googlecloudplatform / weasis-chcapi-extension

Weasis plugin adding support for the Google Cloud Healthcare API

About Weasis Google DICOM Plugin

Plugin enables Weasis Viewer users access to Google Cloud Healthcare API DICOM data. It utilizes DICOMweb REST API to interact with Google Cloud services.

Features

• Login using your Google account
• Interactive exploration of Google Healthcare API Dicom stores
• Download and display all kinds of DICOM data
• Advanced study search capabilities

Running the plugin

The plugin runs as an extension to the main Weasis application, so first you need to download the main Weasis application from https://nroduit.github.io/en/.

Please note, latest supported release of Weasis is 3.6.0

Then you need to have existing data in the Cloud Healthcare API and install the plugin to get up and running. Please see more detailed instructions below.

Setting up Google Cloud Healthcare API:

See https://cloud.google.com/healthcare/docs/ to get started.

Installing plugin

• Get the latest release JAR from this repositories releases tab.
• Follow instructions at installing plug-ins to add this plugin to Weasis.
• Run Weasis Viewer executable
• Switch to Google Dicom Explorer tab and login using your Google Account

NOTE: If you face with some issues when using the plugin, you should remove .Weasis folder wich may cache previous or incorrect settings for the plugin in Weasis.

Using your own OAuth client

The plugin comes with it's own OAuth Client ID for ease of installation, but you can substitute your own if required (e.g. your organization has OAuth policy restriction on external apps). To do this go to the Google API Console and create a set of OAuth 2.0 credentials using the type "Other" and make sure to whitelist the scopes .../auth/cloud-healthcare and .../auth/cloudplatformprojects.readonly. Then download the credentials files in JSON format, name the file client_secrets.json and move it to conf folder, next to the ext-config.properties file.

Building plugin

If you're just trying to run the tool, please see the instructions above. If you need to recompile the plugin for any reason here are the steps to do so.

Weasis requires JDK14. Plugin depends on core Weasis API, that's why you have to clone, build and install core Weasis modules to your local Maven repository first For this purpose follow instructions at building Weasis. After Weasis artifacts installed to your local Maven repository plugin itself can be compiled Detailed build instruction can be found at building Weasis plugins Clone this repository and execute following script:

cd weasis-chcapi-extension

## build plugin
mvn clean install

weasis-chcapi-extension's Issues

Support fuzzymatching on Patient Names

Specify fuzzymatching=true for QIDO requests. See http://dicom.nema.org/medical/dicom/current/output/html/part18.html#sect_8.3.4.2.

Support Weasis v3.6 on MacOS

Add Continuous Integration Builds

Using TravisCI

Upgrade Jackson Dependency

Upgrade com.fasterxml.jackson.core:jackson-databind to version 2.9.9 or later. There is a security vulnerability in the existing version.

Automate Release

Support Pagination of Studies

Use limit/offset query parameters to allow viewing past the first 100 studies.

Have a nice message when a Dataset does not have any DICOM Stores

Right now a pop-up comes up with "unexpected error when fetching google api: null"
Instead, it would be nicer to handle this and pop up: "No DICOM Stores in Dataset"
12:06:26.464 ERROR [AWT-EventQueue-0] org.weasis.dicom.google.api.ui.dicomstore.AbstractDicomSelectorTask: Error on dicom task java.lang.NullPointerException
at org.weasis.dicom.google.api.GoogleAPIClient.fetchDicomstores(GoogleAPIClient.java:365)
at org.weasis.dicom.google.api.ui.dicomstore.LoadDicomStoresTask.doInBackground(LoadDicomStoresTask.java:37)
at org.weasis.dicom.google.api.ui.dicomstore.LoadDicomStoresTask.doInBackground(LoadDicomStoresTask.java:24)

401 for API requests if weasis is running for more than hour

seems like extension does not perform update of auth token when it's expired

switch integration tests to use "gcloud beta"

The alpha endpoint of the Healthcare API is no longer public.

Plugin fails to start: URI is not absolute

I am running Weasis 3.6.0. I did what is says in the "Installing plugin" readme section, but the plugin fails to initialize, throwing the following exception:

19.05.2020 07:43:52.437 *SEVERE* [main] org.weasis.launcher.FileUtil: Cannot install bundle weasis-chcapi-extension-3.0.7
java.lang.IllegalArgumentException: URI is not absolute
	at java.base/java.net.URL.fromURI(URL.java:719)
	at java.base/java.net.URI.toURL(URI.java:1139)
	at org.weasis.launcher.AutoProcessor.installBundle(AutoProcessor.java:530)
	at org.weasis.launcher.AutoProcessor.processAutoProperties(AutoProcessor.java:351)
	at org.weasis.launcher.AutoProcessor.process(AutoProcessor.java:106)
	at org.weasis.launcher.WeasisLoader.setFelix(WeasisLoader.java:248)
	at org.weasis.launcher.WeasisLauncher.launch(WeasisLauncher.java:247)
	at org.weasis.launcher.AppLauncher.main(AppLauncher.java:27)
19.05.2020 07:43:52.450 *SEVERE* [main] org.weasis.launcher.FileUtil: Cannot start bundle weasis-chcapi-extension-3.0.7
java.lang.IllegalArgumentException: URI is not absolute
	at java.base/java.net.URL.fromURI(URL.java:719)
	at java.base/java.net.URI.toURL(URI.java:1139)
	at org.weasis.launcher.AutoProcessor.installBundle(AutoProcessor.java:530)
	at org.weasis.launcher.AutoProcessor.processAutoProperties(AutoProcessor.java:389)
	at org.weasis.launcher.AutoProcessor.process(AutoProcessor.java:106)
	at org.weasis.launcher.WeasisLoader.setFelix(WeasisLoader.java:248)
	at org.weasis.launcher.WeasisLauncher.launch(WeasisLauncher.java:247)
	at org.weasis.launcher.AppLauncher.main(AppLauncher.java:27)

Error when displaying the error message during authentication

The component must be created in EDT:

org.pushingpixels.substance.api.UiThreadingViolationException: Component creation must be done on Event Dispatch Thread
at org.pushingpixels.substance.internal.utils.SubstanceCoreUtilities.testComponentCreationThreadingViolation(SubstanceCoreUtilities.java:1832)
at org.pushingpixels.substance.internal.ui.SubstanceOptionPaneUI.createUI(SubstanceOptionPaneUI.java:99)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at sun.reflect.misc.Trampoline.invoke(MethodUtil.java:71)
at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at sun.reflect.misc.MethodUtil.invoke(MethodUtil.java:275)
at javax.swing.UIDefaults.getUI(UIDefaults.java:770)
at javax.swing.UIManager.getUI(UIManager.java:1016)
at javax.swing.JOptionPane.updateUI(JOptionPane.java:1882)
at javax.swing.JOptionPane.(JOptionPane.java:1845)
at javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:857)
at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:666)
at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:637)
at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:608)
at org.weasis.dicom.google.api.ui.dicomstore.GoogleLoginTask.doInBackground(GoogleLoginTask.java:49)
at org.weasis.dicom.google.api.ui.dicomstore.GoogleLoginTask.doInBackground(GoogleLoginTask.java:24)
at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at javax.swing.SwingWorker.run(SwingWorker.java:334)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
UIDefaults.getUI() failed: createUI() failed for javax.swing.JOptionPane[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=,flags=0,maximumSize=,minimumSize=,preferredSize=,icon=,initialValue=,message=Error occured on fetching google API.
Make sure you created OAuth Client ID credential
in Google Cloud console at https://console.cloud.google.com/apis/credentials
and copied your client_secrets.json to Weasis root folder.
Error message:400 Bad Request
{
"error" : "invalid_grant",
"error_description" : "Bad Request"
},messageType=INFORMATION_MESSAGE,optionType=DEFAULT_OPTION,wantsInput=false] java.lang.reflect.InvocationTargetException
java.lang.Error
at javax.swing.UIDefaults.getUIError(UIDefaults.java:731)

incorrect display of multiseries studies

if study is multiseries, frames from all series will be displayed as one series.

if these series multiframe, then frames will be displayed with strange sequence - sorted by frame first

series0frame0-series1frame0-series2frame0-series0frame1...

also if sum of all series is more than some limit, extension will fail to display frames as described #6

The plugin opens each slice in a separate viewer tab

It is quite a weird behavior when you have a study with multiple series, each of which has multiple slices. Is this expected behavior, or am I doing something wrong?

The plugin finds the study, but does not open it in the viewer

I got the plugin working up to the point where I get a study in the list. When I double-click on it, I see the loading indicator in the Status column "dancing" for several seconds, then stops, but nothing happens. The viewer does not open.

The last log entry I see in ~/.weasis/log/boot-0.log is this:

07.08.2020 15:45:55.298 *CONFIG* [Google Dicom Explorer-pool-4-thread-1] com.google.api.client.http.HttpTransport: -------------- REQUEST  --------------
GET https://healthcare.googleapis.com/v1beta1/projects/chuck-dev-[REDACTED]/locations/europe-west4/datasets/veye-feedback/dicomStores/veye-feedback/dicomWeb/studies/1.2.840.113745.101000.1186002.40721.8111.13846623
Accept: multipart/related; type=application/dicom; transfer-syntax=*
Accept-Encoding: gzip
Authorization: <Not Logged>
User-Agent: Google-HTTP-Java-Client/1.28.0 (gzip)

07.08.2020 15:45:55.298 *CONFIG* [Google Dicom Explorer-pool-4-thread-1] com.google.api.client.http.HttpTransport: curl -v --compressed -H 'Accept: multipart/related; type=application/dicom; transfer-syntax=*' -H 'Accept-Encoding: gzip' -H 'Authorization: <Not Logged>' -H 'User-Agent: Google-HTTP-Java-Client/1.28.0 (gzip)' -- 'https://healthcare.googleapis.com/v1beta1/projects/chuck-dev-[REDACTED]/locations/europe-west4/datasets/veye-feedback/dicomStores/veye-feedback/dicomWeb/studies/1.2.840.113745.101000.1186002.40721.8111.13846623'
07.08.2020 15:45:55.557 *CONFIG* [Google Dicom Explorer-pool-4-thread-1] com.google.api.client.http.HttpTransport: -------------- RESPONSE --------------
HTTP/1.1 200 OK
X-Frame-Options: SAMEORIGIN
Transfer-Encoding: chunked
Alt-Svc: h3-29=":443"; ma=2592000,h3-27=":443"; ma=2592000,h3-T050=":443"; ma=2592000,h3-Q050=":443"; ma=2592000,h3-Q046=":443"; ma=2592000,h3-Q043=":443"; ma=2592000,quic=":443"; ma=2592000; v="46,43"
Server: ESF
X-Content-Type-Options: nosniff
Vary: Referer
Vary: X-Origin
Vary: Origin
X-XSS-Protection: 0
Date: Fri, 07 Aug 2020 13:45:55 GMT
Content-Type: multipart/related; boundary=4ffba0f755780eec54b75fcc0e1d4c2f558da714b127b04b7431d4b6c770; transfer-syntax=*; type="application/dicom"

The window as I see it:

I am kinda suspecting that something is probably wrong with my GCP project setup. Is there any way I can debug this further?

Can't substitute custom OAuth client

Using https://github.com/GoogleCloudPlatform/weasis-chcapi-extension/releases/tag/v3.0.8 with Weasis 3.6 on MacOS installed using native installer.

I tried putting the client_secrets.json file in /Applications/Weasis.app/Contents/app/ as well as adding google.client.secret=file:///Applications/Weasis.app/Contents/app/client_secrets.json to ext-config.properties, but it still loads the packaged client secrets in both cases.

latest plugin does not load

I have installed Weasis v3.6.0 and downloaded the latest jar file v3.0.13 and followed the instructions for installing the plugin. I have placed the plugin in the plugins directory (which I created) and modified the ext-config.properties file to include the absolute path (felix.auto.start.85=file:///C:/Program%20Files/Weasis/app/plugins/weasis-chcapi-extension-3.0.13.jar). After starting, it never properly loads the jar file. Internal logs for the app do not show the plugin trying to load. What am I missing?

fail to display big series

extension fails to display series bigger than some limit(something near 70MB, 100MB definitely won't be displayed) but according to network activity it seems to be downloaded

20.05.2019 22:05:37.517 *ERROR* [Google Dicom Explorer-pool-5-thread-1] org.weasis.dicom.google.explorer.DownloadManager$LoadGoogleDicom: Error occured javax.net.ssl.SSLException: SSL peer shut down incorrectly at sun.security.ssl.InputRecord.readV3Record(InputRecord.java:596) at sun.security.ssl.InputRecord.read(InputRecord.java:532) at sun.security.ssl.SSLSocketImpl.readRecord(SSLSocketImpl.java:975)

Google Sign-In Shouldn't Happen on Start-up

Right now Google sign-in happens when the plugin get's loaded. There should be a dedicated "Sign-in" button instead.

Linux: Google sign-in requires clicking link in terminal output

The application should open the browser window for you instead of you having to look through the terminal output. This only happens on Linux, not Mac.