merge offline to master

Niema-Lab · Sep 11, 2023 · 8d5023e · 8d5023e
2 parents ea49c30 + 4f62a4b
commit 8d5023e
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Showing 20 changed files with 7,812 additions and 39 deletions.
diff --git a/.gitignore b/.gitignore
@@ -8,7 +8,6 @@ pnpm-debug.log*
 lerna-debug.log*
 
 node_modules
-dist
 dist-ssr
 *.local
 

diff --git a/README.md b/README.md
@@ -1,3 +1,5 @@
 ## ViralWasm-Consensus 
 
-A client-side WebAssembly pipeline for viral consensus sequence calling. For an offline version of this site, please see the offline-mode branch: https://github.com/Niema-Lab/ViralWasm-Consensus/tree/offline-mode
+A client-side WebAssembly pipeline for viral consensus sequence calling. To run the pipeline locally without internet, download the **offline** version of ViralWasm-Consensus. To do so, download the latest release / repository (https://github.com/Niema-Lab/ViralWasm-Consensus/releases/latest/master.zip) and run the following command:
+
+```python3 run_website.py```
diff --git a/index.html b/index.html
@@ -13,7 +13,6 @@
 
 <body>
 	<div id="root"></div>
-	<script src="https://biowasm.com/cdn/v3/aioli.js"></script>
 	<script type="module" src="/src/main.jsx"></script>
 </body>
 

diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -10,6 +10,7 @@
     "preview": "vite preview"
   },
   "dependencies": {
+    "@biowasm/aioli": "^3.1.0",
     "bootstrap": "^5.3.1",
     "bootstrap-icons": "^1.10.5",
     "pako": "^2.1.0",

diff --git a/public/tools/fastp/fastp.data b/public/tools/fastp/fastp.data
diff --git a/public/tools/fastp/fastp.js b/public/tools/fastp/fastp.js
diff --git a/public/tools/fastp/fastp.wasm b/public/tools/fastp/fastp.wasm
diff --git a/public/tools/minimap2/minimap2-simd.data b/public/tools/minimap2/minimap2-simd.data
diff --git a/public/tools/minimap2/minimap2-simd.js b/public/tools/minimap2/minimap2-simd.js
diff --git a/public/tools/minimap2/minimap2-simd.wasm b/public/tools/minimap2/minimap2-simd.wasm
diff --git a/public/tools/minimap2/minimap2.data b/public/tools/minimap2/minimap2.data
diff --git a/public/tools/minimap2/minimap2.js b/public/tools/minimap2/minimap2.js
diff --git a/public/tools/minimap2/minimap2.wasm b/public/tools/minimap2/minimap2.wasm
diff --git a/public/tools/viral_consensus/viral_consensus.js b/public/tools/viral_consensus/viral_consensus.js
diff --git a/public/tools/viral_consensus/viral_consensus.wasm b/public/tools/viral_consensus/viral_consensus.wasm
diff --git a/run_website.py b/run_website.py
@@ -0,0 +1,49 @@
+import http.server
+import socketserver
+import subprocess
+import socket
+
+PORT = 5000
+DIRECTORY = "dist"
+
+def kill_port_unix(port):
+    command = f"lsof -i :{port} -t"
+    try:
+        result = subprocess.check_output(command, shell=True).decode("utf-8")
+        pids = result.strip().split("\n")
+        for pid in pids:
+            subprocess.run(f"kill -9 {pid}", shell=True)
+    except subprocess.CalledProcessError as e:
+        return
+
+def kill_port_windows(port):
+    command = f"netstat -ano | findstr :{port}"
+    try:
+        result = subprocess.check_output(command, shell=True).decode("utf-8").strip().split("\n")
+        for line in result:
+            pid = line.split()[-1]
+            subprocess.run(f"taskkill /F /PID {pid}", shell=True)
+    except subprocess.CalledProcessError as e:
+        return
+
+# Check if port is already in use
+sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+port_in_use = sock.connect_ex(('127.0.0.1', PORT)) == 0
+sock.close()
+
+# If port is in use, suggest using --force option
+if port_in_use:
+	force_port = input(f"Port {PORT} is already in use. Try to close the port and continue [Y/n]? ")
+	if force_port.lower() == "y":
+		kill_port_unix(PORT)
+		kill_port_windows(PORT)
+	else: 
+		exit(1)
+
+class Handler(http.server.SimpleHTTPRequestHandler):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, directory=DIRECTORY, **kwargs)
+
+with socketserver.TCPServer(("", PORT), Handler) as httpd:
+    print(f'Serving at port {PORT}. Visit http://localhost:{PORT}/index.html')
+    httpd.serve_forever()
diff --git a/src/App.jsx b/src/App.jsx
@@ -1,9 +1,14 @@
+// TODO: automatically create dist/
+// TODO: don't manually download aioli, tools
+// TODO: PWA? 
 import React, { Component } from 'react'
 import Pako from 'pako';
 
 import 'bootstrap/dist/css/bootstrap.min.css';
 import "bootstrap-icons/font/bootstrap-icons.css";
 
+import Aioli from "@biowasm/aioli/dist/aioli";
+
 import {
 	VIRAL_CONSENSUS_VERSION,
 	MINIMAP2_VERSION,
@@ -21,9 +26,6 @@ import {
 	EXAMPLE_REF_FILE,
 	DEFAULT_REF_FILE_NAME,
 	DEFAULT_PRIMER_FILE_NAME,
-	DEFAULT_VALS_FILE,
-	DEFAULT_VALS_FALLBACK_FILE,
-	DEFAULT_VALS_MAPPING,
 	ARE_FASTQ,
 	IS_GZIP,
 	INPUT_IS_NONNEG_INTEGER,
@@ -75,7 +77,20 @@ export class App extends Component {
 
 	async componentDidMount() {
 		this.setState({
-			CLI: await new Aioli(["ViralConsensus/viral_consensus/" + VIRAL_CONSENSUS_VERSION, "minimap2/" + MINIMAP2_VERSION, "fastp/" + FASTP_VERSION], {
+			CLI: await new Aioli([{
+				tool: "ViralConsensus",
+				program: "viral_consensus",
+				version: VIRAL_CONSENSUS_VERSION,
+				urlPrefix: `${window.location.origin}${import.meta.env.BASE_URL || ''}tools/viral_consensus`,
+			}, {
+				tool: "minimap2",
+				version: MINIMAP2_VERSION,
+				urlPrefix: `${window.location.origin}${import.meta.env.BASE_URL || ''}tools/minimap2`,
+			}, {
+				tool: "fastp",
+				version: FASTP_VERSION,
+				urlPrefix: `${window.location.origin}${import.meta.env.BASE_URL || ''}tools/fastp`,
+			}], {
 				printInterleaved: false,
 			})
 		}, () => {
@@ -85,7 +100,6 @@ export class App extends Component {
 
 		this.preventNumberInputScrolling();
 		this.fetchExampleFiles();
-		this.loadDefaults();
 	}
 
 	preventNumberInputScrolling = () => {
@@ -105,27 +119,6 @@ export class App extends Component {
 		this.setState({ exampleRefFile, exampleAlignmentFile: exampleAlignmentFile })
 	}
 
-	// Fetch and load ViralConsensus default values
-	loadDefaults = async () => {
-		let defaultTextFile;
-		try {
-			defaultTextFile = await (await fetch(DEFAULT_VALS_FILE)).text();
-		} catch (e) {
-			defaultTextFile = await (await fetch(`${import.meta.env.BASE_URL || ''}${DEFAULT_VALS_FALLBACK_FILE}`)).text();
-		}
-		const defaultText = [...defaultTextFile.matchAll(/#define DEFAULT.*$/gm)].map((line) => line[0].split(' '));
-		for (const defaultValue of defaultText) {
-			if (DEFAULT_VALS_MAPPING[defaultValue[1]]) {
-				if (isNaN(defaultValue[2])) {
-					defaultValue[2] = defaultValue[2].replace(/"|'/g, '');
-				} else {
-					defaultValue[2] = Number(defaultValue[2]);
-				}
-				this.setState({ [DEFAULT_VALS_MAPPING[defaultValue[1]] + "Default"]: defaultValue[2], [DEFAULT_VALS_MAPPING[defaultValue[1]]]: defaultValue[2] })
-			}
-		}
-	}
-
 	uploadRefFile = (e) => {
 		this.setState({ refFile: e.target.files[0], refFileValid: true, inputChanged: true })
 	}

diff --git a/src/constants.js b/src/constants.js
@@ -14,14 +14,17 @@ export const TEMP_FASTP_OUTPUT = BIOWASM_WORKING_DIR + 'temp-trimmed.fastq.gz';
 export const COMBINED_SEQUENCES_FILE_NAME = BIOWASM_WORKING_DIR + 'sequences.fastq.gz';
 export const FASTP_OUTPUT_FILE_NAME = BIOWASM_WORKING_DIR + 'trimmed-sequences.fastq.gz';
 export const MINIMAP_OUTPUT_FILE_NAME = BIOWASM_WORKING_DIR + 'reads.sam';
-export const DEFAULT_VALS_FILE = "https://raw.githubusercontent.com/niemasd/ViralConsensus/main/common.h";
-export const DEFAULT_VALS_FALLBACK_FILE = "data/common.h";
-export const DEFAULT_VALS_MAPPING = {
-	"DEFAULT_MIN_QUAL": "minBaseQuality",
-	"DEFAULT_MIN_DEPTH": "minDepth",
-	"DEFAULT_MIN_FREQ": "minFreq",
-	"DEFAULT_AMBIG": "ambigSymbol",
-	"DEFAULT_PRIMER_OFFSET": "primerOffset",
+export const DEFAULT_VALS = {
+	minBaseQuality: 20,
+	minBaseQualityDefault: 20,
+	minDepth: 10,
+	minDepthDefault: 10,
+	minFreq: 0.5,
+	minFreqDefault: 0.5,
+	ambigSymbol: "N",
+	ambigSymbolDefault: "N",
+	primerOffset: 0,
+	primerOffsetDefault: 0,
 }
 export const CONSENSUS_FILE_NAME = BIOWASM_WORKING_DIR + 'consensus.fa';
 export const POSITION_COUNTS_FILE_NAME = BIOWASM_WORKING_DIR + 'positionCounts.tsv';
@@ -72,7 +75,9 @@ export const DEFAULT_INPUT_STATE = {
 	ambigSymbolValid: true,
 
 	genPosCounts: false,
-	genInsCounts: false
+	genInsCounts: false,
+
+	...DEFAULT_VALS,
 }
 
 export const ARE_FASTQ = (files) => {

diff --git a/vite.config.js b/vite.config.js
@@ -3,7 +3,7 @@ import react from '@vitejs/plugin-react-swc'
 
 // https://vitejs.dev/config/
 export default defineConfig({
-  base: '/ViralWasm-Consensus/',
+  base: '/',
   plugins: [react()],
   build: {
     sourcemap: true,