tripal/tripal_analysis/tripal_analysis.install

<?php
/**
 * @file
 * @todo Add file header description
 */

/*******************************************************************************
 * Implementation of hook_install().
 */
function tripal_analysis_install() {

  // create the module's data directory
  tripal_create_moddir('tripal_analysis');

  // Use schema API to create database table.
  drupal_install_schema('tripal_analysis');

  // Create analysisfeatureprop table in chado. This cannot be accomplished
  // by calling drupal_install_schema because it's not in the drupal db. This
  // table is used to store Blast xml and Interpro html/goterms
  $previous_db = tripal_db_set_active('chado');
  if (!db_table_exists('analysisfeatureprop')) {
    $sql = "CREATE TABLE {analysisfeatureprop} (".
            "  analysisfeatureprop_id SERIAL PRIMARY KEY, ".
            "  analysisfeature_id INTEGER NOT NULL REFERENCES analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, ".
            "  type_id INTEGER NOT NULL REFERENCES cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, ".
            "  value TEXT, ".
            "  rank INTEGER NOT NULL, ".
            "  CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank)".
            ")";
    db_query($sql);
  }
  tripal_db_set_active($previous_db);

  tripal_cv_add_cvterm(array('name' => 'analysis_type', 'def' => 'The type of analysis was performed. This value is automatically set by each Tripal Analysis module and should be equal to the module name (e.g. tripal_analysis_blast, tripal_analysis_go).'), 'tripal', 0, 1, 'tripal');
  tripal_cv_add_cvterm(array('name' => 'analysis_date', 'def' => 'The date that an analysis was performed.'), 'tripal', 0, 1, 'tripal');
  tripal_cv_add_cvterm(array('name' => 'analysis_short_name', 'def' => 'A computer legible (no spaces ' .
      'or special characters) abbreviation for the analysis.'), 'tripal', 0, 1 , 'tripal');
}

/*******************************************************************************
 * Implementation of hook_uninstall().
 */
function tripal_analysis_uninstall() {
  // Use schema API to delete database table.
  drupal_uninstall_schema('tripal_analysis');
  // Remove analysis nodes from drupal.
  $sql_ana_id = "SELECT nid, vid ".
                 "FROM {node} ".
                 "WHERE type like 'chado_analysi%'";
  $result = db_query($sql_ana_id);
  while ($ana = db_fetch_object($result)) {
    node_delete($ana->nid);
  }
}

/*******************************************************************************
 * Implementation of hook_schema() creates two tables. chado_analysis table
 * stores nodes that are also saved in the analysis table of chado database.
 * tripal_analysis table stores the sub-module names, such as
 * tripal_analysis_blast, that are registered with this module.
 */
function tripal_analysis_schema() {
  // chado_analysis table
  $schema['chado_analysis'] = array(
      'fields' => array(
         'vid' => array(
            'type' => 'int',
            'unsigned' => TRUE,
            'not null' => TRUE,
            'default' => 0
  ),
         'nid' => array(
            'type' => 'int',
            'unsigned' => TRUE,
            'not null' => TRUE,
            'default' => 0
  ),
         'analysis_id' => array(
            'type' => 'int',
            'not null' => TRUE,
            'default' => 0
  )
  ),
      'indexes' => array(
         'analysis_id' => array('analysis_id')
  ),
      'unique keys' => array(
         'nid_vid' => array('nid', 'vid'),
         'vid' => array('vid')
  ),
      'primary key' => array('nid'),
  );

  // tripal_analysis table
  $schema['tripal_analysis'] = array(
      'description' => t('Table to store analysis sub-modules'),
      'fields' => array(
         'modulename' => array(
            'type' => 'text',
            'size' => 'small',
            'not null' => TRUE,
            'description' => t('The module name. Tripal Analysis will use the '.
                               'module name to call module_setting_form()')
  )
  ),
      'unique keys' => array(
         'modulename' => array('modulename')
  )
  );
  return $schema;
}

/*******************************************************************************
 * Implementation of hook_requirements(). Make sure 'Tripal Core' is enabled
 * before installation
 */
function tripal_analysis_requirements($phase) {
  $requirements = array();
  if ($phase == 'install') {
    if (!function_exists('tripal_create_moddir')) {
      $requirements ['tripal_analysis'] = array(
            'title' => "tripal_analysis",
            'value' => "error. Some required modules are just being installed. Please try again.",
            'severity' => REQUIREMENT_ERROR,
      );
      }
  }
  return $requirements;
}

/*******************************************************************************
 * Provide update script for adding new cvterms
 */
function tripal_analysis_update_6001() {
   // we have some new cvterms to add
  tripal_cv_add_cvterm(array('name' => 'based_on_analysis', 'def' => 'The analysis that this analysis was based on. For example, blast/kegg/interpro analyses are based on a unigene analysis. The unigene analysis_id should be stored in analysisprop as the rank using this cvterm. The name of said unigene analysis can be inserted as the value in analysisprop.'), 'tripal', 0, 1, 'tripal');
  tripal_cv_add_cvterm(array('name' => 'additional_files', 'def' => 'Additional files for this analysis. Each file should be separated by a semi-colon and have this format: <file description>, <file path>;'), 'tripal', 0, 1, 'tripal');
  $ret = array(
      '#finished' => 1,
  );
  return $ret;
}