tripal/tripal_chado/includes/tripal_chado.setup.inc

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

/**
 * Prepares Chado for Tripal use
 */
function tripal_chado_prepare_form($form, $form_state) {
  $form = array();

  if (variable_get('tripal_chado_is_prepared') == TRUE) {
    drupal_set_message('Your site is prepared.');
  }
  $form['instructions'] = array(
    '#type' => 'item',
    '#title' => 'Prepare Drupal for Chado.',
    '#description' => t("Before a Drupal site can use Chado (via Tripal), both
        Chado and Drupal must be prepared a bit more.  Tripal will add some new
        materialized views, custom tables and controlled vocabularies to Chado.
        It will also add some management tables to Drupal. You only are
        required to prepare your Drupal site if this is a brand-new Drupal
        installation or if Chado was installed outside of Tripal.  If you
        installed Chado using Tripal then you do not need to run this step.
        If you are upgrading from a previous version of Tripal, you do not
        need to prepare your site, and you can click the 'Skip' button."),
  );

  $form['prepare-button'] = array(
    '#type' => 'submit',
    '#value' => t('Prepare this site'),
    '#name' => 'prepare-chado',
  );
  $form['skip-button'] = array(
    '#type' => 'submit',
    '#value' => t('Skip'),
    '#name' => 'prepare-skip',
  );
  return $form;
}

/**
 * Submit function for the tripal_chado_prepare_form().
 *
 * @param $form
 * @param $form_state
 */
function tripal_chado_prepare_form_submit($form, $form_state) {
   if ($form_state['clicked_button']['#name'] == "prepare-chado") {
     global $user;
     $args = array();
     $includes = array(
        module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.setup'),
        module_load_include('inc', 'tripal_chado', 'includes/loaders/tripal_chado.obo_loader'),
     );
     tripal_add_job('Prepare Chado', 'tripal_chado',
       'tripal_chado_prepare_chado', $args,
       $user->uid, 10, $includes);
   }
   if ($form_state['clicked_button']['#name'] == "prepare-skip") {
     variable_set('tripal_chado_is_prepared', TRUE);
   }
}

/**
 * Prepares Chado for use by Tripal.
 */
function tripal_chado_prepare_chado() {

  try {
    // 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, FALSE);


    ///////////////////////////////////////////////////////////////////////////
    //                          Chado DB Module
    ///////////////////////////////////////////////////////////////////////////
    tripal_insert_db(array(
      'name' => 'null',
      'description' => 'No online database.'
    ));
    tripal_insert_db(array(
      'name' => 'local',
      'description' => variable_get('site_name', 'This site.'),
    ));

    ///////////////////////////////////////////////////////////////////////////
    //                          Chado CV Module
    ///////////////////////////////////////////////////////////////////////////
    // Add the cv_root_mview.
    tripal_cv_add_cv_root_mview();


    // Create the temp table we will use for loading OBO files.
    tripal_cv_create_tripal_obo_temp();


    /////////////////////////////////////////////////////////////////////////////
    //                        Chado CompAnalysis Module
    /////////////////////////////////////////////////////////////////////////////
    // we may need the analysisfeatureprop table if it doesn't already exist
    tripal_analysis_create_analysisfeatureprop();

    // add materialized views
    tripal_analysis_add_mview_analysis_organism();

    // set the default vocabularies
    //tripal_set_default_cv('analysisprop', 'type_id', 'analysis_property');

    /////////////////////////////////////////////////////////////////////////////
    //                        Chado Contact Module
    /////////////////////////////////////////////////////////////////////////////
    // Add the contactprop table to Chado.
    tripal_contact_add_custom_tables();

    tripal_insert_db(array(
      'name' => 'TContact',
      'description' => 'The Tripal Contact controlled vocabulary.',
    ));
    tripal_insert_db(array(
      'name' => 'TPUB',
      'description' => 'The Tripal Publication controlled vocabulary.',
    ));

    // Set the default vocabularies.
    //('contact', 'type_id', 'tripal_contact');
    //tripal_set_default_cv('contactprop', 'type_id', 'tripal_contact');
    //tripal_set_default_cv('contact_relationship', 'type_id', 'contact_relationship');

    /////////////////////////////////////////////////////////////////////////////
    //                        Chado Feature Module
    /////////////////////////////////////////////////////////////////////////////
    // Note: the feature_property OBO that came with Chado v1.2 should not
    // be automatically installed.  Some of the terms are duplicates of
    // others in better maintained vocabularies.  New Tripal sites should
    // use those.

    // Add the materialized view.
    tripal_feature_add_organism_count_mview();

    // Add the custom tables.
    tripal_feature_add_tripal_gff_temp_table();
    tripal_feature_add_tripal_gffcds_temp_table();
    tripal_feature_add_tripal_gffprotein_temp_table();

    // Set the default vocabularies.
    //tripal_set_default_cv('feature', 'type_id', 'sequence');
    //tripal_set_default_cv('featureprop', 'type_id', 'feature_property');
    //tripal_set_default_cv('feature_relationship', 'type_id', 'feature_relationship');

    /////////////////////////////////////////////////////////////////////////////
    //                            Chado Map Module
    /////////////////////////////////////////////////////////////////////////////
    // add the featuremapprop table to Chado
    tripal_featuremap_add_custom_tables();

    // set the default vocabularies
    //tripal_set_default_cv('featuremapprop', 'type_id', 'featuremap_property');
    //tripal_set_default_cv('featureposprop', 'type_id', 'featurepos_property');
    //tripal_set_default_cv('featuremap', 'unittype_id', 'featuremap_units');

    /////////////////////////////////////////////////////////////////////////////
    //                          Chado Library Module
    /////////////////////////////////////////////////////////////////////////////
    // add the materialized view
    tripal_library_add_mview_library_feature_count();

    // set the default vocabularies
    //tripal_set_default_cv('libraryprop', 'type_id', 'library_property');
    //tripal_set_default_cv('library', 'type_id', 'library_type');


    /////////////////////////////////////////////////////////////////////////////
    //                          Chado Project Module
    /////////////////////////////////////////////////////////////////////////////

    // set the default vocabularies
    //tripal_set_default_cv('projectprop', 'type_id', 'project_property');
    ///tripal_set_default_cv('project_relationship', 'type_id', 'project_relationship');

    /////////////////////////////////////////////////////////////////////////////
    //                          Chado Pub Module
    /////////////////////////////////////////////////////////////////////////////
    global $base_path;

    tripal_pub_add_dbs();

    // add the custom tables
    tripal_pub_add_custom_tables();

    // set the default vocabularies
    //tripal_set_default_cv('pub', 'type_id', 'tripal_pub');
    //tripal_set_default_cv('pubprop', 'type_id', 'tripal_pub');
    //tripal_set_default_cv('pub_relationship', 'type_id', 'pub_relationship');

    // Add the supported loaders
    variable_set('tripal_pub_supported_dbs', array('PMID', 'AGL'));

    /////////////////////////////////////////////////////////////////////////////
      //                          Chado Stock Module
      /////////////////////////////////////////////////////////////////////////////
    // set the default vocabularies
    //tripal_set_default_cv('stock', 'type_id', 'stock_type');
    //tripal_set_default_cv('stockprop', 'type_id', 'stock_property');
    //tripal_set_default_cv('stock_relationship', 'type_id', 'stock_relationship');

    // add the materialized view
    tripal_stock_add_organism_count_mview();

    /////////////////////////////////////////////////////////////////////////////
    //                              Entity Bundles
    /////////////////////////////////////////////////////////////////////////////

    // First, populate the semantic web associations for Chado tables/fields.
    module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.semweb');
    tripal_chado_populate_chado_semweb_table();

    // Unfortunately, some Chado base tables do not have a type_id, so we must
    // take special action for those tables.  These include: organism and
    // analysis. Until we can find an appropriate controlled vocabulary
    // that is well supported by the community with types for these tables we
    // will have to use in-house terms.

    // Add a term to be used for an inherent 'type_id' for the organism table.
    tripal_insert_cvterm(array(
      'id' => 'local:analysis',
      'name' => 'analysis',
      'definition' => 'A process as a method of studying the nature of something ' .
        'or of determining its essential features and their relations. ' .
        '(Random House Kernerman Webster\'s College Dictionary, © 2010 K ' .
        'Dictionaries Ltd).',
      'cv_name' => 'local',
    ));

    // TODO: change this to foaf:Project
    tripal_insert_cvterm(array(
      'id' => 'local:project',
      'name' => 'project',
      'definition' => 'A plan or proposal for accomplishing something. ' .
        '(American Heritage® Dictionary of the English Language, Fifth Edition. ' .
        'Copyright © 2011 by Houghton Mifflin Harcourt Publishing Company).',
      'cv_name' => 'local',
    ));

    tripal_insert_cvterm(array(
      'id' => 'local:contact',
      'name' => 'contact',
      'definition' => 'An entity (e.g. individual or organization) through ' .
         'whom a person can gain access to information, favors, ' .
         'influential people, and the like.',
      'cv_name' => 'local',
    ));

    tripal_insert_cvterm(array(
      'id' => 'local:relationship',
      'name' => 'relationship',
      'definition' => 'The way in which two things are connected.',
      'cv_name' => 'local',
    ));

    tripal_insert_cvterm(array(
      'id' => 'local:biomaterial',
      'name' => 'biomaterial',
      'definition' => 'A biomaterial represents the MAGE concept of BioSource, BioSample, ' .
        'and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that ' .
        'may have been processed. Processed biomaterials should be traceable back to raw ' .
        'biomaterials via the biomaterialrelationship table.',
      'cv_name' => 'local',
    ));

    // We want to provide a set of commonly used entity types by default. This
    // way when a user first installs Tripal there are some commonly used
    // formats.
    module_load_include('inc', 'tripal', 'api/tripal.api');
    module_load_include('inc', 'tripal', 'includes/tripal.admin');

    // Create the 'Organism' entity type. This uses the obi:organism term.
    $error = '';
    $args = array(
     'vocabulary' => 'OBI',
     'accession' => '0100026',
     'term_name' => 'organism',
     'storage_args' => array(
       'data_table' => 'organism',
     )
    );
    if (!tripal_create_bundle($args, $error)) {
      throw new Exception($error['!message']);
    }

    // Create the 'Analysis' entity type. This uses the local:analysis term.
    $error = '';
    $args = array(
      'vocabulary' => 'local',
      'accession' => 'analysis',
      'term_name' => 'analysis',
      'storage_args' => array(
        'data_table' => 'analysis',
      )
    );
    if (!tripal_create_bundle($args, $error)) {
      throw new Exception($error['!message']);
    }

    // Create the 'Project' entity type. This uses the local:project term.
    $error = '';
    $args = array(
      'vocabulary' => 'local',
      'accession' => 'project',
      'term_name' => 'project',
      'storage_args' => array(
        'data_table' => 'project',
      )
    );
    if (!tripal_create_bundle($args, $error)) {
      throw new Exception($error['!message']);
    }

    // Create the 'Genetic Map' entity type. This uses the local:project term.
    $error = '';
    $args = array(
      'vocabulary' => 'data',
      'accession' => '1274',
      'term_name' => 'Map',
      'storage_args' => array(
        'data_table' => 'featuremap',
      )
    );
    if (!tripal_create_bundle($args, $error)) {
      throw new Exception($error['!message']);
    }

    // Create the 'Publication' entity type.
    $error = '';
    $args = array(
      'vocabulary' => 'TPUB',
      'accession' => '0000002',
      'term_name' => 'Publication',
      'storage_args' => array(
        'data_table' => 'pub',
      )
    );
    if (!tripal_create_bundle($args, $error)) {
      throw new Exception($error['!message']);
    }

    // Initialize the population of the chado_cvterm_mapping table.
    tripal_chado_map_cvterms();

    // Set a variable to indicate the site is prepared.
    variable_set('tripal_chado_is_prepared', TRUE);
  }
  catch (Exception $e) {
    throw new Exception($e);
  }
}

/**
 * Creates a materialized view that stores the type & number of stocks per organism
 *
 * @ingroup tripal_stock
 */
function tripal_stock_add_organism_count_mview() {
  $view_name = 'organism_stock_count';
  $comment = 'Stores the type and number of stocks per organism';

  $schema = array(
    'description' => $comment,
    'table' => $view_name,
    'fields' => array(
      'organism_id' => array(
        'size' => 'big',
        'type' => 'int',
        'not null' => TRUE,
      ),
      'genus' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'species' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'common_name' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => FALSE,
      ),
      'num_stocks' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'cvterm_id' => array(
        'size' => 'big',
        'type' => 'int',
        'not null' => TRUE,
      ),
      'stock_type' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
    ),
    'indexes' => array(
      'organism_stock_count_idx1' => array('organism_id'),
      'organism_stock_count_idx2' => array('cvterm_id'),
      'organism_stock_count_idx3' => array('stock_type'),
    ),
  );

  $sql = "
    SELECT
        O.organism_id, O.genus, O.species, O.common_name,
        count(S.stock_id) as num_stocks,
        CVT.cvterm_id, CVT.name as stock_type
     FROM organism O
        INNER JOIN stock S  ON O.Organism_id = S.organism_id
        INNER JOIN cvterm CVT ON S.type_id     = CVT.cvterm_id
     GROUP BY
        O.Organism_id, O.genus, O.species, O.common_name, CVT.cvterm_id, CVT.name
  ";

  tripal_add_mview($view_name, 'tripal_stock', $schema, $sql, $comment);
}

/**
 * Add custom table related to publications
 *  - pubauthor_contact
 *
 * @ingroup tripal_pub
 */
function tripal_pub_add_custom_tables() {
  $schema = array (
    'table' => 'pubauthor_contact',
    'fields' => array (
      'pubauthor_contact_id' => array (
        'type' => 'serial',
        'not null' => true,
      ),
      'contact_id' => array (
        'type' => 'int',
        'not null' => true,
      ),
      'pubauthor_id' => array (
        'type' => 'int',
        'not null' => true,
      ),
    ),
    'primary key' => array (
      0 => 'pubauthor_contact_id',
    ),
    'unique keys' => array (
      'pubauthor_contact_c1' => array (
        0 => 'contact_id',
        1 => 'pubauthor_id',
      ),
    ),
    'foreign keys' => array (
      'contact' => array (
        'table' => 'contact',
        'columns' => array (
          'contact_id' => 'contact_id',
        ),
      ),
      'pubauthor' => array (
        'table' => 'pubauthor',
        'columns' => array (
          'pubauthor_id' => 'pubauthor_id',
        ),
      ),
    ),
  );
  chado_create_custom_table('pubauthor_contact', $schema, TRUE);
}

/**
 * Adds dbs related to publications
 *
 * @ingroup tripal_pub
 */
function tripal_pub_add_dbs() {
  // make sure we have our supported databases
  tripal_insert_db(
      array(
        'name' => 'PMID',
        'description' => 'PubMed',
        'url' => 'http://www.ncbi.nlm.nih.gov/pubmed',
        'urlprefix' => 'http://www.ncbi.nlm.nih.gov/pubmed/'
      ),
      array('update_existing' => TRUE)
  );
  tripal_insert_db(
      array(
        'name' => 'AGL',
        'description' => 'USDA National Agricultural Library',
        'url' => 'http://agricola.nal.usda.gov/'
      ),
      array('update_existing' => TRUE)
  );
}

/**
 * Adds a materialized view keeping track of the type of features associated with each library
 *
 * @ingroup tripal_library
 */
function tripal_library_add_mview_library_feature_count(){
  $view_name = 'library_feature_count';
  $comment = 'Provides count of feature by type that are associated with all libraries';

  $schema = array(
    'table' => $view_name,
    'description' => $comment,
    'fields' => array(
      'library_id' => array(
        'size' => 'big',
        'type' => 'int',
        'not null' => TRUE,
      ),
      'name' => array(
        'type' => 'varchar',
        'length' => 255,
        'not null' => TRUE,
      ),
      'num_features' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'feature_type' => array(
        'type' => 'varchar',
        'length' => 255,
        'not null' => TRUE,
      ),
    ),
    'indexes' => array(
      'library_feature_count_idx1' => array('library_id'),
    ),
  );

  $sql = "
    SELECT
      L.library_id, L.name,
      count(F.feature_id) as num_features,
      CVT.name as feature_type
    FROM library L
      INNER JOIN library_feature LF  ON LF.library_id = L.library_id
      INNER JOIN feature F           ON LF.feature_id = F.feature_id
      INNER JOIN cvterm CVT          ON F.type_id     = CVT.cvterm_id
    GROUP BY L.library_id, L.name, CVT.name
  ";

  tripal_add_mview($view_name, 'tripal_library', $schema, $sql, $comment);
}

/**
 * Add custom tables needed by the feature map module
 *  - featuremapprop
 *  - featuremap_dbxref
 *  - featureposprop
 *
 * @ingroup tripal_featuremap
 */
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',
        ),
      ),
    ),
  );
  chado_create_custom_table('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,
  );
  chado_create_custom_table('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',
        ),
      ),
    ),
  );
  chado_create_custom_table('featureposprop', $schema, TRUE);
}

/**
 *
 */
function tripal_feature_add_tripal_gff_temp_table() {
  $schema = array(
    'table' => 'tripal_gff_temp',
    'fields' => array(
      'feature_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'organism_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'uniquename' => array(
        'type' => 'text',
        'not null' => TRUE,
      ),
      'type_name' => array(
        'type' => 'varchar',
        'length' => '1024',
        'not null' => TRUE,
      ),
    ),
    'indexes' => array(
      'tripal_gff_temp_idx0' => array('feature_id'),
      'tripal_gff_temp_idx0' => array('organism_id'),
      'tripal_gff_temp_idx1' => array('uniquename'),
    ),
    'unique keys' => array(
      'tripal_gff_temp_uq0' => array('feature_id'),
      'tripal_gff_temp_uq1' => array('uniquename', 'organism_id', 'type_name'),
    ),
  );
  chado_create_custom_table('tripal_gff_temp', $schema, TRUE);
}

/**
 *
 */
function tripal_feature_add_tripal_gffcds_temp_table($skip_recreate = TRUE) {
  $schema = array(
    'table' => 'tripal_gffcds_temp',
    'fields' => array(
      'feature_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'parent_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'phase' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'strand' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'fmin' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'fmax' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
    ),
    'indexes' => array(
      'tripal_gff_temp_idx0' => array('feature_id'),
      'tripal_gff_temp_idx0' => array('parent_id'),
    ),
  );
  chado_create_custom_table('tripal_gffcds_temp', $schema, $skip_recreate);
}

/**
 *
 */
function tripal_feature_add_tripal_gffprotein_temp_table() {
  $schema = array(
    'table' => 'tripal_gffprotein_temp',
    'fields' => array(
      'feature_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'parent_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'fmin' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'fmax' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
    ),
    'indexes' => array(
      'tripal_gff_temp_idx0' => array('feature_id'),
      'tripal_gff_temp_idx0' => array('parent_id'),
    ),
    'unique keys' => array(
      'tripal_gff_temp_uq0' => array('feature_id'),
    ),
  );
  chado_create_custom_table('tripal_gffprotein_temp', $schema, TRUE);
}
/**
 * Creates a materialized view that stores the type & number of features per organism
 *
 * @ingroup tripal_feature
 */
function tripal_feature_add_organism_count_mview() {
  $view_name = 'organism_feature_count';
  $comment = 'Stores the type and number of features per organism';

  $schema = array(
    'description' => $comment,
    'table' => $view_name,
    'fields' => array(
      'organism_id' => array(
        'size' => 'big',
        'type' => 'int',
        'not null' => TRUE,
      ),
      'genus' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'species' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'common_name' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => FALSE,
      ),
      'num_features' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'cvterm_id' => array(
        'size' => 'big',
        'type' => 'int',
        'not null' => TRUE,
      ),
      'feature_type' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
    ),
    'indexes' => array(
      'organism_feature_count_idx1' => array('organism_id'),
      'organism_feature_count_idx2' => array('cvterm_id'),
      'organism_feature_count_idx3' => array('feature_type'),
    ),
  );

  $sql = "
    SELECT
        O.organism_id, O.genus, O.species, O.common_name,
        count(F.feature_id) as num_features,
        CVT.cvterm_id, CVT.name as feature_type
     FROM organism O
        INNER JOIN feature F  ON O.Organism_id = F.organism_id
        INNER JOIN cvterm CVT ON F.type_id     = CVT.cvterm_id
     GROUP BY
        O.Organism_id, O.genus, O.species, O.common_name, CVT.cvterm_id, CVT.name
  ";

  tripal_add_mview($view_name, 'tripal_feature', $schema, $sql, $comment);
}
/**
 * Add any custom tables needed by this module.
 * - Contactprop: keep track of properties of contact
 *
 * @ingroup tripal_contact
 */
function tripal_contact_add_custom_tables(){
  $schema = array (
    'table' => 'contactprop',
    'fields' => array (
      'contactprop_id' => array (
        'type' => 'serial',
        'not null' => true,
      ),
      'contact_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 => 'contactprop_id',
    ),
    'unique keys' => array (
      'contactprop_c1' => array (
        0 => 'contact_id',
        1 => 'type_id',
        2 => 'rank',
      ),
    ),
    'indexes' => array (
      'contactprop_idx1' => array (
        0 => 'contact_id',
      ),
      'contactprop_idx2' => array (
        0 => 'type_id',
      ),
    ),
    'foreign keys' => array (
      'cvterm' => array (
        'table' => 'cvterm',
        'columns' => array (
          'type_id' => 'cvterm_id',
        ),
      ),
      'contact' => array (
        'table' => 'contact',
        'columns' => array (
          'contact_id' => 'contact_id',
        ),
      ),
    ),
  );
  chado_create_custom_table('contactprop', $schema, TRUE);
}
/**
 * Create a legacy custom chado table (analysisfeatureprop) to store properties of
 * analysisfeature links.
 *
 * @ingroup tripal_analysis
 */
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('chado.analysisfeatureprop')) {
    $sql = "
      CREATE TABLE {analysisfeatureprop} (
        analysisfeatureprop_id SERIAL PRIMARY KEY,
        analysisfeature_id     INTEGER NOT NULL,
        type_id                INTEGER NOT NULL,
        value                  TEXT,
        rank                   INTEGER NOT NULL,
        CONSTRAINT analysisfeature_id_type_id_rank UNIQUE (analysisfeature_id, type_id, rank),
        CONSTRAINT analysisfeatureprop_analysisfeature_id_fkey FOREIGN KEY (analysisfeature_id) REFERENCES {analysisfeature}(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
        CONSTRAINT analysisfeatureprop_type_id_fkey FOREIGN KEY (type_id) REFERENCES {cvterm}(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
      )
    ";
    chado_query($sql);
  }
}
/**
 * Creates a view showing the link between an organism & it's analysis through associated features.
 *
 * @ingroup tripal_analysis
 */
function tripal_analysis_add_mview_analysis_organism() {
  $view_name = 'analysis_organism';
  $comment = t('This view is for associating an organism (via it\'s associated features) to an analysis.');

  // 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' => $view_name,
    'description' => $comment,
    'fields' => array(
      'analysis_id' => array(
        'size' => 'big',
        'type' => 'int',
        'not null' => TRUE,
      ),
      'organism_id' => array(
        'size' => 'big',
        '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 the view
  tripal_add_mview($view_name, 'tripal_analysis', $schema, $sql, $comment);
}

/**
 * Add a materialized view of root terms for all chado cvs. This is needed for viewing cv trees
 *
 * @ingroup tripal_cv
 */
function tripal_cv_add_cv_root_mview() {
  $mv_name = 'cv_root_mview';
  $comment = 'A list of the root terms for all controlled vocabularies. This is needed for viewing CV trees';
  $schema = array(
    'table' => $mv_name,
    'description' => $comment,
    'fields' => array(
      'name' => array(
        'type' => 'varchar',
        'length' => 255,
        'not null' => TRUE,
      ),
      'cvterm_id' => array(
        'size' => 'big',
        'type' => 'int',
        'not null' => TRUE,
      ),
      'cv_id' => array(
        'size' => 'big',
        'type' => 'int',
        'not null' => TRUE,
      ),
      'cv_name' => array(
        'type' => 'varchar',
        'length' => 255,
        'not null' => TRUE,
      ),
    ),
    'indexes' => array(
      'cv_root_mview_indx1' => array('cvterm_id'),
      'cv_root_mview_indx2' => array('cv_id'),
    ),
  );

  $sql = "
    SELECT DISTINCT CVT.name,CVT.cvterm_id, CV.cv_id, CV.name
    FROM cvterm_relationship CVTR
      INNER JOIN cvterm CVT on CVTR.object_id = CVT.cvterm_id
      INNER JOIN cv CV on CV.cv_id = CVT.cv_id
    WHERE CVTR.object_id not in
      (SELECT subject_id FROM cvterm_relationship)
  ";

  // Create the MView
  tripal_add_mview($mv_name, 'tripal_cv', $schema, $sql, $comment);
}
/**
 * Creates a temporary table to store obo details while loading an obo file
 *
 * @ingroup tripal_cv
 */
function tripal_cv_create_tripal_obo_temp() {
  // the tripal_obo_temp table is used for temporary housing of records when loading OBO files
  // we create it here using plain SQL because we want it to be in the chado schema but we
  // do not want to use the Tripal Custom Table API because we don't want it to appear in the
  // list of custom tables.  It needs to be available for the Tripal Chado API so we create it
  // here and then define it in the tripal_cv/api/tripal_cv.schema.api.inc
  if (!db_table_exists('chado.tripal_obo_temp')) {
    $sql = "
      CREATE TABLE {tripal_obo_temp} (
        id character varying(255) NOT NULL,
        stanza text NOT NULL,
        type character varying(50) NOT NULL,
        CONSTRAINT tripal_obo_temp_uq0 UNIQUE (id)
      );
    ";
    chado_query($sql);
    $sql = "CREATE INDEX tripal_obo_temp_idx0 ON {tripal_obo_temp} USING btree (id)";
    chado_query($sql);
    $sql = "CREATE INDEX tripal_obo_temp_idx1 ON {tripal_obo_temp} USING btree (type)";
    chado_query($sql);
  }
}