Module configuration on a local server

[KrisRousseau]

Hi,
On my local server, I created a study with subjects, design and sample.
I'm ready to upload data, but there's no modules and I don't understand how I could create one.

My module configuration:

Module Configuration

modules.showInMenu=true
modules.sam.baseurl=http://${ipaddr}:8080/gscf/measurements/SAM
modules.sam.url=gscf/measurements/SAM
modules.metabolomics.url=http://${ipaddr}:8083/metabolomicsModule
modules.massSequencing.url=http://${ipaddr}:8184/massSequencing

Where ${ipaddr} is set to my server IP address.

What should I do to upload data (platforms, features and measurements) ?

Thanks for your help.

[ferryjagers]

Hi Kris,

A more convenient way to configure your modules is via 'Admin' -> 'Manage modules'

To add a new module (I assume that you only want to use local modules for now):

• Click 'New AssayModule' at the top.
• UUID: leave blank (system will generate a UUID)
• Base URL: http://${ipaddr}:8080/gscf/measurements/${moduleName}
• Name: ${moduleName}
• URL: /gscf/measurements/${moduleName}
• Click create. It should now be shown in your 'Admin' -> 'Manage modules' overiew. If so, restart your server and the module will be initialised on startup.

For your next step, data upload, this might be useful:
ENPADASI PhenotypeDatabase Tutorial

[KrisRousseau]

Hi Ferry,
I create a new module, but I have this message when I go to Module/My module:
"404 The page your are looking for could not be found. Please make sure you entered the right address, or use the menu to find your way. "

I succeed to import data on https://dashin.eu/interventionstudies.
I didn't found more information about modules on enpadasi.eu/wp6.html

[KrisRousseau]

Should I upload something to be able to use Modules on local server ?

[ferryjagers]

Could you please make a screenshot of your 'Manage modules' (/assayModule/index) page?

[mikkeltullin]

Hi Kris and Ferry,
I have the same problem. This is how it looks when I am under "Manage modules"

http://enpadasitest.science.ku.dk/gscf/assayModule/index

However, I have access to the modules from the start page.

http://enpadasitest.science.ku.dk/

But when I am in the modules section in this case "Clinical chemistry" it is not possible to use the "back to design" button.

http://enpadasitest.science.ku.dk/gscf/measurements/ClinicalChem

Then this error i popping up

http://localhost:8080/gscf

Best Mikkel

[KrisRousseau]

I propably forgot something yesterday. I can access to Modules now and I succeed to upload all my datas.
Mikkel, do you restart your server (that's probably what I'd forgoten) ?

For information, my modules list:

Ferry, thank a lot for your help.

Kris.

[ferryjagers]

@mikkeltullin
I see a error in your overview: 'Url' has to start with a forward slash (**/**gscf/measurements/ClinicalChem).
For the 'Back to design' issue:
Change 'gscf.baseURL' in default.properties or overwrite it in your external config.

Great work both :-)

Best,
Ferry

[mikkeltullin]

Dear Kris,

Yes I rebooted the server and after that I can see the modules, but only access them from the start page.

[mikkeltullin]

it is supposed to start with a "/"? or just gscf/ ....

/Mikkel

[ferryjagers]

It is supposed to start with a "/"

/Ferry

[mikkeltullin]

Ok

[mikkeltullin]

Ok

From: Ferry Jagers [mailto:[email protected]]
Sent: 6. oktober 2016 14:26
To: PhenotypeFoundation/PhenotypeDatabase
Cc: Mikkel Tullin; Mention
Subject: Re: [PhenotypeFoundation/PhenotypeDatabase] Module configuration on a local server (#164)

It is supposed to start with a "/"

/Ferry

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHubhttps://github.com//issues/164#issuecomment-251946476, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVB96U12Y4hayHdxN6KP3Py5tDU8r6OSks5qxOjRgaJpZM4KNqAW.

[mikkeltullin]

Ok, done! I believe I have to reboot again?

Regarding the 'Back to design' issue:

I don't know how access the the default.properties is it possible explain here?

/Mikkel

[ferryjagers]

Yes, you need to reboot for 'Manage module' changes as well as config changes (Grails behaviour).

It is located at ${projectRoot}/grails-app/conf/default.properties
Did you configure your database etc. in an external configuration file (.gscf folder in tomcat home)?
If so, it is better to keep all your config together over there.

[fsando]

I placed two config files in tomcat/.gscf/:

tomcat/.gscf/production.properties
tomcat/.gscf/production.groovy

(the last one to get to the mail server settings)

I don't have access to the server right now but my local copy of the of production.properties looks like this (where I believe ipaddr is the domain name, but could also be the public ip, I will check Monday):

## Module Configuration ##
modules.showInMenu=true
modules.sam.baseurl=http://${ipaddr}:8080/gscf/measurements/SAM
modules.sam.url=gscf/measurements/SAM
modules.metabolomics.url=http://${ipaddr}:8083/metabolomicsModule
modules.massSequencing.url=http://${ipaddr}:8184/massSequencing

## Number of seconds to keep rest results from modules in cache ##
modules.cacheDuration=900

[ferryjagers]

For your convenience; you could move it all to one production.groovy (note: in this file all lines should be real groovy code, so you will need to change modules.sam.url=gscf/measurements/SAM to modules.sam.url="gscf/measurements/SAM" etc).
The .groovy config file option was introduced after we written the installation guides, now I see it causes confusion I will fix it soon.