Python virtual environment for linux

desktopApp/TurboPutative.sh

@@ -1,7 +1,22 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 # Get script current directory
 SRC_HOME="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
 
+# Check if virtual environment is created
+if ! [ -f "$SRC_HOME/env/log.info" ]
+then
+    bash "$SRC_HOME/install/install_linux.sh"
+fi
+
+# Electron path
+ELECTRON="$SRC_HOME/electron-v11.0.3-linux-x64/electron"
+
 # Execute electron with app
-"$SRC_HOME/node_modules/electron/dist/electron" "$SRC_HOME/app"
+"$ELECTRON" "$SRC_HOME/app"
+
+# If user closed before finishing process, kill processes
+if [ $? -eq 99 ]
+then
+    kill -9 $(ps -o pid= | grep -v -E "($$|$PPID)" ) > /dev/null 2>&1
+fi

desktopApp/app/index.js

@@ -2,7 +2,7 @@ const { app, BrowserWindow, ipcMain } = require('electron');
 const path = require('path');
 const fs = require('fs');
 const os = require('os');
-const { spawn, spawnSync, exec } = require('child_process');
+const { spawn, spawnSync, execSync } = require('child_process');
 const { finished } = require('stream');
 
 // Global variables
@@ -64,6 +64,8 @@ app.on('window-all-closed', () => {
 
             if (process.platform == "win32") {
                 spawnSync("TASKKILL", ["/F", "/T", "/PID", batch.pid]);
+            } else if (process.platform == "linux") {
+                app.exit(99)
             }
         }
     }
@@ -107,7 +109,7 @@ ipcMain.on('go-back', (e, workflow) => {
 ipcMain.on('run-workflow', (e, workflow) => {
     // Run workflow and send waiting page
 
-    console.log(workflow);
+    // console.log(workflow);
     var loadURL = win.loadURL(loader);
 
     // Define workflow jobID
@@ -182,7 +184,7 @@ ipcMain.on('see-results', (e, workflow) => {
         });
 
         bash.stderr.on(`data`, (data) => {
-            console.error(`stderr: ${data}`);
+            console.error(`stdout: ${data}`);
         });
 
         bash.on('close', (code) => {
@@ -250,8 +252,8 @@ function runWorkflow (osType, modulesString, infile_user, workflowPath, infile_f
         batch = spawn('CMD', ['/C', script, modulesString, infile_user, workflowPath, infile_feature_info, nCores]);
     }
 
-    console.log(script);
-    console.log("PID: ", batch.pid);
+    // console.log(script);
+    // console.log("PID: ", batch.pid);
 
     batch.stdout.on('data', (data) => {
         console.log(`stdout: ${data}`);

desktopApp/app/src/integrator.sh

@@ -4,7 +4,11 @@
 SRC_HOME="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
 
 # PYTHON ENGINE
-PYTHON="$SRC_HOME/python/bin/python3"
+# PYTHON="$SRC_HOME/python/bin/python3"
+PYTHON="$SRC_HOME/../../env/bin/python"
+#PYTHON=python
+
+PY_MODULES="$SRC_HOME/pyModules"
 
 # INPUT VARIABLES
 WORKFLOW="$1"
@@ -30,7 +34,7 @@ do
     if [ $MOD_NUM == '1' ]
     then
         echo Running Tagger >> "$JOB_DIR/WF.log"
-        $PYTHON "$PWD/app/PPUMA/pyModules/Tagger.py" -i "$INFILE" -c "$JOB_DIR/Tagger.ini" -od "$JOB_DIR" -cpu $CPU
+        $PYTHON "$PY_MODULES/Tagger.py" -i "$INFILE" -c "$JOB_DIR/Tagger.ini" -od "$JOB_DIR" -cpu $CPU
 
         # Handle errors
         STATUS_CODE=$?
@@ -46,7 +50,7 @@ do
     if [ $MOD_NUM == '2' ]
     then
         echo Running REname >> "$JOB_DIR/WF.log"
-        $PYTHON "$PWD/app/PPUMA/pyModules/Mod.py" -i "$INFILE" -pr "$JOB_DIR/REname.ini"  -od "$JOB_DIR" -re "$JOB_DIR/regex.ini"  -cpu $CPU
+        $PYTHON "$PY_MODULES/REname.py" -i "$INFILE" -pr "$JOB_DIR/REname.ini"  -od "$JOB_DIR" -re "$JOB_DIR/regex.ini"  -cpu $CPU
 
         # Handle errors
         STATUS_CODE=$?
@@ -62,7 +66,7 @@ do
     if [ $MOD_NUM == '3' ]
     then
         echo Running RowMerger >> "$JOB_DIR/WF.log"
-        $PYTHON "$PWD/app/PPUMA/pyModules/Table.py" -i "$INFILE" -c "$JOB_DIR/rowMerger.ini" -od "$JOB_DIR"
+        $PYTHON "$PY_MODULES/RowMerger.py" -i "$INFILE" -c "$JOB_DIR/rowMerger.ini" -od "$JOB_DIR"
 
         # Handle errors
         STATUS_CODE=$?
@@ -77,7 +81,7 @@ do
     if [ $MOD_NUM == '4' ]
     then
         echo Running TableMerger >> "$JOB_DIR/WF.log"
-        $PYTHON "$PWD/app/PPUMA/pyModules/FeatureInfo.py" -id "$INFILE" -c "$JOB_DIR/tableMerger.ini" -if "$FEATURE_INFO_INFILE" -od "$JOB_DIR"
+        $PYTHON "$PY_MODULES/TableMerger.py" -id "$INFILE" -c "$JOB_DIR/tableMerger.ini" -if "$FEATURE_INFO_INFILE" -od "$JOB_DIR"
 
         # Handle errors
         STATUS_CODE=$?

desktopApp/install/install_linux.sh

@@ -0,0 +1,140 @@
+#!/usr/bin/env bash
+
+
+###################
+# Local functions #
+###################
+
+function checkPython {
+    "$PYTHON" --version > /dev/null 2>&1
+
+    if [ $? -eq 0 ]
+    then
+        # if python is in path, check version
+        local PY_VERSION="$("$PYTHON" --version)"
+        checkVersion "$PY_VERSION"
+
+    else
+        # if python is not in path, ask user to give it
+        getPython
+    fi
+}
+
+
+function checkVersion {
+    # get version 
+    local VERSION=$(grep -E -o "Python\s[0-9]" <(echo "$1"))
+    local SUB_VERSION=$(grep -E -o "Python\s[0-9]\.[0-9]" <(echo "$1") | grep -E -o "[0-9]$")
+
+    if [ "$VERSION" != "Python 3" ]
+    then
+        echo "** ERROR: Using $VERSION instead of Python 3"
+        getPython
+    fi
+
+    if ! [ "$SUB_VERSION" -ge "6" ]
+    then
+        echo "** ERROR: Using $VERSION.$SUB_VERSION instead of Python 3.6 or greater"
+        getPython
+    fi
+
+    createVENV
+
+}
+
+
+function getPython {
+    echo "** Python not found"
+    read -p "** Enter full path to Python (or q to exit): " PYTHON
+
+    if [ $PYTHON -eq "q" ]
+    then
+        endInstall
+
+    else
+        checkPython
+    fi
+}
+
+
+function createVENV {
+
+    echo "** Creating virtual environment"
+    rm -rf "$SRC_HOME/../env"
+    "$PYTHON" -m venv "$SRC_HOME/../env"
+
+    if ! [ $? -eq 0 ]
+    then
+        echo "** ERROR: An error occurred while creating virtual environment"
+        rm -rf "$SRC_HOME/../env"
+        endInstall
+    fi
+
+    local PYTHON_ENV="$SRC_HOME/../env/bin/python"
+    local PIP_ENV="$SRC_HOME/../env/bin/pip"
+
+    echo "** Updating pip"
+    "$PYTHON_ENV" -m pip install --upgrade pip
+
+    if ! [ $? -eq 0 ]
+    then
+        echo "** ERROR: An error occurred while updating pip"
+        rm -rf "$SRC_HOME/../env"
+        endInstall
+    fi
+
+    echo "** Installing modules"
+    "$PIP_ENV" install numpy pandas xlrd xlwt --no-warn-script-location
+    if ! [ $? -eq 0 ]
+    then
+        echo "** ERROR: An error occurred while installing modules"
+        rm -rf "$SRC_HOME/../env"
+        endInstall
+    fi
+
+    echo "$(date) - INFO: Python Virtual Environment for TurboPutative created" > "$SRC_HOME/../env/log.info"
+    checkVENV
+}
+
+
+function checkVENV {
+
+    if [ -f "$SRC_HOME/../env/log.info" ]
+    then
+    # if it exists, exit...
+        envCreated
+    fi
+
+}
+
+
+function envCreated {
+    echo "** Python virtual environment created"
+    endInstall
+}
+
+
+function endInstall {
+    echo "** Installation process finished"
+    exit
+}
+
+##############
+# Start main #
+##############
+
+echo "**"
+echo "** CREATING PYTHON VIRTUAL ENVIRONMENT"
+echo "**"
+
+# Define SRC_HOME
+SRC_HOME="$( cd "$(dirname "$0")" >/dev/null 2>&1 ; pwd -P )"
+
+# Default python
+PYTHON="python"
+
+# Check if env folder already exists
+checkVENV
+
+# Start checking default python
+checkPython