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Merge pull request #15 from Syntist/interface-update
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Interface Updated and Fix for windows/Linux (folder with spaces)
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@Prof-S
Prof-S authored Dec 18, 2024
2 parents 7ee004a + 8713653 commit e7de930
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Showing 10 changed files with 151 additions and 115 deletions.
2 changes: 1 addition & 1 deletion electron-app/package.json
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@@ -1,6 +1,6 @@
{
"name": "maestro",
"version": "1.2.0",
"version": "1.3.0",
"description": "An Electron application with React and TypeScript",
"main": "./out/main/index.js",
"author": "example.com",
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12 changes: 7 additions & 5 deletions electron-app/src/main/index.ts
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@@ -1,7 +1,7 @@
import { app, shell, BrowserWindow, ipcMain, dialog } from 'electron'
import path, { join } from 'path'
import { electronApp, optimizer, is } from '@electron-toolkit/utils'
import icon from '../../resources/icon.png?asset'
import icon from '../../resources/saeedlogo.png?asset'
import { spawn } from 'child_process'
import fs from 'fs'

Expand All @@ -25,14 +25,16 @@ const config = JSON.parse(rawData)

let cmd

function createWindow(): void {


function createWindow(): void {
// Create the browser window.
const mainWindow = new BrowserWindow({
width: 900,
height: 670,
width: 1280,
height: 720,
show: false,
autoHideMenuBar: true,
...(process.platform === 'linux' ? { icon } : {}),
icon,
webPreferences: {
preload: join(__dirname, '../preload/index.js'),
sandbox: false,
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2 changes: 1 addition & 1 deletion electron-app/src/renderer/index.html
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Expand Up @@ -2,7 +2,7 @@
<html>
<head>
<meta charset="UTF-8" />
<title>Electron</title>
<title>Maestro</title>
<!-- https://developer.mozilla.org/en-US/docs/Web/HTTP/CSP -->
<meta
http-equiv="Content-Security-Policy"
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2 changes: 1 addition & 1 deletion electron-app/src/renderer/src/App.tsx
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Expand Up @@ -6,7 +6,7 @@ import { Runner } from './components/Runner'

// const specollate = `${await window.electron.getEnvVariable('SPECOLLATE')} -c ${await window.electron.getEnvVariable('SPECOLLATE_CONFIG')}`

const proteorift = `${await window.electron.getEnvVariable('PROTEORIFT')} -c ${await window.electron.getEnvVariable('SPECOLLATE_CONFIG')}`
let proteorift = `\"${await window.electron.getEnvVariable('python')}\" \"${await window.electron.getEnvVariable('PROTEORIFT')}\" -c \"${await window.electron.getEnvVariable('SPECOLLATE_CONFIG')}\"`

function App(): JSX.Element {
const [show, setShow] = useState(false)
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147 changes: 81 additions & 66 deletions electron-app/src/renderer/src/components/ConfigForm/index.tsx
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Expand Up @@ -16,6 +16,7 @@ import {
import FolderSelector from '../FolderSelector'
import { configBuilderV2 } from '@renderer/utils/helper'
import { useState } from 'react'
import Divider from '@mui/material/Divider'

const ConfigForm = ({ run }: any) => {
const [useGpu, setUseGpu] = useState(false)
Expand All @@ -29,17 +30,17 @@ const ConfigForm = ({ run }: any) => {
} = useForm({
mode: 'onTouched',
defaultValues: {
spec_batch_size: 16384,
pep_batch_size: 4096,
spec_batch_size: 4,
pep_batch_size: 1,

search_spec_batch_size: 1024,
search_spec_batch_size: 0.5,

precursor_tolerance: 20,
precursor_tolerance_type: 'ppm',

keep_psms: 5,
num_mods: 1,
charge: 8,
charge: 4,

length_filter: true,
len_tol_neg: -1,
Expand Down Expand Up @@ -75,7 +76,7 @@ const ConfigForm = ({ run }: any) => {
<form onSubmit={handleSubmit(onSubmit)}>
<Box>
<FolderSelector
label="MGF Directory"
label="Spectra Directory (MGF)"
{...register('mgf_dir', { required: true })}
error={errors.mgf_dir ? 'This field is required' : ''}
onChange={(path) => setValue('mgf_dir', path, { shouldValidate: true })}
Expand All @@ -84,16 +85,7 @@ const ConfigForm = ({ run }: any) => {
</Box>
<Box margin="normal">
<FolderSelector
label="Preprocessed Directory"
{...register('prep_dir', { required: true })}
error={errors.prep_dir ? 'This field is required' : ''}
onChange={(path) => setValue('prep_dir', path, { shouldValidate: true })}
value={watch('prep_dir')}
/>
</Box>
<Box margin="normal">
<FolderSelector
label="Peptide Directory"
label="Peptide Database Directory (fasta)"
error={errors.pep_dir ? 'This field is required' : ''}
{...register('pep_dir', { required: true })}
onChange={(path) => setValue('pep_dir', path, { shouldValidate: true })}
Expand All @@ -115,9 +107,12 @@ const ConfigForm = ({ run }: any) => {
<TextField
margin="normal"
fullWidth
label="Spectra Batch Size"
label="Spectra Batch Size (GiB)"
variant="outlined"
type="number"
inputProps={{
step: 0.01
}}
{...register('spec_batch_size', { required: true })}
error={!!errors.spec_batch_size}
helperText={errors.spec_batch_size ? 'This field is required' : ''}
Expand All @@ -127,9 +122,12 @@ const ConfigForm = ({ run }: any) => {
<TextField
margin="normal"
fullWidth
label="Peptide Batch Size"
label="Peptide Batch Size (GiB)"
variant="outlined"
type="number"
inputProps={{
step: 0.01
}}
{...register('pep_batch_size', { required: true })}
error={!!errors.pep_batch_size}
helperText={errors.pep_batch_size ? 'This field is required' : ''}
Expand All @@ -139,14 +137,29 @@ const ConfigForm = ({ run }: any) => {
<TextField
margin="normal"
fullWidth
label="Search Spectra Batch Size"
label="Search Spectra Batch Size (GiB)"
variant="outlined"
type="number"
inputProps={{
step: 0.01
}}
{...register('search_spec_batch_size', { required: true })}
error={!!errors.search_spec_batch_size}
helperText={errors.search_spec_batch_size ? 'This field is required' : ''}
/>
</Grid>
<Grid item xs={6}>
<TextField
margin="normal"
fullWidth
label="Number of Top Scoring PSMs to Keep"
variant="outlined"
type="number"
{...register('keep_psms', { required: true })}
error={!!errors.keep_psms}
helperText={errors.keep_psms ? 'This field is required' : ''}
/>
</Grid>
<Grid item xs={6}>
<TextField
margin="normal"
Expand Down Expand Up @@ -174,18 +187,7 @@ const ConfigForm = ({ run }: any) => {
</Select>
</FormControl>
</Grid>
<Grid item xs={6}>
<TextField
margin="normal"
fullWidth
label="Number of Top Scoring PSMs to Keep"
variant="outlined"
type="number"
{...register('keep_psms', { required: true })}
error={!!errors.keep_psms}
helperText={errors.keep_psms ? 'This field is required' : ''}
/>
</Grid>

<Grid item xs={6}>
<TextField
margin="normal"
Expand All @@ -211,18 +213,56 @@ const ConfigForm = ({ run }: any) => {
/>
</Grid>

<Box width={'100%'} sx={{ marginLeft: 2, marginTop: 2, fontFamily: 500 }}>
<Divider />
<Typography variant="h5" mt={2} mb={2}>
Search space reduction using the following
</Typography>
</Box>
{/* Filters */}
<Box display="flex" justifyContent="center" width={'100%'}>
<FormControlLabel
control={
<Checkbox
checked={watch('length_filter')}
onChange={(e) => setValue('length_filter', e.target.checked)}
/>
}
label="Length Filter"
/>
</Box>
{watch('length_filter') && (
<>
<Grid item xs={6}>
<TextField
margin="normal"
fullWidth
label="Length Tolerance Negative"
variant="outlined"
type="number"
{...register('len_tol_neg', { required: true })}
error={!!errors.len_tol_neg}
helperText={errors.len_tol_neg ? 'This field is required' : ''}
/>
</Grid>

<Grid item xs={6}>
<TextField
margin="normal"
fullWidth
label="Length Tolerance Positive"
variant="outlined"
type="number"
{...register('len_tol_pos', { required: true })}
error={!!errors.len_tol_pos}
helperText={errors.len_tol_pos ? 'This field is required' : ''}
/>
</Grid>
</>
)}
<Box></Box>
<Grid item xs={12}>
<Box display="flex" justifyContent="center">
<FormControlLabel
control={
<Checkbox
checked={watch('length_filter')}
onChange={(e) => setValue('length_filter', e.target.checked)}
/>
}
label="Length Filter"
/>
<FormControlLabel
control={
<Checkbox
Expand All @@ -245,35 +285,10 @@ const ConfigForm = ({ run }: any) => {
</Grid>

{/* Text fields at the bottom */}
<Grid item xs={6}>
<TextField
margin="normal"
fullWidth
label="Length Tolerance Negative"
variant="outlined"
type="number"
{...register('len_tol_neg', { required: true })}
error={!!errors.len_tol_neg}
helperText={errors.len_tol_neg ? 'This field is required' : ''}
/>
</Grid>

<Grid item xs={6}>
<TextField
margin="normal"
fullWidth
label="Length Tolerance Positive"
variant="outlined"
type="number"
{...register('len_tol_pos', { required: true })}
error={!!errors.len_tol_pos}
helperText={errors.len_tol_pos ? 'This field is required' : ''}
/>
</Grid>
</Grid>

<Button type="submit" variant="contained" color="primary">
Run ProteoRift
<Button sx={{ marginTop: 2 }} type="submit" variant="contained" color="primary">
Run Maestro
</Button>
</form>
</Container>
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47 changes: 28 additions & 19 deletions electron-app/src/renderer/src/components/SideBar/index.tsx
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Expand Up @@ -6,10 +6,12 @@ import {
ListItemIcon,
ListItemText,
Divider,
Typography
Typography,
Box
} from '@mui/material'
import HomeIcon from '@mui/icons-material/Home'
import { styled } from '@mui/material/styles'
import logo from '../../assets/logo-1.png'

const drawerWidth = 240

Expand All @@ -33,24 +35,31 @@ const Toolbar = styled('div')(({ theme }) => ({
const Sidebar = () => {
return (
<StyledDrawer variant="permanent" anchor="left">
<Toolbar>
<Typography variant="h6">Maestro</Typography>
</Toolbar>
<Divider />
<List>
<ListItem button>
<ListItemIcon>
<HomeIcon />
</ListItemIcon>
<ListItemText primary="Home" />
</ListItem>
{/* <ListItem button>
<ListItemIcon>
<ListIcon />
</ListItemIcon>
<ListItemText primary="Previous Runs Data" />
</ListItem> */}
</List>
<Box sx={{ display: 'flex', flexDirection: 'column', height: '100%' }}>
<Toolbar>
<Typography variant="h6">
<b>MAESTRO</b>
</Typography>
</Toolbar>
<Divider />
<List sx={{ flexGrow: 1 }}>
<ListItem>
<ListItemIcon>
<HomeIcon />
</ListItemIcon>
<ListItemText primary="Home" />
</ListItem>
{/* <ListItem button>
<ListItemIcon>
<ListIcon />
</ListItemIcon>
<ListItemText primary="Previous Runs Data" />
</ListItem> */}
</List>
<Box sx={{ p: 2 }}>
<img src={logo} width={150} />
</Box>
</Box>
</StyledDrawer>
)
}
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10 changes: 5 additions & 5 deletions electron-app/src/renderer/src/utils/helper.tsx
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Expand Up @@ -151,19 +151,19 @@ rank : 1
[search]
mgf_dir: ${data.mgf_dir}
prep_path: ${data.prep_dir}
prep_path: ${data.mgf_dir}${isWindows ? '\\preprocess' : '/preprocessed'}
pep_dir: ${data.pep_dir}
out_pin_dir : ${data.out_pin_dir}
model_name : ${isWindows ? MODEL_2?.replaceAll('/', '\\') : MODEL_2}
specollate_model_path: ${isWindows ? MODEL?.replaceAll('/', '\\'): MODEL}
specollate_model_path: ${isWindows ? MODEL?.replaceAll('/', '\\') : MODEL}
# Batch sizes for forward pass through the network
spec_batch_size : ${data.spec_batch_size}
pep_batch_size : ${data.pep_batch_size}
spec_batch_size : ${data.spec_batch_size * 1024}
pep_batch_size : ${data.pep_batch_size * 1024}
# Batch size for database search
search_spec_batch_size : ${data.search_spec_batch_size}
search_spec_batch_size : ${data.search_spec_batch_size * 1024}
precursor_tolerance : ${data.precursor_tolerance} # Precursor tolerance to use during database search (Da or ppm)
precursor_tolerance_type : ${data.precursor_tolerance_type} # either ppm or Da
Expand Down
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