<?php
/**
* @file
* @todo Add file header description
*/
/**
* @defgroup tripal_feature Feature
* @{
* Provides functions for managing chado features including creating details pages for each feature
* @}
* @ingroup tripal_modules
*/
require_once "includes/tripal_feature.admin.inc";
require_once "includes/syncFeatures.inc";
require_once "includes/indexFeatures.inc";
require_once "includes/fasta_loader.inc";
require_once "includes/gff_loader.inc";
require_once "api/tripal_feature.api.inc";
require_once "includes/tripal_feature-delete.inc";
require_once "includes/tripal_feature-secondary_tables.inc";
require_once "includes/tripal_feature-properties.inc";
require_once "includes/tripal_feature-relationships.inc";
require_once "includes/tripal_feature-db_references.inc";
/**
*
* @ingroup tripal_feature
*/
function tripal_feature_init() {
drupal_add_js(drupal_get_path('theme', 'tripal') . '/js/tripal_feature.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') {
if (!user_access('create chado_feature content', $account)) {
return FALSE;
}
}
if ($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['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_feature_gff3_load_form'),
'access arguments' => array('access administration pages'),
'type' => MENU_NORMAL_ITEM,
);
$items['admin/tripal/tripal_feature/delete'] = array(
'title' => ' Delete Features',
'description' => 'Delete multiple features from Chado',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_feature_delete_form'),
'access arguments' => array('access administration pages'),
'type' => MENU_NORMAL_ITEM,
);
$items['admin/tripal/tripal_feature/sync'] = array(
'title' => ' Sync Features',
'description' => 'Sync features from Chado with Drupal',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_feature_sync_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/edit_feature_properties'] = array(
'title' => 'Edit Properties',
'description' => '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' => 'Edit References',
'description' => '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,
);
// the menu link for addressing any feature (by name, uniquename, synonym)
$items['feature/%'] = array(
'title' => 'Matched Features',
'description' => 'Shows all features that match the provided ID. If multiple features match even by name, uniquename or synonym then a page is presented to allow the user to select which one they intended.',
'page callback' => 'tripal_feature_match_features_page',
'page arguments' => array(1),
'access arguments' => array('access chado_feature content'),
'type' => MENU_NORMAL_ITEM,
);
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['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;
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 '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', $node);
break;
case 'org_feature_browser':
$block['subject'] = t('Feature Browser');
$block['content'] = theme('tripal_organism_feature_browser', $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) {
// remove spaces, newlines from residues
$residues = preg_replace("/[\n\r\s]/", "", $node->residues);
$obsolete = 'FALSE';
if ($node->is_obsolete) {
$obsolete = 'TRUE';
}
// check to see if we are inserting a duplicate record.
$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' => $residues,
'seqlen' => drupal_strlen($residues),
'is_obsolete' => $obsolete,
'type_id' => $type[0]->cvterm_id,
'md5checksum' => md5($residues)
);
$options = array('is_duplicate' => TRUE, 'has_record' => TRUE);
$exists = tripal_core_chado_select('feature', array('*'), $values, $options);
// if the record is not a duplicate then add it
if (!$exists) {
$istatus = tripal_core_chado_insert('feature', $values);
if (!$istatus) {
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);
}
}
// now get the newly added record
$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) {
// 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', $node) ;
if (sizeof($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', $node);
// if we don't have a library id for this node then this isn't a node of
// type chado_library or the entry in the chado_library table was lost.
if (!$feature_id) {
return;
}
// remove the drupal content
$sql_del = "DELETE FROM {chado_feature} ".
"WHERE nid = %d ".
"AND vid = %d";
db_query($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
chado_query("DELETE FROM {feature} WHERE feature_id = %d", $feature_id);
drupal_set_message(t("The feature and all associated data were removed from") .
"chado");
}
/**
*
*
* @ingroup tripal_feature
*/
function chado_feature_add_synonyms($synonyms, $feature_id) {
// 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);
// remove any old synonyms
$feature_syn_dsql = "DELETE FROM {feature_synonym} WHERE feature_id = %d";
if (!chado_query($feature_syn_dsql, $feature_id)) {
$error .= "Could not remove synonyms from feature. ";
}
// return if we don't have any synonmys to add
if (!$synonyms) {
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'";
$synonym = db_fetch_object(chado_query($synonym_sql, $syn));
if (!$synonym) {
$synonym_isql = "INSERT INTO {synonym} (name,synonym_sgml,type_id) ".
"VALUES ('%s','%s', ".
" (SELECT cvterm_id ".
" FROM {CVTerm} CVT ".
" INNER JOIN CV ON CVT.cv_id = CV.cv_id ".
" WHERE CV.name = 'feature_property' and CVT.name = 'synonym'))";
if (!chado_query($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'";
$synonym = db_fetch_object(chado_query($synonym_sql, $syn));
}
// now add in our new sysnonym
$feature_syn_isql = "INSERT INTO {feature_synonym} (synonym_id,feature_id,pub_id) ".
"VALUES (%d,%d,1)";
if (!chado_query($feature_syn_isql, $synonym->synonym_id, $feature_id)) {
$error .= "Could not add synonyms to feature. ";
}
}
// return to the drupal database
return $error;
}
/**
*
*
* @ingroup tripal_feature
*/
function chado_feature_add_gbaccession($accession, $feature_id) {
// use chado database
// remove any old accession from genbank dbEST
$fdbxref_dsql = "DELETE FROM {feature_dbxref} ".
"WHERE feature_id = %d and dbxref_id IN ".
" (SELECT DBX.dbxref_id FROM {dbxref} DBX ".
" INNER JOIN DB ON DB.db_id = DBX.db_id ".
" INNER JOIN feature_dbxref FDBX ON DBX.dbxref_id = FDBX.dbxref_id ".
" WHERE DB.name = 'DB:Genbank' and FDBX.feature_id = %d)";
if (!chado_query($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) {
return;
}
// get the db_id
$db_sql = "SELECT db_id FROM {DB} ".
"WHERE name = 'DB:Genbank_est'";
$db = db_fetch_object(chado_query($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'";
$dbxref = db_fetch_object(chado_query($dbxref_sql, $db->db_id, $accession));
if (!$dbxref) {
// add the accession number
$dbxref_isql = "INSERT INTO {dbxref} (db_id,accession) ".
" VALUES (%d, '%s') ";
if (!chado_query($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'";
$dbxref = db_fetch_object(chado_query($dbxref_sql, $db->db_id, $accession));
}
// associate the accession number with the feature
$feature_dbxref_isql = "INSERT INTO {feature_dbxref} (feature_id,dbxref_id) ".
" VALUES (%d, %d) ";
if (!chado_query($feature_dbxref_isql, $feature_id, $dbxref->dbxref_id)) {
$error .= 'Could not add feature database reference. ';
}
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[''] = '';
$supported_ftypes = split("[ \n]", variable_get('tripal_feature_type_setting', 'gene mRNA EST contig'));
foreach ($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";
$org_rset = chado_query($sql);
//
$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";
$result = db_fetch_object(chado_query($sql, $node->uniquename, $node->organism_id, $node->feature_type, $node->feature_id));
if ($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'";
$result = db_fetch_object(chado_query($sql, $node->uniquename, $node->organism_id, $node->feature_type));
if ($result) {
form_set_error('uniquename', t("Feature insert cannot proceed. The feature name '$node->uniquename' already exists for this organism. Please provide a unique name for this feature."));
}
}
// we don't allow a genbank accession number for a contig
if ($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', $values);
if (strcmp($feature->name, $feature->uniquename)==0) {
$node->title = $feature->name . " (" . $feature->type_id->name . ") " . $feature->organism_id->genus . " " . $feature->organism_id->species ;
}
$additions = new stdClass();
$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";
$organism = db_fetch_object(chado_query($sql, $organism_id));
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 ";
$results = chado_query($sql, $feature_id);
$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";
$results = chado_query($sql, $feature_id);
$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 ";
$results = chado_query($sql, $feature_id);
$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 ";
}
$flresults = chado_query($sql, $feature_id);
// 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
$results = chado_query($sql, $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 = %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 $relationships;
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_get_aggregate_relationships($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;
$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.
$sql = "SELECT substring(residues from %d for %d) as residues ".
"FROM {feature} ".
"WHERE feature_id = %d";
$floc_sequences = array();
foreach ($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;
$sequence = db_fetch_object(chado_query($sql, $featureloc->fmin + 1, ($featureloc->fmax - $featureloc->fmin), $featureloc->srcfeature_id->feature_id));
$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 feature F3 on FL2.srcfeature_id = F3.feature_id ".
" INNER JOIN cvterm CVT2 on F2.type_id = CVT2.cvterm_id ".
"WHERE F1.feature_id = %d and NOT F3.feature_id = %d ".
" AND (CVT2.name = 'match' or CVT2.name like '%_match') ".
"ORDER BY FL1.fmin";
$results = chado_query($sql, $feature->feature_id, $feature->feature_id);
// iterate through the results and add them to our featurelocs array
$featurelocs = array();
while ($fl = db_fetch_object($results)) {
$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", $temp);
foreach ($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) {
$names[] = rtrim($temp2[1]);
}
else {
$names[] = $feature_type;
}
$where .= "OFC.feature_type = '%s' OR \n";
}
if ($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 = %d
ORDER BY num_features desc
";
$args[] = $organism->organism_id;
$org_features = chado_query($sql, $args);
// iterate through the types
$types = array();
while ($type = db_fetch_object($org_features)) {
$types[$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' => $names, 'enabled' => TRUE );
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_load_organism_feature_browser($organism) {
if (!$organism) {
return array();
}
// 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_browser_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 ";
}
$where_cvt = drupal_substr($where_cvt, 0, drupal_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' => $pager, 'enabled' => TRUE );
}
/**
* This generates the Feature Browser which can optionally be included on library pages
* and shows all features belonging to the given library. This Browse can be shown/hidden
* on the Feature Configuration page.
*
* @ingroup tripal_feature
*/
function tripal_feature_load_library_feature_browser($library) {
// 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
$show_browser = variable_get('tripal_library_feature_browse_setting', 'show_feature_browser');
if (strcmp($show_browser, 'show_feature_browser')!=0) {
return array('enabled' => FALSE);
}
// get a list of feature types to include in the browser
$allowed_types = variable_get('chado_browser_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 ";
}
$where_cvt = drupal_substr($where_cvt, 0, drupal_strlen($where_cvt)-3); # strip trailing 'OR'
// get the features for this library
$sql = "SELECT F.name,F.feature_id,F.uniquename,CVT.name as cvname ".
"FROM {feature} F ".
" INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id ".
" INNER JOIN {library_feature} LF on F.feature_id = LF.feature_id ".
" INNER JOIN {library} L on LF.library_id = L.library_id ".
"WHERE LF.library_id = %d and ($where_cvt) ".
"ORDER BY feature_id ASC";
// the counting SQL
$csql = "SELECT count(*) ".
"FROM {feature} F".
" INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id ".
" INNER JOIN {library_feature} LF on F.feature_id = LF.feature_id ".
" INNER JOIN {library} L on LF.library_id = L.library_id ".
"WHERE LF.library_id = %d and ($where_cvt) ".
"GROUP BY L.library_id ";
$previous_db = tripal_db_set_active('chado'); // use chado database
$org_features = pager_query($sql, 10, 0, $csql, $library->library_id);
tripal_db_set_active($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' => $pager, 'enabled' => TRUE );
}
/**
* This generates the Feature Browse which can optionally be included on library pages
* and shows all features belonging to the given library. This Browse can be shown/hidden
* on the Feature Configuration page.
*
* @ingroup tripal_feature
*/
function tripal_feature_load_analysis_feature_browser($analysis) {
// 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
$show_browser = variable_get('tripal_analysis_feature_browse_setting', 'show_feature_browser');
if (strcmp($show_browser, 'show_feature_browser')!=0) {
return array('enabled' => FALSE);
}
// get a list of feature types to include in the browser
$allowed_types = variable_get('chado_browser_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 ";
}
$where_cvt = drupal_substr($where_cvt, 0, drupal_strlen($where_cvt)-3); # strip trailing 'OR'
// get the features for this library
$sql = "SELECT F.name,F.feature_id,F.uniquename,CVT.name as cvname ".
"FROM {feature} F ".
" INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id ".
" INNER JOIN {analysisfeature} AF on F.feature_id = AF.feature_id ".
" INNER JOIN {analysis} A on AF.analysis_id = A.analysis_id ".
"WHERE A.analysis_id = %d and ($where_cvt) ".
"ORDER BY feature_id ASC";
// the counting SQL
$csql = "SELECT count(*) ".
"FROM {feature} F".
" INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id ".
" INNER JOIN {analysisfeature} AF on F.feature_id = AF.feature_id ".
" INNER JOIN {analysis} A on AF.analysis_id = A.analysis_id ".
"WHERE A.analysis_id = %d and ($where_cvt) ".
"GROUP BY A.analysis_id ";
$previous_db = tripal_db_set_active('chado'); // use chado database
$org_features = pager_query($sql, 10, 0, $csql, $analysis->analysis_id);
tripal_db_set_active($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, $b->fmin);
}
/**
* used to sort the list of relationship parts by start position
*
* @ingroup tripal_feature
*/
function tripal_feature_sort_rel_parts_by_start($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.
$ends = array();
foreach ($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 $newseq;
}
/**
* This function customizes the view of the chado_feature node. It allows
* us to generate the markup.
*
* @ingroup tripal_feature
*/
function chado_feature_view($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;
}
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_terms' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_feature_terms',
),
'tripal_feature_alignments' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_feature_alignments',
),
'tripal_feature_relationships' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_feature_relationships',
),
'tripal_feature_edit_ALL_properties_form' => array(
'arguments' => array('form' => NULL),
'function' => 'theme_tripal_feature_edit_ALL_properties_form',
),
);
}
/**
*
*
* @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;
// expand the feature object to include the feature relationships.
$options = array(
'return_array' => 1,
'order_by' => array('rank' => 'ASC'),
);
$feature = tripal_core_expand_chado_vars($feature, 'table',
'feature_relationship', $options);
// get the subject relationships
$srelationships = $feature->feature_relationship->subject_id;
$orelationships = $feature->feature_relationship->object_id;
// get alignment as child. The $feature->featureloc element
// is already populated from the alignment preprocess function
$feature = tripal_core_expand_chado_vars($feature, 'table', 'featureloc');
$cfeaturelocs = $feature->featureloc->feature_id;
if (!$cfeaturelocs) {
$cfeaturelocs = array();
}
elseif (!is_array($cfeaturelocs)) {
$cfeaturelocs = array($cfeaturelocs);
}
// prepare the SQL statement to get the featureloc for the
// feature in the relationships.
$connection = tripal_db_persistent_chado();
$psql = "
PREPARE sel_featureloc_preprocess_relationships (int, int) AS
SELECT
FL.featureloc_id, F.name as srcfeature_name, FL.srcfeature_id,
FL.feature_id, FL.fmin, FL.fmax, FL.strand, FL.phase
FROM featureloc FL
INNER JOIN feature F ON F.feature_id = FL.srcfeature_id
WHERE FL.feature_id = $1 and FL.srcfeature_id = $2
";
tripal_core_chado_prepare('sel_featureloc_preprocess_relationships', $psql, array('int', 'int'));
// combine both object and subject relationshisp into a single array
$relationships = array();
$relationships['object'] = array();
$relationships['subject'] = array();
// iterate through the object relationships
if ($orelationships) {
foreach ($orelationships as $relationship) {
$rel = new stdClass();
// get locations where the child feature and this feature overlap with the
// same landmark feature.
$rel->child_featurelocs = array();
foreach ($cfeaturelocs as $featureloc) {
$res = chado_query("EXECUTE sel_featureloc_preprocess_relationships (%d, %d)",
$relationship->subject_id->feature_id,
$featureloc->srcfeature_id->feature_id);
while ($loc = db_fetch_object($res)) {
// add in the node id of the src feature if it exists and save this location
$loc->nid = $featureloc->srcfeature_id->nid;
$rel->child_featurelocs[] = $loc;
}
}
$rel->record = $relationship;
// get the relationship and child types
$rel_type = t(preg_replace('/_/', " ", $relationship->type_id->name));
$child_type = $relationship->subject_id->type_id->name;
// get the node id of the subject
$sql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d";
$n = db_fetch_object(db_query($sql, $relationship->subject_id->feature_id));
if ($n) {
$rel->record->nid = $n->nid;
}
if (!array_key_exists($rel_type, $relationships['object'])) {
$relationships['object'][$rel_type] = array();
}
if (!array_key_exists($child_type, $relationships['object'][$rel_type])) {
$relationships['object'][$rel_type][$child_type] = array();
}
$relationships['object'][$rel_type][$child_type][] = $rel;
}
}
// now add in the subject relationships
if ($srelationships) {
foreach ($srelationships as $relationship) {
$rel = new stdClass();
// get locations where this feature overlaps with the parent
$rel->parent_featurelocs = array();
foreach ($cfeaturelocs as $featureloc) {
$res = chado_query("EXECUTE sel_featureloc_preprocess_relationships (%d, %d)",
$relationship->object_id->feature_id,
$featureloc->srcfeature_id->feature_id);
while ($loc = db_fetch_object($res)) {
// add in the node id of the src feature if it exists and save this location
$loc->nid = $featureloc->srcfeature_id->nid;
$rel->parent_featurelocs[] = $loc;
}
}
$rel->record = $relationship;
$rel_type = t(preg_replace('/_/', " ", $relationship->type_id->name));
$parent_type = $relationship->object_id->type_id->name;
// get the node id of the subject
$sql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d";
$n = db_fetch_object(db_query($sql, $relationship->object_id->feature_id));
if ($n) {
$rel->record->nid = $n->nid;
}
if (!array_key_exists($rel_type, $relationships['subject'])) {
$relationships['subject'][$rel_type] = array();
}
if (!array_key_exists($child_type, $relationships['subject'][$rel_type])) {
$relationships['subject'][$rel_type][$parent_type] = array();
}
$relationships['subject'][$rel_type][$parent_type][] = $rel;
}
}
$feature->all_relationships = $relationships;
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_preprocess_tripal_feature_alignments(&$variables) {
// we want to provide a new variable that contains the matched features.
$feature = $variables['node']->feature;
$feature = tripal_core_expand_chado_vars($feature, 'table', 'featureloc');
// get alignments as child
$cfeaturelocs = $feature->featureloc->feature_id;
if (!$cfeaturelocs) {
$cfeaturelocs = array();
}
elseif (!is_array($cfeaturelocs)) {
$cfeaturelocs = array($cfeaturelocs);
}
// get alignment as parent
$pfeaturelocs = $feature->featureloc->srcfeature_id;
if (!$pfeaturelocs) {
$pfeaturelocs = array();
}
elseif (!is_array($pfeaturelocs)) {
$pfeaturelocs = array($pfeaturelocs);
}
// get matched alignments (those with an itermediate 'match' or 'EST_match', etc
$mfeaturelocs = tripal_feature_get_matched_alignments($feature);
$feature->matched_featurelocs = tripal_feature_get_matched_alignments($feature);
// 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)$/', $featureloc->feature_id->type_id->name)) {
continue;
}
$alignment = new stdClass();
$alignment->record = $featureloc;
$alignment->name = $featureloc->feature_id->name;
$alignment->nid = $featureloc->feature_id->nid;
$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[] = $alignment;
}
foreach ($cfeaturelocs as $featureloc) {
// if type is a 'match' then ignore it. We will handle those below
if (preg_match('/(^match$|^.*?_match)$/', $featureloc->feature_id->type_id->name)) {
continue;
}
$alignment = new stdClass();
$alignment->record = $featureloc;
$alignment->name = $featureloc->srcfeature_id->name;
$alignment->nid = $featureloc->srcfeature_id->nid;
$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[] = $alignment;
}
// in matching features, the left feature is always the feature
// provided to this function.
foreach ($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->nid = $rfeature->nid;
$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;
}
$feature->all_featurelocs = $alignments;
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_preprocess_tripal_organism_feature_counts(&$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);
}
/**
* Preprocessor function for the Library Feature Browser
*
* @ingroup tripal_feature
*/
function tripal_feature_preprocess_tripal_library_feature_browser(&$variables) {
$library = $variables['node']->library;
$library->feature_browser = tripal_feature_load_library_feature_browser($library);
}
/**
* Preprocessor function for the Analysis Feature Browser
*
* @ingroup tripal_feature
*/
function tripal_feature_preprocess_tripal_analysis_feature_browser(&$variables) {
$analysis = $variables['node']->analysis;
$analysis->feature_browser = tripal_feature_load_analysis_feature_browser($analysis);
}
/**
*
*
* @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 $options;
}
/**
* This function is an extension of the chado_feature_view by providing
* the markup for the feature object THAT WILL BE INDEXED.
*
* @ingroup tripal_feature
*/
function theme_tripal_feature_search_index($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";
$feature = db_fetch_object(chado_query($sql));
// 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 ";
$library = db_fetch_object(chado_query($sql, $feature_id));
$tags["$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 ";
$results = chado_query($sql);
$analysis_terms = array();
while ($analysis=db_fetch_object($results)) {
$tags2["$an_vid"] = "$analysis->name";
$terms['tags'] = $tags2;
taxonomy_node_save($node, $terms);
}
}
}
/**
*
* Remove orphaned drupal nodes
*
* @param $dummy
* Not Used -kept for backwards compatibility
* @param $job_id
* The id of the tripal job executing this function
*
* @ingroup tripal_feature
*/
function tripal_features_cleanup($dummy = NULL, $job_id = NULL) {
return tripal_core_clean_orphaned_nodes('feature', $job_id);
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_feature_return_fasta($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 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";
$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;
$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'] = $args[13];
}
if ($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) {
$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 chado_feature CF on CF.feature_id = F.feature_id
WHERE
F.uniquename = '%s' or
F.name = '%s' or
S.name = '%s'
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, $id, $id, $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 = db_fetch_object($results)) {
$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(url("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;
}