Updating unit test

Author: pnrobinson

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "ga4ghphetools"
-version = "0.5.20"
+version = "0.5.21"
 edition = "2021"
 keywords = ["GA4GH", "Phenopacket Schema", "Human Phenotype Ontology"]
 description = "Generate GA4GH phenopackets from tabular data"

src/etl/etl_tools.rs

@@ -208,19 +208,19 @@ impl EtlTools {
         key: HpoTermDuplet, 
         value: String) 
     -> Result<(), String> {
-            match map.entry(key) {
-                Entry::Occupied(mut entry) => {
-                    if entry.get() != &value {
-                        let resolved_val = Self::resolve_hpo_conflict(entry.get(), &value)?;
-                        *entry.get_mut() = resolved_val;
-                    }
-                },
-                Entry::Vacant(entry) => {
-                    entry.insert(value);
+        match map.entry(key) {
+            Entry::Occupied(mut entry) => {
+                if entry.get() != &value {
+                    let resolved_val = Self::resolve_hpo_conflict(entry.get(), &value)?;
+                    *entry.get_mut() = resolved_val;
                 }
+            },
+            Entry::Vacant(entry) => {
+                entry.insert(value);
             }
-            Ok(())
         }
+        Ok(())
+    }
 
     /// Insert multiple HPO term observations into the given map.
     ///
@@ -263,17 +263,17 @@ impl EtlTools {
             let obs_pair: Vec<&str> = obs.split("-").collect();
             if obs_pair.len() == 3 {
                 // something like  "current": "HP:0008846-observed-Congenital onset",
+                // or "HP:0008846-observed-na" (i.e., not onset)
                 let hp_id = obs_pair[0];
                 let status = obs_pair[1];
                 let onset = obs_pair[2];
-                if crate::age::is_valid_age_string(onset) {
+                if onset == "na" {
+                    observation_map.insert(hp_id.to_string(), status.to_string());
+                } else if crate::age::is_valid_age_string(onset) {
                     observation_map.insert(hp_id.to_string(), onset.to_string());
                 } else {
                     return Err(format!("Malformed observation data onset='{onset}' ({obs})"))
                 }
-            } else if obs_pair.len() == 2 {
-                // i.e., no observation data
-                observation_map.insert(obs_pair[0].to_string(), obs_pair[1].to_string());
             } else {
                 return Err(format!("Malformed observation pair '{obs}'"))
             }

tests/integration_etl_dto.rs

@@ -138,7 +138,7 @@ fn delayed_gross_motor() -> ColumnDto {
 
 #[fixture]
 fn gdd_column_valid() -> ColumnDto {
-    let observed = transformed_from_string("HP:0001263-observed");
+    let observed = transformed_from_string("HP:0001263-observed-na");
     ColumnDto {
         id: "61d07214-abb0-45cf-aa67-3218730416c0".to_string(),
         header: EtlColumnHeader{
@@ -156,8 +156,8 @@ fn gdd_column_valid() -> ColumnDto {
 
 #[fixture]
 fn hypertelorism_column_valid() -> ColumnDto {
-    let observed = transformed_from_string("HP:0000601-observed;HP:0000316-excluded");
-    let o2 = transformed_from_string("HP:0000601-excluded;HP:0000316-observed");
+    let observed = transformed_from_string("HP:0000601-observed-na;HP:0000316-excluded-na");
+    let o2 = transformed_from_string("HP:0000601-excluded-na;HP:0000316-observed-na");
     ColumnDto {
         id: "5697a6ef-4855-4230-9bb1-a8511acadcb3".to_string(),
         header: EtlColumnHeader {
@@ -514,6 +514,7 @@ fn test_missing_hgvs(
     assert!(removed.is_some(), "Entry was not found in hgvs_variants"); // make sure we actually remove the variant
     // This should be an error because the Variant row has an allele key that is not in our map
     let result = ga4ghphetools::etl::get_cohort_data_from_etl_dto(hpo, etl_dto);
+    println!("{:?}", result);
     assert!(result.is_ok());
 }
 
@@ -677,9 +678,6 @@ fn test_from_file(hpo: Arc<FullCsrOntology>) {
                     .map_err(|e| format!("Failed to deserialize JSON: {}", e)).unwrap(); 
     let result = ga4ghphetools::etl::get_cohort_data_from_etl_dto(hpo.clone(), dto);
     println!("{:?}", result);
-
-
-
 }