fix(dataset): make api fields optional and add guards to prevent null fields

[belfhi]

fixes #2386

Description

Motivation

Fixes

• Bug fixed (#X)

Changes:

• changes made

Tests included

• Included for each change/fix?
• Passing?

Documentation

• swagger documentation updated (required for API changes)
• official documentation updated

official documentation info

Summary by Sourcery

Make dataset-related API response fields safer by allowing optional version metadata, preventing null array values, and improving include-parameter handling and relation loading.

Bug Fixes:

• Avoid null-related errors in dataset lookup aggregation when relationships are missing.
• Ensure include query parameters are correctly parsed when passed as comma-separated values from OpenAPI-generated clients.

Enhancements:

• Treat API version fields on dataset, origdatablock, and sample output DTOs as optional metadata instead of required properties.
• Normalize array-like dataset properties by filtering out null/undefined entries and defaulting schema arrays to empty lists.
• Expose includable dataset relations (origdatablocks, datablocks, attachments, instruments, proposals, samples) as documented optional fields in the dataset output DTO.
• Clarify OpenAPI definitions for include array parameters using form style with explode for dataset and origdatablock controllers.

[sourcery-ai]

Hey - I've found 1 issue

Prompt for AI Agents

Please address the comments from this code review:

## Individual Comments

### Comment 1
<location path="src/common/utils.ts" line_range="1343-1350" />
<code_context>
   return keys.map((key) => decodeURIComponentExtended(key));
 }

+export function filterNullFromArray<T>(
+  value: (T | null | undefined)[] | undefined,
+): T[] | undefined {
+  if (!value) return undefined;
+  const filtered = value.filter(
+    (item): item is T => item !== null && item !== undefined,
+  );
+  return filtered.length > 0 ? filtered : undefined;
+}
+
</code_context>
<issue_to_address>
**suggestion (bug_risk):** Consider whether converting empty arrays to `undefined` is desirable for DTO transformations

Because this helper returns `undefined` for empty arrays, DTO fields using `@Transform(({ value }) => filterNullFromArray<string>(value))` (e.g. `keywords`, `proposalIds`) will emit `undefined` instead of `[]` when stored arrays are empty. This changes the API surface and may break consumers that expect these properties to always exist (even when empty), especially given the new Mongoose defaults to `[]`. If callers rely on that stability, consider returning `filtered` even when empty.
</issue_to_address>

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