Executable installer and GUI launcher

README.md

@@ -45,11 +45,11 @@ The human genome is composed of over 3 billion base pairs, making human analysis
 
 ### DNA
 
-In a nutshell, DNA is found in every cell of your body and contains the instructions for building over 200 different types of cells. DNA is similar to a programming language, but only for living organisms. We can crack the code to reading and interpreting it by using Artificial Intelligence and Machine Learning, which can have life-saving benefits as well as key insights.
+DNA, present in every cell of the body, holds the blueprint for creating over 200 distinct cell types. Like a programming language, it is exclusive to living organisms. With the aid of Artificial Intelligence and Machine Learning, we can decode and comprehend DNA, leading to potentially life-saving discoveries and valuable insights.
 
 ### Databases
 
-Having a database of DNA is the best way to interpret the DNA, and when combined with machine learning, the ML model can make accurate predictions on DNA it has never seen before. This is how current DNA tests function.
+A DNA database is crucial for interpreting DNA sequences. By leveraging machine learning, predictions can be made on previously unseen DNA sequences. This is the foundation on which current DNA analysis programs operate.
 
 ## Getting Started
 
@@ -58,13 +58,20 @@ A [video tutorial](https://youtu.be/dOwkInn6eDw) covering the instructions below
 ### System Requirements
 
 * JDK [17](https://www.oracle.com/java/technologies/downloads/#jdk17-windows)+
-* A `JAVA_HOME` environment variable pointing to your JDK, or the Java executable in your PATH
-* [Gradle](https://gradle.org/install/)
+   * A `JAVA_HOME` environment variable pointing to your JDK, or the Java executable in your PATH
+* [Gradle](https://gradle.org/install/) (included)
 
 ### Build & Run
 
+The easiest way to run the program on Windows is by using the executable file located in the [releases](https://github.com/Verisimilitude11/DNAnalyzer/releases/latest) section to install the program, build gradle and run the GUI.
+
+* Note: Ensure you have Java [17](https://www.oracle.com/java/technologies/downloads/#jdk17-windows) or higher installed and a `JAVA_HOME` path variable set for the program to function correctly!
+
 We use [Gradle](https://gradle.org) for building. The Gradle wrapper takes care of downloading dependencies, testing, compiling, linking, and packaging the code.
 
+<details>
+      <summary>Linux and compilation from source</summary>
+
 ```pwsh
 ./gradlew build
 ```
@@ -111,13 +118,18 @@ DNAnalyzer also comes with a (very basic) GUI; to start DNAnalyzer with the GUI,
 ./gradlew run --args="--gui assets/dna/random/dnalong.fa"
 ```
 
+
 Then:
 
 * Enter the file name of the DNA file in the text field
 * Set min and max
 * Click analyze
 
+
 The results of your analysis will be shown in the right pane.
+</details>
+
+#
 
 #### Help message
 

src/main/resources/Powershell/Installer.md

@@ -0,0 +1,2 @@
+
+## How to edit the Powershell files and create your own executable!

src/main/resources/Powershell/JavaInstaller.ps1

@@ -0,0 +1,2 @@
+[System.Environment]::SetEnvironmentVariable("JAVA_HOME", "C:\Program Files\Java\jdk-17.0.5")
+[System.Environment]::SetEnvironmentVariable("Path", [System.Environment]::GetEnvironmentVariable('Path', [System.EnvironmentVariableTarget]::Machine) + ";$($env:JAVA_HOME)\bin")

src/main/resources/Powershell/download-installer.ps1

@@ -0,0 +1,203 @@
+# Specify the downloads folder
+$downloads_folder = (New-Object -ComObject Shell.Application).NameSpace('shell:Downloads').Self.Path
+
+$ErrorActionPreference = 'SilentlyContinue' 
+$ProgressPreference = 'SilentlyContinue'  # adds increased downloading speed
+
+# Set the path for the DNAnalyzer directory in the downloads folder
+$dir_path = "$downloads_folder/DNAnalyzer"
+
+try {
+    # Check if the directory already exists
+    if ([System.IO.Directory]::Exists($dir_path)) {
+        Write-Host "The directory already exists."
+    } else {
+        # Try to create the directory for DNAnalyzer in the downloads folder
+        New-Item -Path "$downloads_folder/DNAnalyzer/" -ItemType Directory
+    }
+} catch [System.Exception] {
+    # Catch any errors and print a message
+    Write-Host "Something went wrong..." -ForegroundColor Red
+    Write-Error $_.Exception.Message
+}
+
+# Set the URL for the latest release and the source code
+$url = 'https://github.com/Verisimilitude11/DNAnalyzer/releases/latest'
+$alt_url = 'https://github.com/Verisimilitude11/DNAnalyzer/archive/refs/tags/'
+
+# Make a request to the URL and get the response
+$request = [System.Net.WebRequest]::Create($url)
+$response = $request.GetResponse()
+
+# Get the original URL of the response
+$realTagUrl = $response.ResponseUri.OriginalString
+
+# Split the URL by '/' and get the last element, then remove the 'v' prefix
+$version = $realTagUrl.split('/')[-1].Trim('v')
+
+# Set the published asset download URL and the source code download URL
+$realDownloadUrl = "$realTagUrl/download/DNAnalyzer-$version.zip"
+$Alt_realDownloadUrl = "$alt_url" + 'v' + "$version.zip"
+
+Function Installation {
+    param($version, $Download_URL, $dir_path, $fileName, $Live_URL)
+
+    Write-Host "Attempting to fetch file, please wait..."
+
+    try {
+        # Download the file from the specified URL
+        Invoke-WebRequest -Uri $Download_URL[$Live_URL] -OutFile "$($dir_path)/$($fileName[$Live_URL]).zip"
+    } catch {
+        # Catch any errors and print a message
+        Write-Host "Fetch Failed," "StatusCode:" $Error -ForegroundColor Red
+        Pause
+    }
+
+    # Check if the file was successfully downloaded
+    if ([System.IO.File]::Exists("$($dir_path)/$($fileName[$Live_URL]).zip")) {
+        Write-Host "Fetch Sucessful!" -ForegroundColor Green
+        Write-Host "Version:" -ForegroundColor Green $version
+
+        try {
+            # Uncompress the archive
+            Expand-Archive -Path "$($dir_path)/$($fileName[$Live_URL]).zip" -DestinationPath "$($dir_path)/$($fileName[$Live_URL])"
+        } catch { 
+            # Catch any errors and print a message
+            Write-Host "Failed to uncomperess archieve!"
+        }        
+    }
+}
+
+function Before_installation_checks {
+    param($version, $dir_path, $Download_URL, $fileName, $Live_URL)
+
+    # Check if already installed
+    if ([System.IO.File]::Exists("$($dir_path)/$($fileName[$Live_URL])")) {
+        Write-Host ("Latest verison already installed") -ForegroundColor Green
+        Write-Host "Version:" -ForegroundColor Green $version
+        Pause
+    }
+    # Check if the zipped file for the correct version exists, but the folder does not
+    elseif ([System.IO.File]::Exists("$($dir_path)/$($fileName[$Live_URL]).zip")) {
+        Write-Host 'Trying to uncompress archieve...' 
+        try {
+            # Attempt to expand the zip file
+            Expand-Archive -Path "$($dir_path)/$($fileName[$Live_URL]).zip" -DestinationPath "$($dir_path)/$($fileName[$Live_URL])"
+        } catch {
+            Write-Host "Failed to uncomperss archieve!" -ForegroundColor Red
+            Pause  
+        } else {
+            try {
+                # Attempt to remove the zip file
+                Remove-Item "$($dir_path)/$($fileName[$Live_URL]).zip"
+                } catch {
+                Write-Host 'Failed to remove zipped folder.' -ForegroundColor Red
+                Write-Host 'Permisson Error?'
+            } else {
+                # Check if the folder for the correct version already exists
+                if ([System.IO.File]::Exists("$($dir_path)/$($fileName[$Live_URL])")) {
+                    Write-Host ("Latest verison sucessfully unzipped!") -ForegroundColor Green
+                    Write-Host "Location:"  $dir_path/$fileName[$Live_URL] -ForegroundColor Green
+                    }
+            }
+        }
+    }
+    if (-not (Test-Path -Path ("$($dir_path)/$($fileName[$Live_URL]).zip")) -and -not (Test-Path -Path "$($dir_path)/$($fileName[$Live_URL])")) {
+        # If neither zipped file or folder exists with the correct version, start installation
+        Write-Host 'File/Folder not already found on system.'
+        Installation $version $Download_URL $dir_path $fileName $Live_URL # Call installation process function
+    }
+}
+
+## Introduction
+
+# Store the URLs in an array
+$Download_URL = @("$realDownloadUrl", "$Alt_realDownloadUrl")
+
+try {
+    # Check the content type of the source code asset and published asset
+    $alt_response = Invoke-WebRequest -Method Head -Uri $Download_URL[1] -UseBasicParsing 
+    $alt_content = $alt_response.Headers."Content-Type"
+    # $alt_content source code
+
+    $response = Invoke-WebRequest -Method Head -Uri $Download_URL[0] -UseBasicParsing
+    $content = $response.Headers."Content-Type"
+    # $content  actual release
+}
+catch [System.Net.WebException] {
+    if ($null -eq $content -and $null -eq $alt_content) {
+        Write-Host 'Internet error maybe?' -ForegroundColor Red
+        Pause
+    }
+}
+catch {
+    # Catch any other errors and print a message
+    Write-Host 'Something went wrong...' -ForegroundColor Red
+    $Error
+}
+
+finally {
+    # If the 'actual release' content type is a zip file, proceed with installation
+
+    $fileName = @("DNAnalyzer-$version", "DNAnalyzer-$version-BETA_SOURCE")
+
+    if ($content -eq 'application/zip') {
+        # Actual Release
+        $Live_URL = 0 
+        Before_installation_checks $version $dir_path $Download_URL $fileName $Live_URL
+    }
+
+    # If the 'source code' content type is a zip file, proceed with installation
+    elseif ($alt_content -eq 'application/zip') {
+        # Source code
+        $Live_URL = 1
+        Before_installation_checks $version $dir_path $Download_URL $fileName $Live_URL
+    }
+
+    else {
+        # If the content type is not a zip file, print an error message
+        Write-Host 'Something went wrong...' -ForegroundColor Red
+        $Error
+        Pause
+    }
+
+}
+
+# Clean up and compilation
+if ([System.IO.File]::Exists("$($dir_path)/$($fileName[$Live_URL]).zip")) { # if zipped file exists
+    # Remove the zip file
+    try {
+        # Attempt to remove the zip file
+        Remove-Item "$($dir_path)/$($fileName[$Live_URL]).zip"
+    }
+    catch {
+        Write-Host 'Failed to remove zipped folder.' -ForegroundColor Red
+        $Error
+    }
+    $subfolder_location = Get-ChildItem -Path "$($dir_path)/$($fileName[$Live_URL])/" -Filter "*DNAnalyzer*" -Directory
+    $items = Get-ChildItem -Path "$($dir_path)/$($fileName[$Live_URL])/$($subfolder_location)"
+    $items | ForEach-Object {
+        Move-Item -Path $_.FullName -Destination "$($dir_path)/$($fileName[$Live_URL])"
+    }
+
+    if (Test-Path "$($dir_path)/$($fileName[$Live_URL])/$($fileName[0])") {
+        Remove-Item -Path "$($dir_path)/$($fileName[$Live_URL])/$($fileName[0])" -Recurse
+    }
+}
+
+# Change the location to the unzipped folder
+Set-Location -Path "$($dir_path)/$($fileName[$Live_URL])/$($subfolder_location)"
+$installer_location = Get-Location
+explorer "$installer_location"
+# Runs the gradle build and run commands
+try {
+    ./gradlew build
+    ./gradlew run --args="--gui assets/dna/random/dnalong.fa"
+}
+catch { # prints the error
+    Write-Host ($Error) -ForegroundColor Red
+}
+
+# Print a success message
+Write-Host ("Installation Complete!") -ForegroundColor Green
+Write-Host "Version:" -ForegroundColor Green $version 

src/main/resources/Powershell/install_config.yml

@@ -0,0 +1 @@
+