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='

' . t("Displays links to nodes created on this date") . '

'; 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', 'administer tripal features', ); } /** * Implement hook_access(). * * This hook allows node modules to limit access to the node types they define. * * @param $op * The operation to be performed * * @param $node * The node on which the operation is to be performed, or, if it does not yet exist, the * type of node to be created * * @param $account * A user object representing the user for whom the operation is to be performed * * @return * If the permission for the specified operation is not set then return FALSE. If the * permission is set then return NULL as this allows other modules to disable * access. The only exception is when the $op == 'create'. We will always * return TRUE if the permission is set. * * @ingroup tripal_feature */ function chado_feature_access($op, $node, $account) { if ($op == 'create') { if (!user_access('create chado_feature content', $account)) { return FALSE; } return TRUE; } if ($op == 'update') { if (!user_access('edit chado_feature content', $account)) { return FALSE; } } if ($op == 'delete') { if (!user_access('delete chado_feature content', $account)) { return FALSE; } } if ($op == 'view') { if (!user_access('access chado_feature content', $account)) { return FALSE; } } return NULL; } /** * Menu items are automatically added for the new node types created * by this module to the 'Create Content' Navigation menu item. This function * adds more menu items needed for this module. * * @ingroup tripal_feature */ function tripal_feature_menu() { $items = array(); // the administative settings menu $items['find/sequences'] = array( 'title' => 'Sequence Retrieval', 'description' => 'Download a file of sequences', 'page callback' => 'tripal_feature_seq_extract_page', 'access arguments' => array('access chado_feature content'), 'type' => MENU_CALLBACK, ); $items['find/sequences/ajax'] = array( 'title' => 'Sequence Retrieval', 'page callback' => 'tripal_feature_seq_extract_form_ahah_update', 'access arguments' => array('access chado_feature content'), 'type' => MENU_CALLBACK, ); // the administative settings menu $items['admin/tripal/tripal_feature'] = array( 'title' => 'Features', 'description' => 'Basic Description of Tripal Organism Module Functionality', 'page callback' => 'theme', 'page arguments' => array('tripal_feature_admin'), 'access arguments' => array('administer tripal features'), 'type' => MENU_NORMAL_ITEM, ); $items['admin/tripal/tripal_feature/configuration'] = array( 'title' => 'Configuration', 'description' => 'Configure the Tripal Feature module.', 'page callback' => 'drupal_get_form', 'page arguments' => array('tripal_feature_admin'), 'access arguments' => array('administer tripal features'), 'type' => MENU_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 tripal features'), '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('administer tripal features'), '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('administer tripal features'), '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('administer tripal features'), 'type' => MENU_NORMAL_ITEM, ); // the menu link for addressing any feature (by name, uniquename, synonym) $items['feature/%'] = array( 'page callback' => 'tripal_feature_match_features_page', 'page arguments' => array(1), 'access arguments' => array('access chado_feature content'), 'type' => MENU_LOCAL_TASK, ); return $items; } /** * We need to let drupal know about our theme functions and their arguments. * We create theme functions to allow users of the module to customize the * look and feel of the output generated in this module * * @ingroup tripal_feature */ function tripal_feature_theme() { 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_proteins' => array( 'arguments' => array('node' => NULL), 'template' => 'tripal_feature_proteins', ), 'tripal_feature_synonyms' => array( 'arguments' => array('node' => NULL), 'template' => 'tripal_feature_synonyms', ), 'tripal_feature_phenotypes' => array( 'arguments' => array('node' => NULL), 'template' => 'tripal_feature_phenotypes', ), 'tripal_feature_featurepos' => array( 'arguments' => array('node' => NULL), 'template' => 'tripal_feature_featurepos', ), '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', ), 'tripal_feature_admin' => array( 'template' => 'tripal_feature_admin', 'arguments' => array(NULL), 'path' => drupal_get_path('module', 'tripal_feature') . '/theme' ), // themed forms 'tripal_feature_seq_extract_form' => array( 'arguments' => array('form'), ) ); } /** * * * @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) { // separate synomys by carriage returns $synonyms = preg_replace("/[\n\r]+/", " ", $synonyms); // split the synonyms into an array based on a space as the delimieter $syn_array = array(); $syn_array = explode(" ", $synonyms); // remove any old synonyms $feature_syn_dsql = "DELETE FROM {feature_synonym} WHERE feature_id = %d"; if (!chado_query($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.'), '#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.'), '#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.'), '#maxlength' => 255 ); // get the sequence ontology CV ID $values = array('name' => 'sequence'); $cv = tripal_core_chado_select('cv', array('cv_id'), $values); $cv_id = $cv[0]->cv_id; $form['feature_type'] = array( '#title' => t('Feature Type'), '#type' => 'textfield', '#description' => t("Choose the feature type."), '#required' => TRUE, '#default_value' => $feature->type_id->name, '#autocomplete_path' => "admin/tripal/tripal_cv/cvterm/auto_name/$cv_id", ); // 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' => $organisms, ); // Get synonyms if ($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 each on different lines.'), ); $form['residues']= array( '#type' => 'textarea', '#title' => t('Residues'), '#required' => FALSE, '#default_value' => $feature->residues, '#description' => t('Enter the nucelotide sequences for this feature'), ); $checked = ''; if ($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.'), ); return $form; } /** * * * @ingroup tripal_feature */ function chado_feature_validate($node) { $result = 0; // make sure the feature type is a real sequence ontology term $type = tripal_cv_get_cvterm_by_name($node->feature_type, NULL, 'sequence'); if (!$type) { form_set_error('feature_type', t("The feature type is not a valid name from the Sequence Ontology.")); } // if this is an update, we want to make sure that a different feature for // the organism doesn't already have this uniquename. We don't want to give // two sequences the same uniquename if ($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); // by default, the titles are saved using the unique constraint. We will // keep it the same, but remove the duplicate name if the unique name and name // are identical $title_type = variable_get('chado_feature_title', 'unique_constraint'); if($title_type == 'unique_constraint') { if (strcmp($feature->name, $feature->uniquename)==0) { $node->title = $feature->name . " (" . $feature->type_id->name . ") " . $feature->organism_id->genus . " " . $feature->organism_id->species ; } // in previous version of Tripal, the feature title was simply the unique name. // so, we recreate the title just to be sure all of our feature pages are consistent else { $node->title = $feature->name . ", " . $feature->uniquename . " (" . $feature->type_id->name . ") " . $feature->organism_id->genus . " " . $feature->organism_id->species ; } } // set the title to be the feature name or uniquename as configured if($title_type == 'feature_name') { $node->title = $feature->name; } if($title_type == 'feature_unique_name') { $node->title = $feature->uniquename; } $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 == $depth) { return NULL; } // first get the relationships for this feature return tripal_feature_load_relationships($feature_id, 'as_object'); } /** * * * @ingroup tripal_feature */ function tripal_feature_load_featureloc_sequences($feature_id, $featurelocs) { // if we don't have any featurelocs then no point in continuing if (!$featurelocs) { return array(); } // get the list of relationships (including any aggregators) and iterate // through each one to find information needed to color-code the reference sequence $relationships = tripal_feature_get_aggregate_relationships($feature_id); if (!$relationships) { return array(); } // iterate through each of the realtionships features and get their // locations foreach ($relationships as $rindex => $rel) { // get the featurelocs for each of the relationship features $rel_featurelocs = tripal_feature_load_featurelocs($rel->subject_id, 'as_child', 0); foreach ($rel_featurelocs as $rfindex => $rel_featureloc) { // keep track of this unique source feature $src = $rel_featureloc->src_feature_id ."-". $rel_featureloc->src_cvterm_id; // copy over the results to the relationship object. Since there can // be more than one feature location for each relationship feature we // use the '$src' variable to keep track of these. $rel->featurelocs = new stdClass(); $rel->featurelocs->$src = new stdClass(); $rel->featurelocs->$src->src_uniquename = $rel_featureloc->src_uniquename; $rel->featurelocs->$src->src_cvterm_id = $rel_featureloc->src_cvterm_id; $rel->featurelocs->$src->src_cvname = $rel_featureloc->src_cvname; $rel->featurelocs->$src->fmin = $rel_featureloc->fmin; $rel->featurelocs->$src->fmax = $rel_featureloc->fmax; $rel->featurelocs->$src->src_name = $rel_featureloc->src_name; // keep track of the individual parts for each relationship $start = $rel->featurelocs->$src->fmin; $end = $rel->featurelocs->$src->fmax; $type = $rel->subject_type; $rel_locs[$src]['parts'][$start][$type]['start'] = $start; $rel_locs[$src]['parts'][$start][$type]['end'] = $end; $rel_locs[$src]['parts'][$start][$type]['type'] = $type; } } // the featurelocs array provided to the function contains the locations // where this feature is found. We want to get the sequence for each // location and then annotate it with the parts found from the relationships // locations determiend above. $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 {cvterm} CVT2 on F2.type_id = CVT2.cvterm_id ". "WHERE F1.feature_id = %d " . " AND (CVT2.name = 'match' or CVT2.name like '%_match') ". "ORDER BY FL1.fmin"; $results = chado_query($sql, $feature->feature_id); // iterate through the results and add them to our featurelocs array $featurelocs = array(); while ($fl = db_fetch_object($results)) { // ignore featurelocs where the left and right srcfeature is the same if (strcmp($fl->left_srcfeature_id, $fl->right_srcfeature_id) == 0) { continue; } $featurelocs[] = $fl ; } return $featurelocs; } /** * * * @ingroup tripal_feature */ function tripal_feature_load_organism_feature_counts($organism) { // don't show the browser if the settings in the admin page is turned off // instead return the array indicating the status of the browser $show_counts = variable_get('tripal_feature_summary_setting', 'show_feature_summary'); if (strcmp($show_counts, 'show_feature_summary')!=0) { return array('enabled' => FALSE ); } $args = array(); $names = array(); $order = array(); // build the where clause for the SQL statement if we have a custom term list // we'll also keep track of the names the admin provided (if any) and the // order that the terms should appear. $is_custom = 0; $temp = rtrim(variable_get('tripal_feature_summary_report_mapping', '')); $where = ''; if ($temp) { $is_custom = 1; $temp = explode("\n", $temp); foreach ($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); // perform the query $values = array( 'organism_id' => $organism->organism_id, 'type_id' => array( 'name' => $so_terms ), ); $columns = array('feature_id', 'name', 'uniquename', 'type_id'); $options = array( 'pager' => array('limit' => 10, 'element' => 0), 'order_by' => array('name' => 'ASC'), ); $features = tripal_core_chado_select('feature', $columns, $values, $options); $pager = theme('pager'); // add the node ids and types $nsql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d"; $tsql = "SELECT name FROM {cvterm} WHERE cvterm_id = %d"; foreach ($features as $feature) { $node = db_fetch_object(db_query($nsql, $feature->feature_id)); $type = db_fetch_object(chado_query($tsql, $feature->type_id)); $feature->nid = $node->nid; $feature->type_name = $type->name; } 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; } } $newseq .= "
Legend: "; foreach ($types as $type_name => $present) { $newseq .= "$type_name"; } $newseq .= "
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 .= "
";
  $newseq .= ">$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 .= "";
        }
      }
      $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 .= "";
      // 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 .= "";
      }
    }
    $pos++;
  }

  $newseq .= "
"; 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) { // set the title to ensure it is always unique case 'presave': switch ($node->type) { case 'chado_feature': $values = array('organism_id' => $node->organism_id); $organism = tripal_core_chado_select('organism', array('genus','species'), $values); $node->title = $node->fname . ', ' . $node->uniquename . ' (' . $node->feature_type . ') ' . $organism[0]->genus . ' ' . $organism[0]->species; break; } break; // set the URL path after inserting. We do it here because we do not // know the feature_id in the presave case 'insert': switch ($node->type) { case 'chado_feature': if (!$node->feature_id) { $sql = "SELECT * FROM {chado_feature} WHERE nid = %d"; $chado_feature = db_fetch_object(db_query($sql, $node->nid)); $node->feature_id = $chado_feature->feature_id; } // remove any previous alias db_query("DELETE FROM {url_alias} WHERE src = '%s'", "node/$node->nid"); // set the URL for this feature page $url_alias = tripal_feature_get_feature_url($node); path_set_alias("node/$node->nid", $url_alias); break; } break; // set the URL path after inserting. We do it here because we do not // know the feature_id in the presave case 'update': switch ($node->type) { case 'chado_feature': // remove any previous alias db_query("DELETE FROM {url_alias} WHERE src = '%s'", "node/$node->nid"); // set the URL for this feature page $url_alias = tripal_feature_get_feature_url($node); path_set_alias("node/$node->nid", $url_alias); break; } break; // add items to other nodes, build index and search results case 'view': switch ($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', $node), ); } break; } break; } } /** * * * @ingroup tripal_feature */ function tripal_feature_preprocess_tripal_feature_relationships(&$variables) { // we want to provide a new variable that contains the matched features. $feature = $variables['node']->feature; if (!$feature->all_relationships) { $feature->all_relationships = tripal_feature_get_feature_relationships($feature); } } /** * * * @ingroup tripal_feature */ function tripal_feature_preprocess_tripal_feature_proteins(&$variables) { // we want to provide a new variable that contains the matched features. $feature = $variables['node']->feature; if (!$feature->all_relationships) { $feature->all_relationships = tripal_feature_get_feature_relationships($feature); } } /** * * * @ingroup tripal_feature */ function tripal_feature_preprocess_tripal_feature_alignments(&$variables) { // we want to provide a new variable that contains the matched features. $feature = $variables['node']->feature; $feature = tripal_core_expand_chado_vars($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 = mfeaturelocs; // combine all three alignments into a single array for printing together in // a single list $alignments = array(); foreach ($pfeaturelocs as $featureloc) { // if type is a 'match' then ignore it. We will handle those below if (preg_match('/(^match$|^.*?_match|match_part)$/', $featureloc->feature_id->type_id->name)) { continue; } $alignment = new stdClass(); $alignment->record = $featureloc; $alignment->name = $featureloc->feature_id->name; $alignment->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|match_part)$/', $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; } /** * * * @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($vocab->vid); } } } /** * * * @ingroup tripal_feature */ function tripal_feature_return_fasta($feature, $desc) { $fasta = ">" . variable_get('chado_feature_accession_prefix', 'FID') . "$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]; $new_args['Create Organism'] = ($args[14] == 1) ? "Yes" : "No"; } if ($callback == 'tripal_feature_sync_features') { if ($args[0]) { $organism = tripal_core_chado_select('organism', array('genus', 'species'), array('organism_id' => $args[0])); $new_args['Organism'] = $organism[0]->genus . " " . $organism[0]->species; } else { $new_args['Organism'] = ''; } $new_args['Feature Types'] = $args[1]; } return $new_args; } /** * Implements hook_coder_ignore(). * Defines the path to the file (tripal_core.coder_ignores.txt) where ignore rules for coder are stored */ function tripal_feature_coder_ignore() { return array( 'path' => drupal_get_path('module', 'tripal_feature'), 'line prefix' => drupal_get_path('module', 'tripal_feature'), ); } /* * Uses the value provided in the $id argument to find all features that match * that ID by name, featurename or synonym. If it matches uniquenly to a single * feature it will redirect to that feature page, otherwise, a list of matching * features is shown. */ function tripal_feature_match_features_page($id) { // if the URL alias configuration is set such that the URL // always begins with 'feature' then we want to use the ID as it is and // forward it on. Otherwise, try to find the matching feature. $url_alias = variable_get('chado_feature_url_string', '/feature/[genus]/[species]/[type]/[uniquename]'); if (!$url_alias) { $url_alias = '/feature/[genus]/[species]/[type]/[uniquename]'; } $url_alias = preg_replace('/^\//', '', $url_alias); // remove any preceeding forward slash if (preg_match('/^feature\//', $url_alias)) { drupal_goto($id); } $sql = " SELECT F.name, F.uniquename, F.feature_id, O.genus, O.species, O.organism_id, CVT.cvterm_id, CVT.name as type_name, CF.nid, array_agg(S.name) as synonyms FROM {feature} F INNER JOIN {organism} O on F.organism_id = O.organism_id INNER JOIN {cvterm} CVT on CVT.cvterm_id = F.type_id LEFT JOIN {feature_synonym} FS on FS.feature_id = F.feature_id LEFT JOIN {synonym} S on S.synonym_id = FS.synonym_id INNER JOIN public.chado_feature CF on CF.feature_id = F.feature_id WHERE F.uniquename = '%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, "nid) ."\">" . $match->name . "", $match->type_name, '' . $match->genus . ' ' . $match->species . '', $synonyms, ); $num_matches++; } // if we have more than one match then generate the table, otherwise, redirect // to the matched feature if ($num_matches == 1) { drupal_goto("node/" . $curr_match->nid); } if ($num_matches == 0) { return "

No features matched the given name '$id'

"; } $table_attrs = array( 'class' => 'tripal-table tripal-table-horz' ); $output = "

The following features match the name '$id'.

"; $output .= theme_table($header, $rows, $table_attrs, $caption); return $output; } /** * * @param unknown_type $form * @param unknown_type $form_state * @param unknown_type $form_id */ function tripal_feature_form_alter(&$form, &$form_state, $form_id) { if ($form_id == "tripal_feature_seq_extract_form") { // updating the form through the ahah callback sets the action of // the form to the ahah callback URL. We need to set it back // to the normal form URL $form['#action'] = url("find/sequences"); } }