tripal/tripal_stock/tripal_stock.module

<?php

/**
 * @file
 * Implements Tripal Stock Module hooks
 */

/**
 * @defgroup tripal_stock Stock Module
 * @ingroup tripal_modules
 * @{
 * Provides functions for managing chado stocks including creating details pages for each stock
 *
 * The Tripal Stock Module provides functionality for adding, editing, deleting and accessing chado
 * stocks. The stock module was designed to store information about stock collections in a
 * laboratory. What is called a stock could also be called a strain or an accession. There is a lot
 * in common between a Drosophila stock and a Saccharomyces strain and an Arabidopsis line. They all
 * come from some taxon, have genotypes, physical locations in the lab, some conceivable
 * relationship with a publication, some conceivable relationship with a sequence feature (such as a
 * transgene), and could be described by some ontology term. For more information about the chado
 * Stock Module see the GMOD Wiki Page (http://gmod.org/wiki/Chado_Stock_Module)
 * @}
 */
require_once("includes/tripal_stock.admin.inc");
require_once("includes/tripal_stock.sync_stocks.inc");
require_once("includes/other_module_api_functions.inc");
require_once("includes/tripal_stock-secondary_tables.inc");
require_once("includes/tripal_stock-properties.inc");
require_once("includes/tripal_stock-relationships.inc");
require_once("includes/tripal_stock-db_references.inc");
require_once("includes/tripal_stock.chado_node.inc");
require_once("api/tripal_stock.api.inc");

/**
 * Implements hook_menu(): Adds menu items for the tripal_stock
 *
 * @return
 *   Menu definitions for the tripal_stock
 *
 * @ingroup tripal_stock
 */
function tripal_stock_menu() {
  $items = array();

  //Administrative settings menu-----------------
  $items['admin/tripal/chado/tripal_stock'] = array(
    'title' => 'Stocks',
    'description' => 'A stock is the physical entities of an organism, either living or preserved.',
    'page callback' => 'tripal_stock_admin_stock_view',
    'access arguments' => array('administer tripal stocks'),
    'type' => MENU_NORMAL_ITEM
  );

  $items['admin/tripal/chado/tripal_stock/configuration'] = array(
    'title' => 'Settings',
    'description' => 'Settings for Chado Stocks',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_stock_admin'),
    'access arguments' => array('administer tripal stocks'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 5
  );

  $items['admin/tripal/chado/tripal_stock/sync'] = array(
    'title' => ' Sync',
    'description' => 'Sync stocks from Chado with Drupal',
    'page callback' => 'drupal_get_form',
    //'page arguments' => array('tripal_stock_sync_form'),
    'page arguments' => array('tripal_core_chado_node_sync_form', 'tripal_stock', 'chado_stock'),
    'access arguments' => array('administer tripal stocks'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 0
  );

  $items['admin/tripal/chado/tripal_stock/help'] = array(
    'title' => 'Help',
    'description' => 'Basic Description of Tripal Stock Module Functionality',
    'page callback' => 'theme',
    'page arguments' => array('tripal_stock_help'),
    'access arguments' => array('administer tripal stocks'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10
  );

  // Adding Secondary Properties-----------------
  $items['node/%cs_node/properties'] = array(
    'title' => 'Add Properties & Synonyms',
    'description' => 'Settings for Chado Stocks',
    'page callback' => 'tripal_stock_add_ALL_property_page',
    'page arguments' => array(1),
    'access arguments' => array('create chado_stock content'),
    'type' => MENU_CALLBACK
  );

  $items['node/%cs_node/db_references'] = array(
    'title' => 'Add Database References',
    'description' => 'Settings for Chado Stocks',
    'page callback' => 'tripal_stock_add_ALL_dbreferences_page',
    'page arguments' => array(1),
    'access arguments' => array('create chado_stock content'),
    'type' => MENU_CALLBACK
  );

  $items['node/%cs_node/relationships'] = array(
    'title' => 'Add Relationships',
    'description' => 'Settings for Chado Stocks',
    'page callback' => 'tripal_stock_add_ALL_relationships_page',
    'page arguments' => array(1),
    'access arguments' => array('create chado_stock content'),
    'type' => MENU_CALLBACK
  );

  //Edit/Deleting Secondary Properties-------------
  $items['node/%cs_node/edit_properties'] = array(
    'title' => 'Edit Properties',
    'description' => 'Settings for Chado Stocks',
    'page callback' => 'tripal_stock_edit_ALL_properties_page',
    'page arguments' => array(1),
    'access arguments' => array('edit chado_stock content'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 8,
  );

    $items['node/%cs_node/edit_relationships'] = array(
    'title' => 'Edit Relationships',
    'description' => 'Settings for Chado Stocks',
    'page callback' => 'tripal_stock_edit_ALL_relationships_page',
    'page arguments' => array(1),
    'access arguments' => array('edit chado_stock content'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 9,
  );

  $items['node/%cs_node/edit_db_references'] = array(
    'title' => 'Edit DB References',
    'description' => 'Settings for Chado Stocks',
    'page callback' => 'tripal_stock_edit_ALL_dbreferences_page',
    'page arguments' => array(1),
    'access arguments' => array('edit chado_stock content'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10,
  );

  // the menu link for addressing any stock (by name, uniquename, synonym)
  $items['stock/%'] = array(
    'page callback' => 'tripal_stock_match_stocks_page',
    'page arguments' => array(1),
    'access arguments' => array('access chado_stock content'),
    'type' => MENU_LOCAL_TASK,
  );
  return $items;
}

/**
 * Implements Menu wildcard_load hook
 *
 * Purpose: Allows the node ID of a chado stock to be dynamically
 *   pulled from the path. The node is loaded from this node ID
 *   and supplied to the page as an arguement. This is an example
 *   of dynamic argument replacement using wildcards in the path.
 *
 * @param $nid
 *   The node ID passed in from the path
 *
 * @return
 *   The node object with the passed in nid
 *
 * @ingroup tripal_stock
 */
function cs_node_load($nid) {
  if (is_numeric($nid)) {
    $node = node_load($nid);
    if ($node->type == 'chado_stock') {
      return $node;
    }
  }

  return FALSE;
}

/**
 * Implementation of hook_perm().
 *
 * Purpose: Set the permission types that the chado stock module uses
 *
 * @return
 *   Listing of the possible permission catagories
 *
 * @ingroup tripal_stock
 */
function tripal_stock_permissions() {
  return array(
    'access chado_stock content' => array(
      'title' => t('View Stocks'),
      'description' => t('Allow users to view stock pages.'),
    ),
    'create chado_stock content' => array(
      'title' => t('Create Stocks'),
      'description' => t('Allow users to create new stock pages.'),
    ),
    'delete chado_stock content' => array(
      'title' => t('Delete Stocks'),
      'description' => t('Allow users to delete stock pages.'),
    ),
    'edit chado_stock content' => array(
      'title' => t('Edit Stocks'),
      'description' => t('Allow users to edit stock pages.'),
    ),
    'adminster tripal stock' => array(
      'title' => t('Administer Stocks'),
      'description' => t('Allow users to administer all stocks.'),
    ),
  );
}

/**
 * Implement hook_access().
 *
 * This hook allows node modules to limit access to the node types they define.
 *
 *  @param $node
 *  The node on which the operation is to be performed, or, if it does not yet exist, the
 *  type of node to be created
 *
 *  @param $op
 *  The operation to be performed
 *
 *  @param $account
 *  A user object representing the user for whom the operation is to be performed
 *
 *  @return
 *  If the permission for the specified operation is not set then return FALSE. If the
 *  permission is set then return NULL as this allows other modules to disable
 *  access.  The only exception is when the $op == 'create'.  We will always
 *  return TRUE if the permission is set.
 *
 * @ingroup tripal_stock
 */
function chado_stock_node_access($node, $op, $account) {
  if ($op == 'create') {
    if (!user_access('create chado_stock content', $account)) {
      return FALSE;
    }
    return TRUE;
  }
  if ($op == 'update') {
    if (!user_access('edit chado_stock content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'delete') {
    if (!user_access('delete chado_stock content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'view') {
    if (!user_access('access chado_stock content', $account)) {
      return FALSE;
    }
  }
  return NULL;
}

/**
 * Implements hook_views_api()
 *
 * Purpose: Essentially this hook tells drupal that there is views support for
 *  for this module which then includes tripal_stock.views.inc where all the
 *  views integration code is
 *
 * @return
 *   An array with fields important for views integration
 *
 * @ingroup tripal_stock
 */
function tripal_stock_views_api() {
  return array(
    'api' => 2.0,
  );
}

/**
 * Implements hook_theme(): Register themeing functions for this module
 *
 * @return
 *   An array of themeing functions to register
 *
 * @ingroup tripal_stock
 */
function tripal_stock_theme() {
  $theme_path = drupal_get_path('module', 'tripal_stock') . '/theme';
  $items = array(

    // property edit forms function templates
    'tripal_stock_edit_ALL_properties_form' => array(
      'arguments' => array('form'),
      'function' => 'theme_tripal_stock_edit_ALL_properties_form',
    ),
    'tripal_stock_edit_ALL_db_references_form' => array(
      'arguments' => array('form'),
      'function' => 'theme_tripal_stock_edit_ALL_db_references_form',
    ),
    'tripal_stock_edit_ALL_relationships_form' => array(
      'arguments' => array('form'),
      'function' => 'theme_tripal_stock_edit_ALL_relationships_form',
    ),
    // tripal_stock templates
    'node__chado_stock' => array(
      'template' => 'node--chado-generic',
      'path' => drupal_get_path('module', 'tripal_core') . '/theme',
      'render element' => 'node',
      'base hook' => 'node',
    ),
    'tripal_stock_base' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_base',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_properties' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_properties',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_publications' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock.publications',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_references' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_references',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_relationships' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_relationships',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_synonyms' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_synonyms',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_collections' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_collections',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_collections' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_collections',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_phenotypes' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_phenotypes',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_locations' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_locations',
      'path' => "$theme_path/tripal_stock",
    ),
    // tripal_organism templates
    'tripal_organism_stocks' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_organism_stocks',
      'path' => "$theme_path/tripal_organism",
    ),
    // help template
    'tripal_stock_help' => array(
      'template' => 'tripal_stock_help',
      'arguments' =>  array(NULL),
      'path' => $theme_path,
    ),
  );
  return $items;
}
/**
 * Implements hook_help()
 * Purpose: Adds a help page to the module list
 */
function tripal_stock_help ($path, $arg) {
  if ($path == 'admin/help#tripal_stock') {
    return theme('tripal_stock_help', array());
  }
}

/**
 * @ingroup tripal_stock
 */
function tripal_stock_block_info() {
  $blocks['base']['info'] = t('Tripal Stock Details');
  $blocks['base']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['properties']['info'] = t('Tripal Stock Properties');
  $blocks['properties']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['references']['info'] = t('Tripal Stock References');
  $blocks['references']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['relationships_as_object']['info'] = t('Tripal Stock Relationships');
  $blocks['relationships_as_object']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['synonyms']['info'] = t('Tripal Stock Synonyms');
  $blocks['synonyms']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['collections']['info'] = t('Tripal Stock Collections');
  $blocks['collections']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['phenotypes']['info'] = t('Tripal Stock Phenotypes');
  $blocks['phenotypes']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['genotypes']['info'] = t('Tripal Stock Genotypes');
  $blocks['genotypes']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['locations']['info'] = t('Tripal Stock Locations');
  $blocks['locations']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['orgstocks']['info'] = t('Tripal Organism Stocks');
  $blocks['orgstocks']['cache'] = 'BLOCK_NO_CACHE';

  return $blocks;
}
/**
 *
 * @ingroup tripal_stock
 */
function tripal_stock_block_view($delta = '') {

  if (user_access('access chado_stock content') and arg(0) == 'node' and is_numeric(arg(1))) {
    $nid = arg(1);
    $node = node_load($nid);

    $block = array();
    switch ($delta) {
      case 'base':
        $block['subject'] = t('Stock Details');
        $block['content'] = theme('tripal_stock_base', $node);
        break;

      case 'properties':
        $block['subject'] = t('Properties');
        $block['content'] = theme('tripal_stock_properties', $node);
        break;

      case 'references':
        $block['subject'] = t('References');
        $block['content'] = theme('tripal_stock_references', $node);
        break;

      case 'relationships':
        $block['subject'] = t('Relationships');
        $block['content'] = theme('tripal_stock_relationships', $node);
        break;

      case 'synonyms':
        $block['subject'] = t('Synonyms');
        $block['content'] = theme('tripal_stock_synonyms', $node);
        break;

      case 'collections':
        $block['subject'] = t('Stock Collections');
        $block['content'] = theme('tripal_stock_collections', $node);
        break;

      case 'phenotypes':
        $block['subject'] = t('Stock Phenotypes');
        $block['content'] = theme('tripal_stock_phenotypes', $node);
        break;

      case 'genotypes':
        $block['subject'] = t('Stock Genotypes');
        $block['content'] = theme('tripal_stock_genotypes', $node);
        break;

      case 'locations':
        $block['subject'] = t('Stock Locations');
        $block['content'] = theme('tripal_stock_locations', $node);
        break;

      case 'orgstocks':
        $block['subject'] = t('Organism Stocks');
        $block['content'] = theme('tripal_organism_stocks', $node);
        break;

    }
    return $block;
  }
}

/**
 *
 *
 * @ingroup tripal_stock
 */
function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
  // we want to provide a new variable that contains the matched stocks.
  $stock = $variables['node']->stock;

  // normally we would use tripal_core_expand_chado_vars to expand our
  // organism object and add in the relationships, however whan a large
  // number of relationships are present this significantly slows the
  // query, therefore we will manually perform the query
  $sql = "
    SELECT
      S.name, S.uniquename, S.stock_id, CS.nid,
      CVT.name as rel_type, CVTs.name as obj_type,
      SR.value
    FROM {stock_relationship} SR
      INNER JOIN {stock} S on SR.object_id = S.stock_id
      INNER JOIN {cvterm} CVT on SR.type_id = CVT.cvterm_id
      INNER JOIN {cvterm} CVTs on S.type_id = CVTs.cvterm_id
      LEFT JOIN public.chado_stock CS on S.stock_id = CS.stock_id
    WHERE SR.subject_id = :stock_id
  ";
  $as_subject = chado_query($sql, array(':stock_id' => $stock->stock_id));
  $sql = "
    SELECT
      S.name, S.uniquename,  S.stock_id, CS.nid,
      CVT.name as rel_type, CVTs.name as sub_type,
      SR.value
    FROM {stock_relationship} SR
      INNER JOIN {stock} S on SR.subject_id = S.stock_id
      INNER JOIN {cvterm} CVT on SR.type_id = CVT.cvterm_id
      INNER JOIN {cvterm} CVTs on S.type_id = CVTs.cvterm_id
      LEFT JOIN public.chado_stock CS on S.stock_id = CS.stock_id
    WHERE SR.object_id = :stock_id
  ";
  $as_object = chado_query($sql, array(':stock_id' => $stock->stock_id));

  // combine both object and subject relationshisp into a single array
  $relationships = array();
  $relationships['object'] = array();
  $relationships['subject'] = array();

  // iterate through the object relationships
  while ($relationship = $as_object->fetchObject()) {

     // get the relationship and child types
     $rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
     $sub_type = t(preg_replace('/_/', " ", $relationship->sub_type));

     if (!array_key_exists($rel_type, $relationships['object'])) {
       $relationships['object'][$rel_type] = array();
     }
     if (!array_key_exists($sub_type, $relationships['object'][$rel_type])) {
       $relationships['object'][$rel_type][$sub_type] = array();
     }
     $relationships['object'][$rel_type][$sub_type][] = $relationship;
  }

  // now add in the subject relationships
  while ($relationship = $as_subject->fetchObject()) {

     // get the relationship and child types
     $rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
     $obj_type = t(preg_replace('/_/', " ", $relationship->obj_type));

     if (!array_key_exists($rel_type, $relationships['subject'])) {
       $relationships['subject'][$rel_type] = array();
     }
     if (!array_key_exists($obj_type, $relationships['subject'][$rel_type])) {
       $relationships['subject'][$rel_type][$obj_type] = array();
     }
     $relationships['subject'][$rel_type][$obj_type][] = $relationship;
  }


  $stock->all_relationships = $relationships;

}

/*
 * Uses the value provided in the $id argument to find all stocks that match
 * that ID by name, stockname or synonym.  If it matches uniquenly to a single
 * stock it will redirect to that stock page, otherwise, a list of matching
 * stocks is shown.
 */
function tripal_stock_match_stocks_page($id) {

  // if the URL alias configuration is set such that the URL
  // always begins with 'stock' then we want to use the ID as it is and
  // forward it on. Otherwise, try to find the matching stock.
  $url_alias = variable_get('chado_stock_url_string', '/stock/[genus]/[species]/[type]/[uniquename]');
  if (!$url_alias) {
    $url_alias = '/stock/[genus]/[species]/[type]/[uniquename]';
  }
  $url_alias = preg_replace('/^\//', '', $url_alias); // remove any preceeding forward slash
  if (preg_match('/^stock\//', $url_alias)) {
    drupal_goto($id);
  }


  $sql = "
    SELECT
      S.name, S.uniquename, S.stock_id,
      O.genus, O.species, O.organism_id,
      CVT.cvterm_id, CVT.name as type_name,
      CS.nid
    FROM {stock} S
      INNER JOIN {organism} O on S.organism_id = O.organism_id
      INNER JOIN {cvterm} CVT on CVT.cvterm_id = S.type_id
      INNER JOIN public.chado_stock CS on CS.stock_id = S.stock_id
    WHERE
      S.uniquename = :uname or S.name = :name
  ";
  $results = chado_query($sql, array(':uname' => $id, ':name' => $id));

  $num_matches = 0;

  // iterate through the matches and build the table for showing matches
  $header = array('Uniquename', 'Name', 'Type', 'Species');
  $rows = array();
  $curr_match;
  while ($match = $results->fetchObject()) {
    $curr_match = $match;
    $rows[] = array(
       $match->uniquename,
       "<a href=\"" . url("node/". $match->nid) ."\">" . $match->name . "</a>",
       $match->type_name,
       '<i>' . $match->genus . ' ' . $match->species . '</i>',
    );
    $num_matches++;
  }

  // if we have more than one match then generate the table, otherwise, redirect
  // to the matched stock
  if ($num_matches == 1) {
    drupal_goto("node/" . $curr_match->nid);
  }
  if ($num_matches == 0) {
    return "<p>No stocks matched the given name '$id'</p>";
  }

  $table_attrs = array(
    'class' => 'tripal-table tripal-table-horz'
  );
  $output = "<p>The following stocks match the name '$id'.</p>";
  $output .= theme_table($header, $rows, $table_attrs, $caption);
  return $output;
}

/**
 * Implementation of hook_form_alter()
 *
 * @param $form
 * @param $form_state
 * @param $form_id
 */
function tripal_stock_form_alter(&$form, &$form_state, $form_id) {
  // turn of preview button for insert/updates
  if ($form_id == "chado_stock_node_form") {
    $form['actions']['preview']['#access'] = FALSE;
  }
}