ -1,3 +1,31 @@
+# [0.35.0](https://github.com/ImagingDataCommons/slim/compare/v0.34.0...v0.35.0) (2024-11-21)
+
+
+### Features
+
+* bump dmv version ([#254](https://github.com/ImagingDataCommons/slim/issues/254)) ([fe9bb49](https://github.com/ImagingDataCommons/slim/commit/fe9bb496aa503c54ee65ffba86a0cf14b7e7c20f))
+
+# [0.34.0](https://github.com/ImagingDataCommons/slim/compare/v0.33.0...v0.34.0) (2024-11-20)
+
+
+### Features
+
+* improve dicom tag browser ([#251](https://github.com/ImagingDataCommons/slim/issues/251)) ([7e57859](https://github.com/ImagingDataCommons/slim/commit/7e57859287ea3b758f9d2cf4e53729063c589569))
+
+# [0.33.0](https://github.com/ImagingDataCommons/slim/compare/v0.32.0...v0.33.0) (2024-10-31)
+
+
+### Features
+
+* dicom tag browser ([#248](https://github.com/ImagingDataCommons/slim/issues/248)) ([177ed8f](https://github.com/ImagingDataCommons/slim/commit/177ed8f6b6e82614f9563eb22584c2c6b8bc8de4))
+
+# [0.32.0](https://github.com/ImagingDataCommons/slim/compare/v0.31.4...v0.32.0) (2024-10-29)
+
+
+### Features
+
+* remove unused white space ([#247](https://github.com/ImagingDataCommons/slim/issues/247)) ([155e001](https://github.com/ImagingDataCommons/slim/commit/155e0018c2fd8b87eee70c207051de9df55f0ada))
+
 ## [0.31.4](https://github.com/ImagingDataCommons/slim/compare/v0.31.3...v0.31.4) (2024-07-29)
 
 

package.json

@@ -1,6 +1,6 @@
 {
   "name": "slim",
-  "version": "0.31.4",
+  "version": "0.35.0",
   "homepage": "https://github.com/imagingdatacommons/slim",
   "private": true,
   "author": "ImagingDataCommons",
@@ -56,9 +56,9 @@
     "classnames": "^2.2.6",
     "copy-webpack-plugin": "^10.2.4",
     "craco-less": "^2.0.0",
-    "dcmjs": "^0.29.8",
+    "dcmjs": "^0.35.0",
     "detect-browser": "^5.2.1",
-    "dicom-microscopy-viewer": "^0.47.0",
+    "dicom-microscopy-viewer": "^0.47.2",
     "dicomweb-client": "^0.10.3",
     "gh-pages": "^5.0.0",
     "oidc-client": "^1.11.5",

src/App.tsx

@@ -453,6 +453,7 @@ class App extends React.Component<AppProps, AppState> {
               onServerSelection={this.handleServerSelection}
               showServerSelectionButton={false}
               appConfig={this.props.config}
+              clients={this.state.clients}
             />
             <Layout.Content style={layoutContentStyle}>
               <FaSpinner />

src/AppConfig.d.ts

@@ -64,6 +64,7 @@ export interface ServerSettings {
   retry?: RetryRequestSettings
   errorMessages?: ErrorMessageSettings[]
   storageClasses?: string[]
+  upgradeInsecureRequests?: boolean
 }
 
 export interface OidcSettings {
@@ -103,4 +104,9 @@ export default interface AppConfig {
   mode?: string
   preload?: boolean
   downloadStudyDialog?: DownloadStudyDialogSettings
+  messages?: {
+    disabled?: boolean | string[]
+    top?: number
+    duration?: number
+  }
 }

src/DicomWebManager.ts

@@ -1,4 +1,6 @@
 import * as dwc from 'dicomweb-client'
+import * as dcmjs from 'dcmjs'
+import * as dmv from 'dicom-microscopy-viewer'
 
 import { ServerSettings, DicomWebManagerErrorHandler } from './AppConfig'
 import { joinUrl } from './utils/url'
@@ -7,6 +9,9 @@ import { CustomError, errorTypes } from './utils/CustomError'
 import NotificationMiddleware, {
   NotificationMiddlewareContext
 } from './services/NotificationMiddleware'
+import DicomMetadataStore, { Instance } from './services/DICOMMetadataStore'
+
+const { naturalizeDataset } = dcmjs.data.DicomMetaDictionary
 
 interface Store {
   id: string
@@ -58,9 +63,20 @@ export default class DicomWebManager implements dwc.api.DICOMwebClient {
           )
         )
       }
+
+      const hasHttpsUrl = (url?: string): boolean => url?.startsWith('https') ?? false
+
       const clientSettings: dwc.api.DICOMwebClientOptions = {
         url: serviceUrl
       }
+
+      const shouldUpgradeInsecure = serverSettings.upgradeInsecureRequests === true && [
+        serviceUrl,
+        serverSettings.qidoPathPrefix,
+        serverSettings.wadoPathPrefix,
+        serverSettings.stowPathPrefix
+      ].some(hasHttpsUrl)
+
       if (serverSettings.qidoPathPrefix !== undefined) {
         clientSettings.qidoURLPrefix = serverSettings.qidoPathPrefix
       }
@@ -70,6 +86,14 @@ export default class DicomWebManager implements dwc.api.DICOMwebClient {
       if (serverSettings.stowPathPrefix !== undefined) {
         clientSettings.stowURLPrefix = serverSettings.stowPathPrefix
       }
+
+      if (shouldUpgradeInsecure) {
+        clientSettings.headers = {
+          ...clientSettings.headers,
+          'Content-Security-Policy': 'upgrade-insecure-requests'
+        }
+      }
+
       if (serverSettings.retry !== undefined) {
         clientSettings.requestHooks = [getXHRRetryHook(serverSettings.retry)]
       }
@@ -144,13 +168,21 @@ export default class DicomWebManager implements dwc.api.DICOMwebClient {
   retrieveStudyMetadata = async (
     options: dwc.api.RetrieveStudyMetadataOptions
   ): Promise<dwc.api.Metadata[]> => {
-    return await this.stores[0].client.retrieveStudyMetadata(options)
+    const studySummaryMetadata = await this.stores[0].client.retrieveStudyMetadata(options)
+    const naturalized = naturalizeDataset(studySummaryMetadata)
+    DicomMetadataStore.addStudy(naturalized)
+    return studySummaryMetadata
   }
 
   retrieveSeriesMetadata = async (
     options: dwc.api.RetrieveSeriesMetadataOptions
   ): Promise<dwc.api.Metadata[]> => {
-    return await this.stores[0].client.retrieveSeriesMetadata(options)
+    const seriesSummaryMetadata = await this.stores[0].client.retrieveSeriesMetadata(options)
+    console.debug('seriesSummaryMetadata:', seriesSummaryMetadata)
+    const naturalized = seriesSummaryMetadata.map(naturalizeDataset)
+    console.debug('naturalized:', naturalized)
+    DicomMetadataStore.addSeriesMetadata(naturalized, true)
+    return seriesSummaryMetadata
   }
 
   retrieveInstanceMetadata = async (
@@ -162,7 +194,11 @@ export default class DicomWebManager implements dwc.api.DICOMwebClient {
   retrieveInstance = async (
     options: dwc.api.RetrieveInstanceOptions
   ): Promise<dwc.api.Dataset> => {
-    return await this.stores[0].client.retrieveInstance(options)
+    const instance = await this.stores[0].client.retrieveInstance(options)
+    const data = dcmjs.data.DicomMessage.readFile(instance)
+    const { dataset } = dmv.metadata.formatMetadata(data.dict)
+    DicomMetadataStore.addInstances([dataset as Instance])
+    return instance
   }
 
   retrieveInstanceFrames = async (

src/components/AnnotationGroupItem.tsx

@@ -360,7 +360,7 @@ class AnnotationGroupItem extends React.Component<AnnotationGroupItemProps, Anno
         size='small'
         disabled={!this.props.isVisible}
       >
-        {}
+        <></>
       </Select.Option>
     )