Update to enable testing that cohort diseases have specified MOI

Author: pnrobinson

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "ga4ghphetools"
-version = "0.5.31"
+version = "0.5.32"
 edition = "2021"
 keywords = ["GA4GH", "Phenopacket Schema", "Human Phenotype Ontology"]
 description = "Generate GA4GH phenopackets from tabular data"

src/factory/cohort_qc.rs

@@ -126,6 +126,20 @@ impl CohortDataQc {
     }
 
 
+    pub fn check_metadata(&self, cohort: &CohortData) -> Result<(), String> {
+        let diseases = &cohort.disease_list;
+        if diseases.is_empty() {
+            return Err("Disease list empty".to_string());
+        }
+        for disease in diseases {
+            if disease.mode_of_inheritance_list.is_empty() {
+                return Err(format!("No mode of inheritance provided for {} ({})", disease.disease_label, disease.disease_id));
+            }
+        }
+        Ok(())
+    }
+
+
     pub fn sanitize_header(&self, duplets: &Vec<HpoTermDuplet>) -> Result<Vec<HpoTermDuplet>, String> {
         let mut sanitized: Vec<HpoTermDuplet> = Vec::new();
         for duplet in duplets {

src/factory/mod.rs

@@ -103,6 +103,7 @@ pub fn qc_assessment(
 -> Result<(), String> {
     let cohort_qc = CohortDataQc::new(hpo);
     cohort_qc.qc_check(cohort_dto)?;
+    cohort_qc.check_metadata(cohort_dto)?;
     cohort_qc.qc_conflicting_pairs(cohort_dto)
 }
 

tests/integration_etl_dto.rs

@@ -3,6 +3,7 @@ use std::collections::HashMap;
 use std::sync::Arc;
 
 use ga4ghphetools::dto::cohort_dto::GeneTranscriptData;
+use ga4ghphetools::dto::cohort_dto::ModeOfInheritance;
 use ga4ghphetools::dto::etl_dto::ColumnDto;
 use ga4ghphetools::dto::etl_dto::ColumnTableDto;
 use ga4ghphetools::dto::etl_dto::EtlCellValue;
@@ -272,10 +273,15 @@ fn columns_lacking_hpo(
 
 #[fixture]
 fn disease_valid() -> DiseaseData {
+    let moi = ModeOfInheritance { 
+        hpo_id: "HP:0000006".to_string(), 
+        hpo_label: "Autosomal dominant inheritance".to_string(), 
+        citation: "PMID: 39471804".to_string()
+    };
     DiseaseData {
         disease_id: "OMIM:621016".to_string(),
         disease_label: "Neurodevelopmental disorder with variable familial hypercholanemia".to_string(),
-        mode_of_inheritance_list: vec![],
+        mode_of_inheritance_list: vec![moi],
         gene_transcript_list: vec![GeneTranscriptData {
             hgnc_id: "HGNC:30203".to_string(),
             gene_symbol: "WDR83OS".to_string(),