tripal/tripal_cv/tripal_cv.module

<?php

require_once "charts.php";
require_once "trees.php";
require_once "obo_loader.php";

//
// Copyright 2009 Clemson University
//
/*************************************************************************
*
*/
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 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');
}
/*************************************************************************
*
*/
function tripal_cv_menu() {
   $items = array();

   $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'] = array(
     'title' => 'Controlled Vocabulary Management',
     '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/new'] = 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/obo'] = array(
     'title' =>'Add/Update 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' => t('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' => t('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' => t('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' => t('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' => t('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' => t('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' => t('CV Term Editor'),
      'page callback' => 'tripal_cv_cvterm_edit',
      'page arguments' => array(1),
      'access arguments' => array('edit chado_cv content'),
      'type' => MENU_CALLBACK
   );

   return $items;
}
/*******************************************************************************
 *  The following function proves access control for users trying to
 *  perform actions on data managed by this module
 */
function chado_cv_access($op, $node, $account){
  if ($op == 'create') {
      return user_access('create chado_cv content', $account);
   }

   if ($op == 'update') {
      if (user_access('edit chado_cv content', $account)) {
         return TRUE;
      }
   }
   if ($op == 'delete') {
      if (user_access('delete chado_cv content', $account)) {
         return TRUE;
      }
   }
   if ($op == 'view') {
      if (user_access('access chado_cv content', $account)) {
         return TRUE;
      }
   }
   return FALSE;
}
/*******************************************************************************
*  Set the permission types that the chado module uses.  Essentially we
*  want permissionis that protect creation, editing and deleting of chado
*  data objects
*/
function tripal_cv_perm(){
   return array(
      'access chado_cv content',
      'create chado_cv content',
      'delete chado_cv content',
      'edit chado_cv content',
   );
}



/*************************************************************************
*
*/
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;
}
/*************************************************************************
*
*/
function tripal_cv_select_form(){

	$previous_db = 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);
	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;
}
/*************************************************************************
*
*/
function tripal_ajax_cv_edit (){ 
   // get the database id, build the form and then return the JSON object
   $cvid = $_POST['cvid'];
   $form = drupal_get_form('tripal_cv_edit_form',$cvid);
   drupal_json(array('status' => TRUE, 'data' => $form));
}
/*************************************************************************
*
*/
function tripal_cv_add_form(&$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 $form;
}
/*************************************************************************
*
*/
function tripal_cv_obo_form(&$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['instructions']= array(
      '#value' => t('Use this interface to upload a controlled vocabulary in OBO format.  A new vocabulary and its 
                     associated terms will be added to the database the first time an OBO is uploaded.  Each
                     subsequent upload will update the terms.  The format of the OBO should be in v1.2 format,
                     however, this loader does support some older styles formats. '),
      '#weight'        => -2
   );

   $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.  Note that the name of the 
                     ontology provided here may not match the namespace of the vocabulary.  For instance,
                     the Gene Ontology will add three vocabularies: biological_process, cellular_component, and 
                     molecular_function.'),
      '#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';


   return $form;
}
/*************************************************************************
*
*/
function tripal_cv_edit_form(&$form_state = NULL,$cvid = NULL){

  
   $sql = "SELECT * FROM {cv} WHERE cv_id = %d ";
   $previous_db = db_set_active('chado');
   $cv = db_fetch_object(db_query($sql,$cvid));
   db_set_active($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 $form;
}
/************************************************************************
*
*/
function tripal_cv_edit_form_submit($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 = db_set_active('chado');
      $db = db_query($sql,$name,$desc,$cvid);
      db_set_active($previous_db);
      if($db){
        drupal_set_message("Controlled vocabulary updated");
      } else {
        drupal_set_message("Failed to update controlled vocabulary.");
      }
   } 
   if(strcmp($op,'Delete')==0){
      $sql = "
         DELETE FROM {cv}
         WHERE cv_id = %d
      ";
      $previous_db = db_set_active('chado');
      $db = db_query($sql,$cvid);
      db_set_active($previous_db);
      if($db){
        drupal_set_message("Controlled vocabulary deleted");
      } else {
        drupal_set_message("Failed to delete controlled vocabulary.");
      }
   }


   return '';
}
/************************************************************************
*
*/
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 = db_set_active('chado');
   $db = db_query($sql,$name,$desc);
   db_set_active($previous_db);
   if($db){
     drupal_set_message("Controlled vocabulary added");
   } else {
     drupal_set_message("Failed to add controlled vocabulary.");
   }


   return '';
}
/************************************************************************
*
*/
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);
      } 
   }

   return '';
}
/*************************************************************************
*
*/
function tripal_cv_cvtermpath_form () {

	$previous_db = 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);
	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('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 $form;
}
/*************************************************************************
*
*/
function tripal_cv_cvtermpath_form_validate($form, &$form_state) {
   global $user;

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

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

   // first get the controlled vocabulary name:
   $previous_db = 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
   $sql = "SELECT * FROM fill_cvtermpath('%s')";
   db_query($sql,$cv->name);         
   db_set_active($previous_db);
   return;
}

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

/*************************************************************************
*/
function tripal_cv_get_cv_id($cv_name){

   $sql = "
      SELECT cv_id FROM {cv} WHERE name = '%s'
   ";
   $previous_db = db_set_active('chado');
   $cv = db_fetch_object(db_query($sql,$cv_name));
   db_set_active($previous_db);
   return $cv->cv_id;
}
/*************************************************************************
*
*/
function tripal_cv_cvterm_edit($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 = db_set_active('chado');
   $cvterm = db_fetch_object(db_query($sql,$cvterm_id));
   db_set_active($previous_db);
   return theme('tripal_cv_cvterm_edit',$cvterm);
}
/*************************************************************************
*
*/
function theme_tripal_cv_cvterm_edit(&$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;
}