Migration from tdata to teal_data inside your teal modules

[vedhav]

⚠️ Comments will be opened for external users after release.

Migration from tdata to teal_data inside your teal modules

The data argument in both the module UI function and the module server function is used to access the application data. In the recent refactor of teal, we have transitioned from using the tdata class to the teal_data class inside the teal modules. This discussion aims to assist you in modifying your existing modules to be compatible with the new data structure.

Key Changes

Previously, the data obtained was of the tdata class, a named list of reactive data.frame or MultiAssayExperiment objects containing the data after it had been filtered through the filter panel.
After the refactor, the data object received by the UI will be of the teal_data class, which is the same teal_data passed by the teal app developer. While the server will get a reactive(teal_data) which will react to the active filters. This change requires all the modules to adapt the internal module logic and data handling to accommodate the new teal_data structure.

Migration Steps

Quick fix

You could convert the teal_data into tdata using the teal::as_tdata if you need a quick fix to make your module work without making it compatible with teal_data.

# Use this in the ui function
data <- as_tdata(data)
# Use this in the server function
data <- as_tdata(data())

But, we recommend making the complete migration as described below.

Complete migration

Here are the potential changes that need to be taken care of.

1. Update Data Class Assertions

In UI function

Old Code	New Code
checkmate::assert_class(data, "tdata")	checkmate::assert_class(data, "teal_data")

In server function

Old Code	New Code
checkmate::assert_class(data, "tdata")	checkmate::assert_class(data, "reactive") checkmate::assert_class(isolate(data()), "teal_data")

2. Initializing the qenv object

The object teal_data inherits from qenv so we don't need to convert the data -> qenv anymore.

Old Code	New Code
teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data))	data()

3. General use of data inside the module server

Old Code	New Code
data	data()
data[[dataname]]()	data()[[dataname]]
length(data)	length(datanames(data()))

You can have a look at the tdata to teal_data migration in the teal.modules.clinical for reference to these changes.

4. Update the package version dependencies

Ensure that you update your renv.lock or DESCRIPTION with these min-versions of:
TODO: This feature is still not merged, the package versions will be updated once they are merged.

1. teal.code >=
2. teal.data >=
3. teal.slice >=
4. teal.transform >=
5. teal >=