use integevers as input for taxa2lca and taxonomy

unipept · Nov 28, 2024 · 5f14a81 · 5f14a81
1 parent 7c8d1a3
commit 5f14a81
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Showing 3 changed files with 10 additions and 1 deletion.
diff --git a/lib/commands/unipept/taxa2lca.ts b/lib/commands/unipept/taxa2lca.ts
@@ -11,6 +11,8 @@ export class Taxa2lca extends UnipeptSubcommand {
 
 The command will give priority to the first way NCBI Taxonomy Identifiers are passed, in the order as listed above. Text files and standard input should have one taxon id per line.`;
 
+  castInput = true;
+
   constructor() {
     super("taxa2lca");
 

diff --git a/lib/commands/unipept/taxonomy.ts b/lib/commands/unipept/taxonomy.ts
@@ -11,6 +11,8 @@ export class Taxonomy extends UnipeptSubcommand {
 
 The command will give priority to the first way taxon id's are passed, in the order as listed above. Text files and standard input should have one taxon id per line.`;
 
+  castInput = true;
+
   constructor() {
     super("taxonomy");
 

diff --git a/lib/commands/unipept/unipept_subcommand.ts b/lib/commands/unipept/unipept_subcommand.ts
@@ -23,6 +23,7 @@ export abstract class UnipeptSubcommand {
   firstBatch = true;
   selectedFields?: RegExp[];
   fasta: boolean;
+  castInput = false;
 
   // we must save this to be able to close it properly in tests
   private streamInterface?: Interface;
@@ -241,8 +242,12 @@ export abstract class UnipeptSubcommand {
 
   private constructRequestBody(slice: string[]): string {
     const names = this.getSelectedFields().length === 0 || this.getSelectedFields().some(regex => regex.toString().includes("name") || regex.toString().includes(".*$"));
+    let input: string[] | number[] = slice;
+    if (this.castInput) {
+      input = slice.map(s => parseInt(s, 10));
+    }
     return JSON.stringify({
-      input: slice,
+      input: input,
       equate_il: this.options.equate,
       extra: this.options.all,
       names: this.options.all && names