tripal/tripal_core/api/tripal_core.api.inc

<?php

require_once "tripal_core.schema_v1.2.api.inc";
require_once "tripal_core.schema_v1.11.api.inc";

/**
 * @file
 * The Tripal Core API
 *
 * This file provides the API needed for all other Tripal and Tripal dependent
 * modules.
 *
 * @defgroup tripal_api Tripal API
 * @{
 * Provides an application programming interface (API) for Tripal
 *
 * The Tripal API currently provides generic insert/update/select functions for all chado content as
 * well as some module specific functions that insert/update/delete/select specific chado content.
 *
 * This API is currently in its infancy and some necessary functions might be missing. If you find
 * a missing function that you think should be included go to the sourceforge feature request
 * page and request it's inclusion in the API. Such feature requests with a working function
 * definition will be given priority.
 * @}
 *
 * @defgroup tripal_chado_api Core Module Chado API
 * @{
 * Provides an application programming interface (API) to manage data withing the Chado database.
 * This includes functions for selecting, inserting, updating and deleting records
 * in Chado tables.  The functions will ensure proper integrity contraints are met
 * for inserts and updates.
 *
 * Also, a set of functions is provided for creating template variables.  First,
 * is the tripal_core_generate_chado_vars which is used to select one ore more
 * records from a table and return an array with foreign key relationships fully
 * populated.  For example, if selecting a feature, the organism_id and type_id
 * would be present in the returned array as a nested array with their respective
 * foreign keys also nested.  The only fields that are not included are text
 * fields (which may be very large) or many-to-many foreign key relationships.
 * However, these fields and relationships can be expanded using the
 * tripal_core_expand_chado_vars.
 *
 * When a row from a chado table is selected using these two functions, it provides
 * a way for users who want to cutomize Drupal template files to access all data
 * associate with a specific record.
 *
 * Finally, the property tables in Chado generally follow the same format.  Therefore
 * there is a set of functions for inserting, updating and deleting properties for
 * any table.  This provides quick lookup of properties (provided the CV term is
 * known).
 *
 * @}
 * @ingroup tripal_api
 *
 * @defgroup tripal_files_api Core Module Files API
 * @{
 * Provides an application programming interface (API) for managing files within
 * the Tripal data directory structure.
 *
 * @}
 * @ingroup tripal_api

 /**
 * Provides a generic routine for inserting into any Chado table
 *
 * Use this function to insert a record into any Chado table.  The first
 * argument specifies the table for inserting and the second is an array
 * of values to be inserted.  The array is mutli-dimensional such that
 * foreign key lookup values can be specified.
 *
 * @param $table
 *  The name of the chado table for inserting
 * @param $values
 *  An associative array containing the values for inserting.
 * @param $options
 *  An array of options such as:
 *  - statement_name: the name of the prepared statement to use. If the statement
 *     has not yet been prepared it will be prepared automatically. On subsequent
 *     calls with the same statement_name only an execute on the previously
 *     prepared statement will occur.
 *  - is_prepared: TRUE or FALSE. Whether or not the statement is prepared. By
 *     default if the statement is not prepared it will be automatically.
 *     However to avoid this check, which requires a database query you can
 *     set this value to true and the check will not be performed.
 *  - skip_validation: TRUE or FALSE. If TRUE will skip all the validation steps and
 *     just try to insert as is. This is much faster but results in unhandled
 *     non user-friendly errors if the insert fails.
 *  - return_record: by default, the function will return the record but with
 *     the primary keys added after insertion.  To simply return TRUE on success
 *     set this option to FALSE
 *
 * @return
 *  On success this function returns the inserted record with the new primary keys
 *  add to the returned array. On failure, it returns FALSE.
 *
 * Example usage:
 * @code
 *   $values =  array(
 *     'organism_id' => array(
 *         'genus' => 'Citrus',
 *         'species' => 'sinensis',
 *      ),
 *     'name' => 'orange1.1g000034m.g',
 *     'uniquename' => 'orange1.1g000034m.g',
 *     'type_id' => array (
 *         'cv_id' => array (
 *            'name' => 'sequence',
 *         ),
 *         'name' => 'gene',
 *         'is_obsolete' => 0
 *      ),
 *   );
 *   $result = tripal_core_chado_insert('feature',$values);
 * @endcode
 * The above code inserts a record into the feature table.  The $values array is
 * nested such that the organism is selected by way of the organism_id foreign
 * key constraint by specifying the genus and species.  The cvterm is also
 * specified using its foreign key and the cv_id for the cvterm is nested as
 * well.
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_chado_insert($table, $values, $options = array()) {
  // set defaults for options. If we don't set defaults then
  // we get memory leaks when we try to access the elements
  if (!is_array($options)) {
    $options = array();
  }
  if (!array_key_exists('is_prepared', $options)) {
    $options['is_prepared'] = FALSE;
  }
  if (!array_key_exists('statement_name', $options)) {
    $options['statement_name'] = FALSE;
  }
  if (!array_key_exists('skip_validation', $options)) {
    $options['skip_validation'] = FALSE;
  }
  if (!array_key_exists('return_record', $options)) {
    $options['return_record'] = TRUE;
  }

  $insert_values = array();

  // Determine plan of action
  if ($options['statement_name']) {
    // we have a prepared statment (or want to create one) so set $prepared = TRUE
    $prepared = TRUE;

    // we need to get a persistent connection.  If one exists this function
    // will not recreate it, but if not it will create one and store it in
    // a Drupal variable for reuse later.
    $connection = tripal_db_persistent_chado();

    // if we cannot get a connection the abandon the prepared statement
    if (!$connection) {
       $prepared = FALSE;
       unset($options['statement_name']);
    }
  }
  else {
    //print "NO STATEMENT (insert): $table\n";
    //debug_print_backtrace();
  }

  if (array_key_exists('skip_validation', $options)) {
    $validate = !$options['skip_validation'];
  }
  else {
    $validate = TRUE;
  }

  // get the table description
  $table_desc = tripal_core_get_chado_table_schema($table);
  if (empty($table_desc)) {
    watchdog('tripal_core', 'tripal_core_chado_insert: There is no table description for !table_name', array('!table_name' => $table), WATCHDOG_WARNING);
  }

  // iterate through the values array and create a new 'insert_values' array
  // that has all the values needed for insert with all foreign relationsihps
  // resolved.
  foreach ($values as $field => $value) {
    // make sure the field is in the table description. If not then return an error
    // message
    if (!array_key_exists($field, $table_desc['fields'])) {
      watchdog('tripal_core', "tripal_core_chado_insert: The field '%field' does not exist ".
        "for the table '%table'.  Cannot perform insert. Values: %array",
        array('%field' => $field, '%table' => $table, '%array' => print_r($values, 1)), WATCHDOG_ERROR);
      return FALSE;
    }

    if (is_array($value)) {
      $foreign_options = array();
      if ($options['statement_name']) {
        // add the fk relationship info to the prepared statement name so that
        // we can prepare the selects run by the recrusive tripal_core_chado_get_foreign_key
        // function.
        $fk_sname = "fk_" . $table . "_" . $field;
        foreach ($value as $k => $v) {
          $fk_sname .= substr($k, 0, 2);
        }
        $foreign_options['statement_name'] = $fk_sname;
      }
      // select the value from the foreign key relationship for this value
      $results = tripal_core_chado_get_foreign_key($table_desc, $field, $value, $foreign_options);

      if (sizeof($results) > 1) {
        watchdog('tripal_core', 'tripal_core_chado_insert: Too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)), WATCHDOG_ERROR);
      }
      elseif (sizeof($results) < 1) {
        //watchdog('tripal_core', 'tripal_core_chado_insert: no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)), WATCHDOG_ERROR);
      }
      else {
        $insert_values[$field] = $results[0];
      }
    }
    else {
      $insert_values[$field] = $value;
    }
  }

  if ($validate) {

    // check for violation of any unique constraints
    $ukeys = array();
    if (array_key_exists('unique keys', $table_desc)) {
      $ukeys = $table_desc['unique keys'];
    }
    $ukselect_cols = array();
    $ukselect_vals = array();
    if ($ukeys) {
      foreach ($ukeys as $name => $fields) {
        foreach ($fields as $index => $field) {
          // build the arrays for performing a select that will check the contraint
          $ukselect_cols[] = $field;
          if (!array_key_exists($field, $insert_values)) {
            if (array_key_exists('default', $table_desc['fields'][$field])) {
              $ukselect_vals[$field] = $table_desc['fields'][$field]['default'];
            }
          }
          else {
            $ukselect_vals[$field] = $insert_values[$field];
          }
        }
        // now check the constraint
        $coptions = array();
        if ($options['statement_name']) {
          $coptions = array('statement_name' => 'uqsel_' . $table . '_' . $name);
        }
        if (tripal_core_chado_select($table, $ukselect_cols, $ukselect_vals, $coptions)) {
          watchdog('tripal_core', "tripal_core_chado_insert: Cannot insert duplicate record into $table table: " .
            print_r($values, 1), array(), 'WATCHDOG_ERROR');
          return FALSE;
        }
      }
    }

    // if trying to insert a field that is the primary key, make sure it also is unique
    if (array_key_exists('primary key', $table_desc)) {
      $pkey = $table_desc['primary key'][0];
      if (array_key_exists($pkey, $insert_values)) {
        $coptions = array('statement_name' => 'pqsel_' . $table . '_' . $pkey);
        if (tripal_core_chado_select($table, array($pkey), array($pkey => $insert_values[$pkey]), $coptions)) {
          watchdog('tripal_core', "tripal_core_chado_insert: Cannot insert duplicate primary key into $table table: " . print_r($values, 1), array(), 'WATCHDOG_ERROR');
          return FALSE;
        }
      }
    }

    // make sure required fields have a value
    if (!is_array($table_desc['fields'])) {
      $table_desc['fields'] = array();
      watchdog('tripal_core', "tripal_core_chado_insert: %table missing fields: \n %schema",
        array('%table' => $table, '%schema' => print_r($table_desc, 1)), WATCHDOG_WARNING);

    }
    foreach ($table_desc['fields'] as $field => $def) {
      // a field is considered missing if it cannot be NULL and there is no default
      // value for it or it is of type 'serial'
      if (array_key_exists('NOT NULL', $def) and
          !array_key_exists($field, $insert_values) and
          !array_key_exists('default', $def) and
          strcmp($def['type'], serial) != 0) {
        watchdog('tripal_core', "tripal_core_chado_insert: Field $table.$field cannot be NULL: " .
          print_r($values, 1), array(), 'WATCHDOG_ERROR');
        return FALSE;
      }
    }
  } //end of validation

  // Now build the insert SQL statement
  $ifields = array();       // contains the names of the fields
  $ivalues = array();       // contains the values of the fields
  $itypes = array();        // contains %d/%s placeholders for the sql query
  $iplaceholders = array(); // contains $1/$2 placeholders for the prepare query
  $idatatypes = array();    // contains the data type of the fields (int, text, etc.)
  $i = 1;
  foreach ($insert_values as $field => $value) {
    $ifields[] = $field;
    $ivalues[] = $value;
    $iplaceholders[] = '$' . $i;
    $i++;
    if (strcmp($value, '__NULL__')==0) {
      $itypes[] = "NULL";
      $idatatypes[] = "NULL";
    }
    elseif (strcasecmp($table_desc['fields'][$field]['type'], 'serial')==0 OR
    strcasecmp($table_desc['fields'][$field]['type'], 'int')==0 OR
    strcasecmp($table_desc['fields'][$field]['type'], 'integer')==0) {
      $itypes[] = "%d";
      $idatatypes[] = 'int';
    }
    elseif (strcasecmp($table_desc['fields'][$field]['type'], 'boolean')==0) {
      $itypes[] = "%s";
      $idatatypes[] = 'bool';
    }
    elseif (strcasecmp($table_desc['fields'][$field]['type'], 'float')==0) {
      $itypes[] = "%s";
      $idatatypes[] = 'numeric';
    }
    else {
      $itypes[] = "'%s'";
      $idatatypes[] = 'text';
    }
  }

  // create the SQL
  $sql = "INSERT INTO {$table} (" . implode(", ", $ifields) . ") VALUES (" . implode(", ", $itypes) . ")";

  // if this is a prepared statement then execute it
  if ($prepared) {
    // if this is the first time we've run this query
    // then we need to do the prepare, otherwise just execute
    if ($options['is_prepared'] != TRUE) {
      // prepare the statement
      $psql = "PREPARE " . $options['statement_name'] . " (" . implode(', ', $idatatypes) . ") AS INSERT INTO {$table} (" . implode(", ", $ifields) . ") VALUES (" . implode(", ", $iplaceholders) . ")";
      $status = tripal_core_chado_prepare($options['statement_name'], $psql, $idatatypes);

      if (!$status) {
        watchdog('tripal_core', "tripal_core_chado_insert: not able to prepare '%name' statement for: %sql", array('%name' => $options['statement_name'], '%sql' => $sql), 'WATCHDOG ERROR');
        return FALSE;
      }
    }

    $sql = "EXECUTE " . $options['statement_name'] . "(" . implode(", ", $itypes) . ")";
    $result = tripal_core_chado_execute_prepared($options['statement_name'], $sql, $ivalues);
  }
  // if it's not a prepared statement then insert normally
  else {
    $result = chado_query($sql, $ivalues);
  }

  // if we have a result then add primary keys to return array
  if ($options['return_record'] == TRUE and $result) {
    if (array_key_exists('primary key', $table_desc) and is_array($table_desc['primary key'])) {
      foreach ($table_desc['primary key'] as $field) {
        $psql = "PREPARE currval_" . $table . "_" . $field . " AS SELECT CURRVAL('" . $table . "_" . $field . "_seq')";
        $is_prepared = tripal_core_chado_prepare("currval_$table", $psql, array());
        if ($is_prepared) {
           $value = db_fetch_object(chado_query("EXECUTE currval_$table"));
        }
        else {
          $sql = "SELECT CURRVAL('" . $table . "_" . $field . "_seq')";
          $value =  db_result(chado_query($sql));
        } 
        $values[$field] = $value;       
      }
    }
    return $values;
  }
  elseif ($options['return_record'] == FALSE and $result) {
    return TRUE;
  }
  else {
    watchdog('tripal_core', "tripal_core_chado_insert: Cannot insert record into $table table: " . print_r($values, 1), array(), 'WATCHDOG_ERROR');
    return FALSE;
  }

  return FALSE;

}
/**
 * Provides a generic routine for updating into any Chado table
 *
 * Use this function to update a record in any Chado table.  The first
 * argument specifies the table for inserting, the second is an array
 * of values to matched for locating the record for updating, and the third
 * argument give the values to update.  The arrays are mutli-dimensional such
 * that foreign key lookup values can be specified.
 *
 * @param $table
 *  The name of the chado table for inserting
 * @param $match
 *  An associative array containing the values for locating a record to update.
 * @param $values
 *  An associative array containing the values for updating.
 * @param $options
 *  An array of options such as:
 *  - statement_name: the name of the prepared statement to use. If the statement
 *     has not yet been prepared it will be prepared automatically. On subsequent
 *     calls with the same statement_name only an execute on the previously
 *     prepared statement will occur.
 *  - is_prepared: TRUE or FALSE. Whether or not the statement is prepared. By
 *     default if the statement is not prepared it will be automatically.
 *     However to avoid this check, which requires a database query you can
 *     set this value to true and the check will not be performed.
 * @return
 *  On success this function returns TRUE. On failure, it returns FALSE.
 *
 * Example usage:
 * @code
 $umatch = array(
   'organism_id' => array(
     'genus' => 'Citrus',
     'species' => 'sinensis',
   ),
   'uniquename' => 'orange1.1g000034m.g7',
   'type_id' => array (
     'cv_id' => array (
       'name' => 'sequence',
     ),
     'name' => 'gene',
     'is_obsolete' => 0
   ),
 );
 $uvalues = array(
   'name' => 'orange1.1g000034m.g',
   'type_id' => array (
     'cv_id' => array (
       'name' => 'sequence',
     ),
     'name' => 'mRNA',
     'is_obsolete' => 0
   ),
 );
 *   $result = tripal_core_chado_update('feature',$umatch,$uvalues);
 * @endcode
 * The above code species that a feature with a given uniquename, organism_id,
 * and type_id (the unique constraint for the feature table) will be updated.
 * The organism_id is specified as a nested array that uses the organism_id
 * foreign key constraint to lookup the specified values to find the exact
 * organism_id. The same nested struture is also used for specifying the
 * values to update.  The function will find the record that matches the
 * columns specified and update the record with the avlues in the $uvalues array.
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_chado_update($table, $match, $values, $options = NULL) {

  // set defaults for options. If we don't set defaults then
  // we get memory leaks when we try to access the elements
  if (!is_array($options)) {
    $options = array();
  }
  if (!array_key_exists('is_prepared', $options)) {
    $options['is_prepared'] = FALSE;
  }
  if (!array_key_exists('statement_name', $options)) {
    $options['statement_name'] = FALSE;
  }

  $update_values = array();   // contains the values to be updated
  $update_matches = array();  // contains the values for the where clause

  // Determine plan of action
  if ($options['statement_name']) {
    // we have a prepared statment (or want to create one) so set $prepared = TRUE
    $prepared = TRUE;

    // we need to get a persistent connection.  If one exists this function
    // will not recreate it, but if not it will create one and store it in
    // a Drupal variable for reuse later.
    $connection = tripal_db_persistent_chado();

    // if we cannot get a connection the abandon the prepared statement
    if (!$connection ) {
       $prepared = FALSE;
       unset($options['statement_name']);
    }
  }
  else {
    //print "NO STATEMENT (update): $table\n";
    //debug_print_backtrace();
  }

  // get the table description
  $table_desc = tripal_core_get_chado_table_schema($table);

  // get the values needed for matching in the SQL statement
  foreach ($match as $field => $value) {
    if (is_array($value)) {
      $foreign_options = array();
      if ($options['statement_name']) {
        // add the fk relationship info to the prepared statement name so that
        // we can prepare the selects run by the recrusive tripal_core_chado_get_foreign_key
        // function.
        $fk_sname = "fk_" . $table . "_" . $field;
        foreach ($value as $k => $v) {
          $fk_sname .= substr($k, 0, 2);
        }
        $foreign_options['statement_name'] = $fk_sname;
      }
      $results = tripal_core_chado_get_foreign_key($table_desc, $field, $value, $foreign_options);
      if (sizeof($results) > 1) {
        watchdog('tripal_core', 'tripal_core_chado_update: When trying to find record to update, too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)), WATCHDOG_ERROR);
      }
      elseif (sizeof($results) < 1) {
        //watchdog('tripal_core', 'tripal_core_chado_update: When trying to find record to update, no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)), WATCHDOG_ERROR);
      }
      else {
        $update_matches[$field] = $results[0];
      }
    }
    else {
      $update_matches[$field] = $value;
    }
  }

  // get the values used for updating
  foreach ($values as $field => $value) {
    if (is_array($value)) {
      $foreign_options = array();
      // select the value from the foreign key relationship for this value
      if ($options['statement_name']) {
        // add the fk relationship info to the prepared statement name so that
        // we can prepare the selects run by the recrusive tripal_core_chado_get_foreign_key
        // function.
        $fk_sname = "fk_" . $table . "_" . $field;
        foreach ($value as $k => $v) {
          $fk_sname .= substr($k, 0, 2);
        }
        $foreign_options['statement_name'] = $fk_sname;
      }
      $results = tripal_core_chado_get_foreign_key($table_desc, $field, $value, $foreign_options);
      if (sizeof($results) > 1) {
        watchdog('tripal_core', 'tripal_core_chado_update: When trying to find update values, too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)), WATCHDOG_ERROR);
      }
      elseif (sizeof($results) < 1) {
        //watchdog('tripal_core', 'tripal_core_chado_update: When trying to find update values, no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value,TRUE)), WATCHDOG_ERROR);
      }
      else {
        $update_values[$field] = $results[0];
      }
    }
    else {
      $update_values[$field] = $value;
    }
  }

  // now build the SQL statement
  $sql  = "UPDATE {$table} SET ";
  $psql = "UPDATE {$table} SET ";
  $uargs = array();
  $idatatypes = array();
  $pvalues = array();
  $ivalues = array();
  $i = 1;
  foreach ($update_values as $field => $value) {

    if (strcasecmp($table_desc['fields'][$field]['type'], 'serial')==0 OR
        strcasecmp($table_desc['fields'][$field]['type'], 'int')==0 OR
        strcasecmp($table_desc['fields'][$field]['type'], 'integer')==0) {
      if (strcmp($value, '__NULL__') == 0) {
        $sql .= " $field = %s, ";
        $ivalues[] = 'NULL';
        $pvalues[] = '%s';
        $uargs[] = 'NULL';
      }
      else {
        $sql .= " $field = %d, ";
        $ivalues[] = $value;
        $pvalues[] = '%d';
        $uargs[] = $value;
      }
      $idatatypes[] = 'int';

    }
    elseif (strcasecmp($table_desc['fields'][$field]['type'], 'boolean')==0) {
      $sql .= " $field = %s, ";
      $pvalues[] = '%s';
      if (strcmp($value, '__NULL__')==0) {
        $ivalues[] = 'NULL';
        $uargs[] = 'NULL';
      }
      else {
        $ivalues[] = $value;
        $uargs[] = $value;
      }
      $idatatypes[] = 'bool';
    }
    elseif (strcasecmp($table_desc['fields'][$field]['type'], 'float')==0) {
      $sql .= " $field = %s, ";
      $pvalues[] = '%s';
      if (strcmp($value, '__NULL__')==0) {
        $ivalues[] = 'NULL';
        $uargs[] = 'NULL';
      }
      else {
        $ivalues[] = $value;
        $uargs[] = $value;
      }
      $idatatypes[] = 'numeric';
    }
    else {
      if (strcmp($value, '__NULL__') == 0) {
        $sql .= " $field = %s, ";
        $ivalues[] = 'NULL';
        $uargs[] = 'NULL';
        $pvalues[] = '%s';
      }
      else {
        $sql .= " $field = '%s', ";
        $ivalues[] = $value;
        $uargs[] = $value;
        $pvalues[] = "'%s'";
      }
      $idatatypes[] = 'text';
    }
    $psql .= "$field = \$" . $i . ", ";
    $i++;
  }
  $sql = drupal_substr($sql, 0, -2);  // get rid of the trailing comma & space
  $psql = drupal_substr($psql, 0, -2);  // get rid of the trailing comma & space

  $sql .= " WHERE ";
  $psql .= " WHERE ";
  foreach ($update_matches as $field => $value) {

    if (strcasecmp($table_desc['fields'][$field]['type'], 'serial')==0 OR
        strcasecmp($table_desc['fields'][$field]['type'], 'int')==0 OR
        strcasecmp($table_desc['fields'][$field]['type'], 'integer')==0) {
      if (strcmp($value, '__NULL__')==0) {
        $sql .= " $field = %s AND ";
        $ivalues[] = 'NULL';
        $uargs[] = 'NULL';
        $pvalues[] = '%s';
      }
      else {
        $sql .= " $field = %d AND ";
        $ivalues[] = $value;
        $uargs[] = $value;
        $pvalues[] = '%s';
      }
      $idatatypes[] = 'int';
    }
    elseif (strcasecmp($table_desc['fields'][$field]['type'], 'boolean')==0) {
      $sql .= " $field = %s AND ";
      $pvalues[] = '%s';
      if (strcmp($value, '__NULL__')==0) {
        $ivalues[] = 'NULL';
        $uargs[] = 'NULL';
      }
      else {
        $ivalues[] = $value;
        $uargs[] = $value;
      }
      $idatatypes[] = 'bool';
    }
    elseif (strcasecmp($table_desc['fields'][$field]['type'], 'float')==0) {
      $sql .= " $field = %s AND ";
      $pvalues[] = '%s';
      if (strcmp($value, '__NULL__')==0) {
        $ivalues[] = 'NULL';
        $uargs[] = 'NULL';
      }
      else {
        $ivalues[] = $value;
        $uargs[] = $value;
      }
      $idatatypes[] = 'numeric';
    }
    else {
      if (strcmp($value, '__NULL__')==0) {
        $sql .= " $field = %s AND ";
        $ivalues[] = 'NULL';
        $uargs[] = 'NULL';
        $pvalues[] = '%s';
      }
      else {
        $sql .= " $field = '%s' AND ";
        $ivalues[] = $value;
        $uargs[] = $value;
        $pvalues[] = "'%s'";
      }
      $idatatypes[] = 'text';
    }
    $psql .= "$field = \$" . $i . " AND ";
    $i++;
  }
  $sql = drupal_substr($sql, 0, -4);  // get rid of the trailing 'AND'
  $psql = drupal_substr($psql, 0, -4);  // get rid of the trailing 'AND'

  // finish constructing the prepared SQL statement
  $psql =  "PREPARE " . $options['statement_name'] . " (" . implode(', ', $idatatypes) . ") AS " . $psql;

  // finally perform the update.  If successful, return the updated record
  if ($prepared) {
    // if this is the first time we've run this query
    // then we need to do the prepare, otherwise just execute
    if ($options['is_prepared'] != TRUE and
    !tripal_core_is_sql_prepared($options['statement_name'])) {
      $status = chado_query($psql);
      if (!$status) {
        watchdog('tripal_core', "tripal_core_chado_update: not able to prepare '%name' statement for: %sql", array('%name' => $options['statement_name'], '%sql' => $sql), 'WATCHDOG ERROR');
        return FALSE;
      }
    }
    $sql = "EXECUTE " . $options['statement_name'] . "(" . implode(", ", $pvalues) . ")";
    $resource = chado_query($sql, $ivalues);
  }
  // if it's not a prepared statement then insert normally
  else {
    $resource = chado_query($sql, $uargs);
  }

  if ($resource) {
    return TRUE;
  }
  else {
    watchdog('tripal_core', "Cannot update record in $table table.  \nMatch:" . print_r($match, 1) . "\nValues: ". print_r($values, 1), array(), 'WATCHDOG_ERROR');
    return FALSE;
  }

  return FALSE;
}
/**
 * Provides a generic function for deleting a record(s) from any chado table
 *
 * Use this function to delete a record(s) in any Chado table.  The first
 * argument specifies the table to delete from and the second is an array
 * of values to match for locating the record(s) to be deleted.  The arrays
 * are mutli-dimensional such that foreign key lookup values can be specified.
 *
 * @param $table
 *  The name of the chado table for inserting
 * @param $match
 *  An associative array containing the values for locating a record to update.
 * @param $options
 *  An array of options such as:
 *  - statement_name: the name of the prepared statement to use. If the statement
 *     has not yet been prepared it will be prepared automatically. On subsequent
 *     calls with the same statement_name only an execute on the previously
 *     prepared statement will occur.
 *  - is_prepared: TRUE or FALSE. Whether or not the statement is prepared. By
 *     default if the statement is not prepared it will be automatically.
 *     However to avoid this check, which requires a database query you can
 *     set this value to true and the check will not be performed.
 * @return
 *   On success this function returns TRUE. On failure, it returns FALSE.
 *
 * Example usage:
 * @code
 $umatch = array(
   'organism_id' => array(
     'genus' => 'Citrus',
     'species' => 'sinensis',
   ),
   'uniquename' => 'orange1.1g000034m.g7',
   'type_id' => array (
     'cv_id' => array (
       'name' => 'sequence',
     ),
     'name' => 'gene',
     'is_obsolete' => 0
   ),
 );
 $uvalues = array(
   'name' => 'orange1.1g000034m.g',
   'type_id' => array (
     'cv_id' => array (
       'name' => 'sequence',
     ),
     'name' => 'mRNA',
     'is_obsolete' => 0
   ),
 );
 *   $result = tripal_core_chado_update('feature',$umatch,$uvalues);
 * @endcode
 * The above code species that a feature with a given uniquename, organism_id,
 * and type_id (the unique constraint for the feature table) will be deleted.
 * The organism_id is specified as a nested array that uses the organism_id
 * foreign key constraint to lookup the specified values to find the exact
 * organism_id. The same nested struture is also used for specifying the
 * values to update.  The function will find all records that match the
 * columns specified and delete them.
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_chado_delete($table, $match, $options = NULL) {
  // set defaults for options. If we don't set defaults then
  // we get memory leaks when we try to access the elements
  if (!is_array($options)) {
    $options = array();
  }
  if (!array_key_exists('is_prepared', $options)) {
    $options['is_prepared'] = FALSE;
  }
  if (!array_key_exists('statement_name', $options)) {
    $options['statement_name'] = FALSE;
  }

  // Determine plan of action
  if ($options['statement_name']) {
    // we have a prepared statment (or want to create one) so set $prepared = TRUE
    $prepared = TRUE;

    // we need to get a persistent connection.  If one exists this function
    // will not recreate it, but if not it will create one and store it in
    // a Drupal variable for reuse later.
    $connection = tripal_db_persistent_chado();

    // if we cannot get a connection the abandon the prepared statement
    if (!$connection ) {
       $prepared = FALSE;
       unset($options['statement_name']);
    }
  }
  else {
    //print "NO STATEMENT (update): $table\n";
    //debug_print_backtrace();
  }
  
  $delete_matches = array();  // contains the values for the where clause

  // get the table description
  $table_desc = tripal_core_get_chado_table_schema($table);
  $fields = $table_desc['fields'];

  // get the values needed for matching in the SQL statement
  foreach ($match as $field => $value) {
    if (is_array($value)) {
      // if the user has specified an array of values to delete rather than
      // FK relationships the keep those in our match
      if (array_values($value) === $value) {
        $delete_matches[$field] = $value;
      }
      else {
        $results = tripal_core_chado_get_foreign_key($table_desc, $field, $value);
        if (sizeof($results) > 1) {
          watchdog('tripal_core', 'tripal_core_chado_delete: When trying to find record to delete, too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)), WATCHDOG_ERROR);
        }
        elseif (sizeof($results) < 1) {
          //watchdog('tripal_core', 'tripal_core_chado_delete: When trying to find record to delete, no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value,TRUE)), WATCHDOG_ERROR);
        }
        else {
          $delete_matches[$field] = $results[0];
        }
      }
    }
    else {
      $delete_matches[$field] = $value;
    }
  }

  // now build the SQL statement
  $sql = "DELETE FROM {$table} WHERE ";
  $psql = $sql;
  $uargs = array();
  $idatatypes = array();
  $pvalues = array();
  $ivalues = array();
  $dargs = array();
  $void_prepared = 0;
  $i = 1;
  foreach ($delete_matches as $field => $value) {
    
    // if we have an array values then this is an "IN" clasue.
    // we cannot use prepared statements with these
    if (count($value) > 1) {
      $sql .= "$field IN (" . db_placeholders($value, 'varchar') . ") AND ";
      foreach ($value as $v) {
        $dargs[] = $v;
      }
      $void_prepared = 1;
      continue;
    }

    if (strcasecmp($table_desc['fields'][$field]['type'], 'serial') == 0 OR
        strcasecmp($table_desc['fields'][$field]['type'], 'int') == 0 OR
        strcasecmp($table_desc['fields'][$field]['type'], 'integer') == 0) {
      if (strcmp($value, '__NULL__') == 0) {
        $sql .= " $field = NULL AND ";
        $ivalues[] = 'NULL';
        $pvalues[] = '%s';
        $uargs[] = 'NULL';
      } 
      else {
        $sql .= " $field = %d AND ";
        $ivalues[] = $value;
        $pvalues[] = '%d';
        $uargs[] = $value;
      }
      $idatatypes[] = 'int';        
    }
    elseif (strcasecmp($table_desc['fields'][$field]['type'], 'boolean')==0) {
      $sql .= " $field = %s AND ";
      $pvalues[] = '%s';
      if (strcmp($value, '__NULL__')==0) {
        $ivalues[] = 'NULL';
        $uargs[] = 'NULL';
      }
      else {
        $ivalues[] = $value;
        $uargs[] = $value;
      }
      $idatatypes[] = 'bool';
    }
    elseif (strcasecmp($table_desc['fields'][$field]['type'], 'float')==0) {
      $sql .= " $field = %s AND ";
      $pvalues[] = '%s';
      if (strcmp($value, '__NULL__')==0) {
        $ivalues[] = 'NULL';
        $uargs[] = 'NULL';
      }
      else {
        $ivalues[] = $value;
        $uargs[] = $value;
      }
      $idatatypes[] = 'numeric';
    }
    else {
      if (strcmp($value, '__NULL__')==0) {
        $sql .= " $field = %s AND ";
        $ivalues[] = 'NULL';
        $uargs[] = 'NULL';
        $pvalues[] = '%s';
      }
      else {
        $sql .= " $field = '%s' AND ";
        $ivalues[] = $value;
        $uargs[] = $value;
        $pvalues[] = "'%s'";
      }
      $idatatypes[] = 'text';
    }    
    array_push($dargs, $value);  
    $psql .= "$field = \$" . $i . " AND ";
    $i++;
  }
  $sql = drupal_substr($sql, 0, -4);  // get rid of the trailing 'AND'
  $psql = drupal_substr($psql, 0, -4);  // get rid of the trailing 'AND'

  // finish constructing the prepared SQL statement
  $psql =  "PREPARE " . $options['statement_name'] . " (" . implode(', ', $idatatypes) . ") AS " . $psql;
  
  // finally perform the update.  If successful, return the updated record
  if ($prepared and !$void_prepared) {
    // if this is the first time we've run this query
    // then we need to do the prepare, otherwise just execute
    if ($options['is_prepared'] != TRUE and
    !tripal_core_is_sql_prepared($options['statement_name'])) {
      $status = chado_query($psql);
      if (!$status) {
        watchdog('tripal_core', "tripal_core_chado_delete: not able to prepare '%name' statement for: %sql", array('%name' => $options['statement_name'], '%sql' => $sql), 'WATCHDOG ERROR');
        return FALSE;
      }
    }
    $sql = "EXECUTE " . $options['statement_name'] . "(" . implode(", ", $pvalues) . ")";
    $resource = chado_query($sql, $ivalues);
  }
  // if it's not a prepared statement then insert normally
  else {
    $resource = chado_query($sql, $uargs);
  }
  
  // finally perform the delete.  If successful, return the updated record  
  $result = chado_query($sql, $dargs);
  if ($result) {
    return TRUE;
  }
  else {
    watchdog('tripal_core', "Cannot delete record in $table table.  Match:" . print_r($match, 1) . ". Values: ". print_r($values, 1), array(), 'WATCHDOG_ERROR');
    return FALSE;
  }
  return FALSE;
}



/**
 * Provides a generic routine for selecting data from a Chado table
 *
 * Use this function to perform a simple select from any Chado table.
 *
 * @param $table
 *  The name of the chado table for inserting
 * @param $columns
 *  An array of column names
 * @param $values
 *  An associative array containing the values for filtering the results. In the
 *  case where multiple values for the same time are to be selected an additional
 *  entry for the field should appear for each value
 * @param $options
 *  An associative array of additional options where the key is the option
 *  and the value is the value of that option.
 *
 * Additional Options Include:
 *  - has_record
 *     Set this argument to 'TRUE' to have this function return a numeric
 *     value for the number of recrods rather than the array of records.  this
 *     can be useful in 'if' statements to check the presence of particula records.
 *  - return_sql
 *     Set this to 'TRUE' to have this function return an array where the first
 *     element is the sql that would have been run and the second is an array of
 *     arguments.
 *  - case_insensitive_columns
 *     An array of columns to do a case insensitive search on.
 *  - regex_columns
 *     An array of columns where the value passed in should be treated as a regular expression
 *  - order_by
 *     An associative array containing the column names of the table as keys
 *     and the type of sort (i.e. ASC, DESC) as the values.  The results in the
 *     query will be sorted by the key values in the direction listed by the value
 *  - statement_name: the name of the prepared statement to use. If the statement
 *     has not yet been prepared it will be prepared automatically. On subsequent
 *     calls with the same statement_name only an execute on the previously
 *     prepared statement will occur.
 *  - is_prepared: TRUE or FALSE. Whether or not the statement is prepared. By
 *     default if the statement is not prepared it will be automatically.
 *     However to avoid this check, which requires a database query you can
 *     set this value to true and the check will not be performed.
 *  - is_duplicate: TRUE or FALSE.  Checks the values submited to see if
 *     they violate any of the unique constraints. If so, the record
 *     is returned, if not, FALSE is returned.
 *
 *
 * @return
 *  A database query result resource, FALSE if the query was not executed
 *  correctly, or the number of records in the dataset if $has_record is set.
 *  If the option 'is_duplicate' is provided and the record is a duplicate it
 *  will return the duplicated record.  If the 'has_record' option is provided
 *  a value of TRUE will be returned if a record exists and FALSE will bee
 *  returned if there are not records.
 *
 * Example usage:
 * @code
 *   $columns = array('feature_id', 'name');
 *   $values =  array(
 *     'organism_id' => array(
 *         'genus' => 'Citrus',
 *         'species' => array('sinensis', 'clementina'),
 *      ),
 *     'uniquename' => 'orange1.1g000034m.g',
 *     'type_id' => array (
 *         'cv_id' => array (
 *            'name' => 'sequence',
 *         ),
 *         'name' => 'gene',
 *         'is_obsolete' => 0
 *      ),
 *   );
 *   $options = array(
 *     'statement_name' => 'sel_feature_genus_species_cvname'
 *     'order_by' => array(
 *        'name' => 'ASC'
 *     ),
 *   );
 *   $result = tripal_core_chado_select('feature',$columns,$values,$options);
 * @endcode
 * The above code selects a record from the feature table using the three fields
 * that uniquely identify a feature.  The $columns array simply lists the columns
 * to select. The $values array is nested such that the organism is identified by
 * way of the organism_id foreign key constraint by specifying the genus and
 * species.  The cvterm is also specified using its foreign key and the cv_id
 * for the cvterm is nested as well.  In the example above, two different species
 * are allowed to match
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_chado_select($table, $columns, $values, $options = NULL) {

  // set defaults for options. If we don't set defaults then
  // we get memory leaks when we try to access the elements
  if (!is_array($options)) {
    $options = array();
  }
  if (!array_key_exists('case_insensitive_columns', $options)) {
    $options['case_insensitive_columns'] = array();
  }
  if (!array_key_exists('regex_columns', $options)) {
    $options['regex_columns'] = array();
  }
  if (!array_key_exists('order_by', $options)) {
    $options['order_by'] = array();
  }
  if (!array_key_exists('is_prepared', $options)) {
    $options['is_prepared'] = FALSE;
  }
  if (!array_key_exists('return_sql', $options)) {
    $options['return_sql'] = FALSE;
  }
  if (!array_key_exists('has_record', $options)) {
    $options['has_record'] = FALSE;
  }
  if (!array_key_exists('statement_name', $options)) {
    $options['statement_name'] = FALSE;
  }
  if (!array_key_exists('is_duplicate', $options)) {
    $options['is_duplicate'] = FALSE;
  }

  // if this is a prepared statement check to see if it has already been prepared
  $prepared = FALSE;
  if ($options['statement_name']) {
    $prepared = TRUE;
    // we need to get a persistent connection.  If one exists this function
    // will not recreate it, but if not it will create one and store it in
    // a Drupal variable for reuse later.
    $connection = tripal_db_persistent_chado();

    // if we cannot get a connection the abandon the prepared statement
    if (!$connection) {
      $prepared = FALSE;
      unset($options['statement_name']);
    }
  }
  else {
    //print "NO STATEMENT (select): $table\n";
    //debug_print_backtrace();
  }

  // check that our columns and values arguments are proper arrays
  if (!is_array($columns)) {
    watchdog('tripal_core', 'the $columns argument for tripal_core_chado_select must be an array.');
    return FALSE;
  }
  if (!is_array($values)) {
    watchdog('tripal_core', 'the $values argument for tripal_core_chado_select must be an array.');
    return FALSE;
  }

  // get the table description
  $table_desc = tripal_core_get_chado_table_schema($table);
  $select = '';
  $from = '';
  $where = '';
  $args = array();

  // if the 'use_unique' option is turned on then we want
  // to remove all but unique keys
  if ($options['is_duplicate'] and array_key_exists('unique keys', $table_desc)) {
    $ukeys = $table_desc['unique keys'];
    $has_results = 0;

    // iterate through the unique constraints and reset the values and columns
    // arrays to only include these fields
    foreach ($ukeys as $cname => $fields) {
      if ($has_results) {
         continue;
      }
      $new_values = array();
      $new_columns = array();
      $new_options = array();
      $uq_sname = "uq_" . $table . "_";
      $has_pkey = 0;


      // include the primary key in the results returned
      if (array_key_exists('primary key', $table_desc)) {
        $has_pkey = 1;
        $pkeys = $table_desc['primary key'];
        foreach ($pkeys as $index => $key) {
          array_push($new_columns, $key);
        }
      }

      // recreate the $values and $columns arrays
      foreach ($fields as $field) {
        if (array_key_exists($field, $values)) {
          $new_values[$field] = $values[$field];
          $uq_sname .= substr($field, 0, 2);
          // if there is no primary key then use the unique contraint fields
          if (!$has_pkey) {
            array_push($new_columns, $field);
          }
        }
        // if the field doesn't exist in the values array then
        // substitute any default values
        elseif (array_key_exists('default', $table_desc['fields'][$field])) {
          $new_values[$field] = $table_desc['fields'][$field]['default'];
          $uq_sname .= substr($field, 0, 2);
          if (!$has_pkey) {
            array_push($new_columns, $field);
          }
        }
        // if there is no value (default or otherwise) check if this field is
        // allowed to be null
        elseif (!$table_desc['fields'][$field]['not null']) {
        	$new_values[$field] = NULL;
          $uq_sname .= "n".substr($field, 0, 2);
          if (!$has_pkey) {
            array_push($new_columns, $field);
          }
        }
        // if the array key doesn't exist in the values given by the caller
        // and there is no default value then we cannot check if the record
        // is a duplicate so return FALSE
        else {
        	watchdog('tripal_core', "tripal_core_chado_select: There is no value for %field"
        		." thus we cannot check if this record is unique",
        		array('%field' => $field), WATCHDOG_ERROR);
          return FALSE;
        }
      }
      $new_options['statement_name'] = $uq_sname;

      $results = tripal_core_chado_select($table, $new_columns, $new_values, $new_options);
      // if we have a duplicate record then return the results
      if (count($results) > 0) {
        $has_results = 1;
      }
      unset($new_columns);
      unset($new_values);
      unset($new_options);
    }
    if ($options['has_record'] and $has_results) {
      return TRUE;
    }
    else {
      return $results;
    }
  }

  foreach ($values as $field => $value) {
    // make sure the field is in the table description. If not then return an error
    // message
    if (!array_key_exists($field, $table_desc['fields'])) {
      watchdog('tripal_core', "tripal_core_chado_select: The field '%field' does not exist ".
        "for the table '%table'.  Cannot perform query. Values: %array",
        array('%field' => $field, '%table' => $table, '%array' => print_r($values, 1)), WATCHDOG_ERROR);
      return array();
    }

    $select[] = $field;
    if (is_array($value)) {
      // if the user has specified multiple values for matching then this we
      // want to catch that and save them in our $where array, otherwise
      // we'll descend for a foreign key relationship
      if (array_values($value) === $value) {
        $where[$field] = $value;
      }
      else {
        // select the value from the foreign key relationship for this value
        $foreign_options = array(
          'regex_columns' => $options['regex_columns'],
          'case_insensitive_columns' => $options['case_insensitive_columns']
        );
        if (array_key_exists('statement_name', $options) and $options['statement_name']) {
          // add the fk relationship info to the prepared statement name so that
          // we can prepare the selects run by the recrusive tripal_core_chado_get_foreign_key
          // function. we need the statement name to be unique so take the first two characters of each column
          $fk_sname = "fk_" . $table . "_" . $field;
          foreach ($value as $k => $v) {
            $fk_sname .= substr($k, 0, 2);
          }
          $foreign_options['statement_name'] = $fk_sname;
        }

        $results = tripal_core_chado_get_foreign_key($table_desc, $field, $value, $foreign_options);
        if (!$results or count($results)==0) {

          // foreign key records are required
          // thus if none matched then return FALSE and alert the admin through watchdog
          /*watchdog('tripal_core',
           'tripal_core_chado_select: no record in the table referenced by the foreign key (!field)   exists. tripal_core_chado_select table=!table, columns=!columns, values=!values',
           array('!table' => $table,
             '!columns' => '<pre>' . print_r($columns, TRUE) . '</pre>',
             '!values' => '<pre>' . print_r($values, TRUE) . '</pre>',
             '!field' => $field,
           ),
           WATCHDOG_WARNING);*/
          return array();
        }
        else {
          $where[$field] = $results;
        }
      }
    }
    else {
      // need to catch a 0 and make int if integer field
      // but we don't want to catch a NULL
      if ($value === NULL) {
      	$where[$field] = NULL;
      }
      elseif ($table_desc['fields'][$field]['type'] == 'int') {
        $where[$field][] = (int) $value;
      }
      else {
        $where[$field][] = $value;
      }
    }
  }

  // now build the SQL and prepared SQL statements. We may not use
  // the prepared statement if it wasn't requested in the options of if the
  // argument in a where statement has multiple values.
  if (empty($where)) {
    // sometimes want to select everything
    $sql  = "SELECT " . implode(', ', $columns) . " ";
    $sql .= "FROM {$table} ";
    // we don't prepare a statement if there is no where clause
    $prepared = FALSE;
  }
  else {
    $sql  = "SELECT " . implode(', ', $columns) . " ";
    $sql .= "FROM {$table} ";
    $sql .= "WHERE ";
    $psql = $sql;  // prepared SQL statement;
    $i = 1;
    $pvalues = array();
    $itypes = array();
    foreach ($where as $field => $value) {

      // if we have multiple values returned then we need an 'IN' statement
      // in our where statement
      if (count($value) > 1) {
        $sql .= "$field IN (" . db_placeholders($value, 'varchar') . ") AND ";
        foreach ($value as $v) {
          $args[] = $v;
          // we can't do a prepared statement with an 'IN' statement in a
          // where clause because we can't guarantee we'll always have the
          // same number of elements.
          $prepared = FALSE;
        }
      }
      // if we have a null value then we need an IS NULL in our where statement
      elseif ($value === NULL) {
				$sql .= "$field IS NULL AND ";
				$psql .= "$field IS NULL AND ";
				// Need to remove one from the argument count b/c nulls don't add an argument
				$i--;
      }
      // if we have a single value then we need an = in our where statement
      else {
        $operator = '=';
        if (in_array($field, $options['regex_columns'])) {
          $operator = '~*';
        }

        // get the types for the prepared statement. First check if the type
        // is an integer
        if (strcasecmp($table_desc['fields'][$field]['type'], 'serial')==0 OR
        strcasecmp($table_desc['fields'][$field]['type'], 'int')==0 OR
        strcasecmp($table_desc['fields'][$field]['type'], 'integer')==0) {
          $sql .= "$field $operator %d AND ";
          $psql .= "$field $operator \$" . $i . " AND ";
          $args[] = $value[0];
          // set the variables needed for the prepared statement
          $idatatypes[] = 'int';
          $itypes[] = '%d';
          $pvalues[] = $value[0];
        }
        elseif (strcasecmp($table_desc['fields'][$field]['type'], 'boolean')==0) {
          $sql .= "$field $operator %s AND ";
          $psql .= "$field $operator \$" . $i . " AND ";
          $args[] = $value[0];
          // set the variables needed for the prepared statement
          $idatatypes[] = 'bool';
          $itypes[] = '%d';
          $pvalues[] = $value[0];
        }
        elseif (strcasecmp($table_desc['fields'][$field]['type'], 'float')==0) {
          $sql .= "$field $operator %s AND ";
          $psql .= "$field $operator \$" . $i . " AND ";
          $args[] = $value[0];
          // set the variables needed for the prepared statement
          $idatatypes[] = 'numeric';
          $itypes[] = '%f';
          $pvalues[] = $value[0];
        }
        // else the type is a text
        else {
          if (in_array($field, $options['case_insensitive_columns'])) {
            $sql .= "lower($field) $operator lower('%s') AND ";
            $psql .= "lower($field) $operator lower('\$" . $i . "') AND ";
            $args[] = $value;
          }
          else {
            $sql .= "$field $operator '%s' AND ";
            $psql .= "$field $operator \$" . $i . " AND ";
            $args[] = $value[0];
          }
          // set the variables needed for the prepared statement
          $idatatypes[] = 'text';
          $itypes[] = "'%s'";
          $pvalues[] = $value[0];
        }
      }
      $i++;
    }
    $sql = drupal_substr($sql, 0, -4);  // get rid of the trailing 'AND '
    $psql = drupal_substr($psql, 0, -4);  // get rid of the trailing 'AND '

    // finally add any ordering of the results to the SQL statement
    if (count($options['order_by']) > 0) {
      $sql .= " ORDER BY ";
      $psql .= " ORDER BY ";
      foreach ($options['order_by'] as $field => $dir) {
        $sql .= "$field $dir, ";
        $psql .= "$field $dir, ";
      }
      $sql = drupal_substr($sql, 0, -2);  // get rid of the trailing ', '
      $psql = drupal_substr($psql, 0, -2);  // get rid of the trailing ', '
    }
    // finish constructing the prepared SQL statement
    $psql =  "PREPARE " . $options['statement_name'] . " (" . implode(', ', $idatatypes) . ") AS " . $psql;

  } // end if(empty($where)){ } else {

  // if the caller has requested the SQL rather than the results...
  // which happens in the case of wanting to use the Drupal pager, then do so
  if ($options['return_sql'] == TRUE) {
    return array('sql' => $sql, 'args' => $args);
  }

  // prepare the statement
  if ($prepared) {
    // if this is the first time we've run this query
    // then we need to do the prepare, otherwise just execute
    if ($options['is_prepared'] != TRUE) {
      $status = tripal_core_chado_prepare($options['statement_name'], $psql, $idatatypes);
      if (!$status) {
        return FALSE;
      }
    }
    $sql = "EXECUTE " . $options['statement_name'] . "(" . implode(", ", $itypes) . ")";
    // WARNING: This call creates a memory leak:  if you remove the $pvalues it doesn't
    // do this. Got to find out what's causing this.
    $resource = tripal_core_chado_execute_prepared($options['statement_name'], $sql, $pvalues);
  }
  else {
    $resource = chado_query($sql, $args);
  }

  // format results into an array
  $results = array();
  while ($r = db_fetch_object($resource)) {
    $results[] = $r;
  }
  if ($options['has_record']) {
    return count($results);
  }
  return $results;
}

/**
 * Gets the value of a foreign key relationship
 *
 * This function is used by tripal_core_chado_select, tripal_core_chado_insert,
 * and tripal_core_chado_update to iterate through the associate array of
 * values that gets passed to each of those routines.  The values array
 * is nested where foreign key contraints are used to specify a value that.  See
 * documentation for any of those functions for further information.
 *
 * @param $table_desc
 *  A table description for the table with the foreign key relationship to be identified generated by
 *  hook_chado_<table name>_schema()
 * @param $field
 *  The field in the table that is the foreign key.
 * @param $values
 *  An associative array containing the values
 * @param $options
 *  An associative array of additional options where the key is the option
 *  and the value is the value of that option. These options are passed on to tripal_core_chado_select.
 *
 * Additional Options Include:
 *  - case_insensitive_columns
 *     An array of columns to do a case insensitive search on.
 *  - regex_columns
 *     An array of columns where the value passed in should be treated as a regular expression
 *
 * @return
 *  A string containg the results of the foreign key lookup, or FALSE if failed.
 *
 * Example usage:
 * @code
 *
 *   $values = array(
 *     'genus' => 'Citrus',
 *     'species' => 'sinensis',
 *   );
 *   $value = tripal_core_chado_get_foreign_key('feature', 'organism_id',$values);
 *
 * @endcode
 * The above code selects a record from the feature table using the three fields
 * that uniquely identify a feature.  The $columns array simply lists the columns
 * to select. The $values array is nested such that the organism is identified by
 * way of the organism_id foreign key constraint by specifying the genus and
 * species.  The cvterm is also specified using its foreign key and the cv_id
 * for the cvterm is nested as well.
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_chado_get_foreign_key($table_desc, $field, $values, $options = NULL) {

  // set defaults for options. If we don't set defaults then
  // we get memory leaks when we try to access the elements
  if (!is_array($options)) {
    $options = array();
  }
  if (!array_key_exists('case_insensitive_columns', $options)) {
    $options['case_insensitive_columns'] = array();
  }
  if (!array_key_exists('regex_columns', $options)) {
    $options['regex_columns'] = array();
  }

  // get the list of foreign keys for this table description and
  // iterate through those until we find the one we're looking for
  $fkeys = '';
  if (array_key_exists('foreign keys', $table_desc)) {
    $fkeys = $table_desc['foreign keys'];
  }
  if ($fkeys) {
    foreach ($fkeys as $name => $def) {
      if (is_array($def['table'])) {
        //foreign key was described 2X
        $message = "The foreign key " . $name . " was defined twice. Please check modules "
          ."to determine if hook_chado_schema_<version>_" . $table_desc['table'] . "() was "
          ."implemented and defined this foreign key when it wasn't supposed to. Modules "
          ."this hook was implemented in: " . implode(', ',
        module_implements("chado_" . $table_desc['table'] . "_schema")) . ".";
        watchdog('tripal_core', $message);
        drupal_set_message(check_plain($message), 'error');
        continue;
      }
      $table = $def['table'];
      $columns = $def['columns'];

      // iterate through the columns of the foreign key relationship
      foreach ($columns as $left => $right) {
        // does the left column in the relationship match our field?
        if (strcmp($field, $left) == 0) {
          // the column name of the foreign key matches the field we want
          // so this is the right relationship.  Now we want to select
          $select_cols = array($right);
          $result = tripal_core_chado_select($table, $select_cols, $values, $options);
          $fields = array();
          if ($result and count($result) > 0) {
            foreach ($result as $obj) {
              $fields[] = $obj->$right;
            }
            return $fields;
          }
        }
      }
    }
  }
  else {
    // TODO: what do we do if we get to this point and we have a fk
    // relationship expected but we don't have any definition for one in the
    // table schema??
    $version = tripal_core_get_chado_version(TRUE);
    $message = t("There is no foreign key relationship defined for " . $field . ".
       To define a foreign key relationship, determine the table this foreign
       key referrs to (<foreign table>) and then implement
       hook_chado_chado_schema_v<version>_<foreign table>(). See
       tripal_feature_chado_v1_2_schema_feature for an example. Chado version: $version");
    watchdog('tripal_core', $message);
    drupal_set_message(check_plain($message), 'error');
  }

  return array();
}

/**
 * Generates an object containing the full details of a record(s) in chado.
 *
 * This differs from the objects returned by tripal_core_chado_select in so far as all foreign key
 * relationships have been followed meaning you have more complete details. Thus this function
 * should be used whenever you need a full variable and tripal_core_chado_select should be used if
 * you only case about a few columns.
 *
 * @param $table
 *   The name of the base table to generate a variable for
 * @param $values
 *   A select values array that selects the records you want from the base table
 *   (this has the same form as tripal_core_chado_select)
 * @param $base_options
 *   An array containing options for the base table.  For example, an
 *   option of 'order_by' may be used to sort results in the base table
 *   if more than one are returned.  The options must be compatible with
 *   the options accepted by the tripal_core_chado_select() function.
 *   Additionally,  These options are available for this function:
 *   -return_array:
 *     can be provided to force the function to always return an array. Default
 *     behavior is to return a single record if only one record exists or to return
 *     an array if multiple records exist.
 *  - include_fk:
 *     an array of FK relationships to fallow. By default, the
 *     tripal_core_chado_select function will follow all FK relationships but this
 *     may generate more queries then is desired.  Provide an array specifying the
 *     fields to include.  For example, if including the cvterm, cv and dbxref records
 *     for a property the following array would work:
 *        array('type_id' => array('cv_id' => 1, 'dbxref_id' => 1)).
 *     Typicall, to expadn a property, this function would also include the db record
 *     through the db_id foreign key with the dbxref and db tables, but becuase
 *     it is not included in the array it will not be included in the results.
 * @return
 *   Either an object (if only one record was selected from the base table)
 *   or an array of objects (if more than one record was selected from the base table).
 *   If the option 'return_array' is provided the function always returns an array.
 *
 * Example Usage:
 * @code
 $values = array(
   'name' => 'Medtr4g030710'
 );
 $features = tripal_core_generate_chado_var('feature', $values);
 * @endcode
 * This will return an object if there is only one feature with the name Medtr4g030710 or it will
 * return an array of feature objects if more than one feature has that name.
 *
 * Note to Module Designers: Fields can be excluded by default from these objects by implementing
 * one of the following hooks:
 *  - hook_exclude_field_from_tablename_by_default (where tablename is the name of the table):
 *      This hook allows you to add fields to be excluded on a per table basis. Simply implement
 *      this hook to return an array of fields to be excluded. For example:
 * @code
 mymodule_exclude_field_from_feature_by_default() {
   return array('residues' => TRUE);
 }
 * @endcode
 *      will ensure that feature.residues is ecluded from a feature object by default.
 *  - hook_exclude_type_by_default:
 *      This hook allows you to exclude fields from all tables that are of a given postgresql field
 *      type. Simply implement this hook to return an array of postgresql types mapped to criteria.
 *      Then all fields of that type where the criteria supplied returns TRUE will be excluded from
 *      any table. Tokens available in criteria are &gt;field_value&lt;  and &gt;field_name&lt; . For example:
 * @code
 mymodule_exclude_type_by_default() {
   return array('text' => 'length(&gt;field_value&lt; ) > 50');
 }
 * @endcode
 *      will exclude all text fields with a length > 50. Thus if $feature.residues is longer than 50 *      it will be excluded, otherwise it will be added.
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_generate_chado_var($table, $values, $base_options = array()) {
  $all = new stdClass();

  $return_array = 0;
  if (array_key_exists('return_array', $base_options)) {
    $return_array = 1;
  }
  $include_fk = 0;
  if (array_key_exists('include_fk', $base_options)) {
    $include_fk = $base_options['include_fk'];
  }

  // get description for the current table----------------------------------------------------------
  $table_desc = tripal_core_get_chado_table_schema($table);
  if (!$table_desc or count($table_desc) == 0) {
    watchdog('tripal_core', "tripal_core_generate_chado_var: The table '%table' has not been defined. ".
             "and cannot be expanded. If this is a custom table, please add it using the Tripal ".
             "custom table interface.", array('%table' => $table), WATCHDOG_ERROR);
    if ($return_array) {
      return array();
    }
    return FALSE;
  }
  $table_primary_key = $table_desc['primary key'][0];
  $table_columns = array_keys($table_desc['fields']);

  // Expandable fields without value needed for criteria--------------------------------------------
  $all->expandable_fields = array();
  if ($table_desc['referring_tables']) {
    $all->expandable_tables = $table_desc['referring_tables'];
  }
  else {
    $all->expandable_tables = array();
  }
  $all->expandable_nodes = array();

  // Get fields to be removed by name.................................
  $fields_to_remove = module_invoke_all('exclude_field_from_' . $table . '_by_default');
  foreach ($fields_to_remove as $field_name => $criteria) {
    //replace &gt;field_name&lt;  with the current field name &
    $criteria = preg_replace('/&gt;field_name&lt; /', $field_name, $criteria);
    // if field_value needed we can't deal with this field yet
    if (preg_match('/&gt;field_value&lt; /', $criteria)) {
      break;
    }

    //if criteria then remove from query
    // @coder-ignore: only module designers can populate $criteria -not security risk
    $success = drupal_eval('<?php return ' . $criteria . '; ?>');
    //    watchdog('tripal_core',
    //      'Evaluating criteria (%criteria) for field %field in tripal_core_generate_chado_var for %table evaluated to %success',
    //      array('%table' => $table, '%criteria'=>$criteria, '%field' => $field_name, '%success'=>$success),
    //      WATCHDOG_NOTICE
    //    );
    if ($success) {
      unset($table_columns[array_search($field_name, $table_columns)]);
      unset($fields_to_remove[$field_name]);
      $all->expandable_fields[] = $table . '.' . $field_name;
    }
  }

  //Get fields to be removed by type................................
  $types_to_remove = module_invoke_all('exclude_type_by_default');
  $field_types = array();
  foreach ($table_desc['fields'] as $field_name => $field_array) {
    $field_types[$field_array['type']][] = $field_name;
  }
  foreach ($types_to_remove as $field_type => $criteria) {
    // if there are fields of that type to remove
    if (is_array($field_types[$field_type])) {
      //replace &gt;field_name&lt;  with the current field name &
      $criteria = preg_replace('/&gt;field_name&lt; /', $field_name, $criteria);
      foreach ($field_types[$field_type] as $field_name) {
        // if field_value needed we can't deal with this field yet
        if (preg_match('/&gt;field_value&lt; /', $criteria)) {
          $fields_to_remove[$field_name] = $criteria;
          continue;
        }
        // if field_value needed we can't deal with this field yet
        if (preg_match('/&gt;field_value&lt; /', $criteria)) {
          break;
        }
        //if criteria then remove from query
        // @coder-ignore: only module designers can populate $criteria -not security risk
        $success = drupal_eval('<?php return ' . $criteria . '; ?>');
        //        watchdog('tripal_core',
        //          'Evaluating criteria (%criteria) for field %field of $type in tripal_core_generate_chado_var for %table evaluated to %success',
        //          array('%table'=>$table, '%criteria'=>$criteria, '%field'=>$field_name, '%type'=>$field_type, '%success'=>$success),
        //          WATCHDOG_NOTICE
        //        );
        if ($success) {
          unset($table_columns[array_search($field_name, $table_columns)]);
          $all->expandable_fields[] = $table . '.' . $field_name;
        }
      } //end of foreach field of that type
    }
  } //end of foreach type to be removed

  // get the values for the record in the current table---------------------------------------------
  $results = tripal_core_chado_select($table, $table_columns, $values, $base_options);
  if ($results) {
    foreach ($results as $key => $object) {
      // Add empty expandable_x arrays
      $object->expandable_fields = $all->expandable_fields;
      $object->expandable_tables = $all->expandable_tables;
      $object->expandable_nodes = $all->expandable_nodes;
      // add curent table
      $object->tablename = $table;

      // check if the current table maps to a node type-----------------------------------------------
      // if this table is connected to a node there will be a chado_tablename table in drupal
      if (db_table_exists('chado_' . $table)) {
        // that has a foreign key to this one ($table_desc['primary key'][0]
        // and to the node table (nid)
        $sql = "SELECT %s, nid FROM {chado_%s} WHERE %s=%d";
        $mapping = db_fetch_object(db_query($sql, $table_primary_key, $table,
          $table_primary_key, $object->{$table_primary_key}));
        if ($mapping->{$table_primary_key}) {
          $object->nid = $mapping->nid;
          $object->expandable_nodes[] = $table;
        }
      }

      // remove any fields where criteria need to be evalulated---------------------------------------
      foreach ($fields_to_remove as $field_name => $criteria) {
        if (!isset($object->{$field_name})) {
          break;
        }
        $criteria = preg_replace('/&gt;field_value&lt; /', $object->{$field_name}, $criteria);
        //if criteria then remove from query
        // @coder-ignore: only module designers can populate $criteria -not security risk
        $success = drupal_eval('<?php return ' . $criteria . '; ?>');
        //      watchdog('tripal_core',
        //        'Evaluating criteria (%criteria) for field %field in tripal_core_generate_chado_var for   %table evaluated to %success',
        //        array('%table' => $table, '%criteria'=>$criteria, '%field' => $field_name, '%success'=>$success),
        //        WATCHDOG_NOTICE
        //      );
        if ($success) {
          unset($object->{$field_name});
          $object->expandable_fields[] = $table . '.' . $field_name;
        }
      }

      // recursively follow foreign key relationships nesting objects as we go------------------------
      if ($table_desc['foreign keys']) {
        foreach ($table_desc['foreign keys'] as $foreign_key_array) {
          $foreign_table = $foreign_key_array['table'];
          foreach ($foreign_key_array['columns'] as $foreign_key => $primary_key) {
            // Note: Foreign key is the field in the current table whereas primary_key is the field in
            // the table referenced by the foreign key
            //Dont do anything if the foreign key is empty
            if (empty($object->{$foreign_key})) {
              continue;
            }

            if ($include_fk) {
              // don't recurse if the callee has supplied an $fk_include list and this
              // FK table is not in the list.
              if (is_array($include_fk) and !array_key_exists($foreign_key, $include_fk)) {
                continue;
              }
              // if we have the option but it is not an array then we don't recurse any furutehr
              if (!is_array($include_fk)) {
                continue;
              }
            }
            // get the record from the foreign table
            $foreign_values = array($primary_key => $object->{$foreign_key});
            $options = array();
            if (is_array($include_fk)) {
              $options['include_fk'] = $include_fk[$foreign_key];
            }
            $foreign_object = tripal_core_generate_chado_var($foreign_table, $foreign_values, $options);
            // add the foreign record to the current object in a nested manner
            $object->{$foreign_key} = $foreign_object;
            // Flatten expandable_x arrays so only in the bottom object
            if (is_array($object->{$foreign_key}->expandable_fields)) {
              $object->expandable_fields = array_merge(
              $object->expandable_fields,
              $object->{$foreign_key}->expandable_fields
              );
              unset($object->{$foreign_key}->expandable_fields);
            }
            if (is_array($object->{$foreign_key}->expandable_tables)) {
              $object->expandable_tables = array_merge(
              $object->expandable_tables,
              $object->{$foreign_key}->expandable_tables
              );
              unset($object->{$foreign_key}->expandable_tables);
            }
            if (is_array($object->{$foreign_key}->expandable_nodes)) {
              $object->expandable_nodes = array_merge(
              $object->expandable_nodes,
              $object->{$foreign_key}->expandable_nodes
              );
              unset($object->{$foreign_key}->expandable_nodes);
            }
          }
        }
        $results[$key] = $object;
      }
    }
  }

  // check only one result returned
  if (!$return_array) {
    if (sizeof($results) == 1) {
      // add results to object
      return $results[0];
    }
    elseif (!empty($results)) {
      return $results;
    }
    else {
      // no results returned
    }
  }
  // the caller has requested results are always returned as
  // an array
  else {
    if (!$results) {
      return array();
    }
    else {
      return $results;
    }
  }
}

/**
 * Retrieves fields/tables/nodes that were excluded by default from a variable and adds them
 *
 * This function exists to allow tripal_core_generate_chado_var() to excldue some
 * fields/tables/nodes from the default form of a variable without making it extremely difficult for
 * the tripal admin to get at these variables if he/she wants them.
 *
 * @param $object
 *   This must be an object generated using tripal_core_generate_chado_var()
 * @param $type
 *   Must be one of 'field', 'table', 'node'. Indicates what is being expanded.
 * @param $to_expand
 *   The name of the field/table/node to be expanded
 * @param $table_options
 *   An array containing options for the base table.  For example, an
 *   option of 'order_by' may be used to sort results in the base table
 *   if more than one are returned.  The options must be compatible with
 *   the options accepted by the tripal_core_chado_select() function.
 *   Additionally,  The option 'return_array' can be provided to force
 *   the function to expand tables as an array. Default behavior is to expand
 *   a table as single record if only one record exists or to expand as an array if
 *   multiple records exist.
 * @return
 *   A chado object supplemented with the field/table/node requested to be expanded.
 *   If the type is a table and it has already been expanded no changes is made to the
 *   returned object
 *
 * Example Usage:
 * @code
   // Get a chado object to be expanded
   $values = array(
     'name' => 'Medtr4g030710'
   );
   $features = tripal_core_generate_chado_var('feature', $values);
   // Expand the organism node
   $feature = tripal_core_expand_chado_vars($feature, 'node', 'organism');
   // Expand the feature.residues field
   $feature = tripal_core_expand_chado_vars($feature, 'field', 'feature.residues');
   // Expand the feature properties (featureprop table)
   $feature = tripal_core_expand_chado_vars($feature, 'table', 'featureprop');
 * @endcode
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_expand_chado_vars($object, $type, $to_expand, $table_options = array()) {
  $base_table = $object->tablename;

  // check to see if we are expanding an array of objects
  if (is_array($object)) {
    foreach ($object as $index => $o) {
      $object[$index] = tripal_core_expand_chado_vars($o, $type, $to_expand);
    }
    return $object;
  }
  switch ($type) {
    case "field": //--------------------------------------------------------------------------------
      if (preg_match('/(\w+)\.(\w+)/', $to_expand, $matches)) {
        $tablename = $matches[1];
        $fieldname = $matches[2];
        $table_desc = tripal_core_get_chado_table_schema($tablename);
        $values = array();
        foreach ($table_desc['primary key'] as $key) {
          $values[$key] = $object->{$key};
        }
        if ($base_table == $tablename) {
          //get the field
          $results = tripal_core_chado_select($tablename, array($fieldname), $values);
          $object->{$fieldname} = $results[0]->{$fieldname};
          $object->expanded = $to_expand;
        }
        else {
          //We need to recurse -the field is in a nested object
          foreach ((array) $object as $field_name => $field_value) {
            if (is_object($field_value)) {
              $object->{$field_name} = tripal_core_expand_chado_vars(
              $field_value,
                'field',
              $to_expand
              );
            }
          } //end of for each field in the current object
        }
      }
      else {
        watchdog('tripal_core', 'tripal_core_expand_chado_vars: Field (%field) not in the right format. ".
          "It should be <tablename>.<fieldname>', WATCHDOG_ERROR);
      }
      break;
    case "table": //--------------------------------------------------------------------------------
      $foreign_table = $to_expand;

      // don't expand the table it already is expanded
      if (array_key_exists($foreign_table, $object)) {
        return $object;
      }
      $foreign_table_desc = tripal_core_get_chado_table_schema($foreign_table);
      // If it's connected to the base table
      if ($foreign_table_desc['foreign keys'][$base_table]) {
        foreach ($foreign_table_desc['foreign keys'][$base_table]['columns'] as $left => $right) {
          if (!$object->{$right}) {
            continue;
          }
          if (is_array($values)) {
            $values = array_merge($values, array($left => $object->{$right}) );
          }
          else {
            $values = array($left => $object->{$right});
          }
          // if a prepared statement is provide then generate a new name
          $new_options = $table_options;
          if (array_key_exists('statement_name', $table_options)) {
             $new_options['statement_name'] = "exp_" . $foreign_table . "_" . substr($left, 0, 2) . substr($right, 0, 2);
          }
          $foreign_object = tripal_core_generate_chado_var($foreign_table, array($left => $object->{$right}), $new_options);
          if ($foreign_object) {
            // in the case where the foreign key relationships exists more
            // than once with the same table we want to alter the
            // array structure
            if (count($foreign_table_desc['foreign keys'][$base_table]['columns']) > 1) {
              if (!is_object($object->{$foreign_table})) {
                $object->{$foreign_table} = new stdClass();
              }
              $object->{$foreign_table}->{$left} = $foreign_object;
              $object->expanded = $to_expand;
            }
            else {
              $object->{$foreign_table} = $foreign_object;
              $object->expanded = $to_expand;
            }
          }
          // if the object returned is NULL then handle that
          else {
            if (count($foreign_table_desc['foreign keys'][$base_table]['columns']) > 1) {
              $object->{$foreign_table}->{$left} = NULL;
            }
            else {
              $object->{$foreign_table} = NULL;
            }
          }
        }
      }
      else {
        // We need to recurse -the table has a relationship to one of the nested objects
        $did_expansion = 0;
        foreach ((array) $object as $field_name => $field_value) {
          // if we have a nested object ->expand the table in it
          if (is_object($field_value)) {
            $did_expansion = 1;
            $object->{$field_name} = tripal_core_expand_chado_vars($field_value, 'table', $foreign_table);
          }
        }
        // if we did not expand this table we should return a message that the foreign table
        // could not be expanded
        if (!$did_expansion) {
          watchdog('tripal_core', 'tripal_core_expand_chado_vars: Could not expand table, %table. It is ',
            'not in a foreign key relationship with the base object nor with any other expanded table. ' .
            'Check the table definition to ensure that a proper foreign key relationship is present.',
            array('%table' => $foreign_table), WATCHDOG_ERROR);
        }
      }
      break;
    case "node": //---------------------------------------------------------------------------------
      //if the node to be expanded is for our base table, then just expand it
      if ($object->tablename == $to_expand) {
        $node = node_load($object->nid);
        if ($node) {
          $object->expanded = $to_expand;
          $node->expandable_fields = $object->expandable_fields;
          unset($object->expandable_fields);
          $node->expandable_tables = $object->expandable_tables;
          unset($object->expandable_tables);
          $node->expandable_nodes = $object->expandable_nodes;
          unset($object->expandable_nodes);
          $node->{$base_table} = $object;
          $object = $node;
        }
        else {
          watchdog('tripal_core', 'tripal_core_expand_chado_vars: No node matches the nid (%nid) supplied.',
            array('%nid' => $object->nid), WATCHDOG_ERROR);
        } //end of if node
      }
      else {
        //We need to recurse -the node to expand is one of the nested objects
        foreach ((array) $object as $field_name => $field_value) {
          if (is_object($field_value)) {
            $object->{$field_name} = tripal_core_expand_chado_vars(
            $field_value,
              'node',
            $to_expand
            );
          }
        } //end of for each field in the current object
      }
      break;
    default:
      watchdog('tripal_core', 'tripal_core_expand_chado_vars: Unrecognized type (%type). Should be one of "field", "table", "node".',
        array('%type' => $type), WATCHDOG_ERROR);
      return FALSE;
  }

  //move extended array downwards-------------------------------------------------------------------
  if (!$object->expanded) {
    //if there's no extended field then go hunting for it
    foreach ( (array)$object as $field_name => $field_value) {
      if (is_object($field_value)) {
        if (isset($field_value->expanded)) {
          $object->expanded = $field_value->expanded;
          unset($field_value->expanded);
        }
      }
    }
  }
  //try again becasue now we might have moved it down
  if ($object->expanded) {
    $expandable_name = 'expandable_' . $type . 's';
    if ($object->{$expandable_name}) {
      $key_to_remove = array_search($object->expanded, $object->{$expandable_name});
      unset($object->{$expandable_name}[$key_to_remove]);
      unset($object->expanded);
    }
    else {
      // if there is an expandable array then we've reached the base object
      // if we get here and don't have anything expanded then something went wrong
      //      watchdog(
      //        'tripal_core',
      //        'tripal_core_expand_chado_vars: Unable to expand the %type %to_expand',
      //        array('%type'=>$type, '%to_expand'=>$to_expand),
      //        WATCHDOG_ERROR
      //      );
    } //end of it we've reached the base object
  }

  return $object;
}

/**
 * Implements hook_exclude_type_by_default()
 *
 * This hooks allows fields of a specified type that match a specified criteria to be excluded by
 * default from any table when tripal_core_generate_chado_var() is called. Keep in mind that if
 * fields are excluded by default they can always be expanded at a later date using
 * tripal_core_expand_chado_vars().
 *
 * Criteria are php strings that evaluate to either TRUE or FALSE. These strings are evaluated using
 * drupal_eval() which suppresses syntax errors and throws watchdog entries of type php. There are
 * also watchdog entries of type tripal_core stating the exact criteria evaluated. Criteria can
 * contain the following tokens:
 *   - &gt;field_name&lt;
 *       Replaced by the name of the field to be excluded
 *   - &gt;field_value&lt;
 *       Replaced by the value of the field in the current record
 * Also keep in mind that if your criteria doesn't contain the &gt;field_value&lt;  token then it will be
 * evaluated before the query is executed and if the field is excluded it won't be included in the
 * query.
 *
 * @return
 *   An array of type => criteria where the type is excluded if the criteria evaluates to TRUE
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_exclude_type_by_default() {
  return array('text' => "strlen('&gt;field_value&lt; ') > 100");
}

/**
 * Implements hook_exclude_field_from_<tablename>_by_default()
 *
 * This hooks allows fields from a specified table that match a specified criteria to be excluded by
 * default from any table when tripal_core_generate_chado_var() is called. Keep in mind that if
 * fields are excluded by default they can always be expanded at a later date using
 * tripal_core_expand_chado_vars().
 *
 * Criteria are php strings that evaluate to either TRUE or FALSE. These strings are evaluated using
 * drupal_eval() which suppresses syntax errors and throws watchdog entries of type php. There are
 * also watchdog entries of type tripal_core stating the exact criteria evaluated. Criteria can
 * contain the following tokens:
 *   - &gt;field_name&lt;
 *       Replaced by the name of the field to be excluded
 *   - &gt;field_value&lt;
 *       Replaced by the value of the field in the current record
 * Also keep in mind that if your criteria doesn't contain the &gt;field_value&lt;  token then it will be
 * evaluated before the query is executed and if the field is excluded it won't be included in the
 * query.
 *
 * @return
 *   An array of type => criteria where the type is excluded if the criteria evaluates to TRUE
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_exclude_field_from_feature_by_default() {
  return array();
}

/**
 * Use this function instead of db_query() to avoid switching databases
 * when making query to the chado database
 *
 * Will use a chado persistent connection if it already exists
 *
 * @param $sql
 *   The sql statement to execute
 *
 * @returns
 *   A database query result resource or FALSE if the query was not
 *   executed correctly
 */
function chado_query($sql) {

  $args = func_get_args();
  array_shift($args); // remove the $sql from the argument list
  $sql = db_prefix_tables($sql);
  if (isset($args[0]) and is_array($args[0])) { // 'All arguments in one array' syntax
    $args = $args[0];
  }

  _db_query_callback($args, TRUE);
  $sql = preg_replace_callback(DB_QUERY_REGEXP, '_db_query_callback', $sql);

  // Execute the query on the chado database/schema
  // Use the persistent chado connection if it already exists
  $persistent_connection = variable_get('tripal_persistent_chado', NULL);
  if ($persistent_connection) {

    $query = $sql;
    // Duplicate the _db_query code in order to ensure that the drupal
    // $active_db variable is never touched
    // thus changed $active_db to $persistent_connection
    // START COPY FROM _db_query in database.pgsql.inc
    if (variable_get('dev_query', 0)) {
      list($usec, $sec) = explode(' ', microtime());
      $timer = (float) $usec + (float) $sec;
    }

    $previous_db = tripal_db_set_active('chado');
    $last_result = pg_query($persistent_connection, $query);
    tripal_db_set_active($previous_db);

    if (variable_get('dev_query', 0)) {
      $bt = debug_backtrace();
      $query = $bt[2]['function'] . "\n" . $query;
      list($usec, $sec) = explode(' ', microtime());
      $stop = (float) $usec + (float) $sec;
      $diff = $stop - $timer;
      $queries[] = array($query, $diff);
    }

    if ($last_result !== FALSE) {
      return $last_result;
    }
    else {
      // Indicate to drupal_error_handler that this is a database error.
      ${DB_ERROR} = TRUE;
      trigger_error(check_plain(pg_last_error($persistent_connection) . "\nquery: " . $query), E_USER_WARNING);
      return FALSE;
    }
    // END COPY FROM _db_query in database.pgsql.inc
  }
  else {
    $previous_db = tripal_db_set_active('chado');
    $results = _db_query($sql);
    tripal_db_set_active($previous_db);
  }

  return $results;
}

/**
 * Get chado id for a node. E.g, if you want to get 'analysis_id' from the
 * 'analysis' table for a synced 'chado_analysis' node, use:
 * $analysis_id = chado_get_id_for_node ('analysis', $node)
 * Likewise,
 * $organism_id = chado_get_id_for_node ('organism', $node)
 * $feature_id = chado_get_id_for_node ('feature', $node)
 */
function chado_get_id_for_node($table, $node) {
  return db_result(db_query("SELECT %s_id FROM {chado_%s} WHERE nid = %d", $table, $table, $node->nid));
}

/**
 *  Get node id for a chado feature/organism/analysis. E.g, if you want to
 *  get the node id for an analysis, use:
 *  $nid = chado_get_node_id ('analysis', $analysis_id)
 *  Likewise,
 *  $nid = chado_get_node_id ('organism', $organism_id)
 *  $nid = chado_get_node_id ('feature', $feature_id)
 */
function chado_get_node_id($table, $id) {
  return db_result(db_query("SELECT nid FROM {chado_%s} WHERE %s_id = %d", $table, $table, $id));
}

/**
 * Retrieve a property for a given base table record
 *
 * @param $basetable
 *   The base table for which the property should be retrieved. Thus to retrieve a property
 *   for a feature the basetable=feature and property is retrieved from featureprop
 * @param $record_id
 *   The foriegn key field of the base table. This should be in integer.
 * @param $property
 *   The cvterm name describing the type of properties to be retrieved
 * @param $cv_name
 *   The name of the cv that the above cvterm is part of
 *
 * @return
 *   An array in the same format as that generated by the function
 *   tripal_core_generate_chado_var().  If only one record is returned it
 *   is a single object.  If more than one record is returned then it is an array
 *   of objects
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_get_property($basetable, $record_id, $property, $cv_name) {
  // get the foreign key for this property table
  $table_desc = tripal_core_get_chado_table_schema($basetable . 'prop');
  $fkcol = key($table_desc['foreign keys'][$basetable]['columns']);

  // construct the array of values to be selected
  $values = array(
  $fkcol => $record_id,
    'type_id' => array(
      'cv_id' => array(
        'name' => $cv_name,
  ),
     'name' => $property,
     'is_obsolete' => 0
  ),
  );
  $results = tripal_core_generate_chado_var($basetable . 'prop', $values);
  $results = tripal_core_expand_chado_vars($results, 'field', $basetable . 'prop.value');

  return $results;
}

/**
 * Insert a property for a given base table.  By default if the property already
 * exists a new property is added with the next available rank.  If
 * $update_if_present argument is specified then the record will be updated if it
 * exists rather than adding a new property.
 *
 * @param $basetable
 *   The base table for which the property should be inserted. Thus to insert a property
 *   for a feature the basetable=feature and property is inserted into featureprop
 * @param $record_id
 *   The foriegn key field of the base table. This should be in integer.
 * @param $property
 *   The cvterm name describing the type of properties to be inserted
 * @param $cv_name
 *   The name of the cv that the above cvterm is part of
 * @param $value
 *   The value of the property to be inserted (can be empty)
 * @param $update_if_present
 *   A boolean indicating whether an existing record should be updated. If the
 *   property already exists and this value is not specified or is zero then
 *   a new property will be added with the next largest rank.
 *
 * @return
 *   Return True on Insert/Update and False otherwise
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_insert_property($basetable, $record_id, $property,
$cv_name, $value, $update_if_present = 0) {

  // first see if the property already exists, if the user want's to update
  // then we can do that, but otherwise we want to increment the rank and
  // insert
  $props = tripal_core_get_property($basetable, $record_id, $property, $cv_name);
  if (!is_array($props)) {
    $props = array($props);
  }
  $rank = 0;
  if (count($props) > 0) {
    if ($update_if_present) {
      return tripal_core_update_property($basetable, $record_id, $property, $cv_name, $value);
    }
    else {
      // iterate through the properties returned and check to see if the
      // property with this value already exists if not, get the largest rank
      // and insert the same property but with this new value
      foreach ($props as $p) {
        if ($p->rank > $rank) {
          $rank = $p->rank;
        }
        if (strcmp($p->value, $value) == 0) {
          return TRUE;
        }
      }
      // now add 1 to the rank
      $rank++;
    }
  }
  else {
    watchdog('tripal_core', "Cannot find property '!prop_name'.",
    array('!prop_name' => $property), WATCHDOG_ERROR);
  }


  // get the foreign key for this property table
  $table_desc = tripal_core_get_chado_table_schema($basetable . 'prop');
  $fkcol = key($table_desc['foreign keys'][$basetable]['columns']);

  // construct the array of values to be inserted
  $values = array(
  $fkcol => $record_id,
    'type_id' => array(
      'cv_id' => array(
        'name' => $cv_name,
  ),
      'name' => $property,
      'is_obsolete' => 0
  ),
    'value' => $value,
    'rank' => $rank,
  );

  return tripal_core_chado_insert($basetable . 'prop', $values);
}

/**
 * Update a property for a given base table record and property name.  This
 * function should be used only if one record of the property will be present.
 * If the property name can have multiple entries (with increasing rank) then
 * use the function named tripal_core_update_property_by_id
 *
 * @param $basetable
 *   The base table for which the property should be updated. The property table
 *   is constructed using  a combination of the base table name and the suffix
 *   'prop' (e.g. basetable = feature then property tabie is featureprop).
 * @param $record_id
 *   The foreign key of the basetable to update a property for. This should be in integer.
 *   For example, if the basetable is 'feature' then the $record_id should be the feature_id
 * @param $property
 *   The cvterm name of property to be updated
 * @param $cv_name
 *   The name of the cv that the above cvterm is part of
 * @param $value
 *   The value of the property to be inserted (can be empty)
 * @param $insert_if_missing
 *   A boolean indicating whether a record should be inserted if one doesn't exist to update
 *
 * Note: The property to be updated is select via the unique combination of $record_id and
 * $property and then it is updated with the supplied value
 *
 * @return
 *   Return True on Update/Insert and False otherwise
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_update_property($basetable, $record_id, $property,
    $cv_name, $value, $insert_if_missing = 0) {

  // first see if the property is missing (we can't update a missing property
  $prop = tripal_core_get_property($basetable, $record_id, $property, $cv_name);
  if (count($prop)==0) {
    if ($insert_if_missing) {
      return tripal_core_insert_property($basetable, $record_id, $property, $cv_name, $value);
    }
    else {
      return FALSE;
    }
  }

  // get the foreign key for this property table
  $table_desc = tripal_core_get_chado_table_schema($basetable . 'prop');
  $fkcol = key($table_desc['foreign keys'][$basetable]['columns']);

  // construct the array that will match the exact record to update
  $match = array(
  $fkcol => $record_id,
    'type_id' => array(
      'cv_id' => array(
        'name' => $cv_name,
  ),
      'name' => $property,
  ),
  );

  // construct the array of values to be updated
  $values = array(
    'value' => $value,
  );

  return tripal_core_chado_update($basetable . 'prop', $match, $values);
}

/**
 * Update a property for a given base table record.  This function should be
 * used if multiple records of the same property will be present. Also, use this
 * function to change the property name of an existing property.
 *
 * @param $basetable
 *   The base table for which the property should be updated. The property table
 *   is constructed using  a combination of the base table name and the suffix
 *   'prop' (e.g. basetable = feature then property tabie is featureprop).
 * @param $record_id
 *   The primary key of the base table. This should be in integer.
 *   For example, if the basetable is 'feature' then the $record_id should be the featureprop_id
 * @param $property
 *   The cvterm name of property to be updated
 * @param $cv_name
 *   The name of the cv that the above cvterm is part of
 * @param $value
 *   The value of the property to be inserted (can be empty)
 *
 * @return
 *   Return True on Update/Insert and False otherwise
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_update_property_by_id($basetable, $record_id, $property,
$cv_name, $value) {

  // get the primary key for this property table
  $table_desc = tripal_core_get_chado_table_schema($basetable . 'prop');
  $pkcol = $table_desc['primary key'][0];

  // construct the array that will match the exact record to update
  $match = array(
  $pkcol => $record_id,
  );

  // construct the array of values to be updated
  $values = array(
    'type_id' => array(
      'cv_id' => array(
        'name' => $cv_name,
  ),
      'name' => $property,
  ),
    'value' => $value,
  );

  return tripal_core_chado_update($basetable . 'prop', $match, $values);
}

/**
 * Deletes a property for a given base table record using the property name
 *
 * @param $basetable
 *   The base table for which the property should be deleted. Thus to deleted a property
 *   for a feature the basetable=feature and property is deleted from featureprop
 * @param $record_id
 *   The primary key of the basetable to delete a property for. This should be in integer.
 * @param $property
 *   The cvterm name describing the type of property to be deleted
 * @param $cv_name
 *   The name of the cv that the above cvterm is part of
 *
 * Note: The property to be deleted is select via the unique combination of $record_id and $property
 *
 * @return
 *   Return True on Delete and False otherwise
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_delete_property($basetable, $record_id, $property, $cv_name) {

  // get the foreign key for this property table
  $table_desc = tripal_core_get_chado_table_schema($basetable . 'prop');
  $fkcol = key($table_desc['foreign keys'][$basetable]['columns']);

  // construct the array that will match the exact record to update
  $match = array(
  $fkcol => $record_id,
    'type_id' => array(
      'cv_id' => array(
        'name' => $cv_name,
  ),
      'name' => $property,
  ),
  );

  return tripal_core_chado_delete($basetable . 'prop', $match);
}

/**
 * Deletes a property using the property ID
 *
 * @param $basetable
 *   The base table for which the property should be deleted. Thus to deleted a property
 *   for a feature the basetable=feature and property is deleted from featureprop
 * @param $record_id
 *   The primary key of the basetable to delete a property for. This should be in integer.
 *
 * @return
 *   Return True on Delete and False otherwise
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_delete_property_by_id($basetable, $record_id) {

  // get the foreign key for this property table
  $table_desc = tripal_core_get_chado_table_schema($basetable . 'prop');
  $pkcol = $table_desc['primary key'][0];

  // construct the array that will match the exact record to update
  $match = array(
  $pkcol => $record_id,
  );

  return tripal_core_chado_delete($basetable . 'prop', $match);
}

/**
 * This function is typically used in the '.install' file for a Tripal module
 * Each module should call this function during installation to create
 * the module data directory which is sites/default/files/tripal/[module_name]
 * for default Drupal settings.  This directory can then be used by the module
 * for storing files.
 *
 * @param $module_name
 *   the name of the module being installed.
 *
 * @returns
 *   nothing
 *
 * @ingroup tripal_files_api
 */
function tripal_create_moddir($module_name) {

  // make the data directory for this module
  $data_dir = file_directory_path() . "/tripal/$module_name";
  if (!file_check_directory($data_dir, FILE_CREATE_DIRECTORY | FILE_MODIFY_PERMISSIONS)) {
    $message = "Cannot create directory $data_dir. This module may not ".
               "behave correctly without this directory.  Please  create ".
               "the directory manually or fix the problem and reinstall.";
    drupal_set_message(check_plain(t($message)), 'error');
    watchdog('tripal_core', $message, array(), WATCHDOG_ERROR);
  }
}

/**
 * Each Tripal module has a unique data directory which was creatd using the
 * tripal_create_moddir function during installation.  This function
 * retrieves the directory path.
 *
 * @param $module_name
 *   The name of the module
 *
 * @returns
 *   The path within the Drupal installation where the data directory resides
 * @ingroup tripal_files_api
 */
function tripal_get_moddir($module_name) {
  $data_dir = file_directory_path() . "/tripal/$module_name";
  return $data_dir;
}

/**
 * Set the Tripal Database
 *
 * The tripal_db_set_active function is used to prevent namespace collisions
 * when chado and drupal are installed in the same database but in different
 * schemas.  It is also used for backwards compatibility with older versions
 * of tripal or in cases where chado is located outside of the Drupal database.
 *
 * @ingroup tripal_chado_api
 */
function tripal_db_set_active($dbname  = 'default') {
  global $db_url, $db_type, $active_db;
  $chado_exists = 0;

  // only postgres can support search paths.  So if this is MysQL then
  // just run the normal tripal_db_set_active function.
  if (strcmp($db_type, 'pgsql')==0) {

    // if the 'chado' database is in the $db_url variable then chado is
    // not in the same Drupal database, so we don't need to set any
    // search_path and can just change the database
    if (is_array($db_url)) {
      if (isset($db_url[$dbname])) {
        return db_set_active($dbname);
      }
    }

    // if this is the default database then set the search path and return
    if (strcmp($dbname, 'default')==0) {
      tripal_db_set_default_search_path();
      return db_set_active($dbname);
    }
    // if the user requests a database other than the default
    // then we need to try and set the chado search path.  This
    // only works if Chado is local to the Drpual database. If it
    // fails then do nothing.
    else {
      if (tripal_db_set_chado_search_path($dbname)) {
         // if the chado schema is local to Drupal then
         // just return the active database.
         return 'default';
      }
      else {
        watchdog('tripal_core', "Cannot set 'search_path' variable for Postgres to %dbname",
          array('%dbname' => $dbname), WATCHDOG_ERROR);
      }
    }
  }
  // a non postgres database
  else {
    return db_set_active($dbname);
  }
}

/**
 * Gets the current search_path for PostgreSQL
 *
 * @ingroup tripal_chado_api
 */
function tripal_db_get_search_path() {
  $path = db_fetch_object(db_query("show search_path"));
  return $path->search_path;
}

/**
 * Set the chado search_path for PostgreSQL
 *
 * Sets the database search_path for postgreSQL to the
 * chado schema.
 *
 * @ingroup tripal_chado_api
 */
function tripal_db_set_chado_search_path($dbname) {

  // check to make sure the chado schema exists
  $chado_exists = variable_get('chado_schema_exists', FALSE);
  if (!$chado_exists) {
    $chado_exists = tripal_core_chado_schema_exists();
  }

  // here we make the assumption that the default database schema is
  // 'public'.  This will most likely always be the case but if not,
  // then this code will break
  if ($chado_exists) {
    db_query('set search_path to %s', "$dbname,public");
    return TRUE;
  }
  else {
    return FALSE;
  }
}

/**
 * Set the default search_path for PostgreSQL
 *
 * Sets the database search_path for postgreSQL to the
 * default schema.
 *
 * @ingroup tripal_chado_api
 */
function tripal_db_set_default_search_path() {
  // we make the assumption that the default schema is 'public'.
  $chado_exists = variable_get('chado_schema_exists', FALSE);
  if ($chado_exists) {
    db_query('set search_path to %s', 'public,chado');
  }
  else {
    db_query('set search_path to %s', 'public');
  }
}
/**
 * Indicates if the SQL statement is prepapred
 *
 * @param $statement_name
 *   The name of the statement to check if it is prepared.
 *
 * @return
 *   TRUE if the statement is preapred, FALSE otherwise
 */
function tripal_core_is_sql_prepared($statement_name) {

  // to reduce the need for a database query we will check the
  // session variable for this connection to see if the statement
  // has been prepared. If it has then we won't do the database
  // query to find out.  If it hasn't then we'll query the database
  // to see if it is prepared.
  $connection = variable_get('tripal_persistent_chado', NULL);
  if (!isset($_SESSION[$connection])) {
    $_SESSION[$connection] = array();
  }
  if (in_array($statement_name, $_SESSION[$connection])) {
    //print "Is Prepared and in Session var: $statement_name\n";
    return TRUE;
  }

  // @coder-ignore: acting on postgres tables rather then drupal schema therefore, table prefixing does not apply
  $sql = "SELECT name FROM pg_prepared_statements WHERE name = '%s'";
  // do not use 'chado_query' here or it causes memory-leaks
  $result = db_fetch_object(db_query($sql, $statement_name));

  if ($result) {
    $_SESSION[$connection][] = $statement_name;
    //print "Is Prepared but in DB: $statement_name\n";
    return TRUE;
  }
  //print "Is Not prepared: $statement_name\n";
  return FALSE;
}

/**
 * Prepare a chado query
 *
 * @param $statement_name
 *   The name of the prepared statement
 * @param $psql
 *   The SQL statement to be executed via chado_query.
 *   Should be of the form PREPARE <statement name> AS <SQL Statement to be prepared>
 * @param $args
 *   An array of arguements required to execute the prepared statement. The keys of
 *   the array should correspond to the $\d in the prepare statement and the value should
 *   be the type of value needed (ie: text, int, etc.)
 */
function tripal_core_chado_prepare($statement_name, $psql, $args) {
  $connection = variable_get('tripal_persistent_chado', NULL);

  if (!$connection) {
    watchdog('tripal_core', "chado_prepare: not able to prepare '%name' statement as no persistent connection is available", array('%name' => $statement_name, '%sql' => $psql), WATCHDOG_ERROR);
    return FALSE;
  }

  // Check to see if this statement was already prepared
  if (tripal_core_is_sql_prepared($statement_name)) {
    // check that the arguments are the same
    $prepared_args = $_SESSION['prepared_args'][$connection][$statement_name];
    $prepared_sql = $_SESSION['prepared_sql'][$connection][$statement_name];
    if ($prepared_args == $args) {
      // This statement is already prepared
      return TRUE;
    }
    else {
      // Although a statement with this name is already prepared it is not the same!
      watchdog('tripal_core', "chado_prepare: '%name' statement already prepared with different arguments! You want to prepare %sql with %values and the existing statement is %esql with %existing",
        array('%name' => $statement_name, '%sql' => $psql, '%values' => print_r($args, TRUE), '%esql' => $prepared_sql,
          '%existing' => print_r($prepared_args, TRUE)), WATCHDOG_ERROR);
      return FALSE;
    }
  }

  $status = chado_query($psql);
  if (!$status) {
    watchdog('tripal_core', "chado_prepare: not able to prepare '%name' statement for: %sql", array('%name' => $statement_name, '%sql' => $psql), WATCHDOG_ERROR);
    return FALSE;
  }
  else {
    //watchdog('tripal_core', "tripal_core_chado_select: prepared '%name' statement as %sql", array('%name' => $statement_name, '%sql' => $psql), WATCHDOG_NOTICE);
    $_SESSION[$connection][] = $statement_name;
    $_SESSION['prepared_args'][$connection][$statement_name] = $args;
    $_SESSION['prepared_sql'][$connection][$statement_name] = $psql;
    return TRUE;
  }
}

/**
 * Execute a prepared statement with the supplied values
 *
 * @param $statement_name
 *   The name of the prepared statement
 * @param $sql
 *   The SQL to execute using chado query.
 *   Should be of the form EXECUTE <statement_name> (<arg1>,<arg2>...<argn>)
 * @param $values
 *   An array of values in the execute sql statement
 */
function tripal_core_chado_execute_prepared($statement_name, $sql, $values) {
  $connection = variable_get('tripal_persistent_chado', NULL);

  if (!tripal_core_is_sql_prepared($statement_name)) {
    watchdog('tripal_core', "tripal_core_chado_execute_prepared: Cannot execute an unprepared statement: '%name'", array('%name' => $statement_name), WATCHDOG_ERROR);
    return FALSE;
  }

  // Before Executing, Ensure that all the values are supplied
  $required_values = $_SESSION['prepared_args'][$connection][$statement_name];
  if (!$required_values) {
    watchdog('tripal_core', "tripal_core_chado_execute_prepared: missing prepare arguments for this statement: '%name'", array('%name' => $statement_name), WATCHDOG_ERROR);
    return FALSE;
  }

  if (sizeof($required_values) == sizeof($values)) {

    $error = FALSE;
    foreach ($values as $k => $v) {
      if (isset($required_values[$k])) {
        switch ($required_values[$k]) {
          case 'text':
            $check = is_string($v);
            if ($v != '' and !$check) {
              watchdog('tripal_core', "chado_execute_prepared: wrong argument type supplied for '%name' statement, field %k. Expected %required but recieved '%value'",
                array('%name' => $statement_name, '%k' => $k, '%required' => $required_values[$k], '%value' => print_r($v, TRUE)), WATCHDOG_ERROR);
              return FALSE;
            }
            break;
          case 'int':
            $check = is_numeric($v);
            if (!$check) {
              watchdog('tripal_core', "chado_execute_prepared: wrong argument type supplied for '%name' statement. Expected %required but recieved '%value'",
                array('%name' => $statement_name, '%required' => $required_values[$k], '%value' => print_r($v, TRUE)), WATCHDOG_ERROR);
              return FALSE;
            }
            break;
          case 'bool':
            if ($v != 'TRUE' and $v != 'FALSE') {
              watchdog('tripal_core', "chado_execute_prepared: wrong argument type supplied for '%name' statement. Expected %required but recieved '%value'",
                array('%name' => $statement_name, '%required' => $required_values[$k], '%value' => print_r($v, TRUE)), WATCHDOG_ERROR);
              return FALSE;
            }
            break;
          case 'numeric':
            $check = is_numeric($v);
            if (!$check) {
              watchdog('tripal_core', "chado_execute_prepared: wrong argument type supplied for '%name' statement. Expected %required but recieved '%value'",
                array('%name' => $statement_name, '%required' => $required_values[$k], '%value' => print_r($v, TRUE)), WATCHDOG_ERROR);
              return FALSE;
            }
            break;
          default:
            watchdog('tripal_core', "chado_execute_prepared: unsupported argument type (supplied for '%name' statement %type)",

            array('%name' => $statement_name, '%type' => $required_values[$k]), WATCHDOG_WARNING);
            break;
        }
      }
      else {
        watchdog('tripal_core', "chado_execute_prepared: wrong number of arguments supplied for '%name' statement. Expected %required but recieved %values",
          array('%name' => $statement_name, '%required' => print_r($required_values, TRUE), '%values' => print_r($values, TRUE)), WATCHDOG_ERROR);
        return FALSE;
      }
    }

    // Since all values are supplied, execute
    $resource = chado_query($sql, $values);
    return $resource;
  }
  else {
    watchdog('tripal_core', "chado_execute_prepared: wrong number of arguments supplied for '%name' statement. Expected %required but recieved %values. Statement: %statement.",
      array('%name' => $statement_name, '%required' => print_r($required_values, TRUE), '%values' => print_r($values, TRUE), '%statement' => $_SESSION['prepared_sql'][$connection][$statement_name]), WATCHDOG_ERROR);
    return FALSE;
  }
}

/**
 * Instantiate or Return a persistent chado connection
 *
 * NOTE: cannot use $active_db since a new connection is created each time
 * db_set_active() is called
 *
 * @return
 *   A postgresql connection object which can be used by pg_prepare, pg_execute, etc.
 */
function tripal_db_persistent_chado() {
  global $db_url;

  // get connection if it already exists
  // Otherwise we need to set it
  $sconn = variable_get('tripal_persistent_chado', NULL);
  if ($sconn) {
    return $sconn;
  }
  else {
    if (is_array($db_url) && isset($db_url['chado'])) {
      $connection = db_connect($db_url['chado']);
      if (!$connection) {
        watchdog('tripal_core', "Could not create persistant connection", array(), WATCHDOG_ERROR);
        return FALSE;
      }
      variable_set('tripal_persistent_chado', $connection);
    }
    else {
      if (is_array($db_url)) {
        $connection = db_connect($db_url['default']);
      }
      else {
        $connection = db_connect($db_url);
      }
      if (!$connection) {
        variable_set('tripal_persistent_chado', NULL);
        watchdog('tripal_core', "Could not create persistant connection", array(), WATCHDOG_ERROR);
        return FALSE;
      }
      variable_set('tripal_persistent_chado', $connection);
    }
    return $connection;
  }
  return FALSE;
}

/**
 * Release a persistent chado connection
 */
function tripal_db_release_persistent_chado() {
  variable_del('tripal_persistent_chado');
}

/**
 * Start a transaction block. Ensures the use of a persistent chado connection
 */
function tripal_db_start_transaction() {
  $connection = tripal_db_persistent_chado();
  if ($connection) {
    chado_query("BEGIN");
    return $connection;
  }
  return FALSE;
}

/**
 * Set a savepoint to roll the current transaction back to if an error is encountered
 */
function tripal_db_set_savepoint_transaction($savepoint, $release = FALSE) {
  // Postgresql requires a savepoint of the same name to be unset before re-use
  if ($release) {
    chado_query("RELEASE SAVEPOINT %s", $savepoint);
  }
  chado_query("SAVEPOINT %s", $savepoint);
}

/**
 * Commit changes made during the current transaction
 */
function tripal_db_commit_transaction() {
  chado_query("COMMIT");
}

/**
 * Rollback changes.
 *
 * If $savepoint is NULL then rollback to the beginning of the transaction,
 * Otherwise, rollback to the point at which the named $savepoint was created
 *
 * @param $savepoint
 *   The name of the saved point in the transaction to rollback to
 */
function tripal_db_rollback_transaction($savepoint = NULL, $commit = TRUE) {

  if ($savepoint) {
    chado_query("ROLLBACK TO SAVEPOINT %s", $savepoint);
  }
  else {
    chado_query("ROLLBACK");
  }

  if ($commit) {
    tripal_db_commit_transaction();
  }

}

/**
 * Purpose: Get max rank for a given set of criteria
 *   This function was developed with the many property tables in chado in mind
 *
 * @param $tablename
 *    The name of the chado table you want to select the max rank from this table must contain a
 *    rank column of type integer
 * @param $where_options
 *   where options should include the id and type for that table to correctly
 *     group a set of records together where the only difference are the value and rank
 * @code
 *  array(
 *     <column_name> => array(
 *        'type' => <type of column: INT/STRING>,
 *       'value' => <the value you want to filter on>,
 *      'exact' => <if TRUE use =; if FALSE use ~>,
 *    )
 *  )
 * @endcode
 * @return the maximum rank
 *
 * @ingroup tripal_chado_api
 */
function tripal_get_max_chado_rank($tablename, $where_options) {
  $where= array();

  //generate the where clause from supplied options
  // the key is the column name
  foreach ($where_options as $key => $val_array) {
    if (preg_match('/INT/', $val_array['type'])) {
      $where[] = $key . "=" . $val_array['value'];
    }
    else {
      if ($val_array['exact']) {
        $operator='=';
      }
      else {
        $operator='~';
      }
      $where[] = $key . $operator . "'" . $val_array['value'] . "'";
    }
  }
  $previous_db = tripal_db_set_active('chado');
  $result = db_fetch_object(db_query("SELECT max(rank) as max_rank, count(rank) as count FROM %s WHERE %s",
    $tablename,  implode(' AND ', $where)));
  tripal_db_set_active($previous_db);
  //drupal_set_message("Max Rank Query=SELECT max(rank) as max_rank, count(rank) as count FROM ".$tablename." WHERE ".implode(' AND ',$where));
  if ($result->count > 0) {
    return $result->max_rank;
  }
  else {
    return -1;
  }
}

/**
 * Retrieves the schema in an array for the specified custom table.
 *
 * @param $table
 *   The name of the table to create.
 *
 * @return
 *   A Drupal-style Schema API array definition of the table. Returns
 *   FALSE on failure.
 *
 * @ingroup tripal_core_api
 */
function tripal_get_chado_custom_schema($table) {

  $sql = "SELECT schema FROM {tripal_custom_tables} WHERE table_name = '%s'";
  $custom = db_fetch_object(db_query($sql, $table));
  if (!$custom) {
    return FALSE;
  }
  else {
    return unserialize($custom->schema);
  }
}

/**
 * Check that the Chado schema exists
 *
 * @return
 *   TRUE/FALSE depending upon whether it exists
 */
function tripal_core_chado_schema_exists() {

  $exists = variable_get('chado_schema_exists', FALSE);

  if (!$exists) {
    // This is postgresql-specific code to check the existence of the chado schema
    // @coder-ignore: acting on pg_catalog schema rather then drupal schema therefore, table prefixing does not apply
    $sql = "SELECT nspname FROM pg_catalog.pg_namespace WHERE nspname = 'chado'";
    if (db_fetch_object(db_query($sql))) {
      variable_set('chado_schema_exists', TRUE);
      return TRUE;
    }
    else {
      return FALSE;
    }
  }
  return TRUE;
}
/**
 * Check that any given schema exists
 *
 * @param $schema
 *   The name of the schema to check the existence of
 *
 * @return
 *   TRUE/FALSE depending upon whether or not the schema exists
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_schema_exists($schema) {

  // check that the chado schema now exists
  $sql = "SELECT nspname
         FROM pg_namespace
         WHERE has_schema_privilege(nspname, 'USAGE') and nspname = '%s'
         ORDER BY nspname";
  $name = db_fetch_object(db_query($sql, $schema));
  if (strcmp($name->nspname, $schema) != 0) {
    return FALSE;
  }

  return TRUE;
}

/**
 * Retrieves the list tables in the Chado schema.  By default it only retursn
 * the default Chado tables, but may also return custom tables added to the
 * Chado schema as well.
 *
 * @param $include_custom
 *   Optional.  Set as TRUE to include any custom tables created in the
 *   Chado schema. Custom tables are added to Chado using the
 *   tripal_core_chado_create_table() function.
 *
 * @returns
 *   An associative array where the key and value pairs are the Chado table names.
 *
 * @ingroup tripal_core_api
 */
function tripal_core_get_chado_tables($include_custom = NULL) {


  // first get the chado version that is installed
  $v = tripal_core_get_chado_version();

  $tables = array();
  if ($v == '1.2') {
    $tables_v1_2 = tripal_core_chado_get_v1_2_tables();
    foreach ($tables_v1_2 as $table) {
      $tables[$table] = $table;
    }
  }
  if ($v == '1.11' or $v == '1.11 or older') {
    $tables_v1_11 = tripal_core_chado_get_v1_11_tables();
    foreach ($tables_v1_11 as $table) {
      $tables[$table] = $table;
    }
  }

  // now add in the custom tables too if requested
  if ($include_custom) {
    $sql = "SELECT table_name FROM {tripal_custom_tables}";
    $resource = db_query($sql);

    while ($r = db_fetch_object($resource)) {
      $tables[$r->table_name] = $r->table_name;
    }
  }

  asort($tables);
  return $tables;
}
/**
 * Sets a Drupal variable with the current version of Chado.  This variable
 * can then be queried later using the tripal_core_get_chado_Version
 *
 * @returns
 *   The version of Chado
 *
 * @ingroup tripal_core_api
 */
function tripal_core_set_chado_version() {
  global $db_url;

  // check that Chado is installed if not return 'uninstalled as the version'
  $chado_exists = tripal_core_chado_schema_exists();
  if (!$chado_exists) {
    // if it's not in the drupal database check to see if it's specified in the $db_url
    // in the settings.php
    if (!is_array($db_url) or !array_key_exists('chado', $db_url)) {
      // if it's not in the drupal database or specified in the $db_url then
      // return uninstalled as the version
      return 'not installed';
    }
  }

  // if the table doesn't exist then we don't know what version but we know
  // it must be 1.11 or older.
  $previous_db = tripal_db_set_active('chado');
  $prop_exists = db_table_exists('chadoprop');
  tripal_db_set_active($previous_db);
  if (!$prop_exists) {
    return "1.11 or older";
  }

  // we can't use the Tripal API to query this table
  // because the Tripal API depends on this function to
  // tell it the version. So, we need a typical SQL statement
  $sql = "SELECT value "
  ."FROM chadoprop CP "
  ."  INNER JOIN cvterm CVT on CVT.cvterm_id = CP.type_id "
  ."  INNER JOIN cv CV on CVT.cv_id = CV.cv_id "
  ."WHERE CV.name = 'chado_properties' and CVT.name = 'version'";
  $previous_db = tripal_db_set_active('chado');
  $v = db_fetch_object(db_query($sql));
  tripal_db_set_active($previous_db);

  // if we don't have a version in the chadoprop table then it must be
  // v1.11 or older
  if (!$v->value) {
    variable_set('chado_version', "1.11 or older");
    return "1.11 or older";
  }

  variable_set('chado_version', $v->value);
  return $v->value;
}
/**
 * Returns the version number of the currently installed Chado instance.
 * It can return the real or effective version.
 *
 * @param $exact
 *   Set this argument to 1 to retrieve the exact version that is installed.
 *   Otherwise, this function will set the version to the nearest 'tenth'.
 *   Chado versioning numbers in the hundreds represent changes to the
 *   software and not the schema.  Changes in the tenth's represent changes
 *   in the schema.
 *
 * @param $warn_if_unsupported
 *   If the currently installed version of Chado is not supported by Tripal
 *   the generatea a Drupal warning.
 *
 * @returns
 *   The version of Chado
 *
 * @ingroup tripal_core_api
 */
function tripal_core_get_chado_version($exact = FALSE, $warn_if_unsupported = FALSE) {
  // first get the chado version that is installed
  $exact_version = variable_get('chado_version', '');
  if (!$exact_version) {
    $exact_version = tripal_core_set_chado_version();
  }

  // Tripal only supports v1.11 or newer.. really this is the same as v1.1
  // but at the time the v1.11 schema API was written we didn't know that so
  // we'll return the version 1.11 so the schema API will work.
  if (strcmp($exact_version, '1.11 or older') == 0) {
    $exact_version = "1.11";
    if ($warn_if_unsupported) {
      drupal_set_message(t("WARNING: Tripal does not fully support Chado version less than v1.1.  If you are certain this is v1.1
         of if Chado was installed using an earlier version of Tripal then all is well. If not please upgrade to v1.1 or later"),
         'warning');
    }
  }

  // if not returing an exact version, return the version to the nearest 10th.
  // return 1.2 for all versions of 1.2x
  $effective_version = $exact_version;
  if (preg_match('/^1\.2\d+$/', $effective_version)) {
    $effective_version = "1.2";
  }
  if ($warn_if_unsupported and ($effective_version != 1.11 and $effective_version != 1.2)) {
    drupal_set_message(t("WARNING: The currently installed version of Chado, v$exact_version, is not fully compatible with Tripal."), 'warning');
  }
  // if the callee has requested the exact version then return it
  if ($exact) {
    return $exact_version;
  }

  return $effective_version;
}
/**
 * Retrieves the chado tables Schema API array.
 *
 * @param $table
 *   The name of the table to retrieve.  The function will use the appopriate
 *   Tripal chado schema API hooks (e.g. v1.11 or v1.2).
 *
 * @returns
 *   A Drupal Schema API array defining the table.
 *
 * @ingroup tripal_core_api
 */
function tripal_core_get_chado_table_schema($table) {

  // first get the chado version that is installed
  $v = tripal_core_get_chado_version();

  // get the table array from the proper chado schema
  $v = preg_replace("/\./", "_", $v); // reformat version for hook name
  $table_arr = module_invoke_all("chado_schema_v" . $v . "_" . $table);

  // if the table_arr is empty then maybe this is a custom table
  if (!is_array($table_arr) or count($table_arr) == 0) {
    $table_arr = tripal_get_chado_custom_schema($table);
  }

  return $table_arr;
}
/**
 * This function will delete Drupal nodes for any sync'ed table (e.g.
 * feature, organism, analysis, stock, library) if the chado record has been
 * deleted or the entry in the chado_[table] table has been removed.
 *
 * @param $table
 *   The name of the table that corresonds to the node type we want to clean up.
 * @param $job_id
 *   This should be the job id from the Tripal jobs system.  This function
 *   will update the job status using the provided job ID.
 *
 * @ingroup tripal_core_api
 */
function tripal_core_clean_orphaned_nodes($table, $job_id) {
  $count = 0;

  // build the SQL statments needed to check if nodes point to valid analyses
  $dsql = "SELECT * FROM {node} WHERE type = 'chado_%s' order by nid";
  $nsql = "SELECT * FROM {node} WHERE nid = %d";
  $csql = "SELECT * FROM {chado_%s} where nid = %d ";
  $clsql= "SELECT * FROM {chado_%s}";
  $lsql = "SELECT * FROM %s where %s_id = %d ";

  // load into nodes array
  print "Getting nodes\n";
  $nodes = array();
  $res = db_query($dsql, $table);
  while ($node = db_fetch_object($res)) {
    $nodes[$count] = $node;
    $count++;
  }

  // load the chado_$table into an array
  print "Getting chado_$table\n";
  $cnodes = array();
  $res = db_query($clsql, $table);
  while ($node = db_fetch_object($res)) {
    $cnodes[$count] = $node;
    $count++;
  }
  $interval = intval($count * 0.01);
  if ($interval < 1) {
    $interval = 1;
  }

  // iterate through all of the chado_$table entries and remove those
  // that don't have a node or don't have a $table record in chado.libary
  foreach ($cnodes as $nid) {

    // update the job status every 1% analyses
    if ($job_id and $i % $interval == 0) {
      tripal_job_set_progress($job_id, intval(($i / $count) * 100));
    }

    // see if the node exits, if not remove the entry from the chado_$table table
    $node = db_fetch_object(db_query($nsql, $nid->nid));
    if (!$node) {
      db_query("DELETE FROM {chado_%s} WHERE nid = %d", $table, $nid->nid);
      $message = "chado_$table missing node.... DELETING: $nid->nid";
      watchdog('tripal_core', $message, array(), WATCHDOG_WARNING);
    }

    // see if the record in chado exist, if not remove the entry from the chado_$table
    $table_id = $table . "_id";
    $record = db_fetch_object(chado_query($lsql, $table, $table, $nid->$table_id));
    if (!$record) {
      chado_query("DELETE FROM {chado_%s} WHERE %s_id = '%d'", $table, $table, $nid->$table_id);
      $message = "chado_$table missing $table.... DELETING entry.";
      watchdog('tripal_core', $message, array(), WATCHDOG_WARNING);
    }
    $i++;
  }

  // iterate through all of the nodes and delete those that don't
  // have a corresponding entry in chado_$table
  foreach ($nodes as $node) {

    // update the job status every 1% libraries
    if ($job_id and $i % $interval == 0) {
      tripal_job_set_progress($job_id, intval(($i / $count) * 100));
    }

    // check to see if the node has a corresponding entry
    // in the chado_$table table. If not then delete the node.
    $link = db_fetch_object(db_query($csql, $table, $node->nid));
    if (!$link) {
      if (node_access('delete', $node)) {
        $message = "Node missing in chado_$table table.... DELETING node $node->nid";
        watchdog("tripal_core", $message, array(), WATCHDOG_WARNING);
        node_delete($node->nid);
      }
      else {
        $message = "Node missing in chado_$table table.... but cannot delete due to improper permissions (node $node->nid)";
        watchdog("tripal_core", $message, array(), WATCHDOG_WARNING);
      }
    }
    $i++;
  }

  return '';
}

/**
 * Check whether chado is installed (either in the same or a different database)
 *
 * @return
 *   TRUE/FALSE depending upon whether chado is installed.
 *
 * @ingroup tripal_chado_api
 */
function tripal_core_is_chado_installed() {
  global $db_url, $db_type;

  // first check if chado is in the db_url of the
  // settings.php file
  if (is_array($db_url)) {
    if (isset($db_url['chado'])) {
      return TRUE;
    }
  }

  // check to make sure the chado schema exists
  return tripal_core_chado_schema_exists();
}