tripal/tripal_analysis/tripal_analysis.module

<?php

/**
 * @file
 * Contains all the main hook implementations for the tripal_analysis module
 *
 * @defgroup tripal_analysis Analysis Module
 * @{
 * Provides functions for managing chado analysis' including creating details pages for each one
 * @}
 * @ingroup tripal_modules
 */

require('api/tripal_analysis.api.inc');
require('includes/tripal_analysis_privacy.inc');


/**
 * Add tripal javascript to page headers
 *
 * @ingroup tripal_analysis
 */
function tripal_analysis_init() {
  drupal_add_js(drupal_get_path('theme', 'tripal') . '/js/tripal_analysis.js');
}

/**
 * Implementation of hook_menu().
 * Entry points and paths of the module
 *
 * @ingroup tripal_analysis
 */
function tripal_analysis_menu() {
  //Sync analysis
  $items['chado_sync_analyses'] = array(
     'title' => 'Sync Data',
     'page callback' => 'tripal_analysis_sync_analyses',
     'access arguments' => array('administer tripal analyses'),
     'type' => MENU_CALLBACK
  );
  // Tripal Analysis administrative settings
  $items['admin/tripal/tripal_analysis'] = array(
      'title' => 'Analyses',
      'description' => 'Basic Description of Tripal Analysis Module Functionality.',
      'page callback' => 'theme',
      'page arguments' => array('tripal_analysis_admin'),
      'access arguments' => array('administer tripal analyses'),
      'type' => MENU_NORMAL_ITEM,
      'file' => 'includes/tripal_analysis.admin.inc',
  );

  $items['admin/tripal/tripal_analysis/configuration'] = array(
      'title' => 'Configuration',
      'description' => 'Settings for the displays of analysis results.',
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_analysis_admin'),
      'access arguments' => array('administer tripal analyses'),
      'type' => MENU_NORMAL_ITEM,
      'file' => 'includes/tripal_analysis.admin.inc',
  );
  return $items;
}

/**
 * Provide information to drupal about the node types that we're creating
 * in this module
 *
 * @ingroup tripal_analysis
 */
function tripal_analysis_node_info() {
  $nodes = array();
  $nodes['chado_analysis'] = array(
      'name' => t('Analysis'),
      'module' => 'chado_analysis',
      'description' => t('An analysis from the chado database'),
      'has_title' => FALSE,
      'title_label' => t('Analysis'),
      'has_body' => FALSE,
      'body_label' => t('Analysis Description'),
      'locked' => TRUE
  );
  return $nodes;
}

/**
 *  When a new chado_analysis node is created we also need to add information
 *  to our chado_analysis table.  This function is called on insert of a new
 *  node of type 'chado_analysis' and inserts the necessary information.
 *
 * @ingroup tripal_analysis
 */
function chado_analysis_insert($node) {
  global $user;

  // Create a timestamp so we can insert it into the chado database
  $time = $node->timeexecuted;
  $month = $time['month'];
  $day = $time['day'];
  $year = $time['year'];
  $timestamp = $month . '/' . $day . '/' . $year;

  // If this analysis already exists then don't recreate it in chado
  $analysis_id = $node->analysis_id;
  if ($analysis_id) {
    $values = array('analysis_id' => $node->analysis_id);
    $result = tripal_core_chado_select('analysis', array('analysis_id'), $values);
    if($result and count($result) > 0) {
      $analysis = $result[0];
    }
  }
  
  // If the analysis doesn't exist then let's create it in chado.
  if (!$analysis) {
      // insert and then get the newly inserted analysis record
      $values = array(
          'name' => $node->analysisname,
          'description' => $node->description,
          'program' => $node->program,
          'programversion' => $node->programversion,
          'algorithm' => $node->algorithm,
          'sourcename' => $node->sourcename,
          'sourceversion' => $node->sourceversion,
          'sourceuri' => $node->sourceuri,
          'timeexecuted' => $timestamp
      );
      if (tripal_core_chado_insert('analysis', $values)) {
        $analysis = tripal_core_chado_select('analysis', array('*'), $values);
        $analysis_id = $analysis[0]->analysis_id;
      }
  }

  // Make sure the entry for this analysis doesn't already exist in the
  // chado_analysis table if it doesn't exist then we want to add it.
  $node_check_sql = "SELECT * FROM {chado_analysis} ".
                     "WHERE analysis_id = %d";
  $node_check = db_fetch_object(db_query($node_check_sql, $analysis_id));
  if (!$node_check) {
    // next add the item to the drupal table
    $sql = "INSERT INTO {chado_analysis} (nid, vid, analysis_id) ".
             "VALUES (%d, %d, %d)";
    db_query($sql, $node->nid, $node->vid, $analysis_id);
    // Create a title for the analysis node using the unique keys so when the
    // node is saved, it will have a title
    $record = new stdClass();
    // If the analysis has a name, use it as the node title. If not, construct
    // the title using program, programversion, and sourcename
    if ($node->analysisname) {
      $record->title = $node->analysisname;
    }
    else {
      //Construct node title as "program (version)
      $record->title = "$node->program ($node->programversion)";
    }
    $record->nid = $node->nid;
    drupal_write_record('node', $record, 'nid');
    drupal_write_record('node_revisions', $record, 'nid');
  }

   // add the analysis to the node object for
   // use by other analysis modules that may be using this function
    $node->analysis = $analysis;
    $node->analysis_id = $analysis_id; // we need to set this for children
}

/**
 * Removes analysis from the chado database
 *
 * @param $node
 *   The node object specifying which chado record to delete
 *
 * @ingroup tripal_analysis
 */
function chado_analysis_delete($node) {
  $analysis_id = chado_get_id_for_node('analysis', $node);
  
  // if we don't have an organism id for this node then this isn't a node of
  // type chado_organism or the entry in the chado_organism table was lost.
  if (!$analysis_id) {
    return;
  }

  // Remove data from the {chado_analysis}, {node}, and {node_revisions} tables
  $sql_del = "DELETE FROM {chado_analysis} ".
              "WHERE nid = %d ".
              "AND vid = %d";
  db_query($sql_del, $node->nid, $node->vid);
  $sql_del = "DELETE FROM {node} ".
              "WHERE nid = %d ".
              "AND vid = %d";
  db_query($sql_del, $node->nid, $node->vid);
  $sql_del = "DELETE FROM {node_revisions} ".
              "WHERE nid = %d ".
              "AND vid = %d";
  db_query($sql_del, $node->nid, $node->vid);

  //Remove from analysis and analysisprop tables of chado database as well
  chado_query("DELETE FROM {analysis} WHERE analysis_id = %d", $analysis_id);
}

/**
 * Update analyses
 *
 * @param $node
 *   The updated node object
 *
 * @ingroup tripal_analysis
 */
function chado_analysis_update($node) {
  global $user;
  if ($node->revision) {
    // TODO -- decide what to do about revisions
  }
  // Create a timestamp so we can insert it into the chado database
  $time = $node->timeexecuted;
  $month = $time['month'];
  $day = $time['day'];
  $year = $time['year'];
  $timestamp = $month . '/' . $day . '/' . $year;

  // get the analysis_id for this node:
  $sql = "SELECT analysis_id ".
           "FROM {chado_analysis} ".
           "WHERE nid = %d";
  $analysis_id = db_fetch_object(db_query($sql, $node->nid))->analysis_id;

  $sql = "UPDATE {analysis} ".
           "SET name = '%s', ".
           "    description = '%s', ".
           "    program = '%s', ".
           "    programversion = '%s', ".
           "    algorithm = '%s', ".
           "    sourcename = '%s', ".
           "    sourceversion = '%s', ".
           "    sourceuri = '%s', ".
           "    timeexecuted = '%s' ".
           "WHERE analysis_id = %d ";

  chado_query($sql, $node->analysisname, $node->description, $node->program,
    $node->programversion, $node->algorithm, $node->sourcename,
    $node->sourceversion, $node->sourceuri, $timestamp, $analysis_id);

  // Create a title for the analysis node using the unique keys so when the
  // node is saved, it will have a title
  $record = new stdClass();
  // If the analysis has a name, use it as the node title. If not, construct
  // the title using program, programversion, and sourcename
  if ($node->analysisname) {
    $record->title = $node->analysisname;
  }
  else {
    //Construct node title as "program (version)
    $record->title = "$node->program ($node->programversion)";
  }

  $record->nid = $node->nid;
  drupal_write_record('node', $record, 'nid');
  drupal_write_record('node_revisions', $record, 'nid');
}

/**
 *  When editing or creating a new node of type 'chado_analysis' we need
 *  a form.  This function creates the form that will be used for this.
 *
 * @ingroup tripal_analysis
 */
function chado_analysis_form($node) {

  $analysis = $node->analysis;

  // add in the description column. It is a text field and may not be included
  // if the text is too big.
  $analysis = tripal_core_expand_chado_vars($analysis, 'field', 'analysis.description');

  // get form defaults
  $analysis_id = $node->analysis_id;
  if (!$analysis_id) {
    $analysis_id = $analysis->analysis_id;
  }
  $analysisname = $node->analysisname;
  if (!$analysisname) {
    $analysisname = $analysis->name;
  }
  $program = $node->program;
  if (!$program) {
    $program = $analysis->program;
  }
  $programversion = $node->programversion;
  if (!$programversion) {
    $programversion = $analysis->programversion;
  }
  $algorithm = $node->algorithm;
  if (!$algorithm) {
    $algorithm = $analysis->algorithm;
  }
  $sourcename = $node->sourcename;
  if (!$sourcename) {
    $sourcename = $analysis->sourcename;
  }
  $sourceversion = $node->sourceversion;
  if (!$sourceversion) {
    $sourceversion = $analysis->sourceversion;
  }
  $sourceuri = $node->sourceuri;
  if (!$sourceuri) {
    $sourceuri = $analysis->sourceuri;
  }
  $timeexecuted = $node->timeexecuted;
  if (!$timeexecuted) {
    $timeexecuted = $analysis->timeexecuted;
  }
  $description = $node->description;
  if (!$description) {
    $description = $analysis->description;
  }
  $form = array();
  $form['title']= array(
      '#type' => 'hidden',
      '#default_value' => $node->title,
  );
  $form['analysis_id']= array(
      '#type' => 'hidden',
      '#default_value' => $analysis_id,
  );
  $form['analysisname']= array(
      '#type' => 'textfield',
      '#title' => t('Analysis Name'),
      '#required' => TRUE,
      '#default_value' => $analysisname,
      '#description' => t("This should be a brief name that
         describes the analysis succintly. This name will helps the user find analyses."),
  );
  $form['program']= array(
      '#type' => 'textfield',
      '#title' => t('Program'),
      '#required' => TRUE,
      '#default_value' => $program,
      '#description' => t("Program name, e.g. blastx, blastp, sim4, genscan."),
  );
  $form['programversion']= array(
      '#type' => 'textfield',
      '#title' => t('Program Version'),
      '#required' => TRUE,
      '#default_value' => $programversion,
      '#description' => t("Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000]. Enter 'n/a' if no version is available."),
  );
  $form['algorithm']= array(
      '#type' => 'textfield',
      '#title' => t('Algorithm'),
      '#required' => FALSE,
      '#default_value' => $algorithm,
      '#description' => t("Algorithm name, e.g. blast."),
  );
  $form['sourcename']= array(
      '#type' => 'textfield',
      '#title' => t('Source Name'),
      '#required' => TRUE,
      '#default_value' => $sourcename,
      '#description' => t('The name of the source data.  This could be a file name, data set name or a
           small description for how the data was collected.  For long descriptions use the description field below'),

  );
  $form['sourceversion']= array(
      '#type' => 'textfield',
      '#title' => t('Source Version'),
      '#required' => FALSE,
      '#default_value' => $sourceversion,
      '#description' => t('If the source dataset has a version, include it here'),
  );
  $form['sourceuri']= array(
      '#type' => 'textfield',
      '#title' => t('Source URI'),
      '#required' => FALSE,
      '#default_value' => $sourceuri,
      '#description' => t("This is a permanent URL or URI for the source of the analysis.
         Someone could recreate the analysis directly by going to this URI and
         fetching the source data (e.g. the blast database, or the training model)."),
  );
  // Get time saved in chado
  $default_time = $timeexecuted;
  $year = preg_replace("/^(\d+)-\d+-\d+ .*/", "$1", $default_time);
  $month = preg_replace("/^\d+-0?(\d+)-\d+ .*/", "$1", $default_time);
  $day = preg_replace("/^\d+-\d+-0?(\d+) .*/", "$1", $default_time);
  // If the time is not set, use current time
  if (!$default_time) {
    $default_time = time();
    $year = format_date($default_time, 'custom', 'Y');
    $month = format_date($default_time, 'custom', 'n');
    $day = format_date($default_time, 'custom', 'j');
  }
  $form['timeexecuted']= array(
      '#type' => 'date',
      '#title' => t('Time Executed'),
      '#required' => TRUE,
      '#default_value' => array(
         'year' => $year,
         'month' => $month,
         'day' => $day,
      ),
  );
  $form['description']= array(
      '#type' => 'textarea',
      '#rows' => 15,
      '#title' => t('Materials & Methods (Description and/or Program Settings)'),
      '#required' => FALSE,
      '#default_value' => $description,
      '#description' => t('Please provide all necessary information to allow
         someone to recreate the analysis, including materials and methods
         for collection of the source data and performing the analysis'),
  );

  return $form;
}

 /**
  *  When a node is requested by the user this function is called to allow us
  *  to add auxiliary data to the node object.
  *
  * @ingroup tripal_analysis
  */
function chado_analysis_load($node) {

   // get the feature details from chado
  $analysis_id = chado_get_id_for_node('analysis', $node);

  $values = array('analysis_id' => $analysis_id);
  $analysis = tripal_core_generate_chado_var('analysis', $values);

  $additions = new stdClass();
  $additions->analysis = $analysis;
  return $additions;
}

/**
 *  This function customizes the view of the chado_analysis node.  It allows
 *  us to generate the markup.
 *
 * @ingroup tripal_analysis
 */
function chado_analysis_view($node, $teaser = FALSE, $page = FALSE) {
  // use drupal's default node view:
  if (!$teaser) {
    $node = node_prepare($node, $teaser);
    // When previewing a node submitting form, it shows 'Array' instead of
    // correct date format. We need to format the date here
    $time = $node->timeexecuted;
    if (is_array($time)) {
      $month = $time['month'];
      $day = $time['day'];
      $year = $time['year'];
      $timestamp = $year . '-' . $month . '-' . $day;
      $node->timeexecuted = $timestamp;
    }
  }
  return $node;
}



/**
 * Validates the user input before creating an analysis node
 *
 * @ingroup tripal_analysis
 */
function chado_analysis_validate($node, &$form) {
   // use the analysis parent to validate the node
  tripal_analysis_validate($node, $form);
}

/**
 * This validation is being used for three activities:
 *   CASE A: Update a node that exists in both drupal and chado
 *   CASE B: Synchronizing a node from chado to drupal
 *   CASE C: Inserting a new node that exists in niether drupal nor chado
 *
 * @ingroup tripal_analysis
 */
function tripal_analysis_validate($node, &$form) {
  
 
  // Only nodes being updated will have an nid already
  if (!is_null($node->nid)) {    
    // CASE A: We are validating a form for updating an existing node
    
    // get the existing node    
    $values = array('analysis_id' => $node->analysis_id);      
    $result = tripal_core_chado_select('analysis', array('*'), $values);
    $analysis = $result[0];
      
    // if the name has changed make sure it doesn't conflict with an existing name
    if($analysis->name != $node->analysisname) {
      $values = array('name' => $node->analysisname);
      $result = tripal_core_chado_select('analysis', array('analysis_id'), $values);
      if($result and count($result) > 0) {
        form_set_error('analysisname', 'Cannot update the analysis with this analysis name. An analysis with this name already exists.');
        return;
      }  
    }
    
    // if the unique constraint has changed check to make sure it doesn't conflict with an
    // existing record
    if($analysis->program != $node->program or $analysis->programversion != $node->programversion or 
       $analysis->sourcename != $node->sourcename) {
      $values = array(
        'program' => $node->program,
        'programversion' => $node->programversion,
        'sourcename' => $node->sourcename,
      );
      $result = tripal_core_chado_select('analysis', array('analysis_id'), $values);
      if ($result and count($result) > 0) {
        if ($analysis->program != $node->program) {
          $field = 'program';  
        }
        if ($analysis->programversion != $node->programversion) {
          $field = 'programversion';  
        }
        if ($analysis->sourcename != $node->sourcename) {
          $field = 'sourcename';  
        }
        form_set_error($field, 'Cannot update the analysis with this program,
          program version and source name. An analysis with these values already exists.');
        return;
      }  
    }
  }
  else{
    // To differentiate if we are syncing or creating a new analysis altogther, see if an
    // analysis_id already exists
    if ($node->analysis_id and $node->analysis_id != 0) {
      // CASE B: Synchronizing a node from chado to drupal
      // we don't need to do anything.
    }
    else {
      // CASE C: We are validating a form for inserting a new node
      // The unique constraint for the chado analysis table is: program, programversion, sourcename
      $values = array(
        'program' => $node->program,
        'programversion' => $node->programversion,
        'sourcename' => $node->sourcename,
      );
      $analysis = tripal_core_chado_select('analysis', array('analysis_id'), $values);
      if ($analysis and count($analysis) > 0) {
        form_set_error('program', 'Cannot add the analysis with this program,
          program version and source name. An analysis with these values already exists.');
        return;
      }
      
      // make sure we have a unique analysis name. This is not a requirement 
      // for the analysis table but we use the analysis name for the Drupal node
      // title, so it should be unique      
      $values = array('name' => $node->analysisname);
      $result = tripal_core_chado_select('analysis', array('analysis_id'), $values);
      if($result and count($result) > 0) {
        form_set_error('analysisname', 'Cannot add the analysis with this analysis name. An analysis with this name already exists.');
        return;
      }
    }
  }
}

/**
 * Display help and module information
 * @param path which path of the site we're displaying help
 * @param arg array that holds the current path as would be returned from arg()
 * function
 * @return help text for the path
 *
 * @ingroup tripal_analysis
 */
function tripal_analysis_help($path, $arg) {
  $output = '';
  switch ($path) {
    case "admin/help#tripal_analysis":
      $output = '<p>' .
      t("Displays links to nodes created on this date") .
                '</p>';
      break;
  }
  return $output;
}

/**
 *  The following function proves access control for users trying to
 *  perform actions on data managed by this module
 *
 * @ingroup tripal_analysis
 */
function chado_analysis_access($op, $node, $account) {

  if ($op == 'create') {
    if (!user_access('create chado_analysis content', $account)) {
      return FALSE;
      }
  }
  if ($op == 'update') {
    if (!user_access('edit chado_analysis content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'delete') {
    if (!user_access('delete chado_analysis content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'view') {
    if (!user_access('access chado_analysis 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_analysis
 */
function tripal_analysis_perm() {
  return array(
    'access chado_analysis content',
    'create chado_analysis content',
    'delete chado_analysis content',
    'edit chado_analysis content',
    'administer tripal analyses',
  );
}

/**
 *  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_analysis
 */
function tripal_analysis_theme() {
  return array(
    'tripal_analysis_base' => array(
       'arguments' => array('node' => NULL),
       'template' => 'tripal_analysis_base',
    ),
    'tripal_feature_analyses' => array(
      'template' => 'tripal_feature_analyses',  
      'arguments' =>  array('node' => NULL),  
    ),
    'tripal_analysis_admin' => array(
      'template' => 'tripal_analysis_admin',  
      'arguments' =>  array(NULL),  
      'path' => drupal_get_path('module', 'tripal_analysis') . '/theme', 
    ),
  );
}
/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_analysis_block($op = 'list', $delta = 0, $edit=array()) {
  switch ($op) {
    case 'list':
      $blocks['base']['info'] = t('Tripal Analysis Details');
      $blocks['base']['cache'] = BLOCK_NO_CACHE;
      
      $blocks['featureblast']['info'] = t('Tripal Feature Analyses');
      $blocks['featureblast']['cache'] = BLOCK_NO_CACHE;
      
      return $blocks;

  case 'view':
    if (user_access('access chado_analysis 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('Analysis Details');
          $block['content'] = theme('tripal_analysis_base', $node);
          break;
        case 'tripal_feature_analyses':
          $block['subject'] = t('Feature Analyses');
          $block['content'] = theme('tripal_feature_analyses', $node);
          break;
        default :
      }
      return $block;
    }
  }
}

/*******************************************************************************
 * tripal_analysis_nodeapi()
 * HOOK: Implementation of hook_nodeapi()
 * Display blast results for allowed node types
 */
function tripal_analysis_nodeapi(&$node,  $op, $teaser, $page) {

  switch ($op) {
    case 'view':

      if ($teaser) {
        return '';
      }
      // Abort if this node is not one of the types we should show.
      if (strcmp($node->type, 'chado_feature') == 0) {
        if ($node->build_mode == NODE_BUILD_SEARCH_INDEX) {
           // return results for searching
        } 
        else {
           // return normal results
           $node->content['tripal_feature_analyses'] = array(
                  '#value' => theme('tripal_feature_analyses',   $node),
                  '#weight' => 8
           );
        }
      }
      break;
  }
}

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