Parse path name lines live and festoon callbacks with error handling

scripts/prepare_vg.sh

@@ -10,11 +10,10 @@ fi
 echo "${1}"
 echo "${1%.vg}"
 
-if [[ -e "${1%.vg}.vcf.gz" && -e "${1%.vg}.vcf.gz.tbi" ]]
-then
-    echo "Generating xg index and gbwt index from vg file and VCF"
-    vg index "${1}" -v "${1%.vg}.vcf.gz" -x "${1}.xg" --gbwt-name "${1}.gbwt"
-else
-    echo "Generating xg index from vg file"
-    vg index "${1}" -x "${1}.xg"
+echo "Generating xg index ${1}.xg from vg file"
+vg convert "${1}" -x >"${1}.xg"
+
+if [[ -e "${1%.vg}.vcf.gz" && -e "${1%.vg}.vcf.gz.tbi" ]] ; then
+    echo "Generating gbwt index ${1}.gbwt from vg file and VCF"
+    vg gbwt -x "${1}" -v "${1%.vg}.vcf.gz" -o "${1}.gbwt"
 fi

src/errors.mjs

@@ -0,0 +1,38 @@
+/// errors.mjs: Error type definitions for the tube map server
+
+// We can throw this error to trigger our error handling code instead of
+// Express's default. It covers input validation failures, and vaguely-expected
+// server-side errors we want to report in a controlled way (because they could
+// be caused by bad user input to vg).
+export class TubeMapError extends Error {
+  constructor(message) {
+    super(message);
+  }
+}
+
+// We can throw this error to make Express respond with a bad request error
+// message. We should throw it whenever we detect that user input is
+// unacceptable.
+export class BadRequestError extends TubeMapError {
+  constructor(message) {
+    super(message);
+    this.status = 400;
+  }
+}
+
+// We can throw this error to make Express respond with an internal server
+// error message
+export class InternalServerError extends TubeMapError {
+  constructor(message) {
+    super(message);
+    this.status = 500;
+  }
+}
+
+// We can throw this error to make Express respond with an internal server
+// error message about vg.
+export class VgExecutionError extends InternalServerError {
+  constructor(message) {
+    super(message);
+  }
+}

src/scripts.test.js

@@ -0,0 +1,62 @@
+// Tests for data imp[ort scripts, to make sure vg still supports them.
+
+import "./config-server.mjs";
+
+import { find_vg } from "./vg.mjs";
+
+import { mkdtemp, rm, cp, open, access } from 'node:fs/promises';
+import { join } from 'node:path';
+import { tmpdir } from 'node:os';
+import child_process from 'node:child_process';
+import { promisify } from 'node:util';
+
+// This runs a command string and returns a promise for {stdout, stderr} that
+// rejects if the command fails.
+const exec = promisify(child_process.exec);
+
+// This takes a command file and an array of arguments and returns a promise
+// for {stdout, stderr} that rejects if the command fails.
+const execFile = promisify(child_process.execFile);
+
+const EXAMPLE_DATA = join(__dirname, "..", "exampleData");
+const SCRIPTS = join(__dirname, "..", "scripts");
+
+// We set this to a fresh empty directory for each test.
+let workDir = null;
+
+beforeEach(async () => {
+  // Each test gets a fresh directory
+  workDir = await mkdtemp(join(tmpdir(), 'test-'));
+});
+
+afterEach(async () => {
+  if (workDir) {
+    rm(workDir, {force: true, recursive: true});
+  }
+});
+
+it("can run prepare_vg.sh", async () => {
+  for (let filename of ["x.fa", "x.vcf.gz", "x.vcf.gz.tbi"]) {
+    // Get all the input data
+    await cp(join(EXAMPLE_DATA, filename), join(workDir, filename));
+  }
+
+  // Build the graph
+  const vgBuffer = (await execFile(find_vg(), ["construct", "-r", join(workDir, "x.fa"), "-v", join(workDir, "x.vcf.gz"), "-a"], {encoding: "buffer"})).stdout
+  const graphPath = join(workDir, "x.vg");
+  console.log("Save graph to " + graphPath);
+  let file = await open(graphPath, "w");
+  await file.writeFile(vgBuffer);
+  await file.close();
+
+  // Do the call under test
+  // We can't use expect here because await expect(...).resolves doesn't actually detect rejections.
+  console.log("Call script");
+  let {stdout, stderr} = await execFile(join(SCRIPTS, "prepare_vg.sh"), [join(workDir, "x.vg")]);
+  console.log("stdout:", stdout);
+  console.log("stderr:", stderr);
+  await access(join(workDir, "x.vg.xg"));
+  await access(join(workDir, "x.vg.gbwt"));
+});
+
+