add basic csv formatter

lib/commands/unipept/unipept_subcommand.ts

@@ -2,6 +2,8 @@ import { Command, Option } from "commander";
 import { createReadStream, readFileSync } from "fs";
 import { createInterface } from "node:readline";
 import { Interface } from "readline";
+import { Formatter } from "../../formatters/formatter.js";
+import { FormatterFactory } from "../../formatters/formatter_factory.js";
 
 export abstract class UnipeptSubcommand {
   public command: Command;
@@ -14,6 +16,8 @@ export abstract class UnipeptSubcommand {
   url?: string;
   selectedFields?: RegExp[];
   fasta: boolean;
+  formatter?: Formatter;
+  firstBatch = true;
 
   constructor(name: string) {
     this.name = name;
@@ -48,6 +52,7 @@ export abstract class UnipeptSubcommand {
     this.options = options;
     this.host = this.getHost();
     this.url = `${this.host}/api/v2/${this.name}.json`;
+    this.formatter = FormatterFactory.getFormatter(this.options.format);
 
     let slice = [];
 
@@ -62,6 +67,8 @@ export abstract class UnipeptSubcommand {
   }
 
   async processBatch(slice: string[]): Promise<void> {
+    if (!this.formatter) throw new Error("Formatter not set");
+
     const r = await fetch(this.url as string, {
       method: "POST",
       body: this.constructRequestBody(slice),
@@ -70,7 +77,14 @@ export abstract class UnipeptSubcommand {
         "User-Agent": this.user_agent,
       }
     });
-    console.log(await r.json());
+    const result = await r.json();
+
+    if (this.firstBatch) {
+      this.firstBatch = false;
+      process.stdout.write(this.formatter.header(result, this.fasta));
+    }
+
+    process.stdout.write(this.formatter.format(result, this.fasta));
   }
 
   private constructRequestBody(slice: string[]): URLSearchParams {
@@ -84,9 +98,9 @@ export abstract class UnipeptSubcommand {
   }
 
   private getSelectedFields(): RegExp[] {
-    if (this.selectedFields) return this.getSelectedFields();
+    if (this.selectedFields) return this.selectedFields;
 
-    const fields = (this.options.fields as string[]).flatMap(f => f.split(","));
+    const fields = (this.options.select as string[])?.flatMap(f => f.split(",")) ?? [];
     if (this.fasta && fields.length > 0) {
       fields.push(...this.requiredFields());
     }

lib/formatters/csv_formatter.ts

@@ -0,0 +1,21 @@
+import { Formatter } from "./formatter.js";
+import { stringify } from "csv-stringify/sync";
+
+export class CSVFormatter extends Formatter {
+
+  header(sampleData: { [key: string]: string }[], fastaMapper?: boolean | undefined): string {
+    return stringify([this.getKeys(sampleData, fastaMapper)]);
+  }
+
+  footer(): string {
+    return "";
+  }
+
+  convert(data: object[]): string {
+    return stringify(data);
+  }
+
+  getKeys(data: { [key: string]: string }[], fastaMapper?: boolean | undefined): string[] {
+    return fastaMapper ? ["fasta_header", ...Object.keys(data[0])] : Object.keys(data[0]);
+  }
+}

lib/formatters/formatter.ts

@@ -0,0 +1,19 @@
+import { CSVFormatter } from "./csv_formatter.js";
+
+export abstract class Formatter {
+
+  abstract header(sampleData: object, fastaMapper?: boolean): string;
+  abstract footer(): string;
+  abstract convert(data: any, first?: boolean): string;
+
+  format(data, fastaMapper?: boolean, first?: boolean): string {
+    if (fastaMapper) {
+      data = this.integrateFastaHeaders(data, fastaMapper);
+    }
+    return this.convert(data, first);
+  }
+
+  integrateFastaHeaders(data: any, fastaMapper: boolean): any {
+    return data;
+  }
+}

lib/formatters/formatter_factory.ts

@@ -0,0 +1,11 @@
+import { CSVFormatter } from "./csv_formatter.js";
+import { Formatter } from "./formatter.js";
+
+export class FormatterFactory {
+  static getFormatter(name: string): Formatter {
+    if (name === "csv") {
+      return new CSVFormatter();
+    }
+    return new CSVFormatter();
+  }
+}

package.json

@@ -24,7 +24,8 @@
     "uniprot": "yarn run tsx bin/uniprot.ts"
   },
   "dependencies": {
-    "commander": "^12.1.0"
+    "commander": "^12.1.0",
+    "csv-stringify": "^6.5.0"
   },
   "devDependencies": {
     "@eslint/js": "^9.5.0",

yarn.lock

@@ -1307,6 +1307,11 @@ cross-spawn@^7.0.2, cross-spawn@^7.0.3:
     shebang-command "^2.0.0"
     which "^2.0.1"
 
+csv-stringify@^6.5.0:
+  version "6.5.0"
+  resolved "https://registry.yarnpkg.com/csv-stringify/-/csv-stringify-6.5.0.tgz#7b1491893c917e018a97de9bf9604e23b88647c2"
+  integrity sha512-edlXFVKcUx7r8Vx5zQucsuMg4wb/xT6qyz+Sr1vnLrdXqlLD1+UKyWNyZ9zn6mUW1ewmGxrpVwAcChGF0HQ/2Q==
+
 debug@^4.1.0, debug@^4.1.1, debug@^4.3.1, debug@^4.3.2, debug@^4.3.4:
   version "4.3.5"
   resolved "https://registry.yarnpkg.com/debug/-/debug-4.3.5.tgz#e83444eceb9fedd4a1da56d671ae2446a01a6e1e"