Tissue Sample Image files for local cbio instance (?)

[John]

Can you host your own tissue sample files on local servers and have your local cBioPortal instance reference those internal servers via the url in the Sample Resource data file?  

Is it as straight forward as that? Or is there more to it?

I am using cBioPortal version 5.3.6.

Thank you,

John Francis  

[JJ Gao]

Hi John,

Yes, it is as straightforward as that. Please feel free to reach out to us if you have additional questions when implementing it.

-JJ

--
You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cbioportal+...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/cbioportal/834f28fb-f032-44a7-ad0f-576e2b794b61n%40googlegroups.com.

[John Francis]

Hi JJ,

I received some additional information: our images are hosted on an external server, and the image URL does not link directly to the file. Instead, it redirects to a login page, and the image becomes accessible only after successful authentication.

Will this workflow be compatible with cBioPortal (version 5.3.6)?

Thank you,

John Francis

[JJ Gao]

Hi John,

Thanks for the clarification.

Just to confirm: is there a URL that points directly to a specific image? If not, then unfortunately it's not possible to link directly from cBioPortal.

If such a URL does exist, and the authentication flow redirects back to that specific image URL after login, then it should work. However, if the authentication ends up on a general landing page instead of the original image URL, then the first login won't lead directly to the image, and cBioPortal won't be able to display it.

Let me know if that matches your understanding.

Best,

-JJ

To view this discussion visit https://groups.google.com/d/msgid/cbioportal/fa63ba39-0ff6-479e-87b4-36ce71c1eedbn%40googlegroups.com.

[John Francis]

Hi JJ,

Here is the flow:

* The URL brings users to a landing page where they log in with their user ID and password. 

* Once authenticated, they are then automatically taken directly to the image.  

Could you please explain why cBioPortal cannot display this?

Thank you!

John Francis 

[JJ Gao]

Hi John,

That should work. If not, please let us know if some details of the issue. 

You might find this thread help for troubleshooting: https://groups.google.com/g/cbioportal/c/inLUq8iywgw/m/z2PUQ9M-AgAJ

Best,

-JJ

To view this discussion visit https://groups.google.com/d/msgid/cbioportal/0f5218aa-4290-43ec-ae8b-1b7ddea17c5an%40googlegroups.com.

[John Francis]

Hi JJ,

I imported the sample resource files and a have a few questions:

*  When I click the "Pathology Slide" link - it opens a "Pathology" tab and it says - "xxx.xxxx.xxx refused to connect."

    (our local cbio is https and so is the external site that stores the files).

     Could you please explain why can't it connect??  Is there any way to make it connect?

* When I click "Open in a New Window" link from the "Files and Links" tab - it works - takes me to a landing page where user enter user id and password - once authenticated - goes directly to the image.

Is there any correction I can make to get the "Pathology" tab to work?  As I believe this will be very confusing to our users.

Thank you,

John Francis

meta_resource_definition.txt

cancer_study_identifier: neu_brain_cancer.s
resource_type: DEFINITION
data_filename: data_resource_definition.txt

meta_resource_sample.txt
cancer_study_identifier: neu_brain_cancer.s
resource_type: SAMPLE

data_filename: data_resource_sample.txt 

data_resource_definition.txt
RESOURCE_ID     DISPLAY_NAME    RESOURCE_TYPE
PATHOLOGY_SLIDE Pathology Slide SAMPLE

data_resource_sample.txt
PATIENT_ID      SAMPLE_ID       RESOURCE_ID     URL
XXX      XXX_SLXXX     PATHOLOGY_SLIDE https://xxxx.xxx.xxxx.xxx/webclient/img_detail/999/

[Gaofei Zhao]

Hi John,

I think it's a good idea to double-check the image hosting site's configuration.

Most likely the imaging site sends one of these headers:

- X-Frame-Options: DENY (blocks all framing)

- X-Frame-Options: SAMEORIGIN (only allows framing by itself)

- Content-Security-Policy: frame-ancestors 'none' or only certain origins

When the "Pathology" tab tries to show the site inside an iframe, the browser enforces those headers and shows: "[domain] refused to connect."

New window navigation is not framing, so those headers don’t apply and it loads fine.

Best,

Gaofei

To view this discussion visit https://groups.google.com/d/msgid/cbioportal/145713fd-c411-467c-a3a3-0d59858b9167n%40googlegroups.com.

[John Francis]

Hi JJ,

Thank you very much.....You have been very helpful.

Regards,

John Francis