tripal/tripal_featuremap/tripal_featuremap.install

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

/**
 * Implementation of hook_install().
 *
 * @ingroup tripal_featuremap
 */
function tripal_featuremap_install() {
  // create the module's data directory
  tripal_create_moddir('tripal_featuremap');

  // create the tables that correlate drupal nodes with chado
  // features, maps, etc....
  drupal_install_schema('tripal_featuremap');
  
  // add the featuremapprop table to Chado
  tripal_featuremap_add_custom_tables();
  
  // Add cvterms
  tripal_featuremap_add_cvterms();

}

/**
 * Implementation of hook_schema().
 *
 * @ingroup tripal_featuremap
 */
function tripal_featuremap_schema() {
  $schema = tripal_featuremap_get_schemas();
  return $schema;
}

/**
 * Implementation of hook_uninstall().
 *
 * @ingroup tripal_featuremap
 */
function tripal_featuremap_uninstall() {
  drupal_uninstall_schema('tripal_featuremap');

  // Get the list of nodes to remove
  $sql_lib_id = "SELECT nid, vid ".
                "FROM {node} ".
                "WHERE type='chado_featuremap'";
  $result = db_query($sql_lib_id);
  while ($node = db_fetch_object($result)) {
    node_delete($node->nid);
  }
}

/**
 * This function simply defines all tables needed for the module to work
 * correctly.  By putting the table definitions in a separate function we
 * can easily provide the entire list for hook_install or individual
 * tables for an update.
 *
 * @ingroup tripal_featuremap
 */
function tripal_featuremap_get_schemas() {
  $schema = array();
  $schema['chado_featuremap'] = 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
      ),
      'featuremap_id' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0
        )
      ),
      'indexes' => array(
        'featuremap_id' => array('featuremap_id')
      ),
      'unique keys' => array(
        'nid_vid' => array('nid', 'vid'),
        'vid' => array('vid')
      ),
      'primary key' => array('nid'),
  );
  return $schema;
}

/**
 * Implementation of hook_requirements(). 
 */
function tripal_featuremap_requirements($phase) {
  $requirements = array();
  if ($phase == 'install') {
    // make sure chado is installed
    if (!tripal_core_is_chado_installed()) {
      $requirements ['tripal_featuremap'] = array(
            'title' => "tripal_featuremap",
            'value' => "ERROR: Chado most be installed before this module can be enabled",
            'severity' => REQUIREMENT_ERROR,
      );
    }
  }
  return $requirements;
}

/*
 * 
 */
function tripal_featuremap_add_cvterms() {
  
   // add cvterms for the map unit types
   tripal_cv_add_cvterm(array('name' => 'cM','def' => 'Centimorgan units'), 
     'featuremap_units', 0, 1, 'tripal');
   tripal_cv_add_cvterm(array('name' => 'bp','def' => 'Base pairs units'), 
     'featuremap_units', 0, 1, 'tripal');
   tripal_cv_add_cvterm(array('name' => 'bin_unit','def' => 'The bin unit'), 
     'featuremap_units', 0, 1, 'tripal');   
   tripal_cv_add_cvterm(array('name' => 'marker_order','def' => 'Units simply to define marker order.'), 
     'featuremap_units', 0, 1, 'tripal');
   tripal_cv_add_cvterm(array('name' => 'undefined','def' => 'A catch-all for an undefined unit type'), 
     'featuremap_units', 0, 1, 'tripal');
   
   tripal_cv_add_cvterm(array('name' => 'start','def' => 'The start coordinate for a map feature.'), 
     'featurepos_property', 0, 1, 'tripal');
   tripal_cv_add_cvterm(array('name' => 'stop','def' => 'The end coordinate for a map feature'), 
     'featurepos_property', 0, 1, 'tripal');
   
   // add cvterms for map properties
   tripal_cv_add_cvterm(array('name' => 'Map Dbxref','def' => 'A unique identifer for the map in a remote database.  The format is a database abbreviation and a unique accession separated by a colon.  (e.g. Gramene:tsh1996a)'), 
     'featuremap_property', 0, 1, 'tripal');
   tripal_cv_add_cvterm(array('name' => 'Map Type','def' => 'The type of Map (e.g. QTL, Physical, etc.)'), 
     'featuremap_property', 0, 1, 'tripal');
   tripal_cv_add_cvterm(array('name' => 'Genome Group','def' => ''), 
     'featuremap_property', 0, 1, 'tripal');
   tripal_cv_add_cvterm(array('name' => 'URL','def' => 'A univeral resource locator (URL) reference where the publication can be found.  For maps found online, this would be the web address for the map.'), 
     'featuremap_property', 0, 1, 'tripal');
   tripal_cv_add_cvterm(array('name' => 'Population Type','def' => 'A brief descriptoin of the population type used to generate the map (e.g. RIL, F2, BC1, etc).'), 
     'featuremap_property', 0, 1, 'tripal');
   tripal_cv_add_cvterm(array('name' => 'Population Size','def' => 'The size of the population used to construct the map.'), 
     'featuremap_property', 0, 1, 'tripal');
   tripal_cv_add_cvterm(array('name' => 'Methods','def' => 'A brief description of the methods used to construct the map.'), 
     'featuremap_property', 0, 1, 'tripal');
   tripal_cv_add_cvterm(array('name' => 'Software','def' => 'The software used to construct the map.'), 
     'featuremap_property', 0, 1, 'tripal');

}

/*
 * 
 */
function tripal_featuremap_add_custom_tables(){
  // add the featuremaprop table to Chado
  $schema = array (
    'table' => 'featuremapprop',
    'fields' => array (
      'featuremapprop_id' => array (
        'type' => 'serial',
        'not null' => true,
      ),
      'featuremap_id' => array (
        'type' => 'int',
        'not null' => true,
      ),
      'type_id' => array (
        'type' => 'int',
        'not null' => true,
      ),
      'value' => array (
        'type' => 'text',
        'not null' => false,
      ),
      'rank' => array (
        'type' => 'int',
        'not null' => true,
        'default' => 0,
      ),
    ),
    'primary key' => array (
      0 => 'featuremapprop_id',
    ),
    'unique keys' => array (
      'featuremapprop_c1' => array (
        0 => 'featuremap_id',
        1 => 'type_id',
        2 => 'rank',
      ),
    ),
    'indexes' => array (
      'featuremapprop_idx1' => array (
        0 => 'featuremap_id',
      ),
      'featuremapprop_idx2' => array (
        0 => 'type_id',
      ),
    ),
    'foreign keys' => array (
      'cvterm' => array (
        'table' => 'cvterm',
        'columns' => array (
          'type_id' => 'cvterm_id',
        ),
      ),
      'featuremap' => array (
        'table' => 'featuremap',
        'columns' => array (
          'featuremap_id' => 'featuremap_id',
        ),
      ),
    ),
  );  
  tripal_core_create_custom_table($ret, 'featuremapprop', $schema, TRUE);
  
  // add the featuremap_dbxref table to Chado
  $schema = array (
    'table' => 'featuremap_dbxref',
    'fields' => array (
      'featuremap_dbxref_id' => array (
        'type' => 'serial',
        'not null' => true,
      ),
      'featuremap_id' => array (
        'type' => 'int',
        'not null' => true,
      ),
      'dbxref_id' => array (
        'type' => 'int',
        'not null' => true,
      ),
    ),
    'primary key' => array (
      0 => 'featuremap_dbxref_id',
    ),
    'unique keys' => array (
      'featuremap_dbxref_c1' => array (
        0 => 'featuremap_id',
        1 => 'dbxref_id',
      ),
    ),
    'indexes' => array (
      'featuremap_dbxref_idx1' => array (
        0 => 'featuremap_dbxref_id',
      ),
      'featuremap_dbxref_idx2' => array (
        0 => 'dbxref_id',
      ),
    ),
    'foreign keys' => array (
      'dbxref' => array (
        'table' => 'dbxref',
        'columns' => array (
          'dbxref_id' => 'dbxref_id',
        ),
      ),
      'featuremap' => array (
        'table' => 'featuremap',
        'columns' => array (
          'featuremap_id' => 'featuremap_id',
        ),
      ),
    ),
    'referring_tables' => NULL,
  );
  tripal_core_create_custom_table($ret, 'featuremap_dbxref', $schema, TRUE);
  
  $schema = array (
    'table' => 'featureposprop',
    'fields' => array (
      'featureposprop_id' => array (
        'type' => 'serial',
        'not null' => true,
      ),
      'featurepos_id' => array (
        'type' => 'int',
        'not null' => true,
      ),
      'type_id' => array (
        'type' => 'int',
        'not null' => true,
      ),
      'value' => array (
        'type' => 'text',
        'not null' => false,
      ),
      'rank' => array (
        'type' => 'int',
        'not null' => true,
        'default' => 0,
      ),
    ),
    'primary key' => array (
      0 => 'featureposprop_id',
    ),
    'unique keys' => array (
      'featureposprop_id' => array (
        0 => 'featurepos_id',
        1 => 'type_id',
        2 => 'rank',
      ),
    ),
    'indexes' => array (
      'featureposprop_c1' => array (
        0 => 'featurepos_id',
      ),
      'featureposprop_idx2' => array (
        0 => 'type_id',
      ),
    ),
    'foreign keys' => array (
      'cvterm' => array (
        'table' => 'cvterm',
        'columns' => array (
          'type_id' => 'cvterm_id',
        ),
      ),
      'featurepos' => array (
        'table' => 'featurepos',
        'columns' => array (
          'featurepos_id' => 'featurepos_id',
        ),
      ),
    ),
  );
  tripal_core_create_custom_table($ret, 'featureposprop', $schema, TRUE);
}

/**
 *  Update for Drupal 6.x, Tripal 1.1, FeatureMap Module 1.1
 *  This update adds a new featuremapprop, featureposprop, and featuremap_dbxref tables and 
 *  CV terms for the featuremap_property CV
 *
 */
function tripal_featuremap_update_6100() {

  tripal_featuremap_add_custom_tables();  
  tripal_featuremap_add_cvterms();
   
  $ret = array(
    '#finished' => 1,
  );

  return $ret;
}