StringApp fails on Mac after CS update to 3.6.1

[M.Z. Rogon]

Hi All,

After updating Cytoscape to 3.6.1 the StringApp is unable to complete the query.

• "Unexpected error when parsing JSON from server: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target"

Downgrading to 3.6.0 doesn't help.

Seems to work on Linux, but not on my Mac OS 10.13.4

Latest Java was downloaded by CS during the installation of 3.6.1, I've tried another update from the Oracle website, same error.

Cleaned the entire environment, doesn't help.

Can someone please double-check?

Cheers

Matt

[Scooter Morris]

Hi Matt,
    I'm not having a problem.  What version of the stringApp are you using?

-- scooter

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[M.Z. Rogon]

Then I don't know what else to do. String App is the latest, downloaded after installation from the cs app store.

[Scooter Morris]

On 05/09/2018 09:08 AM, M.Z. Rogon wrote:
> Then I don't know what else to do. String App is the latest, downloaded after installation from the cs app store.
>

Can you send me your query?  I'll try it here.

-- scooter

[M.Z. Rogon]

Seems to be this issue.
https://stackoverflow.com/questions/9619030/resolving-javax-net-ssl-sslhandshakeexception-sun-security-validator-validatore
I'll try to update the certificate locally in my Java environment tomorrow...

[M.Z. Rogon]

It's any query, not a specific one.

[Scooter Morris]

On 05/09/2018 09:24 AM, M.Z. Rogon wrote:
> It's any query, not a specific one.
>

Got it.  I just tested on my Mac (10.13.4) with stringApp 1.4.0 and I'm
not seeing any issues.  Let me know if adding your certificates locally
helps.  I haven't done anything special on my system as far as I know.

-- scooter

[Barry Demchak]

Can you tell us what the Java VM version is? (It's listed on the Splash screen as Cytoscape starts.) We have seen this kind of thing before when Cytoscape tries to access HTTPS, but the JVM has an old list of trusted CAs. Have you tried getting the latest JVM??

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[M.Z. Rogon]

So here we go.

The version that was failing was 1.8.0_112 as well as the updated version 1.8.0_171

The only way to fix this was to actually import the certificate straight into Java store after cleaning up.

It seems that the cloudflare certificate used by String (recent change?) is not trusted.

Fortunately we don't care, and we can get the certificate throught the REST API web page (download the certificate when you see the popup, or click the button next to the url).

https://string-db.org/api/json/get_string_ids?species=9606&identifiers=ENSG00000002016&caller_identity=string_app_v1_3_2

Then it's a matter of cleaning up Java on the machine - had to drop the latest 171 in favor of 112

$ java -version

Adding the certificate to the java store:

sudo keytool -importcert -alias dev -file CloudFlareOriginCertificate.crt -keystore /Library/Java/JavaVirtualMachines/jdk1.8.0_112.jdk/Contents/Home/jre/lib/security/cacerts

ClueGO, and a couple of other things are still at least partially broken, we'll have to wait for updates.

Probably the last time I do a Cytoscape update before running a course ;P

Cheers

Matt

[Barry Demchak]

Wow, Matt …

 

An unhappy report, but I’m glad you’re navigating well.

 

I see the string web site certificate was issued about 6 months ago … but that’s not necessarily the same as the one for the web service.

 

On my Windows 10 system, Chrome, Firefox and Edge all trust Cloudflare … so I didn’t get the certificate dialog when I went to that link.

 

On my old Mac (El Capitan, Java 1.8.0_60) Stringapp seems to run just fine.

 

Interestingly, too, on my Mac, “keytool –list” complains that I don’t even have a .keystore file. Same on my Windows box.

 

Based on this, it seems like your configuration doesn’t match what we expect to see …

 

How about this as an ignorant theory … could it be that you have a keystore and it overrides the Java defaults, and doesn’t have Cloudflare in it??

 

I don’t play with keys very often, so I’ll defer to you …

 

 

From: cytoscape...@googlegroups.com <cytoscape...@googlegroups.com> On Behalf Of M.Z. Rogon
Sent: Friday, May 11, 2018 2:46 AM
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Subject: Re: [cytoscape-helpdesk] StringApp fails on Mac after CS update to 3.6.1

 

So here we go.

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[M.Z. Rogon]

I agree, it has to be specific to my system, as my windows and Linux installations run fine... but... whatever happened happened with the Java downloaded by CS...

As far as I can remember the last CS update also downloaded Java and that was fine.
On this particular machine I only have one jvm 1.8
The latest version I installed only after realizing that something was wrong. That one really confused my Mac and I really didn't have time to mess with environment variables, even the path for the installation was wrong...

No idea what is happening... most importantly it works now, plus I have a clean and fresh CS, which is always nice. I'll worry about this again when we move to 3.6.2 ;)

[Barry Demchak]

Thanks, Matt --

We'll be on the lookout for similar reports. Sorry this was so painful for you. If we can latch onto a good reproduce case, we'll run this down.

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From: cytoscape...@googlegroups.com <cytoscape...@googlegroups.com> On Behalf Of M.Z. Rogon
Sent: Friday, May 11, 2018 11:22 AM
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>

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[kevin....@gmail.com]

Dear,

I also encounter exactly the same issues as Matt.

My version of Cytoscape in 3.6.1, and my java version is 1.8.0_162.

Kevin