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saezlab / Omnipath_Cytoscape

a plug-in to access Omnipath from Cytoscape
http://apps.cytoscape.org/apps/omnipath
GNU General Public License v3.0
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Querying list of databases from the server fails #4

Open ChloeJKim opened 2 years ago

ChloeJKim commented 2 years ago

Hi,

I tried the 'Installation' Steps and open the Cytoscape to see Omnipath. But every time I load the dataset, I get the following error message (see picture), can you please help? Thank you so much!! The version I'm using Omnipath 2.3 with Cytoscape 3_9_1_windows_64bit

image

deeenes commented 2 years ago

Hi Chloe,

It looks like an SSL error, perhaps your OS or your Java is missing some root certificates, or doesn't support any modern ciphers. What is the version of your OS? What happens if you open an URL from our server (e.g. https://omnipathdb.org/resources/interactions) in the built-in web browser of your OS (Edge or IE)? What is the exact version of Java that you use to run Cytoscape?

Best,

Denes

ChloeJKim commented 2 years ago

@deeenes thanks for looking into this, OS version: 20H2, Windows 10 Enterprise, when I open the url I see (below pic) image

Exact version of Java: version 8 Update 51

deeenes commented 2 years ago

We see the error doesn't happen in the browser, as it can be expected also based on the version of your OS. It means the OS is not the source of outdated SSL key store. Then it can only be Java.

Your Java is 1.8.0_u51b16, released in July 2015. It means applications running in this Java can not access a quite large portion of today's web servers as the encryption keys shipped with this release are at least 7 years old. The root certificate (ISRG Root X1) signing the certificate of our server dates back to June 2015, but hasn't been included yet in the Java release used by you. It wasn't a problem until Oct 2021 when another root certificate (DST Root CA X3), that signs the above mentioned new root certificate, expired.

Updating Java Runtime Environment to the current version of Java 8 (1.8.0u321) should fix this issue. Oracle also recommends to remove the old Java before installing a new one.

However, Cytoscape suggests that it works only with Java 11, a version that Oracle made non-free, so the only option is to use the OpenJDK version. In this case you should remove the old Java and Cytoscape, and install OpenJDK 11 and Cytoscape 3.9, and re-install the OmniPath plug-in if necessary.

ps. I recommend you to consider using our R client as it supports a much broader range of OmniPath features, and implementing your analysis in R makes your work more efficient and reproducible.