kp_nodes.module

<?php

require_once 'theme/template.php';

/**
 * Implementation of hook_init()
 */
function kp_nodes_init() {

  if (drupal_is_front_page()) {
    libraries_load('tether');
    libraries_load('shepherd');
    drupal_add_css(drupal_get_path('theme','kptheme') . '/css/shepherd_tour.css');
    drupal_add_js(drupal_get_path('theme','kptheme') . '/js/shepherdScrollingButtons.js');
    drupal_add_js(drupal_get_path('module','kp_nodes') . '/theme/js/siteTour-FrontPage.js');
  }
}

/**
 * Implements hook_menu().
 */
function kp_nodes_menu() {
  $items = array();

/**
  $items['contact'] = array(
    'title' => 'Contact us',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('kp_contact_form'),
    'access arguments' => array('access content'),
    'file' => 'includes/contact_form.inc',
  );
*/

  // Export germplasm list to csv file for download
  // in Projects node.
  $items['project/project_germplasm/%'] = array(
    'title' => 'Germplasm List',
    'page callback' => 'kp_project_germplasm_list',
    'page arguments' => array(2),
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK,
  );

  return $items;
}

/**
 * Implements hook_theme().
 */
function kp_nodes_theme($existing, $type, $theme, $path) {

  $items = array(
    'node__uofs_research_area' => array(
      'template' => 'node--generic',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$path/theme"
    ),

    'tripal_research_area_teaser' => array(
      'template' => 'tripal-research-area-teaser',
      'render element' => 'node',
      'path' => "$path/theme"
    ),

    'node__jbrowse_instance' => array(
      'template' => 'node--jbrowse-instance',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$path/theme"
    ),

    'kp_worldmap' => array(
      'template' => 'worldmap.svg',
      'path' => "$path/theme"
    ),

    'kp_nodes_project_stocks' => array(
      'template' => 'kp_nodes_project_stocks',
      'render element' => 'node',
      'path' => "$path/theme"
    ),

    'kp_nodes_project_stocks_AGILE' => array(
      'template' => 'kp_nodes_project_stocks',
      'render element' => 'node',
      'path' => "$path/theme"
    )
  );

  return $items;
}

/**
 * Implements hook_libraries_info().
 */
function kp_nodes_libraries_info() {

  $libraries['shepherd'] = array(
    'name' => 'Shepherd Site Tour',
    'vendor url' => 'http://github.hubspot.com/shepherd/docs/welcome/',
    'download url' => 'https://github.com/HubSpot/Shepherd',
    'version' => '1.2.0',
    'files' => array(
        'js' => array('shepherd.min.js'),
        'css' => array(
          'shepherd-theme-arrows.css'
        ),
    ),
  );

  $libraries['tether'] = array(
    'name' => 'Tether',
    'vendor url' => 'http://github.hubspot.com/tether/',
    'download url' => 'http://github.hubspot.com/tether/',
    'version' => '1.1.1',
    'files' => array(
        'js' => array('tether.min.js'),
        'css' => array(
          'tether.min.css'
        ),
    ),
  );

  return $libraries;
}

/**
 * Implements hook_node_view().
 * Acts on all content types.
 */
function kp_nodes_node_view($node, $view_mode, $langcode) {
  // Update the breadcrumbs to include link back to projects page.
  $breadcrumbs[] = l('Home', '');
  $breadcrumbs[] = l('Projects', '/research/projects');

  drupal_set_breadcrumb($breadcrumbs);

  switch ($node->type) {
    case 'uofs_research_area':
      if ($view_mode == 'full') {
        $node->content['kp_toc'] = array(
          '#markup' => "<div id=\"$node->type-tripal-toc-block\" class=\"tripal-toc-block\"></div>"
        );

        // create a base section including the body and thumbnail image field
        $node->content['uofs_research_area_base'] = array(
          '#type' => 'container',
          '#tripal_toc_id'    => 'base',
          '#tripal_toc_title' => 'Overview',
          '#attributes' => array(
            'class' => array('uofs-research-area-base'),
          ),
          'body' => $node->content['body'],
          'field_page_thumnail' => $node->content['field_page_thumnail'],
          '#weight' => -100,
        );
        unset($node->content['body'], $node->content['field_page_thumnail']);

      } elseif($view_mode == 'teaser') {
          $node->content['uofs_research_area_pane'] = array(
            '#theme' => 'tripal_research_area_teaser',
            '#node' => $node
          );

          //stop displaying same entry in the same page
          unset($node->content['body'],
                $node->content['field_page_thumnail'],
                $node->content['links']);
      }
      break;

    case 'chado_organism':
      if ($view_mode == 'full') {

        unset($node->content['tripal_organism_feature_browser']);

        // Remove the field image with source since it will be rendered
        // in the overview instead of as it's own pane.
        unset($node->content['field_image_with_source']);

        // Remove the nurtient facts if it's empty.
        $field_collection = $node->content['field_nutrition'][0]['entity']['field_collection_item'];
        $nutrient_facts = array_shift($field_collection);
        if (sizeof($nutrient_facts['field_nutrition_data'][0]['#rows']) == 1) {
          unset($node->content['field_nutrition']);
        }

        $node->content['tripal_organism_feature_counts']['#tripal_toc_title'] = 'Sequence & Variant Data';
        $node->content['tripal_organism_feature_counts']['#weight'] = 2;

        $node->content['tripal_organism_stocks']['#tripal_toc_title'] = 'Germplasm Data';
        $node->content['tripal_organism_stocks']['#weight'] = 1;
      }
      break;
    case 'chado_project':
      // Determine if project is AGILE.
      $use_theme = ($node->title == 'AGILE: Application of Genomic Innovation in the Lentil Economy')
        ? 'kp_nodes_project_stocks_AGILE' : 'kp_nodes_project_stocks';

      // Germplasm Pane.
      $node->content[$use_theme] = array(
        '#theme' => $use_theme,
        '#node' => $node,
        '#tripal_toc_id'    => 'germplasm',
        '#tripal_toc_title' => 'Germplasm',
        '#weight' => 4,
      );


      // Hide the date field since we will render it manually in the overview.
      unset($node->content['field_date_month_year']);

      // Change the name of the relationships pane.
      $node->content['tripal_project_relationships']['#tripal_toc_title'] = 'Related Projects';

      // Remove the Long description since it will be rendered manually in
      // the overview.
      unset($node->content['field_long_description']);

      break;

    case 'chado_contact':

      // Get rid of Publications list since it's been added onto the overview.
      unset($node->content['tripal_contact_publications']);
      break;

    case 'chado_pub':

      unset(
        $node->content['tripal_pub_properties'],
        $node->content['tripal_pub_authors']
      );
      break;
  }
}

/**
 * After the node is built, we want to add instructions to each
 * content section letting the administrator know which template
 * they can customize
 *
 * @param $build
 */
function kp_nodes_node_view_alter(&$build) {
  global $theme;

  $node_types = array('uofs_research_area');

  // if the $build['kp_toc'] element is not present, then this is not
  // a full node view so we do not want to alter
  if (!array_key_exists('kp_toc', $build)) {
    return;
  }

  $cache = cache_get("theme_registry:$theme", 'cache');
  $node = $build['#node'];
  $toc = array();
  $toc_html = '';

  // if we are looking at a Tripal node template then we want to
  // make some changes to each block of content so that we can associate
  // a table of contents and add administrator and curator messages
  if (in_array($node->type, $node_types)) {

    // iterate through all the elements of the $build array and for those
    // that are wanting to provide content for this node
    $markup = array();
    foreach ($build as $key => $value) {

      // examine elements without a '#' prefix as these should be adding
      // contents to the page. Skip the table of contents and links as those
      // will be placed elsewhere
      if (!preg_match('/^#/', $key) and $key != 'kp_toc' and $key != 'links') {

        //-----------------------
        // INITIALIZE THE CONTENT VARIABLES
        //-----------------------
        $toc_item_title = $key;
        $toc_item_id    = $key;
        $toc_item_link  = '';

        // get the title for the table of contents.  Tripal templates should
        // have a '#tripal_toc_title' element in the build array
        if (array_key_exists('#tripal_toc_title', $build[$key])) {
          $toc_item_title = $build[$key]['#tripal_toc_title'];
        }
        // other elements in the $build array may just have a '#title' element,
        if (array_key_exists('#title', $build[$key])) {
          $toc_item_title = $build[$key]['#title'];
        }
        $toc_item_title = ucwords($toc_item_title);

        if (array_key_exists('#tripal_toc_id', $build[$key])) {
          $toc_item_id = $build[$key]['#tripal_toc_id'];
        }
        $toc_item_link = "<div class=\"tripal_toc_list_item\"><a id=\"$toc_item_id\" class=\"tripal_toc_list_item_link\" href=\"?block=$toc_item_id\">$toc_item_title</a></div>";

        //-----------------------
        // SET THE WEIGHTS FOR THE TOC ELEMENTS
        //-----------------------
        // set the weight of the TOC item and add it to our $toc array
        // for building of the TOC below
        $weight = 0;
        if (array_key_exists('#weight', $build[$key])) {
          $weight = $build[$key]['#weight'];
        }

        //-----------------------
        // GET THE MARKUP FOR EACH ELEMENT
        //-----------------------
        $markup = '';

        // find the markup. Some fields will have a '#markup' and others, such
        // as CCK elements may have a set of '#markup' elements organized by
        // numerical keys.
        if (array_key_exists('#markup', $build[$key]) and trim($build[$key]['#markup'])) {
          $markup = $build[$key]['#markup'];
        }
        // For backwards copmatibility we should support the '#value' element as well.
        elseif (array_key_exists('#value', $build[$key]) and trim($build[$key]['#value'])) {
          $markup = $build[$key]['#markup'];
        }

        // if we have no '#markup' field then this element has not yet
        // been rendered.  Let's render it and substitute that for markup
        if (!$markup) {
          $markup = trim(render($build[$key]));
          $build[$key] = array(
            '#markup' => $markup,
          );
        }

        // if we still don't have markup then skip this one
        if (!$markup) {
          continue;
        }

        //-----------------------
        // FIND THE TEMPLATE PATH
        //-----------------------
        // get the template path so we can put it in an admin message box
        $path = '';
        if (array_key_exists($key, $cache->data) and array_key_exists('path', $cache->data[$key])) {

          $path = $cache->data[$key]['path'] . '/' . $key . '.tpl.php';

          $path = tripal_set_message("Administrators, you can
            customize the way the content above is presented.  Tripal provides a template
            file for each block of content.  To customize, copy the template file to your
            site's default theme, edit then " .
            l('clear the Drupal cache', 'admin/config/development/performance', array('attributes' => array('target' => '_blank'))) . ".
            Currently, the content above is provided by this template: <br><br>$path",
            TRIPAL_INFO,
            array('return_html' => 1)
          );
        }

        //-----------------------
        // CREATE THE DATA BLOCK
        //-----------------------
        // add a surrounding <div> box around the content
        $updated_markup = "
          <div id=\"$toc_item_id-tripal-data-block\" class=\"tripal-data-block\">
            <div class=\"$toc_item_id-tripal-data-block-title tripal-data-block-title\">$toc_item_title</div>
              $markup
              $path
            </div>
          </div>
        ";

        $build[$key]['#markup'] = $updated_markup;
        $build[$key]['#weight'] = $weight;

        //-----------------------
        // Set the TOC Item
        //-----------------------
        $toc[$weight][$toc_item_title] = $toc_item_link;
      }
    }
  }

  //-----------------------
  // BUILD THE TABLE OF CONTENTS LINKS
  //-----------------------
  // first sort the links numerically by their weight
  ksort($toc, SORT_NUMERIC);
  $toc_html = '';
  foreach ($toc as $weight => $links) {
    // for links in the same weight, sort them alphabetically
    ksort($links);
    foreach ($links as $toc_item_title => $toc_item_link) {
      $toc_html .= $toc_item_link;
    }
  }
  $build['kp_toc']['#markup'] = "<div id=\"$node->type-tripal-toc-block\" class=\"tripal-toc-block\">$toc_html</div>";
}

/**
 * Function callback: create a list of germplasm and export to csv file for download.
 *
 * @param $project:
 *    A sting encoded using base64_encode() that comprises the keyword kp_nodes_project: followed by
 *    a project id number.
 */
function kp_project_germplasm_list($project = null) {
  // FOR SECURITY REASON SINCE THIS IS PUBLICLY ACCESSIBLE, WE DEFAULT THE PROJECT TO AGILE,
  // TO PREVENT USER FROM MODIFYING LINK AND DOWNLOAD OTHER GERMPLASM LIST OF OTHER PROJECT.

  // THIS DOWNLOAD LIST FUNCTIONALITY IS EXCLUSIVE TO AGILE PROJECT ONLY AS REQUESTED.
  // SHOULD THIS BE USED TO APPLY TO THE REST OF PROJECTS, DISCARD THE FOLLOWING LINE.
  // USE base64_encode('kp_modes_project:project id number') as the href value to generate
  // download link for other projects.

  // THIS LINE WILL REFERENCE AGILE PROJECT.
  $project = base64_encode('kp_nodes_project:63');

  if (empty($project)) {
    // See if the link contained a query string, if not stop processing.
    die('Project not found.');
  }
  else {
    // Decode the query string and extract the project_id.
    $p = base64_decode($project);
    $project_id = trim(str_replace('kp_nodes_project:', '', $p));

    // Test if project id is valid, that is if it is less or 0, not a numeric value or
    // the length is 4 or more charactres long.
    if ($project_id <= 0 || !is_numeric($project_id) || strlen($project_id) >= 4) {
      die('Project not found.');
    }
    else {
      $project_id = (int)$project_id;

      // Test if project_stock exists.
      $sql = "SELECT relname FROM pg_class WHERE relname = 'project_stock'";
      $exists = db_query($sql)
        ->rowCount();

      // Project Id matches a project.
      $project = chado_query("SELECT name FROM {project} WHERE project_id = :project_id LIMIT 1", array(
        ':project_id' => $project_id
      ));

      // Ensure that project stock exists and that the project_id number matches a project
      // in chado.projects table.
      if ($exists && $project->rowCount() == 1) {
        // Fetch the cvterm_id of type the origin of the organism.
        $cvterm_id_origin = tripal_get_cvterm(array('name' => 'country_of_origin'));

        $sql = "SELECT
          s.name,
          s.uniquename,
          INITCAP(o.genus) || ' ' || LOWER(o.species) AS species,
          cvt.name AS type,
          STRING_AGG(CASE WHEN sprop.type_id = :origin THEN sprop.value END, '') AS origin
        FROM
          {stock} AS s
          LEFT JOIN {project_stock} AS projs USING(stock_id)
          LEFT JOIN {organism} AS o USING(organism_id)
          LEFT JOIN {cvterm} AS cvt ON cvt.cvterm_id = s.type_id
          LEFT JOIN {stockprop} AS sprop USING(stock_id)
        WHERE
          projs.project_id = :project_id
        GROUP BY s.name, s.uniquename, o.genus, o.species, cvt.name
        ORDER BY s.name ASC";

        $args = array(
          ':origin' => $cvterm_id_origin->cvterm_id,
          ':project_id' => $project_id
        );

        $stocks = chado_query($sql, $args);

        // See if in project_stocks table, a project has been assigned a set of stocks.
        if ($stocks->rowCount() > 0) {
          // Prepare csv.
          // PHP write to output stream (like echo).
          $csv = fopen('php://output', 'w');

          $csv_filename =  'AGILE_germplasm_list_' . date('Ymd') . '.csv';
          drupal_add_http_header('Content-Type', 'text/csv; utf-8');
          drupal_add_http_header('Content-Disposition', 'attachment; filename = ' . $csv_filename);

          // Warning:
          fwrite($csv, "#WARNING: Some germplasm names may have converted into dates in Microsoft Excel.\n");

          // Headers.
          fputcsv($csv, array(t('NAME'), t('ORIGIN'), t('SPECIES'), t('TYPE')));

          foreach($stocks as $s) {
            fputcsv($csv, array($s->name, $s->origin, $s->species, $s->type));
          }

          fclose($csv);
        }
        else {
          die('Project has no stocks assigned...');
        }
      }
      else {
        die('Project not found.');
      }
    }
  }
}

/**
 * Implements hook_alter().
 * Match stock name to stock with AGL prefix in rawphenotypes module.
 * Note: only when saving data in Stage 3.
 *
 * @param $data
 *   An array containing the stock name and project name.
 *
 * @return
 *   A string, stock name with AGL as required.
 *
 * NOTE: This applies to check stock names in stage 3: save spreadsheet.
 */
function kp_nodes_rawpheno_AGILE_stock_name_alter(&$stock_name, &$project_name) {
  if ($project_name == 'AGILE: Application of Genomic Innovation in the Lentil Economy') {

    $AGILE_stock_token = 'AGL';

    // Only applies when project is AGILE.
    if (strpos($stock_name, $AGILE_stock_token) === FALSE) {
      // Stock name does not contain AGL.
      // Alter stockname to contain AGL.

      // Space required!
      $stock_name .= ' AGL';
    }
  }
}

/**
 * Implements hook_alter().
 * Ignore columns in a spreadsheet file.
 *
 * @param &$header
 *   An array, a set of column headers from a spreadsheet file.
 * @param &$project_name
 *   A string value, the name of the project.
 *
 * @return
 *   An array, a new set of column headers with the specified header(s) omitted.
 *   Array will be passed back to processing script ignoring data from indicated headers.
 *
 * @see
 *   modules/rawpheno/include/rawpheno.upload.form.inc.
 */
function kp_nodes_rawpheno_ignorecols_newcolumn_alter(&$header, &$project_name) {
  // Referenced parameters in functions: rawpheno_upload_form_stage_review() in @see.

  if ($project_name == 'AGILE: Application of Genomic Innovation in the Lentil Economy') {
    $index = kp_nodes_rawpheno_ignorecols_match($header);

    if (count($index) > 0) {
      foreach($index as $i) {
        unset($header[$i]);
      }
    }
  }
}


/**
 * Implements hook_alter().
 * Ignore columns in a spreadsheet file.
 *
 * @param &$skip
 *   An array, a set of column headers from a spreadsheet file.
 * @param &$project_name
 *   A string value, the name of the project.
 *
 * @return
 *   An array, containing the index numbers of headers in reference to the spreadsheet file.
 *   Array will be passed back to processing script ignoring data from indicated headers.
 *
 * @see
 *   modules/rawpheno/include/rawpheno.upload.excel.inc
 *   kp_nodes_rawpheno_ignorecols().
 */
function kp_nodes_rawpheno_ignorecols_valsave_alter(&$skip, &$project_name) {
  // Referenced parameters in functions:
  // rawpheno_validate_excel_file() and rawpheno_load_spreadsheet() in @see.

  if ($project_name == 'AGILE: Application of Genomic Innovation in the Lentil Economy') {
    $t = kp_nodes_rawpheno_ignorecols();
    $index = array_map('rawpheno_function_delformat', $t);

    if (count($index) > 0) {
      $skip = $index;
    }
  }
}


/**
 * Helper function: Search headers for omission from headers in the spreadsheet file.
 *
 * @param $header
 *   An array, headers from spreadsheet file.
 *
 * @return
 *   An array containing the index numbers of headers that matched header for omission.
 *
 * @see
 *   kp_nodes_rawpheno_ignorecols_valsave_alter().
 *   kp_nodes_rawpheno_ignorecols().
 */
function kp_nodes_rawpheno_ignorecols_match($header) {
  // Ignore columns: type in lowercase.
  $t = kp_nodes_rawpheno_ignorecols();
  $ignore_cols = array_map('rawpheno_function_delformat', $t);

  // Index of match found.
  $cols_i = array();

  // Find columns.
  foreach($header as $i => $col) {
    $col = rawpheno_function_delformat($col);
    $c = (is_array($col)) ? $col['no format'] : strtolower($col);

    if (in_array($c, $ignore_cols)) {
      $cols_i[] = $i;
    }
  }

  return $cols_i;
}


/**
 * Helper function: Define/list column header names for rawphenotypes module to ignore.
 *
 * @return
 *   Array of column header names to be ignored.
 */
function kp_nodes_rawpheno_ignorecols() {
  // As it appears in the spreadsheet file.
  return array('Origin');
}