tripal/tripal_analysis/tripal_analysis.install

<?php
/**
 * @file
 * Implements hooks from the Schema API
 */

/**
 * 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');

  // we may need the analysisfeatureprop table if it doesn't already exist
  tripal_analysis_create_analysisfeatureprop();
  
  // add cvterms
  tripal_analysis_add_cvterms();
  
  // add materialized views
  tripal_analysis_add_mview_analysis_organism();
}

/*
 * 
 */
function tripal_analysis_create_analysisfeatureprop(){
  // Create analysisfeatureprop table in chado.  This is needed for Chado 
  // version 1.11, the table exists in Chado 1.2. 
  if (!db_table_exists('analysisfeatureprop')) {
    $sql = "CREATE TABLE analysisfeatureprop (".
            "  analysisfeatureprop_id SERIAL PRIMARY KEY, ".
            "  analysisfeature_id     INTEGER NOT NULL REFERENCES analysisfeature(analysisfeature_id) " .
            "    ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, ".
            "  type_id                INTEGER NOT NULL REFERENCES cvterm(cvterm_id) ".
            "    ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, ".
            "  value                  TEXT, ".
            "  rank                   INTEGER NOT NULL, ".
            "  CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank)".
            ")";
    chado_query($sql);
  } 
}
/*
 * 
 */
function tripal_analysis_add_cvterms(){
  
  tripal_cv_add_cv('tripal_analysis', 'Terms used for managing analyses in Tripal');
  
  // add analysis_type. This goes in the 'tripal_analysis' CV so that site admins
  // change change this property
  $term = array(
    'name' => 'analysis_type', 
    'def' => 'The type of analysis was performed. This value is automatically set by '.
             'each Tripal Analysis module and should be equal to the module name '.
             '(e.g. tripal_analysis_blast, tripal_analysis_go).'
  );
  tripal_cv_add_cvterm($term, 'tripal_analysis', 0, 1, 'tripal');
  
  // add analysis_date.  This is no longer used (as far as we can tell) but we don't
  // get rid of it in case it is used, so just keep it in the Tripal CV
  $term = array(
    'name' => 'analysis_date', 
    'def' => 'The date that an analysis was performed.'
  );
  tripal_cv_add_cvterm($term, 'tripal', 0, 1, 'tripal');
  
  // add analysis_short_name.  This is no longer used (as far as we can tell) but we don't
  // get rid of it in case it is used, so just keep it in the Tripal CV
  $term = array(
    'name' => 'analysis_short_name', 
    'def' => 'A computer legible (no spaces or special characters) abbreviation for the analysis.'
  );     
  tripal_cv_add_cvterm($term, 'tripal', 0, 1 , 'tripal');     
  
  
  // the 'analysis_property' vocabulary is for user definable properties.  Even though we already have
  // an analysis_type term in the 'tripal_analysis' vocabular we duplicate it here because the 
  // tripal_analysis vocabulary is intended for use by the extension modules.  user's should not be able
  // to directly modify properties set by extension modules for an analysis.
  tripal_cv_add_cvterm(array('name' => 'Analysis Type','def' => 'The type of analysis was performed.'), 
     'analysis_property', 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;
}

/**
 *  Update for Drupal 6.x, Tripal 1.1, Analysis Module 1.1
 *  This update adds a new analysis_organism materialized view
 *
 */
function tripal_analysis_update_6100() {
  // add the new materialized view
  tripal_analysis_add_mview_analysis_organism();
  
  // move the analysis_type property into a new CV so that user's can change this property if
  // they want too  
  tripal_cv_add_cv('tripal_analysis', 'Terms used for managing analyses in Tripal');
  
  $sql = "
    UPDATE {cvterm} SET cv_id = 
      (SELECT cv_id FROM {cv} WHERE name = 'tripal_analysis')
    WHERE cv_id = (SELECT cv_id FROM {cv} WHERE name = 'tripal') AND
      name = 'analysis_type'
  ";
  chado_query($sql);
  
  $ret = array(
    '#finished' => 1,
  );

  return $ret;
}

/**
 * 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;
}

/**
 *  Update for Drupal 6.x, Tripal 1.1, Analysis Module 1.1
 *  This update adds a new analysis_property cv and 'Analysis Type' cvterm
 */
function tripal_analysis_update_6101() {
  // the 'analysis_property' vocabulary is for user definable properties.  Even though we already have
  // an analysis_type term in the 'tripal_analysis' vocabular we duplicate it here because the 
  // tripal_analysis vocabulary is intended for use by the extension modules.  user's should not be able
  // to directly modify properties set by extension modules for an analysis.
   tripal_cv_add_cvterm(array('name' => 'Analysis Type','def' => 'The type of analysis was performed.'), 
     'analysis_property', 0, 1, 'tripal');

  $ret = array(
      '#finished' => 1,
  );
  return $ret;
}
/**
 * Implementation of hook_requirements(). 
 */
function tripal_analysis_requirements($phase) {
  $requirements = array();
  if ($phase == 'install') {
    // make sure chado is installed
    if (!tripal_core_is_chado_installed()) {
      $requirements ['tripal_analysis'] = array(
            'title' => "tripal_analysis",
            'value' => "ERROR: Chado most be installed before this module can be enabled",
            'severity' => REQUIREMENT_ERROR,
      );
    }
  }
  return $requirements;
}

/*
 * 
 * @ingroup tripal_network
 */
function tripal_analysis_add_mview_analysis_organism() {
  
  // this is the SQL used to identify the organism to which an analsysis
  // has been used.  This is obtained though the analysisfeature -> feature -> organism
  // joins
  $sql = "
    SELECT DISTINCT A.analysis_id, O.organism_id
    FROM analysis A
      INNER JOIN analysisfeature AF ON A.analysis_id = AF.analysis_id
      INNER JOIN feature F          ON AF.feature_id = F.feature_id
      INNER JOIN organism O         ON O.organism_id = F.organism_id
  ";
  
  // the schema array for describing this view
  $schema = array(
    'table' => 'analysis_organism',
    'fields' => array(  
      'analysis_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'organism_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),       
    ),
    'indexes' => array(
      'networkmod_qtl_indx0' => array('analysis_id'),
      'networkmod_qtl_indx1' => array('organism_id'),
    ),
    'foreign keys' => array(
      'analysis' => array(
        'table' => 'analysis',
        'columns' => array(
          'analysis_id' => 'analysis_id',
        ),
      ),
      'organism' => array(
        'table' => 'organism',
        'columns' => array(
          'organism_id' => 'organism_id',
        ),
      ),      
    ),
  );
  
  // add a comment to make sure this view makes sense to the site administator
  $comment = t('This view is for associating an organism (via it\'s associated features) to an analysis.');
  
  // add the view
  tripal_add_mview('analysis_organism', 'tripal_analysis', NULL, NULL, NULL,
    $sql, NULL, $comment, $schema);
}