cidgoh / DataHarmonizer

A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the Centre for Infectious Disease Genomics and One Health (CIDGOH), at Simon Fraser University, is now an open-source collaboration with contributions from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.
MIT License
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Proposal: UI configuration #359

Open pkalita-lbl opened 1 year ago

pkalita-lbl commented 1 year ago

This is just a starting point of a discussion and not necessarily fully thought-out yet.

The basic idea is that a schema (LinkML or otherwise) generally can't capture everything about how a tool to collect data adhering to that schema should look or behave. Obviously the schema can inform some sensible defaults (i.e. provide a dropdown menu when a value must be chosen from an enumeration) but it can't capture things like "suggest terms retrieved from this arbitrary endpoint". Or "this field should be omitted from the entry UI because it will be populated by a separate process" (see https://github.com/cidgoh/DataHarmonizer/issues/337). For use cases like these that are common enough, it would be nice for data-harmonizer clients to not have to write a lot of custom code and instead simply provide some configuration.

The changes here represent a very basic sketch of what a UI configuration approach might look like. A data-harmonizer application (i.e. web/index.js) provides a UI configuration object to the DataHarmonizer constructor (an application could even store this configuration in a standalone JSON file). The DataHarmonizer class is responsible for interpreting this configuration and applying the correct settings internally. The specific example implemented here is directing the DataHarmonizer instance to use an OLS-based autocomplete for a particular field.

It's not implemented in this proof-of-concept, but you could also imagine a UI config like:

{
  "fields": {
    "internal_id": {
      "hidden": true
    },
    "look_but_dont_touch": {
      "readonly": true
    }
  }
}

I could also imagine non-field-specific configuration going outside of the "fields" key (e.g. https://github.com/cidgoh/DataHarmonizer/issues/334):

{
  "numFrozenColumns": 2
  "fields": {
    ...
  }
}

Again, this is just a conversation starter. I'd be interested to know if this might address (or not) other cases.

cc: @ddooley

pkalita-lbl commented 1 year ago

Tangentially related: the idea of a separate UI configuration is not uncommon in the world of libraries that generate forms from JSONSchema. For example: here and here.

ddooley commented 1 year ago

Hi Patrick, sorry for delay in looking at this closely - I'm realizing discussion was held up. I totally see need to add DH interface configuration such as number of columns to freeze, but it seems like there are two types of configuration - ones that don't depend on a specific schema/class at hand, and those that do, i.e. with some classes it makes sense to freeze 2 panes, or hide x columns.

I was wondering for configuration how much mileage we could get out of encoding user interface behaviour right into a class or slot annotation, such that it could apply to any tool that displays it, if desired? Or name that tool explicitly in the annotation, e.g.

class_X: {
  annotations: {
    ui_behaviour: {
       DataHarmonizer: { // Optional layer ???
         numFrozenColumns": 2
       }
    }
  ...
   slots: {
     "internal_id": {
       "annotations": {
          ui_behaviour: {
             DataHarmonizer: { // Optional layer ???
                "hidden": true,
                "readonly": true  // e.g.
              }
           }
       }
    }

Or this structure could be separate from schema content, but could be added to new DH instance as you have it:

const uiConfig = { ...

What this would do is enable better code synchronization and not have it that people are manually adapting their code to match a change or deprecation in a class or slot reference.

ddooley commented 1 year ago

Your dynamic OLS lookup example looks neat; I assume the query part of it remains to be flushed out? Here I can see why we wouldn't necessarily want references to the widget baked into the LinkML schema. In other words, it seems much more consumer application specific whether users can be provided with application functionality to do dynamic lookups for particular fields, given their particular agency/project needs, their firewall etc, .... but ... say we had an open source such as OLS that could broadly be used for term lookup and OLS had no objections to serving all comers, then I'm also tempted to allow the LinkML spec to include the details of invoking that widget on a particular slot, again via annotations on that slot in a similar fashion to above? But maybe that's a misstep - all widget-specific configuration needs to be kept out of a schema itself? But perhaps we could ensure the Widget specific config can then contain an echo of the schema class/slot structure just for the fields that it pertains to?!