tripal/tripal_chado/includes/tripal_chado.install.inc

<?php
/**
 * @file
 * Functions to install chado schema through Drupal
 */

/**
 * Load Chado Schema Form
 *
 * @ingroup tripal_chado
 */
function tripal_chado_load_form($form, $form_state) {

  // we want to force the version of Chado to be set properly
  $real_version = chado_get_version(TRUE);

  // get the effective version.  Pass true as second argument
  // to warn the user if the current version is not compatible
  $version = chado_get_version(FALSE, TRUE);

  if (array_key_exists('values', $form_state)) {
    if ($form_state['values']['action_to_do'] == "Upgrade Chado v1.2 to v1.3") {
      $tables_list = implode(', ', [
        'analysis_cvterm',
        'analysis_dbxref',
        'analysis_pub',
        'analysis_relationship',
        'contactprop',
        'dbprop',
        'feature_contact',
        'featuremap_contact',
        'featuremap_dbxref',
        'featuremap_organism',
        'featuremapprop',
        'featureposprop',
        'library_contact',
        'library_expression',
        'library_expressionprop',
        'library_featureprop',
        'library_relationship',
        'library_relationship_pub',
        'nd_experiment_analysis',
        'organism_cvterm',
        'organism_cvtermprop',
        'organism_pub',
        'organism_relationship',
        'organismprop_pub',
        'phenotypeprop',
        'phylotreeprop',
        'project_analysis',
        'project_dbxref',
        'project_feature',
        'project_stock',
        'pubauthor_contact',
        'stock_feature',
        'stock_featuremap',
        'stock_library',
        'stockcollection_db',
      ]);
      $items = [
        'PostgreSQL version 9.5 is required to perform this upgrade. If your Tripal
         site uses an older version please upgrade before proceeding.',
        'A major change between Chado v1.2 and v1.3 is that primary and foreign
         keys were upgraded from integers to big integers. If your site has custom
         materialized views that will hold data derived from fields changed to
         big integers then you may need to alter the views to change the fields
         from integers to big integers and repopulate those views. If you have not
         added any materialized views you can ignore this issue.',
        'Custom PL/pgSQL functions that expect primary and
         foreign key fields to be integers will not work after the upgrade.
         Those functions will need to be altered to accept big integers. If you
         do not have any custom PL/pgSQL functions you can ignore this issue.',
        'PostgreSQL Views that use fields that are converted to big
         integers will cause this upgrade to fail.  You must first remove
         those views, perform the upgrade and then recreate them with the
         appropriate fields change to big integers. If you do not have custom
         PostgreSQL Views you can ignore this issue.',
        'Several new tables were added to Chado v1.3.  However, some groups have
         added these tables to their Chado v1.2 installation.  The Tripal upgrader
         will alter the primary and foreign keys of those tables to be "bigints"
         if they already exist but will otherwise leave them the same.  You should
         verify that any tables with Chado v1.3 names correctly match the v1.3 schema.
         Otherwise you may have problems using Tripal. If you have not added any
         Chado v1.3 tables to your Chado v1.2 database you can ignore this issue.
         These are the newly added tables:  ' .
        $tables_list . '.',
      ];
      $list = theme_item_list([
        'items' => $items,
        'title' => '',
        'type' => 'ul',
        'attributes' => [],
      ]);
      drupal_set_message('Please note: the upgrade of Chado from v1.2 to v1.3 may
          require several fixes to your database. Please review the following
          list to ensure a safe upgrade. The Tripal upgrader is
          not able to fix these problems automatically: ' . $list, 'warning');
    }
    if ($form_state['values']['action_to_do'] == "Install Chado v1.3" or
      $form_state['values']['action_to_do'] == "Install Chado v1.2" or
      $form_state['values']['action_to_do'] == "Install Chado v1.11") {
      drupal_set_message('Please note: if Chado is already installed it will
          be removed and recreated and all data will be lost. If this is
          desired or if this is the first time Chado has been installed
          you can ignore this issue.', 'warning');
    }
  }

  $form['current_version'] = [
    '#type' => 'item',
    '#title' => t("Current installed version of Chado:"),
    '#description' => $real_version,
  ];

  $form['action_to_do'] = [
    '#type' => 'select',
    '#title' => 'Installation/Upgrade Action',
    '#options' => [
      'Install Chado v1.3' => t('New Install of Chado v1.3 (erases all existing Chado data if Chado already exists)'),
      'Upgrade Chado v1.2 to v1.3' => t('Upgrade existing Chado v1.2 to v1.3 (no data is lost)'),
      'Install Chado v1.2' => t('New Install of Chado v1.2 (erases all existing Chado data if Chado already exists)'),
      'Upgrade Chado v1.11 to v1.2' => t('Upgrade existing Chado v1.11 to v1.2 (no data is lost)'),
      'Install Chado v1.11' => t('New Install of Chado v1.11 (erases all existing Chado data if Chado already exists)'),
    ],
    '#description' => t('Select an action to perform.'),
    '#required' => TRUE,
    '#ajax' => [
      'callback' => "tripal_chado_load_form_ajax_callback",
      'wrapper' => 'tripal_chado_load_form',
      'effect' => 'fade',
      'method' => 'replace',
    ],
  ];

  $form['button'] = [
    '#type' => 'submit',
    '#value' => t('Install/Upgrade Chado'),
  ];

  $form['#prefix'] = '<div id="tripal_chado_load_form">';
  $form['#suffix'] = '</div>';
  return $form;
}

/**
 * Ajax callback function for the gensas_job_view_panel_form.
 *
 * @param $form
 * @param $form_state
 */
function tripal_chado_load_form_ajax_callback($form, $form_state) {

  return $form;
}

function tripal_chado_load_form_validate($form, &$form_state) {
  // We do not want to allow re-installation of Chado if other
  // Tripal modules are installed.  This is because the install files
  // of those modules may add content to Chado and reinstalling Chado
  // removes that content which may break the modules.
  if ($form_state['values']['action_to_do'] == "Install Chado v1.3" or
    $form_state['values']['action_to_do'] == "Install Chado v1.2" or
    $form_state['values']['action_to_do'] == "Install Chado v1.11") {

    $modules = system_get_info('module');
    // The tripal_chado_views module should not be included as it's a required
    // dependency of tripal_chado
    unset($modules['tripal_chado_views']);
    $list = [];
    foreach ($modules as $mname => $module) {
      if (array_key_exists('dependencies', $module) and in_array('tripal_chado', $module['dependencies'])) {
        $list[] = $module['name'] . " ($mname)";
      }
    }
    if (count($list) > 0) {
      form_set_error("action_to_do", "Chado cannot be installed while other Tripal modules
          are enabled.  You must fully uninstall the following modules if you
          would like to install or re-install chado.<br>" .
        implode("<br>", $list));
    }
  }
  if ($form_state['values']['action_to_do'] == "Upgrade Chado v1.11 to v1.2") {
    // Make sure we are already not at v1.2
    $real_version = chado_get_version(TRUE);
    if ($real_version == "1.2") {
      form_set_error("action_to_do", "You are already at v1.2.  There is no need to upgrade.");
    }
  }
  if ($form_state['values']['action_to_do'] == "Upgrade Chado v1.2 to v1.3") {
    // Make sure we are already not at v1.3
    $real_version = chado_get_version(TRUE);
    if ($real_version == "1.3") {
      form_set_error("action_to_do", "You are already at v1.3.  There is no need to upgrade.");
    }
  }
}

/**
 * Submit Load Chado Schema Form
 *
 * @ingroup tripal_chado
 */
function tripal_chado_load_form_submit($form, &$form_state) {
  global $user;
  $action_to_do = trim($form_state['values']['action_to_do']);
  $args = [$action_to_do];

  $includes = [module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.install')];
  tripal_add_job($action_to_do, 'tripal_chado',
    'tripal_chado_install_chado', $args, $user->uid, 10, $includes);
}

/**
 * Submit Load Chado Schema Form
 *
 * @ingroup tripal_chado
 */
function tripal_chado_load_drush_submit($version) {
  $args = [$version];
  $includes = [module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.install')];
  tripal_add_job($version, 'tripal_chado',
    'tripal_chado_install_chado', $args, 1, 10, $includes);
}

/**
 * Install Chado Schema
 *
 * @ingroup tripal_chado
 */
function tripal_chado_install_chado($action, TripalJob $job = NULL) {

  $vsql = "
    INSERT INTO {chadoprop} (type_id, value)
      VALUES (
       (SELECT cvterm_id
        FROM {cvterm} CVT
          INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
         WHERE CV.name = 'chado_properties' AND CVT.name = 'version'),
       :version)
  ";

  $vusql = "
    UPDATE {chadoprop}
    SET value = :version
    WHERE type_id = (SELECT cvterm_id
        FROM {cvterm} CVT
          INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
         WHERE CV.name = 'chado_properties' AND CVT.name = 'version')
  ";

  $transaction = db_transaction();
  try {
    if ($action == 'Install Chado v1.3') {
      tripal_chado_install_chado_1_3();
      chado_query($vsql, [':version' => '1.3']);
    }
    elseif ($action == 'Upgrade Chado v1.2 to v1.3') {
      tripal_chado_upgrade_chado_1_2_to_1_3();
      chado_query($vusql, [':version' => '1.3']);
    }
    elseif ($action == 'Install Chado v1.2') {
      tripal_chado_install_chado_1_2();
      chado_query($vsql, [':version' => '1.2']);
    }
    elseif ($action == 'Upgrade Chado v1.11 to v1.2') {
      tripal_chado_upgrade_chado_1_11_to_1_2();
      chado_query($vsql, [':version' => '1.2']);
    }
    elseif ($action == 'Install Chado v1.11') {
      tripal_chado_install_chado_1_11();
    }
  } catch (Exception $e) {
    $transaction->rollback();
    tripal_chado_install_done();
    tripal_report_error('tripal_chado', TRIPAL_ERROR, $e->getMessage(), ['print' => TRUE]);
    return FALSE;
  }
  return TRUE;


}

/**
 * Installs Chado v1.3.
 */
function tripal_chado_install_chado_1_3(TripalJob $job = NULL) {
  // Get the path to the schema and init SQL files.
  $schema_file = drupal_get_path('module', 'tripal_chado') .
    '/chado_schema/default_schema-1.3.sql';
  $init_file = drupal_get_path('module', 'tripal_chado') .
    '/chado_schema/initialize-1.3.sql';

  // Erase the Chado schema if it exists and perform the install.
  if (tripal_chado_reset_chado_schema()) {
    $success = tripal_chado_install_sql($schema_file);
    if ($success) {
      print "Install of Chado v1.3 (Step 1 of 2) Successful!\n";
    }
    else {
      throw new Exception("Installation (Step 1 of 2) Problems!  Please check output above for errors.");
    }
    $success = tripal_chado_install_sql($init_file);
    if ($success) {
      print "Install of Chado v1.3 (Step 2 of 2) Successful.\nInstallation Complete\n";
    }
    else {
      throw new Exception("Installation (Step 2 of 2) Problems!  Please check output above for errors.");
    }
  }
  else {
    throw new Exception("ERROR: cannot install chado.  Please check database permissions");
  }
}

/**
 * Installs Chado v1.2.
 */
function tripal_chado_install_chado_1_2() {
  // Get the path to the schema and init SQL files.
  $schema_file = drupal_get_path('module', 'tripal_chado') .
    '/chado_schema/default_schema-1.2.sql';
  $init_file = drupal_get_path('module', 'tripal_chado') .
    '/chado_schema/initialize-1.2.sql';

  // Erase the Chado schema if it exists and perform the install.
  if (tripal_chado_reset_chado_schema()) {
    $success = tripal_chado_install_sql($schema_file);
    if ($success) {
      print "Install of Chado v1.2 (Step 1 of 2) Successful!\n";
    }
    else {
      throw new Exception("Installation (Step 1 of 2) Problems!  Please check output above for errors.");
    }
    $success = tripal_chado_install_sql($init_file);
    if ($success) {
      print "Install of Chado v1.2 (Step 2 of 2) Successful.\nInstallation Complete\n";
    }
    else {
      throw new Exception("Installation (Step 2 of 2) Problems!  Please check output above for errors.");
    }
  }
  else {
    throw new Exception("ERROR: cannot install chado.  Please check database permissions");
  }
}

/**
 *
 */
function tripal_chado_install_chado_1_11() {

  // Get the path to the schema and init SQL files.
  $schema_file = drupal_get_path('module', 'tripal_chado') .
    '/chado_schema/default_schema-1.11.sql';
  $init_file = drupal_get_path('module', 'tripal_chado') .
    '/chado_schema/initialize-1.11.sql';

  // Erase the Chado schema if it exists and perform the install.
  if (tripal_chado_reset_chado_schema()) {
    $success = tripal_chado_install_sql($schema_file);
    if ($success) {
      print "Install of Chado v1.11 (Step 1 of 2) Successful!\n";
    }
    else {
      throw new Exception("Installation (Step 1 of 2) Problems!  Please check output above for errors.");
    }
    $success = tripal_chado_install_sql($init_file);
    if ($success) {
      print "Install of Chado v1.11 (Step 2 of 2) Successful.\nInstallation Complete!\n";
    }
    else {
      throw new Exception("Installation (Step 2 of 2) Problems!  Please check output above for errors.");
    }
  }
  else {
    throw new Exception("ERROR: cannot install chado.  Please check database permissions");
  }
}

/**
 * Upgrades Chado from v1.2 to v1.3
 */
function tripal_chado_upgrade_chado_1_2_to_1_3() {

  // Upgrade some of the custom tables that Tripal created that are now in
  // Chado v1.3.  We'll do this ahead of time because the upgrade script won't
  // upgrade tables if they already exist.
  print "Checking for existing v1.3 tables in v1.2 and fixing bigints...\n";
  tripal_chado_upgrade_chado_1_2_to_1_3_pre_alter();

  // Get the path to the diff schema and upgrade SQL files.
  print "Incorporating additional changes...\n";
  $diff_file = drupal_get_path('module', 'tripal_chado') .
    '/chado_schema/default_schema-1.2-1.3-diff.sql';

  $success = tripal_chado_install_sql($diff_file);
  if ($success) {
    print "Upgrade from v1.2 to v1.3 Successful!\n";
  }
  else {
    throw new Exception("Upgrade problems!  Please check output above for errors.");
  }
}

/**
 * Upgrade custom tables that may match the tables now in Chado v1.3.
 *
 * There were many new tables that were added to Chado v1.3 that were
 * suggested by the Chado user community.  Some of those were Tripal users.
 * Therefore, to help these Tripal users upgrade more seemlessly this function
 * checks if those custom tables already exists, and if so updates them as
 * best it can to match.  At a minimum it will create the table if it doesn't
 * exist and if it does it will change the primary keys and foreign keys to
 * be big ints.
 */
function tripal_chado_upgrade_chado_1_2_to_1_3_pre_alter() {

  // Include the Chado v1.3 schema definitions.
  module_load_include('inc', 'tripal_chado', '/api/tripal_chado.schema_v1.3.api');

  // The list of new tables in Chado v1.3
  $new_tables = [
    'analysis_cvterm',
    'analysis_dbxref',
    'analysis_pub',
    'analysis_relationship',
    'contactprop',
    'dbprop',
    'feature_contact',
    'featuremap_contact',
    'featuremap_dbxref',
    'featuremap_organism',
    'featuremapprop',
    'featureposprop',
    'library_contact',
    'library_expression',
    'library_expressionprop',
    'library_featureprop',
    'library_relationship',
    'library_relationship_pub',
    'nd_experiment_analysis',
    'organism_cvterm',
    'organism_cvtermprop',
    'organism_pub',
    'organism_relationship',
    'organismprop_pub',
    'phenotypeprop',
    'phylotreeprop',
    'project_analysis',
    'project_dbxref',
    'project_feature',
    'project_stock',
    'pubauthor_contact',
    'stock_feature',
    'stock_featuremap',
    'stock_library',
    'stockcollection_db',
  ];

  // Get the name of the chado schema.
  $chado_schema = chado_get_schema_name('chado');

  // Iterate through the new Chado tables and create them or if they already
  // exist then update them.
  foreach ($new_tables as $table) {

    // Get the schema for this table.
    $function = 'tripal_chado_chado_schema_v1_3_' . $table;
    $schema = $function();

    // If the table exists then fix the pkeys and fkeys.
    if (chado_table_exists($table)) {

      // Update the primary key fields to be bigints.
      $fields = $schema['fields'];
      foreach ($fields as $field_name => $field) {
        if ($field['type'] == 'serial') {
          if (chado_column_exists($table, $field_name)) {
            $sql = 'ALTER TABLE {' . $table . '} ALTER COLUMN ' . $field_name . ' TYPE bigint';
            chado_query($sql);
          }
          else {
            throw new Exception('Could not alter primary key to bigint: ' . $table . '.' . $field_name);
          }
        }
      }

      // Update the foreign key fields to be bigints.
      $fkeys = $schema['foreign keys'];
      foreach ($fkeys as $fktable => $details) {
        foreach ($details['columns'] as $leftkey => $rightkey) {
          if (chado_column_exists($table, $leftkey)) {
            $sql = 'ALTER TABLE {' . $table . '} ALTER COLUMN ' . $leftkey . ' TYPE bigint';
            chado_query($sql);
          }
          else {
            throw new Exception('Could not alter foreign key to bigint: ' . $table . '.' . $leftkey);
          }
        }
      }

    }
  }
}

/**
 * Upgrades Chado from v1.11 to v1.2
 */
function tripal_chado_upgrade_chado_1_11_to_1_2() {

  // Get the path to the schema diff and upgarde SQL files.
  $schema_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/default_schema-1.11-1.2-diff.sql';
  $init_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/upgrade-1.11-1.2.sql';

  $success = tripal_chado_install_sql($schema_file);
  if ($success) {
    print "Upgrade from v1.11 to v1.2 (Step 1 of 2) Successful!\n";
  }
  else {
    throw new Exception("Upgrade (Step 1 of 2) problems!  Please check output above for errors.");
  }
  $success = tripal_chado_install_sql($init_file);
  if ($success) {
    print "Upgrade from v1.11 to v1.2 (Step 2 of 2) Successful.\nUpgrade Complete!\n";
  }
  else {
    throw new Exception("Upgrade (Step 2 of 2) problems!  Please check output above for errors.");
  }
}

/**
 * Reset the Chado Schema
 * This drops the current chado and chado-related schema and re-creates it
 *
 * @ingroup tripal_chado
 */
function tripal_chado_reset_chado_schema() {

  // determine the schema name.
  $chado_schema = chado_get_schema_name('chado');
  $chado_dot = $chado_schema . '.';

  // drop current chado and chado-related schema
  if (chado_dbschema_exists('genetic_code')) {
    print "Dropping existing 'genetic_code' schema\n";
    db_query("drop schema genetic_code cascade");
  }
  if (chado_dbschema_exists('so')) {
    print "Dropping existing 'so' schema\n";
    db_query("drop schema so cascade");
  }
  if (chado_dbschema_exists('frange')) {
    print "Dropping existing 'frange' schema\n";
    db_query("drop schema frange cascade");
  }
  if (chado_dbschema_exists($chado_schema)) {
    if ($chado_schema != 'chado') {
      print "Dropping existing Chado ('$chado_schema') schema\n";
    }
    else {
      print "Dropping existing 'chado' schema\n";
    }
    db_query("drop schema $chado_schema cascade");
  }

  // create the new chado schema
  print "Creating 'chado' schema\n";
  db_query("create schema $chado_schema");
  if (chado_dbschema_exists('chado')) {
    // before creating the plpgsql language let's check to make sure
    // it doesn't already exists
    $sql = "SELECT COUNT(*) FROM pg_language WHERE lanname = 'plpgsql'";
    $results = db_query($sql);
    $count = $results->fetchObject();
    if (!$count or $count->count == 0) {
      db_query("create language plpgsql");
    }
    return TRUE;
  }

  return FALSE;
}

/**
 * Execute the provided SQL
 *
 * @param $sql_file
 *   Contains SQL statements to be executed
 *
 * @ingroup tripal_chado
 */
function tripal_chado_install_sql($sql_file) {

  $chado_local = chado_dbschema_exists('chado');

  // determine the schema name.
  $chado_schema = chado_get_schema_name('chado');
  $chado_dot = $chado_schema . '.';

  if ($chado_local) {
    db_query("set search_path to $chado_schema");
  }
  print "Loading $sql_file...\n";
  $lines = file($sql_file, FILE_SKIP_EMPTY_LINES);

  if (!$lines) {
    return 'Cannot open $schema_file';
  }

  $stack = [];
  $in_string = 0;
  $in_function = FALSE;
  $query = '';
  $i = 0;
  $success = 1;
  foreach ($lines as $line_num => $line) {
    $i++;
    $type = '';
    // find and remove comments except when inside of strings
    if (preg_match('/--/', $line) and !$in_string and !preg_match("/'.*?--.*?'/", $line)) {
      $line = preg_replace('/--.*$/', '', $line);  // remove comments
    }
    if (preg_match('/\/\*.*?\*\//', $line)) {
      $line = preg_replace('/\/\*.*?\*\//', '', $line);  // remove comments
    }
    // skip empty lines
    if (preg_match('/^\s*$/', $line) or strcmp($line, '') == 0) {
      continue;
    }
    // Find SQL for new objects
    if (preg_match('/^\s*CREATE\s+TABLE/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'table';
      $line = preg_replace("/public\./", $chado_dot, $line);
    }
    if (preg_match('/^\s*ALTER\s+TABLE\s+/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'alter_table';
      $line = preg_replace("/public\./", $chado_dot, $line);
    }
    if (preg_match('/^\s*SET/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'set';
    }
    if (preg_match('/^\s*CREATE\s+SCHEMA/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'schema';
    }
    if (preg_match('/^\s*CREATE\s+SEQUENCE/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'sequence';
      $line = preg_replace("/public\./", $chado_dot, $line);
    }
    if (preg_match('/^\s*CREATE\s+(?:OR\s+REPLACE\s+)*VIEW/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'view';
      $line = preg_replace("/public\./", $chado_dot, $line);
    }
    if (preg_match('/^\s*COMMENT/i', $line) and !$in_string and sizeof($stack) == 0 and !$in_function) {
      $stack[] = 'comment';
      $line = preg_replace("/public\./", $chado_dot, $line);
    }
    if (preg_match('/^\s*CREATE\s+(?:OR\s+REPLACE\s+)*FUNCTION/i', $line) and !$in_string and !$in_function) {
      $in_function = TRUE;
      $stack[] = 'function';
      $line = preg_replace("/public\./", $chado_dot, $line);
    }
    if (preg_match('/^\s*CREATE\s+INDEX/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'index';
    }
    if (preg_match('/^\s*INSERT\s+INTO/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'insert';
      $line = preg_replace("/public\./", $chado_dot, $line);
    }
    if (preg_match('/^\s*CREATE\s+TYPE/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'type';
    }
    if (preg_match('/^\s*GRANT/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'grant';
    }
    if (preg_match('/^\s*CREATE\s+AGGREGATE/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'aggregate';
    }
    if (preg_match('/^\s*DROP\s+FUNCTION/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'drop_function';
    }
    if (preg_match('/^\s*DROP\s+VIEW/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'drop_view';
    }
    if (preg_match('/^\s*DROP\s+INDEX/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'drop_index';
    }
    if (preg_match('/^\s*DROP\s+SEQUENCE/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'drop_seq';
    }
    if (preg_match('/^\s*ALTER\s+TYPE\s+/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'alter_type';
    }
    if (preg_match('/^\s*ALTER\s+SEQUENCE\s+/i', $line) and !$in_string and !$in_function) {
      $stack[] = 'alter_seq';
    }

    // determine if we are in a string that spans a line
    $matches = preg_match_all("/[']/i", $line, $temp);
    $in_string = $in_string - ($matches % 2);
    $in_string = abs($in_string);

    // if we've reached the end of an object then pop the stack
    if (strcmp($stack[sizeof($stack) - 1], 'table') == 0 and preg_match('/\);\s*$/', $line)) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'alter_table') == 0 and preg_match('/;\s*$/', $line)) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'set') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'schema') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'sequence') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'view') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'comment') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'function') == 0) {

      if (preg_match('/LANGUAGE.*?;\s*$/i', $line)) {
        $type = array_pop($stack);
        $in_function = FALSE;
        //print "FUNCTION DONE ($i): $line";
      }
      else {
        if (preg_match('/\$_\$;\s*$/i', $line)) {
          $type = array_pop($stack);
          $in_function = FALSE;
          //print "FUNCTION DONE ($i): $line";
        }
        else {
          if (preg_match('/\$\$;\s*$/i', $line)) {
            $type = array_pop($stack);
            $in_function = FALSE;
            // print "FUNCTION DONE ($i): $line";
          }
          else {
            // print "FUNCTION ($i): $line";
          }
        }
      }
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'index') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'insert') == 0 and preg_match('/\);\s*$/', $line)) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'type') == 0 and preg_match('/\);\s*$/', $line)) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'grant') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'aggregate') == 0 and preg_match('/\);\s*$/', $line)) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'drop_function') == 0 and preg_match('/;\s*$/i', $line)) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'drop_view') == 0 and preg_match('/;\s*$/i', $line)) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'drop_index') == 0 and preg_match("/;\s*$/i", $line)) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'drop_seq') == 0 and preg_match("/;\s*$/i", $line)) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'alter_type') == 0 and preg_match('/;\s*$/i', $line)) {
      $type = array_pop($stack);
    }
    elseif (strcmp($stack[sizeof($stack) - 1], 'alter_seq') == 0 and preg_match('/;\s*$/i', $line)) {
      $type = array_pop($stack);
    }
    // if we're in a recognized SQL statement then let's keep track of lines
    if ($type or sizeof($stack) > 0) {
      $query .= "$line";
    }
    else {
      throw new Exception("UNHANDLED $i, $in_string: $line");
    }
    if (preg_match_all("/\n/", $query, $temp) > 1000) {
      throw new Exception("SQL query is too long.  Terminating:\n$query\n");
    }
    if ($type and sizeof($stack) == 0) {
      //print "Adding $type: line $i\n";
      // rewrite the set search_path to make 'public' be 'chado', but only if the
      // chado schema exists
      if (strcmp($type, 'set') == 0 and $chado_local) {
        $query = preg_replace("/public/m", $chado_schema, $query);
      }

      // execute the statement
      try {
        $result = db_query($query);
      } catch (Exception $e) {
        $error = $e->getMessage();
        throw new Exception("FAILED. Line  $i, $in_string\n$error:\n$query\n\n");
      }

      if (!$result) {
        $error = pg_last_error();
        throw new Exception("FAILED. Line  $i, $in_string\n$error:\n$query\n\n");
      }
      $query = '';
    }
  }
  tripal_chado_install_done();
  return $success;
}

/**
 * Finish the Chado Schema Installation
 *
 * @ingroup tripal_chado
 */
function tripal_chado_install_done() {

  $drupal_schema = chado_get_schema_name('drupal');
  db_query("set search_path to $drupal_schema");
}