Frequently Asked Questions¶

Data Dictionary¶

I'm customizing the data schema, where I can find information about the data dictionary customization, variables' definition, and files formatting?¶

Please refer documentation about Creating New Dictionary and Data Types.

I have a dictionary in my local schemas folder, how can I generate the `schema.json`?¶

You can use our dictionaryutils tool. You can find an example on how to generate JSON in the README

Cloud Automation (Legacy)¶

I'm setting up a CSOC-free instance, what should I set for the `config_folder`?¶

The config_folder variable sets the location of your user.yaml file. If you are using a local file, you can put any value - it won't be used. If you are using any of our user.yaml files, then you may need to know which one. If you are neither using ours nor local, you can also put a random value, and then later when deploying kubernetes, you will be able to point the location of your permissions file.

I modified the `user.yaml` file. How do I update Arborist?¶

If you run gen3 job run usersync changes should be picked up automatically. If you don't want to run that command every time you make changes to your user.yaml, you can deploy the cronjob gen3 job run usersync-cronjob and kubernetes will check for changes every hour and update services accordingly.

How do I change the title of my webpage from the default "Generic Data Commons"? Automation?¶

You can override the default configuration in your commons by using gitops.json file. Set your portal_app to gitops in your file cdis-manifest/your-commons-name/manifest.json. Then create cdis-manifest/your-commons-name/portal/gitops.json file. You can use this file as a template for your own gitops.json file. Set navigation title and login title at your choice. Then reroll portal with gen3 kube-setup-portal.

I updated the Fence configuration. Why haven't the changes taken effect?¶

After updating the Fence configuration, run kubectl delete secret fence-config, gen3 kube-setup-fence and roll Fence for configuration changes to take effect with gen3 roll fence.

I receive errors when running queries on the GraphiQL "Query" page, e.g., Cannot query field "field" on type "Root".¶

You may need to hit the Switch to Graph Model button in the upper right corner.

Please refer to Cloud Automation documentation.

Arborist and Sheepdog don't work as expected, what should I check?¶

kubectl logs <name of pod> can show you corresponding errors in the logs.

I've updated the data dictionary, what services should I restart for the change to take effect?¶

First, restart Peregrine gen3 roll peregrine and Sheepdog gen3 roll sheepdog. After these two services restarted, please portal with gen3 roll portal. Please note, if you are making significant changes to the dictionary, you will also need to update portal_app in the manifest.

I branched out the Windmill portal, should I update manifest with a new version of portal?¶

Yes, you can update the manifest to use your version of the portal and use gen3\ kube-setup-portal or gen3 roll portal to changes to take effect.

How can I update the APP for the portal?¶

You can set the global.portal_app setting in your manifest to the name of your windmill configuration file and run gen3 kube-setup-portal.

What do I need to restart if I updated Fence configuration with OAuth credentials?¶

Please run kubectl delete secret fence-config and gen3 kube-setup-fence. If you also updated the user.yaml in the folder apis_configs, you need to run gen3 job run useryaml-job.

I'm storing `user.yaml` in S3 (not locally) and updated it, how do I ensure changes take effect?¶

After you change user.yaml, run gen3 kube-setup-secrets and gen3 job run usersync.

I see my data on a Query page, but not in the Exploration page. What other services do I need to deploy/configure to have it running?¶

The Exploration page needs to be set up with Elastic Search using Guppy. Please refer to the relevant Guppy and Cloud Automation documentation, and see an Sample Configuration for the Guppy.

Compose Services (Deprecated)¶

I installed Compose Services, how do I create a program and a project?¶

Please refer to corresponding Gen3 Documentation to create your first program and project.

I created a program, but I see a `NotFound` error when I try to create a project within my program.¶

Please make sure you inserted program name in the URL, not dbgap_accession_number.

I can not submit data to the project I just created.¶

Please ensure you granted yourself permissions in the user.yaml file. You can find this file in the Secrets folder within your Compose Services folder. Follow provided in the file example to grant yourself relevant permissions. You can find more information in the Setting Up Users documentation.

User.yaml contains information about program/project, but I still cannot access it.¶

Please ensure you are using dbgap_accession_number value as an identifier for the auth_id field, not program's name or project's code.

I see a warning about my connection not being private.¶

Don't worry. The warning about connection not being private appears because creds_setup.sh script generated self-signed SSL certificate to allow microservices to communicate with each other without bypassing SSL verification. Your browser can not verify this certificate. Once you install a trusted SSL certificate instead of generated by our script, this warning will go away.

I want to run Compose Services on the server, how do I configure it?¶

To configure Compose Services with your domain, please change the BASE_URL field in the fence_config.yaml file, and the hostname field in the peregrine.json and sheepdog.json files.

I'm trying to upload files with gen3-client, but received an error `x509: certificate signed by unknown authority`.¶

You can add self-signed certificate to your trusted certificates. Steps may vary depending on Operating System you use.