fixed wasm calls in reporting

rust/bioscript-cli/src/report_observations.rs

@@ -17,11 +17,22 @@ fn app_observation_from_manifest_row(
         &manifest_path.display().to_string(),
     )?;
     let manifest = task.manifest;
-    let (gene, observed_alt_alleles, source) = if row_path.contains('#') {
-        (String::new(), Vec::new(), serde_json::Value::Null)
+    let (gene, alt_alleles, observed_alt_alleles, source) = if row_path.contains('#') {
+        (
+            String::new(),
+            manifest
+                .spec
+                .alternate
+                .clone()
+                .into_iter()
+                .collect::<Vec<_>>(),
+            manifest.spec.observed_alternates.clone(),
+            serde_json::Value::Null,
+        )
     } else {
         (
             variant_manifest_gene(&manifest_path)?,
+            variant_alt_alleles(&manifest_path)?,
             variant_observed_alt_alleles(&manifest_path)?,
             variant_primary_source(&manifest_path)?,
         )
@@ -34,6 +45,7 @@ fn app_observation_from_manifest_row(
             manifest,
             gene,
             source,
+            alt_alleles,
             observed_alt_alleles,
             inferred_sex,
             fallback_assembly,
@@ -117,3 +129,24 @@ fn variant_observed_alt_alleles(path: &Path) -> Result<Vec<String>, String> {
         .map(ToOwned::to_owned)
         .collect())
 }
+
+fn variant_alt_alleles(path: &Path) -> Result<Vec<String>, String> {
+    let text = fs::read_to_string(path)
+        .map_err(|err| format!("failed to read variant YAML {}: {err}", path.display()))?;
+    let value: serde_yaml::Value = serde_yaml::from_str(&text)
+        .map_err(|err| format!("failed to parse variant YAML {}: {err}", path.display()))?;
+    let Some(items) = value
+        .as_mapping()
+        .and_then(|mapping| mapping.get(serde_yaml::Value::String("alleles".to_owned())))
+        .and_then(serde_yaml::Value::as_mapping)
+        .and_then(|mapping| mapping.get(serde_yaml::Value::String("alts".to_owned())))
+        .and_then(serde_yaml::Value::as_sequence)
+    else {
+        return Ok(Vec::new());
+    };
+    Ok(items
+        .iter()
+        .filter_map(serde_yaml::Value::as_str)
+        .map(ToOwned::to_owned)
+        .collect())
+}

rust/bioscript-wasm/src/report_helpers.rs

@@ -124,6 +124,23 @@ pub(super) fn variant_observed_alt_alleles_from_yaml(value: &serde_yaml::Value)
         .unwrap_or_default()
 }
 
+pub(super) fn variant_alt_alleles_from_yaml(value: &serde_yaml::Value) -> Vec<String> {
+    value
+        .as_mapping()
+        .and_then(|mapping| mapping.get(serde_yaml::Value::String("alleles".to_owned())))
+        .and_then(serde_yaml::Value::as_mapping)
+        .and_then(|mapping| mapping.get(serde_yaml::Value::String("alts".to_owned())))
+        .and_then(serde_yaml::Value::as_sequence)
+        .map(|items| {
+            items
+                .iter()
+                .filter_map(serde_yaml::Value::as_str)
+                .map(ToOwned::to_owned)
+                .collect()
+        })
+        .unwrap_or_default()
+}
+
 #[cfg(test)]
 mod tests {
     use super::participant_id_from_name;

rust/bioscript-wasm/src/report_workspace.rs

@@ -68,13 +68,22 @@ impl bioscript_reporting::ReportWorkspace for PackageWorkspace {
         fallback_assembly: Option<Assembly>,
     ) -> Result<serde_json::Value, String> {
         let row_path = row.get("path").cloned().unwrap_or_default();
-        let (manifest, gene, source, observed_alt_alleles) = if row_path.contains('#') {
+        let (manifest, gene, source, alt_alleles, observed_alt_alleles) = if row_path.contains('#') {
             let task = bioscript_reporting::load_variant_manifest_task_by_path(self, &row_path)?;
+            let alt_alleles = task
+                .manifest
+                .spec
+                .alternate
+                .clone()
+                .into_iter()
+                .collect::<Vec<_>>();
+            let observed_alt_alleles = task.manifest.spec.observed_alternates.clone();
             (
                 task.manifest,
                 String::new(),
                 serde_json::Value::Null,
-                Vec::new(),
+                alt_alleles,
+                observed_alt_alleles,
             )
         } else {
             let manifest = self
@@ -85,6 +94,7 @@ impl bioscript_reporting::ReportWorkspace for PackageWorkspace {
                 manifest,
                 yaml_string(&value, "gene").unwrap_or_default(),
                 variant_primary_source_from_yaml(&value),
+                variant_alt_alleles_from_yaml(&value),
                 variant_observed_alt_alleles_from_yaml(&value),
             )
         };
@@ -96,6 +106,7 @@ impl bioscript_reporting::ReportWorkspace for PackageWorkspace {
                 manifest,
                 gene,
                 source,
+                alt_alleles,
                 observed_alt_alleles,
                 inferred_sex,
                 fallback_assembly,