SORMAS-Project

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Feature Description

After adding IPI to the Disease Enum (#13339), update the case form to capture IPI-specific clinical and epidemiological data. This includes clinical presentation types, sterile site validation, sample-type restrictions, serotype, and antibiotic susceptibility fields.

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Added Value/Benefit

• Record IPI-specific clinical manifestations (e.g., meningitis, septicaemia, pneumonia, etc.)
• Track serotype and antibiotic susceptibility data for surveillance and reporting
• Ensure SORMAS data model and UI are consistent with IPI workflow

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Acceptance Criteria

Entities, DTOs, and Enums

• [x] Update Case entity and CaseDataDto with:
  • clinicalPresentation (String array for checkboxes: Bacterial pneumonia, Meningitis, Septicaemia, Asymptomatic, Unknown, Other).
  • ~~sterileSiteValidated (Boolean flag for sample validation).~~ This validation should happens based on Type of Test+ Disease+ Lab Result. E.g, Serogrouping(TT)+IPI(D)+Possitive(LR), then serotype and its method should capture.
• [x] Update Sample entity and SampleDto with:
  • Restrict sampleMaterial to validated sterile sites for IPI:
    • Blood
    • Cerebrospinal fluid (CSF)
    • Pleural fluid
    • Synovial fluid
    • Urine
    • Peritoneal fluid
    • Other (free text)
  • Exclude non-sterile samples (e.g., ~~urine~~, swabs) from IPI confirmation and ECDC reporting . Urine is required for sampleMaterial.
  • Add serotype (String for serotype entry, e.g., "19A", "Non-typable")
• [x] Update PathogenTest entity with:
  • serotypingMethod (Enum: MPCR, QUELLUNG_REACTION, COAGGLUTINATION, OTHER)
• [ ] Update Therapy entity with:
  • Antibiotic Susceptibility Testing (AST) fields for Penicillin, Ceftriaxone, Erythromycin (MIC + S/I/R/UNK)

Case Form Updates

• [x] Clinical Presentation Section:
  • Add checkboxes for Bacterial pneumonia, Meningitis, Septicaemia, Asymptomatic, Unknown, Other (with free-text)
• [x] Sample Validation:
  • Auto-validate samples against allowed sterile site types (see above)
  • Show warning for non-sterile samples (e.g., urine) and exclude them from ECDC reporting
• [ ] Serotype Field:
  • Add free-text entry for serotype under the Samples tab
  • Add dropdown for serotyping method
• [ ] Therapy Tab:
  • Add fields for Antibiotic Susceptibility Testing (AST):
    • Penicillin, Ceftriaxone, Erythromycin MIC values (numeric)
    • Susceptibility dropdowns (S/I/R/UNK)

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Implementation Details

1. Backend:
   • Add clinicalPresentation and sterileSiteValidated to Case entity
   • Restrict IPI samples to sterile sites in validation logic
   • Add serotype and serotypingMethod to sample/pathogen test entities
   • Add AST fields to Therapy entity
2. Frontend:
   • Add clinical presentation checkboxes to Symptoms tab
   • Display sterile site validation warnings in Samples tab
   • Integrate serotype and AST fields into Therapy tab
   • Hide/disable non-sterile sample types for IPI

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Additional Information

• Dependencies: Requires #13339 (Add IPI to Disease Enum)
• References:
  • See IPIs v1.1 rev_XC section 5.3, 6.2, and 7.2 for sample/material and AST requirements.
  • ECDC case definition: Only cases with S. pneumoniae detected in a normally sterile site are confirmed.