details.inc

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<?php

function tpps_details($accession = NULL) {
  global $base_url;
  global $user;
  $output = "";

  if (empty($accession)) {
    $query = db_select('chado.plusgeno_view', 'pg');
    $query->addExpression('count(distinct(accession))', 'count');
    $query = $query->execute();
    $num_studies = $query->fetchObject()->count;

    $query = db_select('chado.plusgeno_view', 'pg');
    $query->addExpression('count(distinct(species))', 'count');
    $query = $query->execute();
    $num_species = $query->fetchObject()->count;

    $tpps_link = "<b><a target=\"blank\" href=\"/tpps\">submit your study</a></b>";
    $output .= "This page reflects community submissions associated with published studies. Each submission is associated with a longterm identifier that connects the genotype, phenotype, and/or environmental metrics assessed. These studies represent diversity assessements, association mapping, and landscape genomics. We accept studies with a variety of marker types. We encourage you to $tpps_link to TreeGenes and utilize the provided accession in your publication. We currently have <b>$num_studies</b> studies representing <b>$num_species</b> species.";
    if (module_exists('cartogratree')) {
      $output .= " Studies that have georeferenced accessions associated with them can be queried on <b><a href=\"cartogratree\">CartograPlant.</a></b>";
    }
    $form = drupal_get_form('tpps_details_search');
    $output .= render($form);
    $output .= tpps_details_tags_sort();
    $output .= "<div id='tpps-details-table'>" . tpps_details_top() . "</div>";
    drupal_add_css(drupal_get_path('module', 'tpps') . TPPS_CSS_PATH);
    drupal_add_js(drupal_get_path('module', 'tpps') . TPPS_JS_PATH);
    return $output;
  }

  $output = "<a href=\"$base_url/tpps/details\">Return to TPPS Details</a>$output";
  $state = tpps_load_submission($accession);
  if (!empty($state)) {
    if ($state['status'] != 'Approved') {
      drupal_set_message(t('This submission is still under construction. Some of the information may be available here, but please keep in mind that it may be incomplete or subject to change in the near future.'), 'warning');
      if (function_exists('tpps_details_byaccession_page')) {
        $output .= @tpps_details_byaccession_page()['raw_markup']['#markup'];
        drupal_add_js(drupal_get_path('module', 'tpps') . TPPS_JS_PATH);
        return $output;
      }
    }

    if (empty($state['saved_values'][TPPS_PAGE_3]['skip_validation'])) {
      $map_api_key = variable_get('tpps_maps_api_key', NULL);
      $map_api_tools = "<script src=\"https://developers.google.com/maps/documentation/javascript/examples/markerclusterer/markerclusterer.js\"></script><script src=\"https://maps.googleapis.com/maps/api/js?key=$map_api_key&callback=initMap\"
        async defer></script>"
        . "<div id=\"_map_wrapper\"></div>";
      $tree_info = array();
      if (!empty($state['tree_info'])) {
        foreach ($state['tree_info'] as $name => $info) {
          if (!empty($info['lat']) and !empty($info['lng'])) {
            $tree_info[] = array(
              $name,
              $info['lat'],
              $info['lng'],
            );
          }
        }
        drupal_add_js(array('tpps' => array('tree_info' => $tree_info)), 'setting');
      }
      $output .= $map_api_tools;
    }
    drupal_add_js(drupal_get_path('module', 'tpps') . TPPS_JS_PATH);
    drupal_add_css(drupal_get_path('module', 'tpps') . TPPS_CSS_PATH);

    $pub_link = $state['title'];
    $pub_id = db_select('chado.project_pub', 'p')
      ->fields('p', array('pub_id'))
      ->condition('project_id', $state['ids']['project_id'])
      ->execute()->fetchObject()->pub_id;
    if (!empty($pub_id)) {
      $bundle = tripal_load_bundle_entity(array('label' => 'Publication'));
      $pub_id = chado_get_record_entity_by_bundle($bundle, $pub_id);
      $pub_link = "<a href='$base_url/Publication/$pub_id'>$pub_link</a>";
    }

    if (!empty($state['saved_values'][TPPS_PAGE_3]['skip_validation'])) {
      $image_path = drupal_get_path('module', 'tpps') . '/images/';
      $pub_link .= "<img title=\"This submission contains no location information\" src=\"/{$image_path}no_location.png\">";
    }

    $output .= "<h2>$pub_link</h2>";
    $output .= tpps_show_tags(tpps_submission_get_tags($state['accession']));
    $primary_author = $state['authors'][0];
    if (preg_match('/,/', $primary_author)) {
      $parts = explode(',', $primary_author);
      $lastname = trim($parts[0]);
    }
    else {
      $parts = explode(' ', $primary_author);
      $lastname = $parts[count($parts) - 1];
    }
    $output .= "<h4>$lastname et al {$state['pyear']}";
    if (!empty($state['journal'])) {
      $output .= " published in {$state['journal']}";
    }
    $output .= "</h4>";
    $output .= "<div id=\"abstract\"><a href=\"#abstract\">Click to show abstract</a></div>"
      . "<script>jQuery(document).ready(jQuery('#abstract').on('click', function() {
          jQuery('#abstract')[0].innerHTML = `{$state['abstract']}`;
        }));</script>";
    if (empty($state['saved_values'][TPPS_PAGE_3]['skip_validation']) and module_exists('cartogratree')) {
      $output .= "<a href=\"$base_url/cartogratree?accession=$accession\" target=\"blank\">View in CartograPlant</a><br>";
    }
    $output .= "<a href=\"$base_url/tpps/api/files/$accession\">Download compressed raw files</a><br>";
    if ($state['saved_values'][TPPS_PAGE_1]['publication']['status'] != 'Published' and $user->uid == tpps_load_submission($accession, FALSE)->uid) {
      $output .= "<a href=\"$base_url/tpps/$accession/edit-publication\">Edit publication information</a>";
    }

    $output .= tpps_details_tabs($state);
    return $output;
  }

  drupal_set_message(t('This submission is pending resubmission through the new TPPS pipeline. Some of the information may be available here, but please keep in mind that it may be incomplete or subject to change in the near future.'), 'warning');

  if (function_exists('tpps_details_byaccession_page')) {
    $output .= @tpps_details_byaccession_page()['raw_markup']['#markup'];
    drupal_add_js(drupal_get_path('module', 'tpps') . TPPS_JS_PATH);
  }
  return $output;
}

function tpps_details_tabs(array &$state) {
  $output = '<ul class="nav nav-tabs" role="tablist">
    <li class="nav-item"><a class="nav-link active" role="tab" data-toggle="tab" href="#species">Species</a></li>
    <li class="nav-item"><a class="nav-link" role="tab" data-toggle="tab" href="#study">Study Details</a></li>
    <li class="nav-item"><a class="nav-link" role="tab" data-toggle="tab" href="#trees">Plants</a></li>';
  $p_exist = FALSE;
  $g_exist = FALSE;
  $mass_spectro_exist = FALSE;
  for ($i = 1; $i <= $state['stats']['species_count']; $i++) {
    if (!empty($state['saved_values'][TPPS_PAGE_4]["organism-$i"]['phenotype'])) {
      $p_exist = TRUE;
    }
    if (!empty($state['saved_values'][TPPS_PAGE_4]["organism-$i"]['genotype'])) {
      $g_exist = TRUE;
    }
    if ($state['saved_values'][TPPS_PAGE_4]["organism-$i"]['phenotype']['iso-check'] == TRUE) {
      $mass_spectro_exist = TRUE;
    }
  }
  
  $output .= $p_exist ? '<li class="nav-item"><a class="nav-link" role="tab" data-toggle="tab" href="#phenotype">Phenotypes / Environments</a></li>' : "";
  $output .= $g_exist ? '<li class="nav-item"><a class="nav-link" role="tab" data-toggle="tab" href="#genotype">Genotypes</a></li>' : "";
  $output .= $mass_spectro_exist ? '<li class="nav-item"><a class="nav-link" role="tab" data-toggle="tab" href="#mass_spectrometry">Mass Spectrometry</a></li>' : "";
  $output .= '</ul><div id="tab-content" class="tab-content">';

  $output .= "<div id=\"species\" role=\"tabpanel\" class=\"tab-pane fade in active\"></div>";
  $output .= "<div id=\"study\" role=\"tabpanel\" class=\"tab-pane fade\"></div>";
  $output .= "<div id=\"trees\" role=\"tabpanel\" class=\"tab-pane fade\"></div>";

  $output .= $p_exist ? "<div id=\"phenotype\" role=\"tabpanel\" class=\"tab-pane fade\"></div>" : "";
  $output .= $g_exist ? "<div id=\"genotype\" role=\"tabpanel\" class=\"tab-pane fade\"></div>" : "";
  $output .= $mass_spectro_exist ? "<div id=\"mass_spectrometry\" role=\"tabpanel\" class=\"tab-pane fade\"></div>" : "";

  $output .= '</div>';
  return $output;
}

function tpps_details_tab($accession, $type) {
  $function = "tpps_details_$type";
  $state = tpps_load_submission($accession);
  print($function($state));
}

function tpps_details_top() {
  global $base_url;
  $params = drupal_get_query_parameters($_POST);
  $page = 0;
  if (empty($params)) {
    $params = drupal_get_query_parameters();
  }
  if (!empty($params['page'])) {
    $page = $params['page'];
  }
  $per_page = 20;

  $query = db_select('chado.plusgeno_view', 'pg');
  $query->addExpression('count(distinct(pg.accession))', 'count');
  if (!empty($params['type']) and !empty($params['value']) and !empty($params['op'])) {
    switch ($params['type']) {
      case 'title':
      case 'species':
      case 'project_id':
      case 'accession':
      case 'author':
      case 'year':
        $query->condition($params['type'], $params['value'], $params['op']);
        break;

      case 'phenotype_name':
        $query->innerJoin('chado.project_stock', 'ps', 'ps.project_id = pg.project_id');
        $query->innerJoin('chado.stock_phenotype', 'sp', 'sp.stock_id = ps.stock_id');
        $query->innerJoin('chado.phenotype', 'ph', 'ph.phenotype_id = sp.phenotype_id');
        $query->condition('ph.name', $params['value'], $params['op']);
        break;

      case 'phenotype_ontology':
        $query->innerJoin('chado.project_stock', 'ps', 'ps.project_id = pg.project_id');
        $query->innerJoin('chado.stock_phenotype', 'sp', 'sp.stock_id = ps.stock_id');
        $query->innerJoin('chado.phenotype', 'ph', 'ph.phenotype_id = sp.phenotype_id');
        $query->innerJoin('chado.cvterm', 'cvt', 'cvt.cvterm_id = ph.attr_id');
        $query->innerJoin('chado.cv', 'cv', 'cv.cv_id = cvt.cv_id');
        $query->condition('cv.name', $params['value'], $params['op']);
        break;

      case 'genotype_name':
        $query->innerJoin('chado.tpps_search_genotype_name', 'g', 'g.project_id = pg.project_id');
        $query->condition('g.name', $params['value'], $params['op']);
        break;

      case 'genotype_marker':
        $query->innerJoin('chado.tpps_search_genotype_marker', 'g', 'g.project_id = pg.project_id');
        $query->condition('g.name', $params['value'], $params['op']);
        break;

      case 'tags':
        $query->innerJoin('public.tpps_submission', 'ts', 'ts.accession = pg.accession');
        $query->innerJoin('public.tpps_submission_tag', 'st', 'st.tpps_submission_id = ts.tpps_submission_id');
        $query->innerJoin('public.tpps_tag', 'tt', 'tt.tpps_tag_id = st.tpps_tag_id');
        $query->condition('tt.name', $params['value'], $params['op']);
        break;

      default:
        break;
    }
  }
  $query = $query->execute();
  $total = $query->fetchObject()->count;

  $_GET['page'] = $page;
  $page = pager_default_initialize($total, $per_page);
  $start = $page * $per_page;

  $submissions = db_select('chado.plusgeno_view', 'pg');
  $submissions->distinct();
  $submissions->innerJoin('chado.project', 'p', 'p.project_id = pg.project_id');
  if (!empty($params['type']) and !empty($params['value']) and !empty($params['op'])) {
    switch ($params['type']) {
      case 'title':
      case 'species':
      case 'project_id':
      case 'accession':
      case 'author':
      case 'year':
        $submissions->condition($params['type'], $params['value'], $params['op']);
        break;

      case 'phenotype_name':
        $submissions->innerJoin('chado.project_stock', 'ps', 'ps.project_id = pg.project_id');
        $submissions->innerJoin('chado.stock_phenotype', 'sp', 'sp.stock_id = ps.stock_id');
        $submissions->innerJoin('chado.phenotype', 'ph', 'ph.phenotype_id = sp.phenotype_id');
        $submissions->condition('ph.name', $params['value'], $params['op']);
        break;

      case 'phenotype_ontology':
        $submissions->innerJoin('chado.project_stock', 'ps', 'ps.project_id = pg.project_id');
        $submissions->innerJoin('chado.stock_phenotype', 'sp', 'sp.stock_id = ps.stock_id');
        $submissions->innerJoin('chado.phenotype', 'ph', 'ph.phenotype_id = sp.phenotype_id');
        $submissions->innerJoin('chado.cvterm', 'cvt', 'cvt.cvterm_id = ph.attr_id');
        $submissions->innerJoin('chado.cv', 'cv', 'cv.cv_id = cvt.cv_id');
        $submissions->condition('cv.name', $params['value'], $params['op']);
        break;

      case 'genotype_name':
        $submissions->innerJoin('chado.tpps_search_genotype_name', 'g', 'g.project_id = pg.project_id');
        $submissions->condition('g.name', $params['value'], $params['op']);
        break;

      case 'genotype_marker':
        $submissions->innerJoin('chado.tpps_search_genotype_marker', 'g', 'g.project_id = pg.project_id');
        $submissions->condition('g.name', $params['value'], $params['op']);
        break;

      case 'tags':
        $submissions->innerJoin('public.tpps_submission', 'ts', 'ts.accession = pg.accession');
        $submissions->innerJoin('public.tpps_submission_tag', 'st', 'st.tpps_submission_id = ts.tpps_submission_id');
        $submissions->innerJoin('public.tpps_tag', 'tt', 'tt.tpps_tag_id = st.tpps_tag_id');
        $submissions->condition('tt.name', $params['value'], $params['op']);
        break;

      default:
        break;
    }
  }
  $submissions->fields('pg', array(
    'title',
    'project_id',
    'accession',
    'tree_count',
    'phenotypes_assessed',
    'phen_count',
    'gen_count',
  ));
  $submissions->range($start, $per_page);
  $submissions->orderBy('pg.accession');
  $submissions = $submissions->execute();

  $rows = array();
  while (($sub = $submissions->fetchObject())) {
    $proj_id = $sub->project_id;

    $query = db_select('chado.organism', 'o');
    $query->join('chado.pub_organism', 'po', 'o.organism_id = po.organism_id');
    $query->join('chado.project_pub', 'pp', 'pp.pub_id = po.pub_id');
    $query->fields('o', array('organism_id', 'genus', 'species'));
    $query->condition('pp.project_id', $proj_id);
    $query->distinct();
    $query = $query->execute();

    $species = array();
    while (($result = $query->fetchObject())) {
      $species[] = tpps_entity_link($result->organism_id, "{$result->genus} {$result->species}", 'Organism');
    }

    $warning = "";
    if (empty(tpps_load_submission($sub->accession))) {
      $warning = "<img src='$base_url/misc/message-16-warning.png' title='This study has not yet been resubmitted through the new TPPS pipeline'> ";
    }

    $row = array(
      "<a href=\"$base_url/tpps/details/{$sub->accession}\">{$sub->accession}</a>",
      "$warning<a href=\"$base_url/tpps/details/{$sub->accession}\">{$sub->title}</a>",
      tpps_show_tags(tpps_submission_get_tags($sub->accession)),
      implode('<br>', $species),
      $sub->tree_count,
      $sub->phenotypes_assessed,
      $sub->phen_count,
      $sub->gen_count,
    );
    $rows[$sub->accession] = $row;
  }

  ksort($rows);

  $vars = array(
    'header' => array(
      'Accession',
      'Title',
      'Tags',
      'Species',
      'Plant Count',
      'Phenotypes Assessed',
      'Phenotypic Measures',
      'Genotype Count',
    ),
    'rows' => $rows,
    'attributes' => array(
      'class' => array('view'),
      'id' => 'tpps_table_display',
    ),
    'caption' => '',
    'colgroups' => NULL,
    'sticky' => FALSE,
    'empty' => '',
  );

  $output = theme('table', $vars);
  $pager = theme('pager', array('quantity', $total));
  return $pager . $output;
}

function tpps_details_top_callback() {
  print(tpps_details_top());
}

function tpps_details_search(array $form, array $form_state) {
  $params = drupal_get_query_parameters();
  $form['details_type'] = array(
    '#type' => 'select',
    '#options' => array(
      'title' => t('Title'),
      'species' => t('Species'),
      'accession' => t('Accession'),
      'author' => t('Primary Author'),
      'year' => t('Publication Year'),
      'phenotype_name' => t('Phenotype Name'),
      'phenotype_ontology' => t('Phenotype Ontology Name'),
      'genotype_name' => t('Genotype Name'),
      'genotype_marker' => t('Genotype Marker Type'),
      'tags' => t('Tags'),
    ),
    '#ajax' => array(
      'wrapper' => 'tpps-details-form',
      'callback' => 'tpps_details_form_callback',
    ),
    '#prefix' => '<div id="tpps-details-form">',
    '#default_value' => $params['type'] ?? NULL,
  );

  $ops = array(
    '~*' => '~*',
    'LIKE' => 'LIKE',
    '=' => '=',
  );

  $form['details_op'] = array(
    '#type' => 'select',
    '#options' => $ops,
    '#default_value' => $params['op'] ?? NULL,
  );

  $form['details_value'] = array(
    '#type' => 'textfield',
    '#suffix' => '</div>',
    '#autocomplete_path' => 'tpps/autocomplete/project_title',
    '#default_value' => $params['value'] ?? NULL,
  );

  if (empty($form_state['values']['details_type'])) {
    $form_state['values']['details_type'] = $params['type'] ?? NULL;
  }

  if (!empty($form_state['values']['details_type'])) {
    switch ($form_state['values']['details_type']) {
      case 'title':
        $form['details_value']['#autocomplete_path'] = 'tpps/autocomplete/project_title';
        break;

      case 'species':
        $form['details_value']['#autocomplete_path'] = 'tpps/autocomplete/species';
        break;

      case 'accession':
        $form['details_value']['#autocomplete_path'] = 'tpps/autocomplete/project_accession';
        break;

      case 'author':
        $form['details_value']['#autocomplete_path'] = 'tpps/autocomplete/author';
        break;

      case 'phenotype_name':
        $form['details_value']['#autocomplete_path'] = 'tpps/autocomplete/phenotype';
        break;

      case 'phenotype_ontology':
        $form['details_value']['#autocomplete_path'] = 'tpps/autocomplete/phenotype_ontology';
        break;

      case 'genotype_name':
        $form['details_value']['#autocomplete_path'] = 'tpps/autocomplete/genotype';
        break;

      case 'genotype_marker':
        $form['details_value']['#autocomplete_path'] = 'tpps/autocomplete/genotype_marker';
        break;

      default:
        $form['details_value']['#autocomplete_path'] = NULL;
        break;
    }
  }

  $form['details_search'] = array(
    '#type' => 'button',
    '#button_type' => 'button',
    '#value' => t('Search'),
  );

  $form['reset_button'] = array(
    '#markup' => '<button class="btn btn-primary form-button" type="reset"/>Reset</button>',
  ); 

  $form['#attributes'] = array(
    'style' => 'text-align:center',
  );

  return $form;
}

function tpps_details_tags_sort() {
  $output = "";

  $query = db_select('tpps_tag', 't')
    ->fields('t')
    ->orderBy('static', 'DESC')
    ->orderBy('tpps_tag_id')
    ->execute();
  $tags = array();
  while (($result = $query->fetchObject())) {
    $tags[$result->tpps_tag_id] = array(
      'id' => $result->tpps_tag_id,
      'name' => $result->name,
      'color' => $result->color,
      'static' => $result->static,
    );
  }

  $output .= tpps_show_tags($tags);

  return "<label for=\"tpps-tags-filter\">Sort by tags:</label><div id=\"tpps-tags-filter\">" . $output . "</div>";
}

function tpps_details_form_callback(array $form, array $form_state) {
  return array(
    'details_type' => $form['details_type'],
    'details_op' => $form['details_op'],
    'details_value' => $form['details_value'],
  );
}

function tpps_details_species(array &$state) {
  $query = db_select('chado.organism', 'o');
  $query->join('chado.pub_organism', 'po', 'o.organism_id = po.organism_id');
  $query->join('chado.project_pub', 'pp', 'pp.pub_id = po.pub_id');
  $query->fields('o', array('organism_id', 'genus', 'species', 'common_name'));
  $query->condition('pp.project_id', $state['ids']['project_id']);
  $query = $query->execute();
  $rows = array();

  while (($result = $query->fetchObject())) {
    $id = $result->organism_id;
    $common_name = $result->common_name;
    $family = $order = "";

    if (tpps_chado_prop_exists('organism', $id, 'family')) {
      $family = db_select('chado.organismprop', 'o')
        ->fields('o', array('value'))
        ->condition('organism_id', $id)
        ->condition('type_id', tpps_load_cvterm('family')->cvterm_id)
        ->execute()->fetchObject()->value;
    }

    if (tpps_chado_prop_exists('organism', $id, 'order')) {
      $order = db_select('chado.organismprop', 'o')
        ->fields('o', array('value'))
        ->condition('organism_id', $id)
        ->condition('type_id', tpps_load_cvterm('order')->cvterm_id)
        ->execute()->fetchObject()->value;
    }

    if (empty($common_name) and tpps_chado_prop_exists('organism', $id, 'common name')) {
      $common_name = db_select('chado.organismprop', 'o')
        ->fields('o', array('value'))
        ->condition('organism_id', $id)
        ->condition('type_id', tpps_load_cvterm('common name')->cvterm_id)
        ->execute()->fetchObject()->value;
    }

    $name = "{$result->genus} {$result->species}";
    $link = tpps_entity_link($id, $name, 'Organism');
    $rows[$name] = array(
      $order,
      $family,
      $link,
      $common_name,
    );
  }
  
  $vars = array(
    'header' => array(
      'Order',
      'Family',
      'Species',
      'Common Name',
    ),
    'rows' => $rows,
    'attributes' => array(
      'class' => array('view'),
      'id' => 'tpps_table_display',
    ),
    'caption' => '',
    'colgroups' => NULL,
    'sticky' => FALSE,
    'empty' => '',
  );
  return theme('table', $vars);
}

function tpps_details_study(array &$state) {
  $rows = array();

  $species = array();
  for ($i = 1; $i <= $state['stats']['species_count']; $i++) {
    $id = $state['ids']['organism_ids'][$i];
    $species_name = $state['saved_values'][TPPS_PAGE_1]['organism'][$i]['name'];
    $species[] = tpps_entity_link($id, $species_name, 'Organism');
  }

  $study_types = array(
    1 => 'Natural Population (Landscape)',
    2 => 'Growth Chamber',
    3 => 'Greenhouse',
    4 => 'Experimental/Common Garden',
    5 => 'Plantation',
  );

  $files = array();
  $study_file_ids = tpps_details_get_study_file_ids($state);
  // foreach ($state['files'] as $fid) {
  foreach ($study_file_ids as $fid) {
    $file = file_load($fid);
    if ($file) {
      $file_url = check_plain(file_create_url($file->uri));
      if(stripos($file_url, 'core/labs') === FALSE) {
        $files[] = "<a href='$file_url' target='blank'>$file->filename</a>";
      }
      
    }
  }

  $pub_link = $state['title'];
  $pub_id = db_select('chado.project_pub', 'p')
    ->fields('p', array('pub_id'))
    ->condition('project_id', $state['ids']['project_id'])
    ->execute()->fetchObject()->pub_id;
  if (!empty($pub_id)) {
    $bundle = tripal_load_bundle_entity(array('label' => 'Publication'));
    $pub_id = chado_get_record_entity_by_bundle($bundle, $pub_id);
    $pub_link = "<a href='$base_url/Publication/$pub_id'>$pub_link</a>";
  }
  $rows[] = array('Accession', $state['accession']);
  $rows[] = array('Title', $pub_link);
  $rows[] = array('Authors', implode(', ', $state['authors']));
  $rows[] = array('Species', implode('<br>', $species));
  $rows[] = array('Data Type', $state['saved_values'][TPPS_PAGE_2]['data_type']);
  $rows[] = array(
    'Study Type',
    $study_types[$state['saved_values'][TPPS_PAGE_2]['study_type']],
  );
  $rows[] = array('File Downloads', implode('<br>', $files));
  $rows[] = array('Population Size', $state['stats']['tree_count']);
  if (!empty($state['stats']['phenotype_count'])) {
    $rows[] = array('Phenotype Count', $state['stats']['phenotype_count']);
  }
  if (!empty($state['stats']['unique_phenotypes'])) {
    $rows[] = array('Unique Phenotypes', $state['stats']['unique_phenotypes']);
  }
  // @todo genotype counts.
  // $rows[] = array('Genotype Count', $state['stats']['genotype_count']);
  $vars = array(
    'header' => array(),
    'rows' => $rows,
    'attributes' => array(
      'class' => array('view'),
      'id' => 'tpps_table_display',
    ),
    'caption' => '',
    'colgroups' => NULL,
    'sticky' => FALSE,
    'empty' => '',
  );
  return theme('table', $vars);
}

function tpps_details_get_study_file_ids($state) {
  $saved_values = $state['saved_values'];
  // print_r($saved_values);
  $organism_count = $saved_values['1']['organism']['number'];
  $file_ids = [];
  for($i=1; $i<=4; $i++) {
    if ($i == 3) {
      for($j=1; $j<=$organism_count; $j++) {
        if(isset($saved_values[$i]['tree-accession']['species-' . $j]['file'])) {
          array_push($file_ids, $saved_values[$i]['tree-accession']['species-' . $j]['file']);
        }
      }
    }
    if ($i == 4) {
      // Phenotype files
      for($j=1; $j<=$organism_count; $j++) {
        if(isset($saved_values[$i]['organism-' . $j]['phenotype']['file'])) {
          array_push($file_ids, $saved_values[$i]['organism-' . $j]['phenotype']['file']);
        }
        if(isset($saved_values[$i]['organism-' . $j]['phenotype']['metadata'])) {
          array_push($file_ids, $saved_values[$i]['organism-' . $j]['phenotype']['metadata']);
        }        
      }
      for($j=1; $j<=$organism_count; $j++) {
        if(isset($saved_values[$i]['organism-' . $j]['genotype']['files']['snps-assay'])) {
          array_push($file_ids, $saved_values[$i]['organism-' . $j]['genotype']['files']['snps-assay']);
        }
        if(isset($saved_values[$i]['organism-' . $j]['genotype']['files']['snps-association'])) {
          array_push($file_ids, $saved_values[$i]['organism-' . $j]['genotype']['files']['snps-association']);
        }
        if(isset($saved_values[$i]['organism-' . $j]['genotype']['files']['vcf'])) {
          array_push($file_ids, $saved_values[$i]['organism-' . $j]['genotype']['files']['vcf']);
        }
        if(isset($saved_values[$i]['organism-' . $j]['genotype']['files']['ssrs'])) {
          array_push($file_ids, $saved_values[$i]['organism-' . $j]['genotype']['files']['ssrs']);
        } 
        if(isset($saved_values[$i]['organism-' . $j]['genotype']['files']['ssrs_extra'])) {
          array_push($file_ids, $saved_values[$i]['organism-' . $j]['genotype']['files']['ssrs_extra']);
        }                        
      }
    }
  }
  // check summarypage for supplemental files
  if(count($saved_values['summarypage']['files']) > 2) {
    $files = $saved_values['summarypage']['files'];
    foreach ($files as $file_index => $file_id) {
      if(is_numeric($file_id) && $file_id > 0) {
        // print_r($file_index);
        // array_push($file_ids, $file_id);
      }
    }
  }
  return $file_ids;
}

function tpps_details_trees(array &$state) {
  $path = current_path();
  $args = explode('/', $path);
  $params = drupal_get_query_parameters($_POST);
  $page = 0;
  if (!empty($params['page'])) {
    $page = $params['page'];
  }
  $rows = array();
  $per_page = 20;

  if (empty($state['tree_info'])) {
    $output = t('The plant information for this study has not been properly updated. Please contact your site administrator.');
    return $output;
  }

  $skip = !empty($state['saved_values'][TPPS_PAGE_3]['skip_validation']);

  $_GET['page'] = $page;
  pager_default_initialize(count($state['tree_info']), $per_page);
  $chunks = array_chunk($state['tree_info'], $per_page, TRUE);

  foreach ($chunks[$page] as $name => $info) {
    $id = $info['organism_id'];
    $form_number = array_search($id, $state['ids']['organism_ids']);
    $species_name = $state['saved_values'][TPPS_PAGE_1]['organism'][$form_number]['name'];

    $tree_id = tpps_entity_link($info['stock_id'], $name, 'Stock');

    $row = array(
      strtoupper($args[2]) . '-' . strip_tags($tree_id),
      tpps_entity_link($info['stock_id'], $name, 'Stock'),
      tpps_entity_link($id, $species_name, 'Organism'),
    );
    if (!$skip) {
      $row[] = $info['lat'];
      $row[] = $info['lng'];
    }
    $rows[] = $row;
  }

  $header = array(
    'TreeGenes Identifier',
    'Identifier',
    'Species',
  );
  if (!$skip) {
    $header[] = 'Latitude';
    $header[] = 'Longitude';
  }

  $vars = array(
    'header' => $header,
    'rows' => $rows,
    'attributes' => array(
      'class' => array('view'),
      'id' => 'tpps_table_display',
    ),
    'caption' => '',
    'colgroups' => NULL,
    'sticky' => FALSE,
    'empty' => '',
  );
  $table = theme('table', $vars);
  $pager = theme('pager', array('quantity', count($state['tree_info'])));
  return $pager . $table;
}

function tpps_details_phenotype(array &$state) {
  $params = drupal_get_query_parameters($_POST);
  $page = 0;
  if (!empty($params['page'])) {
    $page = $params['page'];
  }
  $rows = array();
  $per_page = 20;
  $start = $page * $per_page;

  $query = db_select('chado.phenotype', 'p');
  $query->join('chado.stock_phenotype', 'sp', 'sp.phenotype_id = p.phenotype_id');
  $query->join('chado.project_stock', 'ps', 'ps.stock_id = sp.stock_id');
  $query->join('chado.stock', 's', 's.stock_id = sp.stock_id');
  $query->addExpression('count(p.phenotype_id)', 'count');
  $query->condition('ps.project_id', $state['ids']['project_id']);
  $query = $query->execute();
  $total = $query->fetchObject()->count;

  $_GET['page'] = $page;
  pager_default_initialize($total, $per_page);

  $query = db_select('chado.phenotype', 'p');
  $query->join('chado.stock_phenotype', 'sp', 'sp.phenotype_id = p.phenotype_id');
  $query->join('chado.project_stock', 'ps', 'ps.stock_id = sp.stock_id');
  $query->join('chado.stock', 's', 's.stock_id = sp.stock_id');
  $query->fields('p', array(
    'phenotype_id',
    'name',
    'attr_id',
    'observable_id',
    'value',
  ));
  $query->fields('s', array('uniquename', 'stock_id'));
  $query->condition('ps.project_id', $state['ids']['project_id']);
  $query->range($start, $per_page);
  $query = $query->execute();

  // $query = db_select('chado.new_pheno_view_update', 'p');
  // $query->addField('p', 'phenotype_id', 'phenotype_id');
  // $query->addField('p', 'synonym', 'name');
  // $query->addField('p', 'structure_id', 'attr_id');
  // $query->addField('p', 'observable_id', 'observable_id');
  // $query->addField('p', 'value', 'value');
  // $query->addField('p', 'tree_acc', 'uniquename');
  // $query->addField('p', 'stock_id', 'stock_id');
  // $query->condition('p.project_id', $state['ids']['project_id']);
  // $query->range($start, $per_page);
  // $query = $query->execute();

  while (($result = $query->fetchObject())) {
    // preg_match('/^TGDR...-(.*)$/', $result->uniquename, $matches);
    preg_match('/^TGDR.{1,4}-(.*)$/', $result->uniquename, $matches);
    $tree = $matches[1];
    $obs = chado_get_cvterm(array(
      'cvterm_id' => $result->observable_id,
    ))->name ?? "";
    $attr = chado_get_cvterm(array(
      'cvterm_id' => $result->attr_id,
    ))->name ?? "";

    $rows[] = array(
      tpps_entity_link($result->stock_id, $tree, 'Stock'),
      tpps_entity_link($result->phenotype_id, $result->name, 'Phenotype'),
      $attr,
      $obs,
      $result->value,
    );
  }

  $vars = array(
    'header' => array(
      'Plant',
      'Name',
      'Attribute',
      'Entity',
      'Value',
    ),
    'rows' => $rows,
    'attributes' => array(
      'class' => array('view'),
      'id' => 'tpps_table_display',
    ),
    'caption' => '',
    'colgroups' => NULL,
    'sticky' => FALSE,
    'empty' => '',
  );
  $table = theme('table', $vars);
  $pager = theme('pager', array('quantity', $total));
  return $pager . $table;
}

function tpps_details_genotype(array &$state) {
  $params = drupal_get_query_parameters($_POST);
  $page = 0;
  if (!empty($params['page'])) {
    $page = $params['page'];
  }
  $rows = array();
  $per_page = 20;
  $start = $page * $per_page;

  // Set total check = false to begin with
  $total_check = false;

  // Check cache to see if a total is available
  $total_array = variable_get('tpps_tab_genotype_' + $state['ids']['project_id'] + '_total');
  if($total_array == NULL) {
    $total_check = true;
  }
  else {
    // total array should have an expire_time
    if($total_array['expire_time'] < time()) {
      $total_check = true;
    }
    else {
      $total = $total_array['total'];
    }

  }


  $dev = FALSE;
  if($dev == TRUE) {
    $total_check = true;
  }

  if($total_check) {
    $query = db_select('chado.genotype', 'g');
    $query->join('chado.stock_genotype', 'sg', 'sg.genotype_id = g.genotype_id');
    $query->join('chado.project_stock', 'ps', 'ps.stock_id = sg.stock_id');
    $query->addExpression('count(g.genotype_id)', 'count');
    $query->condition('ps.project_id', $state['ids']['project_id']);
    $query = $query->execute();
    $total = $query->fetchObject()->count;
    
    $total_array = array(
      'expire_time' => time() + variable_get('tpps_tab_genotype_total_cache_time', 30*(24*60*60)),
      'total' => $total
    );
    variable_set('tpps_tab_genotype_' + $state['ids']['project_id'] + '_total', $total_array);
  }

  $_GET['page'] = $page;
  pager_default_initialize($total, $per_page);

  $query = db_select('chado.genotype', 'g');
  $query->join('chado.stock_genotype', 'sg', 'sg.genotype_id = g.genotype_id');
  $query->join('chado.project_stock', 'ps', 'ps.stock_id = sg.stock_id');
  $query->join('chado.stock', 's', 's.stock_id = sg.stock_id');
  $query->fields('g', array(
    'genotype_id',
    'name',
    'uniquename',
    'description',
    'type_id',
  ));
  $query->fields('s', array('uniquename', 'stock_id'));
  $query->condition('ps.project_id', $state['ids']['project_id']);
  $query->range($start, $per_page);
  $query = $query->execute();

  while (($result = $query->fetchObject())) {
    // preg_match('/^TGDR...-(.*)$/', $result->s_uniquename, $matches);
    preg_match('/^TGDR.{1,4}-(.*)$/', $result->s_uniquename, $matches);
    $tree = $matches[1];
    $type = chado_get_cvterm(array(
      'cvterm_id' => $result->type_id,
    ))->name ?? "";
    $rows[] = array(
      tpps_entity_link($result->stock_id, $tree, 'Stock'),
      tpps_entity_link($result->genotype_id, $result->uniquename, 'Genotype'),
      $result->description,
      $type,
    );
  }

  $vars = array(
    'header' => array(
      'Plant',
      'Name',
      'Description',
      'Marker Type',
    ),
    'rows' => $rows,
    'attributes' => array(
      'class' => array('view'),
      'id' => 'tpps_table_display',
    ),
    'caption' => '',
    'colgroups' => NULL,
    'sticky' => FALSE,
    'empty' => '',
  );
  $table = theme('table', $vars);
  $pager = theme('pager', array('quantity', $total));
  return $pager . $table;
}


function tpps_details_mass_spectrometry(array &$state) {
  $params = drupal_get_query_parameters($_POST);
  $page = 0;
  if (!empty($params['page'])) {
    $page = $params['page'];
  }
  $rows = array();
  $per_page = 20;
  $start = $page * $per_page;

  $query = db_select('chado.phenotype', 'p');
  $query->join('chado.stock_phenotype', 'sp', 'sp.phenotype_id = p.phenotype_id');
  $query->join('chado.project_stock', 'ps', 'ps.stock_id = sp.stock_id');
  $query->join('chado.stock', 's', 's.stock_id = sp.stock_id');
  $query->addExpression('count(p.phenotype_id)', 'count');
  $query->condition('ps.project_id', $state['ids']['project_id']);
  $query = $query->execute();
  $total = $query->fetchObject()->count;

  $_GET['page'] = $page;
  pager_default_initialize($total, $per_page);

  $query = db_select('chado.phenotype', 'p');
  $query->join('chado.stock_phenotype', 'sp', 'sp.phenotype_id = p.phenotype_id');
  $query->join('chado.project_stock', 'ps', 'ps.stock_id = sp.stock_id');
  $query->join('chado.stock', 's', 's.stock_id = sp.stock_id');
  $query->fields('p', array(
    'phenotype_id',
    'name',
    'attr_id',
    'observable_id',
    'value',
  ));
  $query->fields('s', array('uniquename', 'stock_id'));
  $query->condition('p.attr_id', tpps_load_cvterm('Intensity')->cvterm_id);
  //$query->condition('ps.project_id', $state['ids']['project_id']);
  $query->range($start, $per_page);
  $query = $query->execute();

  while (($result = $query->fetchObject())) {
    preg_match('/^TGDR...-(.*)$/', $result->uniquename, $matches);
    $tree = $matches[1];
    $obs = chado_get_cvterm(array(
      'cvterm_id' => $result->observable_id,
    ))->name ?? "";
    $attr = chado_get_cvterm(array(
      'cvterm_id' => $result->attr_id,
    ))->name ?? "";

    $rows[] = array(
      tpps_entity_link($result->stock_id, $tree, 'Stock'),
      tpps_entity_link($result->phenotype_id, $result->name, 'Phenotype'),
      $attr,
      $obs,
      $result->value,
    );
  }

  $vars = array(
    'header' => array(
      'Plant',
      'Name',
      'Attribute',
      'Entity',
      'Value',
    ),
    'rows' => $rows,
    'attributes' => array(
      'class' => array('view'),
      'id' => 'tpps_table_display',
    ),
    'caption' => '',
    'colgroups' => NULL,
    'sticky' => FALSE,
    'empty' => '',
  );
  $table = theme('table', $vars);
  $pager = theme('pager', array('quantity', $total));
  return $pager . $table;
}