schematic: allow using labels as column headers in templates instead of display names

[mialy-defelice]

This issue is based on a request by @lopierra that began as a slack conversation, which can be viewed here.

in this example manifest, the column headers are the displayNames (e.g. Condition Source Text) that are more readable, but I would prefer to have the column headers be the labels (e.g. conditionSourceText) because they don't have spaces and are easier to work with programmatically.

User Story: As a data curator I would like the choice to generate the manifest tables column headers with schema labels instead display names for programatic ease of use.

AC:

• API and CLI have option to --use_schema_label as the column header when generating a manifest. Calling this label will set it to True, default is False and will default to using the display name.
• Manifest validation does not throw an error when --use_schema_label used to generate the manifest

Confirm the following: Use several models -- Example, HTAN, iAtlas

• [x] Manifests use schema label
• [x] Conditional formatting
• [x] Required formatting
• [x] Dropdowns
• [x] XSLX output
• [x] Download manifest from synapse
• [x] Submit manifest
• [x] Validate manifest

[lopierra]

To clarify the above, I am only able to use --use_schema_label with submit. I am not able to use get to generate a manifest with schema labels as columns headers, and if I manually create a CSV with schema labels as column headers, validate will throw an error. So I am forced to use display names in R, which is not ideal.

[mialy-defelice]

Hey @lopierra,

Can you provide me with your model and a manifest with entries? I would like to validate and submit to test that everything is working as you are intending.

Thanks!

[lopierra]

Hi @mialy-defelice - here is our model in YAML and JSON-LD.

I'm attaching a test manifest for the Study component.

An additional complication is that if I submit my own manifest with schemaLabels as headers, Synapse automatically capitalizes the first letter of each (so studyCode becomes StudyCode). Is there some way to suppress that, or do I need to open a ticket for Platform about this?

[mialy-defelice]

An additional complication is that if I submit my own manifest with schemaLabels as headers, Synapse automatically capitalizes the first letter of each (so studyCode becomes StudyCode). Is there some way to suppress that, or do I need to open a ticket for Platform about this?

@lopierra Are you submitting through the python or R client (using a table upload) or are you using Schematic?

[lopierra]

I am using schematic.

[mialy-defelice]

I am using schematic.

@lopierra Okay, this is intentional in schematic to conform to synapse standards. We convert all headers to PascalCase during the final submission step. Are you always using camelCase? You can open a ticket with us.

@milen-sage do they need to be Class Labels or can they be Property Labels?

[lopierra]

Thanks - I will open a ticket. We chose camelCase as the standard for slot names in our LinkML model and PascalCase for the classes, so it would be good to have the option for submitting camelCase headers to Synapse.

[milen-sage]

Based on conversation with @lopierra this is not an urgent blocker and we'll resolve after refactoring schema parsers #857