' . 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 $nodes; } /** * Set the permission types that the chado module uses. Essentially we * want permissionis that protect creation, editing and deleting of chado * data objects * * @ingroup tripal_feature */ function tripal_feature_perm() { return array( 'access chado_feature content', 'create chado_feature content', 'delete chado_feature content', 'edit chado_feature content', 'manage chado_feature aggregator', ); } /** * Set the permission types that the module uses. * * @ingroup tripal_feature */ function chado_feature_access($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, ); // managing relationship aggregates $items['admin/tripal/tripal_feature/aggregate'] = array( 'title' => 'Feature Relationship Aggegators', 'description' => 'Features have relationships with other features and it may be desirable to aggregate the content from one ore more child or parent feature.', 'page callback' => 'tripal_feature_aggregator_page', 'access arguments' => array('manage chado_feature aggregator'), 'type' => MENU_NORMAL_ITEM, ); $items['admin/tripal/tripal_feature/aggregate/new'] = array( 'title' => 'Add an Aggregator', 'page callback' => 'drupal_get_form', 'page arguments' => array('tripal_feature_aggregator_form'), 'access arguments' => array('manage chado_feature aggregator'), 'type' => MENU_NORMAL_ITEM, ); $items['admin/tripal/tripal_feature/aggregate/edit/js'] = array( 'title' => 'Edit an Aggegator', 'page callback' => 'tripal_feature_aggregator_ajax_edit', 'access arguments' => array('manage chado_feature aggregator'), 'type' => MENU_CALLBACK, ); return $items; } /** * Implements Menu wildcard_load hook * Purpose: Allows the node ID of a chado feature to be dynamically * pulled from the path. The node is loaded from this node ID * and supplied to the page as an arguement * * @ingroup tripal_feature */ function tf_node_load($nid) { if (is_numeric($nid)) { $node = node_load($nid); if ($node->type == 'chado_feature') { return $node; } } return FALSE; } /** * * * @ingroup tripal_feature */ function tripal_feature_block($op = 'list', $delta = 0, $edit=array()) { switch ($op) { case 'list': $blocks['references']['info'] = t('Tripal Feature References'); $blocks['references']['cache'] = BLOCK_NO_CACHE; $blocks['base']['info'] = t('Tripal Feature Details'); $blocks['base']['cache'] = BLOCK_NO_CACHE; $blocks['sequence']['info'] = t('Tripal Feature Sequence'); $blocks['sequence']['cache'] = BLOCK_NO_CACHE; $blocks['synonyms']['info'] = t('Tripal Feature Synonyms'); $blocks['synonyms']['cache'] = BLOCK_NO_CACHE; $blocks['properties']['info'] = t('Tripal Feature Properties'); $blocks['properties']['cache'] = BLOCK_NO_CACHE;; $blocks['featureloc_sequences']['info'] = t('Tripal Formatted Sequence'); $blocks['featureloc_sequences']['cache'] = BLOCK_NO_CACHE; $blocks['alignments']['info'] = t('Tripal Feature Alignments'); $blocks['alignments']['cache'] = BLOCK_NO_CACHE; $blocks['object_relationships']['info'] = t('Tripal Feature Object Relationships'); $blocks['object_relationships']['cache'] = BLOCK_NO_CACHE; $blocks['subject_relationships']['info'] = t('Tripal Feature Subject Relationships'); $blocks['subject_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; $blocks['library_feature_browser']['info'] = t('Tripal Library Feature Browser'); $blocks['library_feature_browser']['cache'] = BLOCK_NO_CACHE; $blocks['analysis_feature_browser']['info'] = t('Tripal Analysis Feature Browser'); $blocks['analysis_feature_browser']['cache'] = BLOCK_NO_CACHE; return $blocks; case 'view': if (user_access('access chado_feature content') and arg(0) == 'node' and is_numeric(arg(1))) { $nid = arg(1); $node = node_load($nid); $block = array(); switch ($delta) { case 'references': $block['subject'] = t('References'); $block['content'] = theme('tripal_feature_references', $node); break; case 'base': $block['subject'] = t('Feature Details'); $block['content'] = theme('tripal_feature_base', $node); break; case 'synonyms': $block['subject'] = t('Synonyms'); $block['content'] = theme('tripal_feature_synonyms', $node); break; case 'properties': $block['subject'] = t('Properties'); $block['content'] = theme('tripal_feature_properties', $node); break;; case 'sequence': $block['subject'] = t('Sequence'); $block['content'] = theme('tripal_feature_sequence', $node); break; case 'featureloc_sequences': $block['subject'] = t('Formatted Sequences'); $block['content'] = theme('tripal_feature_featureloc_sequences', $node); break; case 'alignments': $block['subject'] = t('Alignments'); $block['content'] = theme('tripal_feature_alignments', $node); break; case 'object_relationships': $block['subject'] = t('Object Relationships'); $block['content'] = theme('tripal_feature_object_relationships', $node); break; case 'subject_relationships': $block['subject'] = t('Subject Relationships'); $block['content'] = theme('tripal_feature_object_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'; } $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) ); $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 ); } $values = array( 'organism_id' => $node->organism_id, 'uniquename' => $node->uniquename, 'type_id' => $type[0]->cvterm_id, ); $feature = tripal_core_chado_select('feature', array('feature_id'), $values); // add the genbank accession and synonyms chado_feature_add_synonyms($node->synonyms, $feature[0]->feature_id); // make sure the entry for this feature doesn't already exist in the chado_feature table // if it doesn't exist then we want to add it. $node_check_sql = "SELECT * FROM {chado_feature} " . "WHERE feature_id = '%s'"; $node_check = db_fetch_object(db_query($node_check_sql, $feature[0]->feature_id)); if (!$node_check) { // next add the item to the drupal table $sql = "INSERT INTO {chado_feature} (nid, vid, feature_id, sync_date) ". "VALUES (%d, %d, %d, " . time() . ")"; db_query($sql, $node->nid, $node->vid, $feature[0]->feature_id); } } /** * * * @ingroup tripal_feature */ function chado_feature_update($node) { if ($node->revision) { // TODO -- decide what to do about revisions } else { $residues = preg_replace("/[\n\r\s]/", "", $node->residues); $obsolete = 'FALSE'; if ($node->is_obsolete) { $obsolete = 'TRUE'; } // get the feature type id $values = array( 'cv_id' => array( 'name' => 'sequence' ), 'name' => $node->feature_type ); $type = tripal_core_chado_select('cvterm', array('cvterm_id'), $values); $feature_id = chado_get_id_for_node('feature', $node) ; if (sizeof($type) > 0) { $match = array( 'feature_id' => $feature_id, ); $values = array( 'organism_id' => $node->organism_id, 'name' => $node->fname, 'uniquename' => $node->uniquename, 'residues' => $residues, 'seqlen' => drupal_strlen($residues), 'is_obsolete' => $obsolete, 'type_id' => $type[0]->cvterm_id, 'md5checksum' => md5($residues) ); $status = tripal_core_chado_update('feature', $match, $values); // add the genbank synonyms chado_feature_add_synonyms($node->synonyms, $feature_id); } else { drupal_set_message(t('Unable to update feature.'), 'warning'); watchdog('tripal_feature', 'Update feature: Unable to update feature where values: %values', array('%values' => print_r($values, TRUE)), WATCHDOG_WARNING ); } } } /** * * * @ingroup tripal_feature */ function chado_feature_delete($node) { $feature_id = chado_get_id_for_node('feature', $node); // remove the drupal content $sql_del = "DELETE FROM {chado_feature} ". "WHERE nid = %d ". "AND vid = %d"; db_query($sql_del, $node->nid, $node->vid); $sql_del = "DELETE FROM {node} ". "WHERE nid = %d ". "AND vid = %d"; db_query($sql_del, $node->nid, $node->vid); $sql_del = "DELETE FROM {node_revisions} ". "WHERE nid = %d ". "AND vid = %d"; db_query($sql_del, $node->nid, $node->vid); // Remove data from feature tables of chado database. This will // cause a cascade delete and remove all data in referencing tables // for this feature $previous_db = tripal_db_set_active('chado'); db_query("DELETE FROM {feature} WHERE feature_id = %d", $feature_id); tripal_db_set_active($previous_db); drupal_set_message(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); // use the chado database $previous_db = tripal_db_set_active('chado'); // remove any old synonyms $feature_syn_dsql = "DELETE FROM {feature_synonym} WHERE feature_id = %d"; if (!db_query($feature_syn_dsql, $feature_id)) { $error .= "Could not remove synonyms from feature. "; } // return if we don't have any synonmys to add if (!$synonyms) { tripal_db_set_active($previous_db); return; } // iterate through each synonym and add it to the database foreach ($syn_array as $syn) { // skip this item if it's empty if (!$syn) { break; } // check to see if we have this accession number already in the database // if so then don't add it again. it messes up drupal if the insert fails. // It is possible for the accession number to be present and not the feature $synonym_sql = "SELECT synonym_id FROM {synonym} ". "WHERE name = '%s'"; $synonym = db_fetch_object(db_query($synonym_sql, $syn)); if (!$synonym) { $synonym_isql = "INSERT INTO {synonym} (name,synonym_sgml,type_id) ". "VALUES ('%s','%s', ". " (SELECT cvterm_id ". " FROM {CVTerm} CVT ". " INNER JOIN CV ON CVT.cv_id = CV.cv_id ". " WHERE CV.name = 'feature_property' and CVT.name = 'synonym'))"; if (!db_query($synonym_isql, $syn, $syn)) { $error .= "Could not add synonym. "; } // now get the synonym we just added $synonym_sql = "SELECT synonym_id FROM {synonym} ". "WHERE name = '%s'"; $synonym = db_fetch_object(db_query($synonym_sql, $syn)); } // now add in our new sysnonym $feature_syn_isql = "INSERT INTO {feature_synonym} (synonym_id,feature_id,pub_id) ". "VALUES (%d,%d,1)"; if (!db_query($feature_syn_isql, $synonym->synonym_id, $feature_id)) { $error .= "Could not add synonyms to feature. "; } } // return to the drupal database tripal_db_set_active($previous_db); return $error; } /** * * * @ingroup tripal_feature */ function chado_feature_add_gbaccession($accession, $feature_id) { // use chado database $previous_db = tripal_db_set_active('chado'); // remove any old accession from genbank dbEST $fdbxref_dsql = "DELETE FROM {feature_dbxref} ". "WHERE feature_id = %d and dbxref_id IN ". " (SELECT DBX.dbxref_id FROM {dbxref} DBX ". " INNER JOIN DB ON DB.db_id = DBX.db_id ". " INNER JOIN feature_dbxref FDBX ON DBX.dbxref_id = FDBX.dbxref_id ". " WHERE DB.name = 'DB:Genbank' and FDBX.feature_id = %d)"; if (!db_query($fdbxref_dsql, $feature_id, $feature_id)) { $error .= "Could not remove accession from feature. "; } // if we don't have an accession number to add then just return if (!$accession) { tripal_db_set_active($previous_db); return; } // get the db_id $db_sql = "SELECT db_id FROM {DB} ". "WHERE name = 'DB:Genbank_est'"; $db = db_fetch_object(db_query($db_sql)); // check to see if we have this accession number already in the database // if so then don't add it again. it messes up drupal if the insert fails. // It is possible for the accession number to be present and not the feature $dbxref_sql = "SELECT dbxref_id FROM {dbxref} ". "WHERE db_id = %d and accession = '%s'"; $dbxref = db_fetch_object(db_query($dbxref_sql, $db->db_id, $accession)); if (!$dbxref) { // add the accession number $dbxref_isql = "INSERT INTO {dbxref} (db_id,accession) ". " VALUES (%d, '%s') "; if (!db_query($dbxref_isql, $db->db_id, $accession)) { $error .= 'Could not add accession as a database reference '; } // get the dbxref_id for the just added accession number $dbxref_sql = "SELECT dbxref_id FROM {dbxref} ". "WHERE db_id = %d and accession = '%s'"; $dbxref = db_fetch_object(db_query($dbxref_sql, $db->db_id, $accession)); } // associate the accession number with the feature $feature_dbxref_isql = "INSERT INTO {feature_dbxref} (feature_id,dbxref_id) ". " VALUES (%d, %d) "; if (!db_query($feature_dbxref_isql, $feature_id, $dbxref->dbxref_id)) { $error .= 'Could not add feature database reference. '; } tripal_db_set_active($previous_db); return $error; } /** * * * @ingroup tripal_feature */ function chado_feature_form($node, $param) { $type = node_get_types('type', $node); $form = array(); $feature = $node->feature; // add the residues to the feature object $feature = tripal_core_expand_chado_vars($feature, 'field', 'feature.residues'); // if the node has synonyms then use that as the form may be returning // from an error. Otherwise try to find synonyms from the database $synonyms = $node->synonyms; $feature = tripal_core_expand_chado_vars($feature, 'table', 'feature_synonym'); $feature_synonyms = $feature->feature_synonym; if (!$synonyms) { if (!is_array($feature_synonyms)) { $synonyms = $feature_synonyms->synonym_id->name; } elseif (is_array($feature_synonyms)) { foreach ($feature_synonyms as $index => $synonym) { $synonyms .= $synonym->synonym_id->name . "\n"; } } } $analyses = $node->analyses; $references = $node->references; // We need to pass above variables for preview to show $form['feature'] = array( '#type' => 'value', '#value' => $feature ); // This field is read when previewing a node $form['synonyms'] = array( '#type' => 'value', '#value' => $synonyms ); // This field is read when previewing a node $form['analyses'] = array( '#type' => 'value', '#value' => $analyses ); // This field is read when previewing a node $form['references'] = array( '#type' => 'value', '#value' => $references ); // keep track of the feature id if we have one. If we do have one then // this would indicate an update as opposed to an insert. $form['feature_id'] = array( '#type' => 'value', '#value' => $feature->feature_id, ); $form['title']= array( '#type' => 'textfield', '#title' => t('Title'), '#required' => TRUE, '#default_value' => $node->title, '#description' => t('The title must be a unique identifier for this feature. It is recommended to use a combination of uniquename, organism and feature type in the title as this is guranteed to be unique.'), '#weight' => 1, '#maxlength' => 255 ); $form['uniquename']= array( '#type' => 'textfield', '#title' => t('Unique Feature Name'), '#required' => TRUE, '#default_value' => $feature->uniquename, '#description' => t('Enter a unique name for this feature. This name must be unique for the organism and feature type.'), '#weight' => 1, '#maxlength' => 255 ); $form['fname']= array( '#type' => 'textfield', '#title' => t('Feature Name'), '#required' => TRUE, '#default_value' => $feature->name, '#description' => t('Enter the name used by humans to refer to this feature.'), '#weight' => 1, '#maxlength' => 255 ); // get the list of supported feature types $ftypes = array(); $ftypes[''] = ''; $supported_ftypes = split("[ \n]", variable_get('tripal_feature_type_setting', 'gene mRNA EST contig')); foreach ($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"; $previous_db = tripal_db_set_active('chado'); // use chado database $org_rset = db_query($sql); tripal_db_set_active($previous_db); // now use drupal database // $organisms = array(); $organisms[''] = ''; while ($organism = db_fetch_object($org_rset)) { $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)"; } $form['organism_id'] = array( '#title' => t('Organism'), '#type' => t('select'), '#description' => t("Choose the organism with which this feature is associated"), '#required' => TRUE, '#default_value' => $feature->organism_id->organism_id, '#options' => $organisms, '#weight' => 3, ); // Get synonyms if ($synonyms) { if (is_array($synonyms)) { foreach ($synonyms as $synonym) { $syn_text .= "$synonym->name\n"; } } else { $syn_text = $synonyms; } } $form['synonyms']= array( '#type' => 'textarea', '#title' => t('Synonyms'), '#required' => FALSE, '#default_value' => $syn_text, '#description' => t('Enter alternate names (synonmys) for this feature to help in searching and identification. You may enter as many alternate names as needed separated by spaces or on different lines.'), '#weight' => 5, ); $form['residues']= array( '#type' => 'textarea', '#title' => t('Residues'), '#required' => FALSE, '#default_value' => $feature->residues, '#description' => t('Enter the nucelotide sequences for this feature'), '#weight' => 6 ); $checked = ''; if ($feature->is_obsolete == 't') { $checked = '1'; } $form['is_obsolete']= array( '#type' => 'checkbox', '#title' => t('Is Obsolete'), '#required' => FALSE, '#default_value' => $checked, '#description' => t('Check this box if this sequence should be retired and no longer included in further analysis.'), '#weight' => 8 ); return $form; } /** * * * @ingroup tripal_feature */ function chado_feature_validate($node) { $result = 0; // if this is an update, we want to make sure that a different feature for // the organism doesn't already have this uniquename. We don't want to give // two sequences the same uniquename if ($node->feature_id) { $sql = "SELECT * FROM {Feature} F INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id WHERE uniquename = '%s' AND organism_id = %d AND CVT.name = '%s' AND NOT feature_id = %d"; $previous_db = tripal_db_set_active('chado'); $result = db_fetch_object(db_query($sql, $node->uniquename, $node->organism_id, $node->feature_type, $node->feature_id)); tripal_db_set_active($previous_db); if ($result) { form_set_error('uniquename', t("Feature update cannot proceed. The feature name '$node->uniquename' is not unique for this organism. Please provide a unique name for this feature.")); } } // if this is an insert then we just need to make sure this name doesn't // already exist for this organism if it does then we need to throw an error else { $sql = "SELECT * FROM {Feature} F INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id WHERE uniquename = '%s' AND organism_id = %d AND CVT.name = '%s'"; $previous_db = tripal_db_set_active('chado'); $result = db_fetch_object(db_query($sql, $node->uniquename, $node->organism_id, $node->feature_type)); tripal_db_set_active($previous_db); if ($result) { form_set_error('uniquename', t("Feature insert cannot proceed. The feature name '$node->uniquename' already exists for this organism. Please provide a unique name for this feature.")); } } // we want to remove all characters except IUPAC nucleotide characters from the // the residues. however, residues are not required so if blank then we'll skip // this step if ($node->residues) { $residues = preg_replace("/[^\w]/", '', $node->residues); if (!preg_match("/^[ACTGURYMKSWBDHVN]+$/i", $residues)) { form_set_error('residues', t("The residues in feature $node->name contains more than the nucleotide IUPAC characters. Only the following characters are allowed: A,C,T,G,U,R,Y,M,K,S,W,B,D,H,V,N: '" . $residues . "'")); } } // we don't allow a genbank accession number for a contig if ($node->feature_type == 'contig' and $node->gbaccession) { form_set_error('gbaccession', t("Contigs cannot have a genbank accession number. Please change the feature type or remove the accession number")); } } /** * When a node is requested by the user this function is called to allow us * to add auxiliary data to the node object. * * @ingroup tripal_feature */ function chado_feature_load($node) { // get the feature details from chado $feature_id = chado_get_id_for_node('feature', $node); $values = array('feature_id' => $feature_id); $feature = tripal_core_generate_chado_var('feature', $values); $additions = 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"; $previous_db = tripal_db_set_active('chado'); // use chado database $organism = db_fetch_object(db_query($sql, $organism_id)); tripal_db_set_active($previous_db); // now use drupal database return $organism; } /** * * * @ingroup tripal_feature */ function tripal_feature_load_synonyms($feature_id) { $sql = "SELECT S.name ". "FROM {Feature_Synonym} FS ". " INNER JOIN {Synonym} S ". " ON FS.synonym_id = S.Synonym_id ". "WHERE FS.feature_id = %d ". "ORDER BY S.name "; $previous_db = tripal_db_set_active('chado'); // use chado database $results = db_query($sql, $feature_id); tripal_db_set_active($previous_db); // now use drupal database $synonyms = array(); $i=0; while ($synonym = db_fetch_object($results)) { $synonyms[$i++] = $synonym; } return $synonyms; } /** * * * @ingroup tripal_feature */ function tripal_feature_load_properties($feature_id) { $sql = "SELECT CVT.name as cvname, FS.type_id, FS.value, FS.rank, CVT.definition, CVT.is_obsolete, DBX.dbxref_id,DBX.accession,DB.name as dbname, DB.urlprefix, DB.description as db_description, DB.url FROM {featureprop} FS INNER JOIN {cvterm} CVT ON FS.type_id = CVT.cvterm_id INNER JOIN {dbxref} DBX ON CVT.dbxref_id = DBX.dbxref_id INNER JOIN {db} DB ON DB.db_id = DBX.db_id WHERE FS.feature_id = %d ORDER BY FS.rank ASC"; $previous_db = tripal_db_set_active('chado'); // use chado database $results = db_query($sql, $feature_id); tripal_db_set_active($previous_db); // now use drupal database $i=0; $properties = array(); while ($property = db_fetch_object($results)) { $properties[$i++] = $property; } return $properties; } /** * * * @ingroup tripal_feature */ function tripal_feature_load_references($feature_id) { $sql = "SELECT F.uniquename,F.Feature_id,DBX.accession,DB.description as dbdesc, ". " DB.db_id, DB.name as db_name, DB.urlprefix,DBX.dbxref_id ". "FROM {feature} F ". " INNER JOIN {feature_dbxref} FDBX on F.feature_id = FDBX.feature_id ". " INNER JOIN {dbxref} DBX on DBX.dbxref_id = FDBX.dbxref_id ". " INNER JOIN {db} on DB.db_id = DBX.db_id ". "WHERE F.feature_id = %d ". "ORDER BY DB.name "; $previous_db = tripal_db_set_active('chado'); // use chado database $results = db_query($sql, $feature_id); tripal_db_set_active($previous_db); // now use drupal database $references = array(); $i=0; while ($accession = db_fetch_object($results)) { $references[$i++] = $accession; } return $references; } /** * * * @ingroup tripal_feature */ function tripal_feature_load_featurelocs($feature_id, $side = 'as_parent', $aggregate = 1) { $sql = "SELECT F.name, F.feature_id, F.uniquename, FS.name as src_name, FS.feature_id as src_feature_id, FS.uniquename as src_uniquename, CVT.name as cvname, CVT.cvterm_id, CVTS.name as src_cvname, CVTS.cvterm_id as src_cvterm_id, FL.fmin, FL.fmax, FL.is_fmin_partial, FL.is_fmax_partial,FL.strand, FL.phase FROM {featureloc} FL INNER JOIN {feature} F on FL.feature_id = F.feature_id INNER JOIN {feature} FS on FS.feature_id = FL.srcfeature_id INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id INNER JOIN {cvterm} CVTS on FS.type_id = CVTS.cvterm_id "; if (strcmp($side, 'as_parent')==0) { $sql .= "WHERE FL.srcfeature_id = %d "; } if (strcmp($side, 'as_child')==0) { $sql .= "WHERE FL.feature_id = %d "; } $previous_db = tripal_db_set_active('chado'); // use chado database $flresults = db_query($sql, $feature_id); tripal_db_set_active($previous_db); // now use drupal database // copy the results into an array $i=0; $featurelocs = array(); while ($loc = db_fetch_object($flresults)) { // if a drupal node exists for this feature then add the nid to the // results object $sql = 'SELECT nid FROM {chado_feature} WHERE feature_id = %d'; $ffeature = db_fetch_object(db_query($sql, $loc->feature_id)); $sfeature = db_fetch_object(db_query($sql, $loc->src_feature_id)); $loc->fnid = $ffeature->nid; $loc->snid = $sfeature->nid; // add the result to the array $featurelocs[$i++] = $loc; } // Add the relationship feature locs if aggregate is turned on if ($aggregate and strcmp($side, 'as_parent')==0) { // get the relationships for this feature without substituting any children // for the parent. We want all relationships $relationships = tripal_feature_get_aggregate_relationships($feature_id, 0); foreach ($relationships as $rindex => $rel) { // get the featurelocs for each of the relationship features $rel_featurelocs = tripal_feature_load_featurelocs($rel->subject_id, 'as_child', 0); foreach ($rel_featurelocs as $findex => $rfloc) { $featurelocs[$i++] = $rfloc; } } } usort($featurelocs, 'tripal_feature_sort_locations'); return $featurelocs; } /** * used to sort the feature locs by start position * * @ingroup tripal_feature */ function tripal_feature_sort_locations($a, $b) { return strnatcmp($a->fmin, $b->fmin); } /** * * * @ingroup tripal_feature */ function tripal_feature_load_relationships($feature_id, $side = 'as_subject') { // get the relationships for this feature. The query below is used for both // querying the object and subject relationships $sql = "SELECT FS.name as subject_name, FS.uniquename as subject_uniquename, CVTS.name as subject_type, CVTS.cvterm_id as subject_type_id, FR.subject_id, FR.type_id as relationship_type_id, CVT.name as rel_type, FO.name as object_name, FO.uniquename as object_uniquename, CVTO.name as object_type, CVTO.cvterm_id as object_type_id, FR.object_id, FR.rank FROM {feature_relationship} FR INNER JOIN {cvterm} CVT ON FR.type_id = CVT.cvterm_id INNER JOIN {feature} FS ON FS.feature_id = FR.subject_id INNER JOIN {feature} FO ON FO.feature_id = FR.object_id INNER JOIN {cvterm} CVTO ON FO.type_id = CVTO.cvterm_id INNER JOIN {cvterm} CVTS ON FS.type_id = CVTS.cvterm_id "; if (strcmp($side, 'as_object')==0) { $sql .= " WHERE FR.object_id = %d"; } if (strcmp($side, 'as_subject')==0) { $sql .= " WHERE FR.subject_id = %d"; } $sql .= " ORDER BY FR.rank"; // get the relationships $previous_db = tripal_db_set_active('chado'); // use chado database $results = db_query($sql, $feature_id); tripal_db_set_active($previous_db); // now use drupal database // iterate through the relationships, put these in an array and add // in the Drupal node id if one exists $i=0; $nodesql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d"; $relationships = array(); while ($rel = db_fetch_object($results)) { $node = db_fetch_object(db_query($nodesql, $rel->subject_id)); if ($node) { $rel->subject_nid = $node->nid; } $node = db_fetch_object(db_query($nodesql, $rel->object_id)); if ($node) { $rel->object_nid = $node->nid; } $relationships[$i++] = $rel; } return $relationships; } /** * * * @ingroup tripal_feature */ function tripal_feature_get_aggregate_types($feature_id) { // get the feature details $sql = 'SELECT type_id FROM {feature} WHERE feature_id = %d'; $previous_db = tripal_db_set_active('chado'); // use chado database $feature = db_fetch_object(db_query($sql, $feature_id)); tripal_db_set_active($previous_db); // now use drupal database // check to see if this feature is of a type with an aggregate $sql = "SELECT * FROM {tripal_feature_relagg} WHERE type_id = %d"; $types = array(); $results = db_query($sql, $feature->type_id); while ($agg = db_fetch_object($results)) { $types[] = $agg->rel_type_id; } return $types; } /** * * * @ingroup tripal_feature */ function tripal_feature_get_aggregate_relationships($feature_id, $substitute=1, $levels=0, $base_type_id=NULL, $depth=0) { // we only want to recurse to as many levels deep as indicated by the // $levels variable, but only if this variable is > 0. If 0 then we // recurse until we reach the end of the relationships tree. if ($levels > 0 and $levels == $depth) { return NULL; } // first get the relationships for this feature $relationships = tripal_feature_load_relationships($feature_id, 'as_object'); // next, iterate through these relationships and descend, adding in those // that are specified by the aggregator. $i=0; $new_relationships = array(); foreach ($relationships as $rindex => $rel) { // set the base type id if (!$base_type_id) { $base_type_id = $rel->object_type_id; } // check to see if we have an aggregator for this base type $sql = "SELECT * FROM {tripal_feature_relagg} WHERE type_id = %d and rel_type_id = %d"; $agg = db_fetch_object(db_query($sql, $base_type_id, $rel->subject_type_id)); if ($agg) { // if we're not going to substitute the resulting relationships for the // parent then we need to add the parent to our list if (!$substitute) { $new_relationships[$i++] = $rel; } // recurse all relationships $agg_relationships = tripal_feature_get_aggregate_relationships( $rel->subject_id, $levels, $base_type_id, $depth++); // if we have an aggregate defined but we have no relationships beyond // this point then there's nothing we can substitute if (!$agg_relationships and $substitute) { $new_relationships[$i++] = $rel; } // merge all relationships into one array foreach ($agg_relationships as $aindex => $arel) { $new_relationships[$i++] = $arel; } } else { // if we don't have an aggregate then keep the current relationship $new_relationships[$i++] = $rel; } } return $new_relationships; } /** * * * @ingroup tripal_feature */ function tripal_feature_load_featureloc_sequences($feature_id, $featurelocs) { // if we don't have any featurelocs then no point in continuing if (!$featurelocs) { return array(); } // get the list of relationships (including any aggregators) and iterate // through each one to find information needed to color-code the reference sequence $relationships = tripal_feature_get_aggregate_relationships($feature_id); if (!$relationships) { return array(); } // iterate through each of the realtionships features and get their // locations foreach ($relationships as $rindex => $rel) { // get the featurelocs for each of the relationship features $rel_featurelocs = tripal_feature_load_featurelocs($rel->subject_id, 'as_child', 0); foreach ($rel_featurelocs as $rfindex => $rel_featureloc) { // keep track of this unique source feature $src = $rel_featureloc->src_feature_id ."-". $rel_featureloc->src_cvterm_id; // copy over the results to the relationship object. Since there can // be more than one feature location for each relationship feature we // use the '$src' variable to keep track of these. $rel->featurelocs->$src->src_uniquename = $rel_featureloc->src_uniquename; $rel->featurelocs->$src->src_cvterm_id = $rel_featureloc->src_cvterm_id; $rel->featurelocs->$src->src_cvname = $rel_featureloc->src_cvname; $rel->featurelocs->$src->fmin = $rel_featureloc->fmin; $rel->featurelocs->$src->fmax = $rel_featureloc->fmax; $rel->featurelocs->$src->src_name = $rel_featureloc->src_name; // keep track of the individual parts for each relationship $start = $rel->featurelocs->$src->fmin; $end = $rel->featurelocs->$src->fmax; $rel_locs[$src]['parts'][$start]['type'] = $rel->subject_type; $rel_locs[$src]['parts'][$start]['start'] = $start; $rel_locs[$src]['parts'][$start]['end'] = $end; } } // the featurelocs array provided to the function contains the locations // where this feature is found. We want to get the sequence for each // location and then annotate it with the parts found from the relationships // locations determiend above. $sql = "SELECT residues FROM {feature} WHERE feature_id = %d"; $floc_sequences = array(); foreach ($featurelocs as $featureloc) { // get the residues for this feature $previous_db = tripal_db_set_active('chado'); // use chado database $feature = db_fetch_object(db_query($sql, $featureloc->srcfeature_id->feature_id)); tripal_db_set_active($previous_db); // now use drupal database $src = $featureloc->srcfeature_id->feature_id ."-". $featureloc->srcfeature_id->type_id->cvterm_id; // orient the parts to the beginning of the feature sequence if (!empty($rel_locs[$src]['parts'])) { $parts = $rel_locs[$src]['parts']; usort($parts, 'tripal_feature_sort_rel_parts'); foreach ($parts as $start => $attrs) { $parts[$start]['start'] = $parts[$start]['start'] - $featureloc->fmin; $parts[$start]['end'] = $parts[$start]['end'] - $featureloc->fmin; } $floc_sequences[$src]['src'] = $src; $floc_sequences[$src]['type'] = $featureloc->feature_id->type_id->name; $sequence = drupal_substr($feature->residues, $featureloc->fmin-1, ($featureloc->fmax - $featureloc->fmin)+1); $floc_sequences[$src]['formatted_seq'] = tripal_feature_color_sequence( $sequence, $parts); } } return $floc_sequences; } /** * * * @ingroup tripal_feature */ function tripal_feature_get_matched_alignments($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"; $results = db_query($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; $previous_db = tripal_db_set_active('chado'); // use chado database $org_features = db_query($sql, $args); tripal_db_set_active($previous_db); // now use drupal database // 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) { // 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, $b->fmin); } /** * used to sort the list of relationship parts by start position * * @ingroup tripal_feature */ function tripal_feature_sort_rel_parts($a, $b) { return strnatcmp($a['start'], $b['start']); } /** * * * @ingroup tripal_feature */ function tripal_feature_color_sequence($sequence, $parts) { $types = array(); // first get the list of types so we can create a color legend foreach ($parts as $index => $child) { $type = $child['type']; if (!in_array($type, $types)) { $types[] = $type; } } $newseq .= "";
foreach ($parts as $index => $child) {
$type = $child['type'];
$start = $child['start'];
$end = $child['end']+1;
$class = "class=\"tripal_feature-featureloc_sequence-$type\"";
// iterate through the sequence up to the end of the child
for ($i = $pos; $i < $end; $i++) {
// if we're at the beginning of the child sequence then set the
// appropriate text color
if ($pos == $start) {
$newseq .= "";
$func = 'uc'; // nucleotides within the child should be uppercase
}
$newseq .= $sequence{$pos};
$seqcount++;
if ($seqcount % 60 == 0) {
$newseq .= "\n";
}
$pos++;
if ($pos == $end) {
$newseq .= "";
$func = 'lc';
}
}
}
$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) {
// Note that this function only adds feature view to an organism node.
// The view of a feature node is controled by the theme *.tpl file
case 'view':
switch ($node->type) {
case 'chado_organism':
// Show feature browser
$types_to_show = array('chado_organism', 'chado_library');
if (in_array($node->type, $types_to_show, TRUE)) {
$node->content['tripal_organism_feature_counts'] = array(
'#value' => theme('tripal_organism_feature_counts', $node),
);
$node->content['tripal_organism_feature_browser'] = array(
'#value' => theme('tripal_organism_feature_browser', $node),
);
}
break;
case 'chado_library':
$node->content['tripal_library_feature_browser'] = array(
'#value' => theme('tripal_library_feature_browser', $node),
);
break;
case 'chado_analysis':
$node->content['tripal_analysis_feature_browser'] = array(
'#value' => theme('tripal_analysis_feature_browser', $node),
);
break;
default:
}
break;
}
}
/**
* We need to let drupal know about our theme functions and their arguments.
* We create theme functions to allow users of the module to customize the
* look and feel of the output generated in this module
*
* @ingroup tripal_feature
*/
function tripal_feature_theme() {
return array(
'tripal_feature_search_index' => array(
'arguments' => array('node'),
),
'tripal_feature_search_results' => array(
'arguments' => array('node'),
),
'tripal_organism_feature_browser' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_organism_feature_browser',
),
'tripal_organism_feature_counts' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_organism_feature_counts',
),
'tripal_library_feature_browser' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_library_feature_browser',
),
'tripal_analysis_feature_browser' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_analysis_feature_browser',
),
'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_alignments' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_feature_alignments',
),
'tripal_feature_object_relationships' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_feature_object_relationships',
),
'tripal_feature_subject_relationships' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_feature_subject_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_alignments(&$variables) {
// we want to provide a new variable that contains the matched features.
$feature = $variables['node']->feature;
// 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 .= "