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

/**
 * Register tripal_analysis sub-modules
 *
 * @param $modulename
 *  The name of the module to be registered as a tripal analysis submodule
 *
 * @ingroup tripal_analysis
 */
function tripal_analysis_register_child($modulename) {
  $sql = "INSERT INTO {tripal_analysis} (modulename) VALUES ('%s')";
  db_query($sql, $modulename);
}

/**
 * Un-register a tripal analysis sub-module
 *
 * @param $modulename
 *  The name of the module to un-register
 *
 * @ingroup tripal_analysis
 */
function tripal_analysis_unregister_child($modulename) {
  if (db_table_exists('tripal_analysis')) {
      $sql = "DELETE FROM {tripal_analysis} WHERE modulename = '%s'";
      db_query($sql, $modulename);
  }
}

/**
 * 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() {
  // Display available analyses
  $items['analyses'] = array(
      'menu_name' => ('primary-links'), //Enable the 'Analysis' primary link
      'title' => 'Analyses',
      'page callback' => 'tripal_analysis_show_analyses',
      'access arguments' => array('access chado_analysis content'),
      'type' => MENU_NORMAL_ITEM
  );
  //Sync analysis
  $items['chado_sync_analyses'] = array(
     'title' => 'Sync Data',
     'page callback' => 'tripal_analysis_sync_analyses',
     'access arguments' => array('administer site configuration'),
     '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' => 'tripal_analysis_module_description_page',
      'access arguments' => array('administer site configuration'),
      'type' => MENU_NORMAL_ITEM,
      'file' => '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 site configuration'),
      'type' => MENU_NORMAL_ITEM,
      'file' => 'tripal_analysis.admin.inc',
  );
  return $items;
}

/**
 * Display the summary view of analyses when click on the 'Analyses'
 * primary-link
 *
 * @ingroup tripal_analysis
 */
function tripal_analysis_show_analyses() {
  // Show libraries stored in Drupal's {chado_analysis} table
  $sql = "SELECT COUNT(analysis_id) FROM {chado_analysis}";
  $no_ana = db_result(db_query($sql));
  if ($no_ana != 0) {
    $analyses = get_chado_analyses();
    return theme('tripal_analysis_analysis_page', $analyses);
  }
  else {
    return t("No analysis available at this time.");
  }

}

/**
 * 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) {
    $sql = "SELECT analysis_id ".
             "FROM {Analysis} ".
             "WHERE analysis_id = %d ";
    $previous_db = tripal_db_set_active('chado');
    $analysis = db_fetch_object(db_query($sql, $node->analysis_id));
    tripal_db_set_active($previous_db);
  }

  // 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');
  }

  if ($node->setpermissions) {
    $job_args[0] = $analysis_id;
    $job_args[1] = $node->nid;
    tripal_add_job("Set permission for analysis associated features", 'tripal_analysis',
                                'tripal_analysis_set_feature_permission', $job_args, $user->uid);
  }

   // 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) {
  // Before removing, get analysis_id so we can remove it from chado database
  // later
  $sql_drupal = "SELECT analysis_id ".
                 "FROM {chado_analysis} ".
                 "WHERE nid = %d ".
                 "AND vid = %d";
  $analysis_id = db_result(db_query($sql_drupal, $node->nid, $node->vid));

  // 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
  $previous_db = tripal_db_set_active('chado');
  db_query("DELETE FROM {analysis} WHERE analysis_id = %d", $analysis_id);
  tripal_db_set_active($previous_db);
}

/**
 * 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
  }
  else {
    // 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 ";

    $previous_db = tripal_db_set_active('chado');  // use chado database
    db_query($sql, $node->analysisname, $node->description, $node->program,
    $node->programversion, $node->algorithm, $node->sourcename,
    $node->sourceversion, $node->sourceuri, $timestamp, $analysis_id);
      tripal_db_set_active($previous_db);  // switch back to drupal database

    // 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)";
    }

    if ($node->setpermissions) {
      $job_args[0] = $analysis_id;
      $job_args[1] = $node->nid;
      tripal_add_job("Set permission for analysis associated features", 'tripal_analysis',
                                  'tripal_analysis_set_feature_permission', $job_args, $user->uid);
    }

    $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' => FALSE,
      '#default_value' => $analysisname,
      '#description' => t("This should be a handy short identifier that
         describes the analysis succintly as possible which 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]"),
  );
  $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('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'),
  );
  /* Set permissions for all features associated with this analysis */
  if (module_exists('node_privacy_byrole')) {
    $form['setpermissions'] = array(
        '#type' => 'checkbox',
          '#title' => t('Submit a job to set the same permissions for all features associated with this analysis'),
          '#default_value' => FALSE,
         '#weight' => 10
    );
  }

  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;
}

/**
 * Synchronize analyses from chado to drupal
 *
 * @ingroup tripal_analysis
 */
function tripal_analysis_sync_analyses($analysis_id = NULL, $job_id = NULL) {
  global $user;
  $page_content = '';

  if (!$analysis_id) {
    $sql = "SELECT Analysis_id, name, description, program, ".
        "  programversion, algorithm, sourcename, sourceversion, sourceuri, ".
          "  timeexecuted ".
          "FROM {Analysis} ";
    $previous_db = tripal_db_set_active('chado');  // use chado database
    $results = db_query($sql);
    tripal_db_set_active($previous_db);  // now use drupal database
  }
  else {
    $sql = "SELECT Analysis_id, name, description, program, ".
         "  programversion, algorithm, sourcename, sourceversion, sourceuri, ".
          "  timeexecuted ".
          "FROM {Analysis} ".
          "WHERE analysis_id = %d";
    $previous_db = tripal_db_set_active('chado');  // use chado database
    $results = db_query($sql, $analysis_id);
    tripal_db_set_active($previous_db);  // now use drupal database
  }


  // We'll use the following SQL statement for checking if the analysis
  // already exists as a drupal node.
  $sql = "SELECT * FROM {chado_analysis} ".
          "WHERE analysis_id = %d";

  while ($analysis = db_fetch_object($results)) {
        print "syncing analysis ";
        print $analysis->name;
        print ", ";
        print $analysis->analysis_id;
        print "\n";

    // check if this analysis already exists in the drupal database. if it
    // does then skip this analysis and go to the next one.
    if (!db_fetch_object(db_query($sql, $analysis->analysis_id))) {

      $new_node = new stdClass();

      // try to access analysis type for this analysis
      $sql = "SELECT * FROM {analysisprop}
                    WHERE analysis_id = %d
                    AND type_id =
                        (SELECT cvterm_id from {cvterm} where name = '%s')
            ";
      $previous_db = tripal_db_set_active('chado');
      $analysis_type = db_fetch_object(db_query($sql, $analysis->analysis_id, "analysis_type"));
      tripal_db_set_active($previous_db);

      // Get the type of analysis using cvterm_id
            // Current possibilities: kegg, unigene, interpro, blast
      if ($analysis_type) {

        // This is a unigene analysis
        if ($analysis_type->value == 'tripal_analysis_unigene') {
          $new_node->type = 'chado_analysis_unigene';
        // This is a blast analysis
        }
        elseif ($analysis_type->value == 'tripal_analysis_blast') {
          $new_node->type = 'chado_analysis_blast';
         // This is a interpro analysis
        }
        elseif ($analysis_type->value == 'tripal_analysis_interpro') {
          $new_node->type = 'chado_analysis_interpro';
         // This is a kegg analysis
        }
        elseif ($analysis_type->value == 'tripal_analysis_kegg' ) {
          $new_node->type = 'chado_analysis_kegg';
        }
        else {
          $new_node->type = 'chado_analysis';
        }
      // If it doesn't exist, this analysis is generic
      }
      else {
        $new_node->type = 'chado_analysis';
      }

            print "analysis type is $new_node->type\n";

      $new_node->uid = $user->uid;
      $new_node->analysis_id = $analysis->analysis_id;
      $new_node->analysisname = $analysis->name;
      $new_node->description = $analysis->description;
      $new_node->program = $analysis->program;
      $new_node->programversion = $analysis->programversion;
      $new_node->algorithm = $analysis->algorithm;
      $new_node->sourcename = $analysis->sourcename;
      $new_node->sourceversion = $analysis->sourceversion;
      $new_node->sourceuri = $analysis->sourceuri;
      $new_node->timeexecuted = $analysis->timeexecuted;

      // If the analysis has a name, use it as the node title. If not,
      // construct the title using program, programversion, and sourcename
      if ($new_node->analysisname) {
        $new_node->title = $new_node->analysisname;
      }
      else {
        //Construct node title as "program (version)"
        $new_node->title = "$analysis->program ($analysis->programversion)";
      }

      node_validate($new_node);

            $errors = form_get_errors();

            if ($errors) {
                print_r($errors);
            }
            else{
      // if(!form_get_errors()){
        $node = node_submit($new_node);
        node_save($node);

        if ($node->nid) {
          $page_content .= "Added $new_node->title<br />";
        }
      }
    }
    else {
      $page_content .= "Skipped $new_node->title<br />";
    }
  }
  return $page_content;
}

/**
 * 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 ($node->nid) {
        //---------------------------------------------------
        // CASE A: We are validating a form for updating an existing node
        //---------------------------------------------------

        // TO DO: check that the new fields don't yield a non-unique primary key in chado
    }
    else{
        // To differentiate if we are syncing or creating a new analysis altogther, see if an
        // analysis_id already exists

        if ($node->analysis_id) {

            //---------------------------------------------------
            // CASE B: Synchronizing a node from chado to drupal
            //---------------------------------------------------

        }
        else{

            //---------------------------------------------------
            // CASE C: We are validating a form for inserting a new node
            //---------------------------------------------------
            // The primary key 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'), $values);
            if (sizeof($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;
            }
        }
    }
}

/**
 * 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',
  );
}

/**
 *  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_analysis_page' => array(
         'arguments' => array('analyses'),
      ),
  );
}

/**
 * This function uses analysis_id's of all drupal analysis nodes as input and
 * pull the analysis information (name, description, program, programversion,
 * algorithm, sourcename, sourceversion, sourceuri, timeexecuted) from
 * chado database. The return type is an object array that stores $analysis
 * objects sorted by program
 *
 * @ingroup tripal_analysis
 */
function get_chado_analyses() {

  $sql_drupal = "SELECT COUNT (analysis_id) FROM {chado_analysis}";
  $no_orgs = db_result(db_query($sql_drupal));
  if ($no_orgs != 0) {
    $sql = "SELECT analysis_id, CA.nid, type FROM {chado_analysis} CA INNER JOIN node ON CA.nid = node.nid";
    $result = db_query($sql);
    $previous_db = tripal_db_set_active('chado');
    $sql = "SELECT Analysis_id, name, description, program,
                   programversion, algorithm, sourcename, sourceversion,
                   sourceuri, timeexecuted
            FROM {Analysis} WHERE analysis_id=%d";
    $analyses = array();
    $count = 0;
    while ($data = db_fetch_object($result)) {
      $analysis = db_fetch_object(db_query($sql, $data->analysis_id));
      $analysis->node_id = $data->nid;
      $analysis->node_type = $data->type;
      // Use node_type as the key so we can sort by node type
      // Since node_type is not unique by itself, we need to add
      // $count to the key
      $sortedBy = $analysis->timeexecuted;
      $analyses ["$sortedBy$count"] = $analysis;
      $count ++;
    }
    tripal_db_set_active($previous_db);

    //Sort analyses by time, descending order
    krsort($analyses, SORT_STRING);

    return $analyses;
  }
}

/**
 * Theme the List Analysis page
 *
 * @param $analyses
 *   An array of analyses to list
 *
 * @ingroup tripal_analysis
 */
function theme_tripal_analysis_analysis_page($analyses) {

  $output = "<br />Analyses are listed in the descending order of their execution time.<br /><a id=\"tripal_expandableBox_toggle_button\" onClick=\"toggleExpandableBoxes()\">[-] Collapse All</a>";

  foreach ($analyses as $analysis) {
    // Prepare information for html output
    $ana_node_url = url("node/$analysis->node_id");
    if ($analysis->sourceversion) {
      $ver = "($analysis->sourceversion)";
      }
      $date =  preg_replace("/^(\d+-\d+-\d+) .*/", "$1", $analysis->timeexecuted);

      // Generate html output
    $output .= "<div class=\"tripal_chado_analysis-info-box\" style=\"padding:5px\">
                         <div class=\"tripal_expandableBox\">
                           <h3>$analysis->name ($date)</h3>
                         </div>
                         <div class=\"tripal_expandableBoxContent\">
                           <span>
                             <table class=\"tripal_chado_analysis_content\">
                               <tr><td>
                                 Name: <a href=\"$ana_node_url\">$analysis->name</a>
                               </td></tr>
                               <tr><td>
                                 Program: $analysis->program ($analysis->programversion)
                               </td></tr>
                               <tr><td>
                                 Algorithm: $analysis->algorithm
                               </td></tr>
                             <tr><td>
                                 Source: $analysis->sourcename $ver
                             </td></tr>
                             <tr><td>
                                 Source URI: $analysis->sourceuri
                               </td></tr>
                               <tr><td>
                                 Executed Time:$date
                               </td></tr>
                               <tr><td>
                                 Description: $analysis->description
                               </td></tr>
                             </table>
                           </span>
                         </div>
                       </div>";
  }

  return $output;
}

/**
 * Remove orphaned drupal nodes or chado analysis
 *
 * @param $dummy
 *   Not Used -kept for backwards compatibility
 * @param $job_id
 *   The id of the tripal job executing this function
 *
 * @ingroup tripal_analysis
 */
function tripal_analyses_cleanup($dummy = NULL, $job_id = NULL) {

    // select each node from node table with chado_analysis as type
    // check to make sure it also exists in chado_analysis table, delete if it doesn't
    // (this should never, ever happen, but we'll double check anyway)
  $sql_drupal_node = "SELECT * FROM {node} WHERE type LIKE 'chado_analysis%' order by nid";
    $sql_drupal_ca = "SELECT * from {chado_analysis} WHERE nid = %d";

  $results = db_query($sql_drupal_node);
  while ($node = db_fetch_object($results)) {
        $ca_record = db_fetch_object(db_query($sql_drupal_ca, $node->nid));
        if (!$ca_record) {
            node_delete($node->nid);
      $message = "Missing in chado_analysis table.... DELETING node: $nid->nid\n";
      watchdog('tripal_analysis', $message, array(), WATCHDOG_WARNING);
        }
  }

    // get nodes from chado_analysis table and load into array, saving chado analysis_id
    // as we iterate through, we'll check that they are actual nodes and
    // delete if they aren't
    // (this should never, ever happen, but we'll double check anyway)
  $sql_drupal_ca2 = "SELECT * FROM {chado_analysis}";
  $sql_drupal_node2 = "SELECT * FROM {node} WHERE type LIKE 'chado_analysis%' AND nid = %d";

  $results = db_query($sql_drupal_ca2);
  $nid2aid = array();
  while ($ca_record = db_fetch_object($results)) {
        $node = db_fetch_object(db_query($sql_drupal_node2, $ca_record->nid));
        if (!$node) {
      db_query("DELETE FROM {chado_analysis} WHERE nid = %nid", $ca_record->nid);
      $message = "chado_analysis missing node.... DELETING chado_analysis record with nid: $ca_record->nid\n";
      watchdog('tripal_analysis', $message, array(), WATCHDOG_WARNING);
        }
        else{
        $nid2aid[$ca_record->nid] = $ca_record->analysis_id;
        }
  }

  // iterate through all of the chado_analysis nodes in drupal
    // and delete those that aren't valid in chado
    $sql_chado = "SELECT analysis_id from {analysis} WHERE analysis_id = %d";

  foreach ($nid2aid as $nid => $aid) {
        $previous_db = tripal_db_set_active('chado');
    $chado_record = db_fetch_object(db_query($sql_chado, $aid));
        tripal_db_set_active($previous_db);
    if (!$chado_record) {
            node_delete($nid);
      $message = "Missing in analysis table in chado.... DELETING node: $nid\n";
      watchdog('tripal_analysis', $message, array(), WATCHDOG_WARNING);
    }
  }
  return '';
}

/**
function tripal_analysis_reindex_features ($analysis_id = NULL, $job_id = NULL){
  $i = 0;

  // if the caller provided a analysis_id then get all of the features
  // associated with the analysis. Otherwise get all sequences associated
  // with all libraries.
  if(!$analysis_id){
    $sql = "SELECT Analysis_id, Feature_id ".
          "FROM {Analysisfeature} ".
          "ORDER BY analysis_id";
    $previous_db = tripal_db_set_active('chado');  // use chado database
    $results = db_query($sql);
    tripal_db_set_active($previous_db);  // now use drupal database
  } else {
    $sql = "SELECT Analysis_id, Feature_id ".
             "FROM {Analysisfeature} ".
             "WHERE analysis_id = %d";
             "ORDER BY analysis_id";
    $previous_db = tripal_db_set_active('chado');  // use chado database
    $results = db_query($sql,$analysis_id);
    tripal_db_set_active($previous_db);  // now use drupal database
  }

  // load into ids array
  $count = 0;
  $ids = array();
  while($id = db_fetch_object($results)){
    $ids[$count] = $id->feature_id;
    $count++;
  }

  $interval = intval($count * 0.01);
  foreach($ids as $feature_id){
    // update the job status every 1% features
    if($job_id and $i % interval == 0){
      tripal_job_set_progress($job_id,intval(($i/$count)*100));
    }
    tripal_feature_sync_feature ($feature_id);
    $i++;
  }
} */

/**
function tripal_analysis_taxonify_features ($analysis_id = NULL, $job_id = NULL){
  $i = 0;

  // if the caller provided a analysis_id then get all of the features
  // associated with the analysis. Otherwise get all sequences assoicated
  // with all libraries.
  if(!$analysis_id){
    $sql = "SELECT Analysis_id, Feature_id ".
          "FROM {Analysisfeature} ".
          "ORDER BY analysis_id";
    $previous_db = tripal_db_set_active('chado');  // use chado database
    $results = db_query($sql);
    tripal_db_set_active($previous_db);  // now use drupal database
  } else {
    $sql = "SELECT Analysis_id, Feature_id ".
             "FROM {Analysisfeature} ".
             "WHERE analysis_id = %d";
             "ORDER BY analysis_id";
    $previous_db = tripal_db_set_active('chado');  // use chado database
    $results = db_query($sql,$analysis_id);
    tripal_db_set_active($previous_db);  // now use drupal database
  }

  // load into ids array
  $count = 0;
  $ids = array();
  while($id = db_fetch_object($results)){
    $ids[$count] = $id->feature_id;
    $count++;
  }

  // make sure our vocabularies are set before proceeding
  tripal_feature_set_vocabulary();

  // use this SQL for getting the nodes
  $nsql =  "SELECT * FROM {chado_feature} CF ".
            "  INNER JOIN {node} N ON N.nid = CF.nid ".
            "WHERE feature_id = %d";

  // iterate through the features and set the taxonomy
  $interval = intval($count * 0.01);
  foreach($ids as $feature_id){
    // update the job status every 1% features
    if($job_id and $i % $interval == 0){
      tripal_job_set_progress($job_id,intval(($i/$count)*100));
    }
    $node = db_fetch_object(db_query($nsql,$feature_id));
    tripal_feature_set_taxonomy($node,$feature_id);
    $i++;
  }
}
 */

/**
 * 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,
  );
}