tripal/tripal_analysis/includes/tripal_analysis.admin.inc

<?php

/**
 * @file
 * Contains functions displaying administrative pages and forms
 */


/**
 * Administration page callbacks for the Tripal Analysis module
 *
 * We have defined a hook_get_settings() function. When a sub-module
 * is enabled, we'll look for this function to provide a form for the
 * administrative setting.
 *
 * @return
 *  A form API array describing an administrative form
 *
 * @ingroup tripal_analysis
 */
function tripal_analysis_admin() {
  // Create a new administrative form. We'll add main functions to the form
  // first (Sync, Reindex, Clean, Taxonify). Thereafter, any sub-module that
  // has a setting will be added.
  $form = array();

  // before proceeding check to see if we have any
  // currently processing jobs. If so, we don't want
  // to give the opportunity to sync libraries
  $active_jobs = FALSE;
  if (tripal_get_module_active_jobs('tripal_organism')) {
    $active_jobs = TRUE;
  }

  // add the field set for syncing libraries
  if (!$active_jobs) {
    // add the field set for syncing analyses
    get_tripal_analysis_admin_form_sync_set($form);
//    get_tripal_analysis_admin_form_reindex_set($form);
//    get_tripal_analysis_admin_form_taxonomy_set($form);
    get_tripal_analysis_admin_form_cleanup_set($form);
  }
  else {
    $form['notice'] = array(
       '#type' => 'fieldset',
       '#title' => t('Analysis Management Temporarily Unavailable')
    );
    $form['notice']['message'] = array(
          '#value' => t('Currently, analysis management jobs are waiting or are running. . Managemment features have been hidden until these jobs complete.  Please check back later once these jobs have finished.  You can view the status of pending jobs in the Tripal jobs page.'),
    );
  }

  // Add sub-module settings. Pull all sub-module information from
  // {tripal_analysis} table
  $sql = "SELECT modulename FROM {tripal_analysis}";
  $result = db_query($sql);
  $counter = 0;  //keep track of the number of sub-modules
  while ($data = $result->fetchObject()) {

    // Check if the hook_get_settings() function is already defined.
    $func = $data->modulename . "_get_settings";
    $functions = get_defined_functions();
    $settings;
    foreach ($functions['user'] as $function) {
      if ($function == $func) {
        $settings = $func();
      }
    }

    // Add sub-module's specific settings to the administrative view
    if ($settings) {
      // Define a fieldset for the sub-module
      $form["field$counter"] = array(
            '#type' => 'fieldset',
            '#title' => "$settings->title",
            '#collapsible' => TRUE
      );
      $form["field$counter"]["$settings->title"] = $settings->form;
    }
    $counter ++;
  }
  return system_settings_form($form);
}

/**
 * Displays the Set Drupal Taxonomy for Analysis Features From
 *
 * @param $form
 *  The administrative form as it is currently
 *
 * @return
 *  A form API array describing an administrative form
 *
 * @ingroup tripal_analysis
 */
function get_tripal_analysis_admin_form_taxonomy_set(&$form) {
  $form['taxonify'] = array(
      '#type' => 'fieldset',
      '#title' => t('Assign Drupal Taxonomy to Analysis Features')
  );

  // get the list of analyses
  $sql = "SELECT * FROM {analysis} ORDER BY name";
  $lib_rset = chado_query($sql);

  // iterate through all of the libraries
  $lib_boxes = array();
  while ($analysis = $lib_rset->fetchObject()) {
    $lib_boxes[$analysis->analysis_id] = "$analysis->name";
  }

  $form['taxonify']['description'] = array(
       '#type' => 'item',
       '#value' => t("Drupal allows for assignment of \"taxonomy\" or catagorical terms to " .
          "nodes. These terms allow for advanced filtering during searching. This option allows " .
          "for setting taxonomy only for features that belong to the selected analyses below.  All other features will be unaffected.  To set taxonomy for all features in the site see the Feature Administration page."),
     '#weight' => 1,
  );

  $form['taxonify']['tx-analyses'] = array(
     '#title'       => t('Analyses'),
     '#type'        => t('checkboxes'),
     '#description' => t("Check the analyses whose features you want to reset taxonomy.  Note: this list contains all analyses, even those that may not be synced."),
     '#required'    => FALSE,
     '#prefix'      => '<div id="lib_boxes">',
     '#suffix'      => '</div>',
     '#options'     => $lib_boxes,
     '#weight'      => 2
  );
  $form['taxonify']['tx-button'] = array(
      '#type' => 'submit',
      '#value' => t('Set Feature Taxonomy'),
      '#weight'      => 3
  );
}

/**
 * The "Reindex Analysis Nodes" form
 *
 * @param $form
 *  The administrative form as it is currently
 *
 * @return
 *  A form API array describing an administrative form
 *
 * @ingroup tripal_analysis
 */
function get_tripal_analysis_admin_form_reindex_set(&$form) {
  // define the fieldsets
  $form['reindex'] = array(
      '#type' => 'fieldset',
      '#title' => t('Reindex Analysis Features')
  );

  // get the list of libraries
  $sql = "SELECT * FROM {analysis} ORDER BY name";
  $lib_rset = chado_query($sql);

  // iterate through all of the libraries
  $lib_boxes = array();
  while ($analysis = $lib_rset->fetchObject()) {
    $lib_boxes[$analysis->analysis_id] = "$analysis->name";
  }
  $form['reindex']['description'] = array(
       '#type' => 'item',
       '#value' => t("This option allows for reindexing of only those features that belong to the selected analyses below. All other features will be unaffected.  To reindex all features in the site see the Feature Administration page."),
     '#weight' => 1,
  );

  $form['reindex']['re-analyses'] = array(
     '#title'       => t('Libraries'),
     '#type'        => t('checkboxes'),
     '#description' => t("Check the analyses whoee features you want to reindex. Note: this list contains all analyses, even those that may not be synced."),
     '#required'    => FALSE,
     '#prefix'      => '<div id="lib_boxes">',
     '#suffix'      => '</div>',
     '#options'     => $lib_boxes,
     '#weight' => 2,
  );
  $form['reindex']['re-button'] = array(
      '#type' => 'submit',
      '#value' => t('Reindex Features'),
      '#weight' => 3,
  );
}

/**
 * The "Clean-up orphaned analysis & nodes" Form
 *
 * @param $form
 *  The administrative form as it is currently
 *
 * @return
 *  A form API array describing an administrative form
 *
 * @ingroup tripal_analysis
 */
function get_tripal_analysis_admin_form_cleanup_set(&$form) {
  $form['cleanup'] = array(
      '#type' => 'fieldset',
      '#title' => t('Clean Up')
  );
  $form['cleanup']['description'] = array(
       '#type' => 'item',
       '#value' => t("With Drupal and chado residing in different databases " .
          "it is possible that nodes in Drupal and analyses in Chado become " .
          "\"orphaned\".  This can occur if an analysis node in Drupal is " .
          "deleted but the corresponding chado analysis is not and/or vice " .
          "versa. Click the button below to resolve these discrepancies."),
       '#weight' => 1,
  );
  $form['cleanup']['button'] = array(
      '#type' => 'submit',
      '#value' => t('Clean up orphaned analyses'),
      '#weight' => 2,
  );
}

/**
 * The "sync Analysis in chado with drupal" form
 *
 * @param $form
 *  The administrative form as it is currently
 *
 * @return
 *  A form API array describing an administrative form
 *
 * @ingroup tripal_analysis
 */
function get_tripal_analysis_admin_form_sync_set(&$form) {
  // define the fieldsets
  $form['sync'] = array(
      '#type' => 'fieldset',
      '#title' => t('Sync Analyses')
  );

  // before proceeding check to see if we have any
  // currently processing jobs. If so, we don't want
  // to give the opportunity to sync analyses
  $active_jobs = FALSE;
  if (tripal_get_module_active_jobs('tripal_analysis')) {
    $active_jobs = TRUE;
  }

  if (!$active_jobs) {

    // get the list of analyses
    $sql = "SELECT * FROM {analysis} ORDER BY name";
    $ana_rset = chado_query($sql);

    // if we've added any analyses to the list that can be synced
    // then we want to build the form components to allow the user
    // to select one or all of them.  Otherwise, just present
    // a message stating that all analyses are currently synced.
    $ana_boxes = array();
    $added = 0;
    while ($analysis = $ana_rset->fetchObject()) {
      // check to see if the analysis is already present as a node in drupal.
      // if so, then skip it.
      $sql = "SELECT * FROM {chado_analysis} WHERE analysis_id = :analysis_id";
      if (!db_query($sql, array(':analysis_id' => $analysis->analysis_id))->fetchObject()) {
        $ana_boxes[$analysis->analysis_id] = "$analysis->name";
        $added++;
      }
    }

    // if we have analyses we need to add to the checkbox then
    // build that form element
    if ($added > 0) {
      $ana_boxes['all'] = "All analyses";

      $form['sync']['analyses'] = array(
           '#title'       => t('Available analyses'),
           '#type'        => t('checkboxes'),
           '#description' => t("Check the analyses you want to sync.  Drupal " .
              "content will be created for each of the analyses listed above. " .
              "Select 'All analyses' to sync all of them."),
           '#required'    => FALSE,
           '#prefix'      => '<div id="ana_boxes">',
           '#suffix'      => '</div>',
           '#options'     => $ana_boxes,
      );
      $form['sync']['button'] = array(
            '#type' => 'submit',
            '#value' => t('Submit Sync Job')
      );
    }
    // we don't have any analyses to select from
    else {
      $form['sync']['value'] = array(
            '#value' => t('All analyses in Chado are currently synced with Drupal.')
      );
    }
  }
  // we don't want to present a form since we have an active job running
  else {
    $form['sync']['value'] = array(
          '#value' => t('Currently, jobs exist related to chado analyses. Please check back later for analyses that can by synced once these jobs have finished.  You can view the status of pending jobs in the Tripal jobs page.')
    );
  }
}

/**
 * Validate the administrative form
 * @todo Stephen: Why is validate used rather then submit?
 *
 * @param $form
 *   The form API array of the form to be validated
 * @form_state
 *   The user submitted values
 *
 * @ingroup tripal_analysis
 */
function tripal_analysis_admin_validate($form, &$form_state) {
  global $user;  // we need access to the user info
  $job_args = array();

  if ($form_state['values']['op'] == t('Submit Sync Job')) {

    // check to see if the user wants to sync chado and drupal.  If
    // so then we need to register a job to do so with tripal
    $analyses = $form_state['values']['analyses'];
    $do_all = FALSE;
    $to_sync = array();

    foreach ($analyses as $analysis_id) {
      if (preg_match("/^all$/i", $analysis_id)) {
        $do_all = TRUE;
      }
      if ($analysis_id and preg_match("/^\d+$/i", $analysis_id)) {
        // get the list of analyses
        $sql = "SELECT * FROM {analysis} WHERE analysis_id = :analysis_id";
        $analysis = chado_query($sql, array(':analysis_id' => $analysis_id))->fetchObject();
        $to_sync[$analysis_id] = $analysis->name;
      }
    }

    // submit the job the tripal job manager
    if ($do_all) {
      tripal_add_job('Sync all analyses', 'tripal_analysis', 'tripal_analysis_sync_analyses', $job_args, $user->uid);
    }
    else{
      foreach ($to_sync as $analysis_id => $name) {
        $job_args[0] = $analysis_id;
        tripal_add_job("Sync analysis: $name", 'tripal_analysis', 'tripal_analysis_sync_analyses', $job_args, $user->uid);
      }
    }
  }
  // -------------------------------------
  // Submit the Reindex Job if selected
  if ($form_state['values']['op'] == t('Reindex Features')) {
    global $user;  // we need access to the user info
    $job_args = array();
    $analyses = $form_state['values']['re-analyses'];
    foreach ($analyses as $analysis_id) {
      if ($analysis_id and preg_match("/^\d+$/i", $analysis_id)) {
        // get the analysis info
        $sql = "SELECT * FROM {analysis} WHERE analysis_id = :analysis_id";
        $analysis = chado_query($sql, array(':analysis_id' => $analysis_id))->fetchObject();
        $job_args[0] = $analysis_id;
        tripal_add_job("Reindex features for analysis: $analysis->name", 'tripal_analysis',
             'tripal_analysis_reindex_features', $job_args, $user->uid);
      }
    }
  }

  // -------------------------------------
  // Submit the Taxonomy Job if selected
  if ($form_state['values']['op'] == t('Set Feature Taxonomy')) {
    global $user;  // we need access to the user info
    $job_args = array();
    $analyses = $form_state['values']['tx-analyses'];
    foreach ($analyses as $analysis_id) {
      if ($analysis_id and preg_match("/^\d+$/i", $analysis_id)) {
        // get the analysis info
        $sql = "SELECT * FROM {analysis} WHERE analysis_id = :analysis_id";
        $analysis = chado_query($sql, array(':analysis_id' => $analysis_id))->fetchObject();
        $job_args[0] = $analysis_id;
        tripal_add_job("Set taxonomy for features in analysis: $analysis->name", 'tripal_analysis',
             'tripal_analysis_taxonify_features', $job_args, $user->uid);
      }
    }
  }

  // -------------------------------------
  // Submit the Cleanup Job if selected
  if ($form_state['values']['op'] == t('Clean up orphaned analyses')) {
    tripal_add_job('Cleanup orphaned analyses', 'tripal_analysis',
         'tripal_analyses_cleanup', $job_args, $user->uid);
  }
}

/**
 * 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} ";
    $results = chado_query($sql);
  }
  else {
    $sql = "SELECT Analysis_id, name, description, program, " .
         "  programversion, algorithm, sourcename, sourceversion, sourceuri, " .
          "  timeexecuted " .
          "FROM {analysis} " .
          "WHERE analysis_id = :analysis_id";
    $results = chado_query($sql, array(':analysis_id' => $analysis_id));
  }


  // 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 = :analysis_id";

  while ($analysis = $results->fetchObject()) {
        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_query($sql, array(':analysis_id' => $analysis->analysis_id))->fetchObject()) {

      $new_node = new stdClass();

      // try to access analysis type for this analysis
      $sql = "SELECT * FROM {analysisprop}
                    WHERE analysis_id = :analysis_id
                    AND type_id =
                        (SELECT cvterm_id from {cvterm} where name = :name)
            ";
      $analysis_type = chado_query($sql, array(':analysis_id' => $analysis->analysis_id, ':name' => "analysis_type"))->fetchObject();

      // 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;
}

/**
 * Remove orphaned drupal nodes
 *
 * @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) {

  return tripal_core_clean_orphaned_nodes('analysis', $job_id);
  
}