tripal/tripal_feature/tripal_feature.module

<?php
/**
 * @file
 * Basic functionality for the tripal module
 */

/**
 * @defgroup tripal_feature Feature Module
 * @ingroup tripal_modules
 * @{
 * Integrates the Chado Sequence module with Drupal Nodes & Views
 * @}
 */

require_once 'api/tripal_feature.api.inc';
require_once 'api/tripal_feature.DEPRECATED.inc';

require_once 'theme/tripal_feature.theme.inc';

require_once 'includes/tripal_feature.admin.inc';
require_once 'includes/tripal_feature.fasta_loader.inc';
require_once 'includes/tripal_feature.gff_loader.inc';
require_once 'includes/tripal_feature.seq_extract.inc';
require_once 'includes/tripal_feature.delete.inc';
require_once 'includes/tripal_feature.chado_node.inc';

/**
 * Implements hook_views_api().
 *
 * Essentially this hook tells drupal that there is views support for
 *  for this module which then includes tripal_db.views.inc where all the
 *  views integration code is
 *
 * @ingroup tripal_feature
 */
function tripal_feature_views_api() {
  return array(
    'api' => 3.0,
  );
}

/**
 * Implements hook_help().
 *
 * Display help and module information
 *
 * @param
 *   path which path of the site we're displaying help
 * @param
 *   arg array that holds the current path as would be returned from arg() function
 *
 * @return
 *   help text for the path
 *
 * @ingroup tripal_feature
 */
function tripal_feature_help($path, $arg) {
  $output = '';
  switch ($path) {
  case "admin/help#tripal_feature":
    $output='<p>' . t("Displays links to nodes created on this date") . '</p>';
    break;
  }
  return $output;
}

/**
 * Implements hook_permission().
 *
 *  Set the permission types that the chado module uses.  Essentially we
 *  want permissionis that protect creation, editing and deleting of chado
 *  data objects
 *
 * @ingroup tripal_feature
 */
function tripal_feature_permission() {
  return array(
    'access chado_feature content' => array(
      'title' => t('View Features'),
      'description' => t('Allow users to view feature pages.'),
    ),
    'create chado_feature content' => array(
      'title' => t('Create Features'),
      'description' => t('Allow users to create new feature pages.'),
    ),
    'delete chado_feature content' => array(
      'title' => t('Delete Features'),
      'description' => t('Allow users to delete feature pages.'),
    ),
    'edit chado_feature content' => array(
      'title' => t('Edit Features'),
      'description' => t('Allow users to edit feature pages.'),
    ),
    'administer tripal feature' => array(
      'title' => t('Administer Features'),
      'description' => t('Allow users to administer all features.'),
    ),
  );
}

/**
 * Implements hook_menu().
 *
 * Menu items are automatically added for the new node types created
 *  by this module to the 'Create Content' Navigation menu item.  This function
 *  adds more menu items needed for this module.
 *
 * @ingroup tripal_feature
 */
function tripal_feature_menu() {
  $items = array();

  // the administative settings menu
  $items['find/sequences'] = array(
    'title' => 'Sequence Retrieval',
    'description' => 'Download a file of sequences',
    'page callback' => 'tripal_feature_seq_extract_page',
    'access arguments' => array('access chado_feature content'),
    'type' => MENU_CALLBACK,
  );

  $items['find/sequences/ajax'] = array(
    'title' => 'Sequence Retrieval',
    'page callback' => 'tripal_feature_seq_extract_form_ahah_update',
    'access arguments' => array('access chado_feature content'),
    'type' => MENU_CALLBACK,
  );

  // the menu link for addressing any feature (by name, uniquename, synonym)
  $items['feature/%'] = array(
    'page callback' => 'tripal_feature_match_features_page',
    'page arguments' => array(1),
    'access arguments' => array('access chado_feature content'),
    'type' => MENU_LOCAL_TASK,
  );

  // the administative settings menu
  $items['admin/tripal/chado/tripal_feature'] = array(
    'title' => 'Features',
    'description' => 'A biological sequence or a section of a biological sequence, or a collection of such sections.',
    'page callback' => 'tripal_feature_admin_feature_view',
    'access arguments' => array('administer tripal feature'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['admin/tripal/chado/tripal_feature/delete'] = array(
    'title' => ' Delete',
    'description' => 'Delete multiple features from Chado',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_feature_delete_form'),
    'access arguments' => array('administer tripal feature'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 2
  );
  $items['admin/tripal/chado/tripal_feature/sync'] = array(
    'title' => ' Sync',
    'description' => 'Create pages on this site for features stored in Chado',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('chado_node_sync_form', 'tripal_feature', 'chado_feature'),
    'access arguments' => array('administer tripal feature'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 1
  );
  $items['admin/tripal/chado/tripal_feature/chado_feature_toc'] = array(
    'title' => ' TOC',
    'description' => 'Manage the table of contents for feature nodes.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_core_content_type_toc_form', 'chado_feature'),
    'access arguments' => array('administer tripal feature'),
    'type' => MENU_LOCAL_TASK,
    'file' =>  'includes/tripal_core.toc.inc',
    'file path' => drupal_get_path('module', 'tripal_core'),
    'weight' => 3
  );
  $items['admin/tripal/chado/tripal_feature/configuration'] = array(
    'title' => 'Settings',
    'description' => 'Configure the Tripal Feature module.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_feature_admin'),
    'access arguments' => array('administer tripal feature'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 5
  );
  $items['admin/tripal/chado/tripal_feature/help'] = array(
    'title' => 'Help',
    'description' => 'Help with the Tripal Feature module.',
    'page callback' => 'theme',
    'page arguments' => array('tripal_feature_help'),
    'access arguments' => array('administer tripal feature'),
    'type' => MENU_LOCAL_TASK,
    'weight' =>  10
  );

  /** Loaders */
  $items['admin/tripal/loaders/fasta_loader'] = array(
    'title' => 'FASTA file Loader',
    'description' => 'Load sequences from a multi-FASTA file into Chado',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_feature_fasta_load_form'),
    'access arguments' => array('administer tripal feature'),
    'type' => MENU_NORMAL_ITEM,
  );
  $items['admin/tripal/loaders/gff3_load'] = array(
    'title' => 'GFF3 file Loader',
    'description' => 'Import a GFF3 file into Chado',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_feature_gff3_load_form'),
    'access arguments' => array('administer tripal feature'),
    'type' => MENU_NORMAL_ITEM,
  );

  // Enable admin view
  $items['admin/tripal/chado/tripal_feature/views/features/enable'] = array(
    'title' => 'Enable feature Administrative View',
    'page callback' => 'tripal_enable_view',
    'page arguments' => array('tripal_feature_admin_features', 'admin/tripal/chado/tripal_feature'),
    'access arguments' => array('administer tripal feature'),
    'type' => MENU_CALLBACK,
  );

  return $items;
}

/**
 * Implements hook_search_biological_data_views().
 *
 * Adds the described views to the "Search Data" Page created by Tripal Views
 */
function tripal_feature_search_biological_data_views() {
  return array(
    'tripal_feature_user_features' => array(
      'machine_name' => 'tripal_feature_user_features',
      'human_name' => 'Features',
      'description' => 'A biological sequence or a section of a biological sequence, or a collection of such sections.',
      'link' => 'chado/feature'
    ),
  );
}

/**
 * Implements hook_theme().
 *
 * We need to let drupal know about our theme functions and their arguments.
 *  We create theme functions to allow users of the module to customize the
 *  look and feel of the output generated in this module
 *
 * @ingroup tripal_feature
 */
function tripal_feature_theme($existing, $type, $theme, $path) {
  $core_path = drupal_get_path('module', 'tripal_core');

  // Feature Node Page Templates.
  $items = array(
    'node__chado_feature' => array(
      'template' => 'node--chado-generic',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$core_path/theme/templates",
    ),
    'tripal_feature_alignments' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_alignments',
      'path' => "$path/theme/templates",
    ),
    'tripal_feature_analyses' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_analyses',
      'path' => "$path/theme/templates",
    ),
    'tripal_feature_base' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_base',
      'path' => "$path/theme/templates",
    ),
    'tripal_feature_sequence' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_sequence',
      'path' => "$path/theme/templates",
    ),
    'tripal_feature_proteins' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_proteins',
      'path' => "$path/theme/templates",
    ),
    'tripal_feature_publications' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_publications',
      'path' => "$path/theme/templates",
    ),
    'tripal_feature_synonyms' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_synonyms',
      'path' => "$path/theme/templates",
    ),
    'tripal_feature_references' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_references',
      'path' => "$path/theme/templates",
    ),
    'tripal_feature_properties' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_properties',
      'path' => "$path/theme/templates",
    ),
    'tripal_feature_terms' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_terms',
      'path' => "$path/theme/templates",
    ),
    'tripal_feature_relationships' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_relationships',
      'path' => "$path/theme/templates",
    ),
  );

  // Feature Node Teaser
  $items['tripal_feature_teaser'] = array(
    'variables' => array('node' => NULL),
    'template' => 'tripal_feature_teaser',
    'path' => "$path/theme/templates",
  );

  // Templates for other node pages.
  // Organism Feature Browser.
  $items['tripal_organism_feature_browser'] = array(
    'variables' => array('node' => NULL),
    'template' => 'tripal_organism_feature_browser',
    'path' => "$path/theme/templates",
  );
  $items['tripal_organism_feature_counts'] = array(
    'variables' => array('node' => NULL),
    'template' => 'tripal_organism_feature_counts',
    'path' => "$path/theme/templates",
  );

  // Administrative Help Template.
  $items['tripal_feature_help'] = array(
    'template' => 'tripal_feature_help',
    'variables' =>  array(NULL),
    'path' => "$path/theme/templates"
  );

  // Themed Forms
  $items['tripal_feature_seq_extract_form'] = array(
     'arguments' => array('form'),
  );

  // D3 Charts.
  // Feature Type/Organism Stacked Bar Chart.
  $items['tripal_feature_bar_chart_type_organism_summary'] = array(
    'template' => 'tripal_feature_bar_chart_type_organism_summary',
    'variables' =>  array(NULL),
    'path' => "$path/theme/templates"
  );

  return $items;
}
/**
 * Implements hook_job_describe_args() in order to describe the various feature jobs
 * to the tripal jobs interface.
 *
 * @ingroup tripal_feature
 */
function tripal_feature_job_describe_args($callback, $args) {

  $new_args = array();
  if ($callback == 'tripal_feature_load_fasta') {
    $new_args['FASTA file'] = $args[0];
    $organism = chado_select_record('organism', array('genus', 'species'), array('organism_id' => $args[1]));
    $new_args['Organism'] = $organism[0]->genus . " " . $organism[0]->species;
    $new_args['Sequence Type'] = $args[2];
    $new_args['Name Match Type'] = $args[14];
    $new_args['Name RE'] = $args[4];
    $new_args['Unique Name RE'] = $args[5];

    // add in the relationship arguments
    $new_args['Relationship Type'] = $args[8];
    $new_args['Relationship Parent RE'] = $args[9];
    $new_args['Relationship Parent Type'] = $args[10];

    // add in the database reference arguments
    if ($args[7]) {
      $db = chado_select_record('db', array('name'), array('db_id' => $args[7]));
    }
    $new_args['Database Reference'] = $db[0]->name;
    $new_args['Accession RE'] = $args[6];
    $new_args['Method'] = $args[11];

    // add in the analysis
    if ($args[13]) {
      $analysis = chado_select_record('analysis', array('name'), array('analysis_id' => $args[13]));
    }
    $new_args['Analysis'] = $analysis[0]->name;
  }
  if ($callback == 'tripal_feature_delete_features') {
    if ($args[0]) {
      $organism = chado_select_record('organism', array('genus', 'species'), array('organism_id' => $args[0]));
      $new_args['Organism'] = $organism[0]->genus . " " . $organism[0]->species;
    }
    else {
      $new_args['Organism'] = '';
    }

    if ($args[1]) {
      $analysis = chado_select_record('analysis', array('name'), array('analysis_id' => $args[1]));
      $new_args['Analysis'] = $analysis[0]->name;
    }
    else {
      $new_args['Analysis'] = '';
    }

    $new_args['Sequence Type'] = $args[2];
    $new_args['Is Unique Name'] = $args[3] ? 'Yes' : 'No';
    $new_args['Features Names'] = $args[4];
  }
  elseif ($callback == 'tripal_feature_load_gff3') {

    $new_args['GFF File'] = $args[0];
    $organism = chado_select_record('organism', array('genus', 'species'), array('organism_id' => $args[1]));
    $new_args['Organism'] = $organism[0]->genus . " " . $organism[0]->species;
    $analysis = chado_select_record('analysis', array('name'), array('analysis_id' => $args[2]));
    $new_args['Analysis'] = $analysis[0]->name;
    $new_args['Use a Transaction'] = ($args[7] == 1) ? "Yes" : "No";
    $new_args['Import only new features'] = ($args[3] == 1) ? "Yes" : "No";
    $new_args['Import all and update'] = ($args[4] == 1) ? "Yes" : "No";
    $new_args['Import all and replace'] = ($args[5] == 1) ? "Yes" : "No";
    $new_args['Delete features'] = ($args[6] == 1) ? "Yes" : "No";
    if ($args[8]) {
      $target_organism = chado_select_record('organism', array('genus', 'species'), array('organism_id' => $args[8]));
      $new_args['Target organism'] = $target_organism[0]->genus . " " . $target_organism[0]->species;
    }
    else {
      $new_args['Target organism'] = '';
    }
    $new_args['Target type'] = $args[9];
    $new_args['Create target'] = ($args[10] == 1) ? "Yes" : "No";
    $new_args['Starting line'] = $args[11];
    $new_args['Landmark Type'] = $args[12];
    $new_args['Alternate ID attribute'] = $args[13];
    $new_args['Create Organism'] = ($args[14] == 1) ? "Yes" : "No";
  }
  return $new_args;
}

/**
 * Implements hook_coder_ignore().
 *
 * Defines the path to the file (tripal_core.coder_ignores.txt) where ignore rules for
 * coder are stored
 *
 * @ingroup tripal_feature
 */
function tripal_feature_coder_ignore() {
  return array(
    'path' => drupal_get_path('module', 'tripal_feature'),
    'line prefix' => drupal_get_path('module', 'tripal_feature'),
  );
}

/*
 * Uses the value provided in the $id argument to find all features that match
 * that ID by name, featurename or synonym.  If it matches uniquenly to a single
 * feature it will redirect to that feature page, otherwise, a list of matching
 * features is shown.
 *
 * @ingroup tripal_feature
 */
function tripal_feature_match_features_page($id) {

  // first check to see if the URL (e.g. /feature/$id) is already
  // assigned to a node. If so, then just go there.  Otherwise,
  // try to find the feature.
  $sql = "
    SELECT source
    FROM {url_alias}
    WHERE alias = :alias
  ";
  $match = db_query($sql, array(':alias' => "feature/$id"))->fetchObject();
  if ($match) {
    drupal_goto($match->source);
    return;
  }
  $sql = "
    SELECT
      F.name, F.uniquename, F.feature_id,
      O.genus, O.species, O.organism_id,
      CVT.cvterm_id, CVT.name as type_name,
      CF.nid,
      array_agg(S.name) as synonyms
    FROM {feature} F
      INNER JOIN {organism} O on F.organism_id = O.organism_id
      INNER JOIN {cvterm} CVT on CVT.cvterm_id = F.type_id
      LEFT JOIN {feature_synonym} FS on FS.feature_id = F.feature_id
      LEFT JOIN {synonym} S on S.synonym_id = FS.synonym_id
      INNER JOIN public.chado_feature CF on CF.feature_id = F.feature_id
    WHERE
      F.uniquename = :uname or
      F.name = :fname or
      S.name = :sname
    GROUP BY F.name, F.uniquename, F.feature_id, O.genus, O.species,
      O.organism_id, CVT.cvterm_id, CVT.name, CF.nid
  ";

  $args = array(':uname' => $id, ':fname' => $id, ':sname' => $id);
  $results = chado_query($sql, $args);

  $num_matches = 0;

  // iterate through the matches and build the table for showing matches
  $header = array('Uniquename', 'Name', 'Type', 'Species', 'Synonyms');
  $rows = array();
  $curr_match;
  while ($match = $results->fetchObject()) {
    $curr_match = $match;
    $synonyms = $match->synonyms;
    $synonyms = preg_replace('/[\"\{\}]/', '', $synonyms);
    $rows[] = array(
       $match->uniquename,
       "<a href=\"" . url("node/" . $match->nid) . "\">" . $match->name . "</a>",
       $match->type_name,
       '<i>' . $match->genus . ' ' . $match->species . '</i>',
       $synonyms,
    );
    $num_matches++;
  }

  // if we have more than one match then generate the table, otherwise, redirect
  // to the matched feature
  if ($num_matches == 1) {
    drupal_goto("node/" . $curr_match->nid);
  }
  if ($num_matches == 0) {
    return "<p>No features matched the given name '$id'</p>";
  }

  $table_attrs = array('class' => 'tripal-data-table');
  $output = "<p>The following features match the name '$id'.</p>";
  $output .= theme_table($header, $rows, $table_attrs, $caption);
  return $output;
}

/**
 * Implementation of hook_form_alter()
 *
 * @param $form
 * @param $form_state
 * @param $form_id
 *
 * @ingroup tripal_feature
 */
function tripal_feature_form_alter(&$form, &$form_state, $form_id) {
  if ($form_id == "tripal_feature_seq_extract_form") {
    // updating the form through the ahah callback sets the action of
    // the form to the ahah callback URL. We need to set it back
    // to the normal form URL
    $form['#action'] = url("find/sequences");
  }
  // turn off preview button for insert/updates
  if ($form_id == "chado_feature_node_form") {
    $form['actions']['preview']['#access'] = FALSE;

    //remove the body field
    unset($form['body']);
  }
}

/**
 * Implements hook_exclude_field_from_<tablename>_by_default()
 *
 * This hooks allows fields from a specified table that match a specified criteria to be excluded by
 * default from any table when chado_generate_var() is called. Keep in mind that if
 * fields are excluded by default they can always be expanded at a later date using
 * chado_expand_var().
 *
 * Criteria are php strings that evaluate to either TRUE or FALSE. These strings are evaluated using
 * drupal_eval() which suppresses syntax errors and throws watchdog entries of type php. There are
 * also watchdog entries of type tripal_core stating the exact criteria evaluated. Criteria can
 * contain the following tokens:
 *   - <field_name>
 *       Replaced by the name of the field to be excluded
 *   - <field_value>
 *       Replaced by the value of the field in the current record
 * Also keep in mind that if your criteria doesn't contain the <field_value>  token then it will be
 * evaluated before the query is executed and if the field is excluded it won't be included in the
 * query.
 *
 * @return
 *   An array of field => criteria where the type is excluded if the criteria evaluates to TRUE
 *
 * @ingroup tripal_feature
 */
function tripal_feature_exclude_field_from_feature_by_default() {
  return array('residues' => 'TRUE');
}