From a3aaf6f78e1cf5334bd25ad902e5399c2838194d Mon Sep 17 00:00:00 2001
From: Robert Aboukhalil <robert.aboukhalil@gmail.com>
Date: Wed, 25 Aug 2021 17:19:22 -0700
Subject: [PATCH] Abstract out filesystem setup function so it can be called in
 case apps want to enable custom behavior (e.g. add a new tool after Aioli was
 initialized)

---
 src/worker.js | 73 ++++++++++++++++++++++++++++-----------------------
 1 file changed, 40 insertions(+), 33 deletions(-)

diff --git a/src/worker.js b/src/worker.js
index 9370cbc..b26b6a6 100644
--- a/src/worker.js
+++ b/src/worker.js
@@ -45,39 +45,8 @@ const aioli = {
 		// Initialize WebAssembly modules (downloads .wasm/.js/.json in parallel)
 		await Promise.all(aioli.tools.map(tool => this._setup(tool)));
 
-		// Some tools have preloaded files mounted to their filesystems to hold sample data (e.g. /samtools/examples/).
-		// By default, those are only accessible from the filesystem of the respective tool. Here, we want to allow
-		// other modules to also have access to those sample data files.
-		for(let i in aioli.tools)
-		{
-			// Skip base module
-			if(i == 0)
-				continue;
-
-			for(let j in aioli.tools)
-			{
-				// Skip base module and self
-				if(j == 0 || i == j)
-					continue;
-
-				const fsSrc = aioli.tools[i].module.FS;
-				const fsDst = aioli.tools[j].module.FS;
-				
-				// Make sure source tool actually has such a folder (must be the same as the "module", not "program").
-				// Skip if the destination filesystem already has that folder (could theoretically happen if initialize)
-				// two copies of the same module.
-				const path = `/${aioli.tools[i].tool}`;
-				if(!fsSrc.analyzePath(path).exists || fsDst.analyzePath(path).exists)
-					continue;
-
-				aioli._log(`Mounting ${path} onto ${aioli.tools[j].tool} filesystem`);
-				fsDst.mkdir(path);
-				fsDst.mount(aioli.tools[0].module.PROXYFS, {
-					root: path,
-					fs: fsSrc
-				}, path);
-			}
-		}
+		// Setup filesystems so that tools can access each other's sample data
+		await this._setupFS();
 
 		aioli._log("Ready");
 		return true;
@@ -293,6 +262,44 @@ const aioli = {
 		tool.ready = true;
 	},
 
+	// Setup filesystems so that tools can access each other's sample data
+	async _setupFS()
+	{
+		// Some tools have preloaded files mounted to their filesystems to hold sample data (e.g. /samtools/examples/).
+		// By default, those are only accessible from the filesystem of the respective tool. Here, we want to allow
+		// other modules to also have access to those sample data files.
+		for(let i in aioli.tools)
+		{
+			// Skip base module
+			if(i == 0)
+				continue;
+
+			for(let j in aioli.tools)
+			{
+				// Skip base module and self
+				if(j == 0 || i == j)
+					continue;
+
+				const fsSrc = aioli.tools[i].module.FS;
+				const fsDst = aioli.tools[j].module.FS;
+				
+				// Make sure source tool actually has such a folder (must be the same as the "module", not "program").
+				// Skip if the destination filesystem already has that folder (could theoretically happen if initialize)
+				// two copies of the same module.
+				const path = `/${aioli.tools[i].tool}`;
+				if(!fsSrc.analyzePath(path).exists || fsDst.analyzePath(path).exists)
+					continue;
+
+				aioli._log(`Mounting ${path} onto ${aioli.tools[j].tool} filesystem`);
+				fsDst.mkdir(path);
+				fsDst.mount(aioli.tools[0].module.PROXYFS, {
+					root: path,
+					fs: fsSrc
+				}, path);
+			}
+		}
+	},
+
 	// Common file operations
 	_fileop(operation, path) {
 		aioli._log(`Running ${operation} ${path}`);