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README-datatype.md

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Adding a new datatype to the Workspace

KBase data objects are strongly typed, meaning that each datatype has a structure with required and optional fields. This structure is enforced during creation.

You can add new types to KBase, but please consult the Project Guides before you begin.

The basic steps to adding a new type are: 1) Login and connect to the workspace; 2) Request and approve the new module (i.e, the namespace); 3) Create the typespec; 4) Register, commit and release the typespec.

We will now walk through each step. In this example, we will register a new module called MyModule.

Start a new client session

If you have the workspace tools installed locally you can try using them. Otherwise you can use the client.sh helper script to start a client session. In these instructions, we assume that you've already set up your site.cfg (see deploy_dev/README.md for instructions). In your site.cfig, you should have set PUBLIC_ADDRESS to your public hostname. You will also need to have successfully completed the bootstrap launch (with the deploy.sh script).

Connect to the workspace

./scripts/client.sh
. ./site.cfg
ws-url http://${PUBLIC_ADDRESS}:8080/services/ws
echo $PASSWORD|kbase-login $USER

You can check that you are successfully logged in by typing kbase-whoami

Register the new module

Workspace types have a Namespace. The top-level part of the name is called a module. We must first request the new module and get approval. In the production system, the approvals would be done by a KBase Administrator.

ws-typespec-register --request MyModule
ws-typespec-register --admin '{"command":"listModRequests"}'
ws-typespec-register --admin '{"command":"approveModRequest" , "module":"MyModule"}'
ws-typespec-register --admin '{"command":"listModRequests"}'

Create the typespc file

MyModule.spec


/* my module, hands off */
module MyModule {

typedef structure {
       string name;
       list values;
} ValueSet;

typedef structure {
   string other_name;
   list  values;
} FloatValueSet;

funcdef getValueSet(string id) returns (ValueSet);

};

Register, commit, and release the new type spec

ws-typespec-register  -t MyModule.spec  --add 'ValueSet;FloatValueSet'

This gives you a preview of what will be committed. Now you can do the real commit: ws-typespec-register -t MyModule.spec --add 'ValueSet;FloatValueSet' --commit ws-typespec-register --release MyModule ws-typespec-list MyModule --spec