icsearch/icbasic.module

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<?php
// $Id: icbasic.module,v 1.12 2010-01-02 18:32:27 alexie Exp $


function icbasic_init() {
  $css_file = drupal_get_path('module', 'icbasic') .'/icbasic.css';
  if (file_exists($css_file)) {
    drupal_add_css($css_file, 'module');
  }
}

function icbasic_encode($variable) {
  if (!empty($variable)) {
    $encoded = strtr(base64_encode(addslashes(gzcompress(serialize($variable), 9))), '+/=', '-_,');
    return $encoded;
  }
}

function icbasic_decode($encoded) {
  if (!empty($encoded)) {
    $string = unserialize(gzuncompress(stripslashes(base64_decode(strtr($encoded, '-_,', '+/=')))));
    return $string;
  }
}

function icbasic_array2csv($array = NULL, $quote = NULL, $separator = ',', $key = FALSE) {
  if (empty($array)) {
    return FALSE;
  }
  $quotes = '';
  if (!empty($quote)) {
    if ($quote === TRUE) {
      $quotes = "'";
    }
    else {
      $quotes = $quote;
    }
  }
  // if not an array but a string/integer
  if (is_string($array) || is_int($array)) {
    return $quotes . $array . $quotes;
  }
  //else it is an array. distinguish between using the key or the value
  $str = '';
  if (empty($key)) {
    foreach ($array as $ar) {
      $str .= $quotes . $ar . $quotes . $separator;
    }
  }
  else {
    foreach ($array as $key => $ar) {
      $str .= $quotes . $key . $quotes . $separator;
    }
  }
  $str = rtrim($str, $separator);
  return $str;
}

function icbasic_db_execute($db = NULL, $function = NULL, $variables = NULL) {
  $return_array = array();
  if (!empty($db) && !empty($function)) {
    global $db_url;
    if (empty($db_url[$db])) {
      drupal_set_message("The public database for $db is unavailable at this time.", 'error', 'FALSE');
      return FALSE;
    }
    db_set_active($db);
    $return_array = $function($variables);
    if (!empty($return_array)) {
      db_set_active('default');
      return $return_array;
    }
    else {
      db_set_active('default');
      return 0;
    }
  }
  //simply (re)-connect. Use with care!!!
  elseif (!empty($db)) {
    global $db_url;
    if (!empty($db_url[$db])) {
      db_set_active($db);
      return 1;
    }
    else {
      drupal_set_message("The public database for $db is unavailable at this time.", 'error', 'FALSE');
      return FALSE;
    }
  }
  else {
    // reset to default
    db_set_active('default');
    return 1;
  }
}

function icbasic_validate_ic_id($accession = NULL) {
  $accession = trim($accession);
  $accession = check_plain($accession);
  if (empty($accession)) {
    return FALSE;
  }
  preg_match("/^([A-Z]{2})(\d+)[A-Z][a-z]([A-Z][a-z]+)(\d+)/", $accession, $matches);
  if (isset($matches) && $matches[1] == "IC" && $matches[2] && $matches[3] && $matches[4]) {
    return $accession;
  }
  return FALSE;
}

function icbasic_validate_seq_dna($seq = NULL) {
  $seq = trim($seq);
  if (empty($seq)) {
    return FALSE;
  }
  $seq_array = explode("\r", $seq);
  $seq_new   = '';
  $error     = 0;
  foreach ($seq_array as $line) {
    $line = trim($line);
    $line = str_replace("\n", '', $line);
    if (empty($line)) {
      continue;
    }
    $defline = strpos($line, '>');
    if ($defline !== FALSE) {
      // '>' char does not begin at the begining. delete anything before it
      if ($defline > 0) {
        $seq_new .= substr($line, $defline) ."\n";
      }
      else {
        $seq_new .= $line ."\n";
      }
    }
    else {
      $line = str_replace(" ", '', $line);
      if (preg_match('/[^XatcgURMWYKBDHVSN]/i', $line)) {
        $error++;
      }
      $seq_new .= $line;
    }
  }
  if (!empty($error)) {
    return $error;
  }
  elseif (!empty($seq_new)) {
    // RNA to DNA
    $seq_new = str_ireplace('U', 'T', $seq_new);
    return $seq_new;
  }
  else {
    return FALSE;
  }
}

function icbasic_validate_seq_protein($seq = NULL) {
  $seq = trim($seq);
  if (empty($seq)) {
    return FALSE;
  }
  $seq_array = explode("\r", $seq);
  $seq_new   = '';
  $error     = 0;
  foreach ($seq_array as $line) {
    $line = str_ireplace("\n", '', $line);
    if (empty($line)) {
      continue;
    }
    if (preg_match('/>/', $line) == 0) {
      if (preg_match('/[^XacdefghiklmnpqrstvwyBZJ]/i', $line)) {
        $error++;
      }
      $seq_new .= $line;
    }
  }
  if (!empty($error)) {
    return $error;
  }
  elseif (!empty($seq_new)) {
    return $seq_new;
  }
  else {
    return FALSE;
  }
}

/*
 * Get data from a IC chado table
 * 
 * Possible convinience function to act as a skeleton, not used anywhere yet.
 * TODO: Need to think through security
 * 
 * @param $table
 *   The name of table
 * @param $field
 *   Field is the name of the field used in the WHERE variable (def. uniquename)
 * @param $value
 *  Value is what you search with so that WHERE $field='$value'
 *  
 * @return
 *   Returns an associative array with keys being the column names
 */
function icbasic_chadoapi_get_single_table($table = NULL, $field = 'uniquename', $value = NULL) {
  if (empty($value) || empty($table)) {
    return FALSE;
  }
  $value   = check_plain($value);
  $results = array();
  $sql     = "SELECT * from %s where %s='%s'";
  $results = db_query($sql, $table, $field, $value);
  return $results;
}

function icbasic_checkboxes_results2array($results) {
  if (empty($results)) {
    return FALSE;
  }
  $array = array();
  foreach ($results as $key => $value) {
    if (empty($value)) {
      continue;
    }
    $array[] = $key;
  }
  if (!empty($array)) {
    return $array;
  }
}

function icbasic_add_cv($cv, $cvterm_array) {
  if (empty($cv) || empty($cvterm_array)) {
    return FALSE;
  }
  $sql_insert_cv = "INSERT INTO {ic_cv} (name) VALUES ('%s')";
  $sql_select_cv = "SELECT cv_id from {ic_cv} where name='%s'";
  $res           = db_fetch_array(db_query($sql_select_cv, $cv));
  $cv_id         = $res['cv_id'];
  if (empty($cv_id)) {
    db_query($sql_insert_cv, $cv);
    $res = db_fetch_array(db_query($sql_select_cv, $cv));
    $cv_id = $res['cv_id'];
  }
  if (empty($cv_id)) {
    drupal_set_message('There has been a problem inserting a new controlled vocabulary. Are you sure permissions are properly set?', 'error', FALSE);
    return FALSE;
  }
  $sql_check = "SELECT cvterm_id from {ic_cvterm} where name='%s' and cv_id=%d";
  $sql_insert_cvterm = "INSERT INTO {ic_cvterm} (name,cv_id) VALUES ('%s',%d)";
  foreach ($cvterm_array as $cvterm) {
    $res = db_fetch_array(db_query($sql_check, $cvterm, $cv_id));
    if (empty($res['cvterm_id'])) {
      db_query($sql_insert_cvterm, $cvterm, $cv_id);
    }
  }
  return $cv_id;
}

function icbasic_populate_prop($table_type, $object_name, $cvterm_id, $property_array) {
  if (empty($table_type) || empty($object_name) || empty($cvterm_id) || empty($property_array)) {
    return FALSE;
  }
  $key        = '';
  $table_pkey = '';
  $table_name = '';
  if ($table_type == 'ic_resource') {
    $key        = 'resource_id';
    $table_pkey = 'resourceprop_id';
    $table_name = 'ic_resourceprop';
  }
  elseif ($table_type == 'ic_feature') {
    $key        = 'feature_id';
    $table_pkey = 'featureprop_id';
    $table_name = 'ic_featureprop';
  }
  else {
    drupal_set_message('Currently only resource and feature table types are allowed', 'error', FALSE);
    return FALSE;
  }

  // get object id
  $object_select = "SELECT $key from {". $table_type ."} where uniquename='%s'";
  $res           = db_fetch_array(db_query($object_select, $object_name));
  $object_id     = $res[$key];
  if (empty($object_id)) {
    drupal_set_message("Failed to get $key for $object_name. Are you sure it exists?", 'error', FALSE);
    return FALSE;
  }
  $property_check     = "SELECT $table_pkey from {". $table_name ."} WHERE $key=%d AND type_id=%d and value='%s'";
  $property_next_rank = "SELECT max(rank) from {". $table_name ."} WHERE $key=%d AND type_id=%d ";
  $property_insert    = "INSERT INTO {". $table_name ."} ($key,type_id,value,rank) VALUES (%d,%d,'%s',%d)";
  foreach ($property_array as $value) {
    $res = db_fetch_array(db_query($property_check, $object_id, $cvterm_id, $value));
    if (empty($res[$table_pkey])) {
      $res_rank = db_fetch_array(db_query($property_next_rank, $object_id, $cvterm_id));
      $next_rank = $res_rank['max'] + 1;
      if (empty($next_rank)) {
        $next_rank = 0;
      }
      db_query($property_insert, $object_id, $cvterm_id, $value, $next_rank);
      $res = db_fetch_array(db_query($property_check, $object_id, $cvterm_id, $value));
      if (empty($res[$table_pkey])) {
        drupal_set_message("Failed to add $value into $table_name. Are you sure DB permissions allow INSERT operations?", 'error', FALSE);
        return FALSE;
      }
    }
  }
  return TRUE;
}

function icbasic_populate_cvterms($table_type, $object_name, $cvname, $cvterm_array) {
  if (empty($table_type) || empty($object_name) || empty($cvname) || empty($cvterm_array)) {
    return FALSE;
  }
  $key        = '';
  $table_pkey = '';
  $table_name = '';
  if ($table_type == 'ic_resource') {
    $key        = 'resource_id';
    $table_pkey = 'resource_cvterm_id';
    $table_name = 'ic_resource_cvterm';
  }
  elseif ($table_type == 'ic_feature') {
    $key        = 'feature_id';
    $table_pkey = 'feature_cvterm_id';
    $table_name = 'ic_feature_cvterm';
  }
  else {
    drupal_set_message('Currently only resource and feature table types are allowed', 'error', FALSE);
    return FALSE;
  }
  // cv
  $cv_id = icbasic_add_cv($cvname, $cvterm_array);
  // get object id
  $object_select = "SELECT $key from {". $table_type ."} where uniquename='%s'";
  $res           = db_fetch_array(db_query($object_select, $object_name));
  $object_id     = $res[$key];
  if (empty($object_id)) {
    drupal_set_message("Failed to get $key for $object_name. Are you sure it exists?", 'error', FALSE);
    return FALSE;
  }
  $cvterm_check = "SELECT $table_pkey from {". $table_name ."} WHERE $key=%d AND " . "cvterm_id=(SELECT cvterm_id from {ic_cvterm} WHERE cv_id=%d and name='%s')";
  $cvterm_insert = "INSERT INTO {". $table_name ."} ($key,cvterm_id) VALUES (%d," . "(SELECT cvterm_id from {ic_cvterm} WHERE cv_id=%d and name='%s'))";
  foreach ($cvterm_array as $cvterm_name) {
    $res = db_fetch_array(db_query($cvterm_check, $object_id, $cv_id, $cvterm_name));
    if (empty($res[$table_pkey])) {
      db_query($cvterm_insert, $object_id, $cv_id, $cvterm_name);
      $res = db_fetch_array(db_query($cvterm_check, $object_id, $cv_id, $cvterm_name));
      if (empty($res[$table_pkey])) {
        drupal_set_message("Failed to add $cvterm_name into $table_name. Are you sure DB permissions allow INSERT operations?", 'error', FALSE);
        return FALSE;
      }
    }
  }
  return TRUE;
}

function icbasic_get_add_cv_withnames($cv_name, $cvterm_name = NULL, $name_as_key = FALSE) {
  $return_array = array();
  if (empty($cv_name)) {
    return FALSE;
  }
  if (empty($cvterm_name)) {
    //this is for getting all the cvterms in a cv
    $select_cvterms = 'SELECT cvterm_id,name from {ic_cvterm} as cvterm where cv_id=' . "(SELECT cv_id from {ic_cv} where name='%s')";
    $res = db_query($select_cvterms, $cv_name);
    if (empty($res)) {
      return FALSE;
    }
    while ($row = db_fetch_array($res)) {
      if (!empty($name_as_key) && $name_as_key === 'BOTH') {
        $return_array[$row['name']] = $row['name'];
      }
      elseif (!empty($name_as_key)) {
        $return_array[$row['name']] = $row['cvterm_id'];
      }
      else {
        $return_array[$row['cvterm_id']] = $row['name'];
      }
    }
    if (!empty($return_array)) {
      return $return_array;
    }
    else {
      return FALSE;
    }
  }
  $cvterm_id     = '';
  $select_cvterm = 'SELECT cvterm_id from {ic_cvterm} as cvterm JOIN {ic_cv} as cv ON cvterm.cv_id=cv.cv_id ' . " WHERE cvterm.name='%s' AND cv.name='%s'";
  $res           = db_fetch_array(db_query($select_cvterm, $cvterm_name, $cv_name));
  $cvterm_id     = $res['cvterm_id'];
  if (!empty($cvterm_id)) {
    return $cvterm_id;
  }
  else {
    // does cv exist?
    $cv_id        = '';
    $select_cv_id = "SELECT cv_id from {ic_cv} as cv where name='%s'";
    $res          = db_fetch_array(db_query($select_cv_id, $cv_name));
    $cv_id        = $res['cv_id'];
    if (empty($cv_id)) {
      //add it
      $insert_cv_id = "INSERT INTO {ic_cv} (name) VALUES ('%s')";
      db_query($insert_cv_id, $cv_name);
      $res = db_fetch_array(db_query($select_cv_id, $cv_name));
      $cv_id = $res['cv_id'];
    }
    if (empty($cv_id)) {
      drupal_set_message("I was not able to store the CV data for $cv_name.", 'error', FALSE);
      return FALSE;
    }
    //add cvterm
    $insert_cvterm = "INSERT INTO {ic_cvterm} (name,cv_id) VALUES ('%s',%d)";
    db_query($insert_cvterm, $cvterm_name, $cv_id);
    $res = db_fetch_array(db_query($select_cvterm, $cvterm_name, $cv_id));
    $cvterm_id = $res['cvterm_id'];
    if (!empty($cvterm_id)) {
      return $cvterm_id;
    }
    else {
      drupal_set_message("I was not able to store the cvterm data for $cvterm_name.", 'error', FALSE);
      return FALSE;
    }
  }
}

function icbasic_get_add_dbxref_withnames($dbname, $accession) {
  if (empty($dbname) || empty($accession)) {
    return FALSE;
  }
  $dbxref_id     = '';
  $select_dbxref = 'SELECT dbxref_id from {ic_dbxref} as dbxref JOIN {ic_db} as db ON dbxref.db_id=db.db_id ' . " WHERE dbxref.accession='%s' AND db.name='%s'";
  $res           = db_fetch_array(db_query($select_dbxref, $accession, $dbname));
  $dbxref_id     = $res['dbxref_id'];
  if (!empty($dbxref_id)) {
    return ($dbxref_id);
  }
  else {
    // does db exist?
    $db_id        = '';
    $select_db_id = "SELECT db_id from {ic_db} as db where name='%s'";
    $res          = db_fetch_array(db_query($select_db_id, $dbname));
    $db_id        = $res['db_id'];
    if (empty($db_id)) {
      //add it
      $insert_db_id = "INSERT INTO {ic_db} (name) VALUES ('%s')";
      db_query($insert_db_id, $dbname);
      $res = db_fetch_array(db_query($select_db_id, $dbname));
      $db_id = $res['db_id'];
    }
    if (empty($db_id)) {
      drupal_set_message("I was not able to store the db data for $dbname.", 'error', FALSE);
      return FALSE;
    }
    //add dbxref
    $insert_dbxref = "INSERT INTO {ic_dbxref} (accession,db_id) VALUES ('%s',%d)";
    db_query($insert_dbxref, $accession, $db_id);
    $res = db_fetch_array(db_query($select_dbxref, $accession, $db_id));
    $dbxref_id = $res['dbxref_id'];
    if (!empty($dbxref_id)) {
      return $dbxref_id;
    }
    else {
      drupal_set_message("I was not able to store the dbxref data for $accession.", 'error', FALSE);
      return FALSE;
    }
  }
}

function icbasic_clear_session($var = NULL) {
  if (empty($var)) {
    $_SESSION = array();
  }
  else {
    if (is_array($var)) {
      foreach ($var as $element) {
        unset($_SESSION[$element]);
      }
    }
    else {
      unset($_SESSION[$var]);
    }
  }
  return TRUE;
}

function icbasic_create_uid($sessionid = NULL, $timestamp = NULL, $string = NULL) {
  if (empty($sessionid)) {
    $sessionid = session_id();
  }
  if (empty($timestamp)) {
    $timestamp = time();
  }
  //md5sum
  $uid = md5($sessionid . $timestamp . $string);
  return $uid;
}

function icbasic_get_resource_name_id($resource, $name_as_key = FALSE) {
  if (empty($resource)) {
    return FALSE;
  }
  $return_array = array();
  foreach ((array)$resource as $r) {
    $sql_select = 'SELECT resource_id as id,uniquename from {ic_resource} where ';
    if (is_numeric($r)) {
      $sql_select .= 'resource_id=%d';
    }
    else {
      $sql_select .= "uniquename='%s'";
    }
    $res = db_fetch_array(db_query($sql_select, $r));
    if (!empty($name_as_key)) {
      $return_array[$res['uniquename']] = $res['id'];
    }
    else {
      $return_array[$res['id']] = $res['uniquename'];
    }
  }
}

function icbasic_get_add_resource($type_name, $data = NULL, $add = FALSE, $name_as_key = FALSE) {
  if (empty($type_name)) {
    return FALSE;
  }
  $return_array = array();
  $type_id = icbasic_get_add_cv_withnames('resource_type', $type_name);
  if (empty($type_id)) {
    drupal_set_message('Could not add cvterm for '. $type_name, 'error');
    return FALSE;
  }

  $sql_select = "SELECT resource_id,uniquename from {ic_resource} where type_id=%d";

  // We are going to do an add or delete operation:
  if (!empty($add)) {
    $dbxref_id = icbasic_get_add_dbxref_withnames('local resource', $data['dbxref_name']);
    if (empty($dbxref_id)) {
      drupal_set_message('Could not add resource because could not get dbxref id for '. $data['dbxref_name'], 'error');
      return FALSE;
    }
    $name = $data['uniquename'];
    if (empty($name)) {
      drupal_set_message("Did not $add requested resource because name/id was missing or not given correctly", 'error');
      return FALSE;
    }
    $sql_delete = "DELETE from {ic_resource} where type_id=%d and uniquename='%s'";
    $sql_insert = "INSERT into {ic_resource} (type_id,uniquename,dbxref_id) VALUES (%d,'%s',%d)";
    $sql_check  = "SELECT resource_id from {ic_resource} where uniquename='%s'";

    switch ($add) {
      case 'REPLACE':
        $check = db_fetch_array(db_query($sql_check, $name));
        if (!empty($check)) {
          db_query($sql_delete, $type_id, $name);
        }
        db_query($sql_insert, $type_id, $name, $dbxref_id);
        break;

      case 'ADD':
        $check = db_fetch_array(db_query($sql_check, $name));
        if (empty($check)) {
          db_query($sql_insert, $type_id, $name, $dbxref_id);
        }
        break;

      case 'DELETE':
        $check = db_fetch_array(db_query($sql_check, $name));
        if (!empty($check)) {
          db_query($sql_delete, $type_id, $name);
        }
        return TRUE;
    }
  }
  else {
    // add limits only when we are not adding.
    if (!empty($data)) {
      foreach ($data as $key => $value) {
        $sql_select .= " AND $key='$value'";
      }
    }
  }
  $db_results = db_query($sql_select, $type_id);
  while ($row = db_fetch_array($db_results)) {
    if (!empty($name_as_key) && $name_as_key === 'BOTH') {
      $return_array[$row['uniquename']] = $row['uniquename'];
    }
    elseif (empty($name_as_key)) {
      $return_array[$row['resource_id']] = $row['uniquename'];
    }
    else {
      $return_array[$row['uniquename']] = $row['resource_id'];
    }
  }

  if (!empty($return_array)) {
    return $return_array;
  }
  else {
    return FALSE;
  }
}

function icbasic_get_resource_cvterm_and_prop($resource) {
  $return_array = array();
  if (empty($resource)) {
    return FALSE;
  }
  $cvterm_select = 'SELECT cvterm.name as cvterm_name,cv.name as cv_name from {ic_resource_cvterm} as r ' . ' JOIN {ic_cvterm} as cvterm ON r.cvterm_id=cvterm.cvterm_id' . ' JOIN {ic_cv} as cv ON cv.cv_id=cvterm.cv_id ';

  $prop_select = 'SELECT cvterm.name as cvterm_name,r.value,r.rank from {ic_resourceprop} as r ' . ' JOIN {ic_cvterm} as cvterm ON r.type_id=cvterm.cvterm_id ';
  if (is_numeric($resource)) {
    $cvterm_select .= ' WHERE r.resource_id=%d ';
    $prop_select .= ' WHERE r.resource_id=%d ';
  }
  else {
    $cvterm_select .= " WHERE r.resource_id=(SELECT resource_id from {ic_resource} where uniquename='%s')";
    $prop_select .= " WHERE r.resource_id=(SELECT resource_id from {ic_resource} where uniquename='%s')";
  }

  $prop_select .= ' ORDER by r.rank';
  $cv_res = db_query($cvterm_select, $resource);
  while ($row = db_fetch_array($cv_res)) {
    $return_array['cvterm'][$row['cv_name']][] = $row['cvterm_name'];
  }
  $prop_res = db_query($prop_select, $resource);
  while ($row = db_fetch_array($prop_res)) {
    $return_array['prop'][$row['cvterm_name']][$row['rank']] = $row['value'];
  }
  if (!empty($return_array)) {
    return $return_array;
  }
  else {
    return FALSE;
  }
}

function icbasic_link_unlink_resources($subject, $rel, $object = NULL, $replace = FALSE) {
  if (empty($subject) || empty($rel)) {
    return FALSE;
  }
  $type_id = icbasic_get_add_cv_withnames('relationship', $rel);
  if (empty($type_id)) {
    drupal_set_message('Could not add cvterm for '. $rel, 'error');
    return FALSE;
  }
  $object_grab = '';
  $subject_grab = "(SELECT resource_id from {ic_resource} where uniquename='%s')";
  if (!empty($object)) {
    $object_grab = "(SELECT resource_id from {ic_resource} where uniquename='%s')";
  }
  if (is_numeric($subject)) {
    $subject_grab = '%d';
  }
  if (!empty($object) && is_numeric($object)) {
    $object_grab = '%d';
  }

  if (empty($object)) {
    if ($replace === 'DELETE') {
      $sql_delete_all = 'DELETE FROM {ic_resource_resource} where subject_id='. $subject_grab ."and type_id=%d";
      db_query($sql_delete_all, $subject, $type_id);
      return TRUE;
    }
    return FALSE;
  }

  $sql_check  = 'SELECT resource_resource_id from {ic_resource_resource} where subject_id='. $subject_grab .' AND object_id='. $object_grab;
  $sql_insert = 'INSERT INTO {ic_resource_resource} (subject_id,object_id,type_id) VALUES ('. $subject_grab .','. $object_grab .',%d)';
  $sql_delete = 'DELETE FROM {ic_resource_resource} where subject_id='. $subject_grab .' AND object_id='. $object_grab;

  $res = db_fetch_array(db_query($sql_check, $subject, $object));
  switch ($replace) {
    case FALSE:
      if (empty($res)) {
        db_query($sql_insert, $subject, $object, $type_id);
        //dvm("Inserted $subject $rel $object");
        return TRUE;
      }
      else {
        //dvm("A relationship exists already for subject $subject and object $object.");
        return TRUE;
      }
      break;

    case 'DELETE':
      if (empty($res)) {
        return TRUE;
      }
      else {
        db_query($sql_delete, $subject, $object);
        $res = db_fetch_array(db_query($sql_check, $subject, $object));
        if (empty($res)) {
          //dvm("Deleted previous relationship $subject $object.");
          return TRUE;
        }
        else {
          dvm("Failed to delete previous relationship for $subject $object.");
          return FALSE;
        }
      }
      break;

    case TRUE:
      if (empty($res)) {
        db_query($sql_insert, $subject, $object, $type_id);
        //dvm("Inserted $subject $rel $object");
        return TRUE;
      }
      else {
        db_query($sql_delete, $subject, $object);
        $res = db_fetch_array(db_query($sql_check, $subject, $object));
        if (empty($res)) {
          db_query($sql_insert, $subject, $object, $type_id);
          //dvm("Inserted $subject $rel $object after deleting previous relationship.");
          return TRUE;
        }
        else {
          dvm("Failed to delete previous relationship for $subject $object.");
          return FALSE;
        }
      }
      break;
  }
}

function icbasic_get_linked_resources($resource, $relationship_name = NULL, $name_as_key = FALSE, $limit = NULL) {
  $return_array = array();
  if (empty($resource)) {
    return FALSE;
  }
  $sql_select = 'SELECT rr.object_id,rocvterm.name as object_type,ro.uniquename as object_name ' . 'from {ic_resource_resource} as rr ' . ' JOIN {ic_resource} as ro ON ro.resource_id=rr.object_id ' . ' JOIN {ic_cvterm} as rocvterm ON rocvterm.cvterm_id=ro.type_id ';

  if (is_numeric($resource)) {
    $sql_select .= 'WHERE rr.subject_id=%d';
  }
  else {
    $sql_select .= "WHERE rr.subject_id=(SELECT resource_id from {ic_resource} where uniquename='%s')";
  }
  if (!empty($relationship_name)) {
    $type_id = icbasic_get_add_cv_withnames('relationship', $relationship_name);
    $sql_select .= " AND rr.type_id=$type_id ";
  }
  if (!empty($limit)) {
    $sql_select .= " AND $limit ";
  }
  $res = db_query($sql_select, $resource);
  while ($row = db_fetch_array($res)) {
    if (!empty($name_as_key)) {
      $return_array[$row['object_name']] = array(
        'type_name' => $row['object_type'],
        'uniquename' => $row['object_name'],
        'id' => $row['object_id'],
      );
    }
    else {
      $return_array[$row['object_id']] = array(
        'type_name' => $row['object_type'],
        'uniquename' => $row['object_name'],
        'id' => $row['object_id'],
      );
    }
  }

  if (!empty($return_array)) {
    return $return_array;
  }
  else {
    return FALSE;
  }
}

function icbasic_write_fastafile($infile = NULL, $outfile = NULL, $delete = NULL) {
  if (empty($infile) || empty($outfile)) {
    return FALSE;
  }
  // OS compatibility
  ini_set('auto_detect_line_endings', TRUE);

  /* Decided against this as it would slow it and
   $seq_chars='';
   //$prots='/\W+/';
   // allowed amino acids
   $prots='/[^xacdefghiklmnpqrstvwyBZJ]/i';
   // allowed base pairs
   $nucs='/[^xatcgURMWYKBDHVSN]/i';
   if($type=='protein'){
   $seq_chars=$prots;
   }else{
   $seq_chars=$nucs;
   }
   */



  // check outfile writability
  if (!$outhandle = fopen($outfile, 'wt')) {
    drupal_set_message(t("Could not create $outfile."), 'error');
    return FALSE;
  }
  // read infile and store in outfile as we go along
  if (file_exists($infile)) {
    if ($inhandle = fopen($infile, 'rb')) {
      while (!feof($inhandle)) {
        $line = trim(fgets($inhandle));
        if (!empty($line)) {
          $defline = strpos($line, '>');
          if ($defline !== FALSE) {
            // '>' char does not begin at the begining. delete anything before it
            if ($defline > 0) {
              $line = substr($line, $defline);
            }
          }
          //else{
          //too slow: $line=preg_replace($seq_chars,'',$line);
          //}
          if (!empty($line)) {
            // CAUTION: UNIX only but translated into windows with t flag in fopen
            $data = $line ."\n";
            fwrite($outhandle, $data);
          }
        }
      }
      fclose($inhandle);
    }
  }
  elseif (!empty($infile)) {
    //$infile is a string
    $seq_array = explode("\r", $infile);
    foreach ($seq_array as $line) {
      $line = trim($line);
      if (!empty($line)) {
        $defline = strpos($line, '>');
        if ($defline !== FALSE) {
          if ($defline > 0) {
            $line = substr($line, $defline);
          }
        }
        //else{
        // $line=preg_replace($seq_chars,'',$line);
        //}
        if (!empty($line)) {
          $data = $line ."\n";
          fwrite($outhandle, $data);
        }
      }
    }
  }
  else {
    drupal_set_message(t("Could not find any input data for writing the FASTA."), 'error');
  }

  fclose($outhandle);
  if (!empty($delete) && $delete === TRUE && file_exists($infile)) {
    file_delete($infile);
  }
  return TRUE;
}

---