SUpport for onset in ETL

Author: pnrobinson

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "ga4ghphetools"
-version = "0.5.19"
+version = "0.5.20"
 edition = "2021"
 keywords = ["GA4GH", "Phenopacket Schema", "Human Phenotype Ontology"]
 description = "Generate GA4GH phenopackets from tabular data"
@@ -22,12 +22,12 @@ required-features = ["cli"]
 
 [dependencies]
 calamine = "0.32.0" 
-chrono = "0.4.42"
-derive_more = {version = "2.1.0", features = ["from", "display"]}
+chrono = "0.4.43"
+derive_more = {version = "2.1.1", features = ["from", "display"]}
 home = "0.5.11"
 lazy_static = "1.5.0"
 once_cell = "1.21.3"
-ontolius = "0.7.1"
+ontolius = "0.7.2"
 phenopackets = "0.2.2-post2"
 phenopacket_tools = { git = " https://github.com/P2GX/phenopacket_tools.git", tag = "0.2.4" }
 prost = "0.14.1" 
@@ -42,7 +42,7 @@ clap = { version = "4.5.53", features = ["derive"], optional = true }
 rayon = "=1.10.0"
 tera = "1.20.1"
 uuid = { version = "1.18", features = ["v4"] }
-rust_xlsxwriter = { version = "0.92.2", optional = true }
+rust_xlsxwriter = { version = "0.92.4", optional = true }
 urlencoding = "2.1.3"
 walkdir = "2.5"
 

src/etl/etl_tools.rs

@@ -261,11 +261,22 @@ impl EtlTools {
                 continue;
             }
             let obs_pair: Vec<&str> = obs.split("-").collect();
-            if obs_pair.len() != 2 {
+            if obs_pair.len() == 3 {
+                // something like  "current": "HP:0008846-observed-Congenital 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) {
+                    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}'"))
             }
-            observation_map.insert(obs_pair[0].to_string(), obs_pair[1].to_string());
-
         }
         for hdup in duplet_list {
         let val = observation_map