details.inc File Reference

Go to the source code of this file.

Functions
	tpps_details ($accession=NULL)
	tpps_details_form_callback (array $form, array $form_state)
	tpps_details_genotype (array &$state)
	tpps_details_get_study_file_ids ($state)
	tpps_details_mass_spectrometry (array &$state)
	tpps_details_phenotype (array &$state)
	tpps_details_search (array $form, array $form_state)
	tpps_details_species (array &$state)
	tpps_details_study (array &$state)
	tpps_details_tab ($accession, $type)
	tpps_details_tabs (array &$state)
	tpps_details_tags_sort ()
	tpps_details_top ()
	tpps_details_top_callback ()
	tpps_details_trees (array &$state)

Detailed Description

Defines functions to be used in the TPPS Details pages.

Definition in file details.inc.

Function Documentation

tpps_details()

tpps_details

(

$accession = NULL

)

Starting point for most TPPS Details pages.

Either returns the top details page, which allows users to select from completed studies, or returns the per-submission details page, which allows users to browse the details of a study.

Parameters

string

$accession

The accession to get details from. If NULL, show all submissions.

Returns

string The appropriate output.

Definition at line 21 of file details.inc.

                                         {
  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;
}

tpps_details_form_callback()

tpps_details_form_callback	(	array	$form,
		array	$form_state
	)

AJAX callback for the search form details_op element.

Parameters

array	$form	The form being updated.
array	$form_state	The state of the form being updated.

Returns

array The part of the form to be updated.

Definition at line 568 of file details.inc.

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

tpps_details_genotype()

tpps_details_genotype

(

array &

$state

)

Creates the table of individual plant genotype details for a submission.

Parameters

array

$state

The form state of the submission.

Returns

string The HTML table of plants and genotypes associated with the submission.

Definition at line 981 of file details.inc.

                                              {
  $params = drupal_get_query_parameters($_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;
}

tpps_details_get_study_file_ids()

tpps_details_get_study_file_ids

(

$state

)

Definition at line 738 of file details.inc.

                                                 {
  $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;
}

tpps_details_mass_spectrometry()

tpps_details_mass_spectrometry

(

array &

$state

)

Creates the table for mass spectrometry details for a submission.

Parameters

array

$state

The form state of the submission.

Returns

string The HTML table of plants and genotypes associated with the submission.

Definition at line 1098 of file details.inc.

                                                       {
  $params = drupal_get_query_parameters($_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;
}

tpps_details_phenotype()

tpps_details_phenotype

(

array &

$state

)

Creates the table of individual plant phenotype details for a submission.

Parameters

array

$state

The form state of the submission.

Returns

string The HTML table of plants and phenotypes associated with the submission.

Definition at line 879 of file details.inc.

                                               {
  $params = drupal_get_query_parameters($_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;
}

tpps_details_search()

tpps_details_search	(	array	$form,
		array	$form_state
	)

Define a search form to search and filter through the TPPS Details page.

Parameters

array	$form	The form array object.
array	$form_state	The form state array object.

Returns

array The populated search form.

Definition at line 424 of file details.inc.

                                                             {
  $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;
}

tpps_details_species()

tpps_details_species

(

array &

$state

)

Creates the table for species details for a submission.

Parameters

array

$state

The form state of the submission.

Returns

string The HTML table of species associated with the submission.

Definition at line 585 of file details.inc.

                                             {
  $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);
}

tpps_details_study()

tpps_details_study

(

array &

$state

)

Creates the table for study information details for a submission.

Parameters

array

$state

The form state of the submission.

Returns

string The HTML table of study information of the submission.

Definition at line 662 of file details.inc.

                                           {
  $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);
}

tpps_details_tab()

tpps_details_tab	(		$accession,
			$type
	)

A callback to print a single detail tab.

Parameters

string	$accession	The accession number of the submission.
string	$type	The type of details we want to print.

Definition at line 197 of file details.inc.

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

tpps_details_tabs()

tpps_details_tabs

(

array &

$state

)

Returns a template for details tabs.

Parameters

array

$state

The form state of the submission.

Returns

string HTML for the details tabs.

Definition at line 152 of file details.inc.

                                          {
  $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;
}

tpps_details_tags_sort()

tpps_details_tags_sort

(

)

Display TPPS tags to sort Details page.

Returns

string Tag options as rendered HTML.

Definition at line 534 of file details.inc.

                                  {
  $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>";
}

tpps_details_top()

tpps_details_top

(

)

Builds the TPPS Details page when no accession is provided.

Returns

string The HTML string for the TPPS Details page.

Definition at line 209 of file details.inc.

                            {
  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;
}

tpps_details_top_callback()

tpps_details_top_callback

(

)

Serves as a direct callback to print the contents of tpps_details_top().

Definition at line 409 of file details.inc.

                                     {
  print(tpps_details_top());
}

tpps_details_trees()

tpps_details_trees

(

array &

$state

)

Creates the table of individual plant details for a submission.

Parameters

array

$state

The form state of the submission.

Returns

string The HTML table of plants associated with the submission.

Definition at line 802 of file details.inc.

                                           {
  $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;
}