Set up App-Only Auth with Key for SharePoint Online

#Requires -RunAsAdministrator
<#
.SYNOPSIS
Creates a Self Signed Certificate for use in server to server authentication
.DESCRIPTION
.EXAMPLE
PS C:\> .\Create-SelfSignedCertificate.ps1 -CommonName "MyCert" -StartDate 2015-11-21 -EndDate 2017-11-21
This will create a new self signed certificate with the common name "CN=MyCert". During creation you will be asked to provide a password to protect the private key.
.EXAMPLE
PS C:\> .\Create-SelfSignedCertificate.ps1 -CommonName "MyCert" -StartDate 2015-11-21 -EndDate 2017-11-21 -Password (ConvertTo-SecureString -String "MyPassword" -AsPlainText -Force)
This will create a new self signed certificate with the common name "CN=MyCert". The password as specified in the Password parameter will be used to protect the private key
.EXAMPLE
PS C:\> .\Create-SelfSignedCertificate.ps1 -CommonName "MyCert" -StartDate 2015-11-21 -EndDate 2017-11-21 -Force
This will create a new self signed certificate with the common name "CN=MyCert". During creation you will be asked to provide a password to protect the private key. If there is already a certificate with the common name you specified, it will be removed first.
#>
Param(

   [Parameter(Mandatory=$true)]
   [string]$CommonName,

   [Parameter(Mandatory=$true)]
   [DateTime]$StartDate,

   [Parameter(Mandatory=$true)]
   [DateTime]$EndDate,

   [Parameter(Mandatory=$false, HelpMessage="Will overwrite existing certificates")]
   [Switch]$Force,

   [Parameter(Mandatory=$false)]
   [SecureString]$Password
)

# DO NOT MODIFY BELOW

function CreateSelfSignedCertificate(){

    #Remove and existing certificates with the same common name from personal and root stores
    #Need to be very wary of this as could break something
    if($CommonName.ToLower().StartsWith("cn="))
    {
        # Remove CN from common name
        $CommonName = $CommonName.Substring(3)
    }
    $certs = Get-ChildItem -Path Cert:\LocalMachine\my | Where-Object{$_.Subject -eq "CN=$CommonName"}
    if($certs -ne $null -and $certs.Length -gt 0)
    {
        if($Force)
        {

            foreach($c in $certs)
            {
                remove-item $c.PSPath
            }
        } else {
            Write-Host -ForegroundColor Red "One or more certificates with the same common name (CN=$CommonName) are already located in the local certificate store. Use -Force to remove them";
            return $false
        }
    }

    $name = new-object -com "X509Enrollment.CX500DistinguishedName.1"
    $name.Encode("CN=$CommonName", 0)

    $key = new-object -com "X509Enrollment.CX509PrivateKey.1"
    $key.ProviderName = "Microsoft RSA SChannel Cryptographic Provider"
    $key.KeySpec = 1
    $key.Length = 2048
    $key.SecurityDescriptor = "D:PAI(A;;0xd01f01ff;;;SY)(A;;0xd01f01ff;;;BA)(A;;0x80120089;;;NS)"
    $key.MachineContext = 1
    $key.ExportPolicy = 1 # This is required to allow the private key to be exported
    $key.Create()

    $serverauthoid = new-object -com "X509Enrollment.CObjectId.1"
    $serverauthoid.InitializeFromValue("1.3.6.1.5.5.7.3.1") # Server Authentication
    $ekuoids = new-object -com "X509Enrollment.CObjectIds.1"
    $ekuoids.add($serverauthoid)
    $ekuext = new-object -com "X509Enrollment.CX509ExtensionEnhancedKeyUsage.1"
    $ekuext.InitializeEncode($ekuoids)

    $cert = new-object -com "X509Enrollment.CX509CertificateRequestCertificate.1"
    $cert.InitializeFromPrivateKey(2, $key, "")
    $cert.Subject = $name
    $cert.Issuer = $cert.Subject
    $cert.NotBefore = $StartDate
    $cert.NotAfter = $EndDate
    $cert.X509Extensions.Add($ekuext)
    $cert.Encode()

    $enrollment = new-object -com "X509Enrollment.CX509Enrollment.1"
    $enrollment.InitializeFromRequest($cert)
    $certdata = $enrollment.CreateRequest(0)
    $enrollment.InstallResponse(2, $certdata, 0, "")
    return $true
}

function ExportPFXFile()
{
    if($CommonName.ToLower().StartsWith("cn="))
    {
        # Remove CN from common name
        $CommonName = $CommonName.Substring(3)
    }
    if($Password -eq $null)
    {
        $Password = Read-Host -Prompt "Enter Password to protect private key" -AsSecureString
    }
    $cert = Get-ChildItem -Path Cert:\LocalMachine\my | where-object{$_.Subject -eq "CN=$CommonName"}

    Export-PfxCertificate -Cert $cert -Password $Password -FilePath "$($CommonName).pfx"
    Export-Certificate -Cert $cert -Type CERT -FilePath "$CommonName.cer"
}

function RemoveCertsFromStore()
{
    # Once the certificates have been been exported we can safely remove them from the store
    if($CommonName.ToLower().StartsWith("cn="))
    {
        # Remove CN from common name
        $CommonName = $CommonName.Substring(3)
    }
    $certs = Get-ChildItem -Path Cert:\LocalMachine\my | Where-Object{$_.Subject -eq "CN=$CommonName"}
    foreach($c in $certs)
    {
        remove-item $c.PSPath
    }
}

if(CreateSelfSignedCertificate)
{
    ExportPFXFile
    RemoveCertsFromStore
}

\Create-SelfSignedCertificate.ps1 -CommonName "YourFileName" -StartDate YYYY-MM-DD -EndDate YYYY-MM-DD

Client assertion contains an invalid signature. [Reason - The key used is expired
1AuthenticationException: {"error_description":"AADSTS700027: Client assertion contains an invalid signature. [Reason - The key used is expired., Thumbprint of key used by client:"...]}