function tripal_core_install_chado

2.x tripal_core.chado_install.inc tripal_core_install_chado($action)
1.x chado_install.inc tripal_core_install_chado($action)

Install Chado Schema

Related topics

Tripal Core Module
2 string references to 'tripal_core_install_chado'
tripal_core_chado_load_form_submit in tripal_core/includes/chado_install.inc
Submit Load Chado Schema 1.11 Form
tripal_core_job_describe_args in tripal_core/tripal_core.module
Implements hook_job_describe_args(). Describes the arguements for the tripal_update_mview job to allow for greater readability in the jobs details pages.

File

tripal_core/includes/chado_install.inc, line 80
Functions to install chado schema through Drupal

Code

function tripal_core_install_chado($action) {

  $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'), " .
    "'%s') ";

  if ($action == 'Install Chado v1.2') {
    $schema_file = drupal_get_path('module', 'tripal_core') . '/chado_schema/default_schema-1.2.sql';
    $init_file = drupal_get_path('module', 'tripal_core') . '/chado_schema/initialize-1.2.sql';
    if (tripal_core_reset_chado_schema()) {
      $success = tripal_core_install_sql($schema_file);
      if ($success) {
        print "Install of Chado v1.2 (Step 1 of 2) Successful!\n";
      }
      else {
        print "Installation (Step 1 of 2) Problems!  Please check output above for errors.\n";
        exit;
      }
      $success = tripal_core_install_sql($init_file);
      if ($success) {
        print "Install of Chado v1.2 (Step 2 of 2) Successful.\nInstallation Complete\n";
      }
      else {
        print "Installation (Step 2 of 2) Problems!  Please check output above for errors.\n";
        exit;
      }
      chado_query($vsql, '1.2'); # set the version
    }
    else {
      print "ERROR: cannot install chado.  Please check database permissions\n";
      exit;
    }
  }
  elseif ($action == 'Upgrade Chado v1.11 to v1.2') {
    $schema_file = drupal_get_path('module', 'tripal_core') . '/chado_schema/default_schema-1.11-1.2-diff.sql';
    $init_file = drupal_get_path('module', 'tripal_core') . '/chado_schema/upgrade-1.11-1.2.sql';
    $success = tripal_core_install_sql($schema_file);
    if ($success) {
      print "Upgrade from v1.11 to v1.2 (Step 1 of 2) Successful!\n";
    }
    else {
      print "Upgrade (Step 1 of 2) problems!  Please check output above for errors.\n";
      exit;
    }
    $success = tripal_core_install_sql($init_file);
    if ($success) {
      print "Upgrade from v1.11 to v1.2 (Step 2 of 2) Successful.\nUpgrade Complete!\n";
    }
    else {
      print "Upgrade (Step 2 of 2) problems!  Please check output above for errors.\n";
      exit;
    }
    chado_query($vsql, '1.2'); # set the version
  }
  elseif ($action == 'Install Chado v1.11') {
    $schema_file = drupal_get_path('module', 'tripal_core') . '/chado_schema/default_schema-1.11.sql';
    $init_file = drupal_get_path('module', 'tripal_core') . '/chado_schema/initialize-1.11.sql';
    if (tripal_core_reset_chado_schema()) {
      $success = tripal_core_install_sql($schema_file);
      if ($success) {
        print "Install of Chado v1.11 (Step 1 of 2) Successful!\n";
      }
      else {
        print "Installation (Step 1 of 2) Problems!  Please check output above for errors.\n";
        exit;
      }
      $success = tripal_core_install_sql($init_file);
      if ($success) {
        print "Install of Chado v1.11 (Step 2 of 2) Successful.\nInstallation Complete!\n";
      }
      else {
        print "Installation (Step 2 of 2) Problems!  Please check output above for errors.\n";
        exit;
      }
    }
    else {
      print "ERROR: cannot install chado.  Please check database permissions\n";
      exit;
    }
  }
}