Building pages fails when disorder name is not present

[caufieldjh]

The render_all_disorders function encounters a KeyError if there is not a disorder["name"].

The schema uses name as an identifier in this and other classes but it is not required, so if it needs to be used to render a filename then there will need to be a backup option.
Or this can be a required value for disorder pages.

Example (from https://github.com/monarch-initiative/dismech/actions/runs/21783332536/job/62850730249):

Run just gen-pages
uv run python -m dismech.render --all
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "/home/runner/work/dismech/dismech/src/dismech/render.py", line 622, in <module>
    main()
    ~~~~^^
  File "/home/runner/work/dismech/dismech/src/dismech/render.py", line 613, in main
    render_all_disorders(input_dir, output_dir, template_path)
    ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/dismech/dismech/src/dismech/render.py", line 570, in render_all_disorders
    output_path = output_dir / f'{slugify(disorder["name"])}.html'
                                          ~~~~~~~~^^^^^^^^
KeyError: 'name'
Rendered comorbidity: com_Atopic_Dermatitis__Type_2_Diabetes_Mellitus -> pages/comorbidities/com_Atopic_Dermatitis__Type_2_Diabetes_Mellitus.html
Rendered comorbidity: com_Type_2_Diabetes_Mellitus__Lichen_Simplex_Chronicus__Prurigo_Nodularis -> pages/comorbidities/com_Type_2_Diabetes_Mellitus__Lichen_Simplex_Chronicus__Prurigo_Nodularis.html
Rendered: 22q11.2 Deletion Syndrome -> pages/disorders/22q11.2_Deletion_Syndrome.html
error: Recipe `gen-pages` failed on line 383 with exit code 1
Error: Process completed with exit code 1.

[github-actions]

Issue Summary

This bug occurs when the render_all_disorders function in src/dismech/render.py:570 attempts to access disorder["name"] to generate output filenames, but encounters a disorder YAML file that lacks the name field.

Technical Analysis

Current State

1. Schema Definition: In src/dismech/schema/dismech.yaml:619-623, the name slot is marked as identifier: true but is not required:

   slots:
     name:
       identifier: true
       range: string

2. Code Assumption: The render function assumes name always exists:

   output_path = output_dir / f'{slugify(disorder["name"])}.html'

3. Test Coverage: There exists test_disorder_has_required_fields in tests/test_data.py that checks for the presence of name, suggesting it's expected in practice.

Root Cause Analysis

The issue stems from a schema-code mismatch:

• The LinkML schema treats name as an identifier but doesn't enforce it as required
• The rendering code treats name as a mandatory field
• The test suite expects name to be present
• In practice, nearly all disorder files have name as their first line

Solution Options

Option 1: Make name Required in Schema (Recommended)

Add required: true to the Disease class slot_usage:

Disease:
  slot_usage:
    name:
      required: true

Pros:

• Aligns schema with actual usage patterns
• Prevents future issues at validation time
• Makes expectations explicit
• Matches existing test expectations

Cons:

• May break any existing files without names (though investigation suggests all current files have names)

Option 2: Add Defensive Fallback in Render Function

# Line 570 in render.py
disorder_name = disorder.get("name") or yaml_path.stem
output_path = output_dir / f'{slugify(disorder_name)}.html'

Pros:

• Handles edge cases gracefully
• No schema changes needed

Cons:

• Allows inconsistent state to persist
• Filename might not match expected conventions
• Doesn't solve the underlying inconsistency

Option 3: Hybrid Approach

1. Make name required in schema
2. Add defensive check with clear error message
3. Update validation to catch this earlier

Recommendation

Option 1 is the best path forward because:

1. name is already used as an identifier throughout the codebase
2. All existing disorder files appear to have name fields
3. Making it required prevents this class of errors at validation time
4. It aligns schema semantics with code expectations

The fix should be a one-line schema change adding required: true to the Disease class's name slot usage, followed by running just validate-all to confirm no existing files are broken.

Files to Modify

• src/dismech/schema/dismech.yaml - Add required constraint
• Optionally: Add a more informative error message in render.py for debugging