<?php
/**
* @defgroup tripal_feature Feature
* @{
* Provides functions for managing chado features including creating details pages for each feature
* @}
* @ingroup tripal_modules
*/
require_once "tripal_feature.admin.inc";
require_once "syncFeatures.php";
require_once "indexFeatures.php";
require_once "fasta_loader.php";
require_once "gff_loader.php";
require_once "tripal_feature.api.inc";
require_once "tripal_feature-secondary_tables.inc";
require_once "tripal_feature-properties.inc";
require_once "tripal_feature-relationships.inc";
require_once "tripal_feature-db_references.inc";
/**
*
* @ingroup tripal_feature
*/
function tripal_feature_init(){
// add the jGCharts JS and CSS
drupal_add_js (drupal_get_path('theme', 'tripal').'/js/tripal_feature.js');
drupal_add_js (drupal_get_path('theme', 'tripal').'/js/jgcharts/jgcharts.js');
drupal_add_css(drupal_get_path('theme', 'tripal').
'/css/tripal_feature.css');
}
/**
* 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'),
'module' => '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 $nodes;
}
/**
* Set the permission types that the chado module uses. Essentially we
* want permissionis that protect creation, editing and deleting of chado
* data objects
*
* @ingroup tripal_feature
*/
function tripal_feature_perm(){
return array(
'access chado_feature content',
'create chado_feature content',
'delete chado_feature content',
'edit chado_feature content',
'manage chado_feature aggregator',
);
}
/**
* Set the permission types that the module uses.
*
* @ingroup tripal_feature
*/
function chado_feature_access($op, $node, $account) {
if ($op == 'create') {
return user_access('create chado_feature content', $account);
}
if ($op == 'update') {
if (user_access('edit chado_feature content', $account)) {
return TRUE;
}
}
if ($op == 'delete') {
if (user_access('delete chado_feature content', $account)) {
return TRUE;
}
}
if ($op == 'view') {
if (user_access('access chado_feature content', $account)) {
return TRUE;
}
}
return FALSE;
}
/**
* 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['admin/tripal/tripal_feature'] = array(
'title' => 'Features',
'description' => 'Basic Description of Tripal Organism Module Functionality',
'page callback' => 'tripal_feature_module_description_page',
'access arguments' => array('administer site configuration'),
'type' => MENU_NORMAL_ITEM,
);
$items['admin/tripal/tripal_feature/configuration'] = array(
'title' => 'Feature Configuration',
'description' => 'Settings for Chado Features',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_feature_admin'),
'access arguments' => array('administer site configuration'),
'type' => MENU_NORMAL_ITEM,
);
$items['admin/tripal/tripal_feature/fasta_loader'] = array(
'title' => 'Import a multi-FASTA file',
'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 site configuration'),
'type' => MENU_NORMAL_ITEM,
);
$items['admin/tripal/tripal_feature/gff3_load'] = array(
'title' => 'Import a GFF3 file',
'description' => 'Import a GFF3 file into Chado',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_core_gff3_load_form'),
'access arguments' => array('access administration pages'),
'type' => MENU_NORMAL_ITEM,
);
// Adding Secondary Properties
$items['node/%tf_node/tf_properties'] = array(
'title' => t('Add Properties & Synonyms'),
'description' => t('Settings for Features'),
'page callback' => 'tripal_feature_add_ALL_property_page',
'page arguments' => array(1),
'access arguments' => array('create chado_feature content'),
'type' => MENU_CALLBACK
);
$items['node/%tf_node/tf_db_references'] = array(
'title' => t('Add Database References'),
'description' => t('Settings for Features'),
'page callback' => 'tripal_feature_add_ALL_dbreferences_page',
'page arguments' => array(1),
'access arguments' => array('create chado_feature content'),
'type' => MENU_CALLBACK
);
$items['node/%tf_node/tf_relationships'] = array(
'title' => t('Add Relationships'),
'description' => t('Settings for Features'),
'page callback' => 'tripal_feature_add_ALL_relationships_page',
'page arguments' => array(1),
'access arguments' => array('create chado_feature content'),
'type' => MENU_CALLBACK
);
//Edit/Deleting Secondary Properties-------------
/**
$items['node/%tf_node/tf_edit_properties'] = array(
'title' => t('Edit Properties'),
'description' => t('Settings for Features'),
'page callback' => 'tripal_feature_edit_ALL_properties_page',
'page arguments' => array(1),
'access arguments' => array('edit chado_feature content'),
'type' => MENU_LOCAL_TASK,
'weight' => 8,
);
$items['node/%tf_node/tf_edit_relationships'] = array(
'title' => t('Edit Relationships'),
'description' => t('Settings for Feature'),
'page callback' => 'tripal_feature_edit_ALL_relationships_page',
'page arguments' => array(1),
'access arguments' => array('edit chado_feature content'),
'type' => MENU_LOCAL_TASK,
'weight' => 9,
);
*/
$items['node/%tf_node/tf_edit_db_references'] = array(
'title' => t('Edit References'),
'description' => t('Settings for Feature'),
'page callback' => 'tripal_feature_edit_ALL_dbreferences_page',
'page arguments' => array(1),
'access arguments' => array('edit chado_feature content'),
'type' => MENU_LOCAL_TASK,
'weight' => 10,
);
// managing relationship aggregates
$items['admin/tripal/tripal_feature/aggregate'] = array(
'title' => 'Feature Relationship Aggegators',
'description' => t('Features have relationships with other features and it may be desirable to aggregate the content from one ore more child or parent feature.'),
'page callback' => 'tripal_feature_aggregator_page',
'access arguments' => array('manage chado_feature aggregator'),
'type' => MENU_NORMAL_ITEM,
);
$items['admin/tripal/tripal_feature/aggregate/new'] = array(
'title' => 'Add an Aggregator',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_feature_aggregator_form'),
'access arguments' => array('manage chado_feature aggregator'),
'type' => MENU_NORMAL_ITEM,
);
$items['admin/tripal/tripal_feature/aggregate/edit/js'] = array(
'title' => 'Edit an Aggegator',
'page callback' => 'tripal_feature_aggregator_ajax_edit',
'access arguments' => array('manage chado_feature aggregator'),
'type' => MENU_CALLBACK,
);
return $items;
}
/**
* Implements Menu wildcard_load hook
* Purpose: Allows the node ID of a chado feature to be dynamically
* pulled from the path. The node is loaded from this node ID
* and supplied to the page as an arguement
*
* @ingroup tripal_feature
*/
function tf_node_load($nid) {
if (is_numeric($nid)) {
$node = node_load($nid);
if ($node->type == 'chado_feature') {
return $node;
}
}
return FALSE;
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_block($op = 'list', $delta = 0, $edit=array()){
switch($op) {
case 'list':
$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['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['featureloc_sequences']['info'] = t('Tripal Formatted Sequence');
$blocks['featureloc_sequences']['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;
case 'view':
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 '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');
$block['content'] = theme('tripal_feature_featurelocs',$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', $node);
break;
case 'org_feature_browser':
$block['subject'] = t('Feature Browser');
$block['content'] = theme('tripal_organism_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){
// remove spaces, newlines from residues
$residues = preg_replace("/[\n\r\s]/","",$node->residues);
$obsolete = 'FALSE';
if($node->is_obsolete){
$obsolete = 'TRUE';
}
$values = array(
'cv_id' => array(
'name' => 'sequence'
),
'name' => $node->feature_type
);
$type = tripal_core_chado_select('cvterm',array('cvterm_id'),$values);
$values = array(
'organism_id' => $node->organism_id,
'name' => $node->fname,
'uniquename' => $node->uniquename,
'residues' => $residues,
'seqlen' => strlen($residues),
'is_obsolete' => $obsolete,
'type_id' => $type[0]->cvterm_id,
'md5checksum' => md5($residues)
);
$istatus = tripal_core_chado_insert('feature', $values);
if (!$istatus) {
drupal_set_message('Unable to add feature.', 'warning');
watchdog('tripal_organism',
'Insert feature: Unable to create feature where values: %values',
array('%values' => print_r($values, TRUE)),
WATCHDOG_WARNING
);
}
$values = array(
'organism_id' => $node->organism_id,
'uniquename' => $node->uniquename,
'type_id' => $type[0]->cvterm_id,
);
$feature = tripal_core_chado_select('feature',array('feature_id'),$values);
// add the genbank accession and synonyms
chado_feature_add_synonyms($node->synonyms,$feature[0]->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.
$node_check_sql = "SELECT * FROM {chado_feature} ".
"WHERE feature_id = '%s'";
$node_check = db_fetch_object(db_query($node_check_sql,$feature[0]->feature_id));
if(!$node_check){
// next add the item to the drupal table
$sql = "INSERT INTO {chado_feature} (nid, vid, feature_id, sync_date) ".
"VALUES (%d, %d, %d, " . time() . ")";
db_query($sql,$node->nid,$node->vid,$feature[0]->feature_id);
}
}
/**
*
*
* @ingroup tripal_feature
*/
function chado_feature_update($node){
if($node->revision){
// TODO -- decide what to do about revisions
} else {
$residues = preg_replace("/[\n\r\s]/","",$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) ;
if(sizeof($type) > 0){
$match = array(
'feature_id' => $feature_id,
);
$values = array(
'organism_id' => $node->organism_id,
'name' => $node->fname,
'uniquename' => $node->uniquename,
'residues' => $residues,
'seqlen' => strlen($residues),
'is_obsolete' => $obsolete,
'type_id' => $type[0]->cvterm_id,
'md5checksum' => md5($residues)
);
$status = tripal_core_chado_update('feature', $match,$values);
// add the genbank synonyms
chado_feature_add_synonyms($node->synonyms,$feature_id);
}
else {
drupal_set_message('Unable to update feature.', 'warning');
watchdog('tripal_organism',
'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);
// remove the drupal content
$sql_del = "DELETE FROM {chado_feature} ".
"WHERE nid = %d ".
"AND vid = %d";
db_query($sql_del, $node->nid, $node->vid);
$sql_del = "DELETE FROM {node} ".
"WHERE nid = %d ".
"AND vid = %d";
db_query($sql_del, $node->nid, $node->vid);
$sql_del = "DELETE FROM {node_revisions} ".
"WHERE nid = %d ".
"AND vid = %d";
db_query($sql_del, $node->nid, $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
$previous_db = tripal_db_set_active('chado');
db_query("DELETE FROM {feature} WHERE feature_id = %d", $feature_id);
tripal_db_set_active($previous_db);
drupal_set_message("The feature and all associated data were removed from ".
"chado");
}
/**
*
*
* @ingroup tripal_feature
*/
function chado_feature_add_synonyms($synonyms,$feature_id){
// make sure we only have a single space between each synonym
$synonyms = preg_replace("/[\s\n\r]+/"," ",$synonyms);
// split the synonyms into an array based on a space as the delimieter
$syn_array = array();
$syn_array = explode(" ",$synonyms);
// use the chado database
$previous_db = tripal_db_set_active('chado');
// remove any old synonyms
$feature_syn_dsql = "DELETE FROM {feature_synonym} WHERE feature_id = %d";
if(!db_query($feature_syn_dsql,$feature_id)){
$error .= "Could not remove synonyms from feature. ";
}
// return if we don't have any synonmys to add
if(!$synonyms){
tripal_db_set_active($previous_db);
return;
}
// iterate through each synonym and add it to the database
foreach($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 = '%s'";
$synonym = db_fetch_object(db_query($synonym_sql,$syn));
if(!$synonym){
$synonym_isql = "INSERT INTO {synonym} (name,synonym_sgml,type_id) ".
"VALUES ('%s','%s', ".
" (SELECT cvterm_id ".
" FROM {CVTerm} CVT ".
" INNER JOIN CV ON CVT.cv_id = CV.cv_id ".
" WHERE CV.name = 'feature_property' and CVT.name = 'synonym'))";
if(!db_query($synonym_isql,$syn,$syn)){
$error .= "Could not add synonym. ";
}
// now get the synonym we just added
$synonym_sql = "SELECT synonym_id FROM {synonym} ".
"WHERE name = '%s'";
$synonym = db_fetch_object(db_query($synonym_sql,$syn));
}
// now add in our new sysnonym
$feature_syn_isql = "INSERT INTO {feature_synonym} (synonym_id,feature_id,pub_id) ".
"VALUES (%d,%d,1)";
if(!db_query($feature_syn_isql,$synonym->synonym_id,$feature_id)){
$error .= "Could not add synonyms to feature. ";
}
}
// return to the drupal database
tripal_db_set_active($previous_db);
return $error;
}
/**
*
*
* @ingroup tripal_feature
*/
function chado_feature_add_gbaccession($accession,$feature_id){
// use chado database
$previous_db = tripal_db_set_active('chado');
// remove any old accession from genbank dbEST
$fdbxref_dsql = "DELETE FROM {feature_dbxref} ".
"WHERE feature_id = %d and dbxref_id IN ".
" (SELECT DBX.dbxref_id FROM {dbxref} DBX ".
" INNER JOIN DB ON DB.db_id = DBX.db_id ".
" INNER JOIN feature_dbxref FDBX ON DBX.dbxref_id = FDBX.dbxref_id ".
" WHERE DB.name = 'DB:Genbank' and FDBX.feature_id = %d)";
if(!db_query($fdbxref_dsql,$feature_id,$feature_id)){
$error .= "Could not remove accession from feature. ";
}
// if we don't have an accession number to add then just return
if(!$accession){
tripal_db_set_active($previous_db);
return;
}
// get the db_id
$db_sql = "SELECT db_id FROM {DB} ".
"WHERE name = 'DB:Genbank_est'";
$db = db_fetch_object(db_query($db_sql));
// 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
$dbxref_sql = "SELECT dbxref_id FROM {dbxref} ".
"WHERE db_id = %d and accession = '%s'";
$dbxref = db_fetch_object(db_query($dbxref_sql,$db->db_id,$accession));
if(!$dbxref){
// add the accession number
$dbxref_isql = "INSERT INTO {dbxref} (db_id,accession) ".
" VALUES (%d, '%s') ";
if(!db_query($dbxref_isql,$db->db_id,$accession)){
$error .= 'Could not add accession as a database reference ';
}
// get the dbxref_id for the just added accession number
$dbxref_sql = "SELECT dbxref_id FROM {dbxref} ".
"WHERE db_id = %d and accession = '%s'";
$dbxref = db_fetch_object(db_query($dbxref_sql,$db->db_id,$accession));
}
// associate the accession number with the feature
$feature_dbxref_isql = "INSERT INTO {feature_dbxref} (feature_id,dbxref_id) ".
" VALUES (%d, %d) ";
if(!db_query($feature_dbxref_isql,$feature_id,$dbxref->dbxref_id)){
$error .= 'Could not add feature database reference. ';
}
tripal_db_set_active($previous_db);
return $error;
}
/**
*
*
* @ingroup tripal_feature
*/
function chado_feature_form ($node,$param){
$type = node_get_types('type', $node);
$form = array();
$feature = $node->feature;
// add the residues to the feature object
$feature = tripal_core_expand_chado_vars($feature,'field','feature.residues');
// if the node has synonyms then use that as the form may be returning
// from an error. Otherwise try to find synonyms from the database
$synonyms = $node->synonyms;
$feature = tripal_core_expand_chado_vars($feature,'table','feature_synonym');
$feature_synonyms = $feature->feature_synonym;
if(!$synonyms){
if (!is_array($feature_synonyms)) {
$synonyms = $feature_synonyms->synonym_id->name;
}
elseif(is_array($feature_synonyms)) {
foreach($feature_synonyms as $index => $synonym){
$synonyms .= $synonym->synonym_id->name ."\n";
}
}
}
$analyses = $node->analyses;
$references = $node->references;
// We need to pass above variables for preview to show
$form['feature'] = array(
'#type' => 'value',
'#value' => $feature
);
// This field is read when previewing a node
$form['synonyms'] = array(
'#type' => 'value',
'#value' => $synonyms
);
// This field is read when previewing a node
$form['analyses'] = array(
'#type' => 'value',
'#value' => $analyses
);
// This field is read when previewing a node
$form['references'] = array(
'#type' => 'value',
'#value' => $references
);
// keep track of the feature id if we have one. If we do have one then
// this would indicate an update as opposed to an insert.
$form['feature_id'] = array(
'#type' => 'value',
'#value' => $feature->feature_id,
);
$form['title']= array(
'#type' => 'textfield',
'#title' => t('Title'),
'#required' => TRUE,
'#default_value' => $node->title,
'#description' => t('The title must be a unique identifier for this feature. It is recommended to use a combination of uniquename, organism and feature type in the title as this is guranteed to be unique.'),
'#weight' => 1,
'#maxlength' => 255
);
$form['uniquename']= array(
'#type' => 'textfield',
'#title' => t('Unique Feature Name'),
'#required' => TRUE,
'#default_value' => $feature->uniquename,
'#description' => t('Enter a unique name for this feature. This name must be unique for the organism and feature type.'),
'#weight' => 1,
'#maxlength' => 255
);
$form['fname']= array(
'#type' => 'textfield',
'#title' => t('Feature Name'),
'#required' => TRUE,
'#default_value' => $feature->name,
'#description' => t('Enter the name used by humans to refer to this feature.'),
'#weight' => 1,
'#maxlength' => 255
);
// get the list of supported feature types
$ftypes = array();
$ftypes[''] = '';
$supported_ftypes = split("[ \n]",variable_get('chado_feature_types','EST contig'));
foreach($supported_ftypes as $ftype){
$ftypes["$ftype"] = $ftype;
}
$form['feature_type'] = array (
'#title' => t('Feature Type'),
'#type' => t('select'),
'#description' => t("Choose the feature type."),
'#required' => TRUE,
'#default_value' => $feature->type_id->name,
'#options' => $ftypes,
'#weight' => 2
);
// get the list of organisms
$sql = "SELECT * FROM {Organism} ORDER BY genus, species";
$previous_db = tripal_db_set_active('chado'); // use chado database
$org_rset = db_query($sql);
tripal_db_set_active($previous_db); // now use drupal database
//
$organisms = array();
$organisms[''] = '';
while($organism = db_fetch_object($org_rset)){
$organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
}
$form['organism_id'] = array (
'#title' => t('Organism'),
'#type' => t('select'),
'#description' => t("Choose the organism with which this feature is associated "),
'#required' => TRUE,
'#default_value' => $feature->organism_id->organism_id,
'#options' => $organisms,
'#weight' => 3,
);
// Get synonyms
if ($synonyms) {
if (is_array($synonyms)) {
foreach ($synonyms as $synonym){
$syn_text .= "$synonym->name\n";
}
} else {
$syn_text = $synonyms;
}
}
$form['synonyms']= array(
'#type' => 'textarea',
'#title' => t('Synonyms'),
'#required' => FALSE,
'#default_value' => $syn_text,
'#description' => t('Enter alternate names (synonmys) for this feature to help in searching and identification. You may enter as many alternate names as needed separated by spaces or on different lines.'),
'#weight' => 5,
);
$form['residues']= array(
'#type' => 'textarea',
'#title' => t('Residues'),
'#required' => FALSE,
'#default_value' => $feature->residues,
'#description' => t('Enter the nucelotide sequences for this feature'),
'#weight' => 6
);
$checked = '';
if($feature->is_obsolete == 't'){
$checked = '1';
}
$form['is_obsolete']= array(
'#type' => 'checkbox',
'#title' => t('Is Obsolete'),
'#required' => FALSE,
'#default_value' => $checked,
'#description' => t('Check this box if this sequence should be retired and no longer included in further analysis.'),
'#weight' => 8
);
return $form;
}
/**
*
*
* @ingroup tripal_feature
*/
function chado_feature_validate($node){
$result = 0;
// if this is an update, we want to make sure that a different feature for
// the organism doesn't already have this uniquename. We don't want to give
// two sequences the same uniquename
if($node->feature_id){
$sql = "SELECT *
FROM {Feature} F
INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
WHERE uniquename = '%s'
AND organism_id = %d AND CVT.name = '%s' AND NOT feature_id = %d";
$previous_db = tripal_db_set_active('chado');
$result = db_fetch_object(db_query($sql, $node->uniquename,$node->organism_id,$node->feature_type,$node->feature_id));
tripal_db_set_active($previous_db);
if($result){
form_set_error('uniquename',t("Feature update cannot proceed. The feature name '$node->uniquename' is not unique for this organism. Please provide a unique name for this feature. "));
}
}
// if this is an insert then we just need to make sure this name doesn't
// already exist for this organism if it does then we need to throw an error
else {
$sql = "SELECT *
FROM {Feature} F
INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
WHERE uniquename = '%s'
AND organism_id = %d AND CVT.name = '%s'";
$previous_db = tripal_db_set_active('chado');
$result = db_fetch_object(db_query($sql, $node->uniquename,$node->organism_id,$node->feature_type));
tripal_db_set_active($previous_db);
if($result){
form_set_error('uniquename',t("Feature insert cannot proceed. The feature name '$node->uniquename' already exists for this organism. Please provide a unique name for this feature. "));
}
}
// we want to remove all characters except IUPAC nucleotide characters from the
// the residues. however, residues are not required so if blank then we'll skip
// this step
if($node->residues){
$residues = preg_replace("/[^\w]/",'',$node->residues);
if(!preg_match("/^[ACTGURYMKSWBDHVN]+$/i",$residues)){
form_set_error('residues',t("The residues in feature $node->name contains more than the nucleotide IUPAC characters. Only the following characters are allowed: A,C,T,G,U,R,Y,M,K,S,W,B,D,H,V,N: '" . $residues ."'"));
}
}
// we don't allow a genbank accession number for a contig
if($node->feature_type == 'contig' and $node->gbaccession){
form_set_error('gbaccession',t("Contigs cannot have a genbank accession number. Please change the feature type or remove the accession number"));
}
}
/**
* When a node is requested by the user this function is called to allow us
* to add auxiliary data to the node object.
*
* @ingroup tripal_feature
*/
function chado_feature_load($node){
// get the feature details from chado
$feature_id = chado_get_id_for_node('feature',$node);
$values = array('feature_id' => $feature_id);
$feature = tripal_core_generate_chado_var('feature',$values);
$additions->feature = $feature;
return $additions;
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_load_organism ($organism_id){
// add organism details
$sql = "SELECT * FROM {organism} WHERE organism_id = %d";
$previous_db = tripal_db_set_active('chado'); // use chado database
$organism = db_fetch_object(db_query($sql,$organism_id));
tripal_db_set_active($previous_db); // now use drupal database
return $organism;
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_load_synonyms ($feature_id){
$sql = "SELECT S.name ".
"FROM {Feature_Synonym} FS ".
" INNER JOIN {Synonym} S ".
" ON FS.synonym_id = S.Synonym_id ".
"WHERE FS.feature_id = %d ".
"ORDER BY S.name ";
$previous_db = tripal_db_set_active('chado'); // use chado database
$results = db_query($sql,$feature_id);
tripal_db_set_active($previous_db); // now use drupal database
$synonyms = array();
$i=0;
while($synonym = db_fetch_object($results)){
$synonyms[$i++] = $synonym;
}
return $synonyms;
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_load_properties ($feature_id){
$sql = "SELECT CVT.name as cvname, FS.type_id, FS.value, FS.rank,
CVT.definition, CVT.is_obsolete,
DBX.dbxref_id,DBX.accession,DB.name as dbname,
DB.urlprefix, DB.description as db_description, DB.url
FROM {featureprop} FS
INNER JOIN {cvterm} CVT ON FS.type_id = CVT.cvterm_id
INNER JOIN {dbxref} DBX ON CVT.dbxref_id = DBX.dbxref_id
INNER JOIN {db} DB ON DB.db_id = DBX.db_id
WHERE FS.feature_id = %d
ORDER BY FS.rank ASC";
$previous_db = tripal_db_set_active('chado'); // use chado database
$results = db_query($sql,$feature_id);
tripal_db_set_active($previous_db); // now use drupal database
$i=0;
$properties = array();
while($property = db_fetch_object($results)){
$properties[$i++] = $property;
}
return $properties;
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_load_references ($feature_id){
$sql = "SELECT F.uniquename,F.Feature_id,DBX.accession,DB.description as dbdesc, ".
" DB.db_id, DB.name as db_name, DB.urlprefix,DBX.dbxref_id ".
"FROM {feature} F ".
" INNER JOIN {feature_dbxref} FDBX on F.feature_id = FDBX.feature_id ".
" INNER JOIN {dbxref} DBX on DBX.dbxref_id = FDBX.dbxref_id ".
" INNER JOIN {db} on DB.db_id = DBX.db_id ".
"WHERE F.feature_id = %d ".
"ORDER BY DB.name ";
$previous_db = tripal_db_set_active('chado'); // use chado database
$results = db_query($sql,$feature_id);
tripal_db_set_active($previous_db); // now use drupal database
$references = array();
$i=0;
while($accession = db_fetch_object($results)){
$references[$i++] = $accession;
}
return $references;
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_load_featurelocs ($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){
$sql .= "WHERE FL.srcfeature_id = %d ";
}
if(strcmp($side,'as_child')==0){
$sql .= "WHERE FL.feature_id = %d ";
}
$previous_db = tripal_db_set_active('chado'); // use chado database
$flresults = db_query($sql, $feature_id);
tripal_db_set_active($previous_db); // now use drupal database
// copy the results into an array
$i=0;
$featurelocs = array();
while($loc = db_fetch_object($flresults)){
// if a drupal node exists for this feature then add the nid to the
// results object
$sql = 'SELECT nid FROM {chado_feature} WHERE feature_id = %d';
$ffeature = db_fetch_object(db_query($sql, $loc->feature_id));
$sfeature = db_fetch_object(db_query($sql, $loc->src_feature_id));
$loc->fnid = $ffeature->nid;
$loc->snid = $sfeature->nid;
// 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
$sql = "SELECT
FS.name as subject_name,
FS.uniquename as subject_uniquename,
CVTS.name as subject_type,
CVTS.cvterm_id as subject_type_id,
FR.subject_id,
FR.type_id as relationship_type_id,
CVT.name as rel_type,
FO.name as object_name,
FO.uniquename as object_uniquename,
CVTO.name as object_type,
CVTO.cvterm_id as object_type_id,
FR.object_id,
FR.rank
FROM {feature_relationship} FR
INNER JOIN {cvterm} CVT ON FR.type_id = CVT.cvterm_id
INNER JOIN {feature} FS ON FS.feature_id = FR.subject_id
INNER JOIN {feature} FO ON FO.feature_id = FR.object_id
INNER JOIN {cvterm} CVTO ON FO.type_id = CVTO.cvterm_id
INNER JOIN {cvterm} CVTS ON FS.type_id = CVTS.cvterm_id
";
if(strcmp($side,'as_object')==0){
$sql .= " WHERE FR.object_id = %d";
}
if(strcmp($side,'as_subject')==0){
$sql .= " WHERE FR.subject_id = %d";
}
$sql .= " ORDER BY FR.rank";
// get the relationships
$previous_db = tripal_db_set_active('chado'); // use chado database
$results = db_query($sql, $feature_id);
tripal_db_set_active($previous_db); // now use drupal database
// 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 = %d";
$relationships = array();
while($rel = db_fetch_object($results)){
$node = db_fetch_object(db_query($nodesql,$rel->subject_id));
if($node){
$rel->subject_nid = $node->nid;
}
$node = db_fetch_object(db_query($nodesql,$rel->object_id));
if($node){
$rel->object_nid = $node->nid;
}
$relationships[$i++] = $rel;
}
return $relationships;
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_get_aggregate_types($feature_id){
// get the feature details
$sql = 'SELECT type_id FROM {feature} WHERE feature_id = %d';
$previous_db = tripal_db_set_active('chado'); // use chado database
$feature = db_fetch_object(db_query($sql, $feature_id));
tripal_db_set_active($previous_db); // now use drupal database
// check to see if this feature is of a type with an aggregate
$sql = "SELECT * FROM {tripal_feature_relagg} WHERE type_id = %d";
$types = array();
$results = db_query($sql,$feature->type_id);
while($agg = db_fetch_object($results)){
$types[] = $agg->rel_type_id;
}
return $types;
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_get_aggregate_relationships($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
$relationships = tripal_feature_load_relationships($feature_id,'as_object');
// next, iterate through these relationships and descend, adding in those
// that are specified by the aggregator.
$i=0;
$new_relationships = array();
foreach($relationships as $rindex => $rel){
// set the base type id
if(!$base_type_id){
$base_type_id = $rel->object_type_id;
}
// check to see if we have an aggregator for this base type
$sql = "SELECT * FROM {tripal_feature_relagg} WHERE type_id = %d and rel_type_id = %d";
$agg = db_fetch_object(db_query($sql,$base_type_id,$rel->subject_type_id));
if($agg){
// if we're not going to substitute the resulting relationships for the
// parent then we need to add the parent to our list
if(!$substitute){
$new_relationships[$i++] = $rel;
}
// recurse all relationships
$agg_relationships = tripal_feature_get_aggregate_relationships(
$rel->subject_id,$levels,$base_type_id,$depth++);
// if we have an aggregate defined but we have no relationships beyond
// this point then there's nothing we can substitute
if(!$agg_relationships and $substitute){
$new_relationships[$i++] = $rel;
}
// merge all relationships into one array
foreach($agg_relationships as $aindex => $arel){
$new_relationships[$i++] = $arel;
}
}
else {
// if we don't have an aggregate then keep the current relationship
$new_relationships[$i++] = $rel;
}
}
return $new_relationships;
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_load_featureloc_sequences($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.
$rel->featurelocs->$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;
$rel_locs[$src]['parts'][$start]['type'] = $rel->subject_type;
$rel_locs[$src]['parts'][$start]['start'] = $start;
$rel_locs[$src]['parts'][$start]['end'] = $end;
}
}
// 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.
$sql = "SELECT residues FROM {feature} WHERE feature_id = %d";
$floc_sequences = array();
foreach ($featurelocs as $featureloc){
// get the residues for this feature
$previous_db = tripal_db_set_active('chado'); // use chado database
$feature = db_fetch_object(db_query($sql,$featureloc->srcfeature_id->feature_id));
tripal_db_set_active($previous_db); // now use drupal database
$src = $featureloc->srcfeature_id->feature_id ."-". $featureloc->srcfeature_id->type_id->cvterm_id;
// orient the parts to the beginning of the feature sequence
$parts = $rel_locs[$src]['parts'];
usort($parts, 'tripal_feature_sort_rel_parts');
foreach ($parts as $start => $attrs){
$parts[$start]['start'] = $parts[$start]['start'] - $featureloc->fmin;
$parts[$start]['end'] = $parts[$start]['end'] - $featureloc->fmin;
}
$floc_sequences[$src]['src'] = $src;
$floc_sequences[$src]['type'] = $featureloc->feature_id->type_id->name;
$sequence = substr($feature->residues,$featureloc->fmin-1,($featureloc->fmax - $featureloc->fmin)+1);
$floc_sequences[$src]['formatted_seq'] = tripal_feature_color_sequence (
$sequence,$parts);
}
return $floc_sequences;
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_load_organism_feature_counts($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 );
}
// 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 organism_id = %d
ORDER BY num_features desc
";
$previous_db = tripal_db_set_active('chado'); // use chado database
$org_features = db_query($sql,$organism->organism_id);
tripal_db_set_active($previous_db); // now use drupal database
$i=0;
$types = array();
while($type = db_fetch_object($org_features)){
$types[$i++] = $type;
}
return array ( 'types' => $types, 'enabled' => true );
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_load_organism_feature_browser($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
$show_browser = variable_get('tripal_feature_browse_setting','show_feature_browser');
if(strcmp($show_browser,'show_feature_browser')!=0){
return array ('enabled' => false);
}
# get the list of available sequence ontology terms for which
# we will build drupal pages from features in chado. If a feature
# is not one of the specified typse we won't build a node for it.
$allowed_types = variable_get('chado_feature_types','EST contig');
$allowed_types = preg_replace("/[\s\n\r]+/"," ",$allowed_types);
$so_terms = split(' ',$allowed_types);
$where_cvt = "";
foreach ($so_terms as $term){
$where_cvt .= "CVT.name = '$term' OR ";
}
$where_cvt = substr($where_cvt,0,strlen($where_cvt)-3); # strip trailing 'OR'
// get the features for this organism
$sql = "SELECT F.name,F.feature_id,F.uniquename,CVT.name as cvname ".
"FROM {feature} F ".
" INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id ".
"WHERE organism_id = %s and ($where_cvt) ".
"ORDER BY feature_id ASC";
// the counting SQL
$csql = "SELECT count(*) ".
"FROM {feature} F".
" INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id ".
"WHERE organism_id = %s and ($where_cvt) ".
"GROUP BY organism_id ";
$previous_db = tripal_db_set_active('chado'); // use chado database
$org_features = pager_query($sql,10,0,$csql,$organism->organism_id);
tripal_db_set_active($previous_db); // now use drupal database
$pager = theme('pager');
// prepare the query that will lookup node ids
$sql = "SELECT nid FROM {chado_feature} ".
"WHERE feature_id = %d";
$i=0;
$features = array();
while($feature = db_fetch_object($org_features)){
$node = db_fetch_object(db_query($sql,$feature->feature_id));
$feature->nid = $node->nid;
$features[$i++] = $feature;
}
return array ( 'features' => $features, 'pager' => $pager, 'enabled' => true );
}
/**
* used to sort the list of relationship objects by start position
*
* @ingroup tripal_feature
*/
function tripal_feature_sort_rel_objects($a,$b){
return strnatcmp($a->fmin, $b->fmin);
}
/**
* used to sort the list of relationship parts by start position
*
* @ingroup tripal_feature
*/
function tripal_feature_sort_rel_parts($a,$b){
return strnatcmp($a['start'], $b['start']);
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_color_sequence ($sequence,$parts){
$types = array();
// first get the list of types so we can create a color legend
foreach ($parts as $index => $child){
$type = $child['type'];
if(!in_array($type,$types)){
$types[] = $type;
}
}
$newseq .= "<div id=\"tripal_feature-featureloc_sequence-legend\">Legend: ";
foreach($types as $type){
$newseq .= "<span class=\"tripal_feature-featureloc_sequence-$type\">$type</span>";
}
$newseq .= "</div>";
// set the background color of the rows based on the type
$pos = 0;
$newseq .= "<pre id=\"tripal_feature-featureloc_sequence\">";
foreach ($parts as $index => $child){
$type = $child['type'];
$start = $child['start'];
$end = $child['end']+1;
$class = "class=\"tripal_feature-featureloc_sequence-$type\"";
// iterate through the sequence up to the end of the child
for ($i = $pos; $i < $end; $i++){
// if we're at the beginning of the child sequence then set the
// appropriate text color
if($pos == $start){
$newseq .= "<span $class>";
$func = 'uc'; // nucleotides within the child should be uppercase
}
$newseq .= $sequence{$pos};
$seqcount++;
if($seqcount % 60 == 0){
$newseq .= "\n";
}
$pos++;
if($pos == $end){
$newseq .= "</span>";
$func = 'lc';
}
}
}
$newseq .= "</pre>";
return $newseq;
}
/**
* This function customizes the view of the chado_feature node. It allows
* us to generate the markup.
*
* @ingroup tripal_feature
*/
function chado_feature_view ($node, $teaser = FALSE, $page = FALSE) {
if (!$teaser) {
// use drupal's default node view:
$node = node_prepare($node, $teaser);
// if we're building the node for searching then
// we want to handle this within the module and
// not allow theme customization. We don't want to
// index all items (such as DNA sequence).
if($node->build_mode == NODE_BUILD_SEARCH_INDEX){
$node->content['index_version'] = array(
'#value' => theme('tripal_feature_search_index',$node),
'#weight' => 1,
);
}
elseif($node->build_mode == NODE_BUILD_SEARCH_RESULT){
$node->content['index_version'] = array(
'#value' => theme('tripal_feature_search_results',$node),
'#weight' => 1,
);
}
else {
// do nothing here, let the theme derived template handle display
}
}
return $node;
}
/**
* Display feature information for associated organisms. This function also
* provides contents for indexing
*
* @ingroup tripal_feature
*/
function tripal_feature_nodeapi(&$node, $op, $teaser, $page) {
switch ($op) {
// Note that this function only adds feature view to an organism node.
// The view of a feature node is controled by the theme *.tpl file
case 'view':
switch($node->type){
case 'chado_organism':
// Show feature browser
$types_to_show = array('chado_organism', 'chado_library');
if (in_array($node->type, $types_to_show, TRUE)) {
$node->content['tripal_organism_feature_counts'] = array(
'#value' => theme('tripal_organism_feature_counts', $node),
);
$node->content['tripal_organism_feature_browser'] = array(
'#value' => theme('tripal_organism_feature_browser', $node),
);
}
break;
case 'chado_library':
break;
default:
}
break;
}
}
/**
* We need to let drupal know about our theme functions and their arguments.
* We create theme functions to allow users of the module to customize the
* look and feel of the output generated in this module
*
* @ingroup tripal_feature
*/
function tripal_feature_theme () {
return array(
'tripal_feature_search_index' => array (
'arguments' => array('node'),
),
'tripal_feature_search_results' => array (
'arguments' => array('node'),
),
'tripal_organism_feature_browser' => array (
'arguments' => array('node'=> null),
'template' => 'tripal_organism_feature_browser',
),
'tripal_organism_feature_counts' => array (
'arguments' => array('node'=> null),
'template' => 'tripal_organism_feature_counts',
),
'tripal_feature_base' => array (
'arguments' => array('node'=> null),
'template' => 'tripal_feature_base',
),
'tripal_feature_sequence' => array (
'arguments' => array('node'=> null),
'template' => 'tripal_feature_sequence',
),
'tripal_feature_synonyms' => array (
'arguments' => array('node'=> null),
'template' => 'tripal_feature_synonyms',
),
'tripal_feature_featureloc_sequences' => array (
'arguments' => array('node'=> null),
'template' => 'tripal_feature_featureloc_sequences',
),
'tripal_feature_references' => array (
'arguments' => array('node'=> null),
'template' => 'tripal_feature_references',
),
'tripal_feature_properties' => array (
'arguments' => array('node'=> null),
'template' => 'tripal_feature_properties',
),
'tripal_feature_featurelocs' => array (
'arguments' => array('node'=> null),
'template' => 'tripal_feature_featurelocs',
),
'tripal_feature_relationships' => array (
'arguments' => array('node'=> null),
'template' => 'tripal_feature_relationships',
),
);
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_preprocess_tripal_organism_feature_counts(&$variables){
$organism = $variables['node']->organism;
$organism->feature_counts = tripal_feature_load_organism_feature_counts($organism);
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_preprocess_tripal_organism_feature_browser(&$variables){
$organism = $variables['node']->organism;
$organism->feature_browser = tripal_feature_load_organism_feature_browser($organism);
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_cv_chart($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.
$organism_id = preg_replace("/^tripal_feature_cv_chart_(\d+)$/","$1",$chart_id);
$options = array(
count_mview => 'organism_feature_count',
cvterm_id_column => 'cvterm_id',
count_column => 'num_features',
size => '550x200',
filter => "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 $options;
}
/**
* This function is an extension of the chado_feature_view by providing
* the markup for the feature object THAT WILL BE INDEXED.
*
* @ingroup tripal_feature
*/
function theme_tripal_feature_search_index ($node) {
$feature = $node->feature;
$content = '';
// get the accession prefix
$aprefix = variable_get('chado_feature_accession_prefix','ID');
$content .= "<h1>$feature->uniquename</h1>. ";
$content .= "<strong>$aprefix$feature->feature_id.</strong> ";
$content .= "$feature->cvname ";
$content .= "$feature->common_name ";
// add the synonyms of this feature to the text for searching
$synonyms = $node->synonyms;
if(count($synonyms) > 0){
foreach ($synonyms as $result){
$content .= "$result->name ";
}
}
return $content;
}
/**
* This function is an extension of the chado_feature_view by providing
* the markup for the feature object THAT WILL BE INDEXED.
*
* @ingroup tripal_feature
*/
function theme_tripal_feature_search_results ($node) {
$feature = $node->feature;
$content = '';
// get the accession prefix
$aprefix = variable_get('chado_feature_accession_prefix','ID');
$content .= "Feature Name: <h1>$feature->uniquename</h1>. ";
$content .= "<strong>Accession: $aprefix$feature->feature_id.</strong>";
$content .= "Type: $feature->cvname. ";
$content .= "Organism: $feature->common_name. ";
// add the synonyms of this feature to the text for searching
$synonyms = $node->synonyms;
if(count($synonyms) > 0){
$content .= "Synonyms: ";
foreach ($synonyms as $result){
$content .= "$result->name, ";
}
}
return $content;
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_set_vocabulary (){
//include the file containing the required functions for adding taxonomy vocabs
module_load_include('inc', 'taxonomy', 'taxonomy.admin');
// get the vocabularies so that we make sure we don't recreate
// the vocabs that already exist
$vocabularies = taxonomy_get_vocabularies();
$ft_vid = NULL;
$op_vid = NULL;
$lb_vid = NULL;
$an_vid = NULL;
// These taxonomic terms are hard coded because we
// konw we have these relationships in the chado tables
// through foreign key relationships. The tripal
// modules that correspond to these chado "modules" don't
// need to be installed for the taxonomy to work.
foreach($vocabularies as $vocab){
if($vocab->name == 'Feature Type'){
$ft_vid = $vocab->vid;
}
if($vocab->name == 'Organism'){
$op_vid = $vocab->vid;
}
if($vocab->name == 'Library'){
$lb_vid = $vocab->vid;
}
if($vocab->name == 'Analysis'){
$an_vid = $vocab->vid;
}
}
if(!$ft_vid){
$form_state = array();
$values = array(
'name' => t('Feature Type'),
'nodes' => array('chado_feature' => 'chado_feature'),
'description' => t('The feature type (or SO cvterm for this feature).'),
'help' => t('Select the term that matches the feature '),
'tags' => 0,
'hierarchy' => 1,
'relations' => 1,
'multiple' => 0,
'required' => 0,
'weight' => 1,
);
drupal_execute('taxonomy_form_vocabulary', $form_state,$values);
drupal_execute('taxonomy_form_vocabulary', $form_state);
}
if(!$op_vid){
$form_state = array();
$values = array(
'name' => t('Organism'),
'nodes' => array('chado_feature' => 'chado_feature'),
'description' => t('The organism to which this feature belongs.'),
'help' => t('Select the term that matches the feature '),
'tags' => 0,
'hierarchy' => 1,
'relations' => 1,
'multiple' => 0,
'required' => 0,
'weight' => 2,
);
drupal_execute('taxonomy_form_vocabulary', $form_state,$values);
drupal_execute('taxonomy_form_vocabulary', $form_state);
}
if(!$lb_vid){
$form_state = array();
$values = array(
'name' => t('Library'),
'nodes' => array('chado_feature' => 'chado_feature'),
'description' => t('Chado features associated with a library are assigned the term associated with the library'),
'help' => t('Select the term that matches the feature '),
'tags' => 0,
'hierarchy' => 1,
'relations' => 1,
'multiple' => 0,
'required' => 0,
'weight' => 3,
);
drupal_execute('taxonomy_form_vocabulary', $form_state, $values);
drupal_execute('taxonomy_form_vocabulary', $form_state);
}
if(!$an_vid){
$form_state = array();
$values = array(
'name' => t('Analysis'),
'nodes' => array('chado_feature' => 'chado_feature'),
'description' => t('Any analysis to which this feature belongs.'),
'help' => t('Select the term that matches the feature '),
'tags' => 0,
'hierarchy' => 1,
'relations' => 1,
'multiple' => 1,
'required' => 0,
'weight' => 4,
);
drupal_execute('taxonomy_form_vocabulary', $form_state,$values);
drupal_execute('taxonomy_form_vocabulary', $form_state);
}
}
/**
*
*
* @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_del_vocabulary($vocab->vid);
}
if($vocab->name == 'Organism'){
taxonomy_del_vocabulary($vocab->vid);
}
if($vocab->name == 'Library'){
taxonomy_del_vocabulary($vocab->vid);
}
if($vocab->name == 'Analysis'){
taxonomy_del_vocabulary($vocab->vid);
}
}
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_features_set_taxonomy($max_sync = 0,$job_id = NULL){
// make sure our vocabularies are cleaned and reset before proceeding
tripal_feature_del_vocabulary();
tripal_feature_set_vocabulary();
// iterate through all drupal feature nodes and set the taxonomy
$results = db_query("SELECT * FROM {chado_feature}");
$nsql = "SELECT * FROM {node} ".
"WHERE nid = %d";
$i = 0;
// load into ids array
$count = 0;
$chado_features = array();
while($chado_feature = db_fetch_object($results)){
$chado_features[$count] = $chado_feature;
$count++;
}
// Iterate through features that need to be synced
$interval = intval($count * 0.01);
foreach($chado_features as $chado_feature){
// update the job status every 1% features
if($job_id and $i % $interval == 0){
tripal_job_set_progress($job_id,intval(($i/$count)*100));
}
print "$i of $count: ";
$node = db_fetch_object(db_query($nsql,$chado_feature->nid));
tripal_feature_set_taxonomy($node,$chado_feature->feature_id);
$i++;
}
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_set_taxonomy ($node,$feature_id){
// iterate through the taxonomy classes that have been
// selected by the admin user and make sure we only set those
$tax_classes = variable_get('tax_classes', '');
$do_ft = 0;
$do_op = 0;
$do_lb = 0;
$do_an = 0;
foreach($tax_classes as $class){
if(strcmp($class ,'organism')==0){
$do_op = 1;
}
if(strcmp($class,'feature_type')==0){
$do_ft = 1;
}
if(strcmp($class,'library')==0){
$do_lb = 1;
}
if(strcmp($class,'analysis')==0){
$do_an = 1;
}
}
// get the list of vocabularies and find our two vocabularies of interest
$vocabularies = taxonomy_get_vocabularies();
$ft_vid = NULL;
$op_vid = NULL;
$lb_vid = NULL;
$an_vid = NULL;
foreach($vocabularies as $vocab){
if($vocab->name == 'Feature Type'){
$ft_vid = $vocab->vid;
}
if($vocab->name == 'Organism'){
$op_vid = $vocab->vid;
}
if($vocab->name == 'Library'){
$lb_vid = $vocab->vid;
}
if($vocab->name == 'Analysis'){
$an_vid = $vocab->vid;
}
}
// get the cvterm and the organism for this feature
$sql = "SELECT CVT.name AS cvname, O.genus, O.species ".
"FROM {CVTerm} CVT ".
" INNER JOIN Feature F on F.type_id = CVT.cvterm_id ".
" INNER JOIN Organism O ON F.organism_id = O.organism_id ".
"WHERE F.feature_id = $feature_id";
$previous_db = tripal_db_set_active('chado'); // use chado database
$feature = db_fetch_object(db_query($sql));
tripal_db_set_active($previous_db); // now use drupal database
// Set the feature type for this feature
if($do_ft && $ft_vid){
$tags["$ft_vid"] = "$feature->cvname";
}
// Set the organism for this feature type
if($do_op && $op_vid){
$tags["$op_vid"] = "$feature->genus $feature->species";
}
// get the library that this feature may belong to and add it as taxonomy
if($do_lb && $lb_vid){
$sql = "SELECT L.name ".
"FROM {Library} L ".
" INNER JOIN Library_feature LF ON LF.library_id = L.library_id ".
"WHERE LF.feature_id = %d ";
$previous_db = tripal_db_set_active('chado'); // use chado database
$library = db_fetch_object(db_query($sql,$feature_id));
tripal_db_set_active($previous_db); // now use drupal database
$tags["$lb_vid"] = "$library->name";
}
// now add the taxonomy to the node
$terms['tags'] = $tags;
taxonomy_node_save($node,$terms);
// print "Setting $node->name: " . implode(", ",$tags) . "\n";
// get the analysis that this feature may belong to and add it as taxonomy
// We'll add each one individually since there may be more than one analysis
if($do_an && $an_vid){
$sql = "SELECT A.name ".
"FROM {Analysis} A ".
" INNER JOIN Analysisfeature AF ON AF.analysis_id = A.analysis_id ".
"WHERE AF.feature_id = $feature_id ";
$results = db_query($sql);
$previous_db = tripal_db_set_active('chado'); // use chado database
$analysis_terms = array();
while($analysis=db_fetch_object($results)){
$tags2["$an_vid"] = "$analysis->name";
$terms['tags'] = $tags2;
taxonomy_node_save($node,$terms);
}
tripal_db_set_active($previous_db); // now use drupal database
}
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_features_cleanup($dummy = NULL, $job_id = NULL) {
// build the SQL statments needed to check if nodes point to valid features
$dsql = "SELECT * FROM {node} WHERE type = 'chado_feature' order by nid";
$nsql = "SELECT * FROM {node} WHERE nid = %d";
$csql = "SELECT * FROM {chado_feature} where nid = %d ";
$cfsql= "SELECT * FROM {chado_feature}";
$tsql = "SELECT * FROM {feature} F ".
" INNER JOIN CVTerm CVT ON F.type_id = CVT.cvterm_id ".
"WHERE feature_id = %d AND (";
$supported_ftypes = split("[ \n]",variable_get('chado_feature_types','EST contig'));
foreach($supported_ftypes as $ftype){
$tsql .= " CVT.name = '$ftype' OR ";
}
$tsql .= " 0=1) "; // add a 0=1 just as a filler so we don't have to remove a trailing 'OR'
// load into nodes array
$results = db_query($dsql);
$count = 0;
$nodes = array();
while($node = db_fetch_object($results)){
$nodes[$count] = $node;
$count++;
}
// load the chado_features into an array
$results = db_query($cfsql);
$cnodes = array();
while($node = db_fetch_object($results)){
$cnodes[$count] = $node;
$count++;
}
$interval = intval($count * 0.01);
// iterate through all of the chado_feature nodes and delete those that aren't valid
foreach($nodes as $nid){
// update the job status every 1% features
if($job_id and $i % $interval == 0){
tripal_job_set_progress($job_id,intval(($i/$count)*100));
}
// first check to see if the node has a corresponding entry
// in the chado_feature table. If not then delete the node.
$feature = db_fetch_object(db_query($csql,$nid->nid));
if(!$feature){
node_delete($nid->nid);
$message = "Missing in chado_feature table.... DELETING: $nid->nid\n";
watchdog('tripal_feature',$message,array(),WATCHDOG_WARNING);
continue;
}
// second check to see if the node is for a feature of an allowed type.
// if not, then delete the node. This check will also take care of the
// case when a node exists and an entry in the chado_feature table exists
// but no feature with a matching feature_id exists
$previous_db = tripal_db_set_active('chado'); // use chado database
$ftype = db_fetch_object(db_query($tsql,$feature->feature_id));
tripal_db_set_active($previous_db); // now use drupal database
if(!$ftype){
node_delete($nid->nid);
db_query("DELETE FROM {chado_feature} WHERE feature_id = $feature->feature_id");
$message = "Node of the wrong feature type.... DELETING: $nid->nid\n";
watchdog('tripal_feature',$message,array(),WATCHDOG_WARNING);
}
$i++;
}
// iterate through all of the chado_feature nodes and delete those that aren't valid
foreach($cnodes as $nid){
// update the job status every 1% features
if($job_id and $i % $interval == 0){
tripal_job_set_progress($job_id,intval(($i/$count)*100));
}
$node = db_fetch_object(db_query($nsql,$nid->nid));
if(!$node){
db_query("DELETE FROM {chado_feature} WHERE nid = $nid->nid");
$message = "chado_feature missing node.... DELETING: $nid->nid\n";
watchdog('tripal_feature',$message,array(),WATCHDOG_WARNING);
}
$i++;
}
return '';
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_return_fasta($feature,$desc){
$fasta = ">" . variable_get('chado_feature_accession_prefix','ID') . "$feature->feature_id|$feature->name";
$fasta .= " $desc\n";
$fasta .= wordwrap($feature->residues, 50, "\n", true);
$fasta .= "\n\n";
return $fasta;
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_job_describe_args($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 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'] = $args[6];
if($args[11]){
$new_args['Update and Insert'] = 'Yes';
}
else {
$new_args['Insert Only New Features'] = 'Yes';
}
// add in the analysis
if($args[13]){
$analysis = tripal_core_chado_select('analysis',array('name'),array('analysis_id' => $args[13]));
}
$new_args['Analysis'] = $analysis[0]->name;
}
return $new_args;
}