print_r($identifiers, TRUE)) ); } elseif (empty($identifiers)) { tripal_report_error('tripal_pub_api', TRIPAL_ERROR, "chado_get_publication: You did not pass in anything to identify the publication you want. The identifier is expected to be an array with the key matching a column name in the pub table (ie: pub_id or name). You passed in %identifier.", array('%identifier'=> print_r($identifiers, TRUE)) ); } // If one of the identifiers is property then use // chado_get_record_with_property(). if (array_key_exists('property', $identifiers)) { $property = $identifiers['property']; unset($identifiers['property']); $pub = chado_get_record_with_property( array('table' => 'pub', 'base_records' => $identifiers), array('type_name' => $property), $options ); } elseif (array_key_exists('dbxref', $identifiers)) { if(preg_match('/^(.*?):(.*?)$/', $identifiers['dbxref'], $matches)) { $dbname = $matches[1]; $accession = $matches[2]; // First make sure the dbxref is present. $values = array( 'accession' => $accession, 'db_id' => array( 'name' => $dbname ), ); $dbxref = chado_select_record('dbxref', array('dbxref_id'), $values); if (count($dbxref) == 0) { return FALSE; } $pub_dbxref = chado_select_record('pub_dbxref', array('pub_id'), array('dbxref_id' => $dbxref[0]->dbxref_id)); if (count($pub_dbxref) == 0) { return FALSE; } $pub = chado_generate_var('pub', array('pub_id' => $pub_dbxref[0]->pub_id), $options); } else { tripal_report_error('tripal_pub_api', TRIPAL_ERROR, "chado_get_publication: The dbxref identifier is not correctly formatted.", array('%identifier'=> print_r($identifiers, TRUE)) ); } } elseif (array_key_exists('dbxref_id', $identifiers)) { // First get the pub_dbxref record. $values = array('dbxref_id' => $identifiers['dbxref_id']); $pub_dbxref = chado_select_record('pub_dbxref', array('pub_id'), $values); // Now get the pub. if (count($pub_dbxref) > 0) { $pub = chado_generate_var('pub', array('pub_id' => $pub_dbxref[0]->pub_id), $options); } else { return FALSE; } } // Else we have a simple case and we can just use chado_generate_var to get // the pub. else { // Try to get the pub. $pub = chado_generate_var('pub', $identifiers, $options); } // Ensure the pub is singular. If it's an array then it is not singular. if (is_array($pub)) { tripal_report_error('tripal_pub_api', TRIPAL_ERROR, "chado_get_publication: The identifiers did not find a single unique record. Identifiers passed: %identifier.", array('%identifier'=> print_r($identifiers, TRUE)) ); } // Report an error if $pub is FALSE since then chado_generate_var has failed. elseif ($pub === FALSE) { tripal_report_error('tripal_pub_api', TRIPAL_ERROR, "chado_get_publication: Could not find a publication using the identifiers provided. Check that the identifiers are correct. Identifiers passed: %identifier.", array('%identifier'=> print_r($identifiers, TRUE)) ); } // Else, as far we know, everything is fine so give them their pub :) else { return $pub; } } /** * The publication table of Chado only has a unique constraint for the * uniquename of the publiation, but in reality a publication can be considered * unique by a combination of the title, publication type, published year and * series name (e.g. journal name or conference name). The site administrator * can configure how publications are determined to be unique. This function * uses the configuration specified by the administrator to look for publications * that match the details specified by the $pub_details argument * and indicates if one ore more publications match the criteria. * * @param $pub_details * An associative array with details about the publications. The expected keys * are: * 'Title': The title of the publication. * 'Year': The published year of the publication. * 'Publication Type': An array of publication types. A publication can * have more than one type. * 'Series Name': The series name of the publication. * 'Journal Name': An alternative to 'Series Name'. * 'Conference Name': An alternative to 'Series Name'. * 'Citation': The publication citation (this is the value saved * in the pub.uniquename field and must be unique). * * If this key is present it will also be checked * 'Publication Dbxref': A database cross reference of the form DB:ACCESSION * where DB is the name of the database and ACCESSION * is the unique identifier (e.g PMID:3483139). * * @return * An array containing the pub_id's of matching publications. Returns an * empty array if no pubs match. * * @ingroup tripal_pub_api */ function chado_publication_exists($pub_details) { // First try to find the publication using the accession number if that key // exists in the details array. if (array_key_exists('Publication Dbxref', $pub_details)) { $pub = chado_get_publication(array('dbxref' => $pub_details['Publication Dbxref'])); if($pub) { return array($pub->pub_id); } } // Make sure the citation is unique. if (array_key_exists('Citation', $pub_details)) { $pub = chado_get_publication(array('uniquename' => $pub_details['Citation'])); if($pub) { return array($pub->pub_id); } } // Get the publication type (use the first publication type). if (array_key_exists('Publication Type', $pub_details)) { $type_name = ''; if(is_array($pub_details['Publication Type'])) { $type_name = $pub_details['Publication Type'][0]; } else { $type_name = $pub_details['Publication Type']; } $identifiers = array( 'name' => $type_name, 'cv_id' => array( 'name' => 'tripal_pub', ), ); $pub_type = chado_get_cvterm($identifiers); } else { tripal_report_error('tripal_pub', TRIPAL_ERROR, "chado_publication_exists(): The Publication Type is a " . "required property but is missing", array()); return array(); } if (!$pub_type) { tripal_report_error('tripal_pub', TRIPAL_ERROR, "chado_publication_exists(): Cannot find publication type: '%type'", array('%type' => $pub_details['Publication Type'][0])); return array(); } // Get the series name. The pub.series_name field is only 255 chars so we // must truncate to be safe. $series_name = ''; if (array_key_exists('Series Name', $pub_details)) { $series_name = substr($pub_details['Series Name'], 0, 255); } if (array_key_exists('Journal Name', $pub_details)) { $series_name = substr($pub_details['Journal Name'], 0, 255); } if (array_key_exists('Conference Name', $pub_details)) { $series_name = substr($pub_details['Conference Name'], 0, 255); } // Make sure the publication is unique using the prefereed import // duplication check. $import_dups_check = variable_get('tripal_pub_import_duplicate_check', 'title_year_media'); $pubs = array(); switch ($import_dups_check) { case 'title_year': $identifiers = array( 'title' => $pub_details['Title'], 'pyear' => $pub_details['Year'] ); $pubs = chado_select_record('pub', array('pub_id'), $identifiers); break; case 'title_year_type': $identifiers = array( 'title' => $pub_details['Title'], 'pyear' => $pub_details['Year'], 'type_id' => $pub_type->cvterm_id, ); $pubs = chado_select_record('pub', array('pub_id'), $identifiers); break; case 'title_year_media': $identifiers = array( 'title' => $pub_details['Title'], 'pyear' => $pub_details['Year'], 'series_name' => $series_name, ); $pubs = chado_select_record('pub', array('pub_id'), $identifiers); break; } $return = array(); foreach ($pubs as $pub) { $return[] = $pub->pub_id; } return $return; } /** * Used for autocomplete in forms for identifying for publications. * * @param $field * The field in the publication to search on. * @param $string * The string to search for. * * @return * A json array of terms that begin with the provided string. * * @ingroup tripal_pub_api */ function chado_autocomplete_pub($string = '') { $items = array(); $sql = " SELECT pub_id, title, uniquename FROM {pub} WHERE lower(title) like lower(:str) ORDER by title LIMIT 25 OFFSET 0 "; $pubs = chado_query($sql, array(':str' => $string . '%')); while ($pub = $pubs->fetchObject()) { $val = $pub->title . " [id:" . $pub->pub_id . "]"; $items[$val] = $pub->title; } drupal_json_output($items); } /** * Imports a singe publication specified by a remote database cross reference. * * @param $pub_dbxref * The unique database ID for the record to update. This value must * be of the format DB_NAME:ACCESSION where DB_NAME is the name of the * database (e.g. PMID or AGL) and the ACCESSION is the unique identifier * for the record in the database. * @param $do_contact * Set to TRUE if authors should automatically have a contact record added * to Chado. * @param $publish * Set to TRUE if publications should be published after import. For Tripal * v3 this value can be set to the string 'sync' or 'both' in the event that * the site is in "legacy" mode. Setting this value to 'sync' will create * nodes, setting to 'both' will create nodes and entities. If set to TRUE * only entities are created. * @param $do_update * If set to TRUE then the publication will be updated if it already exists * in the database. * * @ingroup tripal_pub_api */ function chado_import_pub_by_dbxref($pub_dbxref, $do_contact = FALSE, $publish = TRUE, $do_update = TRUE) { $num_to_retrieve = 1; $pager_id = 0; $page = 0; $num_pubs = 0; $pub_id = NULL; module_load_include('inc', 'tripal_chado', 'includes/loaders/tripal_chado.pub_importers'); // These are options for the tripal_report_error function. We do not // want to log messages to the watchdog but we do for the job and to // the terminal $message_type = 'pub_import'; $message_opts = [ 'watchdog' == FALSE, 'print' => TRUE, ]; $message = "Importing of publications is performed using a database transaction. " . "If the load fails or is terminated prematurely then the entire set of " . "deletions is rolled back and will not be found in the database"; tripal_report_error($message_type, TRIPAL_INFO, $message, [], $message_opts); $transaction = db_transaction(); try { if(preg_match('/^(.*?):(.*?)$/', $pub_dbxref, $matches)) { $dbname = $matches[1]; $accession = $matches[2]; $criteria = array( 'num_criteria' => 1, 'remote_db' => $dbname, 'criteria' => array( '1' => array( 'search_terms' => "$dbname:$accession", 'scope' => 'id', 'operation' => '', 'is_phrase' => 0, ), ), ); $remote_db = $criteria['remote_db']; $results = tripal_get_remote_pubs($remote_db, $criteria, $num_to_retrieve, $page); $pubs = $results['pubs']; $search_str = $results['search_str']; $total_records = $results['total_records']; tripal_pub_add_publications($pubs, $do_contact, $do_update); } // Publish as requested by the caller. _chado_execute_pub_importer_publish($publish, NULL, $message_type, $message_opts); } catch (Exception $e) { $transaction->rollback(); print "\n"; // make sure we start errors on new line watchdog_exception('T_pub_import', $e); print "FAILED: Rolling back database changes...\n"; return; } } /** * Imports all publications for all active import setups. * * @param $report_email * A list of email address, separated by commas, that should be notified * once importing has completed. * @param $publish * Set to TRUE if publications should be published after import. For Tripal * v3 this value can be set to the string 'sync' or 'both' in the event that * the site is in "legacy" mode. Setting this value to 'sync' will create * nodes, setting to 'both' will create nodes and entities. If set to TRUE * only entities are created. * @param $do_update * If set to TRUE then publications that already exist in the Chado database * will be updated, whereas if FALSE only new publications will be added. * * @ingroup tripal_pub_api */ function chado_execute_active_pub_importers($report_email = FALSE, $publish = TRUE, $do_update = FALSE) { $report = []; $report['error'] = []; $report['inserted'] = []; $report['skipped'] = []; $report['updated'] = []; // Get all of the loaders. $args = array(); $sql = "SELECT * FROM {tripal_pub_import} WHERE disabled = 0 "; $importers = db_query($sql, $args); $do_contact = FALSE; while ($import = $importers->fetchObject()) { $importer_report = chado_execute_pub_importer($import->pub_import_id, $publish, $do_update); foreach ($importer_report as $action => $pubs) { $report[$action] = array_merge($report[$action], $pubs); } } $site_email = variable_get('site_mail', ''); $params = array( 'report' => $report ); drupal_mail('tripal_chado', 'import_report', $report_email, language_default(), $params, $site_email, TRUE); print "Done.\n"; } /** * Imports all publications for a given publication import setup. * * @param $import_id * The ID of the import setup to use * @param $publish * Set to TRUE if publications should be published after import. For Tripal * v3 this value can be set to the string 'sync' or 'both' in the event that * the site is in "legacy" mode. Setting this value to 'sync' will create * nodes, setting to 'both' will create nodes and entities. If set to TRUE * only entities are created. * @param $do_update * If set to TRUE then publications that already exist in the Chado database * will be updated, whereas if FALSE only new publications will be added. * @param $job * The jobs management object for the job if this function is run as a job. * This argument is added by Tripal during a job run and is not needed if * this function is run directly. * * @return * Returns an array containing the number of publications that were * inserted, updated, skipped and which had an error during import. * * @ingroup tripal_pub */ function chado_execute_pub_importer($import_id, $publish = TRUE, $do_update = FALSE, $job = NULL) { // Holds the list of imported pubs which includes their ID and Citation. $report = []; $report['error'] = []; $report['inserted'] = []; $report['skipped'] = []; $report['updated'] = []; // These are options for the tripal_report_error function. We do not // want to log messages to the watchdog but we do for the job and to // the terminal $message_type = 'pub_import'; $message_opts = [ 'watchdog' == FALSE, 'job' => $job, 'print' => TRUE, ]; $message = "Importing of publications for this importer is performed using a database transaction. " . "If the load fails or is terminated prematurely then the entire set of " . "deletions is rolled back and will not be found in the database"; tripal_report_error($message_type, TRIPAL_INFO, $message, [], $message_opts); // start the transaction $transaction = db_transaction(); try { $page = 0; $do_contact = FALSE; $num_to_retrieve = 100; // get all of the loaders $args = array(':import_id' => $import_id); $sql = "SELECT * FROM {tripal_pub_import} WHERE pub_import_id = :import_id "; $import = db_query($sql, $args)->fetchObject(); tripal_report_error($message_type, TRIPAL_INFO, "Executing Importer: !name.", ['!name' => $import->name], $message_opts); $criteria = unserialize($import->criteria); $remote_db = $criteria['remote_db']; $total_pubs = 0; // Loop until we have a $pubs array that does not have // our requested numer of records. This means we've hit the end do { // retrieve the pubs for this page. We'll retreive 100 at a time tripal_report_error($message_type, TRIPAL_INFO, "Querying !remote_db for up to !num pubs that match the criteria.", ['!num' => $num_to_retrieve, '!remote_db' => $remote_db], $message_opts); $results = tripal_get_remote_pubs($remote_db, $criteria, $num_to_retrieve, $page); $pubs = $results['pubs']; $num_pubs = $results['total_records']; $total_pubs += $num_pubs; tripal_report_error($message_type, TRIPAL_INFO, "Found %num publications.", ['%num' => $num_pubs], $message_opts); $subset_report = tripal_pub_add_publications($pubs, $import->do_contact, $do_update, $job); foreach ($subset_report as $action => $pubs) { $report[$action] = array_merge($report[$action], $pubs); } $page++; } while (count($pubs) == $num_to_retrieve); // Publish as requested by the caller. _chado_execute_pub_importer_publish($publish, $job, $message_type, $message_opts); if ($job) { $job->setProgress(100); } } catch (Exception $e) { $transaction->rollback(); watchdog_exception('T_pub_import', $e); tripal_report_error($message_type, TRIPAL_ERROR, "Rolling back database changes... !message", ['!message' => $e->getMessage()], $message_opts); return FALSE; } tripal_report_error($message_type, TRIPAL_INFO, "Done.", [], $message_opts); return $report; } /** * A helper function to dermine if imported publications should be published. * * It supports backwards compatibility with Tripal v2 legacy mode. * * @param $publish * Set to TRUE if publications should be published after import. For Tripal * v3 this value can be set to the string 'sync' or 'both' in the event that * the site is in "legacy" mode. Setting this value to 'sync' will create * nodes, setting to 'both' will create nodes and entities. If set to TRUE * only entities are created. */ function _chado_execute_pub_importer_publish($publish, $job, $message_type, $message_opts) { // If the user wants to publish then do so. if ($publish === TRUE or $publish === 'both') { // Get the bundle for the Publication content type. $bundle_term = tripal_load_term_entity(['vocabulary' => 'TPUB', 'accession' => '0000002']); $bundle = tripal_load_bundle_entity(['term_id' => $bundle_term->id]); if ($bundle) { tripal_report_error($message_type, TRIPAL_INFO, "Publishing publications with Drupal...", [], $message_opts); chado_publish_records(['bundle_name' => $bundle->name], $job); } // Note: we won't publish contacts as Tripal v2 did because there is // no consisten way to do that. Each site my use a different term for // different contact content types (e.g. all as one 'Contact' type or // specific such as 'Person', 'Organization', etc.). } // For backwords compatibility with legacy module do a sync. if ($publish === 'sync' or $publish === 'both') { if (module_exists('tripal_pub')) { tripal_report_error($message_type, TRIPAL_INFO, "Syncing publications with Drupal...", [], $message_opts); chado_node_sync_records('pub'); if($import->do_contact) { tripal_report_error($message_type, TRIPAL_INFO, "Syncing contacts with Drupal...", [], $message_opts); chado_node_sync_records('contact'); } } } } /** * Updates publication records. * * Updates publication records that currently exist in the Chado pub table * with the most recent data in the remote database. * * @param $do_contact * Set to TRUE if authors should automatically have a contact record added * to Chado. Contacts are added using the name provided by the remote * database. * @param $dbxref * The unique database ID for the record to update. This value must * be of the format DB_NAME:ACCESSION where DB_NAME is the name of the * database (e.g. PMID or AGL) and the ACCESSION is the unique identifier * for the record in the database. * @param $db * The name of the remote database to update. If this value is provided and * no dbxref then all of the publications currently in the Chado database * for this remote database will be updated. * @param $publish * Set to TRUE if publications should be published after import. For Tripal * v3 this value can be set to the string 'sync' or 'both' in the event that * the site is in "legacy" mode. Setting this value to 'sync' will create * nodes, setting to 'both' will create nodes and entities. If set to TRUE * only entities are created. * @ingroup tripal_pub_api */ function chado_reimport_publications($do_contact = FALSE, $dbxref = NULL, $db = NULL, $publish = TRUE) { // These are options for the tripal_report_error function. We do not // want to log messages to the watchdog but we do for the job and to // the terminal $message_type = 'pub_import'; $message_opts = [ 'watchdog' == FALSE, 'print' => TRUE, ]; $message = "Importing of publications for this importer is performed using a database transaction. " . "If the load fails or is terminated prematurely then the entire set of " . "deletions is rolled back and will not be found in the database"; tripal_report_error($message_type, TRIPAL_INFO, $message, [], $message_opts); $transaction = db_transaction(); try { // Get a list of all publications by their Dbxrefs that have supported // databases. $sql = " SELECT DB.name as db_name, DBX.accession FROM {pub} P INNER JOIN {pub_dbxref} PDBX ON P.pub_id = PDBX.pub_id INNER JOIN {dbxref} DBX ON DBX.dbxref_id = PDBX.dbxref_id INNER JOIN {db} DB ON DB.db_id = DBX.db_id "; $args = array(); if ($dbxref and preg_match('/^(.*?):(.*?)$/', $dbxref, $matches)) { $dbname = $matches[1]; $accession = $matches[2]; $sql .= "WHERE DBX.accession = :accession and DB.name = :dbname "; $args[':accession'] = $accession; $args[':dbname'] = $dbname; } elseif ($db) { $sql .= " WHERE DB.name = :dbname "; $args[':dbname'] = $db; } $sql .= "ORDER BY DB.name, P.pub_id"; $results = chado_query($sql, $args); $num_to_retrieve = 100; $i = 0; // count the number of IDs. When we hit $num_to_retrieve we'll do the query. $curr_db = ''; // keeps track of the current current database. $ids = array(); // the list of IDs for the database. $search = array(); // the search array passed to the search function. // Iterate through the pub IDs. while ($pub = $results->fetchObject()) { $accession = $pub->accession; $remote_db = $pub->db_name; // Here we need to only update publications for databases we support. $supported_dbs = variable_get('tripal_pub_supported_dbs', array()); if(!in_array($remote_db, $supported_dbs)) { continue; } $search = array( 'num_criteria' => 1, 'remote_db' => $remote_db, 'criteria' => array( '1' => array( 'search_terms' => "$remote_db:$accession", 'scope' => 'id', 'operation' => '', 'is_phrase' => 0, ), ), ); $qresults = tripal_get_remote_pubs($remote_db, $search, 1, 0); $pubs = $qresults['pubs']; tripal_pub_add_publications($pubs, $do_contact, TRUE); $i++; } // Publish as requested by the caller. _chado_execute_pub_importer_publish($publish, NULL, $message_type, $message_opts); } catch (Exception $e) { $transaction->rollback(); watchdog_exception('T_pub_import', $e); tripal_report_error($message_type, TRIPAL_ERROR, "Rolling back database changes... !message", ['!message' => $e->getMessage()], $message_opts);return; } print "Done.\n"; } /** * Launch the Tripal job to generate citations. * * This function will recreate citations for all publications currently * loaded into Tripal. This is useful to create a consistent format for * all citations. * * @param $options * Options pertaining to what publications to generate citations for. * One of the following must be present: * - all: Create and replace citation for all pubs. * - new: Create citation for pubs that don't already have one. * * @ingroup tripal_pub_api */ function chado_pub_create_citations($options) { $skip_existing = TRUE; $sql = " SELECT cvterm_id FROM {cvterm} WHERE name = 'Citation' AND cv_id = (SELECT cv_id FROM {cv} WHERE name = 'tripal_pub') "; $citation_type_id = chado_query($sql)->fetchField(); // Create and replace citation for all pubs. if ($options == 'all') { $sql = "SELECT pub_id FROM {pub} P WHERE pub_id <> 1"; $skip_existing = FALSE; } // Create citation for pubs that don't already have one. else if ($options == 'new') { $sql = " SELECT pub_id FROM {pub} P WHERE (SELECT value FROM {pubprop} PB WHERE type_id = :type_id AND P.pub_id = PB.pub_id AND rank = 0) IS NULL AND pub_id <> 1 "; $skip_existing = TRUE; } $result = chado_query($sql, array(':type_id' => $citation_type_id)); $counter_updated = 0; $counter_generated = 0; while ($pub = $result->fetchObject()) { $pub_arr = tripal_pub_get_publication_array($pub->pub_id, $skip_existing); if ($pub_arr) { $citation = chado_pub_create_citation($pub_arr); print $citation . "\n\n"; // Replace if citation exists. This condition is never TRUE if // $skip_existing is TRUE. if ($pub_arr['Citation']) { $sql = " UPDATE {pubprop} SET value = :value WHERE pub_id = :pub_id AND type_id = :type_id AND rank = :rank "; chado_query($sql, array(':value' => $citation, ':pub_id' => $pub->pub_id, ':type_id' => $citation_type_id, ':rank' => 0)); $counter_updated ++; // Generate a new citation. } else { $sql = " INSERT INTO {pubprop} (pub_id, type_id, value, rank) VALUES (:pub_id, :type_id, :value, :rank) "; chado_query($sql, array(':pub_id' => $pub->pub_id, ':type_id' => $citation_type_id, ':value' => $citation, ':rank' => 0)); $counter_generated ++; } } } print "$counter_generated citations generated. $counter_updated citations updated.\n"; } /** * This function generates citations for publications. It requires * an array structure with keys being the terms in the Tripal * publication ontology. This function is intended to be used * for any function that needs to generate a citation. * * @param $pub * An array structure containing publication details where the keys * are the publication ontology term names and values are the * corresponding details. The pub array can contain the following * keys with corresponding values: * - Publication Type: an array of publication types. a publication can * have more than one type. * - Authors: a string containing all of the authors of a publication. * - Journal Name: a string containing the journal name. * - Journal Abbreviation: a string containing the journal name abbreviation. * - Series Name: a string containing the series (e.g. conference * proceedings) name. * - Series Abbreviation: a string containing the series name abbreviation * - Volume: the serives volume number. * - Issue: the series issue number. * - Pages: the page numbers for the publication. * - Publication Date: A date in the format "Year Month Day". * * @return * A text string containing the citation. * * @ingroup tripal_pub_api */ function chado_pub_create_citation($pub) { $citation = ''; $pub_type = ''; // An article may have more than one publication type. For example, // a publication type can be 'Journal Article' but also a 'Clinical Trial'. // Therefore, we need to select the type that makes most sense for // construction of the citation. Here we'll iterate through them all // and select the one that matches best. if (is_array($pub['Publication Type'])) { foreach ($pub['Publication Type'] as $ptype) { if ($ptype == 'Journal Article' ) { $pub_type = $ptype; break; } else if ($ptype == 'Conference Proceedings'){ $pub_type = $ptype; break; } else if ($ptype == 'Review') { $pub_type = $ptype; break; } else if ($ptype == 'Book') { $pub_type = $ptype; break; } else if ($ptype == 'Letter') { $pub_type = $ptype; break; } else if ($ptype == 'Book Chapter') { $pub_type = $ptype; break; } else if ($ptype == "Research Support, Non-U.S. Gov't") { $pub_type = $ptype; // We don't break because if the article is also a Journal Article // we prefer that type. } } // If we don't have a recognized publication type, then just use the // first one in the list. if (!$pub_type) { $pub_type = $pub['Publication Type'][0]; } } else { $pub_type = $pub['Publication Type']; } //---------------------- // Journal Article //---------------------- if ($pub_type == 'Journal Article') { if (array_key_exists('Authors', $pub)) { $citation = $pub['Authors'] . '. '; } $citation .= $pub['Title'] . '. '; if (array_key_exists('Journal Name', $pub)) { $citation .= $pub['Journal Name'] . '. '; } elseif (array_key_exists('Journal Abbreviation', $pub)) { $citation .= $pub['Journal Abbreviation'] . '. '; } elseif (array_key_exists('Series Name', $pub)) { $citation .= $pub['Series Name'] . '. '; } elseif (array_key_exists('Series Abbreviation', $pub)) { $citation .= $pub['Series Abbreviation'] . '. '; } if (array_key_exists('Publication Date', $pub)) { $citation .= $pub['Publication Date']; } elseif (array_key_exists('Year', $pub)) { $citation .= $pub['Year']; } if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) { $citation .= '; '; } if (array_key_exists('Volume', $pub)) { $citation .= $pub['Volume']; } if (array_key_exists('Issue', $pub)) { $citation .= '(' . $pub['Issue'] . ')'; } if (array_key_exists('Pages', $pub)) { if (array_key_exists('Volume', $pub)) { $citation .= ':'; } $citation .= $pub['Pages']; } $citation .= '.'; } //---------------------- // Review //---------------------- else if ($pub_type == 'Review') { if (array_key_exists('Authors', $pub)) { $citation = $pub['Authors'] . '. '; } $citation .= $pub['Title'] . '. '; if (array_key_exists('Journal Name', $pub)) { $citation .= $pub['Journal Name'] . '. '; } elseif (array_key_exists('Journal Abbreviation', $pub)) { $citation .= $pub['Journal Abbreviation'] . '. '; } elseif (array_key_exists('Series Name', $pub)) { $citation .= $pub['Series Name'] . '. '; } elseif (array_key_exists('Series Abbreviation', $pub)) { $citation .= $pub['Series Abbreviation'] . '. '; } if (array_key_exists('Publication Date', $pub)) { $citation .= $pub['Publication Date']; } elseif (array_key_exists('Year', $pub)) { $citation .= $pub['Year']; } if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) { $citation .= '; '; } if (array_key_exists('Volume', $pub)) { $citation .= $pub['Volume']; } if (array_key_exists('Issue', $pub)) { $citation .= '(' . $pub['Issue'] . ')'; } if (array_key_exists('Pages', $pub)) { if (array_key_exists('Volume', $pub)) { $citation .= ':'; } $citation .= $pub['Pages']; } $citation .= '.'; } //---------------------- // Research Support, Non-U.S. Gov't //---------------------- elseif ($pub_type == "Research Support, Non-U.S. Gov't") { if (array_key_exists('Authors', $pub)) { $citation = $pub['Authors'] . '. '; } $citation .= $pub['Title'] . '. '; if (array_key_exists('Journal Name', $pub)) { $citation .= $pub['Journal Name'] . '. '; } if (array_key_exists('Publication Date', $pub)) { $citation .= $pub['Publication Date']; } elseif (array_key_exists('Year', $pub)) { $citation .= $pub['Year']; } $citation .= '.'; } //---------------------- // Letter //---------------------- elseif ($pub_type == 'Letter') { if (array_key_exists('Authors', $pub)) { $citation = $pub['Authors'] . '. '; } $citation .= $pub['Title'] . '. '; if (array_key_exists('Journal Name', $pub)) { $citation .= $pub['Journal Name'] . '. '; } elseif (array_key_exists('Journal Abbreviation', $pub)) { $citation .= $pub['Journal Abbreviation'] . '. '; } elseif (array_key_exists('Series Name', $pub)) { $citation .= $pub['Series Name'] . '. '; } elseif (array_key_exists('Series Abbreviation', $pub)) { $citation .= $pub['Series Abbreviation'] . '. '; } if (array_key_exists('Publication Date', $pub)) { $citation .= $pub['Publication Date']; } elseif (array_key_exists('Year', $pub)) { $citation .= $pub['Year']; } if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) { $citation .= '; '; } if (array_key_exists('Volume', $pub)) { $citation .= $pub['Volume']; } if (array_key_exists('Issue', $pub)) { $citation .= '(' . $pub['Issue'] . ')'; } if (array_key_exists('Pages', $pub)) { if (array_key_exists('Volume', $pub)) { $citation .= ':'; } $citation .= $pub['Pages']; } $citation .= '.'; } //----------------------- // Conference Proceedings //----------------------- elseif ($pub_type == 'Conference Proceedings') { if (array_key_exists('Authors', $pub)) { $citation = $pub['Authors'] . '. '; } $citation .= $pub['Title'] . '. '; if (array_key_exists('Conference Name', $pub)) { $citation .= $pub['Conference Name'] . '. '; } elseif (array_key_exists('Series Name', $pub)) { $citation .= $pub['Series Name'] . '. '; } elseif (array_key_exists('Series Abbreviation', $pub)) { $citation .= $pub['Series Abbreviation'] . '. '; } if (array_key_exists('Publication Date', $pub)) { $citation .= $pub['Publication Date']; } elseif (array_key_exists('Year', $pub)) { $citation .= $pub['Year']; } if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) { $citation .= '; '; } if (array_key_exists('Volume', $pub)) { $citation .= $pub['Volume']; } if (array_key_exists('Issue', $pub)) { $citation .= '(' . $pub['Issue'] . ')'; } if (array_key_exists('Pages', $pub)) { if (array_key_exists('Volume', $pub)) { $citation .= ':'; } $citation .= $pub['Pages']; } $citation .= '.'; } //----------------------- // Default //----------------------- else { if (array_key_exists('Authors', $pub)) { $citation = $pub['Authors'] . '. '; } $citation .= $pub['Title'] . '. '; if (array_key_exists('Series Name', $pub)) { $citation .= $pub['Series Name'] . '. '; } elseif (array_key_exists('Series Abbreviation', $pub)) { $citation .= $pub['Series Abbreviation'] . '. '; } if (array_key_exists('Publication Date', $pub)) { $citation .= $pub['Publication Date']; } elseif (array_key_exists('Year', $pub)) { $citation .= $pub['Year']; } if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) { $citation .= '; '; } if (array_key_exists('Volume', $pub)) { $citation .= $pub['Volume']; } if (array_key_exists('Issue', $pub)) { $citation .= '(' . $pub['Issue'] . ')'; } if (array_key_exists('Pages', $pub)) { if (array_key_exists('Volume', $pub)) { $citation .= ':'; } $citation .= $pub['Pages']; } $citation .= '.'; } return $citation; } /** * Retrieves the minimal information to uniquely describe any publication. * * The returned array is an associative array where the keys are * the controlled vocabulary terms in the form [vocab]:[accession]. * * @param $pub * A publication object as created by chado_generate_var(). * * @return * An array with the following keys: 'Citation', 'Abstract', 'Authors', * 'URL'. All keys are term names in the Tripal Publication Ontology :TPUB. * * @ingroup tripal_pub_api */ function chado_get_minimal_pub_info($pub) { if (!$pub) { return array(); } // Chado has a null pub as default. We don't return anything for this. if (isset($pub->uniquename) && $pub->uniquename == 'null') { return array(); } // Expand the title. $pub = chado_expand_var($pub, 'field', 'pub.title'); $pub = chado_expand_var($pub, 'field', 'pub.volumetitle'); // Get the abstract. $values = array( 'pub_id' => $pub->pub_id, 'type_id' => array( 'name' => 'Abstract', ), ); $options = array( 'include_fk' => array( ), ); $abstract = chado_generate_var('pubprop', $values, $options); $abstract = chado_expand_var($abstract, 'field', 'pubprop.value'); $abstract_text = ''; if ($abstract) { $abstract_text = htmlspecialchars($abstract->value); } // Get the author list. $values = array( 'pub_id' => $pub->pub_id, 'type_id' => array( 'name' => 'Authors', ), ); $options = array( 'include_fk' => array( ), ); $authors = chado_generate_var('pubprop', $values, $options); $authors = chado_expand_var($authors, 'field', 'pubprop.value'); $authors_list = 'N/A'; if ($authors) { $authors_list = $authors->value; } // Get the first database cross-reference with a url. $options = array('return_array' => 1); $pub = chado_expand_var($pub, 'table', 'pub_dbxref', $options); $dbxref = NULL; if ($pub->pub_dbxref) { foreach ($pub->pub_dbxref as $index => $pub_dbxref) { if ($pub_dbxref->dbxref_id->db_id->urlprefix) { $dbxref = $pub_dbxref->dbxref_id; } } } // Get the URL. $values = array( 'pub_id' => $pub->pub_id, 'type_id' => array( 'name' => 'URL', ), ); $options = array( 'return_array' => 1, 'include_fk' => array(), ); $url = ''; $urls = chado_generate_var('pubprop', $values, $options); if ($urls) { $urls = chado_expand_var($urls, 'field', 'pubprop.value'); if (count($urls) > 0) { $url = $urls[0]->value; } } // Get the list of database cross references. $values = array( 'pub_id' => $pub->pub_id, ); $options = array( 'return_array' => 1, ); $pub_dbxrefs = chado_generate_var('pub_dbxref', $values, $options); $dbxrefs = array(); foreach ($pub_dbxrefs as $pub_dbxref) { $dbxrefs[] = $pub_dbxref->dbxref_id->db_id->name . ':' . $pub_dbxref->dbxref_id->accession; } // Get the citation. $values = array( 'pub_id' => $pub->pub_id, 'type_id' => array( 'name' => 'Citation', ), ); $options = array( 'include_fk' => array( ), ); $citation = chado_generate_var('pubprop', $values, $options); if ($citation) { $citation = chado_expand_var($citation, 'field', 'pubprop.value'); $citation = $citation->value; } else { $pub_info = array( 'Title' => $pub->title, 'Publication Type' => $pub->type_id->name, 'Authors' => $authors_list, 'Series Name' => $pub->series_name, 'Volume' => $pub->volume, 'Issue' => $pub->issue, 'Pages' => $pub->pages, 'Publication Date' => $pub->pyear, ); $citation = chado_pub_create_citation($pub_info); } return array( 'TPUB:0000039' => $pub->title, 'TPUB:0000003' => $citation, 'TPUB:0000050' => $abstract_text, 'TPUB:0000047' => $authors_list, 'TPUB:0000052' => $url, 'SBO:0000554' => $dbxrefs, ); }