0) { $_GET['page'] = $page; } // now call the callback function to get the rsults $pubs = array(); if (function_exists($callback)) { $pubs = call_user_func($callback, $search_array, $num_to_retrieve, $pager_id); } return $pubs; } /* * @ingroup tripal_pub_api */ function tripal_pub_get_raw_data($dbxref) { if(preg_match('/^(.*?):(.*?)$/', $dbxref, $matches)) { $remote_db = $matches[1]; $accession = $matches[2]; // check that the database is supported $supported_dbs = variable_get('tripal_pub_supported_dbs', array()); if(!in_array($remote_db, $supported_dbs)) { return "Unsupported database: $dbxref"; } // build the search criteria $search = array( 'remote_db' => $remote_db, 'criteria' => array( array( 'search_terms' => $accession, 'scope' => 'id', ), ), ); $search['num_criteria'] = 0; $pubs = tripal_pub_get_remote_search_results($remote_db, $search, 1, 0); return '' . $pubs[0]['raw'] . ''; } return 'Invalid DB xref'; } /* * @ingroup tripal_pub_api */ function tripal_pub_update_publications($do_contact = FALSE, $dbxref = NULL) { // get a persistent connection $connection = tripal_db_persistent_chado(); if (!$connection) { print "A persistant connection was not obtained. Loading will be slow\n"; } // if we cannot get a connection then let the user know the loading will be slow tripal_db_start_transaction(); if ($connection) { print "\nNOTE: Loading of publications is performed using a database transaction. \n" . "If the load fails or is terminated prematurely then the entire set of \n" . "insertions/updates is rolled back and will not be found in the database\n\n"; } // get a list of all publications 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 = '%s' and DB.name = '%s' "; $args[] = $accession; $args[] = $dbname; } $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 = db_fetch_object($results)) { $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, $supported_dbs)) { continue; } // if we're switching databases then reset the search array if($remote_db != $curr_db) { // if we had a previous DB then do the update. if ($curr_db) { $search['num_criteria'] = $i - 1; $pubs = tripal_pub_get_remote_search_results($remote_db, $search, $i, 0); tripal_pub_add_publications($pubs, $do_contact, TRUE); } $curr_db = $remote_db; $search = array( 'remote_db' => $remote_db, 'criteria' => array(), ); $ids = array(); $i = 0; } // if we've hit the maximum number to retrieve then do the search if($i == $num_to_retrieve) { $search['num_criteria'] = $i - 1; $pubs = tripal_pub_get_remote_search_results($remote_db, $search, $i, 0); tripal_pub_add_publications($pubs, $do_contact, TRUE); $search['criteria'] = array(); $i = 0; } // add each accession to the search criteria $search['criteria'][] = array( 'search_terms' => $accession, 'scope' => 'id', 'operation' => 'OR' ); $i++; } // now update any remaining in the search criteria array $search['num_criteria'] = $i - 1; $pubs = tripal_pub_get_remote_search_results($remote_db, $search, $i, 0); tripal_pub_add_publications($pubs, $do_contact, TRUE); // transaction is complete tripal_db_commit_transaction(); print "Transaction Complete\n"; // sync the newly added publications with Drupal print "Syncing publications with Drupal...\n"; tripal_pub_sync_pubs(); // if the caller wants to create contacts then we should sync them if ($do_contact) { print "Syncing contacts with Drupal...\n"; tripal_contact_sync_contacts(); } print "Done.\n"; } /* * @ingroup tripal_pub_api */ function tripal_pub_import_publications($pub_import_id = NULL) { $num_to_retrieve = 100; $pager_id = 0; $page = 0; $num_pubs = 0; // get a persistent connection $connection = tripal_db_persistent_chado(); if (!$connection) { print "A persistant connection was not obtained. Loading will be slow\n"; } // if we cannot get a connection then let the user know the loading will be slow tripal_db_start_transaction(); if ($connection) { print "\nNOTE: Loading of publications is performed using a database transaction. \n" . "If the load fails or is terminated prematurely then the entire set of \n" . "insertions/updates is rolled back and will not be found in the database\n\n"; } // get all of the loaders $args = array(); $sql = "SELECT * FROM {tripal_pub_import} WHERE disabled = 0 "; if ($pub_import_id) { $sql .= " AND pub_import_id = %d"; $args[] = $pub_import_id; } $results = db_query($sql, $args); $do_contact = FALSE; while ($import = db_fetch_object($results)) { print "Importing: " . $import->name . "\n"; // keep track if any of the importers want to create contacts from authors if ($import->do_contact == 1) { $do_contact = TRUE; } $criteria = unserialize($import->criteria); $remote_db = $criteria['remote_db']; do { // retrieve the pubs for this page. We'll retreive 10 at a time $pubs = tripal_pub_get_remote_search_results($remote_db, $criteria, $num_to_retrieve, $pager_id, $page); tripal_pub_add_publications($pubs, $import->do_contact); $page++; } // continue looping until we have a $pubs array that does not have // our requested numer of records. This means we've hit the end while (count($pubs) == $num_to_retrieve); } // transaction is complete tripal_db_commit_transaction(); print "Transaction Complete\n"; // sync the newly added publications with Drupal print "Syncing publications with Drupal...\n"; tripal_pub_sync_pubs(); // if any of the importers wanted to create contacts from the authors then sync them if($do_contact) { print "Syncing contacts with Drupal...\n"; tripal_contact_sync_contacts(); } print "Done.\n"; } /* * */ function tripal_pub_add_publications($pubs, $do_contact, $update = FALSE) { // iterate through the publications and add each one foreach ($pubs as $pub) { // add the publication to Chado and sync it with Chado $pub_id = tripal_pub_add_publication($pub, $do_contact, $update); if (is_numeric($pub_id)){ // add the publication cross reference (e.g. to PubMed) if ($pub_id and $pub['Publication Dbxref']) { $pub_dbxref = tripal_pub_add_pub_dbxref($pub_id, $pub['Publication Dbxref']); } $num_pubs++; print "Success: " . $pub['Publication Dbxref'] . "\n"; } elseif($pub_id) { print "Skipped: " . $pub['Publication Dbxref'] . "\n"; } else { print "Failed: " . $pub['Publication Dbxref'] . "\n"; } } } /* * */ function tripal_pub_add_pub_dbxref($pub_id, $pub_dbxref) { // break apart the dbxref $dbname = ''; $accession = ''; if(preg_match('/^(.*?):(.*?)$/', $pub_dbxref, $matches)) { $dbname = $matches[1]; $accession = $matches[2]; } else { return FALSE; } // check to see if the pub_dbxref record already exist $values = array( 'dbxref_id' => array( 'accession' => $accession, 'db_id' => array( 'name' => $dbname, ), ), 'pub_id' => $pub_id, ); $options = array('statement_name' => 'sel_pubdbxref_dbpu'); $results = tripal_core_chado_select('pub_dbxref', array('*'), $values, $options); // if the pub_dbxref record exist then we don't need to re-add it. if(count($results) > 0) { return $results[0]; } // make sure our database already exists $db = tripal_db_add_db($dbname); // get the database cross-reference $dbxvalues = array( 'accession' => $accession, 'db_id' => $db->db_id, ); $dbxoptions = array('statement_name' => 'sel_dbxref_acdb'); $results = tripal_core_chado_select('dbxref', array('dbxref_id'), $dbxvalues, $dbxoptions); // if the accession doesn't exist then add it if(count($results) == 0){ $dbxref = tripal_db_add_dbxref($db->db_id, $accession); } else { $dbxref = $results[0]; } // now add the record $options = array('statement_name' => 'ins_pubdbxref_dbpu'); $results = tripal_core_chado_insert('pub_dbxref', $values, $options); if (!$results) { watchdog('tripal_pub', "Cannot add publication dbxref: %db:%accession.", array('%db' => $dbname, '%accession' => $accession). WATCHDOG_ERROR); return FALSE; } return $results; } /** * Returns the list of publications that are assigned the database * cross-reference provided * * @param $pub_dbxref * The database cross reference accession. It should be in the form * DB:ACCESSION, where DB is the database name and ACCESSION is the * unique publication identifier (e.g. PMID:4382934) * * @return * Returns an array of all the publications that have the provided * cross reference. If no publications match, then an empty array * is returned. * * @ingroup tripal_pub_api * */ function tripal_pub_get_pubs_by_dbxref($pub_dbxref) { $return = array(); if(preg_match('/^(.*?):(.*?)$/', $pub_dbxref, $matches)) { $dbname = $matches[1]; $accession = $matches[2]; $values = array( 'dbxref_id' => array ( 'accession' => $accession, 'db_id' => array( 'name' => $dbname ), ), ); $options = array('statement_name' => 'sel_pubdbxref_db'); $results = tripal_core_chado_select('pub_dbxref', array('pub_id'), $values, $options); foreach ($results as $index => $pub) { $return[] = $pub->pub_id; } } return $return; } /** * Returns the list of publications that match a given title and year * * @param title * The title of the publication to look for * @param type * The publication type. The value of this field should come from * the Tripal Pub vocabulary * @param year * Optional. The year the publication was published. * * @return * Returns an array of all the publications that have the provided * cross reference. If no publications match, then an empty array * is returned. * * @ingroup tripal_pub_api * */ function tripal_pub_get_pubs_by_title_type_pyear($title, $type, $pyear = '') { $return = array(); // build the values array for the query. The $pyear is not required. $values = array( 'title' => $title, 'type_id' => array( 'name' => $type, 'cv_id' => array( 'name' => 'tripal_pub' ) ) ); $stmnt_suffix = 'tity'; if ($pub_details['Year']) { $values['pyear'] = $pyear; $stmnt_suffix .= 'py'; } $options = array('statement_name' => 'sel_pub_' . $stmnt_suffix); $results = tripal_core_chado_select('pub', array('pub_id'), $values, $options); // iterate through any matches and pull out the pub_id foreach ($results as $index => $pub) { $return[] = $pub->pub_id; } return $return; } /** * Adds a new publication to the Chado, along with all properties and * database cross-references. If the publication does not already exist * in Chado then it is added. If it does exist nothing is done. If * the $update parameter is TRUE then the publication is updated if it exists. * * @param $pub_details * An associative array containing all of the details about the publication. * @param $do_contact * Optional. Set to TRUE if a contact entry should be added to the Chado contact table * for authors of the publication. * @param $update * Optional. If the publication already exists then this function will return * without adding a new publication. However, set this value to TRUE to force * the function to pudate the publication using the $pub_details that are provided. * * @return * On successful addition of the publication, the new publication ID is returned. If * the publication already exists but $update is FALSE then TRUE is returned indicating * that the publication is there already. If $update is TRUE and the publication * exists then the publication ID is returned. * */ function tripal_pub_add_publication($pub_details, $do_contact = FALSE, $update = FALSE) { $pub_id = 0; // first try to find the publication using the accession number. It will have // one if the pub has already been loaded for the publication database if ($pub_details['Publication Dbxref']) { $results = tripal_pub_get_pubs_by_dbxref($pub_details['Publication Dbxref']); if(count($results) == 1) { $pub_id = $results[0]; } elseif(count($results) > 1) { watchdog('tripal_pub', "There are two publications with this accession: %db:%accession. Cannot determine which to update.", array('%db' => $dbname, '%accession' => $accession), WATCHDOG_ERROR); return FALSE; } // If we found the publication and we do not want to do the update then // return true to indicate the publication has been added if (!$update and $pub_id) { return TRUE; } } // if we couldn't find a publication by the accession (which means it doesn't // yet exist or it has been added using a different publication database) then // try to find it using the title and publication year. elseif ($pub_details['Title']) { $results = tripal_pub_get_pubs_by_title_type_pyear($pub_details['Title'], $pub_details['Publication Type'], $pub_details['Year']); if (count($results) == 1) { $pub_id = $results[0]; } elseif (count($results) > 1) { watchdog('tripal_pub', "The publication with the same title, type and year is present multiple times. Cannot ". "determine which to use. Title: '%title'. Type: '%type'. Year: '%year'", array('%title' => $pub_details['Title'], '%type' => $pub_details['Publication Type'], '%year' => $pub_details['Year']), WATCHDOG_ERROR); return FALSE; } // If we found the publication and we do not want to do the update then // return true to indicate the publication has been added if (!$update and $pub_id) { return TRUE; } } // get the publication type (use the first publication type, any others will get stored as properties) $pub_type = tripal_cv_get_cvterm_by_name($pub_details['Publication Type'][0], NULL, 'tripal_pub'); if (!$pub_type) { watchdog('tripal_pub', "Cannot find publication type: '%type'", array('%type' => $pub_details['Publication Type'][0]), WATCHDOG_ERROR); return FALSE; } // if the publication does not exist then create it. $values = array( 'title' => $pub_details['Title'], 'volume' => $pub_details['Volume'], 'series_name' => $pub_details['Journal Name'], 'issue' => $pub_details['Issue'], 'pyear' => $pub_details['Year'], 'pages' => $pub_details['Pages'], 'uniquename' => $pub_details['Citation'], 'type_id' => $pub_type->cvterm_id, ); // if there is no pub_id then we need to do an insert. if (!$pub_id) { $options = array('statement_name' => 'ins_pub_tivoseispypaunty'); $pub = tripal_core_chado_insert('pub', $values, $options); if (!$pub) { watchdog('tripal_pub', "Cannot insert the publication with title: %title", array('%title' => $pub_details['Title']), WATCHDOG_ERROR); return FALSE; } $pub_id = $pub['pub_id']; } elseif($update) { $match = array('pub_id' => $pub_id); $options = array('statement_name' => 'up_pub_tivoseispypaunty'); $success = tripal_core_chado_update('pub', $match, $values, $options); if (!$success) { watchdog('tripal_pub', "Cannot update the publication with title: %title", array('%title' => $pub_details['Title']), WATCHDOG_ERROR); return FALSE; } } // before we add any new properties we need to remove those that are there if this // is an update. The only thing we don't want to remove are the 'Publication Dbxref' if($update) { $sql = " DELETE FROM {pubprop} WHERE pub_id = %d AND NOT type_id in ( SELECT cvterm_id FROM {cvterm} WHERE name = 'Publication Dbxref' ) "; chado_query($sql, $pub_id); } foreach ($pub_details as $key => $value) { // the pub_details may have the raw search data (e.g. in XML from PubMed. We'll irgnore this for now if($key == 'raw') { continue; } // get the cvterm by name or synonym $cvterm = tripal_cv_get_cvterm_by_name($key, NULL, 'tripal_pub'); if (!$cvterm) { $cvterm = tripal_cv_get_cvterm_by_synonym($key, NULL, 'tripal_pub'); } if (!$cvterm) { watchdog('tripal_pub', "Cannot find term: '%prop'. Skipping.", array('%prop' => $key), WATCHDOG_ERROR); continue; } // skip details that won't be stored as properties if ($key == 'Author List') { tripal_pub_add_authors($pub_id, $value, $do_contact); continue; } if ($key == 'Title' or $key == 'Volume' or $key == 'Journal Name' or $key == 'Issue' or $key == 'Year' or $key == 'Pages') { continue; } $success = 0; if (is_array($value)) { foreach ($value as $subkey => $subvalue) { // if the key is an integer then this array is a simple list and // we will insert using the primary key. Otheriwse, use the new key if(is_int($subkey)) { $success = tripal_core_insert_property('pub', $pub_id, $key, 'tripal_pub', $subvalue, FALSE); } else { $success = tripal_core_insert_property('pub', $pub_id, $subkey, 'tripal_pub', $subvalue, FALSE); } } } else { $success = tripal_core_insert_property('pub', $pub_id, $key, 'tripal_pub', $value, TRUE); } if (!$success) { watchdog('tripal_pub', "Cannot add property '%prop' to publication. Skipping.", array('%prop' => $key), WATCHDOG_ERROR); continue; } } return $pub_id; } /* * */ function tripal_pub_add_authors($pub_id, $authors, $do_contact) { $rank = 0; // first remove any of the existing pubauthor entires $sql = "DELETE FROM {pubauthor} WHERE pub_id = %d"; chado_query($sql, $pub_id); // iterate through the authors and add them to the pubauthors and contact // tables of chado, then link them through the custom pubauthors_contact table foreach ($authors as $author) { // skip invalid author entires if ($author['valid'] == 'N') { continue; } // remove the 'valid' property as we don't have a CV term for it unset($author['valid']); // construct the contact.name field using the author information $name = ''; $type = 'Person'; if ($author['Given Name']) { $name .= $author['Given Name']; } if ($author['Surname']) { $name .= ' ' . $author['Surname']; } if ($author['Suffix']) { $name .= ' ' . $author['Suffix']; } if ($author['Collective']) { $name = $author['Collective']; $type = 'Collective'; } $name = trim($name); // add an entry to the pubauthors table $values = array( 'pub_id' => $pub_id, 'rank' => $rank, 'surname' => $author['Surname'] ? $author['Surname'] : $author['Collective'], 'givennames' => $author['Given Name'], 'suffix' => $author['Suffix'], ); $options = array('statement_name' => 'ins_pubauthor_idrasugisu'); $pubauthor = tripal_core_chado_insert('pubauthor', $values, $options); // if the user wants us to create a contact for each author then do it. if ($do_contact) { // Add the contact $contact = tripal_contact_add_contact($name, '', $type, $author); // if we have succesfully added the contact and the pubauthor entries then we want to // link them together if ($contact and $pubauthor) { // link the pubauthor entry to the contact $values = array( 'pubauthor_id' => $pubauthor['pubauthor_id'], 'contact_id' => $contact['contact_id'], ); $options = array('statement_name' => 'ins_pubauthorcontact_puco'); $pubauthor_contact = tripal_core_chado_insert('pubauthor_contact', $values, $options); if (!$pubauthor_contact) { watchdog('tripal_pub', "Cannot link pub authro and contact.", array(), WATCHDOG_ERROR); } } } $rank++; } } /** * Retrieve properties of a given type for a given pub * * @param $pub_id * The pub_id of the properties you would like to retrieve * @param $property * The cvterm name of the properties to retrieve * * @return * An pub chado variable with the specified properties expanded * * @ingroup tripal_pub_api */ function tripal_pub_get_property($pub_id, $property) { return tripal_core_get_property('pub', $pub_id, $property, 'tripal'); } /** * Insert a given property * * @param $pub_id * The pub_id of the property to insert * @param $property * The cvterm name of the property to insert * @param $value * The value of the property to insert * @param $update_if_present * A boolean indicated whether to update the record if it's already present * * @return * True of success, False otherwise * * @ingroup tripal_pub_api */ function tripal_pub_insert_property($pub_id, $property, $value, $update_if_present = 0) { return tripal_core_insert_property('pub', $pub_id, $property, 'tripal_pub', $value, $update_if_present); } /** * Update a given property * * @param $pub_id * The pub_id of the property to update * @param $property * The cvterm name of the property to update * @param $value * The value of the property to update * @param $insert_if_missing * A boolean indicated whether to insert the record if it's absent * * Note: The property will be identified using the unique combination of the $pub_id and $property * and then it will be updated with the supplied value * * @return * True of success, False otherwise * * @ingroup tripal_pub_api */ function tripal_pub_update_property($pub_id, $property, $value, $insert_if_missing = 0) { return tripal_core_update_property('pub', $pub_id, $property, 'tripal_pub', $value, $insert_if_missing); } /** * Delete a given property * * @param $pub_id * The pub_id of the property to delete * @param $property * The cvterm name of the property to delete * * Note: The property will be identified using the unique combination of the $pub_id and $property * and then it will be deleted * * @return * True of success, False otherwise * * @ingroup tripal_pub_api */ function tripal_pub_delete_property($pub_id, $property) { return tripal_core_delete_property('pub', $pub_id, $property, 'tripal'); }