tripal/tripal_project/tripal_project.module

<?php

require('includes/tripal_project.admin.inc');
require('api/tripal_project.api.inc');

/**
 *  @file
 * This file contains the basic functions needed for this drupal module.
 * The drupal tripal_project module maps directly to the chado general module.
 *
 * For documentation regarding the Chado General module:
 * @see http://gmod.org/wiki/Chado_General_Module
 *
 * @defgroup tripal_project Project Module
 * @ingroup tripal_modules
 */

/**
 * Implementation of hook_node_info().
 *
 * This node_info, is a simple node that describes the functionallity of the module. It specifies
 * that the title(Project Name) and body(Description) set to true so that they information can be
 * entered
 *
 *
 * @ingroup tripal_project
 */
function tripal_project_node_info() {
  return array(
    'chado_project' => array(
      'name' => t('Project'),
      'base' => 'chado_project',
      'description' => t('A module for interfacing the GMOD chado database with Drupal, providing viewing of projects'),
      'has_title' => TRUE,
      'title_label' => t('Project Name'),
      'had_body' => TRUE,
      'body_label' => t('Full Description'),
    )
  );
}

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

/**
 * Implements hook_menu
 *
 * @ingroup tripal_project
 */
function tripal_project_menu() {
  $items[ 'admin/tripal/chado/tripal_project' ]= array(
    'title' => 'Projects',
    'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of projects'),
    'access arguments' => array('adminster tripal projects'),
    'type' => MENU_NORMAL_ITEM
  );

  $items[ 'admin/tripal/chado/tripal_project/help' ]= array(
    'title' => 'Help',
    'description' => ("A description of the Tripal Project module including a short description of it's usage."),
    'page callback' => 'theme',
    'page arguments' => array('tripal_project_admin'),
    'access arguments' => array('adminster tripal projects'),
    'type' => MENU_NORMAL_ITEM
  );

  $items[ 'admin/tripal/chado/tripal_project/configuration' ]= array(
    'title' => 'Configuration',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_project_admin'),
    'access arguments' => array('adminster tripal projects'),
    'type' => MENU_NORMAL_ITEM
  );

  return $items;
}

/**
 * Implements hook_help()
 * Purpose: Adds a help page to the module list
 */
function tripal_project_help ($path, $arg) {
  if ($path == 'admin/help#tripal_project') {
    return theme('tripal_project_admin', array());
  }
}

/**
 * Implements hook_perm()
 *
 *  This function sets the permission for the user to access the information in the database.
 *  This includes creating, inserting, deleting and updating of information in the database
 *
 *
 * @ingroup tripal_project
 */
function tripal_project_permission() {
  return array(
    'access chado_project content' => array(
      'title' => t('View Projects'),
      'description' => t('Allow users to view project pages.'),
    ),
    'create chado_project content' => array(
      'title' => t('Create Projects'),
      'description' => t('Allow users to create new project pages.'),
    ),
    'delete chado_project content' => array(
      'title' => t('Delete Projects'),
      'description' => t('Allow users to delete project pages.'),
    ),
    'edit chado_project content' => array(
      'title' => t('Edit Projects'),
      'description' => t('Allow users to edit project pages.'),
    ),
    'adminster tripal project' => array(
      'title' => t('Administer Projects'),
      'description' => t('Allow users to administer all projects.'),
    ),
  );
}

/**
 * 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 $op == 'create'.  We will always
 *  return TRUE if the permission is set.
 *
 * @ingroup tripal_project
 */
function chado_project_node_access($node, $op, $account) {

  if ($op == 'create') {
    if (!user_access('create chado_projects content', $account)) {
      return FALSE;
    }
    return TRUE;
  }
  if ($op == 'update') {
    if (!user_access('edit chado_projects content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'delete') {
    if (!user_access('delete chado_projects content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'view') {
    if (!user_access('access chado_projects content', $account)) {
      return FALSE;
    }
  }
  return NULL;
}

/**
 *  We need to let drupal know about our theme functions and their arguments.
 *  We create theme functions to allow users of the module to customize the
 *  look and feel of the output generated in this module
 *
 * @ingroup tripal_project
 */
function tripal_project_theme() {
  return array(
    'tripal_project_base' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_project_base',
    ),
    'tripal_project_contact' => array(
       'arguments' => array('node' => NULL),
       'template' => 'tripal_project_contact',
    ),
    'tripal_project_publications' => array(
       'arguments' => array('node' => NULL),
       'template' => 'tripal_project_publications',
    ),
    'tripal_project_relationships' => array(
       'arguments' => array('node' => NULL),
       'template' => 'tripal_project_relationships',
    ),
    'tripal_project_properties' => array(
       'arguments' => array('node' => NULL),
       'template' => 'tripal_project_properties',
    ),
    'tripal_project_admin' => array(
      'template' => 'tripal_project_admin',
      'arguments' =>  array(NULL),
      'path' => drupal_get_path('module', 'tripal_project') . '/theme'
    ),
  );
}
/**
 * Implementation of hook_form().
 *
 *  This form takes the Project Title information and description from the user.
 *
 *  @parm $node
 *    The initialized node
 *
 *  @parm $form_state
 *    The state of the form, that has the user entered information that is neccessary for adding
 *    information to the project
 *
 *  @return $form
 *    An array as described by the Drupal Form API
 *
 *
 * @ingroup tripal_project
 */
function chado_project_form(&$node, $form_state) {
  $form = array();

  $project = $node->project;

  // get the project default values.  When this module was first created
  // the project description was incorrectly stored in the $node->body field.
  // It is better to store it in the Chado tables.  However, the 'description'
  // field of the project table is only 255 characters.  So, we are going
  // to follow the same as the project module and store the description in
  // the projectprop table and leave the project.description field blank.
  // however, for backwards compatibitily, we check to see if the description
  // is in the $node->body field. If it is we'll use that.  When the node is
  // edited the text will be moved out of the body and into the projectprop
  // table where it should belong.
  if ($node->body) {
    $project_description = $node->body;
  }
  else {
    $project_description = $node->project_description;
  }
  if (!$project_description) {
    $projectprop = tripal_project_get_property($project->project_id, 'project_description');
    $project_description = $projectprop->value;
  }

  // keep track of the project id if we have.  If we do have one then
  // this is an update as opposed to an insert.
  $form['project_id'] = array(
    '#type' => 'value',
    '#value' => $project->project_id,
  );

  $form['title']= array(
    '#type'          => 'textfield',
    '#title'         => t('Project Title'),
    '#description'   => t('Please enter the title for this project. This appears at the top of the project page.'),
    '#required'      => TRUE,
    '#default_value' => $node->title,
    '#weight'        => 1
  );

  $form['project_description']= array(
    '#type'          => 'textarea',
    '#title'         => t('Project Description'),
    '#description'   => t('A brief description of the project'),
    '#required'      => TRUE,
    '#default_value' => $project_description,
    '#weight'        => 5
  );

  return $form;

}
/**
 *  validates submission of form when adding or updating a project node
 *
 * @ingroup tripal_project
 */
function chado_project_validate($node) {
  $project = 0;
  // check to make sure the name on the project is unique
  // before we try to insert into chado.
  if ($node->project_id) {
    $sql = "SELECT * FROM {project} WHERE name = :name AND NOT project_id = :project_id";
    $project = chado_query($sql, array(':name' => $node->title, ':project_id' => $node->project_id))->fetchObject();
  }
  else {
    $sql = "SELECT * FROM {project} WHERE name = :name";
    $project = chado_query($sql, array(':name' => $node->title))->fetchObject();
  }
  if ($project) {
    form_set_error('title', t('The unique project name already exists. Please choose another'));
  }
}
/**
 * Implementation of hook_insert().
 *
 *  @parm $node
 *    Then node that has the information stored within, accessed given the nid
 *
 *
 * @ingroup tripal_project
 */
function chado_project_insert($node) {

  if ($node->project_id) {
    $project['project_id'] = $node->project_id;
  }
  else {
    $values = array(
      'name' => $node->title,
      'description' => '',
    );
    $project = tripal_core_chado_insert('project', $values);
  }

  if ($project) {
     // add the description property
    tripal_project_insert_property($project['project_id'], 'project_description',
      $node->project_description);

    // make sure the entry for this feature doesn't already exist in the chado_project table
    // if it doesn't exist then we want to add it.
    $project_id = chado_get_id_for_node('project', $node->nid) ;
    if (!$project_id) {
       // next add the item to the drupal table
      $sql = "
        INSERT INTO {chado_project} (nid, vid, project_id) 
        VALUES (:nid, :vid, :project_id)
      ";
      db_query($sql, array(':nid' => $node->nid, ':vid' => $node->vid, ':project_id' => $project['project_id']));
    }
  }
  else {
    drupal_set_message(t('Unable to add project.', 'warning'));
    watchdog('tripal_project', 'Insert feature: Unable to create project where values: %values',
      array('%values' => print_r($values, TRUE)), WATCHDOG_WARNING);
  }
}

/**
 *
 * Implementation of hook_delete().
 *
 * @param $node
 * The node which is to be deleted, only chado project and chado_project need to be dealt with
 * since the drupal node is deleted automagically
 *
 *
 * @ingroup tripal_project
 */
function chado_project_delete($node) {

  $project_id = chado_get_id_for_node('project', $node->nid);

  // if we don't have a project id for this node then this isn't a node of
  // type chado_project or the entry in the chado_project table was lost.
  if (!$project_id) {
    return;
  }

  // Remove data from {chado_project}, {node} and {node_revisions} tables of
  // drupal database
  $sql_del = "DELETE FROM {chado_project} WHERE nid = :nid AND vid = :vid";
  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
  $sql_del = "DELETE FROM {node_revision} WHERE nid = :nid AND vid = :vod";
  db_query($sql_del,  array(':nid' => $node->nid, ':vid' => $node->vid));
  $sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid";
  db_query($sql_del,  array(':nid' => $node->nid, ':vid' => $node->vid));

  // Remove data from project and projectprop tables of chado database as well
  chado_query("DELETE FROM {projectprop} WHERE project_id = :project_id", array(':project_id' => $project_id));
  chado_query("DELETE FROM {project} WHERE project_id = :project_id", array(':project_id' => $project_id));
}

/**
 * Implements hook_update().
 *
 * @param $node
 *  The node which is to have its containing information updated when the user modifies information
 *  pertaining to the specific project
 *
 *
 * @ingroup tripal_project
 */
function chado_project_update($node) {
 if ($node->revision) {
    // there is no way to handle revisions in Chado but leave
    // this here just to make note we've addressed it.
  }

  // update the project and the description
  $project_id = chado_get_id_for_node('project', $node->nid) ;
  $match = array('project_id' => $project_id);
  $values = array(
    'name' => $node->title,
    'description' => '',
  );
  $status = tripal_core_chado_update('project', $match, $values);
  tripal_project_update_property($project_id, 'project_description', $node->project_description, 1);
}

/**
 * Implementation of node_load().
 *
 * @param $node
 *   The node that is to have its containing information loaded
 *
 * @return $node
 *   The node, containing the loaded project with the current nid
 *
 *
 * @ingroup tripal_project
 */
function chado_project_load($node) {

  // get the feature details from chado
  $project_id = chado_get_id_for_node('project', $node->nid);

  $values = array('project_id' => $project_id);
  $project = tripal_core_generate_chado_var('project', $values);

  $additions = new stdClass();
  $additions->project = $project;
  return $additions;

}

/**
 *
 * @ingroup tripal_project
 */
function tripal_project_block_info() {

  $blocks['projectbase']['info'] = t('Tripal Project Details');
  $blocks['projectbase']['cache'] = BLOCK_NO_CACHE;

  $blocks['projectprops']['info'] = t('Tripal Project Properties');
  $blocks['projectprops']['cache'] = BLOCK_NO_CACHE;

  $blocks['projectpubs']['info'] = t('Tripal Project Publications');
  $blocks['projectpubs']['cache'] = BLOCK_NO_CACHE;

  $blocks['projectcont']['info'] = t('Tripal Project Contact');
  $blocks['projectcont']['cache'] = BLOCK_NO_CACHE;

  $blocks['projectrels']['info'] = t('Tripal Project Relationships');
  $blocks['projectrels']['cache'] = BLOCK_NO_CACHE;

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

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

    $block = array();
    switch ($delta) {
      case 'projectbase':
        $block['subject'] = t('Project Details');
        $block['content'] = theme('tripal_project_base', $node);
        break;
      case 'projectprops':
        $block['subject'] = t('Properties');
        $block['content'] = theme('tripal_project_properties', $node);
        break;
      case 'projectpubs':
        $block['subject'] = t('Publications');
        $block['content'] = theme('tripal_project_publications', $node);
        break;
      case 'projectcont':
        $block['subject'] = t('Contact');
        $block['content'] = theme('tripal_project_contact', $node);
        break;
      case 'projectrels':
        $block['subject'] = t('Relationships');
        $block['content'] = theme('tripal_project_relationships', $node);
        break;
      default :
    }
    return $block;
  }
}
/**
 *
 *
 * @ingroup tripal_project
 */
function tripal_project_preprocess_tripal_project_relationships(&$variables) {
  // we want to provide a new variable that contains the matched projects.
  $project = $variables['node']->project;

  // 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 P.name, P.project_id, CP.nid, CVT.name as rel_type
    FROM project_relationship PR
      INNER JOIN {project} P            ON PR.object_project_id = P.project_id
      INNER JOIN {cvterm} CVT           ON PR.type_id           = CVT.cvterm_id
      LEFT JOIN public.chado_project CP ON P.project_id         = CP.project_id
    WHERE PR.subject_project_id = :project_id
  ";
  $as_subject = chado_query($sql, array(':project_id' => $project->project_id));
  $sql = "
    SELECT P.name, P.project_id, CP.nid, CVT.name as rel_type
    FROM project_relationship PR
      INNER JOIN {project} P            ON PR.subject_project_id = P.project_id
      INNER JOIN {cvterm} CVT           ON PR.type_id            = CVT.cvterm_id
      LEFT JOIN public.chado_project CP ON P.project_id          = CP.project_id
    WHERE PR.object_project_id = :project_id
  ";
  $as_object = chado_query($sql, array(':project_id' => $project->project_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;
  }


  $project->all_relationships = $relationships;

}