⚙️ Backend Issue — Extend `/sample/create_with_file_upload` to Support Additional File Formats

🗣️ User Feedback

"XML may not be the best format to use going forward. Other formats (e.g., JSON) can provide more accessible and complete information from additional repositories."

🎯 Goal

Enhance the backend endpoint

POST /sample/create_with_file_upload

to support additional file formats beyond XML, using the existing Connexion + OpenAPI setup.

Currently, it handles only DataCite XML uploads. The goal is to extend it to accept and process:

JSON
CSV
Excel (.xlsx)
YAML
TOML

📄 Endpoint Specification (Updated)

/sample/create_with_file_upload:
  post:
    operationId: "sample.create_with_upload_file"
    tags:
      - Sample
    summary: "Create a sample record in SEPIA by file upload"
    parameters:
      - $ref: "#/components/parameters/session_id_qp"
    requestBody:
      x-body-name: data
      description: "Sample to create by file upload (XML, JSON, CSV, Excel, YAML, or TOML)"
      required: true
      content:
        multipart/form-data:
          schema:
            $ref: "#/components/schemas/Sample_with_file_upload"
    responses:
      '201':
        description: Sample created successfully in SEPIA by file upload
      '400':
        description: Bad request — invalid or unsupported file format
      '403':
        description: Invalid credentials or insufficient access
      '500':
        description: Server-side error (please inform the administrator)

🧩 Implementation Details

Tasks

Update the existing /sample/create_with_file_upload endpoint (replacing /sample/create_with_xml_upload).
Update the OpenAPI spec to include the new accepted formats in the request body description.
Implement file type detection (by extension or MIME type).
Implement parsing and validation logic for each supported format.
Map parsed data to the existing internal Sample schema.
Return consistent error messages for unsupported or malformed input files.

Format Parsing Suggestions

Format	Library	Notes
XML	`lxml`	Already supported
JSON	`json`	Direct structure mapping
CSV	`pandas.read_csv` or `csv`	Convert to dicts
Excel (.xlsx)	`openpyxl`	Tabular data
YAML	`PyYAML`	Configuration-style input
TOML	`tomllib` (Python ≥3.11) / `toml`	Structured metadata

📅 Proposed Rollout Plan

Phase	Format(s)	Notes
Phase 1	JSON	Highest user demand, easiest integration
Phase 2	CSV, Excel	Common tabular formats
Phase 3	YAML, TOML	Developer/config-friendly formats

🏷️ Labels

backend feature enhancement data-import priority::high

📘 References

Frontend Issue: Frontend Issue — Support Additional File Formats for “Create Sample via File”
Framework: Connexion (Python)
API Spec: OpenAPI 3.x

Edited Oct 21, 2025 by Mojeeb Rahman Sedeqi

⚙️ Backend Issue — Extend /sample/create_with_file_upload to Support Additional File Formats