tripal/tripal_feature/tripal_feature.module

<?php

/**
 * @file
 * @todo Add file header description
 */

/**
 * @defgroup tripal_feature Feature Module
 * @ingroup tripal_modules
 * @{
 * Provides functions for managing chado features including creating details pages for each feature
 * @}
 */

require_once "api/tripal_feature.api.inc";
require_once "api/tripal_feature.schema.api.inc";

require_once "includes/tripal_feature.admin.inc";
require_once "includes/tripal_feature.sync_features.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.form.inc";


/**
 *
 * @ingroup tripal_feature
 */
function tripal_feature_init() {
  drupal_add_css(drupal_get_path('module', 'tripal_feature') . '/theme/css/tripal_feature.css');
  drupal_add_js(drupal_get_path('module', 'tripal_feature') . '/theme/js/tripal_feature.js');
}

/**
 * Implements hook_views_api()
 *
 * Purpose: 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' => 2.0,
  );
}

/**
 * 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;
}

/**
 *  Provide information to drupal about the node types that we're creating
 *  in this module
 *
 * @ingroup tripal_feature
 */
function tripal_feature_node_info() {
  $nodes = array();

  $nodes['chado_feature'] = array(
    'name'        => t('Feature'),
    'base'        => 'chado_feature',
    'description' => t('A feature from the chado database'),
    'has_title'   => FALSE,
    'title_label' => t('Feature'),
    'has_body'    => FALSE,
    'body_label'  => t('Feature Description'),
    'locked'      => TRUE
  );
  return $nodes;
}

/**
 *  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_permissions() {
  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.'),
    ),
    'adminster tripal feature' => array(
      'title' => t('Administer Features'),
      'description' => t('Allow users to administer all features.'),
    ),
  );
}

/**
 * Implement hook_access().
 *
 * This hook allows node modules to limit access to the node types they define.
 *
 *  @param $node
 *  The node on which the operation is to be performed, or, if it does not yet exist, the
 *  type of node to be created
 *
 *  @param $op
 *  The operation to be performed
 *
 *  @param $account
 *  A user object representing the user for whom the operation is to be performed
 *
 *  @return
 *  If the permission for the specified operation is not set then return FALSE. If the
 *  permission is set then return NULL as this allows other modules to disable
 *  access.  The only exception is when the $op == 'create'.  We will always
 *  return TRUE if the permission is set.
 *
 * @ingroup tripal_feature
 */
function chado_feature_node_access($node, $op, $account) {
  if ($op == 'create') {
    if (!user_access('create chado_feature content', $account)) {
      return FALSE;
    }
    return TRUE;
  }

  if ($op == 'update') {
    if (!user_access('edit chado_feature content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'delete') {
    if (!user_access('delete chado_feature content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'view') {
    if (!user_access('access chado_feature content', $account)) {
      return FALSE;
    }
  }
  return NULL;
}
/**
 *  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 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 features'),
    'type' => MENU_NORMAL_ITEM,
  );
  $items['admin/tripal/chado/tripal_feature/sync'] = array(
    'title' => 'Sync',
    'description' => 'Sync features from Chado with Drupal',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_feature_sync_form'),
    'access arguments' => array('administer tripal features'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 0
  );
  $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 features'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 2
  );
  $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 features'),
    '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 features'),
    'type' => MENU_LOCAL_TASK,
    'weight' =>  10
  );


  /** Loaders */
  $items['admin/tripal/loaders/fasta_loader'] = array(
    'title' => 'Multi-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 features'),
    '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 features'),
    'type' => MENU_NORMAL_ITEM,
  );

  // 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,
  );

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

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

  $items = array(
    'node__chado_feature' => array(
      'template' => 'node--chado-generic',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$core_path/theme",
    ),
    'tripal_feature_alignments' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_alignments',
      'path' => "$path/theme/tripal_feature",
    ),
    'tripal_feature_analyses' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_analyses',
      'path' => "$path/theme/tripal_feature",
    ),
    'tripal_feature_base' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_base',
      'path' => "$path/theme/tripal_feature",
    ),
    'tripal_feature_featurepos' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_feature_featurepos',
      'path' => "$path/theme/tripal_feature",
    ),
    'tripal_feature_sequence' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_sequence',
      'path' => "$path/theme/tripal_feature",
    ),
    'tripal_feature_proteins' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_proteins',
      'path' => "$path/theme/tripal_feature",
    ),
    'tripal_feature_synonyms' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_synonyms',
      'path' => "$path/theme/tripal_feature",
    ),
    'tripal_feature_phenotypes' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_phenotypes',
      'path' => "$path/theme/tripal_feature",
    ),
    'tripal_feature_references' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_references',
      'path' => "$path/theme/tripal_feature",
    ),
    'tripal_feature_properties' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_properties',
      'path' => "$path/theme/tripal_feature",
    ),
    'tripal_feature_terms' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_terms',
      'path' => "$path/theme/tripal_feature",
    ),
    'tripal_feature_relationships' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_relationships',
      'path' => "$path/theme/tripal_feature",
    ),
    'tripal_feature_help' => array(
      'template' => 'tripal_feature_help',
      'variables' =>  array(NULL),
      'path' => drupal_get_path('module', 'tripal_feature') . '/theme'
    ),

    // template for the organism page
    'tripal_organism_feature_browser' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_organism_feature_browser',
      'path' => "$path/theme/tripal_organism",
    ),
    'tripal_organism_feature_counts' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_organism_feature_counts',
      'path' => "$path/theme/tripal_organism",
    ),

    // themed forms
    'tripal_feature_seq_extract_form' => array(
       'arguments' => array('form'),
    ),

    // themed teaser
    'tripal_feature_teaser' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_teaser',
      'path' => "$path/theme/tripal_feature",
    ),
  );

  return $items;
}
/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_block_info() {

  $blocks['references']['info'] = t('Tripal Feature References');
  $blocks['references']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['base']['info'] = t('Tripal Feature Details');
  $blocks['base']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['sequence']['info'] = t('Tripal Feature Sequence');
  $blocks['sequence']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['featureloc_sequences']['info'] = t('Tripal Feature Annotated Sequence');
  $blocks['featureloc_sequences']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['synonyms']['info'] = t('Tripal Feature Synonyms');
  $blocks['synonyms']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['properties']['info'] = t('Tripal Feature Properties');
  $blocks['properties']['cache'] = 'BLOCK_NO_CACHE';;

  $blocks['terms']['info'] = t('Tripal Annotated Terms');
  $blocks['terms']['cache'] = 'BLOCK_NO_CACHE';;

  $blocks['alignments']['info'] = t('Tripal Feature Alignments');
  $blocks['alignments']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['relationships']['info'] = t('Tripal Feature Relationships');
  $blocks['relationships']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['org_feature_counts']['info'] = t('Tripal Organism Feature Counts');
  $blocks['org_feature_counts']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['org_feature_browser']['info'] = t('Tripal Organism Feature Browser');
  $blocks['org_feature_browser']['cache'] = 'BLOCK_NO_CACHE';

  return $blocks;
}
/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_block_view($delta = '') {

  if (user_access('access chado_feature content') and arg(0) == 'node' and is_numeric(arg(1))) {
    $nid = arg(1);
    $node = node_load($nid);

    $block = array();
    switch ($delta) {
      case 'references':
        $block['subject'] = t('References');
        $block['content'] = theme('tripal_feature_references', $node);
        break;
      case 'base':
        $block['subject'] = t('Feature Details');
        $block['content'] = theme('tripal_feature_base', $node);
        break;
      case 'synonyms':
        $block['subject'] = t('Synonyms');
        $block['content'] = theme('tripal_feature_synonyms', $node);
        break;
      case 'properties':
        $block['subject'] = t('Properties');
        $block['content'] = theme('tripal_feature_properties', $node);
        break;
      case 'terms':
        $block['subject'] = t('Annotated Terms');
        $block['content'] = theme('tripal_feature_terms', $node);
        break;
      case 'sequence':
        $block['subject'] = t('Sequence');
        $block['content'] = theme('tripal_feature_sequence', $node);
        break;
      case 'featureloc_sequences':
        $block['subject'] = t('Formatted Sequences');
        $block['content'] = theme('tripal_feature_featureloc_sequences', $node);
        break;
      case 'alignments':
        $block['subject'] = t('Alignments');
        $block['content'] = theme('tripal_feature_alignments', $node);
        break;
      case 'relationships':
        $block['subject'] = t('Relationships');
        $block['content'] = theme('tripal_feature_relationships', $node);
        break;
      case 'org_feature_counts':
        $block['subject'] = t('Feature Type Summary');
        $block['content'] = theme('tripal_organism_feature_counts', array('node' => $node));
        break;
      case 'org_feature_browser':
        $block['subject'] = t('Feature Browser');
        $block['content'] = theme('tripal_organism_feature_browser', array('node' => $node));
        break;
      case 'library_feature_browser':
        $block['subject'] = t('Library Feature Browser');
        $block['content'] = theme('tripal_library_feature_browser', $node);
        break;
      case 'analysis_feature_browser':
        $block['subject'] = t('Analysis Feature Browser');
        $block['content'] = theme('tripal_analysis_feature_browser', $node);
        break;
      default :
    }
    return $block;
  }
}
/**
 *  When a new chado_feature node is created we also need to add information
 *  to our chado_feature table.  This function is called on insert of a new node
 *  of type 'chado_feature' and inserts the necessary information.
 *
 * @ingroup tripal_feature
 */
function chado_feature_insert($node) {

  $node->uniquename   = trim($node->uniquename);
  $node->fname        = trim($node->fname);
  $node->feature_type = trim($node->feature_type);
  $node->residues     = trim($node->residues);

  // remove spaces, newlines from residues
  $residues = preg_replace("/[\n\r\s]/", "", $node->residues);
  $obsolete = 'FALSE';
  if ($node->is_obsolete) {
    $obsolete = 'TRUE';
  }

  $feature_id = '';

  // if there is an feature_id in the $node object then this must be a sync so
  // we can skip adding the feature as it is already there, although
  // we do need to proceed with the rest of the insert
  if (!property_exists($node, 'feature_id')) {
    $values = array(
      'organism_id' => $node->organism_id,
      'name' => $node->fname,
      'uniquename' => $node->uniquename,
      'residues' => $residues,
      'seqlen' => drupal_strlen($residues),
      'is_obsolete' => $obsolete,
      'type_id' => $type[0]->cvterm_id,
      'md5checksum' => md5($residues)
    );
    $feature = tripal_core_chado_select('feature', array('*'), $values);
    if (!$feature) {
      drupal_set_message(t('Unable to add feature.'), 'warning');
      watchdog('tripal_feature', 'Insert feature: Unable to create feature where values: %values',
        array('%values' => print_r($values, TRUE)), WATCHDOG_WARNING);
      return;
    }
    $feature_id = $feature->feature_id;

    // add the genbank accession and synonyms
    chado_feature_add_synonyms($node->synonyms, $node->feature_id);
  }
  else {
    $feature_id = $node->feature_id;
  }

  // Make sure the entry for this feature doesn't already exist in the
  // chado_feature table if it doesn't exist then we want to add it.
  $check_org_id = chado_get_id_for_node('feature', $node->nid);
  if (!$check_org_id) {
    $record = new stdClass();
    $record->nid = $node->nid;
    $record->vid = $node->vid;
    $record->feature_id = $feature_id;
    drupal_write_record('chado_feature', $record);
  }
}

/**
 *
 *
 * @ingroup tripal_feature
 */
function chado_feature_update($node) {

  $node->uniquename   = trim($node->uniquename);
  $node->fname        = trim($node->fname);
  $node->feature_type = trim($node->feature_type);
  $node->residues     = trim($node->residues);

  if ($node->revision) {
    // there is no way to handle revisions in Chado but leave
    // this here just to make not we've addressed it.
  }

  $residues = preg_replace("/[\n\r\s]/", "", $node->residues);
  $obsolete = 'FALSE';
  if ($node->is_obsolete) {
    $obsolete = 'TRUE';
  }

  // get the feature type id
  $values = array(
    'cv_id' => array(
      'name' => 'sequence'
      ),
    'name' => $node->feature_type
  );
  $type = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);

  $feature_id = chado_get_id_for_node('feature', $node->nid) ;

  if (sizeof($type) > 0) {
    $match = array(
      'feature_id' => $feature_id,
    );
    $values = array(
      'organism_id' => $node->organism_id,
      'name' => $node->fname,
      'uniquename' => $node->uniquename,
      'residues' => $residues,
      'seqlen' => drupal_strlen($residues),
      'is_obsolete' => $obsolete,
      'type_id' => $type[0]->cvterm_id,
      'md5checksum' => md5($residues)
    );
    $options = array('return_record' => TRUE);
    $status = tripal_core_chado_update('feature', $match, $values, $options);

    // add the genbank synonyms
    chado_feature_add_synonyms($node->synonyms, $feature_id);
  }
  else {
    drupal_set_message(t('Unable to update feature.'), 'warning');
    watchdog('tripal_feature',
    'Update feature: Unable to update feature where values: %values',
    array('%values' => print_r($values, TRUE)),
    WATCHDOG_WARNING
    );
  }


}
/**
 *
 *
 * @ingroup tripal_feature
 */
function chado_feature_delete($node) {

  $feature_id  = chado_get_id_for_node('feature', $node->nid);

  // if we don't have a library id for this node then this isn't a node of
  // type chado_library or the entry in the chado_library table was lost.
  if (!$feature_id) {
    return;
  }

  // remove the drupal content
  $sql_del = "DELETE FROM {chado_feature} WHERE nid = :nid AND vid = :vid";
  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
  $sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid";
  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
  $sql_del = "DELETE FROM {node_revision} WHERE nid = :nid AND vid = :vid";
  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));


  // Remove data from feature tables of chado database.  This will
  // cause a cascade delete and remove all data in referencing tables
  // for this feature
  chado_query("DELETE FROM {feature} WHERE feature_id = :feature_id", array(':feature_id' => $feature_id));

  drupal_set_message(t("The feature and all associated data were removed from") .
  "chado");

}
/**
 *
 *
 * @ingroup tripal_feature
 */
function chado_feature_add_synonyms($synonyms, $feature_id) {

  // separate synomys by carriage returns
  $synonyms = preg_replace("/[\n\r]+/", " ", $synonyms);
  // split the synonyms into an array based on a space as the delimieter
  $syn_array = array();
  $syn_array = explode(" ", $synonyms);


  // remove any old synonyms
  $feature_syn_dsql = "DELETE FROM {feature_synonym} WHERE feature_id = :feature_id";
  if (!chado_query($feature_syn_dsql, array(':feature_id' => $feature_id))) {
    watchdog('tripal_feature', "Could not remove synonyms from feature. ", array(), WATCHDOG_ERROR);
    return;
  }

  // return if we don't have any synonmys to add
  if (!$synonyms) {
    return;
  }
  // iterate through each synonym and add it to the database
  foreach ($syn_array as $syn) {
    // skip this item if it's empty
    if (!$syn) {
      break;
    }

    // check to see if we have this accession number already in the database
    // if so then don't add it again. it messes up drupal if the insert fails.
    // It is possible for the accession number to be present and not the feature
    $synonym_sql = "SELECT synonym_id FROM {synonym} WHERE name = :name";
    $synonym = chado_query($synonym_sql, array(':name' => $syn))->fetchObject();
    if (!$synonym) {
      $synonym_isql = "
        INSERT INTO {synonym} (name, synonym_sgml, type_id)
        VALUES (:name, :synonym_sgml,
          (SELECT cvterm_id
           FROM {cvterm} CVT
             INNER JOIN {cv} ON CVT.cv_id = CV.cv_id
           WHERE CV.name = 'feature_property' and CVT.name = 'synonym')
          )
      ";
      if (!chado_query($synonym_isql, array(':name' => $syn, ':synonym_sgml' => $syn))) {
        watchdog('tripal_feature', "Could not add synonym. ", array(), WATCHDOG_WARNING);
        return;
      }
      // now get the synonym we just added
      $synonym_sql = "SELECT synonym_id FROM {synonym} WHERE name = :name";
      $synonym = chado_query($synonym_sql, array(':name' => $syn))->fetchObject();
    }

    // now add in our new sysnonym
    $feature_syn_isql = "
      INSERT INTO {feature_synonym} (synonym_id,feature_id,pub_id)
      VALUES (:synonym_id, :feature_id, :pub_id)";
    $args = array(':synonym_id' => $synonym->synonym_id, ':feature_id' => $feature_id, ':pub_id'=> 1);
    if (!chado_query($feature_syn_isql, $args)) {
      watchdog('tripal_feature', "Could not associate synonym with feature. ", array(), WATCHDOG_WARNING);
      return;
    }
  }
}

/**
 *  When a node is requested by the user this function is called to allow us
 *  to add auxiliary data to the node object.
 *
 * @ingroup tripal_feature
 */
function chado_feature_load($nodes) {

  foreach ($nodes as $nid => $node) {
    // find the feature and add in the details
    $feature_id = chado_get_id_for_node('feature', $nid);

    // build the feature variable
    $values = array('feature_id' => $feature_id);
    $feature = tripal_core_generate_chado_var('feature', $values);
    $nodes[$nid]->feature = $feature;

    // by default, the titles are saved using the unique constraint.  We will
    // keep it the same, but remove the duplicate name if the unique name and name
    // are identical. This doesn't change the title saved in the database, just what is shown
    // to the user on the page
    $title_type = variable_get('chado_feature_title', 'unique_constraint');
    if ($title_type == 'unique_constraint') {
      if (strcmp($feature->name, $feature->uniquename)==0) {
        $node->title = $feature->name . " (" . $feature->type_id->name . ") " . $feature->organism_id->genus . " " . $feature->organism_id->species ;
      }
      // in previous version of Tripal, the feature title was simply the unique name.
      // so, we recreate the title just to be sure all of our feature pages are consistent
      else {
        $node->title = $feature->name . ", " . $feature->uniquename . " (" . $feature->type_id->name . ") " . $feature->organism_id->genus . " " . $feature->organism_id->species ;
      }
    }
    // set the title to be the feature name or uniquename as configured
    if ($title_type == 'feature_name') {
      $node->title = $feature->name;
    }
    if ($title_type == 'feature_unique_name') {
      $node->title = $feature->uniquename;
    }
  }
}
/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_load_featurelocs($feature_id, $side = 'as_parent', $aggregate = 1) {

  $sql = "
    SELECT
       F.name, F.feature_id, F.uniquename,
       FS.name as src_name, FS.feature_id as src_feature_id, FS.uniquename as src_uniquename,
       CVT.name as cvname, CVT.cvterm_id,
       CVTS.name as src_cvname, CVTS.cvterm_id as src_cvterm_id,
       FL.fmin, FL.fmax, FL.is_fmin_partial, FL.is_fmax_partial,FL.strand, FL.phase
     FROM {featureloc} FL
       INNER JOIN {feature} F   ON FL.feature_id = F.feature_id
       INNER JOIN {feature} FS  ON FS.feature_id = FL.srcfeature_id
       INNER JOIN {cvterm} CVT  ON F.type_id     = CVT.cvterm_id
       INNER JOIN {cvterm} CVTS ON FS.type_id    = CVTS.cvterm_id
   ";
  if (strcmp($side, 'as_parent')==0) {
    $sql .= "WHERE FL.srcfeature_id = :feature_id ";
  }
  if (strcmp($side, 'as_child')==0) {
    $sql .= "WHERE FL.feature_id = :feature_id ";
  }

  $flresults = chado_query($sql, array(':feature_id' => $feature_id));

  // copy the results into an array
  $i=0;
  $featurelocs = array();
  while ($loc = $flresults->fetchObject()) {
    // if a drupal node exists for this feature then add the nid to the
    // results object
    $loc->fnid = chado_get_node_id('feature', $loc->feature_id);
    $loc->snid = chado_get_node_id('feature', $loc->src_feature_id);
    // add the result to the array
    $featurelocs[$i++] = $loc;
  }

  // Add the relationship feature locs if aggregate is turned on
  if ($aggregate and strcmp($side, 'as_parent')==0) {
    // get the relationships for this feature without substituting any children
    // for the parent. We want all relationships
    $relationships = tripal_feature_get_aggregate_relationships($feature_id, 0);
    foreach ($relationships as $rindex => $rel) {
      // get the featurelocs for each of the relationship features
      $rel_featurelocs = tripal_feature_load_featurelocs($rel->subject_id, 'as_child', 0);
      foreach ($rel_featurelocs as $findex => $rfloc) {
        $featurelocs[$i++] = $rfloc;
      }
    }
  }

  usort($featurelocs, 'tripal_feature_sort_locations');
  return $featurelocs;
}
/**
 *  used to sort the feature locs by start position
 *
 * @ingroup tripal_feature
 */
function tripal_feature_sort_locations($a, $b) {
  return strnatcmp($a->fmin, $b->fmin);
}
/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_load_relationships($feature_id, $side = 'as_subject') {
  // get the relationships for this feature.  The query below is used for both
  // querying the object and subject relationships
  $sql = "
    SELECT
      FS.name as subject_name, FS.uniquename as subject_uniquename,
      CVTS.name as subject_type, CVTS.cvterm_id as subject_type_id,
      FR.subject_id, FR.type_id as relationship_type_id, FR.object_id, FR.rank,
      CVT.name as rel_type,
      FO.name as object_name, FO.uniquename as object_uniquename,
      CVTO.name as object_type, CVTO.cvterm_id as object_type_id
    FROM {feature_relationship} FR
     INNER JOIN {cvterm} CVT  ON FR.type_id    = CVT.cvterm_id
     INNER JOIN {feature} FS  ON FS.feature_id = FR.subject_id
     INNER JOIN {feature} FO  ON FO.feature_id = FR.object_id
     INNER JOIN {cvterm} CVTO ON FO.type_id    = CVTO.cvterm_id
     INNER JOIN {cvterm} CVTS ON FS.type_id    = CVTS.cvterm_id
  ";
  if (strcmp($side, 'as_object')==0) {
    $sql .= " WHERE FR.object_id = :feature_id";
  }
  if (strcmp($side, 'as_subject')==0) {
    $sql .= " WHERE FR.subject_id = :feature_id";
  }
  $sql .= " ORDER BY FR.rank";

  // get the relationships
  $results = chado_query($sql, array(':feature_id' => $feature_id));


  // iterate through the relationships, put these in an array and add
  // in the Drupal node id if one exists
  $i=0;
  $nodesql = "SELECT nid FROM {chado_feature} WHERE feature_id = :feature_id";
  $relationships = array();
  while ($rel = $results->fetchObject()) {
    $node = db_query($nodesql, array(':feature_id' => $rel->subject_id))->fetchObject();
    if ($node) {
      $rel->subject_nid = $node->nid;
    }
    $node = db_query($nodesql, array(':feature_id' => $rel->object_id))->fetchObject();
    if ($node) {
      $rel->object_nid = $node->nid;
    }
    $relationships[$i++] = $rel;
  }
  return $relationships;
}
/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_get_aggregate_relationships($feature_id, $substitute=1,
  $levels=0, $base_type_id=NULL, $depth=0) {

  // we only want to recurse to as many levels deep as indicated by the
  // $levels variable, but only if this variable is > 0. If 0 then we
  // recurse until we reach the end of the relationships tree.
  if ($levels > 0 and $levels == $depth) {
    return NULL;
  }

  // first get the relationships for this feature
  return tripal_feature_load_relationships($feature_id, 'as_object');

}
/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_load_featureloc_sequences($feature_id, $featurelocs) {

  // if we don't have any featurelocs then no point in continuing
  if (!$featurelocs) {
    return array();
  }

  // get the list of relationships (including any aggregators) and iterate
  // through each one to find information needed to color-code the reference sequence
  $relationships = tripal_feature_get_aggregate_relationships($feature_id);
  if (!$relationships) {
    return array();
  }


  // iterate through each of the realtionships features and get their
  // locations
  foreach ($relationships as $rindex => $rel) {
    // get the featurelocs for each of the relationship features
    $rel_featurelocs = tripal_feature_load_featurelocs($rel->subject_id, 'as_child', 0);
    foreach ($rel_featurelocs as $rfindex => $rel_featureloc) {
      // keep track of this unique source feature
      $src = $rel_featureloc->src_feature_id . "-" . $rel_featureloc->src_cvterm_id;

      // copy over the results to the relationship object.  Since there can
      // be more than one feature location for each relationship feature we
      // use the '$src' variable to keep track of these.
      $rel->featurelocs = new stdClass();
      $rel->featurelocs->$src = new stdClass();
      $rel->featurelocs->$src->src_uniquename = $rel_featureloc->src_uniquename;
      $rel->featurelocs->$src->src_cvterm_id  = $rel_featureloc->src_cvterm_id;
      $rel->featurelocs->$src->src_cvname     = $rel_featureloc->src_cvname;
      $rel->featurelocs->$src->fmin           = $rel_featureloc->fmin;
      $rel->featurelocs->$src->fmax           = $rel_featureloc->fmax;
      $rel->featurelocs->$src->src_name       = $rel_featureloc->src_name;

      // keep track of the individual parts for each relationship
      $start = $rel->featurelocs->$src->fmin;
      $end   = $rel->featurelocs->$src->fmax;
      $type  = $rel->subject_type;
      $rel_locs[$src]['parts'][$start][$type]['start'] = $start;
      $rel_locs[$src]['parts'][$start][$type]['end']   = $end;
      $rel_locs[$src]['parts'][$start][$type]['type']  = $type;
    }
  }

  // the featurelocs array provided to the function contains the locations
  // where this feature is found.   We want to get the sequence for each
  // location and then annotate it with the parts found from the relationships
  // locations determiend above.
  $floc_sequences = array();
  foreach ($featurelocs as $featureloc) {

    // build the src name so we can keep track of the different parts for each feature
    $src = $featureloc->srcfeature_id->feature_id . "-" . $featureloc->srcfeature_id->type_id->cvterm_id;

    // orient the parts to the beginning of the feature sequence
    if (!empty($rel_locs[$src]['parts'])) {
      $parts = $rel_locs[$src]['parts'];
      $rparts = array();  // we will fill this up if we're on the reverse strand

      foreach ($parts as $start => $types) {
        foreach ($types as $type_name => $type) {
          if ($featureloc->strand >= 0) {
             // this is on the forward strand.  We need to convert the start on the src feature to the
             // start on this feature's sequence
             $parts[$start][$type_name]['start'] = $parts[$start][$type_name]['start'] - $featureloc->fmin;
             $parts[$start][$type_name]['end']   = $parts[$start][$type_name]['end'] - $featureloc->fmin;
             $parts[$start][$type_name]['type']  = $type_name;
          }
          else {
             // this is on the reverse strand.  We need to swap the start and stop and calculate from the
             // begining of the reverse sequence
             $size = ($featureloc->fmax - $featureloc->fmin);
             $start_orig = $parts[$start][$type_name]['start'];
             $end_orig = $parts[$start][$type_name]['end'];
             $new_start = $size - ($end_orig - $featureloc->fmin);
             $new_end = $size - ($start_orig - $featureloc->fmin);

             $rparts[$new_start][$type_name]['start'] = $new_start;
             $rparts[$new_start][$type_name]['end']   = $new_end;
             $rparts[$new_start][$type_name]['type']  = $type_name;
          }
        }
      }

      // now sort the parts
      // if we're on the reverse strand we need to resort
      if ($featureloc->strand >= 0) {
        usort($parts, 'tripal_feature_sort_rel_parts_by_start');
      }
      else {
        usort($rparts, 'tripal_feature_sort_rel_parts_by_start');
        $parts = $rparts;
      }

      $floc_sequences[$src]['src'] = $src;
      $floc_sequences[$src]['type'] = $featureloc->feature_id->type_id->name;
      $args = array(':feature_id' => $featureloc->srcfeature_id->feature_id);
      $start = $featureloc->fmin + 1;
      $size = $featureloc->fmax - $featureloc->fmin;
      // TODO: fix the hard coded $start and $size
      // the $start and $size variables are hard-coded in the SQL statement
      // because the db_query function places quotes around all placeholders
      // (e.g. :start & :size) and screws up the substring function
      $sql = "
        SELECT substring(residues from $start for $size) as residues
        FROM {feature}
        WHERE feature_id = :feature_id
      ";
      $sequence = chado_query($sql, $args)->fetchObject();
      $residues = $sequence->residues;
      if ($featureloc->strand < 0) {
         $residues = tripal_feature_reverse_complement($residues);
      }
      $strand = '.';
      if ($featureloc->strand == 1) {
        $strand = '+';
      }
      elseif ($featureloc->strand == -1) {
        $strand = '-';
      }
      $defline = $featureloc->feature_id->name . " " . $featureloc->srcfeature_id->name . ":" . ($featureloc->fmin + 1) . ".." . $featureloc->fmax . " " . $strand;
      $floc_sequences[$src]['formatted_seq'] =  tripal_feature_color_sequence($residues, $parts, $defline);
    }
  }
  return $floc_sequences;
}
/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_get_matched_alignments($feature) {
  // This function is for features that align through an intermediate such
  // as 'EST_match' or 'match'.  This occurs in the case where two sequences
  // align but where one does not align perfectly.  Some ESTs may be in a contig
  // but not all of the EST.  Portions may overhang and not be included in the
  // consensus if quality is bad.
  // For example:
  //
  //    Feature 1: Contig --------------------
  //    Feature 2: EST_match           -------
  //    Feature 3: EST                 ---------
  //
  // The feature provided to the function will always be the feature 1.  The
  // featureloc columns prefixed with 'right' (e.g. right_fmin) belong to the
  // alignment of feature 3 with feature 2
  //
  // Features may align to more than one feature and are not matches. We do
  // not want to include these, so we have to filter on the SO terms:
  // match, or %_match
  //
   $sql = "
     SELECT
       FL1.featureloc_id    as left_featureloc_id,
       FL1.srcfeature_id    as left_srcfeature_id,
       FL1.feature_id       as left_feature_id,
       FL1.fmin             as left_fmin,
       FL1.is_fmin_partial  as left_is_fmin_partial,
       FL1.fmax             as left_fmax,
       FL1.is_fmax_partial  as left_is_fmax_partial,
       FL1.strand           as left_strand,
       FL1.phase            as left_phase,
       FL1.locgroup         as left_locgroup,
       FL1.rank             as left_rank,
       FL2.featureloc_id    as right_featureloc_id,
       FL2.srcfeature_id    as right_srcfeature_id,
       FL2.feature_id       as right_feature_id,
       FL2.fmin             as right_fmin,
       FL2.is_fmin_partial  as right_is_fmin_partial,
       FL2.fmax             as right_fmax,
       FL2.is_fmax_partial  as right_is_fmax_partial,
       FL2.strand           as right_strand,
       FL2.phase            as right_phase,
       FL2.locgroup         as right_locgroup,
       FL2.rank             as right_rank
     FROM {feature} F1
       INNER JOIN {featureloc} FL1 on FL1.srcfeature_id = F1.feature_id
       INNER JOIN {feature} F2 on FL1.feature_id = F2.feature_id
       INNER JOIN {featureloc} FL2 on FL2.feature_id = F2.feature_id
       INNER JOIN {cvterm} CVT2 on F2.type_id = CVT2.cvterm_id
     WHERE
       F1.feature_id = :feature_id  AND
       (CVT2.name = 'match' or CVT2.name like '%_match')
     ORDER BY FL1.fmin
   ";

   $results = chado_query($sql, array(':feature_id' => $feature->feature_id));

   // iterate through the results and add them to our featurelocs array
   $featurelocs = array();
   while ($fl = $results->fetchObject()) {
     // ignore featurelocs where the left and right srcfeature is the same
     if (strcmp($fl->left_srcfeature_id, $fl->right_srcfeature_id) == 0) {
       continue;
     }
     $featurelocs[] = $fl ;
   }
   return $featurelocs;
}
/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_load_organism_feature_counts($organism) {

  // don't show the browser if the settings in the admin page is turned off
  // instead return the array indicating the status of the browser
  $show_counts = variable_get('tripal_feature_summary_setting', 'show_feature_summary');
  if (strcmp($show_counts, 'show_feature_summary')!=0) {
    return array('enabled' => FALSE );
  }
  $args = array();
  $names = array();
  $order = array();

  // build the where clause for the SQL statement if we have a custom term list
  // we'll also keep track of the names the admin provided (if any) and the
  // order that the terms should appear.
  $is_custom = 0;
  $temp = rtrim(variable_get('tripal_feature_summary_report_mapping', ''));
  $where = '';
  if ($temp) {
    $is_custom = 1;
    $temp = explode("\n", $temp);
    $i = 0;
    foreach ($temp as $key => $value) {
      // separate the key value pairs
      $temp2 = explode("=", $value);
      $feature_type = rtrim($temp2[0]);
      $args[] = $feature_type;
      $order[] = $feature_type;
      // if a new name is provided then use that otherwise just
      // use the feature type
      if (count($temp2) == 2) {
        $names[":name$i"] = rtrim($temp2[1]);
      }
      else {
        $names[":name$i"] = $feature_type;
      }
      $where .= " OFC.feature_type = :name$i OR ";
      $i++;
    }
    if ($where) {
      $where = drupal_substr($where, 0, -5);  # remove OR from the end
      $where = "($where) AND";
    }
  }

  // get the feature counts.  This is dependent on a materialized view
  // installed with the organism module
  $sql = "
    SELECT OFC.num_features,OFC.feature_type,CVT.definition
    FROM {organism_feature_count} OFC
      INNER JOIN {cvterm} CVT on OFC.cvterm_id = CVT.cvterm_id
    WHERE $where organism_id = :organism_id
    ORDER BY num_features desc
  ";
  $args[':organism_id'] = $organism->organism_id;
  $org_features = chado_query($sql, $args);

  // iterate through the types
  $types = array();
  while ($type = $org_features->fetchObject()) {
    $types[$type->feature_type] = $type;
    // if we don't have an order this means we didn't go through the loop
    // above to set the names, so do that now
    if (!$is_custom) {
      $names[] = $type->feature_type;
      $order[] = $type->feature_type;
    }
  }

  # now reorder the types
  $ordered_types = array();
  foreach ($order as $type) {
    $ordered_types[] = $types[$type];
  }
  return array( 'types' => $ordered_types, 'names' => $names, 'enabled' => TRUE );
}

/**
 *  used to sort the list of relationship parts by start position
 *
 * @ingroup tripal_feature
 */
function tripal_feature_sort_rel_parts_by_start($a, $b) {
  foreach ($a as $type_name => $details) {
     $astart = $a[$type_name]['start'];
     break;
  }
  foreach ($b as $type_name => $details) {
     $bstart = $b[$type_name]['start'];
     break;
  }
  return strnatcmp($astart, $bstart);
}

/**
 *  used to sort the list of relationship parts by start position
 *
 * @ingroup tripal_feature
 */
function tripal_feature_sort_rel_parts_by_end($a, $b) {
  $val = strnatcmp($b['end'], $a['end']);
  if ($val == 0) {
     return strcmp($a['type'], $b['type']);
  }
  return $val;
}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_color_sequence($sequence, $parts, $defline) {


  $types = array();
  // first get the list of types so we can create a color legend
  foreach ($parts as $index => $t) {
    foreach ($t as $type_name => $details) {
       $types[$type_name] = 1;
    }
  }

  $newseq = "<div id=\"tripal_feature-featureloc_sequence-legend\">Legend: ";
  foreach ($types as $type_name => $present) {
    $newseq .= "<span id=\"tripal_feature-legend-$type_name\" class=\"tripal_feature-legend-item tripal_feature-featureloc_sequence-$type_name\" script=\"\">$type_name</span>";
  }
  $newseq .= "</div>Hold the cursor over a type above to highlight its positions in the sequence below. The colors in the sequence below merge when types overlap.";


  // set the background color of the rows based on the type
  $pos = 0;
  $newseq .= "<pre id=\"tripal_feature-featureloc_sequence\">";
  $newseq .= ">$defline\n";

  // iterate through the parts. They should be in order.
  $ends = array();
  $seqcount = 0;
  foreach ($parts as $index => $types) {

    // get the start for this part.  All types in this part start at the
    // same position so we only need the first record
    foreach ($types as $type => $child) {
      $start = $child['start'];
      break;
    }

    // add in the sequence up to the start of this part
    for ($i = $pos; $i < $start; $i++) {
      $newseq .= $sequence{$pos};
      $seqcount++;
      if ($seqcount % 50 == 0) {
        $newseq .= "\n";
      }
      if (array_key_exists($pos, $ends)) {
        foreach ($ends[$pos] as $end) {
          $newseq .= "</span>";
        }
      }
      $pos++;
    }

    // we want to sort the parts by their end. We want the span tag to
    // to be added in the order the parts end.
    usort($types, 'tripal_feature_sort_rel_parts_by_end');

    // now add the child span for all types that start at this position
    foreach ($types as $type) {
      $class = "tripal_feature-featureloc_sequence-" . $type['type'];
      $newseq .= "<span class=\"$class\">";
      // add the end position
      $end = $type['end'];
      $ends[$end][] = $end;
    }
  }

  // add in rest of the sequence
  for ($i = $pos; $i < strlen($sequence); $i++) {
    $newseq .= $sequence{$pos};
    $seqcount++;
    if ($seqcount % 50 == 0) {
      $newseq .= "\n";
    }
    if (array_key_exists($pos, $ends)) {
      foreach ($ends[$pos] as $end) {
        $newseq .= "</span>";
      }
    }
    $pos++;
  }

  $newseq .= "</pre>";
  return $newseq;
}

/**
 *
 * @ingroup tripal_feature
 */
function tripal_feature_node_presave($node) {

  // set the title to ensure it is always unique
  switch ($node->type) {
    case 'chado_feature':
      $values = array('organism_id' => $node->organism_id);
      $organism = tripal_core_chado_select('organism', array('genus', 'species'), $values);
      $node->title = $node->fname . ', ' . $node->uniquename . ' (' . $node->feature_type . ') ' . $organism[0]->genus . ' ' . $organism[0]->species;
      break;
  }
}

/**
 *
 * @ingroup tripal_feature
 */
function tripal_feature_node_insert($node) {

  // set the URL path after inserting.  We do it here because we do not
  // know the feature_id in the presave
  switch ($node->type) {
    case 'chado_feature':
      if (!$node->feature_id) {
        $sql = "SELECT * FROM {chado_feature} WHERE nid = :nid";
        $chado_feature = db_query($sql, array(':nid' => $node->nid))->fetchObject();
        $node->feature_id = $chado_feature->feature_id;
      }

      // remove any previous alias
      db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$node->nid"));

      // set the URL for this feature page
      $url_alias = tripal_feature_get_feature_url($node);
      $path_alias = array("source" => "node/$node->nid", "alias" => $url_alias);
      path_save($path_alias);
      break;
  }
}
/**
 *
 * @ingroup tripal_feature
 */
function tripal_feature_node_view($node, $view_mode, $langcode) {
  switch ($node->type) {
    case 'chado_feature':
      // Show feature browser and counts
      if ($view_mode == 'full') {
        $node->content['tripal_feature_alignments'] = array(
          '#value' => theme('tripal_feature_alignments', array('node' => $node)),
        );
        $node->content['tripal_feature_analyses'] = array(
          '#value' => theme('tripal_feature_analyses', array('node' => $node)),
        );
        $node->content['tripal_feature_base'] = array(
          '#value' => theme('tripal_feature_base', array('node' => $node)),
        );
        $node->content['tripal_feature_phenotypes'] = array(
          '#value' => theme('tripal_feature_phenotypes', array('node' => $node)),
        );
        $node->content['tripal_feature_properties'] = array(
          '#value' => theme('tripal_feature_properties', array('node' => $node)),
        );
        $node->content['tripal_feature_references'] = array(
          '#value' => theme('tripal_feature_references', array('node' => $node)),
        );
        $node->content['tripal_feature_relationships'] = array(
          '#value' => theme('tripal_feature_relationships', array('node' => $node)),
        );
        $node->content['tripal_feature_seqence'] = array(
          '#value' => theme('tripal_feature_sequence', array('node' => $node)),
        );
        $node->content['tripal_feature_synonyms'] = array(
          '#value' => theme('tripal_feature_synonyms', array('node' => $node)),
        );
        $node->content['tripal_feature_terms'] = array(
          '#value' => theme('tripal_feature_terms', array('node' => $node)),
        );
      }
      if ($view_mode == 'teaser') {
        $node->content['tripal_feature_teaser'] = array(
          '#value' => theme('tripal_feature_teaser', array('node' => $node)),
        );
      }
      break;
    case 'chado_organism':
      // Show feature browser and counts
      if ($view_mode == 'full') {
        $node->content['tripal_organism_feature_counts'] = array(
          '#value' => theme('tripal_organism_feature_counts', array('node' => $node)),
        );
        $node->content['tripal_organism_feature_browser'] = array(
          '#value' => theme('tripal_organism_feature_browser', array('node' => $node)),
        );
      }
      break;
    // TODO: handle these node types. Should we also have a feature browser?
    case 'chado_library':
      break;
    case 'chado_stock':
      break;
    case 'chado_analysis':
      break;
  }
}
/**
 *
 * @ingroup tripal_feature
 */
function tripal_feature_node_update($node) {

  // add items to other nodes, build index and search results
  switch ($node->type) {
    case 'chado_feature':
      // remove any previous alias
      db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$node->nid"));

      // set the URL for this feature page
      $url_alias = tripal_feature_get_feature_url($node);
      $path_alias = array("source" => "node/$node->nid", "alias" => $url_alias);
      path_save($path_alias);
      break;
  }
}

/**
 * @ingroup tripal_feature
 */
function tripal_feature_preprocess_tripal_feature_sequence(&$variables) {
  // we want to provide a new variable that contains the matched features.
  $feature = $variables['node']->feature;

  // get the featureloc src features
  $options = array(
    'return_array' => 1,
    'include_fk' => array(
      'srcfeature_id' => array(
        'type_id' => 1
      ),
    ),
  );

  $feature = tripal_core_expand_chado_vars($feature, 'table', 'featureloc', $options);

  // because there are two foriegn keys in the featureloc table with the feature table
  // we have to access the records for each by specifying the field name after the table name:
  $ffeaturelocs = $feature->featureloc->feature_id;

  // now extract the sequences
  $featureloc_sequences = tripal_feature_load_featureloc_sequences($feature->feature_id, $ffeaturelocs);
  $feature->featureloc_sequences = $featureloc_sequences;
}
/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_preprocess_tripal_feature_relationships(&$variables) {
  // we want to provide a new variable that contains the matched features.
  $feature = $variables['node']->feature;

  if (!property_exists($feature, 'all_relationships')) {
    $feature->all_relationships = tripal_feature_get_feature_relationships($feature);
  }
}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_preprocess_tripal_feature_proteins(&$variables) {
  // we want to provide a new variable that contains the matched features.
  $feature = $variables['node']->feature;

  if (!property_exists($feature, 'all_relationships')) {
    $feature->all_relationships = tripal_feature_get_feature_relationships($feature);
  }
}
/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_preprocess_tripal_feature_alignments(&$variables) {

  // we want to provide a new variable that contains the matched features.
  $feature = $variables['node']->feature;
  $options = array(
    'return_array' => 1,
    'include_fk' => array(
      'srcfeature_id' => array(
        'type_id' => 1,
      ),
      'feature_id' => array(
        'type_id' => 1
      ),
    )
  );
  $feature = tripal_core_expand_chado_vars($feature, 'table', 'featureloc', $options);

  // get alignments as child
  $cfeaturelocs = $feature->featureloc->feature_id;
  if (!$cfeaturelocs) {
    $cfeaturelocs = array();
  }
  // get alignment as parent
  $pfeaturelocs = $feature->featureloc->srcfeature_id;
  if (!$pfeaturelocs) {
    $pfeaturelocs = array();
  }

  // get matched alignments (those with an itermediate 'match' or 'EST_match', etc
  $mfeaturelocs = tripal_feature_get_matched_alignments($feature);
  $feature->matched_featurelocs = $mfeaturelocs;

  // combine all three alignments into a single array for printing together in
  // a single list
  $alignments = array();
  foreach ($pfeaturelocs as $featureloc) {
    // if type is a 'match' then ignore it. We will handle those below
    if (preg_match('/(^match$|^.*?_match|match_part)$/', $featureloc->feature_id->type_id->name)) {
       continue;
    }
    $alignment = new stdClass();
    $alignment->record = $featureloc;
    $alignment->name = $featureloc->feature_id->name;
    $alignment->type = $featureloc->feature_id->type_id->name;
    $alignment->fmin = $featureloc->fmin;
    $alignment->fmax = $featureloc->fmax;
    $alignment->phase = $featureloc->phase;
    $alignment->strand = $featureloc->strand;
    $alignments[] = $alignment;
    if (property_exists($featureloc->feature_id, 'nid')) {
      $alignment->nid = $featureloc->feature_id->nid;
    }
  }
  foreach ($cfeaturelocs as $featureloc) {
    // if type is a 'match' then ignore it. We will handle those below
    if (preg_match('/(^match$|^.*?_match|match_part)$/', $featureloc->feature_id->type_id->name)) {
      continue;
    }
    $alignment = new stdClass();
    $alignment->record = $featureloc;
    $alignment->name = $featureloc->srcfeature_id->name;
    $alignment->type = $featureloc->srcfeature_id->type_id->name;
    $alignment->fmin = $featureloc->fmin;
    $alignment->is_fmin_partial = $featureloc->is_fmin_partial;
    $alignment->fmax = $featureloc->fmax;
    $alignment->is_fmax_partial = $featureloc->is_fmax_partial;
    $alignment->phase = $featureloc->phase;
    $alignment->strand = $featureloc->strand;
    $alignments[] = $alignment;
    if (property_exists($featureloc->srcfeature_id, 'nid')) {
      $alignment->nid = $featureloc->srcfeature_id->nid;
    }
  }
  // in matching features, the left feature is always the feature
  // provided to this function.
  foreach ($mfeaturelocs as $featureloc) {
     // get more information about the right feature
     $select = array('feature_id' => $featureloc->right_srcfeature_id);
     $rfeature = tripal_core_generate_chado_var('feature', $select);
     // now add to the list
     $alignment = new stdClass();
     $alignment->record = $featureloc;
     $alignment->right_feature = $rfeature;
     $alignment->name = $rfeature->name;
     $alignment->type = $rfeature->type_id->name;
     $alignment->fmin = $featureloc->left_fmin;
     $alignment->is_fmin_partial = $featureloc->left_is_fmin_partial;
     $alignment->fmax = $featureloc->left_fmax;
     $alignment->is_fmax_partial = $featureloc->left_is_fmax_partial;
     $alignment->phase = $featureloc->left_phase;
     $alignment->strand = $featureloc->left_strand;
     $alignment->right_fmin = $featureloc->right_fmin;
     $alignment->right_is_fmin_partial = $featureloc->right_is_fmin_partial;
     $alignment->right_fmax = $featureloc->right_fmax;
     $alignment->right_is_fmax_partial = $featureloc->right_is_fmax_partial;
     $alignment->right_phase = $featureloc->right_phase;
     $alignment->right_strand = $featureloc->right_strand;
     $alignments[] = $alignment;
     if (property_exists($rfeature, 'nid')) {
       $alignment->nid = $rfeature->nid;
     }
  }
  $feature->all_featurelocs = $alignments;
}
/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_preprocess_tripal_organism_feature_counts(&$variables, $hook) {
  $organism = $variables['node']->organism;
  $organism->feature_counts = tripal_feature_load_organism_feature_counts($organism);
}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_cv_chart($chart_id) {

  // we only want the chart to show feature types setup by the admin
  $temp = rtrim(variable_get('tripal_feature_summary_report_mapping', ''));
  $where = '';
  if ($temp) {
    $temp = explode("\n", $temp);
    foreach ($temp as $key => $value) {
      $temp2 = explode("=", $value);
      $feature_type = rtrim($temp2[0]);
      $where .= "CNT.feature_type = '$feature_type' OR \n";
    }
    if ($where) {
      $where = drupal_substr($where, 0, -5);  # remove OR from the end
      $where = "($where) AND";
    }
  }

  $organism_id = preg_replace("/^tripal_feature_cv_chart_(\d+)$/", "$1", $chart_id);

  // The CV module will create the JSON array necessary for buillding a
  // pie chart using jgChart and Google Charts.  We have to pass to it
  // a table that contains count information, tell it which column
  // contains the cvterm_id and provide a filter for getting the
  // results we want from the table.
  $options = array(
    count_mview      => 'organism_feature_count',
    cvterm_id_column => 'cvterm_id',
    count_column     => 'num_features',
    size             => '550x200',
    filter           => "$where CNT.organism_id = $organism_id",
  );
  return $options;
}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_cv_tree($tree_id) {

  // The CV module will create the JSON array necessary for buillding a
  // pie chart using jgChart and Google Charts.  We have to pass to it
  // a table that contains count information, tell it which column
  // contains the cvterm_id and provide a filter for getting the
  // results we want from the table.
  $organism_id = preg_replace("/^tripal_feature_cv_tree_(\d+)$/", "$1", $tree_id);
  $options = array(
    cv_id            => tripal_cv_get_cv_id('sequence'),
    count_mview      => 'organism_feature_count',
    cvterm_id_column => 'cvterm_id',
    count_column     => 'num_features',
    filter           => "CNT.organism_id = $organism_id",
    label            => 'Features',
  );
  return $options;
}



/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_del_vocabulary() {
  //include the file containing the required functions for adding taxonomy vocabs
  module_load_include('inc', 'taxonomy', 'taxonomy.admin');

  // get the vocabularies
  $vocabularies = taxonomy_get_vocabularies();

  // These taxonomic terms are hard coded because we
  // know we have these relationships in the chado tables
  // through foreign key relationships.  The tripal
  // modules that correspond to these chado "modules" don't
  // need to be installed for the taxonomy to work.
  foreach ($vocabularies as $vocab) {
    if ($vocab->name == 'Feature Type') {
      taxonomy_vocabulary_delete($vocab->vid);
    }
    if ($vocab->name == 'Organism') {
      taxonomy_vocabulary_delete($vocab->vid);
    }
    if ($vocab->name == 'Library') {
      taxonomy_vocabulary_delete($vocab->vid);
    }
    if ($vocab->name == 'Analysis') {
      taxonomy_vocabulary_delete($vocab->vid);
    }
  }

}

/**
 *
 *
 * @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 = tripal_core_chado_select('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 = tripal_core_chado_select('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 = tripal_core_chado_select('analysis', array('name'), array('analysis_id' => $args[13]));
    }
    $new_args['Analysis'] = $analysis[0]->name;
  }
  if ($callback == 'tripal_feature_delete_features') {
    if ($args[0]) {
      $organism = tripal_core_chado_select('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 = tripal_core_chado_select('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];
    $new_args['Features Names'] = $args[4];

  }
  elseif ($callback == 'tripal_feature_load_gff3') {

    $new_args['GFF File'] = $args[0];
    $organism = tripal_core_chado_select('organism', array('genus', 'species'), array('organism_id' => $args[1]));
    $new_args['Organism'] = $organism[0]->genus . " " . $organism[0]->species;
    $analysis = tripal_core_chado_select('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 = tripal_core_chado_select('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";
  }
  if ($callback == 'tripal_feature_sync_features') {
    if ($args[0]) {
      $organism = tripal_core_chado_select('organism', array('genus', 'species'), array('organism_id' => $args[0]));
      $new_args['Organism'] = $organism[0]->genus . " " . $organism[0]->species;
    }
    else {
      $new_args['Organism'] = '';
    }
    $new_args['Feature Types'] = $args[1];
  }
  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
 */
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 $id argument to find all features that match
 * that ID by name, featurename or synonym.  If it matches uniquenly to a single
 * feature it will redirect to that feature page, otherwise, a list of matching
 * features is shown.
 */
function tripal_feature_match_features_page($id) {

  // if the URL alias configuration is set such that the URL
  // always begins with 'feature' then we want to use the ID as it is and
  // forward it on. Otherwise, try to find the matching feature.
  $url_alias = variable_get('chado_feature_url_string', '/feature/[genus]/[species]/[type]/[uniquename]');
  if (!$url_alias) {
    $url_alias = '/feature/[genus]/[species]/[type]/[uniquename]';
  }
  $url_alias = preg_replace('/^\//', '', $url_alias); // remove any preceeding forward slash
  if (preg_match('/^feature\//', $url_alias)) {
    drupal_goto($id);
  }

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

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

/**
 * Implementation of hook_form_alter()
 *
 * @param $form
 * @param $form_state
 * @param $form_id
 */
function tripal_feature_form_alter(&$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;
  }
}