Move twisted server and pydas out of slicer python environment

Notification.php

@@ -7,18 +7,19 @@ class Pyslicer_Notification extends ApiEnabled_Notification
   {
   public $moduleName = 'pyslicer';
   public $_moduleComponents=array('Api');
-  
-  
+
+
   /** Register callbacks */
   public function init()
     {
-    $this->enableWebAPI($this->moduleName);  
+    $this->enableWebAPI($this->moduleName);
     $fc = Zend_Controller_Front::getInstance();
     $this->moduleWebroot = $fc->getBaseUrl().'/modules/'.$this->moduleName;
     $this->coreWebroot = $fc->getBaseUrl().'/core';
     $this->addCallBack('CALLBACK_CORE_GET_FOOTER_HEADER', 'getHeader');
     $this->addCallBack('CALLBACK_CORE_GET_LEFT_LINKS', 'getLeftLink');
     $this->addCallBack('CALLBACK_CORE_GET_FOOTER_LAYOUT', 'getFooter');
+    $this->addCallBack('CALLBACK_CORE_GET_CONFIG_TABS', 'getUserTabs');
     }
 
   /** get layout header */
@@ -34,7 +35,7 @@ public function getFooter()
     $footer .= '<script type="text/javascript" src="'.Zend_Registry::get('webroot').'/modules/'.$this->moduleName.'/public/js/layout/'.$this->moduleName.'.js"></script>';
     return $footer;
     }
-    
+
   /**
    *@method getLeftLink
    * will generate a link for this module to be displayed in the main view.
@@ -45,7 +46,7 @@ public function getLeftLink()
     $baseURL = $fc->getBaseUrl();
     $moduleWebroot = $baseURL . '/'.$this->moduleName;
 
-    
+
     if(isset($this->userSession->Dao))
       {
       $apiComponent = MidasLoader::loadComponent('Api', $this->moduleName);
@@ -55,10 +56,18 @@ public function getLeftLink()
       }
     else
       {
-      return array();    
+      return array();
       }
     }
 
-
+  /** User account tabs */
+  public function getUserTabs($params)
+    {
+    $user = $params['user'];
+    $fc = Zend_Controller_Front::getInstance();
+    $moduleWebroot = $fc->getBaseUrl().'/'.$this->moduleName;
+    return array('Pyslicer' => $moduleWebroot.'/user?userId='.$user->getKey());
+    }
+
 } //end class
 ?>

README.md

@@ -4,65 +4,37 @@ pyslicer
 midas viewable python console to interact with slicer
 
 
-To install and run the twisted based python server that will accept http requests from Midas and
-create Slicer jobs in response, first you will need to install a python2.6.
+1) To install and run the twisted based python server that will accept http requests from Midas and
+create Slicer jobs in response, first you will need to install python (2.6+).
 
+2) Download and extract a Slicer nightly binary, the directory where this is extracted to is SLICER_DIR (where the Slicer exe should be contained in).
 
-
-
-Download and extract a Slicer nightly binary, the directory where this is extracted to is SLICER_DIR (where the Slicer exe should be contained in).
-
-Also, in the library/twserver.cfg file, set the path to your slicer exe like so:
+3) Update the library/twserver.cfg file:  
+3a) Set the path to your slicer exe like so:
 
 slicer_path=SLICER_DIR/Slicer
 
-Now change directories into your SLICER_DIR.
-
-
-cd SLICER_DIR
-
-
-As of Slicer Nightly Build 10-16-2012, you will no longer need to manually create the include path or copy over pyconfig.h
-
-We will need a pyconfig.h header for python26 in order to install pip.  You can get this from an ubuntu python system install of 2.6 at 
-/usr/include/python2.6
-
-
-
-Since we will also be compiling twisted, we will need all headers here, so go ahead and copy them over.
-
-mkdir lib/Python/include
-mkdir lib/Python/include/python2.6
-cp /usr/include/python2.6/*.h lib/Python/include/python2.6/
-
-
-
-
-
-Download and install distribute and pip, you will have to replace the path to the python exe with
-the path to your installed python 2.6 interpreter exe.
-
-curl http://python-distribute.org/distribute_setup.py > distribute_setup.py
-./Slicer --launch /usr/bin/python distribute_setup.py 
-curl https://raw.github.com/pypa/pip/master/contrib/get-pip.py > get_pip.py
-./Slicer --launch /usr/bin/python get_pip.py 
-
-Now that pip is installed in your Slicer Python, you can run pip to install pydas and the pydas depedencies.
-
-./Slicer --launch SLICER_DIR/lib/Python/bin/pip install pydas
+3b) Set the Slicer proxy server URL like so:
 
-You will need to install twisted, but I had trouble with this step:
+proxy_url=YOUR_PROXY_URL
 
-./Slicer --launch SLICER_DIR/lib/Python/bin/pip install twisted
+4) Install pydas and twisted  
+4a) Download and install pip
 
-An alternate approach is to download the source of twisted, extract it yourself to TWISTED_DIR, then run this command there:
+curl http://python-distribute.org/distribute_setup.py > distribute_setup.py  
+[sudo] python distribute_setup.py  
+curl https://raw.github.com/pypa/pip/master/contrib/get-pip.py > get_pip.py  
+[sudo] python get_pip.py 
 
-SLICER_DIR/Slicer --no-main-window --python-script setup.py install
+4b) Run pip to install pydas and the pydas dependencies.
 
+pip install pydas
 
+4c) Run pip to install twisted:
 
+pip install twisted
 
-Now you could run your twserver.py using your Slicer Python like this :
+5) Now you could start twisted server like this :
 
-SLICER_DIR/Slicer --no-main-window --python-script twserver.py
+python library/twserver.py
 

constant/module.php

@@ -24,11 +24,19 @@
 define('MIDAS_PYSLICER_SEGMENTATION_PIPELINE', 'segmentation');
 define('MIDAS_PYSLICER_VOLUMERENDERING_PIPELINE', 'volumerendering');
 define('MIDAS_PYSLICER_REGISTRATION_PIPELINE', 'registration');
-
+define('MIDAS_PYSLICER_PDF_SEGMENTATION_PIPELINE', 'pdfsegmentation');
+
+define('MIDAS_PYSLICER_RELATION_TYPE_INPUT_ITEM', 100);
+define('MIDAS_PYSLICER_RELATION_TYPE_INPUT_LABELMAP', 101);
+define('MIDAS_PYSLICER_RELATION_TYPE_OUTPUT_SURFACE_MODEL', 102);
+define('MIDAS_PYSLICER_RELATION_TYPE_OUTPUT_LABELMAP', 103);
+
 define('MIDAS_PYSLICER_SEGMENTATION_INPUT_COUNT', 1);
 define('MIDAS_PYSLICER_SEGMENTATION_OUTPUT_COUNT', 1);
 define('MIDAS_PYSLICER_REGISTRATION_INPUT_COUNT', 2);
 define('MIDAS_PYSLICER_REGISTRATION_OUTPUT_COUNT', 2);
+define('MIDAS_PYSLICER_PDFSEGMENTATION_INPUT_COUNT', 1);
+define('MIDAS_PYSLICER_PDFSEGMENTATION_OUTPUT_COUNT', 2);
 
 define('MIDAS_PYSLICER_EXPECTED_INPUTS', 'expectedinputs');
 define('MIDAS_PYSLICER_EXPECTED_OUTPUTS', 'expectedoutputs');

controllers/UserController.php

@@ -0,0 +1,150 @@
+<?php
+/*=========================================================================
+ MIDAS Server
+ Copyright (c) Kitware SAS. 26 rue Louis Guérin. 69100 Villeurbanne, FRANCE
+ All rights reserved.
+ More information http://www.kitware.com
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+         http://www.apache.org/licenses/LICENSE-2.0.txt
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+=========================================================================*/
+
+/** User settings management */
+class Pyslicer_UserController extends Pyslicer_AppController
+{
+  public $_models = array('User');
+  public $_moduleModels = array('User');
+
+  /**
+   * Shows this user's default settings for Pyslicer module
+   * @param useAjax If this is an Ajax call
+   * @param userId userId Id of the user.  Must be session user itself.
+   * @param pipeline Pipeline name.
+   */
+  function indexAction()
+    {
+    $this->disableLayout();
+    $useAjax = $this->_getParam('useAjax');
+
+    $userDao = Zend_Registry::get('userSession')->Dao;
+    $userId = $this->_getParam('userId');
+    if(isset($userId))
+      {
+      $userDao = $this->User->load($userId);
+      }
+
+    if(!$userDao)
+      {
+      throw new Zend_Exception('Invalid userId', 404);
+      }
+    if(!$this->logged)
+      {
+      throw new Zend_Exception('Must be logged in', 403);
+      }
+    $pipeline = $this->_getParam('pipeline');
+    if(!isset($pipeline))
+      {
+      $pipeline = MIDAS_PYSLICER_PDF_SEGMENTATION_PIPELINE;
+      }
+
+    $pyslicerUserDao = $this->Pyslicer_User->getByUser($userDao, $pipeline);
+    if (isset($useAjax) && $useAjax == true)
+      {
+      $this->disableView();
+      $pyslicerUserArr = array();
+      if ($pyslicerUserDao)
+        {
+        $pyslicerUserArr = $pyslicerUserDao->toArray();
+        }
+      echo JsonComponent::encode(array('status' => 'ok', 'message' => 'Get Pyslicer User settings', 'pyslicerUser' => $pyslicerUserArr));
+      }
+    else
+      {
+      $this->view->pyslicerUser = $pyslicerUserDao;
+      }
+    }
+
+  /**
+   * Create folders for the given pipeline or return existing folders if rootFolderId are same.
+   * @param userId Id of the user.  Must be session user itself.
+   * @param rootFolderId root folder id for the given pipeline.
+   * @param pipeline Pipeline name.
+   */
+  function createfoldersAction()
+    {
+    $this->disableLayout();
+    $this->disableView();
+
+    $rootFolderId = $this->_getParam('rootFolderId');
+    $userId = $this->_getParam('userId');
+    $userDao = Zend_Registry::get('userSession')->Dao;
+    if(isset($userId))
+      {
+      $userDao = $this->User->load($userId);
+      }
+    if(!$userDao)
+      {
+      throw new Zend_Exception('Invalid userId', 400);
+      }
+    if(!$this->logged)
+      {
+      throw new Zend_Exception('Must be logged in', 401);
+      }
+
+    $pipeline = $this->_getParam('pipeline');
+    if(!isset($pipeline))
+      {
+      $pipeline = MIDAS_PYSLICER_PDF_SEGMENTATION_PIPELINE;
+      }
+    $pyslicerUserDao = $this->Pyslicer_User->createFolders($userDao, $rootFolderId, $pipeline);
+    echo JsonComponent::encode(array('status' => 'ok', 'message' => 'Folders created', 'pyslicerUser' => $pyslicerUserDao));
+    }
+
+  /**
+   * Delete default Pyslicer settings for this user
+   * @param userId Id of the user.  Must be session user itself.
+   * @param pipeline Pipeline name.
+   */
+  function deleteAction()
+    {
+    $this->disableLayout();
+    $this->disableView();
+
+    $userId = $this->_getParam('userId');
+    $userDao = Zend_Registry::get('userSession')->Dao;
+    if(isset($userId))
+      {
+      $userDao = $this->User->load($userId);
+      }
+    if(!$userDao)
+      {
+      throw new Zend_Exception('Invalid userId', 400);
+      }
+    if(!$this->logged)
+      {
+      throw new Zend_Exception('Must be logged in', 401);
+      }
+    $pipeline = $this->_getParam('pipeline');
+    if(!isset($pipeline))
+      {
+      $pipeline = MIDAS_PYSLICER_PDF_SEGMENTATION_PIPELINE;
+      }
+
+    $pyslicerUserDao = $this->Pyslicer_User->getByUser($userDao, $pipeline);
+    if ($pyslicerUserDao)
+      {
+      $this->Pyslicer_User->delete($pyslicerUserDao);
+      }
+    echo JsonComponent::encode(array('status' => 'ok', 'message' => 'No default Folders.'));
+    }
+  } // end class
+?>