how to integrate Cancer Digital Slide Archive (CDSA) into local cbioportal?

[Y Chen]

Hi,

We host a local version of cbioportal. 

How do we integrate Cancer Digital Slide Archive (CDSA) into our cbioportal to get similar interface like this link below?

https://www.cbioportal.org/patient/tissueImage?caseId=TCGA-DH-5142&studyId=lgg_tcga 

We want to host our own images at the end, but maybe start with showing the same interface and the public image from Cancer Digital Slide Archive (CDSA). 

Is there documentation about how to do this, or should I contact people in Cancer Digital Slide Archive (CDSA)?

Thank you so much for your help!

Yingfei

[JJ Gao]

Dear Yingfei,

The cBioPortal CDSI integration is simply an i-frame to the CDSA website (https://cancer.digitalslidearchive.org/). In order for you to achieve similar results, you would need to install CDSA or some other image viewer, which can be integrated into the cBioPortal using Resources format (https://docs.cbioportal.org/file-formats/#resource-data)

Best,

-JJ

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[Y Chen]

Hi,

Now I have Digital Slide Archive (DSA) server running on the same server as cbioportal. 

However, when I try to access the image hosted on DSA in cbioportal, "pathology slide" tab, it get errors below:

"We can't show this URL in the portal. Please use the link below:
http://<ip>:8010/#item/691...d82"

I run DSA on port 8010, if click this link, it will go to the image on DSA server correctly, it just won't embed it in cbioportal.

The image hosted on CSDA works in cbioportal, it is embedded correctly. 

I add "pathology slide" tab according to https://docs.cbioportal.org/file-formats/#resource-data 

vi data_resource_sample.txt

PATIENT_ID      SAMPLE_ID       RESOURCE_ID     URL

P01     P01_Pri PATHOLOGY_SLIDE https://cancer.digitalslidearchive.org/#!/CDSA/lgg/TCGA-DH-5142
P04     P04_Pri PATHOLOGY_SLIDE http://<ip>:8010/#item/691...d84

Is there anything need to change in portal.properties to allow this <ip>:8010?  Is it configuration on cbioportal side or DSA side?

I'm not sure if this is related to reverse proxy. Cbioportal is behind nginx reverse proxy. DSA is currently not using reverse proxy, but I can config it to use it.

Thank you so much for your help!

Yingfei

[Gaofei Zhao]

Hi Yingfei,

This issue occurs because you’re trying to embed an HTTP resource inside an HTTPS cBioPortal application. Enabling HTTPS on your DSA app will fix the issue — once both the portal and the embedded app use HTTPS, the browser will allow the iframe to load properly.

Best,

Gaofei

To view this discussion visit https://groups.google.com/d/msgid/cbioportal/0739e5a2-d889-49b5-a617-b86e3786c737n%40googlegroups.com.