@sjcrh/proteinpaint-rust 2.120.1 → 2.121.0

package/README.md

@@ -2,13 +2,11 @@
 
 This directory holds the source code for rust-compiled utilities.
 
-
 ## Code layout
 
 All source code files should be directly under the `src/` directory. For a source
 code file to be compiled, create a `[[bin]]` entry for it in the Cargo.toml file:
 
-
 ```toml
 [[bin]]
 name="tool0"
@@ -27,10 +25,10 @@ which goes against rust cargo's assumptions of having source code under `src/bin
 ## Using from nodejs
 
 ```js
-// assuming a js file from server/src 
-const run_rust = require('@sjcrh/proteinpaint-rust').run_rust
-// or 
-// import * as utils from './utils'
+// Assuming a js or ts file from server/src 
+
+import { run_rust } from '@sjcrh/proteinpaint-rust'
+
 
 // 'indel' may be replaced by any binary name as specified in Cargo.toml
 const out = await run_rust('indel', input_data)
@@ -39,8 +37,10 @@ const out = await run_rust('indel', input_data)
 ## Test
 
 From the `proteinpaint/server` directory,
+
 ```bash
 npx test
+npx tsc
 ```
 
 ## Build

package/downloadBinariesOrCompileSource.js

@@ -1,12 +1,16 @@
-const https = require('https')
-const fs = require('fs')
-const os = require('os')
-const path = require('path')
-const { exec } = require('child_process')
-const tar = require('tar')
+// Import necessary modules
+import https from 'https'
+import fs from 'fs'
+import os from 'os'
+import path from 'path'
+import { exec } from 'child_process'
+import * as tar from 'tar'
 
-// Read package.json to get version and pp_release_tag
-const packageJson = require(path.join(__dirname, 'package.json'))
+// Setting up directory name
+const __dirname = import.meta.dirname
+
+// Read package.json
+const packageJson = JSON.parse(fs.readFileSync(path.join(__dirname, 'package.json'), 'utf8'))
 const { version, pp_release_tag } = packageJson
 
 const targetDirectory = './target/release'

package/index.js

@@ -1,18 +1,20 @@
-const fs = require('fs')
-const path = require('path'),
-	{ spawn, exec } = require('child_process'),
-	Readable = require('stream').Readable,
-	Transform = require('stream').Transform,
-	{ promisify } = require('util')
+// Import necessary modules
+import fs from 'fs'
+import path from 'path'
+import { spawn, exec } from 'child_process'
+import { Readable, Transform } from 'stream'
+import { promisify } from 'util'
+
+const __dirname = import.meta.dirname
 
 const execPromise = promisify(exec)
 
-// check if rust binary directory exists and is not empty
+// Check if rust binary directory exists and is not empty
 const binaryDir = path.join(__dirname, '/target/release/')
 if (!fs.existsSync(binaryDir)) throw `missing rust binary directory='${binaryDir}'`
 if (!fs.readdirSync(binaryDir).length) throw `empty rust binary directory='${binaryDir}'`
 
-exports.run_rust = function (binfile, input_data) {
+export function run_rust(binfile, input_data) {
 	return new Promise((resolve, reject) => {
 		const binpath = path.join(__dirname, '/target/release/', binfile)
 		const ps = spawn(binpath)
@@ -52,7 +54,7 @@ exports.run_rust = function (binfile, input_data) {
 	})
 }
 
-exports.stream_rust = function (binfile, input_data, emitJson) {
+export function stream_rust(binfile, input_data, emitJson) {
 	const binpath = path.join(__dirname, '/target/release/', binfile)
 
 	const ps = spawn(binpath)

package/package.json

@@ -1,6 +1,7 @@
 {
-	"version": "2.120.1",
+	"version": "2.121.0",
 	"name": "@sjcrh/proteinpaint-rust",
+	"type": "module",
 	"description": "Rust-based utilities for proteinpaint",
 	"main": "index.js",
 	"bin": {
@@ -38,5 +39,5 @@
 	"devDependencies": {
 		"tape": "^5.2.2"
 	},
-	"pp_release_tag": "v2.120.1"
+	"pp_release_tag": "v2.121.0"
 }

package/src/DEanalysis.rs

@@ -664,6 +664,14 @@ fn main() {
                                 //println!("filtering time:{:?}", filtering_time.elapsed());
                                 //println!("filtered_matrix_rows:{:?}", filtered_matrix.nrows());
                                 //println!("filtered_matrix_cols:{:?}", filtered_matrix.ncols());
+                                if filtered_matrix.nrows() == 0 {
+                                    // Its possible after filtering there might not be any genes left in the matrix, in such a case the rust code must exit gracefully with an error.
+                                    panic!("Number of genes after filtering = 0, cannot proceed any further")
+                                }
+                                if filtered_matrix.ncols() == 0 {
+                                    // Its possible after filtering there might not be any samples left in the matrix, in such a case the rust code must exit gracefully with an error.
+                                    panic!("Number of samples after filtering = 0, cannot proceed any further")
+                                }
                                 //let cpm_normalization_time = Instant::now();
                                 let mut normalized_matrix = cpm(&filtered_matrix);
                                 //println!(
@@ -1214,7 +1222,6 @@ fn calc_factor_quantile(
         for i in 0..input_matrix.nrows() {
             row_vec.push(input_matrix[(i, j)] as f64);
         }
-        //println!("row_vec:{:?}", row_vec);
         let quan = calc_quantile(row_vec, P);
         //println!("quan:{}", quan);
         let num = quan / lib_sizes[j];