add 3mf support for 3d processing

application/config/config.php

@@ -452,6 +452,7 @@
 $config['convert'] = '/usr/local/bin/convert';
 $config['cziutils'] = '/usr/local/bin/cziutils';
 $config['tarrific'] = '/usr/local/bin/tarrific';
+$config['3mf2stl'] = '/usr/local/bin/3mf2stl';
 
 // LDAP username and password.
 // Application should bind anonymously if not set, or set to blanks.

application/models/Filecontainer.php

@@ -42,6 +42,7 @@ public function makeLocal() {
 		return FILE_LOCAL;
 	}
 
+
 }
 
 /* End of file filecontainer.php */

application/models/filehandlers/Objhandler.php

@@ -1,7 +1,7 @@
 <?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 
 class ObjHandler extends FileHandlerBase {
-	protected $supportedTypes = array("obj", "stl");
+	protected $supportedTypes = array("obj", "stl", "3mf");
 	protected $noDerivatives = false;
 
 
@@ -123,11 +123,13 @@ public function createDerivative($args) {
 			return JOB_FAILED;
 		}
 
+		$sourceFile = $this->swapLocal3MFForSTL($this->sourceFile);
+
 		$foundMTL = false;
 
-		$localPath = $this->sourceFile->getPathToLocalFile();
+		$localPath = $sourceFile->getPathToLocalFile();
 		$pathparts = pathinfo($localPath);
-		$originalExtension = pathinfo($this->sourceFile->originalFilename, PATHINFO_EXTENSION);
+		$originalExtension = pathinfo($sourceFile->originalFilename, PATHINFO_EXTENSION);
 
 		$objFile = $localPath . "." .$originalExtension;
 
@@ -465,6 +467,35 @@ public function createNxsFileInternal($sourceFileContainer, $args) {
 
 	}
 
+
+	function swapLocal3MFForSTL($sourceFile= null) {
+		if(!$sourceFile) {
+			$sourceFile = $this->sourceFile;
+		}
+		// this is ugly, but we might get passed in an intermediate. We need to look at the original to see if 
+		// it was a whole slide
+		if($sourceFile->getType() != "3mf") {
+			return;
+		}
+
+		$source = $sourceFile->getPathToLocalFile();
+		// use the original filename as well to keep extensions sane
+		$dest = $this->sourceFile->getPathToLocalFile() . ".stl";
+		if(file_exists($dest)) {
+			return new FileContainer($dest);
+		}
+		$convertString = $this->config->item('3mf2stl') . " -i " . $source . " -o " . $dest;
+		$process = new Cocur\BackgroundProcess\BackgroundProcess($convertString);
+		$process->run();
+		while($process->isRunning()) {
+			sleep(5);
+			$this->pheanstalk->touch($this->job);
+			echo ".";
+		}
+		return new FileContainer($dest);
+
+	}
+
 }
 
 /* End of file  */

docker/commands/3mf2stl

@@ -0,0 +1,2 @@
+#!/bin/bash
+docker run --quiet --memory=8g  --rm -i -v /scratch:/scratch ghcr.io/umn-elevator/3mf2stl:latest  "$@"