tripal/tripal_core/mviews.php

<?php

/** 
 * @defgroup tripal_mviews_api Core Module Materalized Views API
 * @{
 * Provides an application programming interface (API) to manage materialized views in Chado.
 * The Perl-based chado comes with an interface for managing materialzed views.  This
 * API provides an alternative Drupal-based method.  
 * @}
 * @ingroup tripal_api
 */

/**
 * Add a materialized view to the chado database to help speed data access. This
 * function supports the older style where postgres column specifications 
 * are provided using the $mv_table, $mv_specs and $indexed variables. It also
 * supports the newer preferred method where the materialized view is described
 * using the Drupal Schema API array.  
 *
 * @param $name 
 *   The name of the materialized view.
 * @param $modulename 
 *   The name of the module submitting the materialized view (e.g. 'tripal_library')
 * @param $mv_table 
 *   The name of the table to add to chado. This is the table that can be queried.
 * @param $mv_specs 
 *   The table definition 
 * @param $indexed 
 *   The columns that are to be indexed
 * @param $query 
 *   The SQL query that loads the materialized view with data
 * @param $special_index  
 *   currently not used
 * @param $comment
 *   A string containing a description of the materialized view
 * @param $mv_schema
 *   If using the newer Schema API array to define the materialized view then
 *   this variable should contain the array.
 *
 * @ingroup tripal_mviews_api
 */
function tripal_add_mview ($name, $modulename, $mv_table, $mv_specs, $indexed,
   $query, $special_index, $comment=NULL, $mv_schema=NULL)
{
   // get the table name from the schema array
   $schema_arr = array();
   if($mv_schema){
      // get the schema from the mv_specs and use it to add the custom table
      eval("\$schema_arr = $mv_schema;");
      $mv_table = $schema_arr['table'];
   }

   $record = new stdClass();
   $record->name = $name;
   $record->modulename = $modulename;
   $record->mv_table = $mv_table;
   $record->mv_specs = $mv_specs;
   $record->indexed = $indexed;
   $record->query = $query;
   $record->special_index = $special_index;
   $record->comment = $comment;
   $record->mv_schema = $mv_schema;

   // add the record to the tripal_mviews table and if successful
   // create the new materialized view in the chado schema
   if(drupal_write_record('tripal_mviews',$record)){

      // drop the table from chado if it exists
      $previous_db = tripal_db_set_active('chado');  // use chado database
      if (db_table_exists($mv_table)) {
         $sql = "DROP TABLE $mv_table";
         db_query($sql);
      }
      tripal_db_set_active($previous_db);  // now use drupal database
      
      // now construct the indexes
      $index = '';
      if($indexed){
        // add to the array of values
        $vals = preg_split("/[\n,]+/",$indexed);
        $index = '';
        foreach ($vals as $field){
           $field = trim($field);
           $index .= "CREATE INDEX idx_${mv_table}_${field} ON $mv_table ($field);";
        }
      }

      // create the table differently depending on if it the traditional method
      // or the Drupal Schema API method
      if($mv_schema){
         if(!tripal_create_chado_table ($ret,$mv_table,$schema_arr)){
            drupal_set_message("Could not create the materialized view. Check Drupal error report logs.");
         } else {
            drupal_set_message(t("View '$name' created"));
         }
      } else {
         // add the table to the database
         $sql = "CREATE TABLE {$mv_table} ($mv_specs); $index"; 
         $previous_db = tripal_db_set_active('chado');  // use chado database
         $results = db_query($sql);
         tripal_db_set_active($previous_db);  // now use drupal database
         if($results){
            drupal_set_message(t("View '$name' created"));
         } else {
            drupal_set_message(t("Failed to create the materialized view table: '$mv_table'"));
         }
      }
   }
}
/**
 * Edits a materialized view to the chado database to help speed data access.This
 * function supports the older style where postgres column specifications 
 * are provided using the $mv_table, $mv_specs and $indexed variables. It also
 * supports the newer preferred method where the materialized view is described
 * using the Drupal Schema API array.  
 *
 * @param $mview_id 
 *   The mview_id of the materialized view to edit
 * @param $name 
 *   The name of the materialized view.
 * @param $modulename 
 *   The name of the module submitting the materialized view (e.g. 'tripal_library')
 * @param $mv_table 
 *   The name of the table to add to chado. This is the table that can be queried.
 * @param $mv_specs 
 *   The table definition 
 * @param $indexed 
 *   The columns that are to be indexed
 * @param $query 
 *   The SQL query that loads the materialized view with data
 * @param $special_index  
 *   currently not used
 * @param $comment
 *   A string containing a description of the materialized view
 * @param $mv_schema
 *   If using the newer Schema API array to define the materialized view then
 *   this variable should contain the array.
 *
 * @ingroup tripal_mviews_api
 */
function tripal_edit_mview ($mview_id,$name,$modulename,$mv_table,$mv_specs,
   $indexed,$query,$special_index,$comment=NULL,$mv_schema=NULL)
{

   // get the table name from the schema array
   $schema_arr = array();
   if($mv_schema){
      // get the schema from the mv_specs and use it to add the custom table
      eval("\$schema_arr = $mv_schema;");
      $mv_table = $schema_arr['table'];
   }

   $record = new stdClass();
   $record->mview_id = $mview_id;
   $record->name = $name;
   $record->modulename = $modulename;
   $record->mv_schema = $mv_schema;
   $record->mv_table = $mv_table;
   $record->mv_specs = $mv_specs;
   $record->indexed = $indexed;
   $record->query = $query;
   $record->special_index = $special_index;
   $record->last_update = 0;
   $record->status = '';
   $record->comment = $comment;

   // drop the table from chado if it exists
   $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = $mview_id ";
   $mview = db_fetch_object(db_query($sql));
   $previous_db = tripal_db_set_active('chado');  // use chado database
   if (db_table_exists($mview->mv_table)) {
      $sql = "DROP TABLE $mview->mv_table";
      db_query($sql);
   }
   tripal_db_set_active($previous_db);  // now use drupal database

   // update the record to the tripal_mviews table and if successful
   // create the new materialized view in the chado schema
   if(drupal_write_record('tripal_mviews',$record,'mview_id')){

      // drop the table from chado if it exists
      $previous_db = tripal_db_set_active('chado');  // use chado database
      if (db_table_exists($mv_table)) {
         $sql = "DROP TABLE $mv_table";
         db_query($sql);
      }
      tripal_db_set_active($previous_db);  // now use drupal database
      
      // now construct the indexes
      $index = '';
      if($indexed){
        // add to the array of values
        $vals = preg_split("/[\n,]+/",$indexed);
        $index = '';
        foreach ($vals as $field){
           $field = trim($field);
           $index .= "CREATE INDEX idx_${mv_table}_${field} ON $mv_table ($field);";
        }
      }
      // re-create the table differently depending on if it the traditional method
      // or the Drupal Schema API method
      if($mv_schema){         
         if(!tripal_create_chado_table ($ret,$mv_table,$schema_arr)){
            drupal_set_message("Could not create the materialized view. Check Drupal error report logs.");
         } else {
            drupal_set_message(t("View '$name' created"));
         }
      } else {
         $sql = "CREATE TABLE {$mv_table} ($mv_specs); $index"; 
         $previous_db = tripal_db_set_active('chado');  // use chado database
         $results = db_query($sql);
         tripal_db_set_active($previous_db);  // now use drupal database
         if($results){
            drupal_set_message(t("View '$name' edited and saved.  All results cleared. Please re-populate the view."));
         } else {
            drupal_set_message(t("Failed to create the materialized view table: '$mv_table'"));
         }
      }
   }
}
/**
 * Retrieve the materialized view_id given the name
 *
 * @param $view_name
 *   The name of the materialized view
 *
 * @return
 *   The unique identifier for the given view
 *
 * @ingroup tripal_mviews_api
 */
function tripal_mviews_get_mview_id ($view_name){

   $sql = "SELECT * FROM {tripal_mviews} ".
          "WHERE name = '%s'";
   if(db_table_exists('tripal_mviews')){
      $mview = db_fetch_object(db_query($sql,$view_name));
	   if($mview){
	      return $mview->mview_id;
	   }
   }
   return 0;
}
/**
*
*
* @ingroup tripal_core
*/
function tripal_mviews_action ($op,$mview_id,$redirect=0){
   global $user;
   $args = array("$mview_id");
   
   if(!$mview_id){
      return '';
   }

   // get this mview details
   $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = $mview_id ";
   $mview = db_fetch_object(db_query($sql));
   
   // add a job or perform the action based on the given operation
   if($op == 'update'){
      tripal_add_job("Populate materialized view '$mview->name'",'tripal_core',
         'tripal_update_mview',$args,$user->uid);
	}
   if($op == 'delete'){
	   // remove the mview from the tripal_mviews table
	   $sql = "DELETE FROM {tripal_mviews} ".
             "WHERE mview_id = $mview_id";
      db_query($sql);
		
	   // drop the table from chado if it exists
      $previous_db = tripal_db_set_active('chado');  // use chado database
      if (db_table_exists($mview->mv_table)) {
         $sql = "DROP TABLE $mview->mv_table";
         db_query($sql);
      }
      tripal_db_set_active($previous_db);  // now use drupal database
   }
   if($redirect){
      drupal_goto("admin/tripal/mviews");
   }
}
/**
* Update a Materialized View
*
* @param $mview_id
*   The unique identifier for the materialized view to be updated
*
* @return
*   True if successful, false otherwise
*
* @ingroup tripal_mviews_api
*/
function tripal_update_mview ($mview_id){
   $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = %d ";
   $mview = db_fetch_object(db_query($sql,$mview_id));
   if($mview){
      $previous_db = tripal_db_set_active('chado');  // use chado database
	   $results = db_query("DELETE FROM {$mview->mv_table}");
      $results = db_query("INSERT INTO {$mview->mv_table} ($mview->query)");
      tripal_db_set_active($previous_db);  // now use drupal database
      if($results){
         $sql = "SELECT count(*) as cnt FROM {$mview->mv_table}";
         $count = db_fetch_object(db_query($sql));
	      $record = new stdClass();
         $record->mview_id = $mview_id;
         $record->last_update = time();
         $record->status = "Populated with " . number_format($count->cnt) . " rows";
		   drupal_write_record('tripal_mviews',$record,'mview_id');
		   return 1;
      } else {
         # print and save the error message
	      $record = new stdClass();
         $record->mview_id = $mview_id;
         $record->status = "ERROR populating. See Drupal's recent log entries for details.";
         print $record->status . "\n";
		   drupal_write_record('tripal_mviews',$record,'mview_id');
	      return 0;
	  }
   }
}
/**
*
*
* @ingroup tripal_mviews_api
*/
function tripal_mview_report ($mview_id) {
   // get this mview details
   $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = $mview_id ";
   $mview = db_fetch_object(db_query($sql));

   // create a table with each row containig stats for
   // an individual job in the results set.

   $return_url = url("admin/tripal/mviews/");

   $output .= "<p><a href=\"$return_url\">Return to table of materialized views.</a></p>";
   $output .= "<br />";
   $output .= "<p>Details for <b>$mview->name</b>:</p>";
   $output .= "<br />";
   $output .= "<table class=\"border-table\">";
   if($mview->name){
      $output .= "  <tr>".
      "    <th>View Name</th>".
      "    <td>$mview->name</td>".
      "  </tr>";
   }   
   if($mview->modulename){
      $output .= "  <tr>".
      "    <th>Module Name</th>".
      "    <td>$mview->modulename</td>".
      "  </tr>";
   }
   if($mview->mv_table){
      $output .= "  <tr>".
      "    <th>Table Name</th>".
      "    <td>$mview->mv_table</td>".
      "  </tr>";
   }   
   if($mview->mv_specs){
      $output .= "  <tr>".
      "    <th>Table Field Definitions</th>".
      "    <td>$mview->mv_specs</td>".
      "  </tr>";
   }   
   if($mview->query){
      $output .= "  <tr>".
      "    <th>Query</th>".
      "    <td><pre>$mview->query</pre></td>".
      "  </tr>";
   }   
   if($mview->indexed){
      $output .= "  <tr>".
      "    <th>Indexed Fields</th>".
      "    <td>$mview->indexed</td>".
      "  </tr>";
   }   
   if($mview->special_index){
      $output .= "  <tr>".
      "    <th>Special Indexed Fields</th>".
      "    <td>$mview->speical_index</td>".
      "  </tr>";
   }   
   if($mview->last_update > 0){
      $update = format_date($mview->last_update);
   } else {
      $update = 'Not yet populated';
   }
   $output .= "  <tr>".
      "    <th>Last Update</th>".
      "    <td>$update</td>".
      "  </tr>";

   // build the URLs using the url function so we can handle installations where
   // clean URLs are or are not used
   $update_url = url("admin/tripal/mviews/action/update/$mview->mview_id");
   $delete_url = url("admin/tripal/mviews/action/delete/$mview->mview_id");
   $edit_url = url("admin/tripal/mviews/edit/$mview->mview_id");

   $output .= "<tr><th>Actions</th>".
              "<td> <a href='$update_url'>Populate</a>, ".
              "     <a href='$edit_url'>Edit</a>, ".
              "     <a href='$delete_url'>Delete</a></td></tr>";

   $output .= "</table>";

   return $output;
}
/**
*
*
* @ingroup tripal_mviews_api
*/
function tripal_mviews_report () {

   $header = array('','MView Name','Last Update','Status','Description','');
   $rows = array();

   $mviews = db_query("SELECT * FROM {tripal_mviews} ORDER BY name");  
   while($mview = db_fetch_object($mviews)){
      if($mview->last_update > 0){
         $update = format_date($mview->last_update);
      } else {
         $update = 'Not yet populated';
      }
      $rows[] = array(
         l('View',"admin/tripal/mviews/report/$mview->mview_id") ." | ".
         l('Edit',"admin/tripal/mviews/edit/$mview->mview_id") ." | ".
         l('Populate',"admin/tripal/mviews/action/update/$mview->mview_id"),
         $mview->name,
         $update,
         $mview->status,
         $mview->comment,
         l('Delete',"admin/tripal/mviews/action/delete/$mview->mview_id"),
      );
   }
   $rows[] = array(
      'data' => array( 
         array('data' => l('Create a new materialized view.',"admin/tripal/mviews/new"), 
               'colspan' => 6),
         )
   );
   $page = theme('table', $header, $rows);

   return $page;
}
/**
*
*
* @ingroup tripal_core
*/
function tripal_mviews_form(&$form_state = NULL,$mview_id = NULL){

   if(!$mview_id){
      $action = 'Add';
   } else {
      $action = 'Edit';
   }

   // get this requested view
   if(strcmp($action,'Edit')==0){
      $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = %d ";
      $mview = db_fetch_object(db_query($sql,$mview_id));
      
      # set the default values.  If there is a value set in the 
      # form_state then let's use that, otherwise, we'll pull 
      # the values from the database 
      $default_name = $form_state['values']['name'];
      $default_mv_table = $form_state['values']['mv_table'];
      $default_mv_specs = $form_state['values']['mv_specs'];
      $default_indexed = $form_state['values']['indexed'];
      $default_mvquery = $form_state['values']['mvquery'];
      $default_special_index = $form_state['values']['special_index'];
      $default_comment = $form_state['values']['cpmment'];
      if(!$default_name){
         $default_name = $mview->name;
      }
      if(!$default_mv_table){
         $default_mv_table = $mview->mv_table;
      }
      if(!$default_mv_specs){
         $default_mv_specs = $mview->mv_specs;
      }
      if(!$default_indexed){
         $default_indexed = $mview->indexed;
      }
      if(!$default_mvquery){
         $default_mvquery = $mview->query;
      }
      if(!$default_special_index){
         $default_special_index = $mview->special_index;
      }
      if(!$default_comment){
         $default_comment = $mview->comment;
      }      
      if(!$default_schema){
         $default_schema = $mview->mv_schema;
      }
      // the mv_table column of the tripal_mviews table always has the table 
      // name even if it is a custom table. However, for the sake of the form,
      // we do not want this to show up as the mv_table is needed for the 
      // traditional style input.  We'll blank it out if we have a custom 
      // table and it will get reset in the submit function using the 
      // 'table' value from the schema array
      if($default_schema){
         $default_mv_table = '';
      }
      
      // set which fieldset is collapsed 
      $schema_collapsed = 0;      
      $traditional_collapsed = 1;
      if(!$default_schema){
         $schema_collapsed = 1;      
         $traditional_collapsed = 0;
      }
   }
   // Build the form
   $form['action'] = array(
      '#type' => 'value',
      '#value' => $action
   );
   $form['mview_id'] = array(
      '#type' => 'value',
      '#value' => $mview_id
   );
   $form['name']= array(
      '#type'          => 'textfield',
      '#title'         => t('View Name'),
      '#description'   => t('Please enter the name for this materialized view.'),
      '#required'      => TRUE,
      '#default_value' => $default_name,
   );
   $form['comment']= array(
      '#type'          => 'textarea',
      '#title'         => t('MView Description'),
      '#description'   => t('Optional.  Please provide a description of the purpose for this materialized vieww.'),
      '#required'      => FALSE,
      '#default_value' => $default_comment,
   );

   // add a fieldset for the Drupal Schema API
   $form['schema'] = array(
     '#type' => 'fieldset',
     '#title' => 'Drupal Schema API Setup',
     '#description' => t('Use the Drupal Schema API array to describe a table. The benefit is that it '.
                         'can be fully integrated with Tripal Views.  Tripal supports an extended '.
                         'array format to allow for descriptoin of foreign key relationships.'),
     '#collapsible' => 1,
     '#collapsed' => $schema_collapsed ,
   );
   $form['schema']['schema']= array(
      '#type'          => 'textarea',
      '#title'         => t('Schema Array'),
      '#description'   => t('Please enter the Drupal Schema API compatible array that defines the table.'),
      '#required'      => FALSE,
      '#default_value' => $default_schema,
      '#rows'          => 25,
   ); 
   // add a fieldset for the Original Table Description fields
   $form['traditional'] = array(
     '#type' => 'fieldset',
     '#title' => 'Traditional MViews Setup',
     '#description' => t('Traidtionally with Tripal MViews were created by specifying PostgreSQL style '.
                         'column types.  This method can be used but is deprecated in favor of the '.
                         'newer Drupal schema API method provided above.'),
     '#collapsible' => 1,
     '#collapsed' => $traditional_collapsed,
   ); 
   $form['traditional']['mv_table']= array(
      '#type'          => 'textfield',
      '#title'         => t('Table Name'),
      '#description'   => t('Please enter the table name that this view will generate in the database.  You can use the schema and table name for querying the view'),
      '#required'      => FALSE,
      '#default_value' => $default_mv_table,
   );
   $form['traditional']['mv_specs']= array(
      '#type'          => 'textarea',
      '#title'         => t('Table Definition'),
      '#description'   => t('Please enter the field definitions for this view. Each field should be separated by a comma or enter each field definition on each line.'),
      '#required'      => FALSE,
      '#default_value' => $default_mv_specs,
   );
   $form['traditional']['indexed']= array(
      '#type'          => 'textarea',
      '#title'         => t('Indexed Fields'),
      '#description'   => t('Please enter the field names (as provided in the table definition above) that will be indexed for this view.  Separate by a comma or enter each field on a new line.'),
      '#required'      => FALSE,
      '#default_value' => $default_indexed,
   );
/**
   $form['traditional']['special_index']= array(
      '#type'          => 'textarea',
      '#title'         => t('View Name'),
      '#description'   => t('Please enter the name for this materialized view.'),
      '#required'      => TRUE,
      '#default_value' => $default_special_index,
   );
*/
   $form['mvquery']= array(
      '#type'          => 'textarea',
      '#title'         => t('Query'),
      '#description'   => t('Please enter the SQL statement used to populate the table.'),
      '#required'      => TRUE,
      '#default_value' => $default_mvquery,
      '#rows'          => 25,
   );
   if($action == 'Edit'){
      $value = 'Save';
   }
   if($action == 'Add'){
      $value = 'Add';
   }
   $form['submit'] = array (
     '#type'         => 'submit',
     '#value'        => t($value),
     '#weight'       => 9,
     '#executes_submit_callback' => TRUE,
   );

   $form['#redirect'] = 'admin/tripal/mviews';
   return $form;
}
/**
*
*
* @ingroup tripal_core
*/
function tripal_mviews_form_validate($form, &$form_state){
   $action = $form_state['values']['action'];
   $mview_id = $form_state['values']['mview_id'];
   $name = $form_state['values']['name'];
   $mv_table = $form_state['values']['mv_table'];
   $mv_specs = $form_state['values']['mv_specs'];
   $indexed = $form_state['values']['indexed'];
   $query = $form_state['values']['mvquery'];
   $special_index = $form_state['values']['special_index'];
   $comment = $form_state['values']['comment'];
   $schema = $form_state['values']['schema'];
   
   if($schema and ($mv_table or $mv_specs or $indexed or $special_index)){
       form_set_error($form_state['values']['schema'], 
          t('You can create an MView using the Drupal Schema API method or the '.
            'traditional method but not both.'));
   }
   if(!$schema){
      if(!$mv_specs){
         form_set_error($form_state['values']['mv_specs'], 
            t('The Table Definition field is required.'));
      }
      if(!$mv_table){
         form_set_error($form_state['values']['mv_table'], 
            t('The Table Name field is required.'));
      }
   }
   
   // make sure the array is valid
   if($schema){
      $success = eval("\$schema_array = $schema;");
      if ($success === FALSE){
         $error = error_get_last();
         form_set_error($form_state['values']['schema'], 
            t("The schema array is improperly formatted. Parse Error : " . $error["message"]));
      }
      if(!array_key_exists('table',$schema_array)){
         form_set_error($form_state['values']['schema'], 
            t("The schema array must have key named 'table'"));
      } 
      // TODO: add in more validation checks of the array to help the user
   }
}
/**
*
*
* @ingroup tripal_core
*/
function tripal_mviews_form_submit($form, &$form_state){
   $ret = array();
   
   $action = $form_state['values']['action'];
   $mview_id = $form_state['values']['mview_id'];
   $name = $form_state['values']['name'];
   $mv_table = $form_state['values']['mv_table'];
   $mv_specs = $form_state['values']['mv_specs'];
   $indexed = $form_state['values']['indexed'];
   $query = $form_state['values']['mvquery'];
   $special_index = $form_state['values']['special_index'];
   $comment = $form_state['values']['comment'];
   $schema = $form_state['values']['schema'];

   if(strcmp($action,'Edit')==0){
      tripal_edit_mview($mview_id,$name, 'tripal_core',$mv_table, $mv_specs,
         $indexed,$query,$special_index,$comment,$schema);
   }
   else if(strcmp($action,'Add')==0){
      tripal_add_mview ($name, 'tripal_core',$mv_table, $mv_specs,
         $indexed,$query,$special_index,$comment,$schema);
   }
   else {
        drupal_set_message("No action performed.");
   }
   return '';
}