Merge pull request #38 from daniel-ji/main

Add stdout/stderr streaming config option: printStream

src/examples/stream-std.html

@@ -0,0 +1,7 @@
+<h4>Streamed Output of <code>tn93</code>:</h4>
+<pre id="output">Loading...</pre>
+
+<h4>Pairwise distances:</h4>
+<pre id="result">Loading...</pre>
+
+<script type="module" src="/src/examples/stream-std.js"></script>

src/examples/stream-std.js

@@ -0,0 +1,17 @@
+import Aioli from "../../dist/aioli.mjs";
+
+const CLI = await new Aioli(["tn93/1.0.11"], {
+	debug: true, 
+	printStream: true, 
+	callback: (d) =>{
+		document.getElementById("output").innerHTML += "\n<span style='color: red'>timestamp: " + performance.now() + "</span>\n";
+		document.getElementById("output").innerHTML += d.stdout;
+	}
+});
+
+// Calculate pairwise distances of sequences in test.fas
+const output = await CLI.exec("tn93 -t 0.05 -o test.dst /shared/tn93/test.fas");
+const result = await CLI.cat("test.dst");
+
+// Output results
+document.getElementById("result").innerHTML = result;

src/main.js

@@ -19,6 +19,8 @@ const CONFIG_DEFAULTS = {
 	dirData: "/data",
 	// Interleave stdout/stderr. If set to false, `.exec()` returns an object { "stdout": <text>, "stderr": <text> }
 	printInterleaved: true,
+	// Stream stdout/stderr continuously to the main thread, instead of waiting for the WebWorker to finish running a command.
+	printStream: false,
 
 	// Callback function to run whenever we receive a message from the WebWorker with payload { type: "biowasm", value: ... }.
 	// See <https://github.com/biowasm/biowasm/tree/main/tools/bhtsne> for an example of how this can be used to send regular updates

src/worker.js

@@ -367,8 +367,28 @@ const aioli = {
 				}
 			},
 			// Setup print functions to store stdout/stderr output
-			print: text => tool.stdout += `${text}\n`,
-			printErr: aioli.config.printInterleaved ? text => tool.stdout += `${text}\n` : text => tool.stderr += `${text}\n`
+			print: text => {
+				tool.stdout += `${text}\n`;
+				if(aioli.config.printStream)
+					postMessage({
+						type: "biowasm",
+						value: {
+							stdout: text,
+						},
+					});
+			},
+			printErr: text => {
+				const destination = aioli.config.printInterleaved ? "stdout" : "stderr";
+				tool[destination] += `${text}\n`;
+				if(aioli.config.printStream)
+					postMessage({
+						type: "biowasm",
+						value: {
+							[destination]: text,
+						},
+					});
+				}
+			}
 		});
 
 		// -----------------------------------------------------------------