tripal/tripal_cv/tripal_cv.module

<?php

require_once "includes/charts.inc";
require_once "includes/trees.inc";
require_once "includes/obo_loader.inc";
require_once "api/tripal_cv.api.inc";

/**
 * @defgroup tripal_cv CV Module
 * @ingroup tripal_modules
 */

/**
 * Implements hook_init().
 * Adds CSS and JS needed for this modules rendered content
 *
 * @ingroup tripal_cv
 */
function tripal_cv_init() {

  // add the tripal_cv JS and CSS
  drupal_add_css(drupal_get_path('theme', 'tripal') . '/css/tripal_cv.css');
  drupal_add_js(drupal_get_path('theme', 'tripal') . '/js/tripal_cv.js');
  
  // add the jgCharts.js
  drupal_add_js(drupal_get_path('theme', 'tripal') . '/js/jgcharts/jgcharts.js');

  // add the jsTree JS and CSS
  drupal_add_css(drupal_get_path('theme', 'tripal') . '/js/jsTree/source/tree_component.css');
  drupal_add_js(drupal_get_path('theme', 'tripal') . '/js/jsTree/source/_lib.js');
  drupal_add_js(drupal_get_path('theme', 'tripal') . '/js/jsTree/source/tree_component.js');
}

/**
 * Implements hook_menu().
 * Registers all menu items associated with this module
 *
 * @ingroup tripal_cv
 */
function tripal_cv_menu() {
  $items = array();

  $items['admin/tripal/tripal_cv'] = array(
    'title' => 'Controlled Vocabularies',
    'description' => 'Basic Description of Tripal CV Module Functionality',
    'page callback' => 'tripal_cv_module_description_page',
    'access arguments' => array('administer site configuration'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['admin/tripal/tripal_cv/cvtermpath'] = array(
    'title' => 'Update Chado cvtermpath tables',
    'description' => 'The Chado cvtermpath table provides lineage for terms and is useful for quickly finding any ancestor parent of a term.  However, this table must be populated.  This page allows for populating of this table one vocabulary at a time',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_cv_cvtermpath_form'),
    'access arguments' => array('administer site configuration'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['admin/tripal/tripal_cv/edit_cv'] = array(
    'title' => 'Update/Delete Controlled Vocabulary',
    'description' => 'Manage controlled vocabularies/ontolgoies in Chado ',
    'page callback' => 'tripal_cv_admin_page',
    'access arguments' => array('administer site configuration'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['admin/tripal/tripal_cv/add_cv'] = array(
    'title' => 'Add a Controlled Vocabulary',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_cv_add_form'),
    'access arguments' => array('access administration pages'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['admin/tripal/tripal_cv/add_cvterm'] = array(
    'title' => 'Add Controlled Vocabulary Terms',
    'description' => 'Manage controlled vocabulary/ontology terms in Chado ',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_cv_add_cvterm_form'),
    'access arguments' => array('administer site configuration'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['admin/tripal/tripal_cv/add_cvterm/js'] = array(
    'page callback' => 'tripal_cv_add_cvterm_callback',
    'access arguments' => array('administer site configuration'),
    'type' => MENU_CALLBACK,
  );

  $items['admin/tripal/tripal_cv/obo_loader'] = array(
    'title' => 'Load Ontology With OBO File',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_cv_obo_form'),
    'access arguments' => array('access administration pages'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['admin/tripal/tripal_cv/edit/js'] = array(
    'title' => 'Edit Controlled Vocabularies',
    'page callback' => 'tripal_ajax_cv_edit',
    'access arguments' => array('access administration pages'),
    'type' => MENU_CALLBACK,
  );

  $items['tripal_cv_chart'] = array(
    'path' => 'tripal_cv_chart',
    'title' => 'CV Chart',
    'page callback' => 'tripal_cv_chart',
    'page arguments' => array(1),
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK
  );

  $items['tripal_cv_tree'] = array(
    'path' => 'tripal_cv_tree',
    'title' => 'CV Term Viewer',
    'page callback' => 'tripal_cv_tree',
    'page arguments' => array(1),
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK
  );

  // menu items for working with the CV module tree browser
  $items['cv_browser'] = array(
    'title' => 'CV Relationship Browser',
    'page callback' => 'tripal_cv_show_browser',
    'access arguments' => array('access chado_cv content'),
    'type' => MENU_CALLBACK
  );

  $items['tripal_cv_init_browser'] = array(
    'path' => 'tripal_cv_init_browser',
    'title' => 'CV Browser',
    'page callback' => 'tripal_cv_init_browser',
    'page arguments' => array(1),
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK
  );

  // menu item for interaction with the tree
  $items['tripal_cv_update_tree'] = array(
    'path' => 'tripal_cv_update_tree',
    'title' => 'CV Tree',
    'page callback' => 'tripal_cv_update_tree',
    'page arguments' => array(2, 3),
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK
  );

  // menu items for working with terms
  $items['tripal_cv_cvterm_info'] = array(
    'path' => 'tripal_cv_cvterm_info',
    'title' => 'CV Term Viewer',
    'page callback' => 'tripal_cv_cvterm_info',
    'page arguments' => array(1),
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK
  );

  $items['tripal_cv_cvterm_edit'] = array(
    'path' => 'tripal_cv_edit',
    'title' => 'CV Term Editor',
    'page callback' => 'tripal_cv_cvterm_edit',
    'page arguments' => array(1),
    'access arguments' => array('edit chado_cv content'),
    'type' => MENU_CALLBACK
  );

  return $items;
}

/**
 *  The following function proves access control for users trying to
 *  perform actions on data managed by this module
 *
 * @ingroup tripal_cv
 */
function chado_cv_access($op, $node, $account) {
  if ($op == 'create') {
    if (!user_access('create chado_cv content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'update') {
    if (!user_access('edit chado_cv content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'delete') {
    if (!user_access('delete chado_cv content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'view') {
    if (!user_access('access chado_cv content', $account)) {
      return FALSE;
    }
  }

  return NULL;
}

/**
 *  Set the permission types that the chado module uses.  Essentially we
 *  want permissionis that protect creation, editing and deleting of chado
 *  data objects
 *
 * @ingroup tripal_cv
 */
function tripal_cv_perm() {
  return array(
    'access chado_cv content',
    'create chado_cv content',
    'delete chado_cv content',
    'edit chado_cv content',
  );
}

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

/**
 *  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_cv
 */
function tripal_cv_theme() {
  return array(
    'tripal_cv_cvterm_edit' => array(
      'arguments' => array('cvterm'),
    ),
  );
}

/**
 * Purpose: Provide Guidance to new Tripal Admin
 *
 * @return HTML Formatted text
 *
 * @ingroup tripal_cv
 */
function tripal_cv_module_description_page() {
  $text = '';

  $text = '<h3>Tripal Controlled Vocabulary Administrative Tools Quick Links</h3>';
    $text .= '<ul>';
      $text .= '<li>' . l('Add CV', 'admin/tripal/tripal_cv/add_cv') . '</li>';
      $text .= '<li>' . l('Update/Delete CV', 'admin/tripal/tripal_cv/edit_cv') . '</li>';
      $text .= '<li>' . l('Add/Update Ontology', 'admin/tripal/tripal_cv/obo_loader') . '</li>';
      $text .= '<li>' . l('Add CV term', 'admin/tripal/tripal_cv/add_cvterm') . '</li>';
      $text .= '<li>' . l('Term Listing', 'admin/tripal/tripal_cv/list_cvterms') . '</li>';
      $text .= '<li>' . l('Update cvtermpath', 'admin/tripal/tripal_cv/cvtermpath') . '</li>';
    $text .= '</ul>';


  $text .= '<h3>Module Description:</h3>';
  $text .= '<p>The Tripal CV (Controlled Vocabularies) Module provides
    functionality for managing controlled vocabularies and the terms they are
    comprised of. The flexibility and extendibility of the chado schema depends
    on controlled vocabularies. For example, by using a controlled vocabulary for
    feature types the chado schema can describe features of any type, even those
    we have not concieved of yet.</p>';

  $text .= '<h3>Setup Instructions:</h3>';
  $text .= '<p>After installation of the controlled vocabulary module, the following tasks should be performed:</p>';
    $text .= '<ol>';
      $text .= '<li><p><b>Set Permissions</b>: The cv module supports the Drupal user permissions interface for
               controlling access to cv content and functions. These permissions include viewing,
               creating, editing or administering of
               cv content. The default is that only the original site administrator has these
               permissions.  You can <a href="' . url('admin/user/roles') . '">add roles</a> for classifying users,
               <a href="' . url('admin/user/user') . '">assign users to roles</a> and
               <a href="' . url('admin/user/permissions') . '">assign permissions</a> for the cv content to
               those roles.  For a simple setup, allow anonymous users access to view organism content and
               allow the site administrator all other permissions.</p></li>';
      $text .= '<li><b>Loading of Ontologies/Controlled Vocabularies</b>: You can access this loader at '.
        l('Admin->Tripal Management->Tripal CV->Add/Update Ontology With OBO File', 'admin/tripal/tripal_cv/obo_loader')
        .'. This loader allows you to choose from a list of common ontologies or
        enter the URL or location to an OBO file. Even the list of common
        ontologies is using a URL ensuring you get the most up to date ontology.</p>';
      $text .= '<p>This loader adds a Tripal Job which then waits in a queue to
        be launched. To launch Tripal Jobs either navidate to the root of your
        drupal installation and execute "php sites/all/modules/tripal/tripal_core/
        tripal_launch_jobs.php <drupal user>" or set up a cron job (See user manual
        for more details).</p>';
      $text .= '<p>NOTE: in some cases, community developed ontologies for your
        data may not yet be developed. In this case, it is suggested that you begin
        developement of an ontology using one of the online tools. You might find
        that many researchers are trying to deal with the same data and are willing
        to help you in this endevor. You can ' . l('create a controlled vocabulary', 'admin/tripal/tripal_cv/add_cv') . ' and '
        . l('add terms to it', 'admin/tripal/tripal_cv/add_cvterm')  . ' to provide functionality to your site while you are waiting
        for the ontology to be developed.</p></li>';
    $text .= '</ol>';

  $text .= '<h3>Features of this Module:</h3>';
  $text .= '<p>Aside from the data loading described above, the Tripal Controlled Vocabulary (CV) module also provides the following functionality:</p>';
    $text .= '<ul>';
      $text .= '<li><b>Create/Update/Delete A Controlled Vocaulbulary</b>: to create your own controlled vocabulary go to '.
        l('Admin->Tripal Management->Tripal CV->Add a Controlled Vocabulary', 'admin/tripal/tripal_cv/add_cv')
        .' and fill out the form provided.To Update/Delete a controlled vocabulary
        go to ' . l('Admin->Tripal Management->Tripal CV->Update/Delete Controlled Vocabulary', 'admin/tripal/tripal_cv/edit_cv')
        .', select the existing controlled vocabulary you want to modify and then
        edit it as desired. This only modifies the name, description of a
        controlled vocabulary. See the next section for adding, removing, editing
        the term a controlled vocabulary contains.</li>';

      $text .= '<li><b>Create a Controlled Vocaulbulary Term</b>: To Add a term to an already existing controlled vocabulary
        go to ' . l('Admin->Tripal Management->Tripal CV->Add a Controlled Vocabulary Term', 'admin/tripal/tripal_cv/add_cvterm')
        .', select the controlled vocabulary you want to add terms to and then fill
        out the form.</li>';
      $text .= '<li><b>Controlled Vocabulary Term Browser</b>: This module provides a ' . l('basic listing', 'admin/tripal/tripal_cv/list_cvterms') . ' of controlled vocabulry terms for
              for all vocabularies currently in chado. It does not require indexing for Drupal searching but relies on Drupal Views.
              <a href="http://drupal.org/project/views">Drupal Views</a> must be installed.</li>';
      $text .= '<li><p><b>Integration with Drupal Views</b>: <a href="http://drupal.org/project/views">Drupal Views</a> is
              a powerful tool that allows the site administrator to create lists or basic searching forms of Chado content.
              It provides a graphical interface within Drupal to allow the site admin to directly query the Chado database
              and create custom lists without PHP programming or customization of Tripal source code.  Views can also
              be created to filter content that has not yet been synced with Druapl in order to protect access to non
              published data (only works if Chado was installed using Tripal).  You can see a list of available pre-existing
              Views <a href="' . url('admin/build/views/') . '">here</a>, as well as create your own. </p></li>';
    $text .= '</ul>';

  return $text;
}

///////////////////////////////////////////
// Edit/Delete CVs
//////////////////////////////////////////

/**
 * Purpose: Provides the form for Updating and Deleteing existing
 *   chado controlled vocabularies (See chado cv table)
 *
 * @ingroup tripal_cv
 */
function tripal_cv_admin_page() {

  $add_url = url("admin/tripal/tripal_cv/new");
  $obo_url = url("admin/tripal/tripal_cv/obo");
  $cvtermpath_url = url("admin/tripal/tripal_cv/cvtermpath");
  $browser_url = url("cv_browser");

  $output = "<a href=\"$add_url\">Add a new controlled vocabulary</a> | ";
  $output .= "<a href=\"$browser_url\">Browse a vocabulary</a> | ";
  $output .= "<a href=\"$obo_url\">Add/Update Ontology With OBO File</a> | ";
  $output .= "<a href=\"$cvtermpath_url\">Update the cvtermpath table</a> ";
  $output .= drupal_get_form('tripal_cv_select_form');
  $output .= '<div id="db-edit-div">Please select a vocabulary above to view or edit</div>';

  return $output;
}

/**
 * Purpose: Provides the actual "Select CV" form on the Update/Delete Controlled
 *   Vocabulary page. This form also triggers the edit javascript
 * @todo Modify this form to use Drupal AJAX
 *
 * @ingroup tripal_cv
 */
function tripal_cv_select_form() {

  $previous_db = tripal_db_set_active('chado');  // use chado database
  // get a list of db from chado for user to choose
  $sql = "SELECT * FROM {cv} WHERE NOT name = 'tripal' ORDER BY name ";
  $results = db_query($sql);
  tripal_db_set_active($previous_db); // use drupal database

  $cvs = array();
  $cvs[] = '';
  while ($cv = db_fetch_object($results)) {
    $cvs[$cv->cv_id] = $cv->name;
  }

  $form['cvid'] = array(
    '#title' => t('Controlled Vocabulary/Ontology Name'),
    '#type' => 'select',
    '#options' => $cvs,
    '#ahah' => array(
      'path' => 'admin/tripal/tripal_cv/edit/js',
      'wrapper' => 'db-edit-div',
      'effect' => 'fade',
      'event' => 'change',
      'method' => 'replace',
    ),
  );

  return $form;
}

/**
 * Purpose: The edit controlled vocabulary javascript
 *
 * @ingroup tripal_cv
 */
function tripal_ajax_cv_edit() {

  // get the database id, build the form and then return the JSON object
  $cvid = filter_xss($_POST['cvid']);
  $form = drupal_get_form('tripal_cv_edit_form', $cvid);
  drupal_json(array('status' => TRUE, 'data' => $form));

}

/**
 * Purpose: Provides a form to allow updating/deleteing of controlled vocabularies
 *
 * @ingroup tripal_cv
 */
function tripal_cv_edit_form(&$form_state = NULL, $cvid = NULL) {

  $sql = "SELECT * FROM {cv} WHERE cv_id = %d ";
  $previous_db = tripal_db_set_active('chado');
  $cv = db_fetch_object(db_query($sql, $cvid));
  tripal_db_set_active($previous_db);

  // set the default values.  If there is a value set in the
  // form_state then let's use that, otherwise, we'll pull
  // the values from the database
  $default_db = $form_state['values']['name'];
  $default_desc = $form_state['values']['description'];
  $default_url = $form_state['values']['url'];
  $default_urlprefix = $form_state['values']['urlprefix'];
  if (!$default_db) {
    $default_cv = $cv->name;
  }
  if (!$default_desc) {
    $default_desc = $cv->definition;
  }

  $form['cvid'] = array(
    '#type' => 'hidden',
    '#value' => $cvid
  );

  $form['name']= array(
    '#type'          => 'textfield',
    '#title'         => t("Controlled Vocabulary name"),
    '#description'   => t('Please enter the name for this vocabulary.'),
    '#required'      => FALSE,
    '#default_value' => $default_cv,
    '#weight'        => 1
  );

  $form['definition']= array(
    '#type'          => 'textarea',
    '#title'         => t('Description'),
    '#description'   => t('Please enter a description for this vocabulary'),
    '#default_value' => $default_desc,
    '#weight'        => 2
  );

  $form['update'] = array(
    '#type'         => 'submit',
    '#value'        => t('Update'),
    '#weight'       => 5,
    '#executes_submit_callback' => TRUE,
  );
  $form['delete'] = array(
    '#type'         => 'submit',
    '#value'        => t('Delete'),
    '#weight'       => 6,
    '#executes_submit_callback' => TRUE,
  );

  $form['#redirect'] = 'admin/tripal/tripal_cv';


  return $form;
}

/**
 * Purpose: The submit function of the update/delete controlled vocabulary form
 *
 * @ingroup tripal_cv
 */
function tripal_cv_edit_form_submit($form, &$form_state) {

  $name =  $form_state['values']['name'];
  $desc =  $form_state['values']['definition'];
  $cvid =  $form_state['values']['cvid'];
  $op   =  $form_state['values']['op'];

  if (strcmp($op, 'Update') == 0) {
    $sql = "
       UPDATE {cv} SET
         name = '%s',
         definition = '%s'
       WHERE cv_id = %d
    ";
    $previous_db = tripal_db_set_active('chado');
    $db = db_query($sql, $name, $desc, $cvid);
    tripal_db_set_active($previous_db);
    if ($db) {
      drupal_set_message(t("Controlled vocabulary updated"));
    }
    else {
      drupal_set_message(t("Failed to update controlled vocabulary."), 'error');
    }
  }
  if (strcmp($op, 'Delete')==0) {
    $sql = "
       DELETE FROM {cv}
       WHERE cv_id = %d
    ";
    $previous_db = tripal_db_set_active('chado');
    $db = db_query($sql, $cvid);
    tripal_db_set_active($previous_db);
    if ($db) {
      drupal_set_message(t("Controlled vocabulary deleted"));
    }
    else {
      drupal_set_message(t("Failed to delete controlled vocabulary."), 'error');
    }
  }

}

/////////////////////////////////////
// Add CVs
////////////////////////////////////

/**
 * Purpose: Provides the Add controlled vocabulary form
 *
  * @ingroup tripal_cv
 */
function tripal_cv_add_form(&$form_state = NULL) {

  $form['cvid'] = array(
    '#type' => 'hidden',
    '#value' => $cvid
  );

  $form['name']= array(
    '#type'          => 'textfield',
    '#title'         => t("Controlled Vocabulary name"),
    '#description'   => t('Please enter the name for this vocabulary.  This field will be ignored if an OBO file or URL is provided above'),
    '#required'      => FALSE,
    '#default_value' => $default_cv,
    '#weight'        => 1
  );

  $form['definition']= array(
    '#type'          => 'textarea',
    '#title'         => t('Description'),
    '#description'   => t('Please enter a description for this vocabulary'),
    '#default_value' => $default_desc,
    '#weight'        => 2
  );

  $form['add'] = array(
    '#type'         => 'submit',
    '#value'        => t('Add'),
    '#weight'       => 5,
    '#executes_submit_callback' => TRUE,
  );

  $form['#redirect'] = 'admin/tripal/tripal_cv';

  return $form;
}

/**
 * Purpose: The submit function for the add controlled vocabulary form
 *
 * @ingroup tripal_cv
 */
function tripal_cv_add_form_submit($form, &$form_state) {

  $name =  $form_state['values']['name'];
  $desc =  $form_state['values']['definition'];

  $sql = "
    INSERT INTO {cv}
     (name,definition)
    VALUES
     ('%s','%s')
  ";
  $previous_db = tripal_db_set_active('chado');
  $db = db_query($sql, $name, $desc);
  tripal_db_set_active($previous_db);
  if ($db) {
    drupal_set_message(t("Controlled vocabulary added"));
  }
  else {
    drupal_set_message(t("Failed to add controlled vocabulary."), 'error');
  }

}

//////////////////////////////////////////
// Add Controlled Vocabulary Term
//////////////////////////////////////////

/**
 * Purpose: Provides the form that allows adding of terms to an existing
 *   controlled vocabulary
 *
  * @ingroup tripal_cv
 */
function tripal_cv_add_cvterm_form(&$form_state) {
  $form = array();

  $results = tripal_core_chado_select(
    'cv',
    array('cv_id', 'name'),
    array()
  );
  $cvs = array();
  $cvs[] = '';
  foreach ($results as $cv) {
    $cvs[$cv->cv_id] = $cv->name;
  }

  $form['cv_id'] = array(
    '#title' => t('Controlled Vocabulary/Ontology Name'),
    '#type' => 'select',
    '#options' => $cvs,
    '#ahah' => array(
       'path' => 'admin/tripal/tripal_cv/add_cvterm/js',
       'wrapper' => 'cvterm-add-div',
       'effect' => 'fade',
       'event' => 'change',
       'method' => 'replace',
    ),
    '#required' => TRUE,
  );

  $form['add_cvterm'] = array(
    '#type'           => 'item',
    '#value'            => t('Please select a vocabulary above to add a term to it'),
    '#prefix'         => '<div id="cvterm-add-div">',
    '#suffix'         => '</div>'
  );

  if ($form_state['values']['cv_id']) {

    $form['add_cvterm'] = array(
      '#type'           => 'fieldset',
      '#title'          => t('Add Term to the current Controlled Vocabulary'),
      '#prefix'         => '<div id="cvterm-add-div">',
      '#suffix'         => '</div>'
    );

    $form['add_cvterm']['name']= array(
      '#type'          => 'textfield',
      '#title'         => t("Term Name"),
      '#description'   => t('Please enter the name for this vocabulary term.'),
      '#required'      => FALSE,
      '#weight'        => 1,
      '#required' => TRUE,
    );

    $form['add_cvterm']['definition']= array(
      '#type'          => 'textarea',
      '#title'         => t('Description'),
      '#description'   => t('Please enter a description for this term'),
      '#weight'        => 2
    );

    $form['add_cvterm']['is_relationshiptype'] = array(
      '#type'          => 'checkbox',
      '#title'         => t('This term describes a relationship?'),
      '#weight'        => 3,
    );

    $form['add_cvterm']['is_obsolete'] = array(
      '#type'          => 'checkbox',
      '#title'         => t('This term is obsolete?'),
      '#weight'        => 3,
    );

    $results = tripal_core_chado_select(
      'db',
      array('db_id', 'name'),
      array()
    );
    $dbs = array();
    $dbs[] = '';
    foreach ($results as $db) {
      $dbs[$db->db_id] = $db->name;
    }
    $form['add_cvterm']['db_id'] = array(
      '#type'         => 'select',
      '#title'         => t('Database'),
      '#description'   => t('All terms must be assocated with an external database.
                          Please select the external database to associate with
                          this term'),
      '#options'      => $dbs,
      '#weight'        => 4,
      '#required' => TRUE,
    );

    $form['add_cvterm']['submit'] = array(
      '#type'          => 'submit',
      '#value'         => 'Add Term',
      '#weight'        => 5
    );

  } //end of if cv selected


  return $form;
}

/**
 * Purpose: Validates the input for adding a cvterm
 *
  * @ingroup tripal_cv
 */
function tripal_cv_add_cvterm_form_validate($form, &$form_state) {

  // Ensure that submit does not get called unless the AHAH in the form was called
  if (!empty($form_state['ahah_submission'])) {
    return;
  }

}

/**
 * Purpose: Adds terms to an existing controlled vocabulary
 *
 * @ingroup tripal_cv
 */
function tripal_cv_add_cvterm_form_submit($form, &$form_state) {

  // Ensure the AHAH in the form was called
  if (!empty($form_state['ahah_submission'])) {
    return;
  }

  // Add dbxref for cvterm
  $dbxref_insert_values = array(
    'db_id' => $form_state['values']['db_id'],
    'accession' => $form_state['values']['name'],
    'description' => 'cvterm reference',
  );
  $dbxref_results = tripal_core_chado_select(
    'dbxref',
    array('dbxref_id'),
    $dbxref_insert_values
  );
  if (!$dbxref_results[0]->dbxref_id) {
    $dbxref_insert_values['version'] = '1';
    $dbxref_success = tripal_core_chado_insert(
      'dbxref',
      $dbxref_insert_values
    );
  }
  else {
    $dbxref_success = TRUE;
  }

  // Add cvterm
  if ($dbxref_success) {
    $insert_values = array(
      'cv_id' => $form_state['values']['cv_id'],
      'name' => $form_state['values']['name'],
      'definition' => $form_state['values']['definition'],
      'dbxref_id' => $dbxref_insert_values,
      'is_obsolete' => (string) $form_state['values']['is_obsolete'],
      'is_relationshiptype' => (string) $form_state['values']['is_relationshiptype'],
    );
    $success = tripal_core_chado_insert(
      'cvterm',
      $insert_values
    );
    if ($success) {
      drupal_set_message(t('Successfully Added Term to Controlled Vocabulary'));
    }
    else {
      drupal_set_message(t('Unable to add controlled vocabulary term'), 'error');
      watchdog(
        'tripal_cv',
        'Cvterm Insert: Unable to insert cvterm where values: %values',
        array('%values' => print_r($insert_values, TRUE)),
        WATCHDOG_ERROR
      );
    }
  }
  else {
    drupal_set_message(t('Unable to add database reference for controlled vocabulary term'), 'error');
    watchdog(
      'tripal_cv',
      'Cvterm Insert: Unable to insert dbxref for cvterm where values: %values',
      array('%values' => print_r($dbxref_insert_values, TRUE)),
      WATCHDOG_ERROR
    );
  }

}

/**
 * Purpose: This function gets called when the selecting of a cv from
 *   the select list triggers it. This function simply rebuilds the form
 *   with new information. No elements are created here
 *
 * @ingroup tripal_cv
 */
function tripal_cv_add_cvterm_callback() {

  // Retrieve the form from the cache
  $form_state = array('storage' => NULL);
  $form_build_id = filter_xss($_POST['form_build_id']);
  $form = form_get_cache($form_build_id, $form_state);

  // Preparing to process the form
  $args = $form['#parameters'];
  $form_id = array_shift($args);
  $form_state['post'] = $form['#post'] = $_POST;
  $form['#programmed'] = $form['#redirect'] = FALSE;

  // Sets the form_state so that the validate and submit handlers can tell
  // when the form is submitted via AHAH
  $form_state['ahah_submission'] = TRUE;

  // Process the form with drupal_process_form. This function calls the submit
  // handlers, which put whatever was worthy of keeping into $form_state.
  drupal_process_form($form_id, $form, $form_state);

  // You call drupal_rebuild_form which destroys $_POST.
  // The form generator function is called and creates the form again but since
  // it knows to use $form_state, the form will be different.
  // The new form gets cached and processed again, but because $_POST is
  // destroyed, the submit handlers will not be called again.
  $form = drupal_rebuild_form($form_id, $form_state, $args, $form_build_id);

  // This is the only piece specific to your form
  // Picks a piece of the form and renders it
  // Specifcally the add cvterm fieldset and all contained fields
  $add_cvterm_form = $form['add_cvterm'];
  unset($add_cvterm_form['#prefix'], $add_cvterm_form['#suffix']);
  $output = theme('status_messages') . drupal_render($add_cvterm_form);

  // Final rendering callback.
  drupal_json(array('status' => TRUE, 'data' => $output));
}

///////////////////////////////
// Ontology Loader
//////////////////////////////

/**
 * Purpose: Provides the form to load an already existing controlled
 *  Vocabulary into chado
 *
  * @ingroup tripal_obo_loader
 */
function tripal_cv_obo_form(&$form_state = NULL) {

  // get a list of db from chado for user to choose
  $sql = "SELECT * FROM {tripal_cv_obo} ORDER BY obo_id";
  $results = db_query($sql);

  $obos = array();
  $obos[] = '';
  while ($obo = db_fetch_object($results)) {
    $obos[$obo->obo_id] = "$obo->name  | $obo->path";
  }

  $form['obo_existing'] = array(
    '#type' => 'fieldset',
    '#title' => t('Use a Saved Ontology OBO Reference')
  );

  $form['obo_new'] = array(
    '#type' => 'fieldset',
    '#title' => t('Use a New Ontology OBO Reference')
  );

  $form['obo_existing']['existing_instructions']= array(
    '#value' => t('The Ontology OBO files listed in the drop down below have been automatically added upon
                   installation of the Tripal CV module or were added from a previous upload.  Select
                   an OBO, then click the submit button to load the vocabulary into the database.  If the
                   vocabularies already exist then the ontology will be updated.'),
    '#weight'        => -1
  );

  $form['obo_existing']['obo_id'] = array(
    '#title' => t('Ontology OBO File Reference'),
    '#type' => 'select',
    '#options' => $obos,
    '#weight'        => 0
  );

  $form['obo_new']['path_instructions']= array(
    '#value' => t('Provide the name and path for the OBO file.  If the vocabulary OBO file
                   is stored local to the server provide a file name. If the vocabulry is stored remotely,
                   provide a URL.  Only provide a URL or a local file, not both.'),
    '#weight'        => 0
  );

  $form['obo_new']['obo_name']= array(
    '#type'          => 'textfield',
    '#title'         => t('New Vocabulary Name'),
    '#description'   => t('Please provide a name for this vocabulary.  After upload, this name will appear in the drop down
                           list above for use again later.'),
    '#weight'        => 1
  );

  $form['obo_new']['obo_url']= array(
    '#type'          => 'textfield',
    '#title'         => t('Remote URL'),
    '#description'   => t('Please enter a URL for the online OBO file.  The file will be downloaded and parsed.
                           (e.g. http://www.obofoundry.org/ro/ro.obo'),
    '#default_value' => $default_desc,
    '#weight'        => 2
  );

  $form['obo_new']['obo_file']= array(
    '#type'          => 'textfield',
    '#title'         => t('Local File'),
    '#description'   => t('Please enter the full system path for an OBO definition file, or a path within the Drupal
                           installation (e.g. /sites/default/files/xyz.obo).  The path must be accessible to the
                           server on which this Drupal instance is running.'),
    '#default_value' => $default_desc,
    '#weight'        => 3
  );

  $form['submit'] = array(
    '#type'         => 'submit',
    '#value'        => t('Submit'),
    '#weight'       => 5,
    '#executes_submit_callback' => TRUE,
  );

  $form['#redirect'] = 'admin/tripal/tripal_cv/obo_loader';

  return $form;
}

/**
 * Purpose: The submit function for the load ontology form. It registers a
 *   tripal job to run the obo_loader.php script
 *
   * @ingroup tripal_obo_loader
 */
function tripal_cv_obo_form_submit($form, &$form_state) {
  global $user;

  $obo_id =  $form_state['values']['obo_id'];
  $obo_name =  $form_state['values']['obo_name'];
  $obo_url =  $form_state['values']['obo_url'];
  $obo_file  = $form_state['values']['obo_file'];

  $sql = "SELECT * FROM {tripal_cv_obo} WHERE obo_id = %d";
  $obo = db_fetch_object(db_query($sql, $obo_id));

  if ($obo_id) {
    $args = array($obo_id);
    tripal_add_job("Load OBO $obo->name", 'tripal_cv',
       "tripal_cv_load_obo_v1_2_id", $args, $user->uid);
  }
  else {
    if ($obo_url) {
      $args = array($obo_name, $obo_url);
      tripal_add_job("Load OBO $obo_name", 'tripal_cv',
        "tripal_cv_load_obo_v1_2_url", $args, $user->uid);
    }
    elseif ($obo_file) {
      $args = array($obo_name, $obo_file);
      tripal_add_job("Load OBO $obo_name", 'tripal_cv',
        "tripal_cv_load_obo_v1_2_file", $args, $user->uid);
    }
  }

}

////////////////////////////////////
// cvterm path management
///////////////////////////////////

/**
 * Form for re-doing the cvterm path
 *
 * @ingroup tripal_cv
 */
function tripal_cv_cvtermpath_form() {

  $previous_db = tripal_db_set_active('chado');  // use chado database
  // get a list of db from chado for user to choose
  $sql = "SELECT * FROM {cv} WHERE NOT name = 'tripal' ORDER BY name ";
  $results = db_query($sql);
  tripal_db_set_active($previous_db); // use drupal database

  $cvs = array();
  $cvs[] = '';
  while ($cv = db_fetch_object($results)) {
    $cvs[$cv->cv_id] = $cv->name;
  }

  $form['cvid'] = array(
    '#title' => t('Controlled Vocabulary/Ontology Name'),
    '#type' => 'select',
    '#options' => $cvs,
    '#description' => t('The Chado cvtermpath is a database table that provides lineage for ontology terms 
      and is useful for quickly finding any ancestor parent of a term.  This table must be populated for each
      ontology.  Select a controlled vocabulary for which you would like to upate the cvtermpath.'),
  );

  $form['description'] = array(
    '#type' => 'item',
    '#value' => t("Submit a job to update chado cvtermpath table."),
    '#weight' => 1,
  );

  $form['button'] = array(
    '#type' => 'submit',
    '#value' => t('Update cvtermpath'),
    '#weight' => 2,
  );

  return $form;
}

/**
 * Cvterm path form submit
 *
 * @ingroup tripal_cv
 */
function tripal_cv_cvtermpath_form_submit($form, &$form_state) {
  global $user;

  $cvid =  $form_state['values']['cvid'];

  // first get the controlled vocabulary name:
  $previous_db = tripal_db_set_active('chado');
  $cv = db_fetch_object(db_query("SELECT * FROM {cv} WHERE cv_id = %d", $cvid));
  tripal_db_set_active($previous_db);

  // Submit a job to update cvtermpath
  $job_args = array($cvid);
  if ($form_state['values']['op'] == t('Update cvtermpath')) {
    tripal_add_job("Update cvtermpath: $cv->name", 'tripal_cv',
       'tripal_cv_update_cvtermpath', $job_args, $user->uid);
  }
}

/**
 * Update the cvtermpath table
 *
 * @ingroup tripal_cv
 */
function tripal_cv_update_cvtermpath($cvid = NULL, $job_id = NULL) {

  // first get the controlled vocabulary name:
  $previous_db = tripal_db_set_active('chado');
  $cv = db_fetch_object(db_query("SELECT * FROM {cv} WHERE cv_id = %d", $cvid));
  print "\nUpdating cvtermpath for $cv->name...\n";

  // now fill the cvtermpath table
  // @coder-ignore: using a function rather then tablename therefore table prefixing doesn't apply
  $sql = "SELECT * FROM fill_cvtermpath('%s')";
  db_query($sql, $cv->name);
  tripal_db_set_active($previous_db);

  return;
}

//////////////////////////////////////
// @section Miscellaneous
// @todo check to see if these functions are still needed and/or if they
//   should be moved to the api file
//////////////////////////////////////

/**
 * Get the CV ID based on name
 *
 * @ingroup tripal_cv
 */
function tripal_cv_get_cv_id($cv_name) {

  $sql = "
    SELECT cv_id FROM {cv} WHERE name = '%s'
  ";
  $previous_db = tripal_db_set_active('chado');
  $cv = db_fetch_object(db_query($sql, $cv_name));
  tripal_db_set_active($previous_db);

  return $cv->cv_id;
}

/**
 * Returns a themed cvterm definition table
 *
 * @ingroup tripal_cv
 */
function tripal_cv_cvterm_edit($cvterm_id) {

  $sql = "
    SELECT CVT.name as cvtermname, CVT.definition, CV.name as cvname
    FROM {CVTerm} CVT
      INNER JOIN CV on CVT.cv_id = CV.cv_id
    WHERE CVT.cvterm_id = %d
  ";
  $previous_db = tripal_db_set_active('chado');
  $cvterm = db_fetch_object(db_query($sql, $cvterm_id));
  tripal_db_set_active($previous_db);

  return theme('tripal_cv_cvterm_edit', $cvterm);
}

/**
 * Does the actual themeing of the cvterm definition table
 *
 * @ingroup tripal_cv
 */
function theme_tripal_cv_cvterm_edit(&$cvterm) {

  $output = "
    <div id=\"cvterm\">
    <table>
      <tr><th>Term</th><td>$cvterm->cvtermname</td></tr>
      <tr><th>Vocabulary</th><td>$cvterm->cvname</td></tr>
      <tr><th>Definition</th><td>$cvterm->definition</td></tr>
    </table>
    </div>
  ";

  return $output;
}

/**
 * Implements hook_coder_ignore().
 * Defines the path to the file (tripal_cv.coder_ignores.txt) where ignore rules for coder are stored
 */
function tripal_cv_coder_ignore() {
  return array(
    'path' => drupal_get_path('module', 'tripal_cv'),
    'line prefix' => drupal_get_path('module', 'tripal_cv'),
  );
}