Migrate dicomextractor module settings to database

modules/dicomextractor/configs/module.ini

@@ -1,17 +1,9 @@
-[global]
-; version of the module
-version = 1.0.0
-; full name
-fullname = DICOM Extractor
-; description
-description = Extract metadata from DICOM files
-; category
-category = DICOM
-; dependencies
-dependencies = scheduler,api,thumbnailcreator
+; MIDAS Server. Copyright Kitware SAS. Licensed under the Apache License 2.0.
 
-; hachoir-metadata command
-dcm2xml = "dcm2xml"
-dcmj2pnm = "dcmj2pnm --write-jpeg --min-max-window"
-dcmftest = "dcmftest"
-dcmdictpath = ""
+[global]
+fullname = "DICOM Extractor"
+description = "Extract metadata from DICOM files"
+category = "DICOM"
+dependencies = api,scheduler,thumbnailcreator
+uuid = "53ef7737-29d8-4873-97f5-d35ffb2c2200"
+version = "1.1.0"

modules/dicomextractor/controllers/forms/ConfigForm.php → modules/dicomextractor/constant/module.php

@@ -18,26 +18,11 @@
  limitations under the License.
 =========================================================================*/
 
-/** Configuration form for the dicom extractor */
-class Dicomextractor_ConfigForm extends AppForm
-{
-    /** create  form */
-    public function createConfigForm()
-    {
-        $form = new Zend_Form();
-
-        $form->setAction($this->webroot.'/dicomextractor/config/index')->setMethod('post');
-
-        $dcm2xml = new Zend_Form_Element_Text('dcm2xml');
-        $dcmj2pnm = new Zend_Form_Element_Text('dcmj2pnm');
-        $dcmftest = new Zend_Form_Element_Text('dcmftest');
-        $dcmdictpath = new Zend_Form_Element_Text('dcmdictpath');
-
-        $submit = new  Zend_Form_Element_Submit('submitConfig');
-        $submit->setLabel('Save configuration');
-
-        $form->addElements(array($dcm2xml, $dcmj2pnm, $dcmftest, $dcmdictpath, $submit));
-
-        return $form;
-    }
-}
+define('DICOMEXTRACTOR_DCM2XML_COMMAND_KEY', 'dcm2xml_command');
+define('DICOMEXTRACTOR_DCM2XML_COMMAND_DEFAULT_VALUE', 'dcm2xml');
+define('DICOMEXTRACTOR_DCMJ2PNM_COMMAND_KEY', 'dcmj2pnm_command');
+define('DICOMEXTRACTOR_DCMJ2PNM_COMMAND_DEFAULT_VALUE', 'dcmj2pnm --write-jpeg --min-max-window');
+define('DICOMEXTRACTOR_DCMFTEST_COMMAND_KEY', 'dcmftest_command');
+define('DICOMEXTRACTOR_DCMFTEST_COMMAND_DEFAULT_VALUE', 'dcmftest');
+define('DICOMEXTRACTOR_DCMDICTPATH_KEY', 'dcmdictpath');
+define('DICOMEXTRACTOR_DCMDICTPATH_DEFAULT_VALUE', '');

modules/dicomextractor/controllers/AdminController.php

@@ -0,0 +1,68 @@
+<?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.
+=========================================================================*/
+
+/** Admin controller for the dicomextractor module. */
+class Dicomextractor_AdminController extends Dicomextractor_AppController
+{
+    /** @var array */
+    public $_models = array('Setting');
+
+    /** Index action */
+    public function indexAction()
+    {
+        $this->requireAdminPrivileges();
+
+        $this->view->pageTitle = 'DICOM Extractor Module Configuration';
+        $form = new Dicomextractor_Form_Admin();
+
+        if ($this->getRequest()->isPost()) {
+            $data = $this->getRequest()->getPost();
+
+            if ($form->isValid($data)) {
+                $values = $form->getValues();
+
+                foreach ($values as $key => $value) {
+                    if ($value !== null) {
+                        $this->Setting->setConfig($key, $value, $this->moduleName);
+                    }
+                }
+            }
+
+            $form->populate($data);
+        } else {
+            $elements = $form->getElements();
+
+            foreach ($elements as $element) {
+                $name = $element->getName();
+
+                if ($name !== 'csrf' && $name !== 'submit') {
+                    $value = $this->Setting->getValueByName($name, $this->moduleName);
+
+                    if (!is_null($value)) {
+                        $form->setDefault($name, $value);
+                    }
+                }
+            }
+        }
+
+        $this->view->form = $form;
+        session_start();
+    }
+}

modules/dicomextractor/controllers/components/ExtractorComponent.php

@@ -23,12 +23,14 @@
 /** Extract dicom metadata */
 class Dicomextractor_ExtractorComponent extends AppComponent
 {
+    public $moduleName = 'dicomextractor';
+
     /**
      * Check whether a given application is configured properly.
      *
      * @param command the command to test with
      * @param appName the human-readable application name
-     * @appendVersion whether we need the --version flag
+     * @param appendVersion whether we need the --version flag
      * @return an array indicating whether the app is valid or not
      */
     public function getApplicationStatus($preparedCommand, $appName, $appendVersion = true)
@@ -76,8 +78,10 @@ private function _getExecutableArg($commandWithParams)
      */
     private function _prependDataDict(&$command)
     {
-        $modulesConfig = Zend_Registry::get('configsModules');
-        $dictPath = $modulesConfig['dicomextractor']->dcmdictpath;
+        /** @var SettingModel $settingModel */
+        $settingModel = MidasLoader::loadModel('Setting');
+        $dictPath = $settingModel->getValueByName(DICOMEXTRACTOR_DCMDICTPATH_KEY, $this->moduleName);
+
         if ($dictPath != "") {
             $command = 'DCMDICTPATH="'.$dictPath.'" '.$command;
         }
@@ -88,18 +92,24 @@ private function _prependDataDict(&$command)
      */
     public function isDCMTKWorking()
     {
-        $ret = array();
-        $modulesConfig = Zend_Registry::get('configsModules');
-        $dcm2xmlCommand = $modulesConfig['dicomextractor']->dcm2xml;
-        $dcmftestCommand = $modulesConfig['dicomextractor']->dcmftest;
+        /** @var SettingModel $settingModel */
+        $settingModel = MidasLoader::loadModel('Setting');
+        $dcm2xmlCommand = $settingModel->getValueByName(DICOMEXTRACTOR_DCM2XML_COMMAND_KEY, $this->moduleName);
+        $dcmftestCommand = $settingModel->getValueByName(DICOMEXTRACTOR_DCMFTEST_COMMAND_KEY, $this->moduleName);
+
         // dcmj2pnmCommand may have some params that will cause it to throw
         // an error when no input is given, hence for existence and configuration
         // testing just get the command itself, without params
-        $dcmj2pnmCommand = $this->_getExecutableArg($modulesConfig['dicomextractor']->dcmj2pnm);
+        $dcmj2pnmCommand = $this->_getExecutableArg($settingModel->getValueByName(DICOMEXTRACTOR_DCMJ2PNM_COMMAND_KEY, $this->moduleName));
+
+        $ret = array();
         $ret['dcm2xml'] = $this->getApplicationStatus($dcm2xmlCommand, 'dcm2xml');
         $ret['dcmftest'] = $this->getApplicationStatus($dcmftestCommand, 'dcmftest', false);
         $ret['dcmj2pnm'] = $this->getApplicationStatus($dcmj2pnmCommand, 'dcmj2pnm');
-        if ($modulesConfig['dicomextractor']->dcmdictpath == "") {
+
+        $dataDictVar = $settingModel->getValueByName(DICOMEXTRACTOR_DCMDICTPATH_KEY, $this->moduleName);
+
+        if ($dataDictVar == "") {
             if (is_readable('/usr/local/share/dcmtk/dicom.dic') ||  // default on OS X
                 is_readable('/usr/share/dcmtk/dicom.dic')
             ) { // default on Ubuntu
@@ -111,7 +121,6 @@ public function isDCMTKWorking()
                 );
             }
         } else {
-            $dataDictVar = $modulesConfig['dicomextractor']->dcmdictpath;
             $dictPaths = explode(":", $dataDictVar);
             $errorInDictVar = false;
             foreach ($dictPaths as $path) {
@@ -154,10 +163,12 @@ public function thumbnail($item)
         $bitstream = $bitstreams[$numBitstreams / 2];
 
         // Turn the DICOM into a JPEG
-        $modulesConfig = Zend_Registry::get('configsModules');
         $tempDirectory = $utilityComponent->getTempDirectory();
         $tmpSlice = $tempDirectory.'/'.$bitstream->getName().'.jpg';
-        $command = $modulesConfig['dicomextractor']->dcmj2pnm;
+
+        /** @var SettingModel $settingModel */
+        $settingModel = MidasLoader::loadModel('Setting');
+        $command = $settingModel->getValueByName(DICOMEXTRACTOR_DCMJ2PNM_COMMAND_KEY, $this->moduleName);
         $preparedCommand = str_replace("'", '"', $command);
         $preparedCommand .= ' "'.$bitstream->getFullPath().'" "'.$tmpSlice.'"';
         $this->_prependDataDict($preparedCommand);
@@ -183,8 +194,10 @@ public function extract($revision)
             return;
         }
         $bitstream = $bitstreams[0];
-        $modulesConfig = Zend_Registry::get('configsModules');
-        $command = $modulesConfig['dicomextractor']->dcm2xml;
+
+        /** @var SettingModel $settingModel */
+        $settingModel = MidasLoader::loadModel('Setting');
+        $command = $settingModel->getValueByName(DICOMEXTRACTOR_DCM2XML_COMMAND_KEY, $this->moduleName);
         $preparedCommand = str_replace("'", '"', $command);
         $preparedCommand .= ' "'.$bitstream->getFullPath().'"';
         $this->_prependDataDict($preparedCommand);

modules/dicomextractor/database/InstallScript.php

@@ -0,0 +1,39 @@
+<?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.
+=========================================================================*/
+
+require_once BASE_PATH.'/modules/dicomextractor/constant/module.php';
+
+/** Install the dicomextractor module. */
+class Dicomextractor_InstallScript extends MIDASModuleInstallScript
+{
+    /** @var string */
+    public $moduleName = 'dicomextractor';
+
+    /** Post database install. */
+    public function postInstall()
+    {
+        /** @var SettingModel $settingModel */
+        $settingModel = MidasLoader::loadModel('Setting');
+        $settingModel->setConfig(DICOMEXTRACTOR_DCM2XML_COMMAND_KEY, DICOMEXTRACTOR_DCM2XML_COMMAND_DEFAULT_VALUE, $this->moduleName);
+        $settingModel->setConfig(DICOMEXTRACTOR_DCMJ2PNM_COMMAND_KEY, DICOMEXTRACTOR_DCMJ2PNM_COMMAND_DEFAULT_VALUE, $this->moduleName);
+        $settingModel->setConfig(DICOMEXTRACTOR_DCMFTEST_COMMAND_KEY, DICOMEXTRACTOR_DCMFTEST_COMMAND_DEFAULT_VALUE, $this->moduleName);
+        $settingModel->setConfig(DICOMEXTRACTOR_DCMDICTPATH_KEY, DICOMEXTRACTOR_DCMDICTPATH_DEFAULT_VALUE, $this->moduleName);
+    }
+}

modules/dicomextractor/database/upgrade/1.1.0.php

@@ -0,0 +1,58 @@
+<?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.
+=========================================================================*/
+
+/** Upgrade the dicomextractor module to version 1.1.0. */
+class Dicomextractor_Upgrade_1_1_0 extends MIDASUpgrade
+{
+    /** @var string */
+    public $moduleName = 'dicomextractor';
+
+    /** Post database upgrade. */
+    public function postUpgrade()
+    {
+        /** @var SettingModel $settingModel */
+        $settingModel = MidasLoader::loadModel('Setting');
+        $configPath = LOCAL_CONFIGS_PATH.DIRECTORY_SEPARATOR.$this->moduleName.'.local.ini';
+
+        if (file_exists($configPath)) {
+            $config = new Zend_Config_Ini($configPath, 'global');
+            $settingModel->setConfig(DICOMEXTRACTOR_DCM2XML_COMMAND_KEY, $config->get('dcm2xml', DICOMEXTRACTOR_DCM2XML_COMMAND_DEFAULT_VALUE), $this->moduleName);
+            $settingModel->setConfig(DICOMEXTRACTOR_DCMJ2PNM_COMMAND_KEY, $config->get('dcmj2pnm', DICOMEXTRACTOR_DCMJ2PNM_COMMAND_DEFAULT_VALUE), $this->moduleName);
+            $settingModel->setConfig(DICOMEXTRACTOR_DCMFTEST_COMMAND_KEY, $config->get('dcmftest', DICOMEXTRACTOR_DCMFTEST_COMMAND_DEFAULT_VALUE), $this->moduleName);
+            $settingModel->setConfig(DICOMEXTRACTOR_DCMDICTPATH_KEY, $config->get('dcmdictpath', DICOMEXTRACTOR_DCMDICTPATH_DEFAULT_VALUE), $this->moduleName);
+
+            $config = new Zend_Config_Ini($configPath, null, true);
+            unset($config->global->dcm2xml);
+            unset($config->global->dcmj2pnm);
+            unset($config->global->dcmftest);
+            unset($config->global->dcmdictpath);
+
+            $writer = new Zend_Config_Writer_Ini();
+            $writer->setConfig($config);
+            $writer->setFilename($configPath);
+            $writer->write();
+        } else {
+            $settingModel->setConfig(DICOMEXTRACTOR_DCM2XML_COMMAND_KEY, DICOMEXTRACTOR_DCM2XML_COMMAND_DEFAULT_VALUE, $this->moduleName);
+            $settingModel->setConfig(DICOMEXTRACTOR_DCMJ2PNM_COMMAND_KEY, DICOMEXTRACTOR_DCMJ2PNM_COMMAND_DEFAULT_VALUE, $this->moduleName);
+            $settingModel->setConfig(DICOMEXTRACTOR_DCMFTEST_COMMAND_KEY, DICOMEXTRACTOR_DCMFTEST_COMMAND_DEFAULT_VALUE, $this->moduleName);
+            $settingModel->setConfig(DICOMEXTRACTOR_DCMDICTPATH_KEY, DICOMEXTRACTOR_DCMDICTPATH_DEFAULT_VALUE, $this->moduleName);
+        }
+    }
+}