allowCrossOriginDataRoot Error Message

[mdhar1980]

Hello, Nick,

Thanks again for this module. I have just installed in on a new Tripal website, and the suggested link for our data says:

However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error.

Now, due to another issue, we haven't yet been able to get the GFF to load on Chado. However, FASTAs are loaded, so there should be data.

At the bottom of the page is the following error message:

Error: Invalid JBrowse dataRoot setting. For security, absolute URLs are not allowed. Set allowCrossOriginDataRoot to true to disable this security check.

How, with the Tripal JBrowse API, can you set that configuration? Or is there another fix that needs to be made.

Thanks!

[njbooher]

It looks like that as of this release JBrowse doesn't allow data to be loaded from external sites by default, so the method in the quickstart no longer works. You will need to install JBrowse on your Tripal server and configure the data root to either point to the API using a relative URL, or add allowCrossOriginDataRoot = true to your JBrowse config file if you want to use the absolute URL method.

[mdhar1980]

Hi, Nick,

OK, thanks for the response. I'm guessing the data root would be set in this file? https://github.com/GMOD/jbrowse/blob/master/jbrowse.conf

And would allowCrossOriginDataRoot be added there too?

What would be the relative path for the API -- that is, where would the API be in the server's file structure? I know the Quick Start says "?data=http://yourtripalsite.com/api/jbrowse", but I don't see an api folder in our HTML root. Should there be one there, or am I just misunderstanding how that URL works (likely)?

Thanks again

[njbooher]

OK, thanks for the response. I'm guessing the data root would be set in this file? https://github.com/GMOD/jbrowse/blob/master/jbrowse.conf

And would allowCrossOriginDataRoot be added there too?

yes

What would be the relative path for the API -- that is, where would the API be in the server's file structure? I know the Quick Start says "?data=http://yourtripalsite.com/api/jbrowse", but I don't see an api folder in our HTML root. Should there be one there, or am I just misunderstanding how that URL works (likely)?

try ?data=/api/jbrowse

it's not an actual file, URLs like that get routed to index.php and eventually handled by this module

[kyrenya]

Hi, I'm trying to follow advice here, but I dont manage to see my data. Dont know if I did something wrong, of I skipped something..
I installed in my server jbrowse-1.15.4
run ./setup.sh
changed jbrowse.conf adding:

alloweCrossOriginDataRoot = true

and tried both
?data=/api/jbrowse

when trying to go to the URL.

and I get this:

and when try with my site
?data=http://yourtripalsite.com/api/jbrowse

I get the warning saying to allow cross origin data (its done)!?

I appreciate any help, thanks!

[njbooher]

alloweCrossOriginDataRoot = true

->

allowCrossOriginDataRoot = true

If that doesn't work please provide a link to your site.

[mdhar1980]

Hi, Nick,

I edited the dataRoot line in the config file, and I get the same error on my website as kyrenya did:
"Unable to load: http://aduae210-lap.abudhabi.nyu.edu/api/jbrowse/seq/refSeqs.json status 404"

I edited the config line to be:
dataRoot = /api/jbrowse

I'm not sure, however, what the URL should be. I tried two different urls (you won't be able to access, as they're behind a firewall, just giving for the filepaths):
http://aduae210-lap.abudhabi.nyu.edu/jbrowse/JBrowse-1.15.4/
http://aduae210-lap.abudhabi.nyu.edu/jbrowse/JBrowse-1.15.4/index.html?data=/api/jbrowse

Both have that same error message on the page: "Unable to load: http://aduae210-lap.abudhabi.nyu.edu/api/jbrowse/seq/refSeqs.json status 404"

The latter is modeled after the filepath I can use to get to the yeast sample data (which does load):
http://aduae210-lap.abudhabi.nyu.edu/jbrowse/JBrowse-1.15.4/index.html?data=sample_data/json/yeast

[njbooher]

Your server isn't publicly accessible.

Here's the URL for a working installation if that helps:

Tripal: https://www.serioladb.org
JBrowse: https://www.serioladb.org/jbrowse/
JBrowse config: https://www.serioladb.org/jbrowse/jbrowse.conf

[mdhar1980]

Hi, Nick,

Yes, it is behind a firewall. So, it seems that our jbrowse using the API should be accessible at the first URL I listed (http://aduae210-lap.abudhabi.nyu.edu/jbrowse/JBrowse-1.15.4/) after I modified the dataRoot, but I get that same error message.

[kyrenya]

sorry I had to restart the installation of my site for other reasons, thats why I have this in standby by now. Did you manage @mdhar1980 ?
thanks!

[mdhar1980]

hi, Kyrenya,

I haven't gotten the module to work yet. For right now, I've just added our data directly to the JBrowse we downloaded on our server. So, I'm not using the module.

[kyrenya]

ok thanks!