tripal/tripal_phenotype/tripal_phenotype.views.inc

<?php

/**
 *  @file
 *  This file contains the basic functions for views integration of
 *  chado/tripal_phenotype tables. Supplementary functions can be found in
 *  ./views/
 *
 *  Documentation on views integration can be found at
 *  http://views2.logrus.com/doc/html/index.html.
 */

/**
 * @defgroup tripal_phenotype_views Phenotype Views Integration
 * @ingroup views
 */

/**
 *
 *
 * @ingroup tripal_phenotype_views
 */
function tripal_phenotype_views_default_views() {
  $views = array();

  if (!module_exists('tripal_views')) {
    return $views;
  }

  // Main default view
  $view = new view;
  $view->name = 'phenotype_listing';
  $view->description = 'A listing of chado phenotypes';
  $view->tag = 'chado default';
  $view->base_table = 'phenotype';
  $view->core = 6;
  $view->api_version = '2';
  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
  $handler = $view->new_display('default', 'Defaults', 'default');
  $handler->override_option('relationships', array(
    'assay_id' => array(
      'label' => 'assay_id to cvterm',
      'required' => 0,
      'id' => 'assay_id',
      'table' => 'phenotype',
      'field' => 'assay_id',
      'relationship' => 'none',
    ),
    'attr_id' => array(
      'label' => 'attr_id to cvterm',
      'required' => 0,
      'id' => 'attr_id',
      'table' => 'phenotype',
      'field' => 'attr_id',
      'relationship' => 'none',
    ),
    'cvalue_id' => array(
      'label' => 'cvalue_id to cvterm',
      'required' => 0,
      'id' => 'cvalue_id',
      'table' => 'phenotype',
      'field' => 'cvalue_id',
      'relationship' => 'none',
    ),
    'observable_id' => array(
      'label' => 'observable_id to cvterm',
      'required' => 0,
      'id' => 'observable_id',
      'table' => 'phenotype',
      'field' => 'observable_id',
      'relationship' => 'none',
    ),
  ));
  $handler->override_option('fields', array(
    'uniquename' => array(
      'label' => 'Unique Name',
      'alter' => array(
        'alter_text' => 0,
        'text' => '',
        'make_link' => 0,
        'path' => '',
        'absolute' => 0,
        'link_class' => '',
        'alt' => '',
        'rel' => '',
        'prefix' => '',
        'suffix' => '',
        'target' => '',
        'help' => '',
        'trim' => 0,
        'max_length' => '',
        'word_boundary' => 1,
        'ellipsis' => 1,
        'html' => 0,
        'strip_tags' => 0,
      ),
      'empty' => '',
      'hide_empty' => 0,
      'empty_zero' => 0,
      'hide_alter_empty' => 1,
      'type' => 'separator',
      'separator' => ', ',
      'exclude' => 0,
      'id' => 'uniquename',
      'table' => 'phenotype',
      'field' => 'uniquename',
      'relationship' => 'none',
    ),
    'name_1' => array(
      'label' => 'Phenotypic Attribute',
      'alter' => array(
        'alter_text' => 0,
        'text' => '',
        'make_link' => 0,
        'path' => '',
        'absolute' => 0,
        'link_class' => '',
        'alt' => '',
        'rel' => '',
        'prefix' => '',
        'suffix' => '',
        'target' => '',
        'help' => '',
        'trim' => 0,
        'max_length' => '',
        'word_boundary' => 1,
        'ellipsis' => 1,
        'html' => 0,
        'strip_tags' => 0,
      ),
      'empty' => '',
      'hide_empty' => 0,
      'empty_zero' => 0,
      'hide_alter_empty' => 1,
      'type' => 'separator',
      'separator' => ', ',
      'exclude' => 0,
      'id' => 'name_1',
      'table' => 'cvterm',
      'field' => 'name',
      'relationship' => 'attr_id',
    ),
    'name_3' => array(
      'label' => 'Controlled Value',
      'alter' => array(
        'alter_text' => 0,
        'text' => '',
        'make_link' => 0,
        'path' => '',
        'absolute' => 0,
        'link_class' => '',
        'alt' => '',
        'rel' => '',
        'prefix' => '',
        'suffix' => '',
        'target' => '',
        'help' => '',
        'trim' => 0,
        'max_length' => '',
        'word_boundary' => 1,
        'ellipsis' => 1,
        'html' => 0,
        'strip_tags' => 0,
      ),
      'empty' => '',
      'hide_empty' => 0,
      'empty_zero' => 0,
      'hide_alter_empty' => 1,
      'type' => 'separator',
      'separator' => ', ',
      'exclude' => 0,
      'id' => 'name_3',
      'table' => 'cvterm',
      'field' => 'name',
      'relationship' => 'cvalue_id',
    ),
    'value' => array(
      'label' => 'Value',
      'alter' => array(
        'alter_text' => 0,
        'text' => '',
        'make_link' => 0,
        'path' => '',
        'absolute' => 0,
        'link_class' => '',
        'alt' => '',
        'rel' => '',
        'prefix' => '',
        'suffix' => '',
        'target' => '',
        'help' => '',
        'trim' => 0,
        'max_length' => '',
        'word_boundary' => 1,
        'ellipsis' => 1,
        'html' => 0,
        'strip_tags' => 0,
      ),
      'empty' => '',
      'hide_empty' => 0,
      'empty_zero' => 0,
      'hide_alter_empty' => 1,
      'type' => 'separator',
      'separator' => ', ',
      'exclude' => 0,
      'id' => 'value',
      'table' => 'phenotype',
      'field' => 'value',
      'relationship' => 'none',
    ),
    'name_2' => array(
      'label' => 'Observation Type',
      'alter' => array(
        'alter_text' => 0,
        'text' => '',
        'make_link' => 0,
        'path' => '',
        'absolute' => 0,
        'link_class' => '',
        'alt' => '',
        'rel' => '',
        'prefix' => '',
        'suffix' => '',
        'target' => '',
        'help' => '',
        'trim' => 0,
        'max_length' => '',
        'word_boundary' => 1,
        'ellipsis' => 1,
        'html' => 0,
        'strip_tags' => 0,
      ),
      'empty' => '',
      'hide_empty' => 0,
      'empty_zero' => 0,
      'hide_alter_empty' => 1,
      'type' => 'separator',
      'separator' => ', ',
      'exclude' => 0,
      'id' => 'name_2',
      'table' => 'cvterm',
      'field' => 'name',
      'relationship' => 'observable_id',
    ),
    'name' => array(
      'label' => 'Evidence Type',
      'alter' => array(
        'alter_text' => 0,
        'text' => '',
        'make_link' => 0,
        'path' => '',
        'absolute' => 0,
        'link_class' => '',
        'alt' => '',
        'rel' => '',
        'prefix' => '',
        'suffix' => '',
        'target' => '',
        'help' => '',
        'trim' => 0,
        'max_length' => '',
        'word_boundary' => 1,
        'ellipsis' => 1,
        'html' => 0,
        'strip_tags' => 0,
      ),
      'empty' => '',
      'hide_empty' => 0,
      'empty_zero' => 0,
      'hide_alter_empty' => 1,
      'type' => 'separator',
      'separator' => ', ',
      'exclude' => 0,
      'id' => 'name',
      'table' => 'cvterm',
      'field' => 'name',
      'relationship' => 'assay_id',
    ),
  ));
  $handler->override_option('filters', array(
    'search_results' => array(
      'operator' => '=',
      'value' => '',
      'group' => '0',
      'exposed' => FALSE,
      'expose' => array(
        'operator' => FALSE,
        'label' => '',
      ),
      'id' => 'search_results',
      'table' => 'views',
      'field' => 'search_results',
      'relationship' => 'none',
      'apply_button' => 'Show',
      'no_results_text' => 'Click "Show" to see a list of all phenotypes matching the entered criteria. If you leave a any of the criteria blank then the phenotypes will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all phenotypes will be listed.',
    ),
    'attr_id' => array(
      'operator' => '=',
      'value' => '',
      'group' => '0',
      'exposed' => TRUE,
      'expose' => array(
        'use_operator' => 0,
        'operator' => 'attr_id_op',
        'identifier' => 'attr_id',
        'label' => 'Phenotypic Attribute',
        'remember' => 0,
      ),
      'case' => 1,
      'id' => 'attr_id',
      'table' => 'phenotype',
      'field' => 'attr_id',
      'relationship' => 'none',
      'agg' => array(
        'records_with' => 1,
        'aggregates_with' => 1,
      ),
      'values_form_type' => 'select',
      'multiple' => 1,
      'optional' => 0,
      'show_all' => 0,
    ),
    'cvalue_id' => array(
      'operator' => '=',
      'value' => '',
      'group' => '0',
      'exposed' => TRUE,
      'expose' => array(
        'use_operator' => 0,
        'operator' => 'cvalue_id_op',
        'identifier' => 'cvalue_id',
        'label' => 'Controlled Value',
        'remember' => 0,
      ),
      'case' => 1,
      'id' => 'cvalue_id',
      'table' => 'phenotype',
      'field' => 'cvalue_id',
      'relationship' => 'none',
      'agg' => array(
        'records_with' => 1,
        'aggregates_with' => 1,
      ),
      'values_form_type' => 'select',
      'multiple' => 1,
      'optional' => 0,
      'show_all' => 0,
    ),
    'observable_id' => array(
      'operator' => '=',
      'value' => '',
      'group' => '0',
      'exposed' => TRUE,
      'expose' => array(
        'use_operator' => 0,
        'operator' => 'observable_id_op',
        'identifier' => 'observable_id',
        'label' => 'Observation Type',
        'remember' => 0,
      ),
      'case' => 1,
      'id' => 'observable_id',
      'table' => 'phenotype',
      'field' => 'observable_id',
      'relationship' => 'none',
      'agg' => array(
        'records_with' => 1,
        'aggregates_with' => 1,
      ),
      'values_form_type' => 'select',
      'multiple' => 1,
      'optional' => 0,
      'show_all' => 0,
    ),
    'assay_id' => array(
      'operator' => '=',
      'value' => '',
      'group' => '0',
      'exposed' => TRUE,
      'expose' => array(
        'use_operator' => 0,
        'operator' => 'assay_id_op',
        'identifier' => 'assay_id',
        'label' => 'Evidence Type',
        'remember' => 0,
      ),
      'case' => 1,
      'id' => 'assay_id',
      'table' => 'phenotype',
      'field' => 'assay_id',
      'relationship' => 'none',
      'agg' => array(
        'records_with' => 1,
        'aggregates_with' => 1,
      ),
      'values_form_type' => 'select',
      'multiple' => 1,
      'optional' => 0,
      'show_all' => 0,
    ),
    'uniquename' => array(
      'operator' => '~',
      'value' => '',
      'group' => '0',
      'exposed' => TRUE,
      'expose' => array(
        'use_operator' => 0,
        'operator' => 'uniquename_op',
        'identifier' => 'uniquename',
        'label' => 'Unique Name Contains',
        'remember' => 0,
      ),
      'case' => 0,
      'id' => 'uniquename',
      'table' => 'phenotype',
      'field' => 'uniquename',
      'relationship' => 'none',
      'agg' => array(
        'records_with' => 1,
        'aggregates_with' => 1,
      ),
    ),
    'value' => array(
      'operator' => '~',
      'value' => '',
      'group' => '0',
      'exposed' => TRUE,
      'expose' => array(
        'use_operator' => 0,
        'operator' => 'value_op',
        'identifier' => 'phen_value',
        'label' => 'Value Contains',
        'remember' => 0,
      ),
      'case' => 0,
      'id' => 'value',
      'table' => 'phenotype',
      'field' => 'value',
      'relationship' => 'none',
      'agg' => array(
        'records_with' => 1,
        'aggregates_with' => 1,
      ),
    ),
  ));
  $handler->override_option('access', array(
    'type' => 'perm',
    'perm' => 'access content',
  ));
  $handler->override_option('cache', array(
    'type' => 'none',
  ));
  $handler->override_option('title', 'Phenotypes');
  $handler->override_option('header', 'Click "Show" to see a list of all phenotypes matching the entered criteria. If you leave a any of the criteria blank then the phenotypes will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all phenotypes will be listed.');
  $handler->override_option('header_format', '2');
  $handler->override_option('header_empty', 0);
  $handler->override_option('empty', 'No phenotypes match the supplied criteria.');
  $handler->override_option('empty_format', '2');
  $handler->override_option('items_per_page', 50);
  $handler->override_option('use_pager', '1');
  $handler->override_option('style_plugin', 'table');
  $handler->override_option('style_options', array(
    'grouping' => '',
    'override' => 1,
    'sticky' => 0,
    'order' => 'asc',
    'summary' => '',
    'columns' => array(
      'uniquename' => 'uniquename',
      'value' => 'value',
    ),
    'info' => array(
      'uniquename' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'value' => array(
        'sortable' => 1,
        'separator' => '',
      ),
    ),
    'default' => 'uniquename',
  ));
  $handler = $view->new_display('page', 'Page', 'page_1');
  $handler->override_option('path', 'chado/phenotypes');
  $handler->override_option('menu', array(
    'type' => 'normal',
    'title' => 'Phenotypes',
    'description' => 'A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function.',
    'weight' => '10',
    'name' => 'navigation',
  ));
  $handler->override_option('tab_options', array(
    'type' => 'none',
    'title' => '',
    'description' => '',
    'weight' => 0,
    'name' => 'navigation',
  ));
  $views[$view->name] = $view;

  return $views;
}