Merge pull request #1457 from nextstrain/feat/clade-optional

nextstrain · May 24, 2024 · 7963ac4 · 7963ac4
2 parents 3475c1b + c4ee360
commit 7963ac4
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Showing 8 changed files with 21 additions and 13 deletions.
diff --git a/packages/nextclade-web/src/components/Results/ColumnClade.tsx b/packages/nextclade-web/src/components/Results/ColumnClade.tsx
@@ -15,7 +15,7 @@ export function ColumnClade({ analysisResult }: ColumnCladeProps) {
 
   const { clade, seqName, index } = analysisResult
   const id = getSafeId('col-clade', { index, seqName })
-  const cladeText = clade ?? t('Pending...')
+  const cladeText = clade ?? ''
 
   const onMouseEnter = useCallback(() => setShowTooltip(true), [])
   const onMouseLeave = useCallback(() => setShowTooltip(false), [])

diff --git a/packages/nextclade-web/src/filtering/filterByClades.ts b/packages/nextclade-web/src/filtering/filterByClades.ts
@@ -11,6 +11,6 @@ export function filterByClades(cladesFilter: string) {
     }
 
     const { clade } = result.result.analysisResult
-    return cladesFilters.some((filter) => clade.toLowerCase().startsWith(filter.toLowerCase()))
+    return cladesFilters.some((filter) => clade?.toLowerCase().startsWith(filter.toLowerCase()))
   }
 }
diff --git a/packages/nextclade/src/io/nextclade_csv.rs b/packages/nextclade/src/io/nextclade_csv.rs
@@ -351,7 +351,7 @@ impl<W: VecWriter> NextcladeResultsCsvWriter<W> {
     self.add_entry("index", index)?;
     self.add_entry("seqName", seq_name)?;
 
-    self.add_entry("clade", clade)?;
+    self.add_entry("clade", &clade.as_deref().unwrap_or_default())?;
     self.add_entry("qc.overallScore", &format_qc_score(qc.overall_score))?;
     self.add_entry("qc.overallStatus", &qc.overall_status.to_string())?;
     self.add_entry("totalSubstitutions", &total_substitutions.to_string())?;

diff --git a/packages/nextclade/src/run/nextclade_run_one.rs b/packages/nextclade/src/run/nextclade_run_one.rs
@@ -58,7 +58,7 @@ struct NextcladeResultWithAa {
 
 #[derive(Default)]
 struct NextcladeResultWithGraph {
-  clade: String,
+  clade: Option<String>,
   private_nuc_mutations: PrivateNucMutations,
   private_aa_mutations: BTreeMap<String, PrivateAaMutations>,
   phenotype_values: Option<Vec<PhenotypeValue>>,
@@ -306,8 +306,10 @@ pub fn nextclade_run_one(
         .iter()
         .filter_map(|phenotype_data| {
           let PhenotypeData { name, cds, ignore, .. } = phenotype_data;
-          if ignore.clades.contains(&clade) {
-            return None;
+          if let Some(clade) = &clade {
+            if ignore.clades.contains(clade) {
+              return None;
+            }
           }
           let phenotype = calculate_phenotype(phenotype_data, &aa_substitutions);
           Some(PhenotypeValue {

diff --git a/packages/nextclade/src/tree/tree.rs b/packages/nextclade/src/tree/tree.rs
@@ -136,7 +136,8 @@ pub struct TreeNodeAttrs {
   #[serde(skip_serializing_if = "Option::is_none")]
   pub div: Option<f64>,
 
-  pub clade_membership: TreeNodeAttr,
+  #[serde(skip_serializing_if = "Option::is_none")]
+  pub clade_membership: Option<TreeNodeAttr>,
 
   #[serde(skip_serializing_if = "Option::is_none")]
   #[serde(rename = "Node type")]
@@ -243,8 +244,12 @@ impl From<&AuspiceTreeNode> for AuspiceGraphNodePayload {
 
 impl AuspiceGraphNodePayload {
   /// Extracts clade of the node
-  pub fn clade(&self) -> String {
-    self.node_attrs.clade_membership.value.clone()
+  pub fn clade(&self) -> Option<String> {
+    self
+      .node_attrs
+      .clade_membership
+      .as_ref()
+      .map(|clade_membership| clade_membership.value.clone())
   }
 
   /// Extracts clade-like node attributes, given a list of key descriptions

diff --git a/packages/nextclade/src/tree/tree_attach_new_nodes.rs b/packages/nextclade/src/tree/tree_attach_new_nodes.rs
@@ -68,7 +68,7 @@ pub fn create_new_auspice_node(
     },
     node_attrs: TreeNodeAttrs {
       div: Some(new_divergence),
-      clade_membership: TreeNodeAttr::new(&result.clade),
+      clade_membership: result.clade.as_ref().map(|clade| TreeNodeAttr::new(clade)),
       node_type: Some(TreeNodeAttr::new("New")),
       region: Some(TreeNodeAttr::new(AUSPICE_UNKNOWN_VALUE)),
       country: Some(TreeNodeAttr::new(AUSPICE_UNKNOWN_VALUE)),

diff --git a/packages/nextclade/src/tree/tree_find_nearest_node.rs b/packages/nextclade/src/tree/tree_find_nearest_node.rs
@@ -149,10 +149,10 @@ mod tests {
 
       node_attrs: TreeNodeAttrs {
         div: None,
-        clade_membership: TreeNodeAttr {
+        clade_membership: Some(TreeNodeAttr {
           value: "Test_Clade".to_owned(),
           other: serde_json::Value::default(),
-        },
+        }),
         node_type: None,
         region: None,
         country: None,

diff --git a/packages/nextclade/src/types/outputs.rs b/packages/nextclade/src/types/outputs.rs
@@ -70,7 +70,8 @@ pub struct NextcladeOutputs {
   pub aa_unsequenced_ranges: BTreeMap<String, Vec<AaRefRange>>,
   pub pcr_primer_changes: Vec<PcrPrimerChange>,
   pub total_pcr_primer_changes: usize,
-  pub clade: String,
+  #[serde(skip_serializing_if = "Option::is_none")]
+  pub clade: Option<String>,
   pub private_nuc_mutations: PrivateNucMutations,
   pub private_aa_mutations: BTreeMap<String, PrivateAaMutations>,
   pub warnings: Vec<PeptideWarning>,