coder cleanup

admin/islandora.admin.inc

@@ -1,11 +1,14 @@
 <?php
 
 /**
- * @file islandora.admin.inc
+ * @file
+ * islandora.admin.inc: This file contains the general islandora admin form and callback functions.
+ */
+
+/**
  * Create admin form
  * @return array
  */
-
 function islandora_repository_admin($form, &$form_state) {
   module_load_include('inc', 'islandora', 'includes/tuque');
   module_load_include('inc', 'islandora', 'includes/utilities');
@@ -77,7 +80,7 @@ function islandora_repository_admin($form, &$form_state) {
     '#type' => 'textfield',
     '#title' => t('Fedora base URL'),
     '#default_value' => variable_get('islandora_base_url', 'http://localhost:8080/fedora'),
-    '#description' => t('The URL to use for REST connections <br>' . $confirmation_message),
+    '#description' => t('The URL to use for REST connections <br />' . $confirmation_message),
     '#required' => TRUE,
     '#ajax' => array(
       'callback' => 'islandora_update_url_div',
@@ -134,7 +137,7 @@ function islandora_repository_admin($form, &$form_state) {
       '#type' => 'textfield',
       '#title' => t('PID namespaces allowed in this Drupal install'),
       '#default_value' => variable_get('islandora_pids_allowed', 'default: demo: changeme: ilives: islandora-book: books: newspapers: '),
-      '#description' => t('A space separated list of PID namespaces that users are permitted to access from this Drupal installation. <br /> This could be more than a simple namespace ie demo:mydemos. <br> islandora: is reserved and is always allowed.'),
+      '#description' => t('A space separated list of PID namespaces that users are permitted to access from this Drupal installation. <br /> This could be more than a simple namespace ie demo:mydemos. <br /> islandora: is reserved and is always allowed.'),
       '#weight' => 0,
     );
   }

includes/breadcrumb.inc

@@ -1,5 +1,10 @@
 <?php
 
+/**
+ * @file
+ * This file contains functions to create breadcrumbs on Islandora object pages.
+ */
+
 function islandora_get_breadcrumbs($object) {
   $breadcrumbs = array();
 

includes/datastream.inc

@@ -1,11 +1,13 @@
 <?php
 
 /**
- * @file datastream.inc 
+ * @file
+ * This file contains the admin form and callback functions for datastream manipulations.
  */
 
 define('DS_COMP_STREAM', 'DS-COMPOSITE-MODEL');
 /**
+ * Callback function to view or download a datastream.
  *
  * @global object $user
  * @param string $object_id
@@ -55,7 +57,9 @@ function islandora_datastream_get_parents($islandora_object) {
       $parent_collections[$pid]['label'] = $object->label;
       $parent_collections[$pid]['label_link'] = l($parent_collections[$pid]['label'], $parent_collections[$pid]['url']);
     }
-    catch (RepositoryException $e) {}
+    catch (RepositoryException $e) {
+
+    }
   }
 
   return $parent_collections;
@@ -168,9 +172,9 @@ function islandora_get_add_datastream_form($object, &$form_state) {
   );
 
   if (!empty($unused_dsids)) {
-    $dsidsForForm = array();
+    $dsids_for_form = array();
     foreach ($unused_dsids as $key => $value) {
-      $dsidsForForm[$key] = $key;
+      $dsids_for_form[$key] = $key;
     }
     $form['add_fieldset']['stream_id'] = array(
       '#type' => 'select',
@@ -179,7 +183,7 @@ function islandora_get_add_datastream_form($object, &$form_state) {
       '#weight' => '-1',
       '#description' => t('Datastream IDs defined by the content model.'),
     );
-    $form['add_fieldset']['stream_id']['#options'] = $dsidsForForm;
+    $form['add_fieldset']['stream_id']['#options'] = $dsids_for_form;
   }
   else {
     $form['add_fieldset']['stream_id'] = array(
@@ -220,11 +224,11 @@ function islandora_add_datastream_form_submit($form, &$form_state) {
   $dsid = $form_state['values']['stream_id'];
   $ds_label = $form_state['values']['stream_label'];
   $dformat = $mimetype->getMimeType($file);
-  $controlGroup = "M";
+  $control_group = "M";
 
   try {
     $fedora_object = islandora_object_load($object_id);
-    $ds = $fedora_object->constructDatastream($dsid, $controlGroup);
+    $ds = $fedora_object->constructDatastream($dsid, $control_group);
     $ds->label = $ds_label;
     $ds->mimetype = $dformat;
     $ds->setContentFromFile($file);
@@ -235,7 +239,7 @@ function islandora_add_datastream_form_submit($form, &$form_state) {
     drupal_set_message(t('@message', array('@message' => check_plain($e->getMessage()))), 'error');
     return;
   }
-  drupal_set_message("Successfully Added Datastream!");
+  drupal_set_message(t("Successfully Added Datastream!"));
   drupal_goto("islandora/object/$object_id");
 }
 
@@ -254,8 +258,8 @@ function islandora_add_datastream_form_validate($form, &$form_state) {
     return;
   }
   $dsid = $form_state['values']['stream_id'];
-  $dsLabel = $form_state['values']['stream_label'];
+  $ds_label = $form_state['values']['stream_label'];
-  if (strlen($dsid) > 64) {
+  if (drupal_strlen($dsid) > 64) {
     form_set_error('', t('Data stream ID cannot be more than 64 characters.'));
     return FALSE;
   }
@@ -263,11 +267,11 @@ function islandora_add_datastream_form_validate($form, &$form_state) {
     form_set_error('', t("Data stream ID (@dsid) has to start with a letter.", array('@dsid' => check_plain($dsid))));
     return FALSE;
   }
-  if (strlen($dsLabel) > 64) {
+  if (drupal_strlen($ds_label) > 64) {
     form_set_error('', t('Data stream Label cannot be more than 64 characters.'));
     return FALSE;
   }
-  if (strpos($dsLabel, '/')) {
+  if (strpos($ds_label, '/')) {
     form_set_error('', t('Data stream Label cannot contain a "/".'));
     return FALSE;
   }
@@ -356,19 +360,19 @@ function islandora_add_datastream_form($form, &$form_state, $object) {
   );
 
   $unused_dsids = islandora_get_unused_dsids($object);
-  $dsidsForForm = '';
+  $dsids_for_form = '';
   $i = 0;
   foreach ($unused_dsids as $key => $value) {
     if ($i++) {
-      $dsidsForForm .= ", ";
+      $dsids_for_form .= ", ";
     }
-    $dsidsForForm .= "'$key'";
+    $dsids_for_form .= "'$key'";
   }
 
   $form['add_fieldset']['stream_id'] = array(
     '#title' => 'Datastream ID',
     '#required' => 'TRUE',
-    '#description' => t('An ID for this stream that is unique to this object. Must start with a letter and contain only alphanumeric characters and dashes and underscores. Datastreams that are defined by the content model dont currently exist: <b>' . $dsidsForForm . '</b>.'),
+    '#description' => t('An ID for this stream that is unique to this object. Must start with a letter and contain only alphanumeric characters and dashes and underscores. Datastreams that are defined by the content model dont currently exist: <b>' . $dsids_for_form . '</b>.'),
     '#type' => 'textfield',
     '#weight' => -1,
     '#autocomplete_path' => "islandora/object/$object->id/manage/datastreams/add/autocomplete",

includes/islandora.ingest.inc

@@ -1,5 +1,10 @@
 <?php
 
+/**
+ * @file
+ * This file contains ingest callback functions
+ */
+
 function islandora_ingest_get_information(AbstractFedoraObject $collection_object) {
   $models = $collection_object->models;
   $collection_info = module_invoke_all('islandora_ingest_get_information', $models, $collection_object);

includes/islandora_dublin_core.inc

@@ -121,10 +121,10 @@ class Dublin_Core {
             $value = $values;
           }
           $dc_label = explode(':', $field);
-          $element_label = ucfirst($dc_label[1]);
+          $element_label = drupal_ucfirst($dc_label[1]);
           $dc_array[$field]['label'] = $element_label;
           $dc_array[$field]['value'] = $value;
-          $dc_array[$field]['class'] = strtolower(preg_replace('/[^A-Za-z0-9]/', '-', $field));
+          $dc_array[$field]['class'] = drupal_strtolower(preg_replace('/[^A-Za-z0-9]/', '-', $field));
         }
       }
     }

includes/mime.detect.inc

@@ -227,7 +227,7 @@ class MimeDetect {
   public function getMimetype($filename, $debug = FALSE) {
 
     $file_name_and_extension = explode('.', $filename);
-    $ext = strtolower(array_pop($file_name_and_extension));
+    $ext = drupal_strtolower(array_pop($file_name_and_extension));
 
     if (!empty($this->protectedMimeTypes[$ext])) {
       if (TRUE === $debug) {

includes/object_properties.inc

@@ -1,7 +1,14 @@
 <?php
 
 /**
- * may want more validation here the only restrictions i see on
+ * @file
+ * Contains admin form functions for object properties
+ */
+
+/**
+ * Validate function for object properties admin form.
+ *
+ * @TODO: may want more validation here the only restrictions i see on
  * the object label and owner is the foxml schema says they should be
  * an xsd:string there maybe further restrictions such as length but they aren't
  * defined in the schema.
@@ -18,6 +25,7 @@ function islandora_edit_properties_form_validate($form, &$form_state) {
 }
 
 /**
+ * Submit function for object properties admin form.
  *
  * @param array $form
  * @param array $form_state
@@ -53,12 +61,16 @@ function islandora_edit_properties_form_submit($form, &$form_state) {
   }
 }
 
+/**
+ * Callback function for object properties admin form delete button.
+ */
 function islandora_edit_properties_form_delete($form, &$form_state) {
   $islandora_object = $form_state['values']['pid'];
   drupal_goto("islandora/object/$islandora_object/delete");
 }
 
 /**
+ * Object properties admin form.
  *
  * @param array $form
  * @param array $form_state
@@ -111,5 +123,3 @@ function islandora_edit_properties_form($form, &$form_state, $object) {
   );
   return $form;
 }
-
-?>

includes/purge.form.inc

@@ -1,5 +1,10 @@
 <?php
 
+/**
+ * @file
+ * This file contains the admin (confirmation) form and callback functions to purge an object.
+ */
+
 /**
  * Gives the option of deleting or purging and object.
  *

includes/tuque.inc

@@ -1,5 +1,10 @@
 <?php
 
+/**
+ * @file
+ * This file contains a class to include the Tuque php library.
+ */
+
 $islandora_module_path = drupal_get_path('module', 'islandora');
 
 //do this until we expost these in a module or library
@@ -61,7 +66,8 @@ class IslandoraTuque {
     if (!isset($user) || $user->uid == 0) {
       $user_string = 'anonymous';
       $pass_string = 'anonymous';
-    } else {
+    }
+    else {
       $user_string = $user->name;
       $pass_string = $user->pass;
     }
@@ -87,7 +93,7 @@ class IslandoraTuque {
     $islandora_doc_link = l(t('Islandora documentation'), 'https://wiki.duraspace.org/display/ISLANDORA/Islandora');
     $tuque_link = l(t('Tuque Fedora API'), 'http://github.com/islandora/tuque');
     $message = t('Islandora requires the !tuque_url. Please install in /sites/all/libraries/tuque before continuing. See the !islandora_url.', array( '!tuque_url' => $tuque_link, '!islandora_url' => $islandora_doc_link));
-    drupal_set_message($message, 'error', FALSE);
+    drupal_set_message(filter_xss($message), 'error', FALSE);
   }
 }
 

includes/utilities.inc

@@ -1,13 +1,17 @@
 <?php
 
+/**
+ * @file
+ * Contains islandora utility functions
+ */
+
 /**
  * Convert bytes to human readable format
  *
  * @param integer bytes Size in bytes to convert
  * @return string
  */
-function islandora_convert_bytes_to_human_readable($bytes, $precision = 2)
+function islandora_convert_bytes_to_human_readable($bytes, $precision = 2) {
-{
   $kilobyte = 1024;
   $megabyte = $kilobyte * 1024;
   $gigabyte = $megabyte * 1024;
@@ -15,19 +19,20 @@ function islandora_convert_bytes_to_human_readable($bytes, $precision = 2)
 
   if (($bytes >= 0) && ($bytes < $kilobyte)) {
     return $bytes . ' B';
-
+  }
-    } elseif (($bytes >= $kilobyte) && ($bytes < $megabyte)) {
+  elseif (($bytes >= $kilobyte) && ($bytes < $megabyte)) {
     return round($bytes / $kilobyte, $precision) . ' KB';
-
+  }
-    } elseif (($bytes >= $megabyte) && ($bytes < $gigabyte)) {
+  elseif (($bytes >= $megabyte) && ($bytes < $gigabyte)) {
     return round($bytes / $megabyte, $precision) . ' MB';
-
+  }
-    } elseif (($bytes >= $gigabyte) && ($bytes < $terabyte)) {
+  elseif (($bytes >= $gigabyte) && ($bytes < $terabyte)) {
     return round($bytes / $gigabyte, $precision) . ' GB';
-
+  }
-    } elseif ($bytes >= $terabyte) {
+  elseif ($bytes >= $terabyte) {
     return round($bytes / $terabyte, $precision) . ' TB';
-    } else {
+  }
+  else {
     return $bytes . ' B';
   }
 }
@@ -54,7 +59,7 @@ function islandora_control_group_to_human_readable($control_group) {
  */
 function islandora_validate_pid($pid) {
   $valid = FALSE;
-  if (strlen(trim($pid)) <= 64 && preg_match('/^([A-Za-z0-9]|-|\.)+:(([A-Za-z0-9])|-|\.|~|_|(%[0-9A-F]{2}))+$/', trim($pid))) {
+  if (drupal_strlen(trim($pid)) <= 64 && preg_match('/^([A-Za-z0-9]|-|\.)+:(([A-Za-z0-9])|-|\.|~|_|(%[0-9A-F]{2}))+$/', trim($pid))) {
     $valid = TRUE;
   }
 
@@ -68,7 +73,7 @@ function islandora_validate_pid($pid) {
  */
 function islandora_validate_dsid($dsid) {
   $valid = FALSE;
-  if (strlen(trim($dsid)) <= 64 && preg_match('/^[a-zA-Z0-9\_\-\.]+$/', trim($dsid))) {
+  if (drupal_strlen(trim($dsid)) <= 64 && preg_match('/^[a-zA-Z0-9\_\-\.]+$/', trim($dsid))) {
     $valid = TRUE;
   }
 

islandora.api.php

@@ -1,4 +1,10 @@
 <?php
+
+/**
+ * @file
+ * This file lists and documents all available hook functions to manipulate data.
+ */
+
 /**
  * remove a datastream from a repository object
  * @param object $fedora_object

islandora.install

@@ -0,0 +1,6 @@
+<?php
+
+/**
+ * @file
+ * This file contains all install functions.
+ */

islandora.module

@@ -1,9 +1,9 @@
 <?php
 
 /*
- * @file islandora.module
+ * @file
- * defines paths (drupal menu items) as entry points and acts as a hub for dispatching tasks to other modules.
  *
+ * islandora.module: defines paths (drupal menu items) as entry points and acts as a hub for dispatching tasks to other modules.
  *
  * This file is part of Islandora.
  *
@@ -36,7 +36,7 @@ define('ISLANDORA_VIEW_HOOK', 'islandora_view_object');
 define('ISLANDORA_EDIT_HOOK', 'islandora_edit_object');
 
 /**
- * Implementation of hook_menu. 
+ * Implements hook_menu().
  * we need some standard entry points so we can have consistent urls for different Object actions
  */
 function islandora_menu() {

theme/islandora-object-edit.tpl.php

@@ -1,30 +1,9 @@
 <?php
 
-/*
+/**
- * islandora-object-edit.tpl.php
+ * @file
- * 
+ * islandora-object-edit.tpl.php: This is a template for objects that do not have
- *
+ * a module to registered to build their display.
- * 
- * This file is part of Islandora.
- * 
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License
- * along with the program.  If not, see <http ://www.gnu.org/licenses/>.
- */
-?>
-<?php
-
-/* 
- * this is a template for objects that do not have a module to registered to build their display.
  *
  * islandora_object is a fedora tuque Object
  *    $object->label
@@ -37,14 +16,9 @@
  * and each element has an array of values.  dc.title can have none, one or many titles
  * this is the case for all dc elements.
  *
- * 
- * 
  */
-
-//dsm($object);
-
-drupal_set_title($islandora_object->label);
-//print($islandora_object->label . ' ' . $islandora_object->id); 
-print (theme_table($variables['datastream_table']));
 ?>
 
+<?php drupal_set_title($islandora_object->label); ?>
+
+<?php print (theme_table($variables['datastream_table'])); ?>

theme/islandora-object.tpl.php

@@ -1,30 +1,8 @@
 <?php
 
 /*
- * islandora-object.tpl.php
+ * @file
- * 
+ * This is a template for objects that do not have a module to registered to build their display.
- *
- * 
- * This file is part of Islandora.
- * 
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License
- * along with the program.  If not, see <http ://www.gnu.org/licenses/>.
- */
-?>
-<?php
-
-/* 
- * this is a template for objects that do not have a module to registered to build their display.
  * 
  * islandora_object is a fedora tuque Object
  *    $object->label             - The label for this object.

theme/islandora.theme.inc

@@ -1,5 +1,10 @@
 <?php
 
+/**
+ * @file
+ * This file contains all theme and preprocess functions.
+ */
+
 /**
  * preprocess the edit template
  * @global string $base_url
@@ -72,9 +77,11 @@ function islandora_preprocess_islandora_default(&$variables) {
       $datastreams[$id]['mimetype'] = $ds->mimetype;
       $datastreams[$id]['size'] = islandora_datastream_get_human_readable_size($ds);
       $datastreams[$id]['created_date'] = $ds->createdDate->format("Y-m-d");
-      $datastreams[$id]['class'] = strtolower(preg_replace('/[^A-Za-z0-9]/', '-', $id));
+      $datastreams[$id]['class'] = drupal_strtolower(preg_replace('/[^A-Za-z0-9]/', '-', $id));
+    }
+    catch (RepositoryException $e) {
+
     }
-    catch (RepositoryException $e) {}
   }
   $variables['datastreams'] = $datastreams;
   try {